# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 04:37:07 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: (2~{S},3~{R})-2-azanyl-~{N}-[(~{E})-4-[6,7-bis(chloranyl)-4-oxidanylidene-quinazolin-3-yl]but-2-enyl]-3-oxidanyl-butanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@H](N)C(=O)NC/C=C/CN1C=Nc2cc(Cl)c(Cl)cc2C1=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
 E4O  E4O  (2~{S},3~{R})-2-azanyl-~{N}-[(~{E})-4-[6,7-bis(chloranyl)-4-oxidanylidene-quinazolin-3-yl]but-2-enyl]-3-oxidanyl-butanamide  ligand  43  25  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_E4O
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
 E4O  C4   C   CR66  0   0.260   2.6160  -0.0102   1.3071
 E4O  C5   C   CR66  0  -0.096   2.7661   0.7940   0.1711
 E4O  C6   C   CR16  0  -0.238   3.8323   0.5892  -0.7044
 E4O  C8   C   CR16  0   0.164   0.7462   1.0981   1.9283
 E4O  C10  C   CR6   0   0.604   1.7898   1.8448  -0.0993
 E4O  C15  C   C1    0  -0.205  -1.3719   2.4200  -0.1465
 E4O  C1   C   CR6   0  -0.008   4.7466  -0.4063  -0.4515
 E4O  C2   C   CR6   0   0.017   4.6002  -1.2157   0.6866
 E4O  C3   C   CR16  0  -0.277   3.5506  -1.0217   1.5538
 E4O  N7   N   N     0  -0.463   1.5777   0.1591   2.1879
 E4O  N9   N   NR6   0  -0.515   0.8026   1.9463   0.8655
 E4O  CL1  CL  CL    0  -0.085   6.0618  -0.6533  -1.5309
 E4O  CL2  CL  CL    0  -0.075   5.7368  -2.4623   1.0077
 E4O  O13  O   O     0  -0.448   1.8111   2.5777  -1.0692
 E4O  C16  C   C1    0  -0.237  -2.6261   2.3160   0.2763
 E4O  C17  C   CH2   0  -0.313  -3.7492   1.8287  -0.5810
 E4O  N18  N   NH1   0  -0.639  -4.3978   0.6890   0.0334
 E4O  C19  C   C     0   0.562  -5.6981   0.3894  -0.1428
 E4O  C20  C   CH1   0  -0.254  -6.1403  -0.9297   0.4918
 E4O  O21  O   O     0  -0.489  -6.4654   1.1052  -0.7653
 E4O  C22  C   CH1   0   0.047  -5.5203  -2.0953  -0.3031
 E4O  C23  C   CH3   0  -0.704  -5.9538  -3.4507   0.2301
 E4O  N24  N   NH2   0  -0.786  -7.5813  -0.9416   0.6052
 E4O  O25  O   OH1   0  -0.668  -5.8962  -1.9107  -1.6516
 E4O  H1   H   HCR6  0   0.296   3.9387   1.2146  -1.5803
 E4O  H2   H   HCR6  0   0.299  -0.0877   1.2620   2.6012
 E4O  H3   H   HCH2  0   0.294   0.1849   3.8379   0.2629
 E4O  H4   H   HCH2  0   0.291  -0.6160   3.2184   1.6942
 E4O  H5   H   H     0   0.265  -1.1147   2.1222  -1.1589
 E4O  H6   H   HCR6  0   0.299   3.4372  -1.6458   2.4296
 E4O  H7   H   H     0   0.263  -2.8847   2.6085   1.2908
 E4O  H8   H   HCH2  0   0.260  -4.4920   2.6200  -0.6955
 E4O  H9   H   HCH2  0   0.250  -3.3841   1.5829  -1.5830
 E4O  H10  H   HNH1  0   0.399  -3.8086   0.0275   0.5140
 E4O  H11  H   HCH1  0   0.270  -5.7237  -0.9797   1.5031
 E4O  H12  H   HCH1  0   0.201  -4.4275  -2.0310  -0.1969
 E4O  H13  H   HCH3  0   0.226  -7.0275  -3.6034   0.1146
 E4O  H14  H   HCH3  0   0.242  -5.4440  -4.2540  -0.3050
 E4O  H15  H   HCH3  0   0.233  -5.7040  -3.5541   1.2868
 E4O  H16  H   HNH2  0   0.343  -8.0025  -1.0512  -0.3088
 E4O  H17  H   HNH2  0   0.356  -7.8722  -1.7400   1.1539
 E4O  H19  H   HOH1  0   0.454  -5.5589  -2.6499  -2.1672
 E4O  C14  C   CH2   0  -0.396  -0.2585   2.9453   0.7021

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
 E4O  CL1  C1   single    1.719  0.020  1.719
 E4O  CL2  C2   single    1.717  0.020  1.717
 E4O  C1   C2   aromatic  1.404  0.020  1.404
 E4O  C1   C6   aromatic  1.375  0.020  1.375
 E4O  O25  C22  single    1.412  0.020  1.412
 E4O  C2   C3   aromatic  1.375  0.020  1.375
 E4O  N24  C20  single    1.446  0.020  1.446
 E4O  C6   C5   aromatic  1.395  0.020  1.395
 E4O  C22  C20  single    1.541  0.020  1.541
 E4O  C22  C23  single    1.520  0.020  1.520
 E4O  C3   C4   aromatic  1.399  0.020  1.399
 E4O  C20  C19  single    1.529  0.020  1.529
 E4O  O21  C19  double    1.220  0.020  1.220
 E4O  C5   C4   aromatic  1.400  0.020  1.400
 E4O  C5   C10  single    1.460  0.020  1.460
 E4O  C4   N7   single    1.372  0.020  1.372
 E4O  C19  N18  single    1.346  0.020  1.346
 E4O  O13  C10  double    1.216  0.020  1.216
 E4O  C10  N9   single    1.384  0.020  1.384
 E4O  N7   C8   double    1.281  0.020  1.281
 E4O  N18  C17  single    1.448  0.020  1.448
 E4O  N9   C8   single    1.361  0.020  1.361
 E4O  N9   C14  single    1.467  0.020  1.467
 E4O  C15  C14  single    1.495  0.020  1.495
 E4O  C15  C16  double    1.328  0.020  1.328
 E4O  C17  C16  single    1.495  0.020  1.495
 E4O  C6   H1   single    0.930  0.020  1.080
 E4O  C8   H2   single    0.930  0.020  1.080
 E4O  C14  H3   single    0.970  0.020  1.090
 E4O  C14  H4   single    0.970  0.020  1.090
 E4O  C15  H5   single    0.930  0.020  1.080
 E4O  C3   H6   single    0.930  0.020  1.080
 E4O  C16  H7   single    0.930  0.020  1.080
 E4O  C17  H8   single    0.970  0.020  1.090
 E4O  C17  H9   single    0.970  0.020  1.090
 E4O  N18  H10  single    0.860  0.020  1.020
 E4O  C20  H11  single    0.970  0.020  1.090
 E4O  C22  H12  single    0.970  0.020  1.090
 E4O  C23  H13  single    0.970  0.020  1.090
 E4O  C23  H14  single    0.970  0.020  1.090
 E4O  C23  H15  single    0.970  0.020  1.090
 E4O  N24  H16  single    0.890  0.020  1.040
 E4O  N24  H17  single    0.890  0.020  1.040
 E4O  O25  H19  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
 E4O  N7   C4   C3   118.78  3.000
 E4O  N7   C4   C5   122.09  3.000
 E4O  C3   C4   C5   119.13  3.000
 E4O  C10  C5   C6   120.05  3.000
 E4O  C10  C5   C4   119.48  3.000
 E4O  C6   C5   C4   120.47  3.000
 E4O  H1   C6   C1   120.14  3.000
 E4O  H1   C6   C5   119.91  3.000
 E4O  C1   C6   C5   119.94  3.000
 E4O  H2   C8   N9   114.99  3.000
 E4O  H2   C8   N7   118.97  3.000
 E4O  N9   C8   N7   126.04  3.000
 E4O  O13  C10  N9   121.63  3.000
 E4O  N9   C10  C5   113.62  3.000
 E4O  O13  C10  C5   124.75  3.000
 E4O  H5   C15  C16  119.94  3.000
 E4O  H5   C15  C14  116.68  3.000
 E4O  C16  C15  C14  123.38  3.000
 E4O  CL1  C1   C2   120.38  3.000
 E4O  C2   C1   C6   119.80  3.000
 E4O  CL1  C1   C6   119.81  3.000
 E4O  CL2  C2   C3   119.32  3.000
 E4O  C3   C2   C1   120.62  3.000
 E4O  CL2  C2   C1   120.07  3.000
 E4O  H6   C3   C2   120.61  3.000
 E4O  H6   C3   C4   119.34  3.000
 E4O  C2   C3   C4   120.04  3.000
 E4O  C8   N7   C4   116.85  3.000
 E4O  C14  N9   C10  119.23  3.000
 E4O  C14  N9   C8   118.79  3.000
 E4O  C10  N9   C8   121.89  3.000
 E4O  H7   C16  C17  116.37  3.000
 E4O  H7   C16  C15  120.06  3.000
 E4O  C17  C16  C15  123.56  3.000
 E4O  H9   C17  H8   107.09  3.000
 E4O  H9   C17  N18  111.17  3.000
 E4O  H8   C17  N18  108.08  3.000
 E4O  H9   C17  C16  110.35  3.000
 E4O  H8   C17  C16  109.58  3.000
 E4O  N18  C17  C16  110.48  3.000
 E4O  H10  N18  C19  118.75  3.000
 E4O  H10  N18  C17  117.20  3.000
 E4O  C19  N18  C17  123.53  3.000
 E4O  O21  C19  C20  122.41  3.000
 E4O  O21  C19  N18  122.94  3.000
 E4O  C20  C19  N18  114.65  3.000
 E4O  H11  C20  N24  107.85  3.000
 E4O  H11  C20  C22  106.79  3.000
 E4O  N24  C20  C22  115.80  3.000
 E4O  H11  C20  C19  108.22  3.000
 E4O  C22  C20  C19  108.79  3.000
 E4O  N24  C20  C19  109.14  3.000
 E4O  H12  C22  O25  110.43  3.000
 E4O  H12  C22  C23  107.56  3.000
 E4O  O25  C22  C23  112.07  3.000
 E4O  H12  C22  C20  107.80  3.000
 E4O  C23  C22  C20  112.27  3.000
 E4O  O25  C22  C20  106.65  3.000
 E4O  H15  C23  H14  107.35  3.000
 E4O  H15  C23  H13  108.35  3.000
 E4O  H14  C23  H13  107.75  3.000
 E4O  H15  C23  C22  111.05  3.000
 E4O  H14  C23  C22  110.56  3.000
 E4O  H13  C23  C22  111.62  3.000
 E4O  H17  N24  H16  106.54  3.000
 E4O  H17  N24  C20  109.61  3.000
 E4O  H16  N24  C20  110.17  3.000
 E4O  H19  O25  C22  108.54  3.000
 E4O  H4   C14  H3   107.18  3.000
 E4O  H4   C14  N9   107.86  3.000
 E4O  H3   C14  N9   107.98  3.000
 E4O  H4   C14  C15  111.14  3.000
 E4O  H3   C14  C15  111.24  3.000
 E4O  N9   C14  C15  111.27  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
 E4O  CONST_01  C1   C2   C3   C4     0.00   0.0  0
 E4O  CONST_02  C1   C6   C5   C4     0.00   0.0  0
 E4O  CONST_03  C2   C1   C6   C5     0.00   0.0  0
 E4O  CONST_04  C2   C3   C4   C5     0.00   0.0  0
 E4O  CONST_05  C3   C2   C1   C6     0.00   0.0  0
 E4O  CONST_06  C3   C4   C5   C6     0.00   0.0  0
 E4O  CONST_07  N9   C8   N7   C4     0.00   0.0  0
 E4O  CONST_08  C8   N9   C10  C5     0.00   0.0  0
 E4O  CONST_09  N7   C8   N9   C10    0.00   0.0  0
 E4O  CONST_10  CL2  C2   C3   C4   180.00   0.0  0
 E4O  CONST_11  CL1  C1   C6   C5   180.00   0.0  0
 E4O  CONST_12  CL2  C2   C1   C6   180.00   0.0  0
 E4O  CONST_13  CL1  C1   C2   C3   180.00   0.0  0
 E4O  CONST_14  C14  N9   C10  C5   180.00   0.0  0
 E4O  CONST_15  O13  C10  N9   C8   180.00   0.0  0
 E4O  CONST_16  N7   C8   N9   C14  180.00   0.0  0
 E4O  CONST_17  H1   C6   C5   C4   180.00   0.0  0
 E4O  CONST_18  H6   C3   C4   C5   180.00   0.0  0
 E4O  CONST_19  H2   C8   N7   C4   180.00   0.0  0
 E4O  CONST_20  O13  C10  N9   C14    0.00   0.0  0
 E4O  CONST_21  C20  C19  N18  C17  180.00   0.0  0
 E4O  CONST_22  O21  C19  N18  C17    0.00   0.0  0
 E4O  CONST_23  H10  N18  C19  C20    0.00   0.0  0
 E4O  Var_01    C15  C14  N9   C8   -91.31  30.0  3
 E4O  Var_02    C16  C15  C14  N9   120.52  30.0  1
 E4O  Var_03    C17  C16  C15  C14  178.17   0.0  2
 E4O  Var_04    N18  C17  C16  C15  123.11  30.0  2
 E4O  Var_05    C19  N18  C17  C16  150.61  30.0  1

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
 E4O  chir_01  C20  N24  C22  C19  negativ
 E4O  chir_02  C22  O25  C20  C23  negativ

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
 E4O  plan-1  C4   0.020
 E4O  plan-1  C5   0.020
 E4O  plan-1  C6   0.020
 E4O  plan-1  C8   0.020
 E4O  plan-1  C10  0.020
 E4O  plan-1  C1   0.020
 E4O  plan-1  C2   0.020
 E4O  plan-1  C3   0.020
 E4O  plan-1  N7   0.020
 E4O  plan-1  N9   0.020
 E4O  plan-1  CL1  0.020
 E4O  plan-1  CL2  0.020
 E4O  plan-1  O13  0.020
 E4O  plan-1  H1   0.020
 E4O  plan-1  H2   0.020
 E4O  plan-1  H6   0.020
 E4O  plan-1  C14  0.020
 E4O  plan-2  C17  0.020
 E4O  plan-2  N18  0.020
 E4O  plan-2  C19  0.020
 E4O  plan-2  C20  0.020
 E4O  plan-2  O21  0.020
 E4O  plan-2  H10  0.020
 E4O  plan-3  C15  0.020
 E4O  plan-3  C16  0.020
 E4O  plan-3  C17  0.020
 E4O  plan-3  H5   0.020
 E4O  plan-3  H7   0.020
 E4O  plan-3  C14  0.020

