# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 09:51:06 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 2,8-difluoro-11-(4-methylpiperazin-1-yl)-5H-dibenzo[b,e][1,4]diazepine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)C2=Nc3cc(F)ccc3Nc4ccc(F)cc24
#
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
 4PV  4PV  2,8-difluoro-11-(4-methylpiperazin-1-yl)-5H-dibenzo[b,e][1,4]diazepine  ligand  42  24  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4PV
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
 4PV  C1   C  C     0  -0.285   2.6682   2.7736  -0.1599
 4PV  C2   C  C     0  -0.328   2.1092   1.9911  -1.3373
 4PV  C3   C  C     0  -0.339   3.0394  -0.0297  -0.4463
 4PV  C11  C  CR6   0   0.210  -1.9301   0.1064   1.0546
 4PV  C12  C  CR6   0   0.260  -0.3300  -1.6039   0.8344
 4PV  C13  C  CR16  0  -0.290  -0.4693  -2.9660   1.0871
 4PV  C14  C  CR16  0  -0.411   0.0453  -3.9054   0.2089
 4PV  C15  C  CR6   0   0.537   0.6691  -3.4649  -0.9430
 4PV  C16  C  CR16  0  -0.449   0.8399  -2.1246  -1.2109
 4PV  C17  C  CR6   0  -0.056   0.3622  -1.1838  -0.3012
 4PV  F1   F  F     0  -0.315   1.1329  -4.3690  -1.8217
 4PV  C5   C  C     0   0.485   0.5920   0.2662  -0.5346
 4PV  N1   N  NR6   0  -0.463   1.8385   0.6112  -0.9680
 4PV  C4   C  C     0  -0.268   3.5995   0.7631   0.7254
 4PV  N    N  NR6   0  -0.412   3.8686   2.1345   0.3455
 4PV  C    C  CH3   0  -0.518   4.4542   2.8822   1.4344
 4PV  N3   N  NH1   0  -0.724  -0.8922  -0.6272   1.6745
 4PV  C6   C  CR6   0   0.268  -1.6105   0.9347  -0.0370
 4PV  N2   N  N     0  -0.500  -0.3176   1.1692  -0.4551
 4PV  C10  C  CR16  0  -0.310  -3.2389   0.0318   1.5103
 4PV  C9   C  CR16  0  -0.431  -4.2561   0.7633   0.9120
 4PV  C8   C  CR6   0   0.523  -3.9294   1.5543  -0.1709
 4PV  F    F  F     0  -0.322  -4.9005   2.2599  -0.7802
 4PV  C7   C  CR16  0  -0.491  -2.6396   1.6581  -0.6461
 4PV  H1   H  H     0   0.242   2.9150   3.7863  -0.4879
 4PV  H2   H  H     0   0.200   1.8905   2.8632   0.6185
 4PV  H3   H  H     0   0.265   1.2011   2.4572  -1.7087
 4PV  H4   H  H     0   0.248   2.8435   1.9785  -2.1476
 4PV  H5   H  H     0   0.275   2.8359  -1.0473  -0.1251
 4PV  H6   H  H     0   0.249   3.7797  -0.0822  -1.2485
 4PV  H7   H  HCR6  0   0.276  -0.9883  -3.2971   1.9777
 4PV  H8   H  HCR6  0   0.288  -0.0603  -4.9634   0.4093
 4PV  H9   H  HCR6  0   0.288   1.3535  -1.8094  -2.1105
 4PV  H10  H  H     0   0.193   2.8885   0.7017   1.5697
 4PV  H11  H  H     0   0.245   4.5293   0.2920   1.0542
 4PV  H13  H  HCH3  0   0.193   3.7931   2.9619   2.3114
 4PV  H14  H  HCH3  0   0.234   5.3804   2.4050   1.7576
 4PV  H15  H  HCH3  0   0.234   4.6954   3.8942   1.1056
 4PV  H16  H  HNH1  0   0.385  -1.1803  -1.0109   2.5643
 4PV  H17  H  HCR6  0   0.267  -3.4719  -0.6072   2.3536
 4PV  H18  H  HCR6  0   0.276  -5.2726   0.7068   1.2771
 4PV  H19  H  HCR6  0   0.271  -2.4106   2.3113  -1.4785

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
 4PV  C    N    single    1.445  0.020  1.445
 4PV  N    C1   single    1.451  0.020  1.451
 4PV  N    C4   single    1.448  0.020  1.448
 4PV  C1   C2   single    1.520  0.020  1.520
 4PV  C4   C3   single    1.522  0.020  1.522
 4PV  C2   N1   single    1.454  0.020  1.454
 4PV  C3   N1   single    1.458  0.020  1.458
 4PV  N1   C5   single    1.364  0.020  1.364
 4PV  N2   C5   double    1.284  0.020  1.284
 4PV  N2   C6   single    1.379  0.020  1.379
 4PV  C5   C17  single    1.487  0.020  1.487
 4PV  C6   C7   aromatic  1.398  0.020  1.398
 4PV  C6   C11  aromatic  1.407  0.020  1.407
 4PV  C7   C8   aromatic  1.378  0.020  1.378
 4PV  C17  C16  aromatic  1.393  0.020  1.393
 4PV  C17  C12  aromatic  1.395  0.020  1.395
 4PV  C16  C15  aromatic  1.377  0.020  1.377
 4PV  C11  N3   single    1.414  0.020  1.414
 4PV  C11  C10  aromatic  1.388  0.020  1.388
 4PV  N3   C12  single    1.406  0.020  1.406
 4PV  C8   F    single    1.346  0.020  1.346
 4PV  C8   C9   aromatic  1.380  0.020  1.380
 4PV  C12  C13  aromatic  1.392  0.020  1.392
 4PV  C15  F1   single    1.343  0.020  1.343
 4PV  C15  C14  aromatic  1.382  0.020  1.382
 4PV  C10  C9   aromatic  1.388  0.020  1.388
 4PV  C13  C14  aromatic  1.385  0.020  1.385
 4PV  C1   H1   single    0.970  0.020  1.090
 4PV  C1   H2   single    0.970  0.020  1.090
 4PV  C2   H3   single    0.970  0.020  1.090
 4PV  C2   H4   single    0.970  0.020  1.090
 4PV  C3   H5   single    0.970  0.020  1.090
 4PV  C3   H6   single    0.970  0.020  1.090
 4PV  C13  H7   single    0.930  0.020  1.080
 4PV  C14  H8   single    0.930  0.020  1.080
 4PV  C16  H9   single    0.930  0.020  1.080
 4PV  C4   H10  single    0.970  0.020  1.090
 4PV  C4   H11  single    0.970  0.020  1.090
 4PV  C    H13  single    0.970  0.020  1.090
 4PV  C    H14  single    0.970  0.020  1.090
 4PV  C    H15  single    0.970  0.020  1.090
 4PV  N3   H16  single    0.890  0.020  1.040
 4PV  C10  H17  single    0.930  0.020  1.080
 4PV  C9   H18  single    0.930  0.020  1.080
 4PV  C7   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
 4PV  H2   C1   H1   107.19  3.000
 4PV  H2   C1   N    111.90  3.000
 4PV  H1   C1   N    109.03  3.000
 4PV  H2   C1   C2   109.19  3.000
 4PV  H1   C1   C2   109.13  3.000
 4PV  N    C1   C2   110.32  3.000
 4PV  H4   C2   H3   108.24  3.000
 4PV  H4   C2   N1   107.60  3.000
 4PV  H3   C2   N1   109.79  3.000
 4PV  H4   C2   C1   109.44  3.000
 4PV  H3   C2   C1   110.57  3.000
 4PV  N1   C2   C1   111.12  3.000
 4PV  H6   C3   H5   107.39  3.000
 4PV  H6   C3   C4   109.93  3.000
 4PV  H5   C3   C4   109.23  3.000
 4PV  H6   C3   N1   108.45  3.000
 4PV  H5   C3   N1   111.30  3.000
 4PV  C4   C3   N1   110.47  3.000
 4PV  C10  C11  C6   120.03  3.000
 4PV  C10  C11  N3   121.35  3.000
 4PV  C6   C11  N3   118.61  3.000
 4PV  N3   C12  C17  118.42  3.000
 4PV  N3   C12  C13  122.09  3.000
 4PV  C17  C12  C13  119.48  3.000
 4PV  H7   C13  C14  119.49  3.000
 4PV  H7   C13  C12  119.76  3.000
 4PV  C14  C13  C12  120.75  3.000
 4PV  H8   C14  C15  120.67  3.000
 4PV  H8   C14  C13  120.63  3.000
 4PV  C15  C14  C13  118.69  3.000
 4PV  F1   C15  C16  119.00  3.000
 4PV  F1   C15  C14  119.11  3.000
 4PV  C16  C15  C14  121.88  3.000
 4PV  H9   C16  C17  120.57  3.000
 4PV  H9   C16  C15  120.24  3.000
 4PV  C17  C16  C15  119.18  3.000
 4PV  C5   C17  C16  120.21  3.000
 4PV  C16  C17  C12  119.90  3.000
 4PV  C5   C17  C12  119.89  3.000
 4PV  N2   C5   N1   119.28  3.000
 4PV  N2   C5   C17  124.52  3.000
 4PV  N1   C5   C17  115.97  3.000
 4PV  C5   N1   C3   121.86  3.000
 4PV  C5   N1   C2   119.40  3.000
 4PV  C3   N1   C2   110.78  3.000
 4PV  H11  C4   H10  107.06  3.000
 4PV  H11  C4   N    109.21  3.000
 4PV  H10  C4   N    111.86  3.000
 4PV  H11  C4   C3   108.68  3.000
 4PV  H10  C4   C3   108.81  3.000
 4PV  N    C4   C3   111.09  3.000
 4PV  C    N    C4   111.57  3.000
 4PV  C4   N    C1   110.78  3.000
 4PV  C    N    C1   111.71  3.000
 4PV  H15  C    H14  107.90  3.000
 4PV  H15  C    H13  107.79  3.000
 4PV  H14  C    H13  107.78  3.000
 4PV  H15  C    N    110.03  3.000
 4PV  H14  C    N    109.94  3.000
 4PV  H13  C    N    113.23  3.000
 4PV  H16  N3   C12  112.11  3.000
 4PV  H16  N3   C11  111.94  3.000
 4PV  C12  N3   C11  113.08  3.000
 4PV  C7   C6   N2   118.05  3.000
 4PV  C7   C6   C11  118.40  3.000
 4PV  N2   C6   C11  123.25  3.000
 4PV  C6   N2   C5   124.29  3.000
 4PV  H17  C10  C9   119.25  3.000
 4PV  H17  C10  C11  119.34  3.000
 4PV  C9   C10  C11  121.40  3.000
 4PV  H18  C9   C8   121.15  3.000
 4PV  H18  C9   C10  121.03  3.000
 4PV  C8   C9   C10  117.81  3.000
 4PV  C7   C8   F    118.65  3.000
 4PV  F    C8   C9   118.99  3.000
 4PV  C7   C8   C9   122.35  3.000
 4PV  H19  C7   C8   120.56  3.000
 4PV  H19  C7   C6   119.45  3.000
 4PV  C8   C7   C6   119.98  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
 4PV  CONST_01  C8   C9   C10  C11    0.00   0.0  0
 4PV  CONST_02  C15  C14  C13  C12    0.00   0.0  0
 4PV  CONST_03  C16  C15  C14  C13    0.00   0.0  0
 4PV  CONST_04  C17  C16  C15  C14    0.00   0.0  0
 4PV  CONST_05  C9   C8   C7   C6     0.00   0.0  0
 4PV  CONST_06  C7   C8   C9   C10    0.00   0.0  0
 4PV  CONST_07  F1   C15  C14  C13  180.00   0.0  0
 4PV  CONST_08  F1   C15  C16  C17  180.00   0.0  0
 4PV  CONST_09  F    C8   C7   C6   180.00   0.0  0
 4PV  CONST_10  F    C8   C9   C10  180.00   0.0  0
 4PV  CONST_11  H18  C9   C10  C11  180.00   0.0  0
 4PV  CONST_12  H8   C14  C13  C12  180.00   0.0  0
 4PV  CONST_13  H9   C16  C15  C14  180.00   0.0  0
 4PV  CONST_14  H7   C13  C14  C15  180.00   0.0  0
 4PV  CONST_15  H19  C7   C8   C9   180.00   0.0  0
 4PV  CONST_16  H17  C10  C9   C8   180.00   0.0  0
 4PV  Var_01    C3   C4   N    C1    57.32  30.0  1
 4PV  Var_02    C3   N1   C2   C1   -56.48  30.0  1
 4PV  Var_03    C4   N    C1   C2   -57.13  30.0  1
 4PV  Var_04    C4   C3   N1   C2    55.86  30.0  1
 4PV  Var_05    N    C1   C2   N1    56.91  30.0  1
 4PV  Var_06    N    C4   C3   N1   -56.46  30.0  1
 4PV  Var_07    H13  C    N    C1    62.29  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
 4PV  plan-1  C2   0.020
 4PV  plan-1  C3   0.020
 4PV  plan-1  C17  0.020
 4PV  plan-1  C5   0.020
 4PV  plan-1  N1   0.020
 4PV  plan-1  C6   0.020
 4PV  plan-1  N2   0.020
 4PV  plan-2  C12  0.020
 4PV  plan-2  C13  0.020
 4PV  plan-2  C14  0.020
 4PV  plan-2  C15  0.020
 4PV  plan-2  C16  0.020
 4PV  plan-2  C17  0.020
 4PV  plan-2  F1   0.020
 4PV  plan-2  C5   0.020
 4PV  plan-2  N3   0.020
 4PV  plan-2  H7   0.020
 4PV  plan-2  H8   0.020
 4PV  plan-2  H9   0.020
 4PV  plan-3  C11  0.020
 4PV  plan-3  N3   0.020
 4PV  plan-3  C6   0.020
 4PV  plan-3  N2   0.020
 4PV  plan-3  C10  0.020
 4PV  plan-3  C9   0.020
 4PV  plan-3  C8   0.020
 4PV  plan-3  F    0.020
 4PV  plan-3  C7   0.020
 4PV  plan-3  H17  0.020
 4PV  plan-3  H18  0.020
 4PV  plan-3  H19  0.020

