# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 21:04:18 2022
#   Inital geometry file: a 104 line input string
#   Ligand name: 3-[(~{S})-dioxidanyl(phenyl)methyl]-4-methyl-2-oxidanyl-1~{H}-1,4-benzodiazepin-5-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)c2ccccc2NC(=C1[C@@H](OO)c3ccccc3)O
#
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
 VJQ  VJQ  "3-[(S)-dioxidanyl(phenyl)methyl]-4-methyl-2-oxidanyl-1H-1,4-benzodiazepin-5-one"
  ligand  39  23  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VJQ
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
 VJQ  C4   C  C     0   0.547  -24.4137  -20.3468  -3.1065
 VJQ  C7   C  C     0   0.055  -24.8056  -22.7265  -3.4490
 VJQ  C8   C  CH1   0   0.002  -23.8043  -23.7563  -3.0013
 VJQ  C10  C  CR16  0  -0.270  -25.1146  -25.1175  -1.3872
 VJQ  C13  C  CR16  0  -0.240  -23.4658  -24.4773   0.7379
 VJQ  C15  C  C     0   0.453  -25.4672  -22.8170  -4.6171
 VJQ  C20  C  CR16  0  -0.250  -24.0253  -19.2275  -7.1952
 VJQ  O16  O  OH1   0  -0.593  -25.6411  -23.9250  -5.3483
 VJQ  N17  N  NH1   0  -0.712  -25.9479  -21.6896  -5.2505
 VJQ  C18  C  CR6   0   0.326  -25.0336  -20.6723  -5.5469
 VJQ  C3   C  CR6   0  -0.151  -24.1733  -20.1549  -4.5684
 VJQ  C19  C  CR16  0  -0.308  -24.9688  -20.1762  -6.8498
 VJQ  C1   C  CR16  0  -0.256  -23.1227  -18.7567  -6.2468
 VJQ  C2   C  CR16  0  -0.270  -23.2214  -19.2022  -4.9436
 VJQ  N6   N  NT    0  -0.516  -24.9141  -21.5308  -2.6912
 VJQ  C23  C  CH3   0  -0.533  -25.5190  -21.5853  -1.3662
 VJQ  O5   O  O     0  -0.468  -24.2488  -19.4074  -2.3424
 VJQ  C9   C  CR6   0   0.048  -24.0196  -24.2832  -1.5999
 VJQ  C14  C  CR16  0  -0.310  -23.1925  -23.9698  -0.5277
 VJQ  C12  C  CR16  0  -0.262  -24.5626  -25.2999   0.9450
 VJQ  C11  C  CR16  0  -0.244  -25.3882  -25.6213  -0.1259
 VJQ  O18  O  O2    0  -0.298  -22.4913  -23.2093  -3.0466
 VJQ  H2   H  HCH1  0   0.244  -23.8415  -24.6208  -3.6756
 VJQ  H3   H  HCR6  0   0.257  -25.7655  -25.3703  -2.2172
 VJQ  H4   H  HCR6  0   0.255  -22.8155  -24.2225   1.5650
 VJQ  H5   H  HCR6  0   0.266  -23.9822  -18.8669  -8.2147
 VJQ  H6   H  HNH1  0   0.404  -26.6195  -21.8755  -5.9839
 VJQ  H7   H  HCR6  0   0.271  -25.6517  -20.5598  -7.5984
 VJQ  H8   H  HCR6  0   0.259  -22.3697  -18.0297  -6.5188
 VJQ  H9   H  HCR6  0   0.262  -22.5628  -18.7957  -4.1873
 VJQ  H10  H  HCH3  0   0.252  -26.1362  -20.7033  -1.2014
 VJQ  H11  H  HCH3  0   0.252  -26.1546  -22.4647  -1.3120
 VJQ  H12  H  HCH3  0   0.244  -24.7808  -21.6442  -0.5670
 VJQ  H13  H  HCR6  0   0.255  -22.3357  -23.3229  -0.6573
 VJQ  H14  H  HCR6  0   0.254  -24.7725  -25.6915   1.9319
 VJQ  H15  H  HCR6  0   0.256  -26.2439  -26.2675   0.0211
 VJQ  H16  H  HOH1  0   0.469  -22.3864  -22.0972  -4.5601
 VJQ  H1   H  HOH1  0   0.490  -25.6591  -24.7138  -4.7925
 VJQ  O17  O  OH1   0  -0.440  -22.1269  -23.0155  -4.3868

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
 VJQ  C20  C19  aromatic  1.382  0.020  1.382
 VJQ  C20  C1   aromatic  1.391  0.020  1.391
 VJQ  C19  C18  aromatic  1.396  0.020  1.396
 VJQ  N17  C18  single    1.399  0.020  1.399
 VJQ  N17  C15  single    1.380  0.020  1.380
 VJQ  C18  C3   aromatic  1.402  0.020  1.402
 VJQ  C1   C2   aromatic  1.381  0.020  1.381
 VJQ  O16  C15  single    1.339  0.020  1.339
 VJQ  O17  O18  single    1.402  0.020  1.402
 VJQ  C15  C7   double    1.345  0.020  1.345
 VJQ  C2   C3   aromatic  1.398  0.020  1.398
 VJQ  C3   C4   single    1.494  0.020  1.494
 VJQ  O18  C8   single    1.423  0.020  1.423
 VJQ  C7   C8   single    1.504  0.020  1.504
 VJQ  C7   N6   single    1.420  0.020  1.420
 VJQ  C4   N6   single    1.351  0.020  1.351
 VJQ  C4   O5   double    1.222  0.020  1.222
 VJQ  C8   C9   single    1.513  0.020  1.513
 VJQ  N6   C23  single    1.458  0.020  1.458
 VJQ  C9   C10  aromatic  1.393  0.020  1.393
 VJQ  C9   C14  aromatic  1.390  0.020  1.390
 VJQ  C10  C11  aromatic  1.385  0.020  1.385
 VJQ  C14  C13  aromatic  1.391  0.020  1.391
 VJQ  C11  C12  aromatic  1.390  0.020  1.390
 VJQ  C13  C12  aromatic  1.387  0.020  1.387
 VJQ  C8   H2   single    0.970  0.020  1.090
 VJQ  C10  H3   single    0.930  0.020  1.080
 VJQ  C13  H4   single    0.930  0.020  1.080
 VJQ  C20  H5   single    0.930  0.020  1.080
 VJQ  N17  H6   single    0.890  0.020  1.040
 VJQ  C19  H7   single    0.930  0.020  1.080
 VJQ  C1   H8   single    0.930  0.020  1.080
 VJQ  C2   H9   single    0.930  0.020  1.080
 VJQ  C23  H10  single    0.970  0.020  1.090
 VJQ  C23  H11  single    0.970  0.020  1.090
 VJQ  C23  H12  single    0.970  0.020  1.090
 VJQ  C14  H13  single    0.930  0.020  1.080
 VJQ  C12  H14  single    0.930  0.020  1.080
 VJQ  C11  H15  single    0.930  0.020  1.080
 VJQ  O17  H16  single    0.850  0.020  0.980
 VJQ  O16  H1   single    0.850  0.020  0.980

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
 VJQ  O5   C4   N6   122.11  3.000
 VJQ  O5   C4   C3   119.43  3.000
 VJQ  N6   C4   C3   118.23  3.000
 VJQ  N6   C7   C15  118.84  3.000
 VJQ  N6   C7   C8   117.94  3.000
 VJQ  C15  C7   C8   122.65  3.000
 VJQ  H2   C8   O18  108.34  3.000
 VJQ  H2   C8   C9   106.86  3.000
 VJQ  O18  C8   C9   107.14  3.000
 VJQ  H2   C8   C7   109.51  3.000
 VJQ  C9   C8   C7   114.80  3.000
 VJQ  O18  C8   C7   109.97  3.000
 VJQ  H3   C10  C11  119.56  3.000
 VJQ  H3   C10  C9   119.64  3.000
 VJQ  C11  C10  C9   120.80  3.000
 VJQ  H4   C13  C12  120.05  3.000
 VJQ  H4   C13  C14  119.43  3.000
 VJQ  C12  C13  C14  120.52  3.000
 VJQ  N17  C15  O16  112.35  3.000
 VJQ  O16  C15  C7   126.42  3.000
 VJQ  N17  C15  C7   121.00  3.000
 VJQ  H5   C20  C1   120.23  3.000
 VJQ  H5   C20  C19  119.43  3.000
 VJQ  C1   C20  C19  120.33  3.000
 VJQ  H1   O16  C15  111.36  3.000
 VJQ  H6   N17  C18  114.44  3.000
 VJQ  H6   N17  C15  114.46  3.000
 VJQ  C18  N17  C15  117.62  3.000
 VJQ  C19  C18  C3   119.46  3.000
 VJQ  C3   C18  N17  121.43  3.000
 VJQ  C19  C18  N17  119.11  3.000
 VJQ  C2   C3   C18  118.82  3.000
 VJQ  C2   C3   C4   117.37  3.000
 VJQ  C18  C3   C4   122.47  3.000
 VJQ  H7   C19  C18  119.33  3.000
 VJQ  H7   C19  C20  120.05  3.000
 VJQ  C18  C19  C20  120.60  3.000
 VJQ  H8   C1   C2   120.28  3.000
 VJQ  H8   C1   C20  120.51  3.000
 VJQ  C2   C1   C20  119.19  3.000
 VJQ  H9   C2   C1   119.66  3.000
 VJQ  H9   C2   C3   118.87  3.000
 VJQ  C1   C2   C3   121.46  3.000
 VJQ  C23  N6   C7   119.04  3.000
 VJQ  C23  N6   C4   117.77  3.000
 VJQ  C7   N6   C4   123.08  3.000
 VJQ  H12  C23  H11  108.42  3.000
 VJQ  H12  C23  H10  108.47  3.000
 VJQ  H11  C23  H10  108.44  3.000
 VJQ  H12  C23  N6   112.81  3.000
 VJQ  H11  C23  N6   108.57  3.000
 VJQ  H10  C23  N6   110.03  3.000
 VJQ  C14  C9   C10  119.02  3.000
 VJQ  C14  C9   C8   123.47  3.000
 VJQ  C10  C9   C8   117.52  3.000
 VJQ  H13  C14  C9   120.92  3.000
 VJQ  H13  C14  C13  118.89  3.000
 VJQ  C9   C14  C13  120.18  3.000
 VJQ  H14  C12  C11  120.25  3.000
 VJQ  H14  C12  C13  120.28  3.000
 VJQ  C11  C12  C13  119.47  3.000
 VJQ  H15  C11  C12  120.20  3.000
 VJQ  H15  C11  C10  119.79  3.000
 VJQ  C12  C11  C10  120.00  3.000
 VJQ  O17  O18  C8   108.86  3.000
 VJQ  H16  O17  O18  103.42  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
 VJQ  CONST_01  C13  C14  C9   C10    0.00  0.0  0
 VJQ  CONST_02  C13  C12  C11  C10    0.00  0.0  0
 VJQ  CONST_03  C3   C2   C1   C20    0.00  0.0  0
 VJQ  CONST_04  C1   C20  C19  C18    0.00  0.0  0
 VJQ  CONST_05  C2   C1   C20  C19    0.00  0.0  0
 VJQ  CONST_06  C12  C11  C10  C9     0.00  0.0  0
 VJQ  CONST_07  C12  C13  C14  C9     0.00  0.0  0
 VJQ  CONST_08  C11  C10  C9   C14    0.00  0.0  0
 VJQ  CONST_09  C11  C12  C13  C14    0.00  0.0  0
 VJQ  CONST_10  C11  C10  C9   C8   180.00  0.0  0
 VJQ  CONST_11  C13  C14  C9   C8   180.00  0.0  0
 VJQ  CONST_12  H13  C14  C9   C10  180.00  0.0  0
 VJQ  CONST_13  H14  C12  C11  C10  180.00  0.0  0
 VJQ  CONST_14  H15  C11  C12  C13  180.00  0.0  0
 VJQ  CONST_15  H9   C2   C1   C20  180.00  0.0  0
 VJQ  CONST_16  H5   C20  C19  C18  180.00  0.0  0
 VJQ  CONST_17  H8   C1   C2   C3   180.00  0.0  0
 VJQ  CONST_18  H8   C1   C20  C19  180.00  0.0  0
 VJQ  CONST_19  H7   C19  C20  C1   180.00  0.0  0
 VJQ  CONST_20  H5   C20  C1   C2   180.00  0.0  0
 VJQ  CONST_21  H15  C11  C10  C9   180.00  0.0  0
 VJQ  CONST_22  H4   C13  C14  C9   180.00  0.0  0
 VJQ  CONST_23  H3   C10  C9   C14  180.00  0.0  0
 VJQ  CONST_24  H14  C12  C13  C14  180.00  0.0  0
 VJQ  CONST_25  H3   C10  C11  C12  180.00  0.0  0
 VJQ  CONST_26  H13  C14  C13  C12  180.00  0.0  0
 VJQ  CONST_27  H4   C13  C12  C11  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
 VJQ  chir_01  C8  O18  C7  C9  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
 VJQ  plan-1  C8   0.020
 VJQ  plan-1  C10  0.020
 VJQ  plan-1  C13  0.020
 VJQ  plan-1  C9   0.020
 VJQ  plan-1  C14  0.020
 VJQ  plan-1  C12  0.020
 VJQ  plan-1  C11  0.020
 VJQ  plan-1  H3   0.020
 VJQ  plan-1  H4   0.020
 VJQ  plan-1  H13  0.020
 VJQ  plan-1  H14  0.020
 VJQ  plan-1  H15  0.020
 VJQ  plan-2  C4   0.020
 VJQ  plan-2  C20  0.020
 VJQ  plan-2  N17  0.020
 VJQ  plan-2  C18  0.020
 VJQ  plan-2  C3   0.020
 VJQ  plan-2  C19  0.020
 VJQ  plan-2  C1   0.020
 VJQ  plan-2  C2   0.020
 VJQ  plan-2  H5   0.020
 VJQ  plan-2  H7   0.020
 VJQ  plan-2  H8   0.020
 VJQ  plan-2  H9   0.020
 VJQ  plan-3  C4   0.020
 VJQ  plan-3  C7   0.020
 VJQ  plan-3  C3   0.020
 VJQ  plan-3  N6   0.020
 VJQ  plan-3  C23  0.020
 VJQ  plan-3  O5   0.020
 VJQ  plan-4  C15  0.020
 VJQ  plan-4  N17  0.020
 VJQ  plan-4  C18  0.020
 VJQ  plan-4  H6   0.020

