# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 09:08:09 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: (3~{Z})-4-methyl-3-[[4-(trifluoromethyl)phenyl]methylidene]-1~{H}-1,4-benzodiazepine-2,5-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)c2ccccc2NC(=O)\C1=C\c3ccc(cc3)C(F)(F)F
#
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
 CV3  CV3  (3~{Z})-4-methyl-3-[[4-(trifluoromethyl)phenyl]methylidene]-1~{H}-1,4-benzodiazepine-2,5-dione  ligand  38  25  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CV3
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
 CV3  C13   C  CR16  0  -0.308  -4.7388  -0.8369   1.2200
 CV3  C15   C  CR16  0  -0.286  -3.0129  -2.4616  -0.1954
 CV3  C17   C  CH3   0  -0.536  -0.4877   1.0663  -2.2869
 CV3  C20   C  CR16  0  -0.276   1.2653  -0.2816   0.1477
 CV3  C21   C  CR6   0  -0.206   3.6274   0.0877   0.3901
 CV3  C01   C  C     0   0.543  -2.0317  -0.5872  -1.4412
 CV3  C02   C  C     0   0.090  -1.4163   1.2836  -0.0080
 CV3  C03   C  C1    0  -0.250  -0.3572   1.5357   0.7645
 CV3  C04   C  CR16  0  -0.282   2.0729   1.8109   0.9996
 CV3  C05   C  CR16  0  -0.254   2.5666  -0.7375   0.0344
 CV3  C06   C  C     0   0.510  -2.7205   1.9469   0.2972
 CV3  C07   C  CR16  0  -0.249  -4.7965  -2.2081   1.3781
 CV3  C08   C  CT    0   1.053   5.0372  -0.3787   0.2068
 CV3  O09   O  O     0  -0.435  -2.8050   3.1304   0.5564
 CV3  N10   N  NH1   0  -0.735  -3.8111   1.1376   0.2464
 CV3  C11   C  CR6   0   0.357  -3.8029  -0.2575   0.3624
 CV3  C12   C  CR6   0  -0.091  -2.9422  -1.0779  -0.3714
 CV3  C14   C  CR16  0  -0.250  -3.9165  -3.0290   0.6812
 CV3  N16   N  NT    0  -0.527  -1.3538   0.5664  -1.2236
 CV3  O18   O  O     0  -0.461  -1.8802  -1.2257  -2.4697
 CV3  C19   C  CR6   0   0.103   0.9989   1.0050   0.6186
 CV3  C23   C  CR16  0  -0.258   3.3774   1.3655   0.8757
 CV3  F81   F  F     0  -0.306   5.8685   0.1525   1.1103
 CV3  F82   F  F     0  -0.305   5.1496  -1.7077   0.3029
 CV3  F83   F  F     0  -0.314   5.5123  -0.0372  -1.0012
 CV3  H131  H  HCR6  0   0.281  -5.4176  -0.1973   1.7704
 CV3  H151  H  HCR6  0   0.269  -2.3485  -3.0965  -0.7660
 CV3  H172  H  HCH3  0   0.266  -1.0428   1.1435  -3.2198
 CV3  H171  H  HCH3  0   0.262  -0.1322   2.0546  -2.0129
 CV3  H173  H  HCH3  0   0.253   0.3730   0.4169  -2.4447
 CV3  H201  H  HCR6  0   0.269   0.4577  -0.9520  -0.1107
 CV3  H031  H  H     0   0.289  -0.5026   2.2373   1.5783
 CV3  H041  H  HCR6  0   0.273   1.8861   2.8037   1.3886
 CV3  H051  H  HCR6  0   0.279   2.7384  -1.7425  -0.3265
 CV3  H071  H  HCR6  0   0.272  -5.5253  -2.6370   2.0530
 CV3  H101  H  HNH1  0   0.416  -4.6802   1.5907   0.4983
 CV3  H141  H  HCR6  0   0.266  -3.9474  -4.1020   0.8112
 CV3  H231  H  HCR6  0   0.278   4.1869   2.0217   1.1666

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
 CV3  C13  C07   aromatic  1.382  0.020  1.382
 CV3  C13  C11   aromatic  1.395  0.020  1.395
 CV3  C07  C14   aromatic  1.391  0.020  1.391
 CV3  N10  C11   single    1.400  0.020  1.400
 CV3  N10  C06   single    1.359  0.020  1.359
 CV3  O09  C06   double    1.214  0.020  1.214
 CV3  C11  C12   aromatic  1.397  0.020  1.397
 CV3  C06  C02   single    1.495  0.020  1.495
 CV3  C14  C15   aromatic  1.381  0.020  1.381
 CV3  C12  C15   aromatic  1.397  0.020  1.397
 CV3  C12  C01   single    1.488  0.020  1.488
 CV3  C02  C03   double    1.335  0.020  1.335
 CV3  C02  N16   single    1.413  0.020  1.413
 CV3  C03  C19   single    1.464  0.020  1.464
 CV3  C01  N16   single    1.356  0.020  1.356
 CV3  C01  O18   double    1.220  0.020  1.220
 CV3  N16  C17   single    1.460  0.020  1.460
 CV3  C19  C04   aromatic  1.396  0.020  1.396
 CV3  C19  C20   aromatic  1.396  0.020  1.396
 CV3  C04  C23   aromatic  1.384  0.020  1.384
 CV3  C20  C05   aromatic  1.383  0.020  1.383
 CV3  C23  C21   aromatic  1.390  0.020  1.390
 CV3  C05  C21   aromatic  1.390  0.020  1.390
 CV3  C21  C08   single    1.496  0.020  1.496
 CV3  F82  C08   single    1.337  0.020  1.337
 CV3  C08  F83   single    1.342  0.020  1.342
 CV3  C08  F81   single    1.338  0.020  1.338
 CV3  C13  H131  single    0.930  0.020  1.080
 CV3  C15  H151  single    0.930  0.020  1.080
 CV3  C17  H172  single    0.970  0.020  1.090
 CV3  C17  H171  single    0.970  0.020  1.090
 CV3  C17  H173  single    0.970  0.020  1.090
 CV3  C20  H201  single    0.930  0.020  1.080
 CV3  C03  H031  single    0.930  0.020  1.080
 CV3  C04  H041  single    0.930  0.020  1.080
 CV3  C05  H051  single    0.930  0.020  1.080
 CV3  C07  H071  single    0.930  0.020  1.080
 CV3  N10  H101  single    0.890  0.020  1.040
 CV3  C14  H141  single    0.930  0.020  1.080
 CV3  C23  H231  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
 CV3  H131  C13  C11   119.18  3.000
 CV3  H131  C13  C07   120.12  3.000
 CV3  C11   C13  C07   120.69  3.000
 CV3  H151  C15  C14   119.71  3.000
 CV3  H151  C15  C12   118.94  3.000
 CV3  C14   C15  C12   121.35  3.000
 CV3  H173  C17  H171  108.70  3.000
 CV3  H173  C17  H172  108.72  3.000
 CV3  H171  C17  H172  108.59  3.000
 CV3  H173  C17  N16   111.72  3.000
 CV3  H171  C17  N16   108.80  3.000
 CV3  H172  C17  N16   110.25  3.000
 CV3  H201  C20  C19   120.65  3.000
 CV3  H201  C20  C05   118.61  3.000
 CV3  C19   C20  C05   120.73  3.000
 CV3  C23   C21  C08   119.93  3.000
 CV3  C08   C21  C05   120.17  3.000
 CV3  C23   C21  C05   119.87  3.000
 CV3  O18   C01  N16   121.24  3.000
 CV3  O18   C01  C12   120.63  3.000
 CV3  N16   C01  C12   118.11  3.000
 CV3  N16   C02  C06   116.08  3.000
 CV3  N16   C02  C03   123.96  3.000
 CV3  C06   C02  C03   119.36  3.000
 CV3  H031  C03  C19   115.70  3.000
 CV3  H031  C03  C02   116.75  3.000
 CV3  C19   C03  C02   127.52  3.000
 CV3  H041  C04  C23   119.34  3.000
 CV3  H041  C04  C19   119.65  3.000
 CV3  C23   C04  C19   121.00  3.000
 CV3  H051  C05  C21   121.05  3.000
 CV3  H051  C05  C20   118.88  3.000
 CV3  C21   C05  C20   120.07  3.000
 CV3  N10   C06  O09   122.17  3.000
 CV3  O09   C06  C02   122.46  3.000
 CV3  N10   C06  C02   115.36  3.000
 CV3  H071  C07  C14   120.32  3.000
 CV3  H071  C07  C13   119.53  3.000
 CV3  C14   C07  C13   120.14  3.000
 CV3  F83   C08  F82   106.73  3.000
 CV3  F83   C08  F81   106.67  3.000
 CV3  F82   C08  F81   107.09  3.000
 CV3  F81   C08  C21   112.27  3.000
 CV3  F83   C08  C21   111.37  3.000
 CV3  F82   C08  C21   112.35  3.000
 CV3  H101  N10  C11   115.51  3.000
 CV3  H101  N10  C06   114.41  3.000
 CV3  C11   N10  C06   125.85  3.000
 CV3  C12   C11  N10   123.04  3.000
 CV3  C12   C11  C13   119.48  3.000
 CV3  N10   C11  C13   117.43  3.000
 CV3  C11   C12  C01   124.12  3.000
 CV3  C01   C12  C15   116.63  3.000
 CV3  C11   C12  C15   118.97  3.000
 CV3  H141  C14  C07   120.49  3.000
 CV3  H141  C14  C15   120.18  3.000
 CV3  C07   C14  C15   119.32  3.000
 CV3  C02   N16  C01   123.23  3.000
 CV3  C01   N16  C17   118.12  3.000
 CV3  C02   N16  C17   118.63  3.000
 CV3  C04   C19  C03   118.45  3.000
 CV3  C04   C19  C20   118.52  3.000
 CV3  C03   C19  C20   123.01  3.000
 CV3  H231  C23  C04   119.08  3.000
 CV3  H231  C23  C21   121.14  3.000
 CV3  C04   C23  C21   119.78  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
 CV3  CONST_01  C15   C14  C07  C13    0.00   0.0  0
 CV3  CONST_02  C23   C04  C19  C20    0.00   0.0  0
 CV3  CONST_03  C23   C21  C05  C20    0.00   0.0  0
 CV3  CONST_04  C19   C04  C23  C21    0.00   0.0  0
 CV3  CONST_05  C19   C20  C05  C21    0.00   0.0  0
 CV3  CONST_06  C05   C20  C19  C04    0.00   0.0  0
 CV3  CONST_07  C05   C21  C23  C04    0.00   0.0  0
 CV3  CONST_08  C12   C15  C14  C07    0.00   0.0  0
 CV3  CONST_09  C14   C07  C13  C11    0.00   0.0  0
 CV3  CONST_10  C08   C21  C05  C20  180.00   0.0  0
 CV3  CONST_11  C23   C04  C19  C03  180.00   0.0  0
 CV3  CONST_12  C05   C20  C19  C03  180.00   0.0  0
 CV3  CONST_13  C08   C21  C23  C04  180.00   0.0  0
 CV3  CONST_14  H141  C14  C07  C13  180.00   0.0  0
 CV3  CONST_15  H071  C07  C14  C15  180.00   0.0  0
 CV3  CONST_16  H041  C04  C19  C20  180.00   0.0  0
 CV3  CONST_17  H201  C20  C05  C21  180.00   0.0  0
 CV3  CONST_18  H231  C23  C21  C05  180.00   0.0  0
 CV3  CONST_19  H151  C15  C14  C07  180.00   0.0  0
 CV3  CONST_20  H131  C13  C07  C14  180.00   0.0  0
 CV3  CONST_21  H051  C05  C20  C19  180.00   0.0  0
 CV3  Var_01    C02   C03  C19  C20  -34.28  30.0  2
 CV3  Var_02    F82   C08  C21  C05  -29.13  30.0  2

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
 CV3  plan-1  C20   0.020
 CV3  plan-1  C21   0.020
 CV3  plan-1  C03   0.020
 CV3  plan-1  C04   0.020
 CV3  plan-1  C05   0.020
 CV3  plan-1  C08   0.020
 CV3  plan-1  C19   0.020
 CV3  plan-1  C23   0.020
 CV3  plan-1  H201  0.020
 CV3  plan-1  H041  0.020
 CV3  plan-1  H051  0.020
 CV3  plan-1  H231  0.020
 CV3  plan-2  C13   0.020
 CV3  plan-2  C15   0.020
 CV3  plan-2  C01   0.020
 CV3  plan-2  C07   0.020
 CV3  plan-2  N10   0.020
 CV3  plan-2  C11   0.020
 CV3  plan-2  C12   0.020
 CV3  plan-2  C14   0.020
 CV3  plan-2  H131  0.020
 CV3  plan-2  H151  0.020
 CV3  plan-2  H071  0.020
 CV3  plan-2  H141  0.020
 CV3  plan-3  C17   0.020
 CV3  plan-3  C01   0.020
 CV3  plan-3  C02   0.020
 CV3  plan-3  C12   0.020
 CV3  plan-3  N16   0.020
 CV3  plan-3  O18   0.020
 CV3  plan-4  C02   0.020
 CV3  plan-4  C06   0.020
 CV3  plan-4  O09   0.020
 CV3  plan-4  N10   0.020
 CV3  plan-4  C11   0.020
 CV3  plan-4  N16   0.020
 CV3  plan-4  H101  0.020

