# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 01:36:49 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: N-{4-[(2-amino-3-cyano-1H-indol-5-yl)oxy]phenyl}-L-serinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CO)C(=O)Nc1ccc(Oc2ccc3[nH]c(N)c(C#N)c3c2)cc1
#
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
 8R2  8R2  N-{4-[(2-amino-3-cyano-1H-indol-5-yl)oxy]phenyl}-L-serinamide  ligand  43  26  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8R2
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
 8R2  CAM   C  CR16  0  -0.437  -2.7580  -0.3014  -0.7384
 8R2  CAY   C  CR56  0   0.129  -3.9408   0.1885  -0.1978
 8R2  CAW   C  CR5   0  -0.169  -4.7092   1.3857  -0.4004
 8R2  CAF   C  CSP   0  -0.037  -4.4025   2.4635  -1.2341
 8R2  NAA   N  NS    0  -0.284  -4.1373   3.3573  -1.9219
 8R2  CAS   C  CR5   0   0.583  -5.8250   1.3035   0.4414
 8R2  NAB   N  NH2   0  -0.839  -6.8015   2.1981   0.6366
 8R2  NAP   N  NR15  0  -0.747  -5.7628   0.1380   1.1229
 8R2  CAX   C  CR56  0   0.351  -4.6328  -0.5707   0.7625
 8R2  CAL   C  CR16  0  -0.295  -4.1750  -1.7979   1.2032
 8R2  CAK   C  CR16  0  -0.345  -2.9877  -2.2772   0.6638
 8R2  CAV   C  CR6   0   0.313  -2.3032  -1.5337  -0.2947
 8R2  OAQ   O  O2    0  -0.518  -1.1657  -2.0720  -0.8519
 8R2  CAU   C  CR6   0   0.354   0.0510  -1.6060  -0.4554
 8R2  CAJ   C  CR16  0  -0.327   1.1497  -2.0313  -1.1932
 8R2  CAH   C  CR16  0  -0.291   2.4287  -1.6158  -0.8631
 8R2  CAI   C  CR16  0  -0.334   0.2424  -0.7636   0.6324
 8R2  CAG   C  CR16  0  -0.323   1.5231  -0.3395   0.9516
 8R2  CAT   C  CR6   0   0.346   2.6285  -0.7493   0.2118
 8R2  NAO   N  NH1   0  -0.733   3.8937  -0.2936   0.6165
 8R2  C     C  C     0   0.503   4.9973  -0.1204  -0.1462
 8R2  O     O  O     0  -0.469   5.0654  -0.4127  -1.3279
 8R2  CA    C  CH1   0  -0.262   6.1814   0.5226   0.5836
 8R2  N     N  NH2   0  -0.770   7.4504  -0.0828   0.2500
 8R2  CB    C  CH2   0  -0.124   6.1768   2.0075   0.2318
 8R2  OG    O  OH1   0  -0.663   7.1703   2.6588   0.9813
 8R2  HAM   H  HCR6  0   0.263  -2.2043   0.2567  -1.4839
 8R2  HAB1  H  HNH2  0   0.414  -6.9027   2.9556  -0.0176
 8R2  HAB2  H  HNH2  0   0.415  -7.6474   1.9181   1.1046
 8R2  HAP   H  HNR5  0   0.425  -6.4643  -0.1814   1.7728
 8R2  HAL   H  HCR6  0   0.273  -4.7176  -2.3712   1.9431
 8R2  HAK   H  HCR6  0   0.268  -2.5951  -3.2341   0.9818
 8R2  HAJ   H  HCR6  0   0.270   1.0054  -2.7001  -2.0330
 8R2  HAI   H  HCR6  0   0.281  -0.5896  -0.4257   1.2363
 8R2  HAH   H  HCR6  0   0.275   3.2590  -1.9791  -1.4473
 8R2  HAG   H  HCR6  0   0.274   1.6581   0.3275   1.7947
 8R2  HAO   H  HNH1  0   0.414   3.9489   0.0345   1.5688
 8R2  HA    H  HCH1  0   0.259   6.0323   0.4248   1.6642
 8R2  HN1   H  HNH2  0   0.354   7.4515  -1.0573   0.5240
 8R2  HN2   H  HNH2  0   0.343   7.5813  -0.0723  -0.7548
 8R2  HB1C  H  HCH2  0   0.201   6.3454   2.1139  -0.8485
 8R2  HB2C  H  HCH2  0   0.206   5.1796   2.4168   0.4409
 8R2  HG    H  HOH1  0   0.456   7.1505   3.5912   0.7480

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
 8R2  CAM  CAY   aromatic  1.390  0.020  1.390
 8R2  CAM  CAV   aromatic  1.386  0.020  1.386
 8R2  CAY  CAW   aromatic  1.437  0.020  1.437
 8R2  CAY  CAX   aromatic  1.406  0.020  1.406
 8R2  CAW  CAF   single    1.397  0.020  1.397
 8R2  CAW  CAS   aromatic  1.400  0.020  1.400
 8R2  CAF  NAA   triple    1.159  0.020  1.159
 8R2  CAS  NAB   single    1.339  0.020  1.339
 8R2  CAS  NAP   aromatic  1.352  0.020  1.352
 8R2  NAP  CAX   aromatic  1.382  0.020  1.382
 8R2  CAX  CAL   aromatic  1.382  0.020  1.382
 8R2  CAL  CAK   aromatic  1.389  0.020  1.389
 8R2  CAK  CAV   aromatic  1.393  0.020  1.393
 8R2  CAV  OAQ   single    1.376  0.020  1.376
 8R2  OAQ  CAU   single    1.362  0.020  1.362
 8R2  CAU  CAJ   aromatic  1.390  0.020  1.390
 8R2  CAU  CAI   aromatic  1.389  0.020  1.389
 8R2  CAJ  CAH   aromatic  1.385  0.020  1.385
 8R2  CAH  CAT   aromatic  1.395  0.020  1.395
 8R2  CAI  CAG   aromatic  1.386  0.020  1.386
 8R2  CAG  CAT   aromatic  1.392  0.020  1.392
 8R2  CAT  NAO   single    1.404  0.020  1.404
 8R2  NAO  C     single    1.353  0.020  1.353
 8R2  C    O     double    1.219  0.020  1.219
 8R2  C    CA    single    1.532  0.020  1.532
 8R2  CA   N     single    1.445  0.020  1.445
 8R2  CA   CB    single    1.526  0.020  1.526
 8R2  CB   OG    single    1.405  0.020  1.405
 8R2  CAM  HAM   single    0.930  0.020  1.080
 8R2  NAB  HAB1  single    0.890  0.020  1.040
 8R2  NAB  HAB2  single    0.890  0.020  1.040
 8R2  NAP  HAP   single    0.860  0.020  1.020
 8R2  CAL  HAL   single    0.930  0.020  1.080
 8R2  CAK  HAK   single    0.930  0.020  1.080
 8R2  CAJ  HAJ   single    0.930  0.020  1.080
 8R2  CAI  HAI   single    0.930  0.020  1.080
 8R2  CAH  HAH   single    0.930  0.020  1.080
 8R2  CAG  HAG   single    0.930  0.020  1.080
 8R2  NAO  HAO   single    0.860  0.020  1.020
 8R2  CA   HA    single    0.970  0.020  1.090
 8R2  N    HN1   single    0.890  0.020  1.040
 8R2  N    HN2   single    0.890  0.020  1.040
 8R2  CB   HB1C  single    0.970  0.020  1.090
 8R2  CB   HB2C  single    0.970  0.020  1.090
 8R2  OG   HG    single    0.850  0.020  0.980

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
 8R2  HAM   CAM  CAV   120.69  3.000
 8R2  HAM   CAM  CAY   121.40  3.000
 8R2  CAV   CAM  CAY   117.91  3.000
 8R2  CAX   CAY  CAW   106.44  3.000
 8R2  CAX   CAY  CAM   119.61  3.000
 8R2  CAW   CAY  CAM   133.95  3.000
 8R2  CAS   CAW  CAF   125.39  3.000
 8R2  CAS   CAW  CAY   107.01  3.000
 8R2  CAF   CAW  CAY   127.57  3.000
 8R2  NAA   CAF  CAW   180.00  3.000
 8R2  NAP   CAS  NAB   122.43  3.000
 8R2  NAP   CAS  CAW   108.49  3.000
 8R2  NAB   CAS  CAW   129.03  3.000
 8R2  HAB2  NAB  HAB1  115.29  3.000
 8R2  HAB2  NAB  CAS   119.67  3.000
 8R2  HAB1  NAB  CAS   118.80  3.000
 8R2  HAP   NAP  CAX   125.08  3.000
 8R2  HAP   NAP  CAS   124.49  3.000
 8R2  CAX   NAP  CAS   110.39  3.000
 8R2  CAL   CAX  NAP   130.03  3.000
 8R2  CAL   CAX  CAY   122.29  3.000
 8R2  NAP   CAX  CAY   107.68  3.000
 8R2  HAL   CAL  CAK   120.75  3.000
 8R2  HAL   CAL  CAX   121.50  3.000
 8R2  CAK   CAL  CAX   117.75  3.000
 8R2  HAK   CAK  CAV   119.73  3.000
 8R2  HAK   CAK  CAL   120.07  3.000
 8R2  CAV   CAK  CAL   120.20  3.000
 8R2  OAQ   CAV  CAK   118.42  3.000
 8R2  OAQ   CAV  CAM   119.29  3.000
 8R2  CAK   CAV  CAM   122.24  3.000
 8R2  CAU   OAQ  CAV   119.12  3.000
 8R2  CAI   CAU  CAJ   119.49  3.000
 8R2  CAI   CAU  OAQ   123.96  3.000
 8R2  CAJ   CAU  OAQ   116.55  3.000
 8R2  HAJ   CAJ  CAH   119.54  3.000
 8R2  HAJ   CAJ  CAU   119.68  3.000
 8R2  CAH   CAJ  CAU   120.78  3.000
 8R2  HAH   CAH  CAT   121.09  3.000
 8R2  HAH   CAH  CAJ   118.75  3.000
 8R2  CAT   CAH  CAJ   120.15  3.000
 8R2  HAI   CAI  CAG   119.10  3.000
 8R2  HAI   CAI  CAU   121.35  3.000
 8R2  CAG   CAI  CAU   119.55  3.000
 8R2  HAG   CAG  CAT   119.73  3.000
 8R2  HAG   CAG  CAI   118.85  3.000
 8R2  CAT   CAG  CAI   121.41  3.000
 8R2  NAO   CAT  CAG   117.82  3.000
 8R2  NAO   CAT  CAH   123.55  3.000
 8R2  CAG   CAT  CAH   118.60  3.000
 8R2  HAO   NAO  C     116.49  3.000
 8R2  HAO   NAO  CAT   115.27  3.000
 8R2  C     NAO  CAT   127.89  3.000
 8R2  CA    C    O     121.27  3.000
 8R2  CA    C    NAO   114.56  3.000
 8R2  O     C    NAO   124.15  3.000
 8R2  HA    CA   CB    108.30  3.000
 8R2  HA    CA   N     108.06  3.000
 8R2  CB    CA   N     110.92  3.000
 8R2  HA    CA   C     109.10  3.000
 8R2  CB    CA   C     107.23  3.000
 8R2  N     CA   C     113.13  3.000
 8R2  HN2   N    HN1   106.16  3.000
 8R2  HN2   N    CA    109.76  3.000
 8R2  HN1   N    CA    109.98  3.000
 8R2  HB2C  CB   HB1C  106.89  3.000
 8R2  HB2C  CB   OG    111.59  3.000
 8R2  HB1C  CB   OG    111.79  3.000
 8R2  HB2C  CB   CA    108.76  3.000
 8R2  HB1C  CB   CA    108.69  3.000
 8R2  OG    CB   CA    109.03  3.000
 8R2  HG    OG   CB    107.80  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
 8R2  CONST_01  CAS   CAW  CAY  CAM   180.00   0.0  0
 8R2  CONST_02  NAP   CAX  CAY  CAM   180.00   0.0  0
 8R2  CONST_03  CAL   CAX  CAY  CAM     0.00   0.0  0
 8R2  CONST_04  CAL   CAK  CAV  CAM     0.00   0.0  0
 8R2  CONST_05  CAK   CAV  CAM  CAY     0.00   0.0  0
 8R2  CONST_06  NAP   CAS  CAW  CAY     0.00   0.0  0
 8R2  CONST_07  CAS   NAP  CAX  CAY     0.00   0.0  0
 8R2  CONST_08  CAK   CAL  CAX  CAY     0.00   0.0  0
 8R2  CONST_09  CAV   CAM  CAY  CAW   180.00   0.0  0
 8R2  CONST_10  NAP   CAX  CAY  CAW     0.00   0.0  0
 8R2  CONST_11  CAL   CAX  CAY  CAW   180.00   0.0  0
 8R2  CONST_12  CAX   NAP  CAS  CAW     0.00   0.0  0
 8R2  CONST_13  CAX   CAY  CAW  CAS     0.00   0.0  0
 8R2  CONST_14  CAL   CAX  NAP  CAS   180.00   0.0  0
 8R2  CONST_15  CAK   CAL  CAX  NAP   180.00   0.0  0
 8R2  CONST_16  CAV   CAM  CAY  CAX     0.00   0.0  0
 8R2  CONST_17  CAV   CAK  CAL  CAX     0.00   0.0  0
 8R2  CONST_18  CAT   CAH  CAJ  CAU     0.00   0.0  0
 8R2  CONST_19  CAT   CAG  CAI  CAU     0.00   0.0  0
 8R2  CONST_20  CAG   CAI  CAU  CAJ     0.00   0.0  0
 8R2  CONST_21  CAG   CAT  CAH  CAJ     0.00   0.0  0
 8R2  CONST_22  CAI   CAU  CAJ  CAH     0.00   0.0  0
 8R2  CONST_23  CAI   CAG  CAT  CAH     0.00   0.0  0
 8R2  CONST_24  CAF   CAW  CAY  CAM     0.00   0.0  0
 8R2  CONST_25  OAQ   CAV  CAM  CAY   180.00   0.0  0
 8R2  CONST_26  NAB   CAS  CAW  CAY   180.00   0.0  0
 8R2  CONST_27  CAX   CAY  CAW  CAF   180.00   0.0  0
 8R2  CONST_28  NAP   CAS  CAW  CAF   180.00   0.0  0
 8R2  CONST_29  CAX   NAP  CAS  NAB   180.00   0.0  0
 8R2  CONST_30  OAQ   CAV  CAK  CAL   180.00   0.0  0
 8R2  CONST_31  CAH   CAJ  CAU  OAQ   180.00   0.0  0
 8R2  CONST_32  CAG   CAI  CAU  OAQ   180.00   0.0  0
 8R2  CONST_33  NAO   CAT  CAH  CAJ   180.00   0.0  0
 8R2  CONST_34  NAO   CAT  CAG  CAI   180.00   0.0  0
 8R2  CONST_35  HAK   CAK  CAV  CAM   180.00   0.0  0
 8R2  CONST_36  HAP   NAP  CAX  CAY   180.00   0.0  0
 8R2  CONST_37  HAL   CAL  CAX  CAY   180.00   0.0  0
 8R2  CONST_38  HAM   CAM  CAY  CAW     0.00   0.0  0
 8R2  CONST_39  HAH   CAH  CAJ  CAU   180.00   0.0  0
 8R2  CONST_40  HAG   CAG  CAI  CAU   180.00   0.0  0
 8R2  CONST_41  HAI   CAI  CAU  CAJ   180.00   0.0  0
 8R2  CONST_42  HAJ   CAJ  CAU  CAI   180.00   0.0  0
 8R2  CONST_45  HAB1  NAB  CAS  CAW     0.00   0.0  0
 8R2  CONST_46  HAB2  NAB  CAS  CAW   180.00   0.0  0
 8R2  CONST_48  O     C    NAO  CAT     0.00   0.0  0
 8R2  CONST_49  CA    C    NAO  CAT   180.00   0.0  0
 8R2  Var_01    CAJ   CAU  OAQ  CAV  -170.29  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 8R2  chir_01  CA  C  N  CB  negativ

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
 8R2  plan-1  OAQ   0.020
 8R2  plan-1  CAU   0.020
 8R2  plan-1  CAJ   0.020
 8R2  plan-1  CAH   0.020
 8R2  plan-1  CAI   0.020
 8R2  plan-1  CAG   0.020
 8R2  plan-1  CAT   0.020
 8R2  plan-1  NAO   0.020
 8R2  plan-1  HAJ   0.020
 8R2  plan-1  HAI   0.020
 8R2  plan-1  HAH   0.020
 8R2  plan-1  HAG   0.020
 8R2  plan-2  CAM   0.020
 8R2  plan-2  CAY   0.020
 8R2  plan-2  CAW   0.020
 8R2  plan-2  CAF   0.020
 8R2  plan-2  NAA   0.020
 8R2  plan-2  CAS   0.020
 8R2  plan-2  NAB   0.020
 8R2  plan-2  NAP   0.020
 8R2  plan-2  CAX   0.020
 8R2  plan-2  CAL   0.020
 8R2  plan-2  CAK   0.020
 8R2  plan-2  CAV   0.020
 8R2  plan-2  OAQ   0.020
 8R2  plan-2  HAM   0.020
 8R2  plan-2  HAP   0.020
 8R2  plan-2  HAL   0.020
 8R2  plan-2  HAK   0.020
 8R2  plan-3  CAT   0.020
 8R2  plan-3  NAO   0.020
 8R2  plan-3  C     0.020
 8R2  plan-3  O     0.020
 8R2  plan-3  CA    0.020
 8R2  plan-3  HAO   0.020
 8R2  plan-4  CAS   0.020
 8R2  plan-4  NAB   0.020
 8R2  plan-4  HAB1  0.020
 8R2  plan-4  HAB2  0.020

