Compounds

The File menu, shown below, contains several ways to import or load compounds into MolModa.

PubChem

Integrating molecular compounds into your drug design workflow is straightforward with direct access to PubChem, a large chemical database. This lets you import compound structures for docking experiments.

PopupEnter molecule nameAuto CID lookup

File Import Load Molecule from PubChem (guided tour) opens an interface for searching PubChem by name, formula, or other identifiers. Matching results are displayed for selection.

If you already know the compound you want, you can enter its name directly. The system queries PubChem for the corresponding compound, which is particularly useful for well-known compounds with unique names.

When a molecule name is provided, MolModa automatically retrieves the PubChem Chemical Identifier (CID), so you don't have to look it up manually.

After selecting the compound, the loaded structure is shown for confirmation and is ready for further analysis.

Text

You can also import molecular structures from text-based representations or files. This supports a variety of formats, including those used by other software in the drug discovery space. Access this option via File Import Molecular Text (guided tour).

Supported formats

The tool accepts molecular data in several widely used formats, ensuring compatibility with other software and databases:

PDB (Protein Data Bank): A standard format for the three-dimensional structural data of proteins and nucleic acids.
mol2: A file format used to describe the structure of chemical molecules containing atoms, bonds, coordinates, and other information.
SDF (Structure-Data File): A file format used to represent multiple chemical compound information, supporting a wide range of chemical data fields.
SMILES (Simplified Molecular Input Line Entry System): A notation that allows a user to represent a chemical structure in a way that can be used by the computer.

smilessdf

CS(=O)(=O)CCNCC1=CC=C(O1)C2=CC3=C(C=C2)N=CN=C3NC4=CC(=C(C=C4)OCC5=CC(=CC=C5)F)Cl

9549299
-OEChem-03062421093D

48 51  0     0  0  0  0  0  0999 V2000
-7.7265   -2.1388   -0.5627 F   0  0  0  0  0  0  0  0  0  0  0  0
-6.5520   -1.2263   -2.1413 F   0  0  0  0  0  0  0  0  0  0  0  0
-5.6635   -2.7526   -0.8726 F   0  0  0  0  0  0  0  0  0  0  0  0
    7.5757   -0.6332   -0.0294 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2336   -0.8701   -0.0887 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5493    2.2571   -0.4496 N   0  0  0  0  0  0  0  0  0  0  0  0
-3.0422    1.5350    0.6638 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5340    0.1541   -0.9145 N   0  0  0  0  0  0  0  0  0  0  0  0
-1.7810   -0.2099   -0.3532 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.6942   -2.7968    0.1058 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9755   -3.4855    1.2123 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4689   -3.3439    1.2527 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5573   -1.3108   -0.0120 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7693    0.4406   -0.2038 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3987    0.6921   -0.2676 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6757    1.4995   -0.2558 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9289    2.0035   -0.3838 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2118    2.8098   -0.3717 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8412    3.0613   -0.4355 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4182    1.4049   -0.4220 C   0  0  0  0  0  0  0  0  0  0  0  0
-4.3134    0.9472    0.8311 C   0  0  0  0  0  0  0  0  0  0  0  0
-0.7476    1.9131    0.1135 C   0  0  0  0  0  0  0  0  0  0  0  0
-1.8328    1.0548    0.1252 C   0  0  0  0  0  0  0  0  0  0  0  0
-6.0093   -0.6133    0.1060 C   0  0  0  0  0  0  0  0  0  0  0  0
-4.7528   -0.0310   -0.0608 C   0  0  0  0  0  0  0  0  0  0  0  0
-5.1305    1.3429    1.8902 C   0  0  0  0  0  0  0  0  0  0  0  0
-6.8264   -0.2175    1.1648 C   0  0  0  0  0  0  0  0  0  0  0  0
-6.3869    0.7606    2.0570 C   0  0  0  0  0  0  0  0  0  0  0  0
-6.4796   -1.6587   -0.8476 C   0  0  0  0  0  0  0  0  0  0  0  0
-0.5878   -0.5881   -0.8497 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7853   -3.3218   -0.8391 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4032   -2.9033    1.9243 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5678   -4.4696    1.0148 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0635   -4.2335    1.0844 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8877   -2.6599    1.9807 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5111   -1.5864   -0.0647 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7301   -0.1577   -0.1951 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7498    1.3839   -0.2121 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9167    3.6352   -0.4124 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4947    4.0879   -0.5260 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3118    3.2421   -0.5278 H   0  0  0  0  0  0  0  0  0  0  0  0
-0.8090    2.9237    0.5017 H   0  0  0  0  0  0  0  0  0  0  0  0
-2.9149    2.3598    1.2457 H   0  0  0  0  0  0  0  0  0  0  0  0
-4.1556   -0.3340   -0.9154 H   0  0  0  0  0  0  0  0  0  0  0  0
-4.8004    2.1031    2.5936 H   0  0  0  0  0  0  0  0  0  0  0  0
-7.8081   -0.6593    1.3114 H   0  0  0  0  0  0  0  0  0  0  0  0
-7.0230    1.0686    2.8818 H   0  0  0  0  0  0  0  0  0  0  0  0
-0.5233   -1.5970   -1.2382 H   0  0  0  0  0  0  0  0  0  0  0  0
1 29  1  0  0  0  0
2 29  1  0  0  0  0
3 29  1  0  0  0  0
4 13  2  0  0  0  0
5 13  1  0  0  0  0
5 14  1  0  0  0  0
5 36  1  0  0  0  0
6 17  1  0  0  0  0
6 20  1  0  0  0  0
6 41  1  0  0  0  0
7 21  1  0  0  0  0
7 23  1  0  0  0  0
7 43  1  0  0  0  0
8 20  2  0  0  0  0
8 30  1  0  0  0  0
9 23  1  0  0  0  0
9 30  2  0  0  0  0
10 11  1  0  0  0  0
10 12  1  0  0  0  0
10 13  1  0  0  0  0
10 31  1  0  0  0  0
11 12  1  0  0  0  0
11 32  1  0  0  0  0
11 33  1  0  0  0  0
12 34  1  0  0  0  0
12 35  1  0  0  0  0
14 15  1  0  0  0  0
14 16  2  0  0  0  0
15 17  2  0  0  0  0
15 37  1  0  0  0  0
16 18  1  0  0  0  0
16 38  1  0  0  0  0
17 19  1  0  0  0  0
18 19  2  0  0  0  0
18 39  1  0  0  0  0
19 40  1  0  0  0  0
20 22  1  0  0  0  0
21 25  1  0  0  0  0
21 26  2  0  0  0  0
22 23  2  0  0  0  0
22 42  1  0  0  0  0
24 25  2  0  0  0  0
24 27  1  0  0  0  0
24 29  1  0  0  0  0
25 44  1  0  0  0  0
26 28  1  0  0  0  0
26 45  1  0  0  0  0
27 28  2  0  0  0  0
27 46  1  0  0  0  0
28 47  1  0  0  0  0
30 48  1  0  0  0  0
M  END
> <PUBCHEM_COMPOUND_CID>
9549299

> <PUBCHEM_CONFORMER_RMSD>
1

> <PUBCHEM_CONFORMER_DIVERSEORDER>
14
103
40
167
262
127
147
237
84
198
256
105
145
213
227
90
139
239
125
85
174
121
157
206
134
132
220
188
224
152
126
143
115
214
7
173
138
202
100
204
124
68
184
60
176
253
196
112
82
104
193
133
89
136
137
251
190
170
233
261
59
98
191
162
32
245
123
250
135
75
208
52
186
88
260
201
93
67
106
172
43
119
217
159
57
81
146
72
11
148
99
240
171
140
6
114
207
131
263
10
116
244
95
164
203
66
179
265
110
234
20
141
111
264
197
77
130
169
192
16
50
17
15
49
257
235
149
47
165
183
156
226
166
241
4
61
153
199
238
48
92
216
219
248
154
200
181
185
150
18
69
225
120
35
151
64
42
254
194
117
144
178
25
41
168
5
9
44
252
247
101
71
246
255
108
189
22
56
80
62
231
46
160
215
19
209
109
175
221
229
128
51
45
155
107
228
259
163
187
122
8
23
129
182
83
218
118
242
177
58
3
158
249
24
2
53
161
113
91
180
21
31
222
94
102
142
65
210
86
205
13
76
12
211
79
195
78
1
30
26
34
54
70
212
63
223
258
230
55
33
38
236
27
243
36
73
97
74
37
232
96
39
87
29
28

> <PUBCHEM_MMFF94_PARTIAL_CHARGES>
48
1 -0.34
10 -0.1
11 -0.2
12 -0.2
13 0.63
14 0.12
15 -0.15
16 -0.15
17 0.1
18 -0.15
19 -0.15
2 -0.34
20 0.41
21 0.1
22 -0.15
23 0.41
24 -0.14
25 -0.15
26 -0.15
27 -0.15
28 -0.15
29 1.16
3 -0.34
30 0.47
31 0.1
32 0.1
33 0.1
34 0.1
35 0.1
36 0.37
37 0.15
38 0.15
39 0.15
4 -0.57
40 0.15
41 0.4
42 0.15
43 0.4
44 0.15
45 0.15
46 0.15
47 0.15
48 0.15
5 -0.55
6 -0.6
7 -0.6
8 -0.62
9 -0.62

> <PUBCHEM_EFFECTIVE_ROTOR_COUNT>
8.6

> <PUBCHEM_PHARMACOPHORE_FEATURES>
10
1 4 acceptor
1 5 donor
1 6 donor
1 7 cation
1 7 donor
3 6 8 20 cation
3 8 9 30 cation
6 14 15 16 17 18 19 rings
6 21 24 25 26 27 28 rings
6 8 9 20 22 23 30 rings

> <PUBCHEM_HEAVY_ATOM_COUNT>
30

> <PUBCHEM_ATOM_DEF_STEREO_COUNT>
0

> <PUBCHEM_ATOM_UDEF_STEREO_COUNT>
0

> <PUBCHEM_BOND_DEF_STEREO_COUNT>
0

> <PUBCHEM_BOND_UDEF_STEREO_COUNT>
0

> <PUBCHEM_ISOTOPIC_ATOM_COUNT>
0

> <PUBCHEM_COMPONENT_COUNT>
1

> <PUBCHEM_CACTVS_TAUTO_COUNT>
18

> <PUBCHEM_CONFORMER_ID>
0091B5F30000000E

> <PUBCHEM_MMFF94_ENERGY>
104.1356

> <PUBCHEM_FEATURE_SELFOVERLAP>
50.882

> <PUBCHEM_SHAPE_FINGERPRINT>
12107183 9 18342183241212946304
12236239 1 18271530879002097409
13008946 170 18265333001093312268
13533116 47 18335706048727083224
13782708 43 17894630310397625948
14251764 18 18272937154426712124
15183329 4 18338236067520474373
15467298 65 18270673276770196654
1577012 14 18272941539235062217
16993089 31 17386303064200624955
1768 124 18343021056726850302
1979834 28 17560240198998601494
19841028 212 18335697260580573562
20028762 73 18342459214648254966
20165401 70 18410572886220721698
21130935 74 18413390964011885409
21267235 1 18338525145280583820
21315759 40 18272375273487429721
21585481 151 17987244326922041294
21585483 132 18336814360089364307
21682296 61 18187650171631417465
21987483 16 18127408071743676331
22002106 203 18262225622593389970
23081809 10 18343028830148261357
23522609 53 18125192469519742537
23569943 247 18261671459066695075
25242607 90 18267015069563660634
3504750 166 18341896238930291433
3663271 9 18059862787105074865
406291 66 18335700478175846466
4073 2 18191594266517978248
4516262 110 18118404175662541724
4616759 239 16343712006828315387
5104073 3 17917992806189255240
513202 73 18187363186322696213
531348 171 18408602540325466821
54039377 194 18190184491338868342
5718773 13 18335698308990001550
5874358 3 17845632842565014583
6299153 45 18341899597378016775
636783 161 18057027035212051447
9555976 147 17702954612764470937
96874 4 18412822482151532363
9962374 69 18334852832230641162

> <PUBCHEM_SHAPE_MULTIPOLES>
564.79
25.87
3.71
1.31
4.57
1.61
0.26
20.2
3.68
-7.66
0.23
2.63
0.4
-4.75

> <PUBCHEM_SHAPE_SELFOVERLAP>
1226.55

> <PUBCHEM_SHAPE_VOLUME>
307

> <PUBCHEM_COORDINATE_TYPE>
2
5
10

$$$$

Draw

For a hands-on approach to molecule design, MolModa includes a drawing tool that lets you build small-molecule compounds atom by atom. Open it with File Import Draw Molecule (guided tour).

How to use the drawing tool

Select a tool: Click on the desired tool from the toolbar to begin creating your molecule. Options include drawing single, double, or triple bonds, adding atoms, and more.
Draw the molecule: Click and drag on the canvas to place atoms and bonds. The interface is intuitive, letting you visualize the molecular structure as it is created.
Edit as needed: Use the selection tool to adjust atoms and bonds. The eraser tool removes specific parts of the structure, while the charge tool adds charges to atoms.
Confirm the structure: Once the molecule is complete, review it to ensure it matches your intended design.

To edit a compound that is already loaded, select it in the Navigator and use Compounds Build Edit Compound (guided tour).

Preparing compounds

Before docking, compounds typically need preparation:

Protonate/Deprotonate Compounds (Compounds Build) (guided tour) assigns protonation states for a given pH.
Rebuild Compound Coordinates (Compounds Build) (guided tour) regenerates 3D atomic coordinates, useful when starting from a SMILES string or a 2D representation.

Finding similar compounds

Compounds Create Library Find Similar Compounds (guided tour) builds a library of chemically similar analogs by searching PubChem. This is a quick way to expand a starting compound into a screening set.

Retrieving compound information

Three plugins under Compounds Information annotate selected compounds with data from PubChem:

Compound Names (guided tour) — retrieves names and synonyms.
PubChem Properties (guided tour) — retrieves chemical properties.
PubChem Bioassays (guided tour) — retrieves bioassay results.

Results appear in the Data panel and can be sorted and filtered alongside docking output.