# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 02:47:20 2022
#   Inital geometry file: a 134 line input string
#   Ligand name: (2~{S})-~{N}-butyl-1-(2-fluorophenyl)carbonyl-2-methyl-4-oxidanylidene-3,5-dihydro-2~{H}-1,5-benzodiazepine-7-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCNC(=O)c1ccc2N([C@@H](C)CC(=O)Nc2c1)C(=O)c3ccccc3F
#
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
 UZQ  UZQ  (2~{S})-~{N}-butyl-1-(2-fluorophenyl)carbonyl-2-methyl-4-oxidanylidene-3,5-dihydro-2~{H}-1,5-benzodiazepine-7-carboxamide  ligand  53  29  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_UZQ
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
 UZQ  C4   C  CR16  0  -0.350  13.7949  -1.4856  15.0126
 UZQ  C5   C  CR6   0  -0.026  13.3200  -2.3538  15.9877
 UZQ  C6   C  CR16  0  -0.305  12.5479  -1.8466  17.0295
 UZQ  C7   C  C     0   0.534  13.6596  -3.8085  15.8493
 UZQ  C10  C  CH2   0  -0.286  13.9584  -5.9400  17.0346
 UZQ  C13  C  CH3   0  -0.666  15.5131  -8.5223  16.1813
 UZQ  C15  C  C     0   0.507  14.5251   1.9512  14.2647
 UZQ  C17  C  CH1   0  -0.101  13.3555   2.7446  16.3718
 UZQ  C20  C  CH3   0  -0.650  13.5436   2.9569  17.8661
 UZQ  C24  C  CR16  0  -0.249   8.9451   0.8785  16.6797
 UZQ  C26  C  CR16  0  -0.237   7.9626  -0.7627  15.2285
 UZQ  C28  C  CR6   0   0.564   9.9718   0.3496  14.5992
 UZQ  C11  C  CH2   0  -0.432  15.4402  -6.2121  17.2781
 UZQ  N9   N  NH1   0  -0.645  13.6431  -4.5280  16.9816
 UZQ  O8   O  O     0  -0.480  13.9275  -4.2842  14.7541
 UZQ  C1   C  CR16  0  -0.248  12.2562  -0.4948  17.0815
 UZQ  C2   C  CR6   0   0.227  12.7001   0.3680  16.0886
 UZQ  C3   C  CR6   0   0.405  13.5055  -0.1293  15.0594
 UZQ  N14  N  NH1   0  -0.722  13.9848   0.7192  14.0595
 UZQ  O19  O  O     0  -0.449  14.8801   2.6523  13.3368
 UZQ  C16  C  CH2   0  -0.630  14.6769   2.3532  15.7126
 UZQ  N18  N  NT    0  -0.539  12.3275   1.7317  16.0932
 UZQ  O22  O  O     0  -0.447  10.6736   3.2562  16.3259
 UZQ  C23  C  CR6   0  -0.274   9.9921   1.0718  15.7809
 UZQ  C25  C  CR16  0  -0.256   7.9440  -0.0418  16.4162
 UZQ  C27  C  CR16  0  -0.396   8.9786  -0.5637  14.3056
 UZQ  H1   H  HCR6  0   0.274  14.4031  -1.8640  14.2009
 UZQ  H2   H  HCR6  0   0.265  12.1436  -2.4896  17.7999
 UZQ  H3   H  HCH2  0   0.245  13.3672  -6.3777  17.8416
 UZQ  H4   H  HCH2  0   0.245  13.6229  -6.4032  16.1080
 UZQ  H5   H  HCH3  0   0.229  15.8161  -9.5592  16.3297
 UZQ  H6   H  HCH3  0   0.222  14.4622  -8.5320  15.8896
 UZQ  H7   H  HCH3  0   0.218  16.0856  -8.1290  15.3391
 UZQ  H8   H  HCH1  0   0.275  13.0113   3.6713  15.9128
 UZQ  H9   H  HCH3  0   0.247  12.6204   3.2903  18.3370
 UZQ  H10  H  HCH3  0   0.232  13.8695   2.0360  18.3527
 UZQ  H11  H  HCH3  0   0.242  14.3047   3.7173  18.0435
 UZQ  H12  H  HCR6  0   0.274   8.9309   1.4431  17.6031
 UZQ  H13  H  HCR6  0   0.273   7.1812  -1.4792  15.0131
 UZQ  H14  H  HCH2  0   0.215  15.1594  -8.1036  18.2651
 UZQ  H15  H  HCH2  0   0.228  16.7976  -7.8011  17.7423
 UZQ  H16  H  HCH2  0   0.222  16.0253  -5.7987  16.4513
 UZQ  H17  H  HCH2  0   0.228  15.7498  -5.6763  18.1797
 UZQ  H18  H  HNH1  0   0.405  13.5585  -4.0517  17.8648
 UZQ  H19  H  HCR6  0   0.282  11.6508  -0.1079  17.8907
 UZQ  H20  H  HNH1  0   0.405  13.9985   0.3675  13.1113
 UZQ  H21  H  HCH2  0   0.279  15.1563   1.5466  16.2754
 UZQ  H22  H  HCH2  0   0.297  15.3404   3.2154  15.7614
 UZQ  H23  H  HCR6  0   0.267   7.1482  -0.1929  17.1328
 UZQ  H24  H  HCR6  0   0.284   8.9985  -1.1033  13.3678
 UZQ  C21  C  C     0   0.534  11.0215   2.1149  16.0867
 UZQ  F29  F  F     0  -0.301  10.9407   0.5563  13.6967
 UZQ  C12  C  CH2   0  -0.434  15.7527  -7.6971  17.4401

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
 UZQ  O19  C15  double    1.216  0.020  1.216
 UZQ  F29  C28  single    1.340  0.020  1.340
 UZQ  N14  C15  single    1.361  0.020  1.361
 UZQ  N14  C3   single    1.396  0.020  1.396
 UZQ  C15  C16  single    1.510  0.020  1.510
 UZQ  C27  C28  aromatic  1.381  0.020  1.381
 UZQ  C27  C26  aromatic  1.387  0.020  1.387
 UZQ  C28  C23  aromatic  1.385  0.020  1.385
 UZQ  O8   C7   double    1.224  0.020  1.224
 UZQ  C4   C3   aromatic  1.388  0.020  1.388
 UZQ  C4   C5   aromatic  1.389  0.020  1.389
 UZQ  C3   C2   aromatic  1.398  0.020  1.398
 UZQ  C26  C25  aromatic  1.390  0.020  1.390
 UZQ  C16  C17  single    1.528  0.020  1.528
 UZQ  C23  C21  single    1.497  0.020  1.497
 UZQ  C23  C24  aromatic  1.393  0.020  1.393
 UZQ  C7   C5   single    1.500  0.020  1.500
 UZQ  C7   N9   single    1.342  0.020  1.342
 UZQ  C21  O22  double    1.217  0.020  1.217
 UZQ  C21  N18  single    1.361  0.020  1.361
 UZQ  C5   C6   aromatic  1.392  0.020  1.392
 UZQ  C2   N18  single    1.414  0.020  1.414
 UZQ  C2   C1   aromatic  1.388  0.020  1.388
 UZQ  N18  C17  single    1.470  0.020  1.470
 UZQ  C17  C20  single    1.521  0.020  1.521
 UZQ  C13  C12  single    1.524  0.020  1.524
 UZQ  C25  C24  aromatic  1.385  0.020  1.385
 UZQ  C10  N9   single    1.448  0.020  1.448
 UZQ  C10  C11  single    1.526  0.020  1.526
 UZQ  C6   C1   aromatic  1.384  0.020  1.384
 UZQ  C11  C12  single    1.526  0.020  1.526
 UZQ  C4   H1   single    0.930  0.020  1.080
 UZQ  C6   H2   single    0.930  0.020  1.080
 UZQ  C10  H3   single    0.970  0.020  1.090
 UZQ  C10  H4   single    0.970  0.020  1.090
 UZQ  C13  H5   single    0.970  0.020  1.090
 UZQ  C13  H6   single    0.970  0.020  1.090
 UZQ  C13  H7   single    0.970  0.020  1.090
 UZQ  C17  H8   single    0.970  0.020  1.090
 UZQ  C20  H9   single    0.970  0.020  1.090
 UZQ  C20  H10  single    0.970  0.020  1.090
 UZQ  C20  H11  single    0.970  0.020  1.090
 UZQ  C24  H12  single    0.930  0.020  1.080
 UZQ  C26  H13  single    0.930  0.020  1.080
 UZQ  C12  H14  single    0.970  0.020  1.090
 UZQ  C12  H15  single    0.970  0.020  1.090
 UZQ  C11  H16  single    0.970  0.020  1.090
 UZQ  C11  H17  single    0.970  0.020  1.090
 UZQ  N9   H18  single    0.860  0.020  1.020
 UZQ  C1   H19  single    0.930  0.020  1.080
 UZQ  N14  H20  single    0.860  0.020  1.020
 UZQ  C16  H21  single    0.970  0.020  1.090
 UZQ  C16  H22  single    0.970  0.020  1.090
 UZQ  C25  H23  single    0.930  0.020  1.080
 UZQ  C27  H24  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
 UZQ  H1   C4   C3   118.96  3.000
 UZQ  H1   C4   C5   119.99  3.000
 UZQ  C3   C4   C5   121.05  3.000
 UZQ  C7   C5   C6   123.21  3.000
 UZQ  C6   C5   C4   119.15  3.000
 UZQ  C7   C5   C4   117.64  3.000
 UZQ  H2   C6   C1   118.36  3.000
 UZQ  H2   C6   C5   121.57  3.000
 UZQ  C1   C6   C5   120.05  3.000
 UZQ  O8   C7   N9   123.34  3.000
 UZQ  N9   C7   C5   116.06  3.000
 UZQ  O8   C7   C5   120.60  3.000
 UZQ  H4   C10  H3   106.95  3.000
 UZQ  H4   C10  N9   108.45  3.000
 UZQ  H3   C10  N9   107.46  3.000
 UZQ  H4   C10  C11  111.05  3.000
 UZQ  H3   C10  C11  109.66  3.000
 UZQ  N9   C10  C11  113.03  3.000
 UZQ  H7   C13  H6   107.58  3.000
 UZQ  H7   C13  H5   107.57  3.000
 UZQ  H6   C13  H5   107.20  3.000
 UZQ  H7   C13  C12  111.08  3.000
 UZQ  H6   C13  C12  112.16  3.000
 UZQ  H5   C13  C12  111.03  3.000
 UZQ  C16  C15  O19  123.28  3.000
 UZQ  C16  C15  N14  115.18  3.000
 UZQ  O19  C15  N14  121.52  3.000
 UZQ  H8   C17  N18  106.57  3.000
 UZQ  H8   C17  C16  108.02  3.000
 UZQ  N18  C17  C16  110.28  3.000
 UZQ  H8   C17  C20  109.51  3.000
 UZQ  N18  C17  C20  111.65  3.000
 UZQ  C16  C17  C20  110.65  3.000
 UZQ  H11  C20  H10  107.90  3.000
 UZQ  H11  C20  H9   107.94  3.000
 UZQ  H10  C20  H9   108.59  3.000
 UZQ  H11  C20  C17  110.09  3.000
 UZQ  H10  C20  C17  110.92  3.000
 UZQ  H9   C20  C17  111.27  3.000
 UZQ  H12  C24  C25  119.96  3.000
 UZQ  H12  C24  C23  119.19  3.000
 UZQ  C25  C24  C23  120.84  3.000
 UZQ  H13  C26  C27  119.45  3.000
 UZQ  H13  C26  C25  120.28  3.000
 UZQ  C27  C26  C25  120.28  3.000
 UZQ  F29  C28  C27  118.61  3.000
 UZQ  C27  C28  C23  122.47  3.000
 UZQ  F29  C28  C23  118.92  3.000
 UZQ  H17  C11  H16  106.65  3.000
 UZQ  H17  C11  C12  109.34  3.000
 UZQ  H16  C11  C12  109.78  3.000
 UZQ  H17  C11  C10  108.61  3.000
 UZQ  H16  C11  C10  109.35  3.000
 UZQ  C12  C11  C10  112.91  3.000
 UZQ  H18  N9   C10  116.58  3.000
 UZQ  H18  N9   C7   119.18  3.000
 UZQ  C10  N9   C7   123.46  3.000
 UZQ  H19  C1   C2   119.44  3.000
 UZQ  H19  C1   C6   119.68  3.000
 UZQ  C2   C1   C6   120.85  3.000
 UZQ  N18  C2   C3   119.82  3.000
 UZQ  N18  C2   C1   120.86  3.000
 UZQ  C3   C2   C1   119.31  3.000
 UZQ  N14  C3   C2   120.57  3.000
 UZQ  C2   C3   C4   119.51  3.000
 UZQ  N14  C3   C4   119.88  3.000
 UZQ  H20  N14  C3   117.69  3.000
 UZQ  H20  N14  C15  116.80  3.000
 UZQ  C3   N14  C15  125.34  3.000
 UZQ  H22  C16  H21  107.07  3.000
 UZQ  H22  C16  C17  107.75  3.000
 UZQ  H21  C16  C17  110.24  3.000
 UZQ  H22  C16  C15  108.36  3.000
 UZQ  H21  C16  C15  109.93  3.000
 UZQ  C17  C16  C15  113.26  3.000
 UZQ  C2   N18  C21  121.63  3.000
 UZQ  C2   N18  C17  118.75  3.000
 UZQ  C21  N18  C17  118.56  3.000
 UZQ  C28  C23  C24  117.84  3.000
 UZQ  C24  C23  C21  118.79  3.000
 UZQ  C28  C23  C21  123.21  3.000
 UZQ  H23  C25  C26  120.25  3.000
 UZQ  H23  C25  C24  119.91  3.000
 UZQ  C26  C25  C24  119.84  3.000
 UZQ  H24  C27  C28  120.05  3.000
 UZQ  H24  C27  C26  121.24  3.000
 UZQ  C28  C27  C26  118.71  3.000
 UZQ  C23  C21  O22  119.81  3.000
 UZQ  O22  C21  N18  122.50  3.000
 UZQ  C23  C21  N18  117.68  3.000
 UZQ  H15  C12  H14  105.94  3.000
 UZQ  H15  C12  C11  108.53  3.000
 UZQ  H14  C12  C11  109.30  3.000
 UZQ  H15  C12  C13  109.10  3.000
 UZQ  H14  C12  C13  109.64  3.000
 UZQ  C11  C12  C13  114.01  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
 UZQ  CONST_01  C1   C6   C5   C4     0.00   0.0  0
 UZQ  CONST_02  C2   C1   C6   C5     0.00   0.0  0
 UZQ  CONST_03  C3   C4   C5   C6     0.00   0.0  0
 UZQ  CONST_04  C27  C28  C23  C24    0.00   0.0  0
 UZQ  CONST_05  C27  C26  C25  C24    0.00   0.0  0
 UZQ  CONST_06  C23  C28  C27  C26    0.00   0.0  0
 UZQ  CONST_07  C23  C24  C25  C26    0.00   0.0  0
 UZQ  CONST_08  C25  C26  C27  C28    0.00   0.0  0
 UZQ  CONST_09  C25  C24  C23  C28    0.00   0.0  0
 UZQ  CONST_10  C3   C4   C5   C7   180.00   0.0  0
 UZQ  CONST_11  C1   C6   C5   C7   180.00   0.0  0
 UZQ  CONST_12  C27  C28  C23  C21  180.00   0.0  0
 UZQ  CONST_13  C25  C24  C23  C21  180.00   0.0  0
 UZQ  CONST_14  F29  C28  C23  C24  180.00   0.0  0
 UZQ  CONST_15  F29  C28  C27  C26  180.00   0.0  0
 UZQ  CONST_16  H2   C6   C5   C4   180.00   0.0  0
 UZQ  CONST_17  H19  C1   C6   C5   180.00   0.0  0
 UZQ  CONST_18  H1   C4   C5   C6   180.00   0.0  0
 UZQ  CONST_19  H13  C26  C25  C24  180.00   0.0  0
 UZQ  CONST_20  H12  C24  C25  C26  180.00   0.0  0
 UZQ  CONST_21  H24  C27  C28  C23  180.00   0.0  0
 UZQ  CONST_22  H23  C25  C24  C23  180.00   0.0  0
 UZQ  CONST_23  C10  N9   C7   C5   180.00   0.0  0
 UZQ  CONST_24  H18  N9   C7   C5     0.00   0.0  0
 UZQ  CONST_25  O8   C7   N9   C10    0.00   0.0  0
 UZQ  Var_01    N18  C21  C23  C24  125.91  30.0  2
 UZQ  Var_02    O8   C7   C5   C4   -24.07  30.0  2
 UZQ  Var_03    C11  C10  N9   C7    90.20  30.0  2
 UZQ  Var_04    C13  C12  C11  C10   65.70  30.0  3
 UZQ  Var_05    N9   C10  C11  C12  175.60  30.0  1
 UZQ  Var_06    H5   C13  C12  C11  176.07  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
 UZQ  chir_01  C17  C16  N18  C20  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
 UZQ  plan-1  C24  0.020
 UZQ  plan-1  C26  0.020
 UZQ  plan-1  C28  0.020
 UZQ  plan-1  C23  0.020
 UZQ  plan-1  C25  0.020
 UZQ  plan-1  C27  0.020
 UZQ  plan-1  H12  0.020
 UZQ  plan-1  H13  0.020
 UZQ  plan-1  H23  0.020
 UZQ  plan-1  H24  0.020
 UZQ  plan-1  C21  0.020
 UZQ  plan-1  F29  0.020
 UZQ  plan-2  C4   0.020
 UZQ  plan-2  C5   0.020
 UZQ  plan-2  C6   0.020
 UZQ  plan-2  C7   0.020
 UZQ  plan-2  C1   0.020
 UZQ  plan-2  C2   0.020
 UZQ  plan-2  C3   0.020
 UZQ  plan-2  N14  0.020
 UZQ  plan-2  N18  0.020
 UZQ  plan-2  H1   0.020
 UZQ  plan-2  H2   0.020
 UZQ  plan-2  H19  0.020
 UZQ  plan-3  C5   0.020
 UZQ  plan-3  C7   0.020
 UZQ  plan-3  C10  0.020
 UZQ  plan-3  N9   0.020
 UZQ  plan-3  O8   0.020
 UZQ  plan-3  H18  0.020
 UZQ  plan-4  C15  0.020
 UZQ  plan-4  C3   0.020
 UZQ  plan-4  N14  0.020
 UZQ  plan-4  O19  0.020
 UZQ  plan-4  C16  0.020
 UZQ  plan-4  H20  0.020
 UZQ  plan-5  C17  0.020
 UZQ  plan-5  C2   0.020
 UZQ  plan-5  N18  0.020
 UZQ  plan-5  O22  0.020
 UZQ  plan-5  C23  0.020
 UZQ  plan-5  C21  0.020

