# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 00:04:30 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: methyl (2~{R})-2-[(4~{S})-6-(4-chlorophenyl)-9-methoxy-1-methyl-4~{H}-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]propanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@H](C)[C@@H]1N=C(c2ccc(Cl)cc2)c3ccc(OC)cc3n4c(C)nnc14
#
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
 9J2  9J2  'methyl (2~{R})-2-[(4~{S})-6-(4-chlorophenyl)-9-methoxy-1-methyl-4~{H}-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]propanoate'  ligand  51  30  .  2022-07-24  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_9J2
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
 9J2  CBD  C   CH3   0  -0.427   0.7982  -2.7714   3.0215
 9J2  OBC  O   O2    0  -0.440  -0.2337  -2.1551   2.2503
 9J2  CAZ  C   C     0   0.614  -0.8772  -2.9096   1.3744
 9J2  OBB  O   O     0  -0.446  -0.6573  -4.0833   1.2086
 9J2  CAV  C   CH1   0  -0.386  -1.9016  -2.1217   0.5868
 9J2  CBA  C   CH3   0  -0.655  -3.2257  -2.8710   0.5068
 9J2  CAJ  C   CH1   0  -0.239  -1.3217  -1.8997  -0.8330
 9J2  NAI  N   N     0  -0.355   0.0780  -1.5190  -0.8494
 9J2  CAK  C   CR5   0   0.418  -2.1036  -0.9372  -1.6548
 9J2  NAO  N   N     0  -0.317  -2.7232  -1.1863  -2.7652
 9J2  NAP  N   N     0  -0.335  -3.1996  -0.0099  -3.2469
 9J2  CAQ  C   CR5   0   0.398  -2.8655   0.9404  -2.4234
 9J2  CAY  C   CH3   0  -0.762  -3.1532   2.3815  -2.6153
 9J2  NAL  N   NR5   0  -0.596  -2.1631   0.3978  -1.3814
 9J2  CAM  C   CR6   0   0.328  -1.6310   1.0208  -0.2356
 9J2  CAR  C   CR16  0  -0.373  -2.3929   1.9655   0.4242
 9J2  CAS  C   CR6   0   0.400  -1.9053   2.5863   1.5748
 9J2  OAW  O   O2    0  -0.460  -2.7148   3.4834   2.1426
 9J2  CAX  C   CH3   0  -0.443  -2.3110   4.0972   3.3554
 9J2  CAT  C   CR16  0  -0.366  -0.6494   2.2306   2.0631
 9J2  CAU  C   CR16  0  -0.266   0.0932   1.2784   1.3903
 9J2  CAN  C   CR6   0  -0.022  -0.3638   0.6500   0.2341
 9J2  CAG  C   C     0   0.236   0.4731  -0.4033  -0.3808
 9J2  CAA  C   CR6   0   0.035   1.9372  -0.1594  -0.4225
 9J2  CAB  C   CR16  0  -0.289   2.8229  -1.2214  -0.2500
 9J2  CAC  C   CR16  0  -0.196   4.1909  -1.0240  -0.3215
 9J2  CAD  C   CR6   0  -0.047   4.6761   0.2488  -0.5870
 9J2  CLA  CL  CL    0  -0.119   6.3851   0.5019  -0.6861
 9J2  CAE  C   CR16  0  -0.193   3.8167   1.3201  -0.7711
 9J2  CAF  C   CR16  0  -0.289   2.4497   1.1102  -0.6789
 9J2  HBE  H   HCH3  0   0.237   1.5802  -3.1846   2.3846
 9J2  HBF  H   HCH3  0   0.253   1.2166  -1.9853   3.6430
 9J2  HBD  H   HCH3  0   0.244   0.3993  -3.5619   3.6564
 9J2  HAV  H   HCH1  0   0.287  -2.0647  -1.1665   1.0862
 9J2  HBA  H   HCH3  0   0.238  -3.1069  -3.8436   0.0301
 9J2  HBB  H   HCH3  0   0.254  -3.6429  -3.0266   1.5013
 9J2  HBC  H   HCH3  0   0.249  -3.9549  -2.2999  -0.0677
 9J2  HAJ  H   HCH1  0   0.293  -1.3912  -2.8569  -1.3550
 9J2  HA2  H   HCH3  0   0.271  -3.9999   2.7155  -2.0155
 9J2  HA0  H   HCH3  0   0.271  -2.2943   2.9997  -2.3565
 9J2  HA1  H   HCH3  0   0.282  -3.4011   2.5527  -3.6602
 9J2  HAR  H   HCR6  0   0.291  -3.3876   2.2125   0.0790
 9J2  HAZ  H   HCH3  0   0.267  -3.1259   4.7518   3.6521
 9J2  HAY  H   HCH3  0   0.237  -2.1421   3.3598   4.1433
 9J2  HAX  H   HCH3  0   0.238  -1.4064   4.6954   3.2259
 9J2  HAT  H   HCR6  0   0.295  -0.2424   2.6732   2.9612
 9J2  HAU  H   HCR6  0   0.277   1.0592   1.0060   1.7935
 9J2  HAB  H   HCR6  0   0.263   2.4394  -2.2125  -0.0473
 9J2  HAC  H   HCR6  0   0.285   4.8704  -1.8515  -0.1712
 9J2  HAE  H   HCR6  0   0.285   4.2026   2.3073  -0.9847
 9J2  HAF  H   HCR6  0   0.274   1.7822   1.9495  -0.8249

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
 9J2  CBD  OBC  single    1.428  0.020  1.428
 9J2  OBC  CAZ  single    1.323  0.020  1.323
 9J2  CAZ  OBB  double    1.206  0.020  1.206
 9J2  CAZ  CAV  single    1.513  0.020  1.513
 9J2  CBA  CAV  single    1.524  0.020  1.524
 9J2  CAV  CAJ  single    1.550  0.020  1.550
 9J2  CAJ  NAI  single    1.451  0.020  1.451
 9J2  CAJ  CAK  single    1.488  0.020  1.488
 9J2  NAO  CAK  aromatic  1.296  0.020  1.296
 9J2  NAO  NAP  aromatic  1.358  0.020  1.358
 9J2  NAI  CAG  double    1.273  0.020  1.273
 9J2  CAK  NAL  aromatic  1.364  0.020  1.364
 9J2  CAB  CAC  aromatic  1.384  0.020  1.384
 9J2  CAB  CAA  aromatic  1.394  0.020  1.394
 9J2  NAP  CAQ  aromatic  1.301  0.020  1.301
 9J2  CAG  CAA  single    1.485  0.020  1.485
 9J2  CAG  CAN  single    1.479  0.020  1.479
 9J2  CAC  CAD  aromatic  1.388  0.020  1.388
 9J2  NAL  CAQ  aromatic  1.369  0.020  1.369
 9J2  NAL  CAM  aromatic  1.409  0.020  1.409
 9J2  CAA  CAF  aromatic  1.393  0.020  1.393
 9J2  CAQ  CAY  single    1.482  0.020  1.482
 9J2  CAN  CAM  aromatic  1.401  0.020  1.401
 9J2  CAN  CAU  aromatic  1.393  0.020  1.393
 9J2  CAM  CAR  aromatic  1.381  0.020  1.381
 9J2  CAD  CLA  single    1.730  0.020  1.730
 9J2  CAD  CAE  aromatic  1.386  0.020  1.386
 9J2  CAU  CAT  aromatic  1.382  0.020  1.382
 9J2  CAF  CAE  aromatic  1.386  0.020  1.386
 9J2  CAR  CAS  aromatic  1.395  0.020  1.395
 9J2  CAT  CAS  aromatic  1.394  0.020  1.394
 9J2  CAS  OAW  single    1.335  0.020  1.335
 9J2  OAW  CAX  single    1.418  0.020  1.418
 9J2  CBD  HBE  single    0.970  0.020  1.090
 9J2  CBD  HBF  single    0.970  0.020  1.090
 9J2  CBD  HBD  single    0.970  0.020  1.090
 9J2  CAV  HAV  single    0.970  0.020  1.090
 9J2  CBA  HBA  single    0.970  0.020  1.090
 9J2  CBA  HBB  single    0.970  0.020  1.090
 9J2  CBA  HBC  single    0.970  0.020  1.090
 9J2  CAJ  HAJ  single    0.970  0.020  1.090
 9J2  CAY  HA2  single    0.970  0.020  1.090
 9J2  CAY  HA0  single    0.970  0.020  1.090
 9J2  CAY  HA1  single    0.970  0.020  1.090
 9J2  CAR  HAR  single    0.930  0.020  1.080
 9J2  CAX  HAZ  single    0.970  0.020  1.090
 9J2  CAX  HAY  single    0.970  0.020  1.090
 9J2  CAX  HAX  single    0.970  0.020  1.090
 9J2  CAT  HAT  single    0.930  0.020  1.080
 9J2  CAU  HAU  single    0.930  0.020  1.080
 9J2  CAB  HAB  single    0.930  0.020  1.080
 9J2  CAC  HAC  single    0.930  0.020  1.080
 9J2  CAE  HAE  single    0.930  0.020  1.080
 9J2  CAF  HAF  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
 9J2  HBD  CBD  HBF  109.44  3.000
 9J2  HBD  CBD  HBE  109.15  3.000
 9J2  HBF  CBD  HBE  109.41  3.000
 9J2  HBD  CBD  OBC  111.30  3.000
 9J2  HBF  CBD  OBC  105.97  3.000
 9J2  HBE  CBD  OBC  111.50  3.000
 9J2  CAZ  OBC  CBD  117.57  3.000
 9J2  CAV  CAZ  OBB  123.97  3.000
 9J2  CAV  CAZ  OBC  112.14  3.000
 9J2  OBB  CAZ  OBC  123.88  3.000
 9J2  HAV  CAV  CAJ  110.50  3.000
 9J2  HAV  CAV  CBA  108.96  3.000
 9J2  CAJ  CAV  CBA  110.34  3.000
 9J2  HAV  CAV  CAZ  108.61  3.000
 9J2  CAJ  CAV  CAZ  107.35  3.000
 9J2  CBA  CAV  CAZ  111.07  3.000
 9J2  HBC  CBA  HBB  107.44  3.000
 9J2  HBC  CBA  HBA  108.06  3.000
 9J2  HBB  CBA  HBA  108.28  3.000
 9J2  HBC  CBA  CAV  110.58  3.000
 9J2  HBB  CBA  CAV  110.80  3.000
 9J2  HBA  CBA  CAV  111.54  3.000
 9J2  HAJ  CAJ  CAK  105.63  3.000
 9J2  HAJ  CAJ  NAI  106.61  3.000
 9J2  CAK  CAJ  NAI  109.34  3.000
 9J2  HAJ  CAJ  CAV  106.77  3.000
 9J2  CAK  CAJ  CAV  113.72  3.000
 9J2  NAI  CAJ  CAV  114.14  3.000
 9J2  CAG  NAI  CAJ  121.69  3.000
 9J2  NAL  CAK  NAO  109.82  3.000
 9J2  NAL  CAK  CAJ  123.05  3.000
 9J2  NAO  CAK  CAJ  126.90  3.000
 9J2  NAP  NAO  CAK  107.78  3.000
 9J2  CAQ  NAP  NAO  108.56  3.000
 9J2  NAL  CAQ  CAY  125.71  3.000
 9J2  CAY  CAQ  NAP  125.34  3.000
 9J2  NAL  CAQ  NAP  108.91  3.000
 9J2  HA1  CAY  HA0  108.59  3.000
 9J2  HA1  CAY  HA2  107.66  3.000
 9J2  HA0  CAY  HA2  107.92  3.000
 9J2  HA1  CAY  CAQ  108.77  3.000
 9J2  HA0  CAY  CAQ  111.59  3.000
 9J2  HA2  CAY  CAQ  112.18  3.000
 9J2  CAM  NAL  CAQ  129.62  3.000
 9J2  CAM  NAL  CAK  125.41  3.000
 9J2  CAQ  NAL  CAK  104.94  3.000
 9J2  CAN  CAM  CAR  121.31  3.000
 9J2  CAR  CAM  NAL  118.85  3.000
 9J2  CAN  CAM  NAL  119.82  3.000
 9J2  HAR  CAR  CAS  118.88  3.000
 9J2  HAR  CAR  CAM  120.73  3.000
 9J2  CAS  CAR  CAM  120.35  3.000
 9J2  CAT  CAS  OAW  124.67  3.000
 9J2  OAW  CAS  CAR  115.96  3.000
 9J2  CAT  CAS  CAR  119.36  3.000
 9J2  CAX  OAW  CAS  118.81  3.000
 9J2  HAX  CAX  HAY  109.10  3.000
 9J2  HAX  CAX  HAZ  108.89  3.000
 9J2  HAY  CAX  HAZ  109.01  3.000
 9J2  HAX  CAX  OAW  111.81  3.000
 9J2  HAY  CAX  OAW  111.63  3.000
 9J2  HAZ  CAX  OAW  106.30  3.000
 9J2  HAT  CAT  CAU  118.96  3.000
 9J2  HAT  CAT  CAS  121.73  3.000
 9J2  CAU  CAT  CAS  119.30  3.000
 9J2  HAU  CAU  CAN  119.26  3.000
 9J2  HAU  CAU  CAT  118.15  3.000
 9J2  CAN  CAU  CAT  122.58  3.000
 9J2  CAG  CAN  CAU  118.73  3.000
 9J2  CAU  CAN  CAM  117.09  3.000
 9J2  CAG  CAN  CAM  124.10  3.000
 9J2  CAA  CAG  CAN  116.91  3.000
 9J2  CAN  CAG  NAI  126.98  3.000
 9J2  CAA  CAG  NAI  116.08  3.000
 9J2  CAF  CAA  CAB  118.91  3.000
 9J2  CAF  CAA  CAG  121.18  3.000
 9J2  CAB  CAA  CAG  119.87  3.000
 9J2  HAB  CAB  CAC  119.39  3.000
 9J2  HAB  CAB  CAA  119.73  3.000
 9J2  CAC  CAB  CAA  120.87  3.000
 9J2  HAC  CAC  CAD  120.58  3.000
 9J2  HAC  CAC  CAB  120.32  3.000
 9J2  CAD  CAC  CAB  119.10  3.000
 9J2  CAE  CAD  CLA  119.46  3.000
 9J2  CAE  CAD  CAC  121.17  3.000
 9J2  CLA  CAD  CAC  119.37  3.000
 9J2  HAE  CAE  CAF  120.23  3.000
 9J2  HAE  CAE  CAD  120.71  3.000
 9J2  CAF  CAE  CAD  119.06  3.000
 9J2  HAF  CAF  CAE  118.80  3.000
 9J2  HAF  CAF  CAA  120.32  3.000
 9J2  CAE  CAF  CAA  120.87  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
 9J2  CONST_01  CAQ  NAP  NAO  CAK     0.00   0.0  0
 9J2  CONST_02  NAL  CAQ  NAP  NAO     0.00   0.0  0
 9J2  CONST_03  CAT  CAS  CAR  CAM     0.00   0.0  0
 9J2  CONST_04  CAU  CAT  CAS  CAR     0.00   0.0  0
 9J2  CONST_05  CAN  CAU  CAT  CAS     0.00   0.0  0
 9J2  CONST_06  CAD  CAC  CAB  CAA     0.00   0.0  0
 9J2  CONST_07  CAD  CAE  CAF  CAA     0.00   0.0  0
 9J2  CONST_08  CAE  CAD  CAC  CAB     0.00   0.0  0
 9J2  CONST_09  CAE  CAF  CAA  CAB     0.00   0.0  0
 9J2  CONST_10  CAF  CAA  CAB  CAC     0.00   0.0  0
 9J2  CONST_11  CAF  CAE  CAD  CAC     0.00   0.0  0
 9J2  CONST_12  CAC  CAB  CAA  CAG   180.00   0.0  0
 9J2  CONST_13  CAE  CAF  CAA  CAG   180.00   0.0  0
 9J2  CONST_14  CAY  CAQ  NAP  NAO   180.00   0.0  0
 9J2  CONST_15  OAW  CAS  CAR  CAM   180.00   0.0  0
 9J2  CONST_16  CAU  CAT  CAS  OAW   180.00   0.0  0
 9J2  CONST_17  CLA  CAD  CAC  CAB   180.00   0.0  0
 9J2  CONST_18  CAF  CAE  CAD  CLA   180.00   0.0  0
 9J2  CONST_19  HAT  CAT  CAS  CAR   180.00   0.0  0
 9J2  CONST_20  HAU  CAU  CAT  CAS   180.00   0.0  0
 9J2  CONST_21  HAR  CAR  CAS  CAT   180.00   0.0  0
 9J2  CONST_22  HAB  CAB  CAA  CAG     0.00   0.0  0
 9J2  CONST_23  HAF  CAF  CAA  CAG     0.00   0.0  0
 9J2  CONST_24  HAC  CAC  CAB  CAA   180.00   0.0  0
 9J2  CONST_25  HAE  CAE  CAF  CAA   180.00   0.0  0
 9J2  Var_01    CAT  CAS  OAW  CAX    -2.36  30.0  2
 9J2  Var_02    HA2  CAY  CAQ  NAP   101.79  30.0  2
 9J2  Var_03    HAZ  CAX  OAW  CAS  -177.85  30.0  3
 9J2  Var_04    OBB  CAZ  OBC  CBD     1.26  30.0  3
 9J2  Var_05    HBE  CBD  OBC  CAZ    59.09  30.0  3

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
 9J2  chir_01  CAV  CAZ  CBA  CAJ  positiv
 9J2  chir_02  CAJ  NAI  CAV  CAK  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
 9J2  plan-1  CAG  0.020
 9J2  plan-1  CAA  0.020
 9J2  plan-1  CAB  0.020
 9J2  plan-1  CAC  0.020
 9J2  plan-1  CAD  0.020
 9J2  plan-1  CLA  0.020
 9J2  plan-1  CAE  0.020
 9J2  plan-1  CAF  0.020
 9J2  plan-1  HAB  0.020
 9J2  plan-1  HAC  0.020
 9J2  plan-1  HAE  0.020
 9J2  plan-1  HAF  0.020
 9J2  plan-2  CAJ  0.020
 9J2  plan-2  CAK  0.020
 9J2  plan-2  NAO  0.020
 9J2  plan-2  NAP  0.020
 9J2  plan-2  CAQ  0.020
 9J2  plan-2  CAY  0.020
 9J2  plan-2  NAL  0.020
 9J2  plan-2  CAM  0.020
 9J2  plan-3  NAL  0.020
 9J2  plan-3  CAM  0.020
 9J2  plan-3  CAR  0.020
 9J2  plan-3  CAS  0.020
 9J2  plan-3  OAW  0.020
 9J2  plan-3  CAT  0.020
 9J2  plan-3  CAU  0.020
 9J2  plan-3  CAN  0.020
 9J2  plan-3  CAG  0.020
 9J2  plan-3  HAR  0.020
 9J2  plan-3  HAT  0.020
 9J2  plan-3  HAU  0.020
 9J2  plan-4  OBC  0.020
 9J2  plan-4  CAZ  0.020
 9J2  plan-4  OBB  0.020
 9J2  plan-4  CAV  0.020

