# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 08:19:07 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: (3Z)-3-{[(2-methoxyethyl)amino]methylidene}-1-methyl-5-phenyl-7-(trifluoromethyl)-1H-1,5-benzodiazepine-2,4(3H,5H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCN\C=C/1C(=O)N(C)c2ccc(cc2N(C/1=O)c3ccccc3)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
 1F6  1F6  (3Z)-3-{[(2-methoxyethyl)amino]methylidene}-1-methyl-5-phenyl-7-(trifluoromethyl)-1H-1,5-benzodiazepine-2,4(3H,5H)-dione  ligand  50  30  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1F6
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
 1F6  C1   C  CR6   0  -0.199   2.9026   0.1436  -1.1638
 1F6  C2   C  CR16  0  -0.323   1.8580  -0.4402  -0.4692
 1F6  C3   C  CR6   0   0.335   1.0113   0.3289   0.3235
 1F6  C4   C  CR6   0   0.310   1.1989   1.7070   0.3965
 1F6  C5   C  CR16  0  -0.291   2.2422   2.2859  -0.3270
 1F6  C6   C  CR16  0  -0.284   3.0960   1.5184  -1.0925
 1F6  N7   N  NT    0  -0.669   0.0073  -0.3145   1.0770
 1F6  C8   C  C     0   0.552  -1.3249   0.0205   0.9797
 1F6  C9   C  C     0  -0.420  -1.6739   1.3608   0.5231
 1F6  C10  C  C     0   0.527  -0.9812   2.5677   0.9761
 1F6  N11  N  NT    0  -0.568   0.3785   2.5073   1.2040
 1F6  C12  C  C1    0   0.125  -2.9059   1.5810  -0.0718
 1F6  N13  N  NH1   0  -0.577  -3.8351   0.6989  -0.3633
 1F6  C14  C  CH2   0  -0.324  -5.0460   0.9957  -1.0976
 1F6  C15  C  CH2   0  -0.143  -5.1692   0.1441  -2.3434
 1F6  O16  O  O2    0  -0.487  -5.2068  -1.2042  -1.9535
 1F6  C17  C  CH3   0  -0.395  -5.2268  -2.0908  -3.0437
 1F6  C18  C  CR6   0   0.262   0.3688  -1.5280   1.7370
 1F6  C19  C  CR16  0  -0.261   1.1228  -1.4383   2.8995
 1F6  C20  C  CR16  0  -0.258   1.5261  -2.5935   3.5546
 1F6  C21  C  CR16  0  -0.248   1.1710  -3.8375   3.0506
 1F6  C22  C  CR16  0  -0.264   0.4174  -3.9230   1.8868
 1F6  C23  C  CR16  0  -0.259   0.0149  -2.7711   1.2262
 1F6  C24  C  CH3   0  -0.557   0.9893   3.6560   1.8565
 1F6  C25  C  CT    0   1.056   3.7856  -0.6899  -2.0364
 1F6  F26  F  F     0  -0.314   3.3725  -0.6773  -3.3135
 1F6  F27  F  F     0  -0.308   5.0486  -0.2473  -2.0398
 1F6  F28  F  F     0  -0.305   3.8177  -1.9712  -1.6549
 1F6  O29  O  O     0  -0.482  -2.1810  -0.8002   1.2891
 1F6  O30  O  O     0  -0.472  -1.5823   3.6093   1.1995
 1F6  H1   H  HCR6  0   0.281   1.6958  -1.5083  -0.5184
 1F6  H2   H  HCR6  0   0.288   2.3973   3.3551  -0.2846
 1F6  H3   H  HCR6  0   0.279   3.9009   2.0038  -1.6275
 1F6  H5   H  H     0   0.294  -3.1406   2.5969  -0.3689
 1F6  H6   H  HCH2  0   0.261  -5.9109   0.8351  -0.4494
 1F6  H7   H  HCH2  0   0.262  -5.0397   2.0473  -1.3822
 1F6  H8   H  HCH2  0   0.218  -6.0834   0.4341  -2.8788
 1F6  H9   H  HCH2  0   0.210  -4.3210   0.3384  -3.0143
 1F6  H10  H  HCH3  0   0.207  -6.1122  -1.9480  -3.6739
 1F6  H11  H  HCH3  0   0.207  -4.3395  -1.9803  -3.6778
 1F6  H12  H  HCH3  0   0.236  -5.2451  -3.1061  -2.6498
 1F6  H13  H  HCR6  0   0.262   1.3901  -0.4641   3.2893
 1F6  H14  H  HCR6  0   0.262   2.1135  -2.5194   4.4602
 1F6  H15  H  HCR6  0   0.262   1.4808  -4.7394   3.5620
 1F6  H16  H  HCR6  0   0.263   0.1452  -4.8908   1.4869
 1F6  H17  H  HCR6  0   0.267  -0.5624  -2.8414   0.3141
 1F6  H18  H  HCH3  0   0.243   1.0631   4.5320   1.2098
 1F6  H19  H  HCH3  0   0.266   0.4073   3.9272   2.7332
 1F6  H20  H  HCH3  0   0.256   1.9874   3.3795   2.1876
 1F6  H4   H  HNH1  0   0.413  -3.7068  -0.2509  -0.0415

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
 1F6  C17  O16  single    1.405  0.020  1.405
 1F6  C15  O16  single    1.404  0.020  1.404
 1F6  C15  C14  single    1.514  0.020  1.514
 1F6  F28  C25  single    1.337  0.020  1.337
 1F6  C14  N13  single    1.447  0.020  1.447
 1F6  N13  C12  single    1.314  0.020  1.314
 1F6  C25  F26  single    1.342  0.020  1.342
 1F6  C25  F27  single    1.338  0.020  1.338
 1F6  C25  C1   single    1.495  0.020  1.495
 1F6  C12  C9   double    1.386  0.020  1.386
 1F6  C1   C2   aromatic  1.384  0.020  1.384
 1F6  C1   C6   aromatic  1.390  0.020  1.390
 1F6  C2   C3   aromatic  1.392  0.020  1.392
 1F6  O29  C8   double    1.226  0.020  1.226
 1F6  C6   C5   aromatic  1.380  0.020  1.380
 1F6  C23  C22  aromatic  1.388  0.020  1.388
 1F6  C23  C18  aromatic  1.390  0.020  1.390
 1F6  C8   C9   single    1.458  0.020  1.458
 1F6  C8   N7   single    1.377  0.020  1.377
 1F6  C9   C10  single    1.463  0.020  1.463
 1F6  C3   N7   single    1.411  0.020  1.411
 1F6  C3   C4   aromatic  1.393  0.020  1.393
 1F6  C22  C21  aromatic  1.389  0.020  1.389
 1F6  N7   C18  single    1.428  0.020  1.428
 1F6  C5   C4   aromatic  1.395  0.020  1.395
 1F6  C4   N11  single    1.402  0.020  1.402
 1F6  C18  C19  aromatic  1.388  0.020  1.388
 1F6  C10  N11  single    1.380  0.020  1.380
 1F6  C10  O30  double    1.223  0.020  1.223
 1F6  N11  C24  single    1.455  0.020  1.455
 1F6  C21  C20  aromatic  1.388  0.020  1.388
 1F6  C19  C20  aromatic  1.388  0.020  1.388
 1F6  C2   H1   single    0.930  0.020  1.080
 1F6  C5   H2   single    0.930  0.020  1.080
 1F6  C6   H3   single    0.930  0.020  1.080
 1F6  C12  H5   single    0.930  0.020  1.080
 1F6  C14  H6   single    0.970  0.020  1.090
 1F6  C14  H7   single    0.970  0.020  1.090
 1F6  C15  H8   single    0.970  0.020  1.090
 1F6  C15  H9   single    0.970  0.020  1.090
 1F6  C17  H10  single    0.970  0.020  1.090
 1F6  C17  H11  single    0.970  0.020  1.090
 1F6  C17  H12  single    0.970  0.020  1.090
 1F6  C19  H13  single    0.930  0.020  1.080
 1F6  C20  H14  single    0.930  0.020  1.080
 1F6  C21  H15  single    0.930  0.020  1.080
 1F6  C22  H16  single    0.930  0.020  1.080
 1F6  C23  H17  single    0.930  0.020  1.080
 1F6  C24  H18  single    0.970  0.020  1.090
 1F6  C24  H19  single    0.970  0.020  1.090
 1F6  C24  H20  single    0.970  0.020  1.090
 1F6  N13  H4   single    0.860  0.020  1.020

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
 1F6  C25  C1   C6   119.93  3.000
 1F6  C6   C1   C2   119.77  3.000
 1F6  C25  C1   C2   120.24  3.000
 1F6  H1   C2   C3   118.71  3.000
 1F6  H1   C2   C1   120.47  3.000
 1F6  C3   C2   C1   120.80  3.000
 1F6  N7   C3   C4   121.28  3.000
 1F6  C4   C3   C2   119.65  3.000
 1F6  N7   C3   C2   119.02  3.000
 1F6  N11  C4   C5   119.95  3.000
 1F6  N11  C4   C3   121.08  3.000
 1F6  C5   C4   C3   118.95  3.000
 1F6  H2   C5   C6   118.88  3.000
 1F6  H2   C5   C4   119.82  3.000
 1F6  C6   C5   C4   121.30  3.000
 1F6  H3   C6   C5   119.03  3.000
 1F6  H3   C6   C1   121.47  3.000
 1F6  C5   C6   C1   119.50  3.000
 1F6  C18  N7   C8   118.96  3.000
 1F6  C18  N7   C3   117.03  3.000
 1F6  C8   N7   C3   122.67  3.000
 1F6  O29  C8   C9   121.83  3.000
 1F6  C9   C8   N7   118.50  3.000
 1F6  O29  C8   N7   119.67  3.000
 1F6  C12  C9   C10  115.00  3.000
 1F6  C10  C9   C8   123.22  3.000
 1F6  C12  C9   C8   119.55  3.000
 1F6  O30  C10  N11  119.42  3.000
 1F6  O30  C10  C9   121.75  3.000
 1F6  N11  C10  C9   118.78  3.000
 1F6  C24  N11  C10  116.94  3.000
 1F6  C24  N11  C4   117.60  3.000
 1F6  C10  N11  C4   120.42  3.000
 1F6  H5   C12  N13  114.53  3.000
 1F6  H5   C12  C9   117.33  3.000
 1F6  N13  C12  C9   128.12  3.000
 1F6  H4   N13  C14  117.41  3.000
 1F6  H4   N13  C12  118.06  3.000
 1F6  C14  N13  C12  124.52  3.000
 1F6  H7   C14  H6   107.54  3.000
 1F6  H7   C14  C15  109.18  3.000
 1F6  H6   C14  C15  109.94  3.000
 1F6  H7   C14  N13  109.01  3.000
 1F6  H6   C14  N13  109.34  3.000
 1F6  C15  C14  N13  111.73  3.000
 1F6  H9   C15  H8   107.34  3.000
 1F6  H9   C15  O16  111.10  3.000
 1F6  H8   C15  O16  111.51  3.000
 1F6  H9   C15  C14  109.88  3.000
 1F6  H8   C15  C14  108.68  3.000
 1F6  O16  C15  C14  108.29  3.000
 1F6  C17  O16  C15  113.01  3.000
 1F6  H12  C17  H11  108.47  3.000
 1F6  H12  C17  H10  108.41  3.000
 1F6  H11  C17  H10  107.94  3.000
 1F6  H12  C17  O16  107.93  3.000
 1F6  H11  C17  O16  111.94  3.000
 1F6  H10  C17  O16  112.04  3.000
 1F6  C23  C18  C19  120.25  3.000
 1F6  C19  C18  N7   118.00  3.000
 1F6  C23  C18  N7   121.72  3.000
 1F6  H13  C19  C20  120.47  3.000
 1F6  H13  C19  C18  119.58  3.000
 1F6  C20  C19  C18  119.95  3.000
 1F6  H14  C20  C21  120.27  3.000
 1F6  H14  C20  C19  119.72  3.000
 1F6  C21  C20  C19  120.01  3.000
 1F6  H15  C21  C22  120.00  3.000
 1F6  H15  C21  C20  120.13  3.000
 1F6  C22  C21  C20  119.87  3.000
 1F6  H16  C22  C23  119.58  3.000
 1F6  H16  C22  C21  120.08  3.000
 1F6  C23  C22  C21  120.34  3.000
 1F6  H17  C23  C22  120.15  3.000
 1F6  H17  C23  C18  120.26  3.000
 1F6  C22  C23  C18  119.59  3.000
 1F6  H20  C24  H19  108.02  3.000
 1F6  H20  C24  H18  108.81  3.000
 1F6  H19  C24  H18  108.30  3.000
 1F6  H20  C24  N11  108.73  3.000
 1F6  H19  C24  N11  109.51  3.000
 1F6  H18  C24  N11  113.34  3.000
 1F6  F28  C25  F27  107.15  3.000
 1F6  F27  C25  F26  106.56  3.000
 1F6  F28  C25  F26  106.73  3.000
 1F6  F27  C25  C1   111.99  3.000
 1F6  F26  C25  C1   111.61  3.000
 1F6  F28  C25  C1   112.44  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
 1F6  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 1F6  CONST_02  C5   C6   C1   C2      0.00   0.0  0
 1F6  CONST_03  C6   C1   C2   C3      0.00   0.0  0
 1F6  CONST_04  C21  C22  C23  C18     0.00   0.0  0
 1F6  CONST_05  C21  C20  C19  C18     0.00   0.0  0
 1F6  CONST_06  C22  C23  C18  C19     0.00   0.0  0
 1F6  CONST_07  C22  C21  C20  C19     0.00   0.0  0
 1F6  CONST_08  C23  C22  C21  C20     0.00   0.0  0
 1F6  CONST_09  C23  C18  C19  C20     0.00   0.0  0
 1F6  CONST_10  C22  C23  C18  N7    180.00   0.0  0
 1F6  CONST_11  C20  C19  C18  N7    180.00   0.0  0
 1F6  CONST_12  C25  C1   C2   C3    180.00   0.0  0
 1F6  CONST_13  C25  C1   C6   C5    180.00   0.0  0
 1F6  CONST_14  H2   C5   C6   C1    180.00   0.0  0
 1F6  CONST_15  H3   C6   C1   C2    180.00   0.0  0
 1F6  CONST_16  H1   C2   C1   C6    180.00   0.0  0
 1F6  CONST_17  H17  C23  C18  N7      0.00   0.0  0
 1F6  CONST_18  H13  C19  C18  N7      0.00   0.0  0
 1F6  CONST_19  H16  C22  C23  C18   180.00   0.0  0
 1F6  CONST_20  H14  C20  C19  C18   180.00   0.0  0
 1F6  CONST_21  H15  C21  C20  C19   180.00   0.0  0
 1F6  Var_01    F28  C25  C1   C2    -25.34  30.0  3
 1F6  Var_02    C14  N13  C12  C9   -174.03  30.0  1
 1F6  Var_03    C15  C14  N13  C12   122.20  30.0  2
 1F6  Var_04    O16  C15  C14  N13    60.69  30.0  2
 1F6  Var_05    H10  C17  O16  C15   -61.29  30.0  3

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
 1F6  plan-1  N7   0.020
 1F6  plan-1  C18  0.020
 1F6  plan-1  C19  0.020
 1F6  plan-1  C20  0.020
 1F6  plan-1  C21  0.020
 1F6  plan-1  C22  0.020
 1F6  plan-1  C23  0.020
 1F6  plan-1  H13  0.020
 1F6  plan-1  H14  0.020
 1F6  plan-1  H15  0.020
 1F6  plan-1  H16  0.020
 1F6  plan-1  H17  0.020
 1F6  plan-2  C1   0.020
 1F6  plan-2  C2   0.020
 1F6  plan-2  C3   0.020
 1F6  plan-2  C4   0.020
 1F6  plan-2  C5   0.020
 1F6  plan-2  C6   0.020
 1F6  plan-2  N7   0.020
 1F6  plan-2  N11  0.020
 1F6  plan-2  C25  0.020
 1F6  plan-2  H1   0.020
 1F6  plan-2  H2   0.020
 1F6  plan-2  H3   0.020
 1F6  plan-3  C3   0.020
 1F6  plan-3  N7   0.020
 1F6  plan-3  C8   0.020
 1F6  plan-3  C9   0.020
 1F6  plan-3  C18  0.020
 1F6  plan-3  O29  0.020
 1F6  plan-4  C4   0.020
 1F6  plan-4  C8   0.020
 1F6  plan-4  C9   0.020
 1F6  plan-4  C10  0.020
 1F6  plan-4  N11  0.020
 1F6  plan-4  C24  0.020
 1F6  plan-4  O30  0.020

