# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 17:47:06 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 4-(2,3-dihydro-1H-perimidin-2-yl)benzene-1,2-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(cc1O)C2Nc3cccc4cccc(N2)c34
#
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
 AV6  AV6  4-(2,3-dihydro-1H-perimidin-2-yl)benzene-1,2-diol  ligand  35  21  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AV6
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
 AV6  C1    C  CR66  0  -0.026  -1.9075  -0.0640  -0.1370
 AV6  C2    C  CR6   0   0.368  -1.4252  -1.1299  -0.9463
 AV6  C3    C  CR16  0  -0.378  -1.7404  -2.4317  -0.6147
 AV6  C4    C  CR16  0  -0.246  -2.5226  -2.6944   0.5222
 AV6  C5    C  CR16  0  -0.367  -2.9899  -1.6850   1.3237
 AV6  C6    C  CR66  0   0.099  -2.7014  -0.3375   1.0031
 AV6  C7    C  CR16  0  -0.364  -3.1959   0.7485   1.7634
 AV6  C8    C  CR16  0  -0.248  -2.9221   2.0357   1.3793
 AV6  C9    C  CR16  0  -0.383  -2.1454   2.3152   0.2425
 AV6  C10   C  CR6   0   0.362  -1.6390   1.2802  -0.5157
 AV6  N11   N  NH1   0  -0.682  -0.9201   1.4780  -1.6732
 AV6  C12   C  CH1   0  -0.032   0.0361   0.4483  -2.0211
 AV6  N13   N  NH1   0  -0.687  -0.6882  -0.7969  -2.0598
 AV6  C15   C  CR6   0   0.095   1.2484   0.4338  -1.0859
 AV6  C16   C  CR16  0  -0.384   1.7521  -0.7504  -0.5579
 AV6  C17   C  CR6   0   0.309   2.8731  -0.7556   0.2591
 AV6  C18   C  CR6   0   0.242   3.5172   0.4494   0.5580
 AV6  C19   C  CR16  0  -0.360   3.0241   1.6312   0.0284
 AV6  C20   C  CR16  0  -0.316   1.9000   1.6242  -0.7861
 AV6  O21   O  OH1   0  -0.645   4.6020   0.3690   1.3629
 AV6  O22   O  OH1   0  -0.636   3.3142  -1.9350   0.7479
 AV6  H3    H  HCR6  0   0.253  -1.3769  -3.2500  -1.2249
 AV6  H4    H  HCR6  0   0.251  -2.7504  -3.7238   0.7689
 AV6  H5    H  HCR6  0   0.243  -3.5880  -1.9058   2.1989
 AV6  H7    H  HCR6  0   0.243  -3.7990   0.5503   2.6406
 AV6  H8    H  HCR6  0   0.251  -3.3048   2.8633   1.9635
 AV6  H9    H  HCR6  0   0.253  -1.9433   3.3416  -0.0384
 AV6  H16   H  HCR6  0   0.249   1.2801  -1.7022  -0.7672
 AV6  H19   H  HCR6  0   0.273   3.5208   2.5685   0.2527
 AV6  H20   H  HCR6  0   0.245   1.5446   2.5681  -1.1805
 AV6  HO21  H  HOH1  0   0.482   4.9981   1.2375   1.4922
 AV6  HO22  H  HOH1  0   0.472   4.1022  -1.8034   1.2877
 AV6  HN11  H  HNH1  0   0.390  -0.6162   2.4234  -1.8457
 AV6  HN13  H  HNH1  0   0.391  -0.2356  -1.5552  -2.5454
 AV6  H12   H  HCH1  0   0.285   0.3838   0.6585  -3.0339

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
 AV6  C6   C1    aromatic  1.416  0.020  1.416
 AV6  C1   C2    aromatic  1.423  0.020  1.423
 AV6  C1   C10   aromatic  1.422  0.020  1.422
 AV6  C3   C2    aromatic  1.380  0.020  1.380
 AV6  C2   N13   single    1.376  0.020  1.376
 AV6  C4   C3    aromatic  1.405  0.020  1.405
 AV6  C3   H3    single    0.930  0.020  1.080
 AV6  C5   C4    aromatic  1.371  0.020  1.371
 AV6  C4   H4    single    0.930  0.020  1.080
 AV6  C5   C6    aromatic  1.415  0.020  1.415
 AV6  C5   H5    single    0.930  0.020  1.080
 AV6  C7   C6    aromatic  1.415  0.020  1.415
 AV6  C7   C8    aromatic  1.371  0.020  1.371
 AV6  C7   H7    single    0.930  0.020  1.080
 AV6  C8   C9    aromatic  1.405  0.020  1.405
 AV6  C8   H8    single    0.930  0.020  1.080
 AV6  C9   C10   aromatic  1.379  0.020  1.379
 AV6  C9   H9    single    0.930  0.020  1.080
 AV6  C10  N11   single    1.377  0.020  1.377
 AV6  N11  C12   single    1.448  0.020  1.448
 AV6  N13  C12   single    1.441  0.020  1.441
 AV6  C12  C15   single    1.531  0.020  1.531
 AV6  C15  C16   aromatic  1.391  0.020  1.391
 AV6  C15  C20   aromatic  1.390  0.020  1.390
 AV6  C16  C17   aromatic  1.387  0.020  1.387
 AV6  C16  H16   single    0.930  0.020  1.080
 AV6  C17  O22   single    1.351  0.020  1.351
 AV6  C17  C18   aromatic  1.399  0.020  1.399
 AV6  C19  C18   aromatic  1.386  0.020  1.386
 AV6  C18  O21   single    1.353  0.020  1.353
 AV6  C20  C19   aromatic  1.388  0.020  1.388
 AV6  C19  H19   single    0.930  0.020  1.080
 AV6  C20  H20   single    0.930  0.020  1.080
 AV6  O21  HO21  single    0.850  0.020  0.980
 AV6  O22  HO22  single    0.850  0.020  0.980
 AV6  N11  HN11  single    0.890  0.020  1.040
 AV6  N13  HN13  single    0.890  0.020  1.040
 AV6  C12  H12   single    0.970  0.020  1.090

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
 AV6  C10   C1   C6   120.19  3.000
 AV6  C10   C1   C2   119.52  3.000
 AV6  C6    C1   C2   120.23  3.000
 AV6  N13   C2   C3   123.03  3.000
 AV6  N13   C2   C1   117.42  3.000
 AV6  C3    C2   C1   119.52  3.000
 AV6  H3    C3   C4   120.09  3.000
 AV6  H3    C3   C2   120.03  3.000
 AV6  C4    C3   C2   119.88  3.000
 AV6  H4    C4   C5   119.67  3.000
 AV6  H4    C4   C3   118.65  3.000
 AV6  C5    C4   C3   121.68  3.000
 AV6  H5    C5   C6   119.34  3.000
 AV6  H5    C5   C4   120.70  3.000
 AV6  C6    C5   C4   119.95  3.000
 AV6  C7    C6   C5   122.54  3.000
 AV6  C7    C6   C1   118.71  3.000
 AV6  C5    C6   C1   118.73  3.000
 AV6  H7    C7   C8   120.67  3.000
 AV6  H7    C7   C6   119.31  3.000
 AV6  C8    C7   C6   120.02  3.000
 AV6  H8    C8   C9   118.68  3.000
 AV6  H8    C8   C7   119.72  3.000
 AV6  C9    C8   C7   121.60  3.000
 AV6  H9    C9   C10  120.00  3.000
 AV6  H9    C9   C8   120.10  3.000
 AV6  C10   C9   C8   119.90  3.000
 AV6  N11   C10  C9   123.10  3.000
 AV6  N11   C10  C1   117.27  3.000
 AV6  C9    C10  C1   119.58  3.000
 AV6  HN11  N11  C12  115.27  3.000
 AV6  HN11  N11  C10  115.85  3.000
 AV6  C12   N11  C10  116.41  3.000
 AV6  H12   C12  C15  108.45  3.000
 AV6  H12   C12  N13  107.56  3.000
 AV6  C15   C12  N13  113.97  3.000
 AV6  H12   C12  N11  107.25  3.000
 AV6  C15   C12  N11  112.52  3.000
 AV6  N13   C12  N11  106.80  3.000
 AV6  HN13  N13  C12  115.93  3.000
 AV6  HN13  N13  C2   116.64  3.000
 AV6  C12   N13  C2   117.16  3.000
 AV6  C20   C15  C16  118.52  3.000
 AV6  C20   C15  C12  119.66  3.000
 AV6  C16   C15  C12  121.78  3.000
 AV6  H16   C16  C17  117.57  3.000
 AV6  H16   C16  C15  121.14  3.000
 AV6  C17   C16  C15  121.29  3.000
 AV6  O22   C17  C18  121.64  3.000
 AV6  C18   C17  C16  119.65  3.000
 AV6  O22   C17  C16  118.71  3.000
 AV6  O21   C18  C19  124.28  3.000
 AV6  O21   C18  C17  116.42  3.000
 AV6  C19   C18  C17  119.29  3.000
 AV6  H19   C19  C20  119.78  3.000
 AV6  H19   C19  C18  119.68  3.000
 AV6  C20   C19  C18  120.54  3.000
 AV6  H20   C20  C19  118.36  3.000
 AV6  H20   C20  C15  120.94  3.000
 AV6  C19   C20  C15  120.70  3.000
 AV6  HO21  O21  C18  110.85  3.000
 AV6  HO22  O22  C17  110.51  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
 AV6  CONST_01  C4   C5   C6   C1     0.00   0.0  0
 AV6  CONST_02  C8   C7   C6   C1     0.00   0.0  0
 AV6  CONST_03  C4   C3   C2   C1     0.00   0.0  0
 AV6  CONST_04  C8   C9   C10  C1     0.00   0.0  0
 AV6  CONST_05  C5   C6   C1   C2     0.00   0.0  0
 AV6  CONST_06  C7   C6   C1   C2   180.00   0.0  0
 AV6  CONST_07  C9   C10  C1   C2   180.00   0.0  0
 AV6  CONST_08  C5   C4   C3   C2     0.00   0.0  0
 AV6  CONST_09  C6   C1   C2   C3     0.00   0.0  0
 AV6  CONST_10  C10  C1   C2   C3   180.00   0.0  0
 AV6  CONST_11  C6   C5   C4   C3     0.00   0.0  0
 AV6  CONST_12  C7   C6   C5   C4   180.00   0.0  0
 AV6  CONST_13  C10  C1   C6   C5   180.00   0.0  0
 AV6  CONST_14  C8   C7   C6   C5   180.00   0.0  0
 AV6  CONST_15  C9   C10  C1   C6     0.00   0.0  0
 AV6  CONST_16  C9   C8   C7   C6     0.00   0.0  0
 AV6  CONST_17  C10  C1   C6   C7     0.00   0.0  0
 AV6  CONST_18  C10  C9   C8   C7     0.00   0.0  0
 AV6  CONST_19  C18  C17  C16  C15    0.00   0.0  0
 AV6  CONST_20  C18  C19  C20  C15    0.00   0.0  0
 AV6  CONST_21  C19  C20  C15  C16    0.00   0.0  0
 AV6  CONST_22  C19  C18  C17  C16    0.00   0.0  0
 AV6  CONST_23  C20  C15  C16  C17    0.00   0.0  0
 AV6  CONST_24  C20  C19  C18  C17    0.00   0.0  0
 AV6  CONST_25  C17  C16  C15  C12  180.00   0.0  0
 AV6  CONST_26  C19  C20  C15  C12  180.00   0.0  0
 AV6  CONST_27  O22  C17  C16  C15  180.00   0.0  0
 AV6  CONST_28  O21  C18  C17  C16  180.00   0.0  0
 AV6  CONST_29  O22  C17  C18  C19  180.00   0.0  0
 AV6  CONST_30  O21  C18  C19  C20  180.00   0.0  0
 AV6  CONST_31  H5   C5   C6   C1   180.00   0.0  0
 AV6  CONST_32  H7   C7   C6   C1   180.00   0.0  0
 AV6  CONST_33  H3   C3   C2   C1   180.00   0.0  0
 AV6  CONST_34  H9   C9   C10  C1   180.00   0.0  0
 AV6  CONST_35  H4   C4   C3   C2   180.00   0.0  0
 AV6  CONST_36  H8   C8   C7   C6   180.00   0.0  0
 AV6  CONST_37  H16  C16  C15  C12    0.00   0.0  0
 AV6  CONST_38  H20  C20  C15  C12    0.00   0.0  0
 AV6  CONST_39  H19  C19  C20  C15  180.00   0.0  0
 AV6  Var_01    C12  N13  C2   C1    27.17  30.0  1
 AV6  Var_02    C12  N11  C10  C1   -30.30  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
 AV6  chir_01  C12  N11  N13  C15  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
 AV6  plan-1  C12  0.020
 AV6  plan-1  C15  0.020
 AV6  plan-1  C16  0.020
 AV6  plan-1  C17  0.020
 AV6  plan-1  C18  0.020
 AV6  plan-1  C19  0.020
 AV6  plan-1  C20  0.020
 AV6  plan-1  O21  0.020
 AV6  plan-1  O22  0.020
 AV6  plan-1  H16  0.020
 AV6  plan-1  H19  0.020
 AV6  plan-1  H20  0.020
 AV6  plan-2  C1   0.020
 AV6  plan-2  C2   0.020
 AV6  plan-2  C3   0.020
 AV6  plan-2  C4   0.020
 AV6  plan-2  C5   0.020
 AV6  plan-2  C6   0.020
 AV6  plan-2  C7   0.020
 AV6  plan-2  C8   0.020
 AV6  plan-2  C9   0.020
 AV6  plan-2  C10  0.020
 AV6  plan-2  N11  0.020
 AV6  plan-2  N13  0.020
 AV6  plan-2  H3   0.020
 AV6  plan-2  H4   0.020
 AV6  plan-2  H5   0.020
 AV6  plan-2  H7   0.020
 AV6  plan-2  H8   0.020
 AV6  plan-2  H9   0.020

