# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 18:59:50 2022
#   Inital geometry file: a 117 line input string
#   Ligand name: 2-[4-[(2~{S})-3-(6-chloranyl-4-oxidanylidene-quinazolin-3-yl)-2-oxidanyl-propoxy]phenoxy]ethanenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H](COc1ccc(OCC#N)cc1)CN2C=Nc3ccc(Cl)cc3C2=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
 V0H  V0H  "2-[4-[(2S)-3-(6-chloranyl-4-oxidanylidene-quinazolin-3-yl)-2-oxidanyl-propoxy]phenoxy]ethanenitrile"
  ligand  43  27  .  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_V0H
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
 V0H  N1   N   NS    0  -0.244  -52.5455  -8.0510  11.4229
 V0H  C9   C   CH2   0  -0.379  -57.1657   0.6573  11.8008
 V0H  C10  C   CR16  0   0.146  -56.1358   1.3503   9.7212
 V0H  O4   O   O     0  -0.448  -54.5733   0.2187  12.6557
 V0H  C8   C   CH1   0   0.040  -57.8203  -0.6956  11.4821
 V0H  C5   C   CR16  0  -0.363  -54.6562  -3.6117  11.8904
 V0H  C6   C   CR6   0   0.384  -54.8521  -2.7102  10.8551
 V0H  C4   C   CR16  0  -0.352  -53.4899  -4.3748  11.9507
 V0H  C7   C   CH2   0  -0.214  -56.9109  -1.8905  11.7413
 V0H  C3   C   CR6   0   0.359  -52.5172  -4.2405  10.9741
 V0H  C2   C   CH2   0  -0.287  -51.1017  -5.9169  11.8944
 V0H  C1   C   CSP   0   0.098  -51.9192  -7.1107  11.6328
 V0H  O2   O   O2    0  -0.490  -55.9319  -1.9097  10.7230
 V0H  O1   O   O2    0  -0.467  -51.3302  -4.9147  10.9501
 V0H  O3   O   OH1   0  -0.657  -58.9397  -0.8722  12.3126
 V0H  N2   N   NR6   0  -0.511  -55.9743   0.9163  11.0021
 V0H  C11  C   CR66  0   0.252  -53.9320   1.1725   9.2412
 V0H  C12  C   CR16  0  -0.319  -52.8897   1.2614   8.3083
 V0H  C13  C   CR16  0  -0.193  -51.6056   0.9213   8.6634
 V0H  C14  C   CR6   0  -0.047  -51.3380   0.4910   9.9666
 V0H  C15  C   CR16  0  -0.223  -52.3380   0.3988  10.9050
 V0H  C16  C   CR66  0  -0.101  -53.6424   0.7401  10.5407
 V0H  C17  C   CR6   0   0.605  -54.7250   0.5941  11.5089
 V0H  C18  C   CR16  0  -0.317  -53.8758  -2.5959   9.8621
 V0H  C19  C   CR16  0  -0.322  -52.7242  -3.3509   9.9204
 V0H  N3   N   N     0  -0.459  -55.2078   1.4990   8.8516
 V0H  CL1  CL  CL    0  -0.117  -49.7179   0.0557  10.3916
 V0H  H10  H   HCH2  0   0.283  -56.8998   0.7050  12.8547
 V0H  H9   H   HCH2  0   0.286  -57.8817   1.4583  11.6057
 V0H  H11  H   HCR6  0   0.297  -57.1576   1.5909   9.4475
 V0H  H7   H   HCH1  0   0.228  -58.1073  -0.7081  10.4205
 V0H  H4   H   HCR6  0   0.284  -55.3915  -3.7474  12.6717
 V0H  H3   H   HCR6  0   0.283  -53.3807  -5.0569  12.7834
 V0H  H5   H   HCH2  0   0.248  -57.5072  -2.8100  11.7181
 V0H  H6   H   HCH2  0   0.233  -56.4555  -1.8100  12.7346
 V0H  H2   H   HCH2  0   0.333  -50.0522  -6.2006  11.8121
 V0H  H1   H   HCH2  0   0.298  -51.2707  -5.5932  12.9263
 V0H  H8   H   HOH1  0   0.461  -59.6096  -0.2225  12.0758
 V0H  H12  H   HCR6  0   0.277  -53.1106   1.5940   7.3026
 V0H  H13  H   HCR6  0   0.289  -50.8060   0.9850   7.9376
 V0H  H14  H   HCR6  0   0.285  -52.1277   0.0564  11.9090
 V0H  H15  H   HCR6  0   0.271  -54.0265  -1.9058   9.0414
 V0H  H16  H   HCR6  0   0.269  -51.9726  -3.2473   9.1480

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
 V0H  C12  C13  aromatic  1.375  0.020  1.375
 V0H  C12  C11  aromatic  1.402  0.020  1.402
 V0H  N3   C11  single    1.373  0.020  1.373
 V0H  N3   C10  double    1.280  0.020  1.280
 V0H  C19  C18  aromatic  1.378  0.020  1.378
 V0H  C19  C3   aromatic  1.394  0.020  1.394
 V0H  C18  C6   aromatic  1.397  0.020  1.397
 V0H  C13  C14  aromatic  1.398  0.020  1.398
 V0H  C11  C16  aromatic  1.400  0.020  1.400
 V0H  C10  N2   single    1.362  0.020  1.362
 V0H  C3   O1   single    1.365  0.020  1.365
 V0H  C3   C4   aromatic  1.385  0.020  1.385
 V0H  C6   O2   single    1.351  0.020  1.351
 V0H  C6   C5   aromatic  1.387  0.020  1.387
 V0H  O2   C7   single    1.413  0.020  1.413
 V0H  O1   C2   single    1.396  0.020  1.396
 V0H  C14  CL1  single    1.731  0.020  1.731
 V0H  C14  C15  aromatic  1.374  0.020  1.374
 V0H  C16  C15  aromatic  1.397  0.020  1.397
 V0H  C16  C17  single    1.460  0.020  1.460
 V0H  C2   C1   single    1.470  0.020  1.470
 V0H  N2   C17  single    1.386  0.020  1.386
 V0H  N2   C9   single    1.458  0.020  1.458
 V0H  C8   C7   single    1.524  0.020  1.524
 V0H  C8   C9   single    1.536  0.020  1.536
 V0H  C8   O3   single    1.405  0.020  1.405
 V0H  C4   C5   aromatic  1.395  0.020  1.395
 V0H  C17  O4   double    1.216  0.020  1.216
 V0H  C1   N1   triple    1.149  0.020  1.149
 V0H  C9   H10  single    0.970  0.020  1.090
 V0H  C9   H9   single    0.970  0.020  1.090
 V0H  C10  H11  single    0.930  0.020  1.080
 V0H  C8   H7   single    0.970  0.020  1.090
 V0H  C5   H4   single    0.930  0.020  1.080
 V0H  C4   H3   single    0.930  0.020  1.080
 V0H  C7   H5   single    0.970  0.020  1.090
 V0H  C7   H6   single    0.970  0.020  1.090
 V0H  C2   H2   single    0.970  0.020  1.090
 V0H  C2   H1   single    0.970  0.020  1.090
 V0H  O3   H8   single    0.850  0.020  0.980
 V0H  C12  H12  single    0.930  0.020  1.080
 V0H  C13  H13  single    0.930  0.020  1.080
 V0H  C15  H14  single    0.930  0.020  1.080
 V0H  C18  H15  single    0.930  0.020  1.080
 V0H  C19  H16  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
 V0H  H9   C9   H10  107.53  3.000
 V0H  H9   C9   N2   107.92  3.000
 V0H  H10  C9   N2   108.86  3.000
 V0H  H9   C9   C8   109.24  3.000
 V0H  H10  C9   C8   110.10  3.000
 V0H  N2   C9   C8   113.02  3.000
 V0H  H11  C10  N3   119.05  3.000
 V0H  H11  C10  N2   114.81  3.000
 V0H  N3   C10  N2   126.13  3.000
 V0H  H7   C8   O3   111.17  3.000
 V0H  H7   C8   C7   108.12  3.000
 V0H  O3   C8   C7   106.05  3.000
 V0H  H7   C8   C9   108.75  3.000
 V0H  O3   C8   C9   109.12  3.000
 V0H  C7   C8   C9   113.63  3.000
 V0H  H4   C5   C4   117.94  3.000
 V0H  H4   C5   C6   121.66  3.000
 V0H  C4   C5   C6   120.40  3.000
 V0H  C18  C6   O2   116.14  3.000
 V0H  O2   C6   C5   124.84  3.000
 V0H  C18  C6   C5   119.01  3.000
 V0H  H3   C4   C3   122.21  3.000
 V0H  H3   C4   C5   117.54  3.000
 V0H  C3   C4   C5   120.24  3.000
 V0H  H6   C7   H5   107.87  3.000
 V0H  H6   C7   O2   111.50  3.000
 V0H  H5   C7   O2   110.50  3.000
 V0H  H6   C7   C8   110.16  3.000
 V0H  H5   C7   C8   109.24  3.000
 V0H  O2   C7   C8   107.56  3.000
 V0H  C19  C3   O1   115.51  3.000
 V0H  O1   C3   C4   125.11  3.000
 V0H  C19  C3   C4   119.37  3.000
 V0H  H1   C2   H2   107.26  3.000
 V0H  H1   C2   O1   113.59  3.000
 V0H  H2   C2   O1   107.05  3.000
 V0H  H1   C2   C1   108.79  3.000
 V0H  H2   C2   C1   108.09  3.000
 V0H  O1   C2   C1   111.81  3.000
 V0H  C2   C1   N1   180.00  3.000
 V0H  C7   O2   C6   119.45  3.000
 V0H  C2   O1   C3   119.01  3.000
 V0H  H8   O3   C8   108.92  3.000
 V0H  C17  N2   C10  121.65  3.000
 V0H  C17  N2   C9   119.67  3.000
 V0H  C10  N2   C9   118.36  3.000
 V0H  N3   C11  C16  121.93  3.000
 V0H  C16  C11  C12  118.93  3.000
 V0H  N3   C11  C12  119.14  3.000
 V0H  H12  C12  C13  120.44  3.000
 V0H  H12  C12  C11  119.10  3.000
 V0H  C13  C12  C11  120.45  3.000
 V0H  H13  C13  C14  120.13  3.000
 V0H  H13  C13  C12  120.16  3.000
 V0H  C14  C13  C12  119.71  3.000
 V0H  CL1  C14  C15  119.78  3.000
 V0H  C15  C14  C13  121.18  3.000
 V0H  CL1  C14  C13  119.04  3.000
 V0H  H14  C15  C16  120.07  3.000
 V0H  H14  C15  C14  120.91  3.000
 V0H  C16  C15  C14  119.02  3.000
 V0H  C17  C16  C15  119.69  3.000
 V0H  C17  C16  C11  119.55  3.000
 V0H  C15  C16  C11  120.72  3.000
 V0H  C16  C17  N2   113.75  3.000
 V0H  N2   C17  O4   121.93  3.000
 V0H  C16  C17  O4   124.32  3.000
 V0H  H15  C18  C19  119.83  3.000
 V0H  H15  C18  C6   119.57  3.000
 V0H  C19  C18  C6   120.59  3.000
 V0H  H16  C19  C18  119.83  3.000
 V0H  H16  C19  C3   119.81  3.000
 V0H  C18  C19  C3   120.36  3.000
 V0H  C11  N3   C10  116.94  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
 V0H  CONST_01  C19  C18  C6   C5      0.00   0.0  0
 V0H  CONST_02  C19  C3   C4   C5      0.00   0.0  0
 V0H  CONST_03  C3   C19  C18  C6      0.00   0.0  0
 V0H  CONST_04  C3   C4   C5   C6      0.00   0.0  0
 V0H  CONST_05  C18  C19  C3   C4      0.00   0.0  0
 V0H  CONST_06  C18  C6   C5   C4      0.00   0.0  0
 V0H  CONST_07  C14  C13  C12  C11     0.00   0.0  0
 V0H  CONST_08  C14  C15  C16  C11     0.00   0.0  0
 V0H  CONST_09  C15  C14  C13  C12     0.00   0.0  0
 V0H  CONST_10  C15  C16  C11  C12     0.00   0.0  0
 V0H  CONST_11  C16  C11  C12  C13     0.00   0.0  0
 V0H  CONST_12  C16  C15  C14  C13     0.00   0.0  0
 V0H  CONST_13  C16  C17  N2   C10     0.00   0.0  0
 V0H  CONST_14  C11  N3   C10  N2      0.00   0.0  0
 V0H  CONST_15  N3   C10  N2   C17     0.00   0.0  0
 V0H  CONST_16  O1   C3   C4   C5    180.00   0.0  0
 V0H  CONST_17  O2   C6   C5   C4    180.00   0.0  0
 V0H  CONST_18  C19  C18  C6   O2    180.00   0.0  0
 V0H  CONST_19  C18  C19  C3   O1    180.00   0.0  0
 V0H  CONST_20  CL1  C14  C13  C12   180.00   0.0  0
 V0H  CONST_21  CL1  C14  C15  C16   180.00   0.0  0
 V0H  CONST_22  N3   C10  N2   C9    180.00   0.0  0
 V0H  CONST_23  C16  C17  N2   C9    180.00   0.0  0
 V0H  CONST_24  O4   C17  N2   C10   180.00   0.0  0
 V0H  CONST_25  H15  C18  C6   C5    180.00   0.0  0
 V0H  CONST_26  H16  C19  C18  C6    180.00   0.0  0
 V0H  CONST_27  H3   C4   C5   C6    180.00   0.0  0
 V0H  CONST_28  H16  C19  C3   C4    180.00   0.0  0
 V0H  CONST_29  H15  C18  C19  C3    180.00   0.0  0
 V0H  CONST_30  H4   C5   C4   C3    180.00   0.0  0
 V0H  CONST_31  H13  C13  C12  C11   180.00   0.0  0
 V0H  CONST_32  H14  C15  C16  C11   180.00   0.0  0
 V0H  CONST_33  H14  C15  C14  C13   180.00   0.0  0
 V0H  CONST_34  H12  C12  C13  C14   180.00   0.0  0
 V0H  CONST_35  H13  C13  C14  C15   180.00   0.0  0
 V0H  CONST_36  H12  C12  C11  C16   180.00   0.0  0
 V0H  CONST_37  H14  C15  C16  C17     0.00   0.0  0
 V0H  CONST_38  H4   C5   C6   C18   180.00   0.0  0
 V0H  CONST_39  H3   C4   C3   C19   180.00   0.0  0
 V0H  CONST_40  H12  C12  C11  N3      0.00   0.0  0
 V0H  CONST_41  H11  C10  N3   C11   180.00   0.0  0
 V0H  CONST_42  H11  C10  N2   C17   180.00   0.0  0
 V0H  CONST_43  O4   C17  N2   C9      0.00   0.0  0
 V0H  CONST_44  H11  C10  N2   C9      0.00   0.0  0
 V0H  Var_01    C8   C9   N2   C10    79.26  30.0  3
 V0H  Var_02    C17  N2   C9   C8    -94.42  30.0  3
 V0H  Var_03    C7   O2   C6   C5      4.79  30.0  2
 V0H  Var_04    C2   O1   C3   C4      6.62  30.0  2
 V0H  Var_05    C18  C6   O2   C7   -175.02  30.0  2
 V0H  Var_06    C19  C3   O1   C2   -173.82  30.0  3
 V0H  Var_07    H10  C9   N2   C10  -158.06  30.0  3
 V0H  Var_08    H9   C9   N2   C10   -41.64  30.0  3
 V0H  Var_09    H10  C9   N2   C17    28.25  30.0  3
 V0H  Var_10    H9   C9   N2   C17   144.68  30.0  3
 V0H  Var_11    C6   O2   C7   C8    167.39  30.0  1
 V0H  Var_12    C1   C2   O1   C3     71.36  30.0  3
 V0H  Var_13    H5   C7   O2   C6    -73.45  30.0  3
 V0H  Var_14    H6   C7   O2   C6     46.51  30.0  3
 V0H  Var_15    H2   C2   O1   C3   -170.44  30.0  3
 V0H  Var_16    H1   C2   O1   C3    -52.23  30.0  3
 V0H  Var_17    O1   C2   C1   N1    105.21  30.0  1
 V0H  Var_18    H2   C2   C1   N1    -12.37  30.0  1
 V0H  Var_19    H1   C2   C1   N1   -128.54  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
 V0H  chir_01  C8  C7  C9  O3  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
 V0H  plan-1  C5   0.020
 V0H  plan-1  C6   0.020
 V0H  plan-1  C4   0.020
 V0H  plan-1  C3   0.020
 V0H  plan-1  O2   0.020
 V0H  plan-1  O1   0.020
 V0H  plan-1  C18  0.020
 V0H  plan-1  C19  0.020
 V0H  plan-1  H4   0.020
 V0H  plan-1  H3   0.020
 V0H  plan-1  H15  0.020
 V0H  plan-1  H16  0.020
 V0H  plan-2  C9   0.020
 V0H  plan-2  C10  0.020
 V0H  plan-2  O4   0.020
 V0H  plan-2  N2   0.020
 V0H  plan-2  C11  0.020
 V0H  plan-2  C12  0.020
 V0H  plan-2  C13  0.020
 V0H  plan-2  C14  0.020
 V0H  plan-2  C15  0.020
 V0H  plan-2  C16  0.020
 V0H  plan-2  C17  0.020
 V0H  plan-2  N3   0.020
 V0H  plan-2  CL1  0.020
 V0H  plan-2  H11  0.020
 V0H  plan-2  H12  0.020
 V0H  plan-2  H13  0.020
 V0H  plan-2  H14  0.020

