# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 23:50:23 2020
#   Inital geometry file: a 137 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]butanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H]([C@@H]1N=C(c2ccc(Cl)cc2)c3ccc(OC)cc3n4c(C)nnc14)C(=O)OC
#
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
 9J5  9J5  '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]butanoate'  ligand  54  31  .  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_9J5
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
 9J5  CBC  C   CH3   0  -0.429  -0.4779  -3.1724  -2.7554
 9J5  OBA  O   O2    0  -0.438   0.4266  -2.3375  -2.0299
 9J5  CAX  C   C     0   0.607   1.0480  -2.8668  -0.9897
 9J5  OBB  O   O     0  -0.446   0.9062  -4.0094  -0.6309
 9J5  CAW  C   CH1   0  -0.380   1.9480  -1.8686  -0.2916
 9J5  CAY  C   CH2   0  -0.420   3.3673  -2.4167  -0.1479
 9J5  CAZ  C   CH3   0  -0.673   4.0357  -2.6872  -1.4888
 9J5  CAJ  C   CH1   0  -0.240   1.3196  -1.5845   1.0927
 9J5  NAI  N   N     0  -0.353  -0.1095  -1.3379   1.0381
 9J5  CAK  C   CR5   0   0.419   1.9805  -0.4886   1.8498
 9J5  NAS  N   N     0  -0.316   2.5784  -0.5887   2.9950
 9J5  NAT  N   N     0  -0.334   2.9266   0.6621   3.3913
 9J5  CAU  C   CR5   0   0.398   2.5375   1.5080   2.4826
 9J5  CAV  C   CH3   0  -0.762   2.6859   2.9801   2.5644
 9J5  NAL  N   NR5   0  -0.598   1.9273   0.8196   1.4685
 9J5  CAM  C   CR6   0   0.330   1.3796   1.2971   0.2620
 9J5  CAO  C   CR16  0  -0.374   2.0703   2.2589  -0.4487
 9J5  CAP  C   CR6   0   0.400   1.5632   2.7455  -1.6544
 9J5  OBD  O   O2    0  -0.460   2.3010   3.6743  -2.2668
 9J5  CBE  C   CH3   0  -0.443   1.8692   4.1707  -3.5229
 9J5  CAQ  C   CR16  0  -0.366   0.3635   2.2349  -2.1467
 9J5  CAR  C   CR16  0  -0.266  -0.3071   1.2666  -1.4230
 9J5  CAN  C   CR6   0  -0.023   0.1685   0.7716  -0.2108
 9J5  CAH  C   C     0   0.233  -0.5873  -0.3071   0.4638
 9J5  CAE  C   CR6   0   0.034  -2.0685  -0.2023   0.4412
 9J5  CAD  C   CR16  0  -0.289  -2.8438  -1.3538   0.3197
 9J5  CAC  C   CR16  0  -0.197  -4.2260  -1.2840   0.3361
 9J5  CAB  C   CR6   0  -0.047  -4.8372  -0.0483   0.4944
 9J5  CLA  CL  CL    0  -0.119  -6.5649   0.0471   0.5236
 9J5  CAG  C   CR16  0  -0.193  -4.0892   1.1109   0.6254
 9J5  CAF  C   CR16  0  -0.288  -2.7061   1.0274   0.5889
 9J5  HBC  H   HCH3  0   0.243   0.0279  -4.0468  -3.1634
 9J5  HBE  H   HCH3  0   0.239  -1.3071  -3.4988  -2.1275
 9J5  HBD  H   HCH3  0   0.255  -0.8595  -2.5629  -3.5686
 9J5  HAY  H   HCH1  0   0.280   1.9814  -0.9584  -0.8922
 9J5  HAZ  H   HCH2  0   0.249   3.9628  -1.6884   0.4075
 9J5  HA0  H   HCH2  0   0.237   3.3501  -3.3259   0.4578
 9J5  HA2  H   HCH3  0   0.227   3.5412  -3.4889  -2.0399
 9J5  HA1  H   HCH3  0   0.227   4.0295  -1.7966  -2.1188
 9J5  HA3  H   HCH3  0   0.243   5.0739  -2.9862  -1.3475
 9J5  HAJ  H   HCH1  0   0.293   1.4604  -2.4846   1.6953
 9J5  HAX  H   HCH3  0   0.270   3.5000   3.3473   1.9398
 9J5  HAV  H   HCH3  0   0.271   1.7737   3.4933   2.2619
 9J5  HAW  H   HCH3  0   0.282   2.9111   3.2510   3.5931
 9J5  HAO  H   HCR6  0   0.291   3.0253   2.6267  -0.0987
 9J5  HBF  H   HCH3  0   0.237   1.7880   3.3741  -4.2655
 9J5  HBG  H   HCH3  0   0.238   0.9095   4.6861  -3.4455
 9J5  HBH  H   HCH3  0   0.267   2.6251   4.8809  -3.8467
 9J5  HAQ  H   HCR6  0   0.296  -0.0560   2.5685  -3.0852
 9J5  HAR  H   HCR6  0   0.278  -1.2294   0.8731  -1.8289
 9J5  HAD  H   HCR6  0   0.263  -2.3617  -2.3150   0.1995
 9J5  HAC  H   HCR6  0   0.285  -4.8195  -2.1809   0.2245
 9J5  HAG  H   HCR6  0   0.285  -4.5738   2.0686   0.7565
 9J5  HAF  H   HCR6  0   0.274  -2.1247   1.9343   0.6943

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
 9J5  CAV  CAU  single    1.482  0.020  1.482
 9J5  CAZ  CAY  single    1.523  0.020  1.523
 9J5  OBD  CBE  single    1.418  0.020  1.418
 9J5  OBD  CAP  single    1.335  0.020  1.335
 9J5  NAT  CAU  aromatic  1.301  0.020  1.301
 9J5  NAT  NAS  aromatic  1.358  0.020  1.358
 9J5  CAU  NAL  aromatic  1.369  0.020  1.369
 9J5  CAO  CAP  aromatic  1.396  0.020  1.396
 9J5  CAO  CAM  aromatic  1.381  0.020  1.381
 9J5  CAY  CAW  single    1.528  0.020  1.528
 9J5  NAS  CAK  aromatic  1.296  0.020  1.296
 9J5  CAP  CAQ  aromatic  1.394  0.020  1.394
 9J5  NAL  CAK  aromatic  1.364  0.020  1.364
 9J5  NAL  CAM  aromatic  1.408  0.020  1.408
 9J5  CAK  CAJ  single    1.487  0.020  1.487
 9J5  CAM  CAN  aromatic  1.402  0.020  1.402
 9J5  CAQ  CAR  aromatic  1.382  0.020  1.382
 9J5  CAW  CAJ  single    1.547  0.020  1.547
 9J5  CAW  CAX  single    1.515  0.020  1.515
 9J5  CAJ  NAI  single    1.451  0.020  1.451
 9J5  CAN  CAR  aromatic  1.393  0.020  1.393
 9J5  CAN  CAH  single    1.480  0.020  1.480
 9J5  CAX  OBA  single    1.322  0.020  1.322
 9J5  CAX  OBB  double    1.206  0.020  1.206
 9J5  OBA  CBC  single    1.429  0.020  1.429
 9J5  NAI  CAH  double    1.273  0.020  1.273
 9J5  CAH  CAE  single    1.485  0.020  1.485
 9J5  CAE  CAD  aromatic  1.393  0.020  1.393
 9J5  CAE  CAF  aromatic  1.393  0.020  1.393
 9J5  CAD  CAC  aromatic  1.384  0.020  1.384
 9J5  CAF  CAG  aromatic  1.386  0.020  1.386
 9J5  CAC  CAB  aromatic  1.388  0.020  1.388
 9J5  CAG  CAB  aromatic  1.386  0.020  1.386
 9J5  CAB  CLA  single    1.731  0.020  1.731
 9J5  CBC  HBC  single    0.970  0.020  1.090
 9J5  CBC  HBE  single    0.970  0.020  1.090
 9J5  CBC  HBD  single    0.970  0.020  1.090
 9J5  CAW  HAY  single    0.970  0.020  1.090
 9J5  CAY  HAZ  single    0.970  0.020  1.090
 9J5  CAY  HA0  single    0.970  0.020  1.090
 9J5  CAZ  HA2  single    0.970  0.020  1.090
 9J5  CAZ  HA1  single    0.970  0.020  1.090
 9J5  CAZ  HA3  single    0.970  0.020  1.090
 9J5  CAJ  HAJ  single    0.970  0.020  1.090
 9J5  CAV  HAX  single    0.970  0.020  1.090
 9J5  CAV  HAV  single    0.970  0.020  1.090
 9J5  CAV  HAW  single    0.970  0.020  1.090
 9J5  CAO  HAO  single    0.930  0.020  1.080
 9J5  CBE  HBF  single    0.970  0.020  1.090
 9J5  CBE  HBG  single    0.970  0.020  1.090
 9J5  CBE  HBH  single    0.970  0.020  1.090
 9J5  CAQ  HAQ  single    0.930  0.020  1.080
 9J5  CAR  HAR  single    0.930  0.020  1.080
 9J5  CAD  HAD  single    0.930  0.020  1.080
 9J5  CAC  HAC  single    0.930  0.020  1.080
 9J5  CAG  HAG  single    0.930  0.020  1.080
 9J5  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
 9J5  HBD  CBC  HBE  109.40  3.000
 9J5  HBD  CBC  HBC  109.47  3.000
 9J5  HBE  CBC  HBC  109.18  3.000
 9J5  HBD  CBC  OBA  105.95  3.000
 9J5  HBE  CBC  OBA  111.35  3.000
 9J5  HBC  CBC  OBA  111.43  3.000
 9J5  CAX  OBA  CBC  117.58  3.000
 9J5  CAW  CAX  OBB  123.86  3.000
 9J5  OBB  CAX  OBA  123.93  3.000
 9J5  CAW  CAX  OBA  112.21  3.000
 9J5  HAY  CAW  CAJ  110.60  3.000
 9J5  HAY  CAW  CAY  108.82  3.000
 9J5  CAJ  CAW  CAY  111.04  3.000
 9J5  HAY  CAW  CAX  108.32  3.000
 9J5  CAJ  CAW  CAX  106.99  3.000
 9J5  CAY  CAW  CAX  111.03  3.000
 9J5  HA0  CAY  HAZ  106.35  3.000
 9J5  HA0  CAY  CAZ  110.32  3.000
 9J5  HAZ  CAY  CAZ  109.07  3.000
 9J5  HA0  CAY  CAW  109.64  3.000
 9J5  HAZ  CAY  CAW  108.36  3.000
 9J5  CAZ  CAY  CAW  112.87  3.000
 9J5  HA3  CAZ  HA1  107.72  3.000
 9J5  HA3  CAZ  HA2  107.20  3.000
 9J5  HA1  CAZ  HA2  107.79  3.000
 9J5  HA3  CAZ  CAY  110.66  3.000
 9J5  HA1  CAZ  CAY  111.17  3.000
 9J5  HA2  CAZ  CAY  112.11  3.000
 9J5  HAJ  CAJ  CAK  105.61  3.000
 9J5  HAJ  CAJ  NAI  106.72  3.000
 9J5  CAK  CAJ  NAI  109.37  3.000
 9J5  HAJ  CAJ  CAW  106.86  3.000
 9J5  NAI  CAJ  CAW  113.43  3.000
 9J5  CAK  CAJ  CAW  114.24  3.000
 9J5  CAH  NAI  CAJ  121.61  3.000
 9J5  NAL  CAK  NAS  109.83  3.000
 9J5  NAL  CAK  CAJ  123.18  3.000
 9J5  NAS  CAK  CAJ  126.74  3.000
 9J5  NAT  NAS  CAK  107.77  3.000
 9J5  CAU  NAT  NAS  108.57  3.000
 9J5  NAL  CAU  CAV  125.80  3.000
 9J5  NAL  CAU  NAT  108.89  3.000
 9J5  CAV  CAU  NAT  125.27  3.000
 9J5  HAW  CAV  HAV  108.58  3.000
 9J5  HAW  CAV  HAX  107.66  3.000
 9J5  HAV  CAV  HAX  107.92  3.000
 9J5  HAW  CAV  CAU  108.69  3.000
 9J5  HAV  CAV  CAU  111.65  3.000
 9J5  HAX  CAV  CAU  112.21  3.000
 9J5  CAM  NAL  CAU  129.59  3.000
 9J5  CAM  NAL  CAK  125.45  3.000
 9J5  CAU  NAL  CAK  104.94  3.000
 9J5  CAN  CAM  CAO  121.29  3.000
 9J5  CAN  CAM  NAL  119.84  3.000
 9J5  CAO  CAM  NAL  118.85  3.000
 9J5  HAO  CAO  CAP  118.81  3.000
 9J5  HAO  CAO  CAM  120.79  3.000
 9J5  CAP  CAO  CAM  120.38  3.000
 9J5  CAQ  CAP  OBD  124.66  3.000
 9J5  CAQ  CAP  CAO  119.36  3.000
 9J5  OBD  CAP  CAO  115.98  3.000
 9J5  CBE  OBD  CAP  118.79  3.000
 9J5  HBH  CBE  HBG  108.91  3.000
 9J5  HBH  CBE  HBF  109.03  3.000
 9J5  HBG  CBE  HBF  109.09  3.000
 9J5  HBH  CBE  OBD  106.32  3.000
 9J5  HBG  CBE  OBD  111.72  3.000
 9J5  HBF  CBE  OBD  111.69  3.000
 9J5  HAQ  CAQ  CAR  118.85  3.000
 9J5  HAQ  CAQ  CAP  121.85  3.000
 9J5  CAR  CAQ  CAP  119.29  3.000
 9J5  HAR  CAR  CAN  119.23  3.000
 9J5  HAR  CAR  CAQ  118.16  3.000
 9J5  CAN  CAR  CAQ  122.60  3.000
 9J5  CAH  CAN  CAR  118.77  3.000
 9J5  CAH  CAN  CAM  124.09  3.000
 9J5  CAR  CAN  CAM  117.07  3.000
 9J5  CAE  CAH  CAN  116.81  3.000
 9J5  CAE  CAH  NAI  116.00  3.000
 9J5  CAN  CAH  NAI  127.17  3.000
 9J5  CAF  CAE  CAD  118.96  3.000
 9J5  CAF  CAE  CAH  121.14  3.000
 9J5  CAD  CAE  CAH  119.86  3.000
 9J5  HAD  CAD  CAC  119.41  3.000
 9J5  HAD  CAD  CAE  119.73  3.000
 9J5  CAC  CAD  CAE  120.85  3.000
 9J5  HAC  CAC  CAB  120.58  3.000
 9J5  HAC  CAC  CAD  120.33  3.000
 9J5  CAB  CAC  CAD  119.09  3.000
 9J5  CAG  CAB  CLA  119.42  3.000
 9J5  CLA  CAB  CAC  119.39  3.000
 9J5  CAG  CAB  CAC  121.20  3.000
 9J5  HAG  CAG  CAF  120.25  3.000
 9J5  HAG  CAG  CAB  120.69  3.000
 9J5  CAF  CAG  CAB  119.06  3.000
 9J5  HAF  CAF  CAG  118.87  3.000
 9J5  HAF  CAF  CAE  120.27  3.000
 9J5  CAG  CAF  CAE  120.84  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
 9J5  CONST_01  CAU  NAT  NAS  CAK     0.00   0.0  0
 9J5  CONST_02  NAT  CAU  NAL  CAK     0.00   0.0  0
 9J5  CONST_05  NAL  CAU  NAT  NAS     0.00   0.0  0
 9J5  CONST_06  CAU  NAL  CAK  NAS     0.00   0.0  0
 9J5  CONST_07  CAM  NAL  CAK  NAS   180.00   0.0  0
 9J5  CONST_08  CAM  NAL  CAU  NAT   180.00   0.0  0
 9J5  CONST_09  NAL  CAK  NAS  NAT     0.00   0.0  0
 9J5  CONST_12  CAP  CAO  CAM  NAL   180.00   0.0  0
 9J5  CONST_13  CAR  CAN  CAM  NAL   180.00   0.0  0
 9J5  CONST_14  CAQ  CAP  CAO  CAM     0.00   0.0  0
 9J5  CONST_15  CAQ  CAR  CAN  CAM     0.00   0.0  0
 9J5  CONST_16  CAR  CAQ  CAP  CAO     0.00   0.0  0
 9J5  CONST_17  CAR  CAN  CAM  CAO     0.00   0.0  0
 9J5  CONST_18  CAN  CAM  CAO  CAP     0.00   0.0  0
 9J5  CONST_19  CAN  CAR  CAQ  CAP     0.00   0.0  0
 9J5  CONST_20  CAB  CAC  CAD  CAE     0.00   0.0  0
 9J5  CONST_21  CAB  CAG  CAF  CAE     0.00   0.0  0
 9J5  CONST_22  CAG  CAF  CAE  CAD     0.00   0.0  0
 9J5  CONST_23  CAG  CAB  CAC  CAD     0.00   0.0  0
 9J5  CONST_24  CAF  CAE  CAD  CAC     0.00   0.0  0
 9J5  CONST_25  CAF  CAG  CAB  CAC     0.00   0.0  0
 9J5  CONST_26  CAC  CAD  CAE  CAH   180.00   0.0  0
 9J5  CONST_27  CAG  CAF  CAE  CAH   180.00   0.0  0
 9J5  CONST_28  CAV  CAU  NAL  CAK   180.00   0.0  0
 9J5  CONST_29  CAV  CAU  NAT  NAS   180.00   0.0  0
 9J5  CONST_30  CAM  NAL  CAU  CAV     0.00   0.0  0
 9J5  CONST_31  OBD  CAP  CAO  CAM   180.00   0.0  0
 9J5  CONST_32  CAR  CAQ  CAP  OBD   180.00   0.0  0
 9J5  CONST_33  CLA  CAB  CAC  CAD   180.00   0.0  0
 9J5  CONST_34  CAF  CAG  CAB  CLA   180.00   0.0  0
 9J5  CONST_35  HAO  CAO  CAM  NAL     0.00   0.0  0
 9J5  CONST_36  HAR  CAR  CAN  CAM   180.00   0.0  0
 9J5  CONST_37  HAQ  CAQ  CAP  CAO   180.00   0.0  0
 9J5  CONST_38  HAD  CAD  CAE  CAH     0.00   0.0  0
 9J5  CONST_39  HAF  CAF  CAE  CAH     0.00   0.0  0
 9J5  CONST_40  HAC  CAC  CAD  CAE   180.00   0.0  0
 9J5  CONST_41  HAG  CAG  CAF  CAE   180.00   0.0  0
 9J5  Var_01    CAN  CAH  NAI  CAJ    -0.22  30.0  1
 9J5  Var_02    CAM  CAN  CAH  NAI   -39.19  30.0  1
 9J5  Var_03    CAD  CAE  CAH  NAI   -34.90  30.0  2
 9J5  Var_04    CAQ  CAP  OBD  CBE    -1.48  30.0  2
 9J5  Var_05    HAX  CAV  CAU  NAT   103.60  30.0  2
 9J5  Var_06    HBF  CBE  OBD  CAP   -59.38  30.0  3
 9J5  Var_07    CAW  CAX  OBA  CBC  -178.58  30.0  1
 9J5  Var_08    HBC  CBC  OBA  CAX   -59.88  30.0  3
 9J5  Var_09    HA2  CAZ  CAY  CAW   -65.72  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
 9J5  chir_01  CAW  CAY  CAJ  CAX  positiv
 9J5  chir_02  CAJ  NAI  CAW  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
 9J5  plan-1  CAH  0.020
 9J5  plan-1  CAE  0.020
 9J5  plan-1  CAD  0.020
 9J5  plan-1  CAC  0.020
 9J5  plan-1  CAB  0.020
 9J5  plan-1  CLA  0.020
 9J5  plan-1  CAG  0.020
 9J5  plan-1  CAF  0.020
 9J5  plan-1  HAD  0.020
 9J5  plan-1  HAC  0.020
 9J5  plan-1  HAG  0.020
 9J5  plan-1  HAF  0.020
 9J5  plan-2  CAJ  0.020
 9J5  plan-2  CAK  0.020
 9J5  plan-2  NAS  0.020
 9J5  plan-2  NAT  0.020
 9J5  plan-2  CAU  0.020
 9J5  plan-2  CAV  0.020
 9J5  plan-2  NAL  0.020
 9J5  plan-2  CAM  0.020
 9J5  plan-3  NAL  0.020
 9J5  plan-3  CAM  0.020
 9J5  plan-3  CAO  0.020
 9J5  plan-3  CAP  0.020
 9J5  plan-3  OBD  0.020
 9J5  plan-3  CAQ  0.020
 9J5  plan-3  CAR  0.020
 9J5  plan-3  CAN  0.020
 9J5  plan-3  CAH  0.020
 9J5  plan-3  HAO  0.020
 9J5  plan-3  HAQ  0.020
 9J5  plan-3  HAR  0.020
 9J5  plan-4  OBA  0.020
 9J5  plan-4  CAX  0.020
 9J5  plan-4  OBB  0.020
 9J5  plan-4  CAW  0.020

