# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 10:38:57 2022
#   Inital geometry file: a 101 line input string
#   Ligand name: 3-(2-hydroxyphenyl)-6-(3-nitrophenyl)-3,4-dihydropyrimidin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccccc1N2CC=C(NC2=O)c3cccc(c3)[N+]([O-])=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
 KX7  KX7  3-(2-hydroxyphenyl)-6-(3-nitrophenyl)-3,4-dihydropyrimidin-2(1H)-one  ligand  36  23  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KX7
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
 KX7  C01   C  CH2    0  -0.282   1.6659   1.7221  -0.0508
 KX7  C02   C  C1     0  -0.404   0.1990   1.8466  -0.2916
 KX7  C03   C  C      0   0.395  -0.6301   0.9452   0.2308
 KX7  N04   N  NH1    0  -0.758  -0.0955  -0.1293   0.9394
 KX7  C05   C  C      0   0.705   1.2070  -0.5150   0.8572
 KX7  O06   O  O      0  -0.544   1.5865  -1.5738   1.3621
 KX7  N07   N  NT     0  -0.584   2.0350   0.3213   0.1858
 KX7  C08   C  CR6    0   0.226   3.3738  -0.0586  -0.1130
 KX7  C09   C  CR16   0  -0.295   3.8083   0.0692  -1.4297
 KX7  C10   C  CR16   0  -0.275   5.1272  -0.1682  -1.7762
 KX7  C11   C  CR16   0  -0.249   6.0290  -0.5552  -0.7925
 KX7  C12   C  CR16   0  -0.347   5.6026  -0.7240   0.5134
 KX7  C13   C  CR6    0   0.318   4.2769  -0.4806   0.8720
 KX7  O14   O  OH1    0  -0.662   3.9193  -0.6449   2.1597
 KX7  C15   C  CR6    0   0.065  -2.0925   0.9683   0.0667
 KX7  C16   C  CR16   0  -0.334  -2.8091  -0.2165  -0.0647
 KX7  C17   C  CR6    0   0.281  -4.1823  -0.1597  -0.2418
 KX7  C18   C  CR16   0  -0.272  -4.8715   1.0416  -0.2897
 KX7  C19   C  CR16   0  -0.233  -4.1506   2.2168  -0.1509
 KX7  C20   C  CR16   0  -0.276  -2.7783   2.1832   0.0329
 KX7  N21   N  N      1   0.329  -4.9220  -1.4072  -0.3856
 KX7  O22   O  O     -1  -0.375  -4.3116  -2.4446  -0.2835
 KX7  O23   O  O      0  -0.373  -6.1088  -1.3397  -0.5985
 KX7  H012  H  HCH2   0   0.276   2.2153   2.0781  -0.9194
 KX7  H011  H  HCH2   0   0.268   1.9874   2.3390   0.7976
 KX7  H021  H  H      0   0.282  -0.1646   2.6563  -0.9071
 KX7  H041  H  HNH1   0   0.422  -0.6933  -0.6988   1.5187
 KX7  H091  H  HCR6   0   0.272   3.0961   0.3706  -2.1887
 KX7  H101  H  HCR6   0   0.258   5.4447  -0.0564  -2.8040
 KX7  H111  H  HCR6   0   0.260   7.0648  -0.7423  -1.0441
 KX7  H121  H  HCR6   0   0.265   6.2968  -1.0440   1.2809
 KX7  H141  H  HOH1   0   0.476   3.0365  -1.0724   2.1643
 KX7  H161  H  HCR6   0   0.300  -2.3008  -1.1705  -0.0522
 KX7  H181  H  HCR6   0   0.303  -5.9429   1.0734  -0.4212
 KX7  H191  H  HCR6   0   0.285  -4.6683   3.1655  -0.1727
 KX7  H201  H  HCR6   0   0.279  -2.2343   3.1087   0.1685

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
 KX7  O23  N21   double    1.208  0.020  1.208
 KX7  C18  C19   aromatic  1.386  0.020  1.386
 KX7  C18  C17   aromatic  1.386  0.020  1.386
 KX7  C19  C20   aromatic  1.385  0.020  1.385
 KX7  N21  C17   single    1.457  0.020  1.457
 KX7  N21  O22   single    1.208  0.020  1.208
 KX7  C17  C16   aromatic  1.386  0.020  1.386
 KX7  C20  C15   aromatic  1.395  0.020  1.395
 KX7  C16  C15   aromatic  1.391  0.020  1.391
 KX7  C15  C03   single    1.472  0.020  1.472
 KX7  N04  C03   single    1.394  0.020  1.394
 KX7  N04  C05   single    1.361  0.020  1.361
 KX7  O06  C05   double    1.233  0.020  1.233
 KX7  C03  C02   double    1.331  0.020  1.331
 KX7  C05  N07   single    1.355  0.020  1.355
 KX7  C02  C01   single    1.492  0.020  1.492
 KX7  N07  C01   single    1.468  0.020  1.468
 KX7  N07  C08   single    1.423  0.020  1.423
 KX7  C08  C09   aromatic  1.392  0.020  1.392
 KX7  C08  C13   aromatic  1.401  0.020  1.401
 KX7  C09  C10   aromatic  1.384  0.020  1.384
 KX7  O14  C13   single    1.346  0.020  1.346
 KX7  C13  C12   aromatic  1.395  0.020  1.395
 KX7  C10  C11   aromatic  1.389  0.020  1.389
 KX7  C12  C11   aromatic  1.384  0.020  1.384
 KX7  C01  H012  single    0.970  0.020  1.090
 KX7  C01  H011  single    0.970  0.020  1.090
 KX7  C02  H021  single    0.930  0.020  1.080
 KX7  N04  H041  single    0.860  0.020  1.020
 KX7  C09  H091  single    0.930  0.020  1.080
 KX7  C10  H101  single    0.930  0.020  1.080
 KX7  C11  H111  single    0.930  0.020  1.080
 KX7  C12  H121  single    0.930  0.020  1.080
 KX7  O14  H141  single    0.850  0.020  0.980
 KX7  C16  H161  single    0.930  0.020  1.080
 KX7  C18  H181  single    0.930  0.020  1.080
 KX7  C19  H191  single    0.930  0.020  1.080
 KX7  C20  H201  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
 KX7  H011  C01  H012  106.59  3.000
 KX7  H011  C01  N07   109.77  3.000
 KX7  H012  C01  N07   108.30  3.000
 KX7  H011  C01  C02   111.48  3.000
 KX7  H012  C01  C02   109.91  3.000
 KX7  N07   C01  C02   110.67  3.000
 KX7  H021  C02  C03   121.44  3.000
 KX7  H021  C02  C01   119.05  3.000
 KX7  C03   C02  C01   119.50  3.000
 KX7  C15   C03  N04   116.74  3.000
 KX7  N04   C03  C02   118.86  3.000
 KX7  C15   C03  C02   124.35  3.000
 KX7  H041  N04  C05   116.23  3.000
 KX7  H041  N04  C03   120.00  3.000
 KX7  C05   N04  C03   123.70  3.000
 KX7  N07   C05  O06   123.01  3.000
 KX7  N07   C05  N04   116.10  3.000
 KX7  O06   C05  N04   120.88  3.000
 KX7  C08   N07  C05   120.94  3.000
 KX7  C08   N07  C01   117.22  3.000
 KX7  C05   N07  C01   121.01  3.000
 KX7  C13   C08  C09   119.42  3.000
 KX7  C13   C08  N07   122.61  3.000
 KX7  C09   C08  N07   117.87  3.000
 KX7  H091  C09  C10   119.91  3.000
 KX7  H091  C09  C08   118.87  3.000
 KX7  C10   C09  C08   121.22  3.000
 KX7  H101  C10  C11   120.73  3.000
 KX7  H101  C10  C09   119.99  3.000
 KX7  C11   C10  C09   119.28  3.000
 KX7  H111  C11  C12   119.54  3.000
 KX7  H111  C11  C10   120.32  3.000
 KX7  C12   C11  C10   120.13  3.000
 KX7  H121  C12  C13   118.59  3.000
 KX7  H121  C12  C11   120.47  3.000
 KX7  C13   C12  C11   120.94  3.000
 KX7  O14   C13  C12   118.49  3.000
 KX7  C12   C13  C08   118.97  3.000
 KX7  O14   C13  C08   122.53  3.000
 KX7  H141  O14  C13   107.26  3.000
 KX7  C20   C15  C16   119.09  3.000
 KX7  C16   C15  C03   120.60  3.000
 KX7  C20   C15  C03   120.31  3.000
 KX7  H161  C16  C17   120.24  3.000
 KX7  H161  C16  C15   120.56  3.000
 KX7  C17   C16  C15   119.18  3.000
 KX7  N21   C17  C18   119.09  3.000
 KX7  N21   C17  C16   118.71  3.000
 KX7  C18   C17  C16   122.20  3.000
 KX7  H181  C18  C19   120.22  3.000
 KX7  H181  C18  C17   121.55  3.000
 KX7  C19   C18  C17   118.23  3.000
 KX7  H191  C19  C20   119.90  3.000
 KX7  H191  C19  C18   119.55  3.000
 KX7  C20   C19  C18   120.55  3.000
 KX7  H201  C20  C19   119.61  3.000
 KX7  H201  C20  C15   119.64  3.000
 KX7  C19   C20  C15   120.75  3.000
 KX7  O23   N21  O22   124.02  3.000
 KX7  O22   N21  C17   118.05  3.000
 KX7  O23   N21  C17   117.93  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
 KX7  CONST_01  C11   C10  C09  C08    0.00   0.0  0
 KX7  CONST_02  C11   C12  C13  C08    0.00   0.0  0
 KX7  CONST_03  C12   C13  C08  C09    0.00   0.0  0
 KX7  CONST_04  C12   C11  C10  C09    0.00   0.0  0
 KX7  CONST_05  C13   C08  C09  C10    0.00   0.0  0
 KX7  CONST_06  C13   C12  C11  C10    0.00   0.0  0
 KX7  CONST_07  C18   C19  C20  C15    0.00   0.0  0
 KX7  CONST_08  C18   C17  C16  C15    0.00   0.0  0
 KX7  CONST_09  C19   C18  C17  C16    0.00   0.0  0
 KX7  CONST_10  C19   C20  C15  C16    0.00   0.0  0
 KX7  CONST_11  C20   C19  C18  C17    0.00   0.0  0
 KX7  CONST_12  C20   C15  C16  C17    0.00   0.0  0
 KX7  CONST_13  C19   C20  C15  C03  180.00   0.0  0
 KX7  CONST_14  C17   C16  C15  C03  180.00   0.0  0
 KX7  CONST_15  C10   C09  C08  N07  180.00   0.0  0
 KX7  CONST_16  C12   C13  C08  N07  180.00   0.0  0
 KX7  CONST_18  N07   C05  N04  C03    0.00   0.0  0
 KX7  CONST_19  C08   N07  C05  N04  180.00   0.0  0
 KX7  CONST_20  O14   C13  C08  N07    0.00   0.0  0
 KX7  CONST_21  O14   C13  C08  C09  180.00   0.0  0
 KX7  CONST_22  O14   C13  C12  C11  180.00   0.0  0
 KX7  CONST_23  N21   C17  C16  C15  180.00   0.0  0
 KX7  CONST_24  N21   C17  C18  C19  180.00   0.0  0
 KX7  CONST_26  O06   C05  N04  C03  180.00   0.0  0
 KX7  CONST_27  C08   N07  C05  O06    0.00   0.0  0
 KX7  CONST_28  H201  C20  C15  C03    0.00   0.0  0
 KX7  CONST_29  H161  C16  C15  C03    0.00   0.0  0
 KX7  CONST_30  H091  C09  C08  N07    0.00   0.0  0
 KX7  CONST_31  H101  C10  C09  C08  180.00   0.0  0
 KX7  CONST_32  H121  C12  C13  C08  180.00   0.0  0
 KX7  CONST_33  H111  C11  C10  C09  180.00   0.0  0
 KX7  CONST_34  H191  C19  C20  C15  180.00   0.0  0
 KX7  CONST_35  H181  C18  C17  C16  180.00   0.0  0
 KX7  CONST_36  H041  N04  C05  N07  180.00   0.0  0
 KX7  CONST_37  O23   N21  C17  C16  180.00   0.0  0
 KX7  CONST_38  O22   N21  C17  C16    0.00   0.0  0
 KX7  CONST_39  O23   N21  C17  C18    0.00   0.0  0
 KX7  CONST_40  O22   N21  C17  C18  180.00   0.0  0
 KX7  Var_01    C15   C03  C02  C01  179.71  30.0  1
 KX7  Var_02    C09   C08  N07  C01  -61.48  30.0  2
 KX7  Var_03    C20   C15  C03  C02  -35.85  30.0  3
 KX7  Var_04    C05   N04  C03  C02  -17.33  30.0  1
 KX7  Var_05    C05   N07  C01  C02  -35.69  30.0  1
 KX7  Var_06    N07   C01  C02  C03   26.84  30.0  1

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
 KX7  plan-1  N07   0.020
 KX7  plan-1  C08   0.020
 KX7  plan-1  C09   0.020
 KX7  plan-1  C10   0.020
 KX7  plan-1  C11   0.020
 KX7  plan-1  C12   0.020
 KX7  plan-1  C13   0.020
 KX7  plan-1  O14   0.020
 KX7  plan-1  H091  0.020
 KX7  plan-1  H101  0.020
 KX7  plan-1  H111  0.020
 KX7  plan-1  H121  0.020
 KX7  plan-2  C03   0.020
 KX7  plan-2  C15   0.020
 KX7  plan-2  C16   0.020
 KX7  plan-2  C17   0.020
 KX7  plan-2  C18   0.020
 KX7  plan-2  C19   0.020
 KX7  plan-2  C20   0.020
 KX7  plan-2  N21   0.020
 KX7  plan-2  H161  0.020
 KX7  plan-2  H181  0.020
 KX7  plan-2  H191  0.020
 KX7  plan-2  H201  0.020
 KX7  plan-3  C17   0.020
 KX7  plan-3  N21   0.020
 KX7  plan-3  O22   0.020
 KX7  plan-3  O23   0.020
 KX7  plan-4  C01   0.020
 KX7  plan-4  C03   0.020
 KX7  plan-4  N04   0.020
 KX7  plan-4  C05   0.020
 KX7  plan-4  O06   0.020
 KX7  plan-4  N07   0.020
 KX7  plan-4  C08   0.020
 KX7  plan-4  H041  0.020

