# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 21:15:45 2022
#   Inital geometry file: a 128 line input string
#   Ligand name: (2S)-(4-chlorophenyl)[(3S)-3-(4-chlorophenyl)-7-iodo-2,5-dioxo-1,2,3,5-tetrahydro-4H-1,4-benzodiazepin-4-yl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H](N1[C@H](C(=O)Nc2ccc(I)cc2C1=O)c3ccc(Cl)cc3)c4ccc(Cl)cc4
#
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
 DIZ  DIZ  '(2S)-(4-chlorophenyl)[(3S)-3-(4-chlorophenyl)-7-iodo-2,5-dioxo-1,2,3,5-tetrahydro-4H-1,4-benzodiazepin-4-yl]ethanoic acid'  ligand  46  32  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DIZ
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
 DIZ  CL1  CL  CL     0  -0.133  -5.4150  -3.7324  -0.8982
 DIZ  C1   C   CR6    0  -0.049  -4.6840  -2.1600  -0.9451
 DIZ  C2   C   CR16   0  -0.202  -3.8179  -1.8410  -1.9780
 DIZ  C3   C   CR16   0  -0.308  -3.2361  -0.5827  -1.9988
 DIZ  C4   C   CR6    0   0.182  -3.5046   0.3613  -1.0101
 DIZ  C5   C   CR16   0  -0.308  -4.3924   0.0158   0.0052
 DIZ  C6   C   CR16   0  -0.203  -4.9788  -1.2406   0.0486
 DIZ  C7   C   CH1    0  -0.391  -2.7511   1.6693  -1.0319
 DIZ  C8   C   C      0   0.445  -3.5220   2.9116  -0.5112
 DIZ  O1   O   O      0  -0.570  -2.8449   3.7727   0.0727
 DIZ  O2   O   OC    -1  -0.583  -4.7302   2.9443  -0.7955
 DIZ  N1   N   NT     0  -0.441  -1.4553   1.5142  -0.3738
 DIZ  C9   C   C      0   0.556  -0.3239   1.5916  -1.1049
 DIZ  O3   O   O      0  -0.478  -0.3276   1.6784  -2.3258
 DIZ  C10  C   CR6    0  -0.069   0.9867   1.5501  -0.3940
 DIZ  C11  C   CR16   0  -0.240   2.0160   0.8739  -1.0515
 DIZ  C12  C   CR6    0  -0.227   3.2972   0.8786  -0.5416
 DIZ  I1   I   I      0   0.064   4.8196  -0.1791  -1.5295
 DIZ  C13  C   CR16   0  -0.223   3.5909   1.5899   0.6161
 DIZ  C14  C   CR16   0  -0.304   2.5764   2.2574   1.2703
 DIZ  C15  C   CR6    0   0.358   1.2652   2.2304   0.7916
 DIZ  N2   N   NH1    0  -0.720   0.3030   2.9250   1.5209
 DIZ  C16  C   C      0   0.537  -0.9522   2.5001   1.8315
 DIZ  O4   O   O      0  -0.444  -1.5955   3.0222   2.7159
 DIZ  C17  C   CH1    0  -0.297  -1.4588   1.2893   1.0571
 DIZ  C18  C   CR6    0   0.124  -0.7715   0.0023   1.4907
 DIZ  C19  C   CR16   0  -0.303  -0.2755  -0.1341   2.7832
 DIZ  C20  C   CR16   0  -0.193   0.3043  -1.3204   3.2068
 DIZ  C21  C   CR6    0  -0.056   0.3782  -2.3880   2.3285
 DIZ  CL2  CL  CL     0  -0.129   1.1048  -3.8737   2.8456
 DIZ  C22  C   CR16   0  -0.193  -0.1235  -2.2833   1.0415
 DIZ  C23  C   CR16   0  -0.284  -0.6961  -1.0897   0.6332
 DIZ  H2   H   HCR6   0   0.278  -3.5974  -2.5594  -2.7557
 DIZ  H3   H   HCR6   0   0.265  -2.5501  -0.3360  -2.8008
 DIZ  H5   H   HCR6   0   0.260  -4.6474   0.7275   0.7793
 DIZ  H6   H   HCR6   0   0.278  -5.6623  -1.4939   0.8477
 DIZ  H7   H   HCH1   0   0.301  -2.5298   1.8929  -2.0770
 DIZ  H11  H   HCR6   0   0.285   1.7867   0.3498  -1.9688
 DIZ  H13  H   HCR6   0   0.289   4.5932   1.6219   1.0201
 DIZ  H14  H   HCR6   0   0.288   2.7992   2.7984   2.1815
 DIZ  HN2  H   HNH1   0   0.413   0.6573   3.6558   2.1243
 DIZ  H17  H   HCH1   0   0.321  -2.5032   1.1961   1.3565
 DIZ  H19  H   HCR6   0   0.266  -0.3297   0.6826   3.4918
 DIZ  H20  H   HCR6   0   0.282   0.6911  -1.4046   4.2130
 DIZ  H22  H   HCR6   0   0.281  -0.0704  -3.1196   0.3580
 DIZ  H23  H   HCR6   0   0.272  -1.0845  -1.0253  -0.3738

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
 DIZ  CL1  C1   single    1.735  0.020  1.735
 DIZ  C1   C2   aromatic  1.385  0.020  1.385
 DIZ  C1   C6   aromatic  1.386  0.020  1.386
 DIZ  C2   C3   aromatic  1.386  0.020  1.386
 DIZ  C2   H2   single    0.930  0.020  1.080
 DIZ  C3   C4   aromatic  1.393  0.020  1.393
 DIZ  C3   H3   single    0.930  0.020  1.080
 DIZ  C4   C5   aromatic  1.392  0.020  1.392
 DIZ  C4   C7   single    1.510  0.020  1.510
 DIZ  C5   C6   aromatic  1.387  0.020  1.387
 DIZ  C5   H5   single    0.930  0.020  1.080
 DIZ  C6   H6   single    0.930  0.020  1.080
 DIZ  C7   C8   single    1.552  0.020  1.552
 DIZ  C7   N1   single    1.462  0.020  1.462
 DIZ  C7   H7   single    0.970  0.020  1.090
 DIZ  C8   O1   deloc     1.241  0.020  1.241
 DIZ  C8   O2   deloc     1.242  0.020  1.242
 DIZ  N1   C9   single    1.349  0.020  1.349
 DIZ  N1   C17  single    1.448  0.020  1.448
 DIZ  C9   O3   double    1.224  0.020  1.224
 DIZ  C9   C10  single    1.492  0.020  1.492
 DIZ  C10  C11  aromatic  1.396  0.020  1.396
 DIZ  C10  C15  aromatic  1.395  0.020  1.395
 DIZ  C11  C12  aromatic  1.379  0.020  1.379
 DIZ  C11  H11  single    0.930  0.020  1.080
 DIZ  C12  I1   single    2.101  0.020  2.101
 DIZ  C12  C13  aromatic  1.390  0.020  1.390
 DIZ  C13  C14  aromatic  1.379  0.020  1.379
 DIZ  C13  H13  single    0.930  0.020  1.080
 DIZ  C14  C15  aromatic  1.396  0.020  1.396
 DIZ  C14  H14  single    0.930  0.020  1.080
 DIZ  C15  N2   single    1.393  0.020  1.393
 DIZ  N2   C16  single    1.361  0.020  1.361
 DIZ  N2   HN2  single    0.890  0.020  1.040
 DIZ  C16  O4   double    1.212  0.020  1.212
 DIZ  C16  C17  single    1.524  0.020  1.524
 DIZ  C17  C18  single    1.522  0.020  1.522
 DIZ  C17  H17  single    0.970  0.020  1.090
 DIZ  C18  C19  aromatic  1.391  0.020  1.391
 DIZ  C18  C23  aromatic  1.390  0.020  1.390
 DIZ  C19  C20  aromatic  1.387  0.020  1.387
 DIZ  C19  H19  single    0.930  0.020  1.080
 DIZ  C20  C21  aromatic  1.384  0.020  1.384
 DIZ  C20  H20  single    0.930  0.020  1.080
 DIZ  C21  CL2  single    1.733  0.020  1.733
 DIZ  C21  C22  aromatic  1.385  0.020  1.385
 DIZ  C22  C23  aromatic  1.385  0.020  1.385
 DIZ  C22  H22  single    0.930  0.020  1.080
 DIZ  C23  H23  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
 DIZ  C6   C1   C2   121.00  3.000
 DIZ  C6   C1   CL1  119.51  3.000
 DIZ  C2   C1   CL1  119.50  3.000
 DIZ  H2   C2   C3   120.43  3.000
 DIZ  H2   C2   C1   120.72  3.000
 DIZ  C3   C2   C1   118.85  3.000
 DIZ  H3   C3   C4   119.53  3.000
 DIZ  H3   C3   C2   118.90  3.000
 DIZ  C4   C3   C2   121.56  3.000
 DIZ  C7   C4   C5   122.94  3.000
 DIZ  C7   C4   C3   118.73  3.000
 DIZ  C5   C4   C3   118.18  3.000
 DIZ  H5   C5   C6   118.28  3.000
 DIZ  H5   C5   C4   120.58  3.000
 DIZ  C6   C5   C4   121.14  3.000
 DIZ  H6   C6   C5   120.16  3.000
 DIZ  H6   C6   C1   120.59  3.000
 DIZ  C5   C6   C1   119.26  3.000
 DIZ  H7   C7   N1   105.85  3.000
 DIZ  H7   C7   C8   104.95  3.000
 DIZ  N1   C7   C8   111.97  3.000
 DIZ  H7   C7   C4   107.01  3.000
 DIZ  N1   C7   C4   110.13  3.000
 DIZ  C8   C7   C4   116.15  3.000
 DIZ  O2   C8   O1   128.33  3.000
 DIZ  O2   C8   C7   115.31  3.000
 DIZ  O1   C8   C7   116.25  3.000
 DIZ  C17  N1   C9   123.10  3.000
 DIZ  C17  N1   C7   117.33  3.000
 DIZ  C9   N1   C7   119.56  3.000
 DIZ  C10  C9   O3   118.69  3.000
 DIZ  C10  C9   N1   118.49  3.000
 DIZ  O3   C9   N1   122.82  3.000
 DIZ  C15  C10  C11  119.29  3.000
 DIZ  C15  C10  C9   124.54  3.000
 DIZ  C11  C10  C9   115.90  3.000
 DIZ  H11  C11  C12  120.83  3.000
 DIZ  H11  C11  C10  118.56  3.000
 DIZ  C12  C11  C10  120.61  3.000
 DIZ  C13  C12  I1   119.75  3.000
 DIZ  C13  C12  C11  120.40  3.000
 DIZ  I1   C12  C11  119.85  3.000
 DIZ  H13  C13  C14  119.36  3.000
 DIZ  H13  C13  C12  121.48  3.000
 DIZ  C14  C13  C12  119.16  3.000
 DIZ  H14  C14  C15  119.44  3.000
 DIZ  H14  C14  C13  119.31  3.000
 DIZ  C15  C14  C13  121.25  3.000
 DIZ  N2   C15  C14  117.36  3.000
 DIZ  N2   C15  C10  123.38  3.000
 DIZ  C14  C15  C10  119.24  3.000
 DIZ  HN2  N2   C16  114.35  3.000
 DIZ  HN2  N2   C15  115.51  3.000
 DIZ  C16  N2   C15  126.93  3.000
 DIZ  C17  C16  O4   122.46  3.000
 DIZ  C17  C16  N2   116.01  3.000
 DIZ  O4   C16  N2   121.44  3.000
 DIZ  H17  C17  C18  106.38  3.000
 DIZ  H17  C17  C16  104.29  3.000
 DIZ  C18  C17  C16  112.14  3.000
 DIZ  H17  C17  N1   106.67  3.000
 DIZ  C18  C17  N1   114.31  3.000
 DIZ  C16  C17  N1   112.20  3.000
 DIZ  C23  C18  C19  118.47  3.000
 DIZ  C23  C18  C17  120.85  3.000
 DIZ  C19  C18  C17  120.57  3.000
 DIZ  H19  C19  C20  117.80  3.000
 DIZ  H19  C19  C18  121.09  3.000
 DIZ  C20  C19  C18  121.12  3.000
 DIZ  H20  C20  C21  120.75  3.000
 DIZ  H20  C20  C19  120.03  3.000
 DIZ  C21  C20  C19  119.22  3.000
 DIZ  C22  C21  CL2  119.60  3.000
 DIZ  C22  C21  C20  120.79  3.000
 DIZ  CL2  C21  C20  119.62  3.000
 DIZ  H22  C22  C23  120.02  3.000
 DIZ  H22  C22  C21  120.73  3.000
 DIZ  C23  C22  C21  119.25  3.000
 DIZ  H23  C23  C22  118.32  3.000
 DIZ  H23  C23  C18  120.54  3.000
 DIZ  C22  C23  C18  121.15  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
 DIZ  CONST_01  C4   C3   C2   C1     0.00  0.0  0
 DIZ  CONST_02  C4   C5   C6   C1     0.00  0.0  0
 DIZ  CONST_03  C5   C6   C1   C2     0.00  0.0  0
 DIZ  CONST_04  C5   C4   C3   C2     0.00  0.0  0
 DIZ  CONST_05  C6   C1   C2   C3     0.00  0.0  0
 DIZ  CONST_06  C6   C5   C4   C3     0.00  0.0  0
 DIZ  CONST_07  C13  C12  C11  C10    0.00  0.0  0
 DIZ  CONST_08  C14  C13  C12  C11    0.00  0.0  0
 DIZ  CONST_09  C15  C14  C13  C12    0.00  0.0  0
 DIZ  CONST_10  C21  C20  C19  C18    0.00  0.0  0
 DIZ  CONST_11  C21  C22  C23  C18    0.00  0.0  0
 DIZ  CONST_12  C22  C23  C18  C19    0.00  0.0  0
 DIZ  CONST_13  C22  C21  C20  C19    0.00  0.0  0
 DIZ  CONST_14  C23  C18  C19  C20    0.00  0.0  0
 DIZ  CONST_15  C23  C22  C21  C20    0.00  0.0  0
 DIZ  CONST_16  C20  C19  C18  C17  180.00  0.0  0
 DIZ  CONST_17  C22  C23  C18  C17  180.00  0.0  0
 DIZ  CONST_18  C3   C2   C1   CL1  180.00  0.0  0
 DIZ  CONST_19  C5   C6   C1   CL1  180.00  0.0  0
 DIZ  CONST_20  C7   C4   C3   C2   180.00  0.0  0
 DIZ  CONST_21  C7   C4   C5   C6   180.00  0.0  0
 DIZ  CONST_22  I1   C12  C11  C10  180.00  0.0  0
 DIZ  CONST_23  C14  C13  C12  I1   180.00  0.0  0
 DIZ  CONST_24  CL2  C21  C20  C19  180.00  0.0  0
 DIZ  CONST_25  C23  C22  C21  CL2  180.00  0.0  0
 DIZ  CONST_26  H3   C3   C2   C1   180.00  0.0  0
 DIZ  CONST_27  H5   C5   C6   C1   180.00  0.0  0
 DIZ  CONST_28  H6   C6   C1   C2   180.00  0.0  0
 DIZ  CONST_29  H2   C2   C3   C4   180.00  0.0  0
 DIZ  CONST_30  H13  C13  C12  C11  180.00  0.0  0
 DIZ  CONST_31  H14  C14  C13  C12  180.00  0.0  0
 DIZ  CONST_32  H11  C11  C12  C13  180.00  0.0  0
 DIZ  CONST_33  H19  C19  C18  C17    0.00  0.0  0
 DIZ  CONST_34  H23  C23  C18  C17    0.00  0.0  0
 DIZ  CONST_35  H20  C20  C19  C18  180.00  0.0  0
 DIZ  CONST_36  H22  C22  C23  C18  180.00  0.0  0

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
 DIZ  chir_01  C7   C4  C8   N1   negativ
 DIZ  chir_02  C17  N1  C16  C18  positiv

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
 DIZ  plan-1  CL1  0.020
 DIZ  plan-1  C1   0.020
 DIZ  plan-1  C2   0.020
 DIZ  plan-1  C3   0.020
 DIZ  plan-1  C4   0.020
 DIZ  plan-1  C5   0.020
 DIZ  plan-1  C6   0.020
 DIZ  plan-1  C7   0.020
 DIZ  plan-1  H2   0.020
 DIZ  plan-1  H3   0.020
 DIZ  plan-1  H5   0.020
 DIZ  plan-1  H6   0.020
 DIZ  plan-2  C17  0.020
 DIZ  plan-2  C18  0.020
 DIZ  plan-2  C19  0.020
 DIZ  plan-2  C20  0.020
 DIZ  plan-2  C21  0.020
 DIZ  plan-2  CL2  0.020
 DIZ  plan-2  C22  0.020
 DIZ  plan-2  C23  0.020
 DIZ  plan-2  H19  0.020
 DIZ  plan-2  H20  0.020
 DIZ  plan-2  H22  0.020
 DIZ  plan-2  H23  0.020
 DIZ  plan-3  C9   0.020
 DIZ  plan-3  C10  0.020
 DIZ  plan-3  C11  0.020
 DIZ  plan-3  C12  0.020
 DIZ  plan-3  I1   0.020
 DIZ  plan-3  C13  0.020
 DIZ  plan-3  C14  0.020
 DIZ  plan-3  C15  0.020
 DIZ  plan-3  N2   0.020
 DIZ  plan-3  H11  0.020
 DIZ  plan-3  H13  0.020
 DIZ  plan-3  H14  0.020
 DIZ  plan-4  C7   0.020
 DIZ  plan-4  N1   0.020
 DIZ  plan-4  C9   0.020
 DIZ  plan-4  O3   0.020
 DIZ  plan-4  C10  0.020
 DIZ  plan-4  C17  0.020
 DIZ  plan-5  C15  0.020
 DIZ  plan-5  N2   0.020
 DIZ  plan-5  C16  0.020
 DIZ  plan-5  O4   0.020
 DIZ  plan-5  C17  0.020
 DIZ  plan-5  HN2  0.020
 DIZ  plan-6  C7   0.020
 DIZ  plan-6  C8   0.020
 DIZ  plan-6  O1   0.020
 DIZ  plan-6  O2   0.020

