# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 16:06:10 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: (4R)-N-benzyl-4-methyl-2-oxo-2,3,4,5-tetrahydro-1H-1,5-benzodiazepine-6-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CC(=O)Nc2cccc(C(=O)NCc3ccccc3)c2N1
#
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
 69A  69A  (4R)-N-benzyl-4-methyl-2-oxo-2,3,4,5-tetrahydro-1H-1,5-benzodiazepine-6-carboxamide  ligand  42  23  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_69A
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
 69A  CAI  C  CR16  0  -0.298  -1.4119   0.9882  -3.2479
 69A  CAJ  C  CR16  0  -0.241  -2.6379   1.6220  -3.1514
 69A  CAK  C  CR16  0  -0.312  -3.2131   1.8317  -1.9103
 69A  CAE  C  CR6   0   0.361  -2.5502   1.4107  -0.7655
 69A  NAF  N  NH1   0  -0.714  -3.1405   1.6231   0.4905
 69A  CAG  C  C     0   0.498  -3.2714   0.6872   1.4713
 69A  OAM  O  O     0  -0.464  -3.8311   0.9475   2.5218
 69A  CAA  C  CH2   0  -0.617  -2.6906  -0.6657   1.1504
 69A  CAB  C  CH1   0  -0.101  -1.1528  -0.6634   1.1016
 69A  CAL  C  CH3   0  -0.657  -0.6485  -1.9852   0.5458
 69A  NAC  N  NH1   0  -0.708  -0.6032   0.4798   0.3577
 69A  CAD  C  CR6   0   0.216  -1.2845   0.8121  -0.8474
 69A  CAH  C  CR6   0  -0.086  -0.7162   0.5852  -2.1088
 69A  CAN  C  C     0   0.542   0.6365  -0.0350  -2.3594
 69A  OAP  O  O     0  -0.501   0.9540  -0.3863  -3.4913
 69A  NAO  N  NH1   0  -0.662   1.4613  -0.1421  -1.3164
 69A  CAQ  C  CH2   0  -0.319   2.7715  -0.7481  -1.4293
 69A  CAR  C  CR6   0   0.057   3.4878  -0.6519  -0.1109
 69A  CAS  C  CR16  0  -0.301   3.6640  -1.7768   0.6878
 69A  CAT  C  CR16  0  -0.241   4.3085  -1.6805   1.9154
 69A  CAU  C  CR16  0  -0.265   4.7792  -0.4527   2.3583
 69A  CAV  C  CR16  0  -0.242   4.6046   0.6777   1.5679
 69A  CAW  C  CR16  0  -0.282   3.9635   0.5773   0.3421
 69A  H1   H  HCR6  0   0.261  -0.9759   0.8137  -4.2210
 69A  H2   H  HCR6  0   0.267  -3.1536   1.9414  -4.0468
 69A  H3   H  HCR6  0   0.278  -4.1812   2.3090  -1.8244
 69A  H4   H  HNH1  0   0.406  -3.6304   2.4963   0.6331
 69A  H5   H  HCH2  0   0.285  -3.0212  -1.3752   1.9082
 69A  H6   H  HCH2  0   0.272  -3.0884  -1.0102   0.1900
 69A  H7   H  HCH1  0   0.264  -0.7807  -0.5482   2.1214
 69A  H8   H  HCH3  0   0.229  -0.9092  -2.1019  -0.5079
 69A  H9   H  HCH3  0   0.237   0.4340  -2.0654   0.6413
 69A  H10  H  HCH3  0   0.243  -1.0954  -2.8176   1.0896
 69A  H11  H  HNH1  0   0.383  -0.5833   1.2949   0.9609
 69A  H12  H  HNH1  0   0.427   1.0754   0.0922  -0.4024
 69A  H13  H  HCH2  0   0.252   2.6855  -1.7953  -1.7326
 69A  H14  H  HCH2  0   0.254   3.3455  -0.2399  -2.2082
 69A  H15  H  HCR6  0   0.254   3.3008  -2.7389   0.3457
 69A  H16  H  HCR6  0   0.257   4.4422  -2.5660   2.5233
 69A  H17  H  HCR6  0   0.257   5.2831  -0.3752   3.3132
 69A  H18  H  HCR6  0   0.257   4.9710   1.6381   1.9069
 69A  H19  H  HCR6  0   0.254   3.8356   1.4613  -0.2718

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
 69A  CAA  CAB  single    1.539  0.020  1.539
 69A  CAA  CAG  single    1.507  0.020  1.507
 69A  CAB  CAL  single    1.520  0.020  1.520
 69A  CAB  NAC  single    1.470  0.020  1.470
 69A  OAP  CAN  double    1.227  0.020  1.227
 69A  CAH  CAN  single    1.509  0.020  1.509
 69A  CAH  CAI  aromatic  1.394  0.020  1.394
 69A  CAH  CAD  aromatic  1.402  0.020  1.402
 69A  CAN  NAO  single    1.334  0.020  1.334
 69A  CAG  OAM  double    1.218  0.020  1.218
 69A  CAG  NAF  single    1.362  0.020  1.362
 69A  CAI  CAJ  aromatic  1.383  0.020  1.383
 69A  NAC  CAD  single    1.424  0.020  1.424
 69A  CAD  CAE  aromatic  1.402  0.020  1.402
 69A  CAJ  CAK  aromatic  1.384  0.020  1.384
 69A  CAE  CAK  aromatic  1.388  0.020  1.388
 69A  CAE  NAF  single    1.404  0.020  1.404
 69A  NAO  CAQ  single    1.448  0.020  1.448
 69A  CAQ  CAR  single    1.504  0.020  1.504
 69A  CAR  CAS  aromatic  1.391  0.020  1.391
 69A  CAR  CAW  aromatic  1.394  0.020  1.394
 69A  CAS  CAT  aromatic  1.390  0.020  1.390
 69A  CAW  CAV  aromatic  1.387  0.020  1.387
 69A  CAT  CAU  aromatic  1.388  0.020  1.388
 69A  CAV  CAU  aromatic  1.390  0.020  1.390
 69A  CAI  H1   single    0.930  0.020  1.080
 69A  CAJ  H2   single    0.930  0.020  1.080
 69A  CAK  H3   single    0.930  0.020  1.080
 69A  NAF  H4   single    0.860  0.020  1.020
 69A  CAA  H5   single    0.970  0.020  1.090
 69A  CAA  H6   single    0.970  0.020  1.090
 69A  CAB  H7   single    0.970  0.020  1.090
 69A  CAL  H8   single    0.970  0.020  1.090
 69A  CAL  H9   single    0.970  0.020  1.090
 69A  CAL  H10  single    0.970  0.020  1.090
 69A  NAC  H11  single    0.890  0.020  1.040
 69A  NAO  H12  single    0.860  0.020  1.020
 69A  CAQ  H13  single    0.970  0.020  1.090
 69A  CAQ  H14  single    0.970  0.020  1.090
 69A  CAS  H15  single    0.930  0.020  1.080
 69A  CAT  H16  single    0.930  0.020  1.080
 69A  CAU  H17  single    0.930  0.020  1.080
 69A  CAV  H18  single    0.930  0.020  1.080
 69A  CAW  H19  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
 69A  H1   CAI  CAH  119.19  3.000
 69A  H1   CAI  CAJ  119.64  3.000
 69A  CAH  CAI  CAJ  121.17  3.000
 69A  H2   CAJ  CAK  119.97  3.000
 69A  H2   CAJ  CAI  120.00  3.000
 69A  CAK  CAJ  CAI  120.03  3.000
 69A  H3   CAK  CAE  119.69  3.000
 69A  H3   CAK  CAJ  120.64  3.000
 69A  CAE  CAK  CAJ  119.67  3.000
 69A  CAD  CAE  NAF  119.75  3.000
 69A  NAF  CAE  CAK  119.41  3.000
 69A  CAD  CAE  CAK  120.81  3.000
 69A  H4   NAF  CAG  116.43  3.000
 69A  H4   NAF  CAE  117.42  3.000
 69A  CAG  NAF  CAE  125.50  3.000
 69A  CAA  CAG  OAM  123.53  3.000
 69A  OAM  CAG  NAF  121.22  3.000
 69A  CAA  CAG  NAF  115.25  3.000
 69A  H6   CAA  H5   107.16  3.000
 69A  H6   CAA  CAB  109.62  3.000
 69A  H5   CAA  CAB  109.05  3.000
 69A  H6   CAA  CAG  109.22  3.000
 69A  H5   CAA  CAG  108.64  3.000
 69A  CAB  CAA  CAG  112.99  3.000
 69A  H7   CAB  NAC  105.26  3.000
 69A  H7   CAB  CAL  108.67  3.000
 69A  NAC  CAB  CAL  111.54  3.000
 69A  H7   CAB  CAA  108.13  3.000
 69A  NAC  CAB  CAA  113.01  3.000
 69A  CAL  CAB  CAA  109.99  3.000
 69A  H10  CAL  H9   107.90  3.000
 69A  H10  CAL  H8   107.58  3.000
 69A  H9   CAL  H8   108.29  3.000
 69A  H10  CAL  CAB  110.22  3.000
 69A  H9   CAL  CAB  111.19  3.000
 69A  H8   CAL  CAB  111.51  3.000
 69A  H11  NAC  CAD  108.98  3.000
 69A  H11  NAC  CAB  109.35  3.000
 69A  CAD  NAC  CAB  115.52  3.000
 69A  CAH  CAD  NAC  121.99  3.000
 69A  NAC  CAD  CAE  118.82  3.000
 69A  CAH  CAD  CAE  119.17  3.000
 69A  CAN  CAH  CAD  125.40  3.000
 69A  CAD  CAH  CAI  119.08  3.000
 69A  CAN  CAH  CAI  115.49  3.000
 69A  NAO  CAN  OAP  122.56  3.000
 69A  NAO  CAN  CAH  117.22  3.000
 69A  OAP  CAN  CAH  120.19  3.000
 69A  H12  NAO  CAQ  120.57  3.000
 69A  H12  NAO  CAN  116.65  3.000
 69A  CAQ  NAO  CAN  122.15  3.000
 69A  H14  CAQ  H13  106.80  3.000
 69A  H14  CAQ  CAR  110.18  3.000
 69A  H13  CAQ  CAR  110.00  3.000
 69A  H14  CAQ  NAO  109.64  3.000
 69A  H13  CAQ  NAO  110.56  3.000
 69A  CAR  CAQ  NAO  109.63  3.000
 69A  CAW  CAR  CAS  118.91  3.000
 69A  CAW  CAR  CAQ  120.27  3.000
 69A  CAS  CAR  CAQ  120.81  3.000
 69A  H15  CAS  CAT  119.71  3.000
 69A  H15  CAS  CAR  119.62  3.000
 69A  CAT  CAS  CAR  120.66  3.000
 69A  H16  CAT  CAU  120.18  3.000
 69A  H16  CAT  CAS  119.78  3.000
 69A  CAU  CAT  CAS  120.03  3.000
 69A  H17  CAU  CAV  120.12  3.000
 69A  H17  CAU  CAT  120.19  3.000
 69A  CAV  CAU  CAT  119.70  3.000
 69A  H18  CAV  CAW  119.84  3.000
 69A  H18  CAV  CAU  120.05  3.000
 69A  CAW  CAV  CAU  120.11  3.000
 69A  H19  CAW  CAV  119.74  3.000
 69A  H19  CAW  CAR  119.67  3.000
 69A  CAV  CAW  CAR  120.59  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
 69A  CONST_01  CAE  CAK  CAJ  CAI    0.00   0.0  0
 69A  CONST_02  CAD  CAH  CAI  CAJ    0.00   0.0  0
 69A  CONST_03  CAH  CAI  CAJ  CAK    0.00   0.0  0
 69A  CONST_04  CAU  CAT  CAS  CAR    0.00   0.0  0
 69A  CONST_05  CAU  CAV  CAW  CAR    0.00   0.0  0
 69A  CONST_06  CAV  CAW  CAR  CAS    0.00   0.0  0
 69A  CONST_07  CAV  CAU  CAT  CAS    0.00   0.0  0
 69A  CONST_08  CAW  CAR  CAS  CAT    0.00   0.0  0
 69A  CONST_09  CAW  CAV  CAU  CAT    0.00   0.0  0
 69A  CONST_10  CAN  CAH  CAI  CAJ  180.00   0.0  0
 69A  CONST_11  CAT  CAS  CAR  CAQ  180.00   0.0  0
 69A  CONST_12  CAV  CAW  CAR  CAQ  180.00   0.0  0
 69A  CONST_13  H3   CAK  CAJ  CAI  180.00   0.0  0
 69A  CONST_14  H1   CAI  CAJ  CAK  180.00   0.0  0
 69A  CONST_15  H2   CAJ  CAK  CAE  180.00   0.0  0
 69A  CONST_16  H16  CAT  CAS  CAR  180.00   0.0  0
 69A  CONST_17  H18  CAV  CAW  CAR  180.00   0.0  0
 69A  CONST_18  H19  CAW  CAR  CAS  180.00   0.0  0
 69A  CONST_19  H17  CAU  CAT  CAS  180.00   0.0  0
 69A  CONST_20  H15  CAS  CAT  CAU  180.00   0.0  0
 69A  CONST_21  CAQ  NAO  CAN  CAH  180.00   0.0  0
 69A  CONST_22  H12  NAO  CAN  CAH    0.00   0.0  0
 69A  CONST_23  CAQ  NAO  CAN  OAP    0.00   0.0  0
 69A  Var_01    OAP  CAN  CAH  CAI  -13.63  30.0  2
 69A  Var_02    CAS  CAR  CAQ  NAO  106.99  30.0  2
 69A  Var_03    CAR  CAQ  NAO  CAN  176.84  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
 69A  chir_01  CAB  CAA  CAL  NAC  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
 69A  plan-1  CAQ  0.020
 69A  plan-1  CAR  0.020
 69A  plan-1  CAS  0.020
 69A  plan-1  CAT  0.020
 69A  plan-1  CAU  0.020
 69A  plan-1  CAV  0.020
 69A  plan-1  CAW  0.020
 69A  plan-1  H15  0.020
 69A  plan-1  H16  0.020
 69A  plan-1  H17  0.020
 69A  plan-1  H18  0.020
 69A  plan-1  H19  0.020
 69A  plan-2  CAI  0.020
 69A  plan-2  CAJ  0.020
 69A  plan-2  CAK  0.020
 69A  plan-2  CAE  0.020
 69A  plan-2  NAF  0.020
 69A  plan-2  NAC  0.020
 69A  plan-2  CAD  0.020
 69A  plan-2  CAH  0.020
 69A  plan-2  CAN  0.020
 69A  plan-2  H1   0.020
 69A  plan-2  H2   0.020
 69A  plan-2  H3   0.020
 69A  plan-3  CAE  0.020
 69A  plan-3  NAF  0.020
 69A  plan-3  CAG  0.020
 69A  plan-3  OAM  0.020
 69A  plan-3  CAA  0.020
 69A  plan-3  H4   0.020
 69A  plan-4  CAH  0.020
 69A  plan-4  CAN  0.020
 69A  plan-4  OAP  0.020
 69A  plan-4  NAO  0.020
 69A  plan-4  CAQ  0.020
 69A  plan-4  H12  0.020

