# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 02:42:10 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 7-pyridin-2-yl-N-(3,4,5-trimethoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(Nc2ncc3ccn(c4ccccn4)c3n2)cc(OC)c1OC
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 7PY  7PY  7-pyridin-2-yl-N-(3,4,5-trimethoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-2-amine  ligand  47  28  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_7PY
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 7PY  CAX   C  CH3   0  -0.408  -3.9467   3.7904   0.3079
 7PY  OAW   O  O2    0  -0.459  -4.5845   2.5541   0.0791
 7PY  CAS   C  CR6   0   0.351  -3.8277   1.4461  -0.0049
 7PY  CAR   C  CR16  0  -0.531  -2.4436   1.4384   0.1154
 7PY  CAT   C  CR6   0   0.149  -4.5238   0.2571  -0.2359
 7PY  OAY   O  O2    0  -0.479  -5.8755   0.2684  -0.3958
 7PY  CAZ   C  CH3   0  -0.384  -6.6070   0.0938   0.8060
 7PY  CAU   C  CR6   0   0.380  -3.8088  -0.9374  -0.3144
 7PY  OBA   O  O2    0  -0.464  -4.5499  -2.0404  -0.5233
 7PY  CBB   C  CH3   0  -0.412  -3.8921  -3.2800  -0.6668
 7PY  CAV   C  CR16  0  -0.525  -2.4211  -0.9606  -0.1915
 7PY  CAF   C  CR6   0   0.432  -1.7365   0.2349   0.0172
 7PY  NAE   N  NH1   0  -0.777  -0.3572   0.3281   0.1247
 7PY  CAD   C  CR6   0   0.589   0.6356  -0.6179   0.0774
 7PY  NAG   N  N     0  -0.485   1.8645  -0.1062   0.0850
 7PY  CAH   C  CR56  0   0.535   2.8235  -1.0088   0.0359
 7PY  NAC   N  N     0  -0.478   0.3091  -1.9100   0.0368
 7PY  CAB   C  CR16  0  -0.001   1.2934  -2.7965   0.0066
 7PY  CAA   C  CR56  0  -0.044   2.6187  -2.4033   0.0085
 7PY  CAL   C  CR15  0  -0.381   3.9054  -3.0255   0.0008
 7PY  CAK   C  CR15  0   0.043   4.8128  -2.0246   0.0268
 7PY  NAI   N  NR5   0  -0.626   4.1715  -0.7875   0.0433
 7PY  CAJ   C  CR6   0   0.503   4.8248   0.4513   0.0812
 7PY  CAM   C  CR16  0  -0.344   5.9829   0.5939   0.8421
 7PY  CAN   C  CR16  0  -0.127   6.6172   1.8214   0.8297
 7PY  CAO   C  CR16  0  -0.315   6.0698   2.8582   0.0881
 7PY  CAP   C  CR16  0  -0.044   4.9030   2.6063  -0.6138
 7PY  NAQ   N  N     0  -0.392   4.2955   1.4288  -0.6290
 7PY  HAX1  H  HCH3  0   0.214  -3.2532   4.0524  -0.4957
 7PY  HAX2  H  HCH3  0   0.250  -4.7309   4.5417   0.3456
 7PY  HAX3  H  HCH3  0   0.215  -3.4055   3.8049   1.2576
 7PY  HAR   H  HCR6  0   0.251  -1.8992   2.3578   0.2885
 7PY  HAZ1  H  HCH3  0   0.210  -6.3702  -0.8549   1.2937
 7PY  HAZ2  H  HCH3  0   0.212  -6.4277   0.9063   1.5144
 7PY  HAZ3  H  HCH3  0   0.221  -7.6639   0.0923   0.5436
 7PY  HBB1  H  HCH3  0   0.217  -3.2025  -3.2844  -1.5148
 7PY  HBB2  H  HCH3  0   0.218  -3.3424  -3.5640   0.2344
 7PY  HBB3  H  HCH3  0   0.247  -4.6676  -4.0202  -0.8473
 7PY  HAV   H  HCR6  0   0.316  -1.8611  -1.8793  -0.2492
 7PY  HAE   H  HNH1  0   0.378   0.0087   1.2638   0.1885
 7PY  HAB   H  HCR6  0   0.249   1.0100  -3.8422  -0.0126
 7PY  HAL   H  HCR5  0   0.235   4.1247  -4.0777  -0.0440
 7PY  HAK   H  HCR5  0   0.274   5.8865  -2.0830  -0.0163
 7PY  HAM   H  HCR6  0   0.261   6.3607  -0.2235   1.4402
 7PY  HAN   H  HCR6  0   0.248   7.5180   1.9709   1.4095
 7PY  HAO   H  HCR6  0   0.240   6.5297   3.8357   0.0582
 7PY  HAP   H  HCR6  0   0.239   4.4379   3.3880  -1.2038

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 7PY  CAX  OAW   single    1.410  0.020  1.410
 7PY  CAX  HAX1  single    0.970  0.020  1.090
 7PY  CAX  HAX2  single    0.970  0.020  1.090
 7PY  CAX  HAX3  single    0.970  0.020  1.090
 7PY  OAW  CAS   single    1.344  0.020  1.344
 7PY  CAS  CAR   aromatic  1.389  0.020  1.389
 7PY  CAS  CAT   aromatic  1.397  0.020  1.397
 7PY  CAR  CAF   aromatic  1.399  0.020  1.399
 7PY  CAR  HAR   single    0.930  0.020  1.080
 7PY  CAT  OAY   single    1.361  0.020  1.361
 7PY  CAT  CAU   aromatic  1.394  0.020  1.394
 7PY  OAY  CAZ   single    1.418  0.020  1.418
 7PY  CAZ  HAZ1  single    0.970  0.020  1.090
 7PY  CAZ  HAZ2  single    0.970  0.020  1.090
 7PY  CAZ  HAZ3  single    0.970  0.020  1.090
 7PY  CAU  OBA   single    1.345  0.020  1.345
 7PY  CAU  CAV   aromatic  1.393  0.020  1.393
 7PY  OBA  CBB   single    1.411  0.020  1.411
 7PY  CBB  HBB1  single    0.970  0.020  1.090
 7PY  CBB  HBB2  single    0.970  0.020  1.090
 7PY  CBB  HBB3  single    0.970  0.020  1.090
 7PY  CAV  CAF   aromatic  1.393  0.020  1.393
 7PY  CAV  HAV   single    0.930  0.020  1.080
 7PY  CAF  NAE   single    1.387  0.020  1.387
 7PY  NAE  CAD   single    1.372  0.020  1.372
 7PY  NAE  HAE   single    0.860  0.020  1.020
 7PY  CAD  NAG   aromatic  1.331  0.020  1.331
 7PY  CAD  NAC   aromatic  1.333  0.020  1.333
 7PY  NAG  CAH   aromatic  1.318  0.020  1.318
 7PY  CAH  CAA   aromatic  1.410  0.020  1.410
 7PY  CAH  NAI   aromatic  1.366  0.020  1.366
 7PY  NAC  CAB   aromatic  1.325  0.020  1.325
 7PY  CAB  CAA   aromatic  1.382  0.020  1.382
 7PY  CAB  HAB   single    0.930  0.020  1.080
 7PY  CAA  CAL   aromatic  1.429  0.020  1.429
 7PY  CAL  CAK   aromatic  1.351  0.020  1.351
 7PY  CAL  HAL   single    0.930  0.020  1.080
 7PY  CAK  NAI   aromatic  1.393  0.020  1.393
 7PY  CAK  HAK   single    0.930  0.020  1.080
 7PY  NAI  CAJ   single    1.401  0.020  1.401
 7PY  CAJ  CAM   aromatic  1.393  0.020  1.393
 7PY  CAJ  NAQ   aromatic  1.319  0.020  1.319
 7PY  CAM  CAN   aromatic  1.382  0.020  1.382
 7PY  CAM  HAM   single    0.930  0.020  1.080
 7PY  CAN  CAO   aromatic  1.387  0.020  1.387
 7PY  CAN  HAN   single    0.930  0.020  1.080
 7PY  CAO  CAP   aromatic  1.385  0.020  1.385
 7PY  CAO  HAO   single    0.930  0.020  1.080
 7PY  CAP  NAQ   aromatic  1.325  0.020  1.325
 7PY  CAP  HAP   single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 7PY  HAX3  CAX  HAX2  108.53  3.000
 7PY  HAX3  CAX  HAX1  108.75  3.000
 7PY  HAX2  CAX  HAX1  108.51  3.000
 7PY  HAX3  CAX  OAW   112.13  3.000
 7PY  HAX2  CAX  OAW   106.58  3.000
 7PY  HAX1  CAX  OAW   112.20  3.000
 7PY  CAS   OAW  CAX   118.56  3.000
 7PY  CAT   CAS  CAR   120.40  3.000
 7PY  CAT   CAS  OAW   115.55  3.000
 7PY  CAR   CAS  OAW   124.06  3.000
 7PY  HAR   CAR  CAF   119.18  3.000
 7PY  HAR   CAR  CAS   120.68  3.000
 7PY  CAF   CAR  CAS   120.14  3.000
 7PY  CAU   CAT  OAY   120.65  3.000
 7PY  CAU   CAT  CAS   118.88  3.000
 7PY  OAY   CAT  CAS   120.47  3.000
 7PY  CAZ   OAY  CAT   114.32  3.000
 7PY  HAZ3  CAZ  HAZ2  108.45  3.000
 7PY  HAZ3  CAZ  HAZ1  108.47  3.000
 7PY  HAZ2  CAZ  HAZ1  108.70  3.000
 7PY  HAZ3  CAZ  OAY   107.26  3.000
 7PY  HAZ2  CAZ  OAY   111.92  3.000
 7PY  HAZ1  CAZ  OAY   111.93  3.000
 7PY  CAV   CAU  OBA   123.29  3.000
 7PY  CAV   CAU  CAT   121.33  3.000
 7PY  OBA   CAU  CAT   115.38  3.000
 7PY  CBB   OBA  CAU   118.65  3.000
 7PY  HBB3  CBB  HBB2  108.59  3.000
 7PY  HBB3  CBB  HBB1  108.57  3.000
 7PY  HBB2  CBB  HBB1  108.74  3.000
 7PY  HBB3  CBB  OBA   106.41  3.000
 7PY  HBB2  CBB  OBA   112.27  3.000
 7PY  HBB1  CBB  OBA   112.12  3.000
 7PY  HAV   CAV  CAF   118.96  3.000
 7PY  HAV   CAV  CAU   121.81  3.000
 7PY  CAF   CAV  CAU   119.23  3.000
 7PY  NAE   CAF  CAV   123.92  3.000
 7PY  NAE   CAF  CAR   116.07  3.000
 7PY  CAV   CAF  CAR   120.01  3.000
 7PY  HAE   NAE  CAD   112.33  3.000
 7PY  HAE   NAE  CAF   115.40  3.000
 7PY  CAD   NAE  CAF   132.13  3.000
 7PY  NAC   CAD  NAG   126.78  3.000
 7PY  NAC   CAD  NAE   119.47  3.000
 7PY  NAG   CAD  NAE   113.75  3.000
 7PY  CAH   NAG  CAD   114.10  3.000
 7PY  NAI   CAH  CAA   107.68  3.000
 7PY  NAI   CAH  NAG   127.37  3.000
 7PY  CAA   CAH  NAG   124.92  3.000
 7PY  CAB   NAC  CAD   117.85  3.000
 7PY  HAB   CAB  CAA   121.69  3.000
 7PY  HAB   CAB  NAC   116.86  3.000
 7PY  CAA   CAB  NAC   121.46  3.000
 7PY  CAL   CAA  CAB   137.67  3.000
 7PY  CAL   CAA  CAH   107.45  3.000
 7PY  CAB   CAA  CAH   114.88  3.000
 7PY  HAL   CAL  CAK   126.05  3.000
 7PY  HAL   CAL  CAA   127.56  3.000
 7PY  CAK   CAL  CAA   106.37  3.000
 7PY  HAK   CAK  NAI   120.52  3.000
 7PY  HAK   CAK  CAL   128.97  3.000
 7PY  NAI   CAK  CAL   110.42  3.000
 7PY  CAJ   NAI  CAK   124.80  3.000
 7PY  CAJ   NAI  CAH   127.12  3.000
 7PY  CAK   NAI  CAH   108.08  3.000
 7PY  NAQ   CAJ  CAM   123.49  3.000
 7PY  NAQ   CAJ  NAI   116.98  3.000
 7PY  CAM   CAJ  NAI   119.53  3.000
 7PY  HAM   CAM  CAN   121.08  3.000
 7PY  HAM   CAM  CAJ   121.02  3.000
 7PY  CAN   CAM  CAJ   117.88  3.000
 7PY  HAN   CAN  CAO   120.79  3.000
 7PY  HAN   CAN  CAM   120.02  3.000
 7PY  CAO   CAN  CAM   119.18  3.000
 7PY  HAO   CAO  CAP   120.60  3.000
 7PY  HAO   CAO  CAN   121.52  3.000
 7PY  CAP   CAO  CAN   117.87  3.000
 7PY  HAP   CAP  NAQ   115.97  3.000
 7PY  HAP   CAP  CAO   120.41  3.000
 7PY  NAQ   CAP  CAO   123.62  3.000
 7PY  CAP   NAQ  CAJ   117.93  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 7PY  CONST_01  CAV   CAF  CAR  CAS     0.00   0.0  0
 7PY  CONST_02  CAV   CAU  CAT  CAS     0.00   0.0  0
 7PY  CONST_03  CAU   CAT  CAS  CAR     0.00   0.0  0
 7PY  CONST_04  CAU   CAV  CAF  CAR     0.00   0.0  0
 7PY  CONST_05  CAF   CAR  CAS  CAT     0.00   0.0  0
 7PY  CONST_06  CAF   CAV  CAU  CAT     0.00   0.0  0
 7PY  CONST_07  CAA   CAH  NAG  CAD     0.00   0.0  0
 7PY  CONST_08  NAI   CAH  NAG  CAD   180.00   0.0  0
 7PY  CONST_09  CAA   CAB  NAC  CAD     0.00   0.0  0
 7PY  CONST_10  CAB   NAC  CAD  NAG     0.00   0.0  0
 7PY  CONST_11  CAB   CAA  CAH  NAG     0.00   0.0  0
 7PY  CONST_12  CAL   CAA  CAH  NAG   180.00   0.0  0
 7PY  CONST_13  CAK   NAI  CAH  NAG   180.00   0.0  0
 7PY  CONST_14  CAJ   NAI  CAH  NAG     0.00   0.0  0
 7PY  CONST_15  NAC   CAD  NAG  CAH     0.00   0.0  0
 7PY  CONST_16  NAC   CAB  CAA  CAH     0.00   0.0  0
 7PY  CONST_17  CAK   CAL  CAA  CAH     0.00   0.0  0
 7PY  CONST_18  CAL   CAK  NAI  CAH     0.00   0.0  0
 7PY  CONST_21  CAL   CAA  CAB  NAC   180.00   0.0  0
 7PY  CONST_22  NAI   CAH  CAA  CAB   180.00   0.0  0
 7PY  CONST_23  CAK   CAL  CAA  CAB   180.00   0.0  0
 7PY  CONST_24  CAK   NAI  CAH  CAA     0.00   0.0  0
 7PY  CONST_25  CAJ   NAI  CAH  CAA   180.00   0.0  0
 7PY  CONST_26  NAI   CAK  CAL  CAA     0.00   0.0  0
 7PY  CONST_27  NAI   CAH  CAA  CAL     0.00   0.0  0
 7PY  CONST_28  CAJ   NAI  CAK  CAL   180.00   0.0  0
 7PY  CONST_31  CAN   CAM  CAJ  NAI   180.00   0.0  0
 7PY  CONST_32  CAP   NAQ  CAJ  NAI   180.00   0.0  0
 7PY  CONST_33  CAO   CAN  CAM  CAJ     0.00   0.0  0
 7PY  CONST_34  CAO   CAP  NAQ  CAJ     0.00   0.0  0
 7PY  CONST_35  CAP   NAQ  CAJ  CAM     0.00   0.0  0
 7PY  CONST_36  CAP   CAO  CAN  CAM     0.00   0.0  0
 7PY  CONST_37  NAQ   CAJ  CAM  CAN     0.00   0.0  0
 7PY  CONST_38  NAQ   CAP  CAO  CAN     0.00   0.0  0
 7PY  CONST_39  CAF   CAR  CAS  OAW   180.00   0.0  0
 7PY  CONST_40  CAU   CAT  CAS  OAW   180.00   0.0  0
 7PY  CONST_41  NAE   CAF  CAR  CAS   180.00   0.0  0
 7PY  CONST_42  OBA   CAU  CAT  CAS   180.00   0.0  0
 7PY  CONST_43  OAY   CAT  CAS  CAR   180.00   0.0  0
 7PY  CONST_44  CAV   CAU  CAT  OAY   180.00   0.0  0
 7PY  CONST_45  NAE   CAF  CAV  CAU   180.00   0.0  0
 7PY  CONST_46  CAF   CAV  CAU  OBA   180.00   0.0  0
 7PY  CONST_47  CAH   NAG  CAD  NAE   180.00   0.0  0
 7PY  CONST_48  CAB   NAC  CAD  NAE   180.00   0.0  0
 7PY  CONST_49  HAV   CAV  CAF  CAR   180.00   0.0  0
 7PY  CONST_50  HAR   CAR  CAS  CAT   180.00   0.0  0
 7PY  CONST_51  HAB   CAB  NAC  CAD   180.00   0.0  0
 7PY  CONST_52  HAL   CAL  CAA  CAH   180.00   0.0  0
 7PY  CONST_53  HAK   CAK  NAI  CAH   180.00   0.0  0
 7PY  CONST_54  HAM   CAM  CAJ  NAI     0.00   0.0  0
 7PY  CONST_55  HAN   CAN  CAM  CAJ   180.00   0.0  0
 7PY  CONST_56  HAP   CAP  NAQ  CAJ   180.00   0.0  0
 7PY  CONST_57  HAO   CAO  CAN  CAM   180.00   0.0  0
 7PY  Var_01    CAD   NAE  CAF  CAR  -179.97  30.0  2
 7PY  Var_02    NAG   CAD  NAE  CAF   173.43  30.0  2
 7PY  Var_03    CAR   CAS  OAW  CAX    -0.24  30.0  2
 7PY  Var_04    CAU   CAT  OAY  CAZ    89.77  30.0  2
 7PY  Var_05    CAV   CAU  OBA  CBB    -2.01  30.0  2
 7PY  Var_06    HAX1  CAX  OAW  CAS    61.65  30.0  3
 7PY  Var_07    HAZ1  CAZ  OAY  CAT   -59.53  30.0  3
 7PY  Var_08    HBB1  CBB  OBA  CAU   -60.17  30.0  3

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 7PY  plan-1  OAW  0.020
 7PY  plan-1  CAS  0.020
 7PY  plan-1  CAR  0.020
 7PY  plan-1  CAT  0.020
 7PY  plan-1  OAY  0.020
 7PY  plan-1  CAU  0.020
 7PY  plan-1  OBA  0.020
 7PY  plan-1  CAV  0.020
 7PY  plan-1  CAF  0.020
 7PY  plan-1  NAE  0.020
 7PY  plan-1  HAR  0.020
 7PY  plan-1  HAV  0.020
 7PY  plan-2  NAI  0.020
 7PY  plan-2  CAJ  0.020
 7PY  plan-2  CAM  0.020
 7PY  plan-2  CAN  0.020
 7PY  plan-2  CAO  0.020
 7PY  plan-2  CAP  0.020
 7PY  plan-2  NAQ  0.020
 7PY  plan-2  HAM  0.020
 7PY  plan-2  HAN  0.020
 7PY  plan-2  HAO  0.020
 7PY  plan-2  HAP  0.020
 7PY  plan-3  NAE  0.020
 7PY  plan-3  CAD  0.020
 7PY  plan-3  NAG  0.020
 7PY  plan-3  CAH  0.020
 7PY  plan-3  NAC  0.020
 7PY  plan-3  CAB  0.020
 7PY  plan-3  CAA  0.020
 7PY  plan-3  CAL  0.020
 7PY  plan-3  CAK  0.020
 7PY  plan-3  NAI  0.020
 7PY  plan-3  CAJ  0.020
 7PY  plan-3  HAB  0.020
 7PY  plan-3  HAL  0.020
 7PY  plan-3  HAK  0.020

