# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 14:59:29 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: 4-chloranyl-1-methyl-2-[4-(4-methylpiperazin-1-yl)phenyl]pyrrolo[2,3-b]pyridine-6-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)c2ccc(cc2)c3cc4c(Cl)cc(nc4n3C)C(N)=O
#
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
 6S3  6S3  4-chloranyl-1-methyl-2-[4-(4-methylpiperazin-1-yl)phenyl]pyrrolo[2,3-b]pyridine-6-carboxamide  ligand  49  27  .  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_6S3
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
 6S3  CAT   C   CH2   0  -0.313  -5.5402   1.2352   0.6170
 6S3  CAU   C   CH2   0  -0.281  -6.9846   1.3199   0.1622
 6S3  NAV   N   NT    0  -0.412  -7.6948   0.0890   0.4274
 6S3  CAY   C   CH3   0  -0.519  -9.0940   0.1935   0.0821
 6S3  CAW   C   CH2   0  -0.284  -7.0450  -0.9975  -0.2717
 6S3  CAX   C   CH2   0  -0.307  -5.6060  -1.1441   0.1794
 6S3  NAS   N   NT    0  -0.517  -4.8671   0.1002   0.0135
 6S3  CAP   C   CR6   0   0.383  -3.4852   0.0577   0.0512
 6S3  CAO   C   CR16  0  -0.329  -2.7732  -1.0210  -0.5065
 6S3  CAN   C   CR16  0  -0.288  -1.3946  -1.0488  -0.5075
 6S3  CAQ   C   CR16  0  -0.353  -2.7200   1.0907   0.6179
 6S3  CAR   C   CR16  0  -0.275  -1.3369   1.0551   0.6062
 6S3  CAM   C   CR6   0   0.011  -0.6379  -0.0112   0.0435
 6S3  CAH   C   CR5   0   0.386   0.8169  -0.1087   0.0680
 6S3  CAI   C   CR15  0  -0.488   1.5660  -1.2356   0.3206
 6S3  CAE   C   CR56  0   0.170   2.9228  -0.8489   0.2533
 6S3  CAD   C   CR6   0  -0.078   4.1647  -1.4502   0.4092
 6S3  CLAK  CL  CL    0  -0.113   4.2611  -3.1296   0.7813
 6S3  CAA   C   CR16  0  -0.295   5.3086  -0.6914   0.2588
 6S3  CAB   C   CR6   0   0.091   5.1807   0.6663  -0.0510
 6S3  CAJ   C   C     0   0.490   6.4230   1.4891  -0.2280
 6S3  OBA   O   O     0  -0.479   7.5339   0.9911  -0.1017
 6S3  NAZ   N   NH2   0  -0.810   6.2054   2.7727  -0.5264
 6S3  NAC   N   N     0  -0.469   4.0146   1.2818  -0.2029
 6S3  CAF   C   CR56  0   0.480   2.9432   0.5355  -0.0480
 6S3  NAG   N   NR5   0  -0.569   1.6542   0.9627  -0.1613
 6S3  CAL   C   CH3   0  -0.551   1.2888   2.3029  -0.5648
 6S3  H1    H   HCH2  0   0.254  -5.0482   2.1575   0.3091
 6S3  H2    H   HCH2  0   0.221  -5.4984   1.1873   1.7147
 6S3  H3    H   HCH2  0   0.244  -7.4651   2.1397   0.7010
 6S3  H4    H   HCH2  0   0.195  -7.0101   1.5801  -0.9107
 6S3  H6    H   HCH3  0   0.193  -9.2625   0.4092  -0.9842
 6S3  H7    H   HCH3  0   0.234  -9.6088  -0.7383   0.3207
 6S3  H8    H   HCH3  0   0.235  -9.5609   0.9922   0.6604
 6S3  H9    H   HCH2  0   0.243  -7.5670  -1.9322  -0.0549
 6S3  H10   H   HCH2  0   0.196  -7.0733  -0.8543  -1.3664
 6S3  H11   H   HCH2  0   0.223  -5.5835  -1.4639   1.2304
 6S3  H12   H   HCH2  0   0.258  -5.1536  -1.9376  -0.4096
 6S3  H13   H   HCR6  0   0.267  -3.2929  -1.8456  -0.9724
 6S3  H14   H   HCR6  0   0.255  -0.8931  -1.8913  -0.9666
 6S3  H15   H   HCR6  0   0.272  -3.1925   1.9339   1.0991
 6S3  H16   H   HCR6  0   0.260  -0.8052   1.8660   1.0862
 6S3  H17   H   HCR5  0   0.265   1.1744  -2.2096   0.5655
 6S3  H18   H   HCR6  0   0.287   6.2880  -1.1314   0.3770
 6S3  H19   H   HNH2  0   0.410   5.2681   3.1228  -0.6333
 6S3  H20   H   HNH2  0   0.405   6.9779   3.3969  -0.6881
 6S3  H21   H   HCH3  0   0.258   1.1314   2.9544   0.2942
 6S3  H22   H   HCH3  0   0.273   2.0907   2.7187  -1.1692
 6S3  H23   H   HCH3  0   0.268   0.3822   2.2759  -1.1635

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
 6S3  CAY  NAV   single    1.445  0.020  1.445
 6S3  CAU  NAV   single    1.446  0.020  1.446
 6S3  CAU  CAT   single    1.517  0.020  1.517
 6S3  NAV  CAW   single    1.446  0.020  1.446
 6S3  CAW  CAX   single    1.515  0.020  1.515
 6S3  CAT  NAS   single    1.451  0.020  1.451
 6S3  NAS  CAX   single    1.457  0.020  1.457
 6S3  NAS  CAP   single    1.383  0.020  1.383
 6S3  CAQ  CAP   aromatic  1.405  0.020  1.405
 6S3  CAQ  CAR   aromatic  1.384  0.020  1.384
 6S3  CAP  CAO   aromatic  1.408  0.020  1.408
 6S3  CAR  CAM   aromatic  1.394  0.020  1.394
 6S3  CAL  NAG   single    1.447  0.020  1.447
 6S3  CAO  CAN   aromatic  1.379  0.020  1.379
 6S3  CAM  CAN   aromatic  1.397  0.020  1.397
 6S3  CAM  CAH   single    1.458  0.020  1.458
 6S3  NAG  CAH   aromatic  1.379  0.020  1.379
 6S3  NAG  CAF   aromatic  1.363  0.020  1.363
 6S3  CAH  CAI   aromatic  1.376  0.020  1.376
 6S3  CAF  NAC   aromatic  1.315  0.020  1.315
 6S3  CAF  CAE   aromatic  1.417  0.020  1.417
 6S3  NAC  CAB   aromatic  1.327  0.020  1.327
 6S3  CAI  CAE   aromatic  1.412  0.020  1.412
 6S3  NAZ  CAJ   single    1.336  0.020  1.336
 6S3  CAE  CAD   aromatic  1.389  0.020  1.389
 6S3  CAB  CAJ   single    1.501  0.020  1.501
 6S3  CAB  CAA   aromatic  1.398  0.020  1.398
 6S3  CAJ  OBA   double    1.224  0.020  1.224
 6S3  CAD  CAA   aromatic  1.381  0.020  1.381
 6S3  CAD  CLAK  single    1.723  0.020  1.723
 6S3  CAT  H1    single    0.970  0.020  1.090
 6S3  CAT  H2    single    0.970  0.020  1.090
 6S3  CAU  H3    single    0.970  0.020  1.090
 6S3  CAU  H4    single    0.970  0.020  1.090
 6S3  CAY  H6    single    0.970  0.020  1.090
 6S3  CAY  H7    single    0.970  0.020  1.090
 6S3  CAY  H8    single    0.970  0.020  1.090
 6S3  CAW  H9    single    0.970  0.020  1.090
 6S3  CAW  H10   single    0.970  0.020  1.090
 6S3  CAX  H11   single    0.970  0.020  1.090
 6S3  CAX  H12   single    0.970  0.020  1.090
 6S3  CAO  H13   single    0.930  0.020  1.080
 6S3  CAN  H14   single    0.930  0.020  1.080
 6S3  CAQ  H15   single    0.930  0.020  1.080
 6S3  CAR  H16   single    0.930  0.020  1.080
 6S3  CAI  H17   single    0.930  0.020  1.080
 6S3  CAA  H18   single    0.930  0.020  1.080
 6S3  NAZ  H19   single    0.860  0.020  1.020
 6S3  NAZ  H20   single    0.860  0.020  1.020
 6S3  CAL  H21   single    0.970  0.020  1.090
 6S3  CAL  H22   single    0.970  0.020  1.090
 6S3  CAL  H23   single    0.970  0.020  1.090

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
 6S3  H2    CAT  H1    107.57  3.000
 6S3  H2    CAT  NAS   111.31  3.000
 6S3  H1    CAT  NAS   109.58  3.000
 6S3  H2    CAT  CAU   109.75  3.000
 6S3  H1    CAT  CAU   107.33  3.000
 6S3  NAS   CAT  CAU   111.14  3.000
 6S3  H4    CAU  H3    106.99  3.000
 6S3  H4    CAU  NAV   111.56  3.000
 6S3  H3    CAU  NAV   109.42  3.000
 6S3  H4    CAU  CAT   109.05  3.000
 6S3  H3    CAU  CAT   108.23  3.000
 6S3  NAV   CAU  CAT   111.43  3.000
 6S3  CAW   NAV  CAY   111.96  3.000
 6S3  CAW   NAV  CAU   109.29  3.000
 6S3  CAY   NAV  CAU   111.73  3.000
 6S3  H8    CAY  H7    107.90  3.000
 6S3  H8    CAY  H6    107.72  3.000
 6S3  H7    CAY  H6    107.87  3.000
 6S3  H8    CAY  NAV   109.92  3.000
 6S3  H7    CAY  NAV   110.05  3.000
 6S3  H6    CAY  NAV   113.20  3.000
 6S3  H10   CAW  H9    107.18  3.000
 6S3  H10   CAW  CAX   109.38  3.000
 6S3  H9    CAW  CAX   108.18  3.000
 6S3  H10   CAW  NAV   111.73  3.000
 6S3  H9    CAW  NAV   109.41  3.000
 6S3  CAX   CAW  NAV   110.83  3.000
 6S3  H12   CAX  H11   107.30  3.000
 6S3  H12   CAX  NAS   110.54  3.000
 6S3  H11   CAX  NAS   110.31  3.000
 6S3  H12   CAX  CAW   107.73  3.000
 6S3  H11   CAX  CAW   109.41  3.000
 6S3  NAS   CAX  CAW   111.42  3.000
 6S3  CAP   NAS  CAX   118.52  3.000
 6S3  CAP   NAS  CAT   118.44  3.000
 6S3  CAX   NAS  CAT   112.68  3.000
 6S3  CAQ   CAP  CAO   116.60  3.000
 6S3  CAO   CAP  NAS   121.21  3.000
 6S3  CAQ   CAP  NAS   122.18  3.000
 6S3  H13   CAO  CAN   117.73  3.000
 6S3  H13   CAO  CAP   120.83  3.000
 6S3  CAN   CAO  CAP   121.43  3.000
 6S3  H14   CAN  CAM   119.62  3.000
 6S3  H14   CAN  CAO   118.63  3.000
 6S3  CAM   CAN  CAO   121.74  3.000
 6S3  H15   CAQ  CAR   117.47  3.000
 6S3  H15   CAQ  CAP   121.04  3.000
 6S3  CAR   CAQ  CAP   121.47  3.000
 6S3  H16   CAR  CAM   120.40  3.000
 6S3  H16   CAR  CAQ   117.92  3.000
 6S3  CAM   CAR  CAQ   121.63  3.000
 6S3  CAH   CAM  CAR   123.01  3.000
 6S3  CAH   CAM  CAN   119.81  3.000
 6S3  CAR   CAM  CAN   117.11  3.000
 6S3  NAG   CAH  CAI   109.64  3.000
 6S3  CAI   CAH  CAM   126.92  3.000
 6S3  NAG   CAH  CAM   123.43  3.000
 6S3  H17   CAI  CAE   127.38  3.000
 6S3  H17   CAI  CAH   125.72  3.000
 6S3  CAE   CAI  CAH   106.85  3.000
 6S3  CAF   CAE  CAD   115.72  3.000
 6S3  CAD   CAE  CAI   137.33  3.000
 6S3  CAF   CAE  CAI   106.95  3.000
 6S3  CAA   CAD  CLAK  120.85  3.000
 6S3  CLAK  CAD  CAE   119.76  3.000
 6S3  CAA   CAD  CAE   119.38  3.000
 6S3  H18   CAA  CAB   120.18  3.000
 6S3  H18   CAA  CAD   121.02  3.000
 6S3  CAB   CAA  CAD   118.81  3.000
 6S3  NAC   CAB  CAJ   117.36  3.000
 6S3  CAJ   CAB  CAA   118.87  3.000
 6S3  NAC   CAB  CAA   123.78  3.000
 6S3  NAZ   CAJ  OBA   124.19  3.000
 6S3  OBA   CAJ  CAB   121.07  3.000
 6S3  NAZ   CAJ  CAB   114.74  3.000
 6S3  H20   NAZ  H19   118.83  3.000
 6S3  H20   NAZ  CAJ   120.46  3.000
 6S3  H19   NAZ  CAJ   120.65  3.000
 6S3  CAF   NAC  CAB   116.05  3.000
 6S3  NAG   CAF  NAC   125.67  3.000
 6S3  NAC   CAF  CAE   126.25  3.000
 6S3  NAG   CAF  CAE   108.07  3.000
 6S3  CAL   NAG  CAF   123.54  3.000
 6S3  CAF   NAG  CAH   108.48  3.000
 6S3  CAL   NAG  CAH   127.80  3.000
 6S3  H23   CAL  H22   108.58  3.000
 6S3  H23   CAL  H21   109.19  3.000
 6S3  H22   CAL  H21   108.44  3.000
 6S3  H23   CAL  NAG   109.96  3.000
 6S3  H22   CAL  NAG   108.86  3.000
 6S3  H21   CAL  NAG   111.75  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
 6S3  CONST_01  CAM   CAR  CAQ  CAP     0.00   0.0  0
 6S3  CONST_02  CAM   CAN  CAO  CAP     0.00   0.0  0
 6S3  CONST_03  CAR   CAQ  CAP  CAO     0.00   0.0  0
 6S3  CONST_04  CAR   CAM  CAN  CAO     0.00   0.0  0
 6S3  CONST_05  CAH   CAM  CAN  CAO   180.00   0.0  0
 6S3  CONST_06  CAQ   CAP  CAO  CAN     0.00   0.0  0
 6S3  CONST_07  CAQ   CAR  CAM  CAN     0.00   0.0  0
 6S3  CONST_10  CAH   CAM  CAR  CAQ   180.00   0.0  0
 6S3  CONST_13  CAF   NAG  CAH  CAM   180.00   0.0  0
 6S3  CONST_14  CAE   CAI  CAH  CAM   180.00   0.0  0
 6S3  CONST_15  NAC   CAF  NAG  CAH   180.00   0.0  0
 6S3  CONST_16  CAE   CAF  NAG  CAH     0.00   0.0  0
 6S3  CONST_17  CAF   CAE  CAI  CAH     0.00   0.0  0
 6S3  CONST_18  CAD   CAE  CAI  CAH   180.00   0.0  0
 6S3  CONST_19  CAF   NAG  CAH  CAI     0.00   0.0  0
 6S3  CONST_20  NAG   CAF  CAE  CAI     0.00   0.0  0
 6S3  CONST_21  NAC   CAF  CAE  CAI   180.00   0.0  0
 6S3  CONST_22  CAA   CAD  CAE  CAI   180.00   0.0  0
 6S3  CONST_23  CAB   NAC  CAF  CAE     0.00   0.0  0
 6S3  CONST_24  NAG   CAH  CAI  CAE     0.00   0.0  0
 6S3  CONST_25  CAB   CAA  CAD  CAE     0.00   0.0  0
 6S3  CONST_26  NAG   CAF  CAE  CAD   180.00   0.0  0
 6S3  CONST_27  NAC   CAF  CAE  CAD     0.00   0.0  0
 6S3  CONST_28  NAC   CAB  CAA  CAD     0.00   0.0  0
 6S3  CONST_29  CAF   NAC  CAB  CAA     0.00   0.0  0
 6S3  CONST_30  CAF   CAE  CAD  CAA     0.00   0.0  0
 6S3  CONST_31  NAG   CAF  NAC  CAB   180.00   0.0  0
 6S3  CONST_32  CAR   CAQ  CAP  NAS   180.00   0.0  0
 6S3  CONST_33  CAN   CAO  CAP  NAS   180.00   0.0  0
 6S3  CONST_34  CAL   NAG  CAH  CAM     0.00   0.0  0
 6S3  CONST_35  CAL   NAG  CAH  CAI   180.00   0.0  0
 6S3  CONST_36  CLAK  CAD  CAE  CAI     0.00   0.0  0
 6S3  CONST_37  CAL   NAG  CAF  CAE   180.00   0.0  0
 6S3  CONST_38  CAJ   CAB  CAA  CAD   180.00   0.0  0
 6S3  CONST_39  CAF   CAE  CAD  CLAK  180.00   0.0  0
 6S3  CONST_40  CAB   CAA  CAD  CLAK  180.00   0.0  0
 6S3  CONST_41  CAF   NAC  CAB  CAJ   180.00   0.0  0
 6S3  CONST_42  CAL   NAG  CAF  NAC     0.00   0.0  0
 6S3  CONST_43  H15   CAQ  CAP  NAS     0.00   0.0  0
 6S3  CONST_44  H13   CAO  CAP  NAS     0.00   0.0  0
 6S3  CONST_45  H16   CAR  CAQ  CAP   180.00   0.0  0
 6S3  CONST_46  H14   CAN  CAO  CAP   180.00   0.0  0
 6S3  CONST_47  H17   CAI  CAH  CAM     0.00   0.0  0
 6S3  CONST_48  H18   CAA  CAD  CAE   180.00   0.0  0
 6S3  CONST_49  H19   NAZ  CAJ  CAB     0.00   0.0  0
 6S3  CONST_50  H20   NAZ  CAJ  CAB   180.00   0.0  0
 6S3  Var_01    CAW   NAV  CAU  CAT   -59.53  30.0  1
 6S3  Var_02    CAW   CAX  NAS  CAT    51.62  30.0  1
 6S3  Var_03    CAQ   CAP  NAS  CAT    -1.83  30.0  2
 6S3  Var_04    CAX   CAW  NAV  CAU    59.56  30.0  1
 6S3  Var_05    CAX   NAS  CAT  CAU   -51.11  30.0  1
 6S3  Var_06    NAS   CAT  CAU  NAV    55.35  30.0  1
 6S3  Var_07    NAS   CAX  CAW  NAV   -55.83  30.0  1
 6S3  Var_08    NAZ   CAJ  CAB  CAA   179.78  30.0  2
 6S3  Var_09    H6    CAY  NAV  CAU    60.91  30.0  3
 6S3  Var_10    H21   CAL  NAG  CAH    91.46  30.0  2

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
 6S3  plan-1  NAS   0.020
 6S3  plan-1  CAP   0.020
 6S3  plan-1  CAO   0.020
 6S3  plan-1  CAN   0.020
 6S3  plan-1  CAQ   0.020
 6S3  plan-1  CAR   0.020
 6S3  plan-1  CAM   0.020
 6S3  plan-1  CAH   0.020
 6S3  plan-1  H13   0.020
 6S3  plan-1  H14   0.020
 6S3  plan-1  H15   0.020
 6S3  plan-1  H16   0.020
 6S3  plan-2  CAM   0.020
 6S3  plan-2  CAH   0.020
 6S3  plan-2  CAI   0.020
 6S3  plan-2  CAE   0.020
 6S3  plan-2  CAD   0.020
 6S3  plan-2  CLAK  0.020
 6S3  plan-2  CAA   0.020
 6S3  plan-2  CAB   0.020
 6S3  plan-2  CAJ   0.020
 6S3  plan-2  NAC   0.020
 6S3  plan-2  CAF   0.020
 6S3  plan-2  NAG   0.020
 6S3  plan-2  CAL   0.020
 6S3  plan-2  H17   0.020
 6S3  plan-2  H18   0.020
 6S3  plan-3  CAB   0.020
 6S3  plan-3  CAJ   0.020
 6S3  plan-3  OBA   0.020
 6S3  plan-3  NAZ   0.020
 6S3  plan-3  H19   0.020
 6S3  plan-3  H20   0.020

