# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 00:21:50 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 2-(ethoxymethyl)-4-(4-fluorophenyl)-3-[2-(2-hydroxyphenoxy)pyrimidin-4-yl]isoxazol-5(2H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOCN1OC(=O)C(=C1c2ccnc(Oc3ccccc3O)n2)c4ccc(F)cc4
#
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
 PGJ  PGJ  2-(ethoxymethyl)-4-(4-fluorophenyl)-3-[2-(2-hydroxyphenoxy)pyrimidin-4-yl]isoxazol-5(2H)-one  ligand  49  31  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PGJ
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
 PGJ  C1    C  CR5   0   0.471  -1.1344   0.8347  -1.7580
 PGJ  N2    N  NR5   0  -0.231  -2.1721   1.1966  -2.5695
 PGJ  O3    O  O     0  -0.349  -1.8337   0.8174  -3.8503
 PGJ  C4    C  CR5   0   0.583  -0.5744   0.2904  -3.8488
 PGJ  C5    C  CR5   0  -0.312  -0.1096   0.3208  -2.4807
 PGJ  C6    C  CH2   0  -0.079  -3.5766   0.9224  -2.2875
 PGJ  O7    O  O2    0  -0.465  -3.9214  -0.4111  -2.3708
 PGJ  C10   C  CH2   0  -0.173  -3.5998  -1.2077  -1.2373
 PGJ  C11   C  CH3   0  -0.683  -4.2980  -2.5404  -1.3711
 PGJ  C17   C  CR6   0   0.186  -1.1760   1.1000  -0.3132
 PGJ  C18   C  CR16  0  -0.343  -1.6359   2.3020   0.2001
 PGJ  C19   C  CR16  0   0.008  -1.5351   2.4449   1.5757
 PGJ  N20   N  N     0  -0.420  -1.0248   1.5024   2.3540
 PGJ  C21   C  CR6   0   0.564  -0.6290   0.4015   1.7455
 PGJ  N22   N  N     0  -0.411  -0.6857   0.1385   0.4575
 PGJ  O23   O  O2    0  -0.499  -0.0944  -0.5938   2.4701
 PGJ  C24   C  CR6   0   0.251   0.2686  -0.3371   3.7791
 PGJ  C25   C  CR16  0  -0.302  -0.6009  -0.6018   4.8193
 PGJ  C26   C  CR16  0  -0.281  -0.1949  -0.3713   6.1258
 PGJ  C27   C  CR16  0  -0.246   1.0780   0.1293   6.3685
 PGJ  C28   C  CR16  0  -0.345   1.9515   0.3826   5.3214
 PGJ  C29   C  CR6   0   0.311   1.5540   0.1498   4.0093
 PGJ  O34   O  OH1   0  -0.625   2.4167   0.4172   3.0070
 PGJ  C35   C  CR6   0   0.059   1.2229  -0.0909  -2.0430
 PGJ  C36   C  CR16  0  -0.287   1.7598  -1.3001  -2.4817
 PGJ  C37   C  CR16  0  -0.398   3.0120  -1.7199  -2.0583
 PGJ  C38   C  CR6   0   0.523   3.7220  -0.9137  -1.1911
 PGJ  C39   C  CR16  0  -0.414   3.2280   0.2979  -0.7441
 PGJ  C40   C  CR16  0  -0.293   1.9787   0.7062  -1.1830
 PGJ  F45   F  F     0  -0.311   4.9330  -1.3136  -0.7753
 PGJ  O47   O  OC    0  -0.438  -0.0593  -0.0632  -4.8778
 PGJ  H61   H  HCH2  0   0.291  -4.1579   1.4686  -3.0282
 PGJ  H62   H  HCH2  0   0.253  -3.7773   1.3553  -1.3022
 PGJ  H101  H  HCH2  0   0.219  -3.9202  -0.6977  -0.3206
 PGJ  H102  H  HCH2  0   0.220  -2.5177  -1.3657  -1.1640
 PGJ  H111  H  HCH3  0   0.237  -4.0530  -3.1670  -0.5142
 PGJ  H112  H  HCH3  0   0.234  -5.3810  -2.4207  -1.4032
 PGJ  H113  H  HCH3  0   0.235  -3.9786  -3.0667  -2.2708
 PGJ  H18   H  HCR6  0   0.306  -2.0211   3.0956  -0.4226
 PGJ  H19   H  HCR6  0   0.301  -1.8684   3.3534   2.0616
 PGJ  H25   H  HCR6  0   0.278  -1.5894  -0.9864   4.6024
 PGJ  H26   H  HCR6  0   0.263  -0.8700  -0.5756   6.9453
 PGJ  H27   H  HCR6  0   0.264   1.4032   0.3140   7.3836
 PGJ  H28   H  HCR6  0   0.273   2.9473   0.7612   5.5141
 PGJ  H34   H  HOH1  0   0.468   2.1702  -0.0564   2.2040
 PGJ  H36   H  HCR6  0   0.266   1.1924  -1.9377  -3.1463
 PGJ  H37   H  HCR6  0   0.284   3.4228  -2.6622  -2.3954
 PGJ  H39   H  HCR6  0   0.289   3.8144   0.9222  -0.0826
 PGJ  H40   H  HCR6  0   0.267   1.6016   1.6677  -0.8585

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
 PGJ  C1   N2    aromatic  1.366  0.020  1.366
 PGJ  C1   C5    aromatic  1.355  0.020  1.355
 PGJ  C1   C17   single    1.469  0.020  1.469
 PGJ  N2   O3    aromatic  1.378  0.020  1.378
 PGJ  N2   C6    single    1.459  0.020  1.459
 PGJ  O3   C4    aromatic  1.365  0.020  1.365
 PGJ  C4   C5    aromatic  1.445  0.020  1.445
 PGJ  C4   O47   double    1.204  0.020  1.204
 PGJ  C5   C35   single    1.462  0.020  1.462
 PGJ  C6   O7    single    1.380  0.020  1.380
 PGJ  C6   H61   single    0.970  0.020  1.090
 PGJ  C6   H62   single    0.970  0.020  1.090
 PGJ  O7   C10   single    1.422  0.020  1.422
 PGJ  C10  C11   single    1.510  0.020  1.510
 PGJ  C10  H101  single    0.970  0.020  1.090
 PGJ  C10  H102  single    0.970  0.020  1.090
 PGJ  C11  H111  single    0.970  0.020  1.090
 PGJ  C11  H112  single    0.970  0.020  1.090
 PGJ  C11  H113  single    0.970  0.020  1.090
 PGJ  C17  C18   aromatic  1.386  0.020  1.386
 PGJ  C17  N22   aromatic  1.326  0.020  1.326
 PGJ  C18  C19   aromatic  1.387  0.020  1.387
 PGJ  C18  H18   single    0.930  0.020  1.080
 PGJ  C19  N20   aromatic  1.325  0.020  1.325
 PGJ  C19  H19   single    0.930  0.020  1.080
 PGJ  N20  C21   aromatic  1.319  0.020  1.319
 PGJ  C21  N22   aromatic  1.316  0.020  1.316
 PGJ  C21  O23   single    1.342  0.020  1.342
 PGJ  O23  C24   single    1.382  0.020  1.382
 PGJ  C24  C25   aromatic  1.381  0.020  1.381
 PGJ  C24  C29   aromatic  1.394  0.020  1.394
 PGJ  C25  C26   aromatic  1.387  0.020  1.387
 PGJ  C25  H25   single    0.930  0.020  1.080
 PGJ  C26  C27   aromatic  1.389  0.020  1.389
 PGJ  C26  H26   single    0.930  0.020  1.080
 PGJ  C27  C28   aromatic  1.387  0.020  1.387
 PGJ  C27  H27   single    0.930  0.020  1.080
 PGJ  C28  C29   aromatic  1.391  0.020  1.391
 PGJ  C28  H28   single    0.930  0.020  1.080
 PGJ  C29  O34   single    1.349  0.020  1.349
 PGJ  O34  H34   single    0.850  0.020  0.980
 PGJ  C35  C36   aromatic  1.394  0.020  1.394
 PGJ  C35  C40   aromatic  1.395  0.020  1.395
 PGJ  C36  C37   aromatic  1.387  0.020  1.387
 PGJ  C36  H36   single    0.930  0.020  1.080
 PGJ  C37  C38   aromatic  1.381  0.020  1.381
 PGJ  C37  H37   single    0.930  0.020  1.080
 PGJ  C38  C39   aromatic  1.383  0.020  1.383
 PGJ  C38  F45   single    1.341  0.020  1.341
 PGJ  C39  C40   aromatic  1.386  0.020  1.386
 PGJ  C39  H39   single    0.930  0.020  1.080
 PGJ  C40  H40   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
 PGJ  C17   C1   C5    127.89  3.000
 PGJ  C17   C1   N2    120.98  3.000
 PGJ  C5    C1   N2    110.98  3.000
 PGJ  C6    N2   O3    111.38  3.000
 PGJ  C6    N2   C1    124.53  3.000
 PGJ  O3    N2   C1    107.02  3.000
 PGJ  C4    O3   N2    109.37  3.000
 PGJ  O47   C4   C5    132.66  3.000
 PGJ  O47   C4   O3    120.48  3.000
 PGJ  C5    C4   O3    106.84  3.000
 PGJ  C35   C5   C4    124.80  3.000
 PGJ  C35   C5   C1    129.53  3.000
 PGJ  C4    C5   C1    105.64  3.000
 PGJ  H62   C6   H61   108.43  3.000
 PGJ  H62   C6   O7    113.00  3.000
 PGJ  H61   C6   O7    108.08  3.000
 PGJ  H62   C6   N2    106.04  3.000
 PGJ  H61   C6   N2    106.76  3.000
 PGJ  O7    C6   N2    114.24  3.000
 PGJ  C10   O7   C6    115.89  3.000
 PGJ  H102  C10  H101  107.43  3.000
 PGJ  H102  C10  C11   109.58  3.000
 PGJ  H101  C10  C11   110.44  3.000
 PGJ  H102  C10  O7    110.93  3.000
 PGJ  H101  C10  O7    109.85  3.000
 PGJ  C11   C10  O7    108.61  3.000
 PGJ  H113  C11  H112  108.65  3.000
 PGJ  H113  C11  H111  107.79  3.000
 PGJ  H112  C11  H111  108.05  3.000
 PGJ  H113  C11  C10   111.32  3.000
 PGJ  H112  C11  C10   111.41  3.000
 PGJ  H111  C11  C10   109.50  3.000
 PGJ  N22   C17  C18   122.43  3.000
 PGJ  N22   C17  C1    115.47  3.000
 PGJ  C18   C17  C1    122.02  3.000
 PGJ  H18   C18  C19   121.49  3.000
 PGJ  H18   C18  C17   122.84  3.000
 PGJ  C19   C18  C17   115.65  3.000
 PGJ  H19   C19  N20   116.86  3.000
 PGJ  H19   C19  C18   120.61  3.000
 PGJ  N20   C19  C18   122.52  3.000
 PGJ  C21   N20  C19   116.01  3.000
 PGJ  O23   C21  N22   113.42  3.000
 PGJ  O23   C21  N20   119.30  3.000
 PGJ  N22   C21  N20   127.28  3.000
 PGJ  C21   N22  C17   116.10  3.000
 PGJ  C24   O23  C21   118.56  3.000
 PGJ  C29   C24  C25   121.54  3.000
 PGJ  C29   C24  O23   117.62  3.000
 PGJ  C25   C24  O23   120.80  3.000
 PGJ  H25   C25  C26   120.99  3.000
 PGJ  H25   C25  C24   119.47  3.000
 PGJ  C26   C25  C24   119.54  3.000
 PGJ  H26   C26  C27   120.52  3.000
 PGJ  H26   C26  C25   119.97  3.000
 PGJ  C27   C26  C25   119.51  3.000
 PGJ  H27   C27  C28   119.21  3.000
 PGJ  H27   C27  C26   120.05  3.000
 PGJ  C28   C27  C26   120.73  3.000
 PGJ  H28   C28  C29   119.30  3.000
 PGJ  H28   C28  C27   120.58  3.000
 PGJ  C29   C28  C27   120.11  3.000
 PGJ  O34   C29  C28   119.01  3.000
 PGJ  O34   C29  C24   122.43  3.000
 PGJ  C28   C29  C24   118.56  3.000
 PGJ  H34   O34  C29   110.97  3.000
 PGJ  C40   C35  C36   118.75  3.000
 PGJ  C40   C35  C5    121.17  3.000
 PGJ  C36   C35  C5    120.08  3.000
 PGJ  H36   C36  C37   118.86  3.000
 PGJ  H36   C36  C35   120.18  3.000
 PGJ  C37   C36  C35   120.94  3.000
 PGJ  H37   C37  C38   120.60  3.000
 PGJ  H37   C37  C36   120.76  3.000
 PGJ  C38   C37  C36   118.65  3.000
 PGJ  F45   C38  C39   118.92  3.000
 PGJ  F45   C38  C37   119.01  3.000
 PGJ  C39   C38  C37   122.07  3.000
 PGJ  H39   C39  C40   120.81  3.000
 PGJ  H39   C39  C38   120.63  3.000
 PGJ  C40   C39  C38   118.55  3.000
 PGJ  H40   C40  C39   118.74  3.000
 PGJ  H40   C40  C35   120.23  3.000
 PGJ  C39   C40  C35   121.02  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
 PGJ  CONST_01  C4    O3   N2   C1     0.00   0.0  0
 PGJ  CONST_02  O3    C4   C5   C1     0.00   0.0  0
 PGJ  CONST_05  C19   C18  C17  C1   180.00   0.0  0
 PGJ  CONST_06  C21   N22  C17  C1   180.00   0.0  0
 PGJ  CONST_07  C4    C5   C1   N2     0.00   0.0  0
 PGJ  CONST_08  C35   C5   C1   N2   180.00   0.0  0
 PGJ  CONST_11  C5    C4   O3   N2     0.00   0.0  0
 PGJ  CONST_12  C5    C1   N2   O3     0.00   0.0  0
 PGJ  CONST_13  C17   C1   N2   O3   180.00   0.0  0
 PGJ  CONST_14  C35   C5   C4   O3   180.00   0.0  0
 PGJ  CONST_15  C17   C1   C5   C4   180.00   0.0  0
 PGJ  CONST_20  C37   C36  C35  C5   180.00   0.0  0
 PGJ  CONST_21  C39   C40  C35  C5   180.00   0.0  0
 PGJ  CONST_22  C35   C5   C1   C17    0.00   0.0  0
 PGJ  CONST_23  N20   C19  C18  C17    0.00   0.0  0
 PGJ  CONST_24  N20   C21  N22  C17    0.00   0.0  0
 PGJ  CONST_25  C21   N22  C17  C18    0.00   0.0  0
 PGJ  CONST_26  C21   N20  C19  C18    0.00   0.0  0
 PGJ  CONST_27  N22   C17  C18  C19    0.00   0.0  0
 PGJ  CONST_28  N22   C21  N20  C19    0.00   0.0  0
 PGJ  CONST_29  C27   C26  C25  C24    0.00   0.0  0
 PGJ  CONST_30  C27   C28  C29  C24    0.00   0.0  0
 PGJ  CONST_31  C28   C29  C24  C25    0.00   0.0  0
 PGJ  CONST_32  C28   C27  C26  C25    0.00   0.0  0
 PGJ  CONST_33  C29   C24  C25  C26    0.00   0.0  0
 PGJ  CONST_34  C29   C28  C27  C26    0.00   0.0  0
 PGJ  CONST_35  C38   C37  C36  C35    0.00   0.0  0
 PGJ  CONST_36  C38   C39  C40  C35    0.00   0.0  0
 PGJ  CONST_37  C39   C40  C35  C36    0.00   0.0  0
 PGJ  CONST_38  C39   C38  C37  C36    0.00   0.0  0
 PGJ  CONST_39  C40   C35  C36  C37    0.00   0.0  0
 PGJ  CONST_40  C40   C39  C38  C37    0.00   0.0  0
 PGJ  CONST_41  O47   C4   C5   C1   180.00   0.0  0
 PGJ  CONST_42  O47   C4   O3   N2   180.00   0.0  0
 PGJ  CONST_46  O23   C21  N22  C17  180.00   0.0  0
 PGJ  CONST_47  O23   C21  N20  C19  180.00   0.0  0
 PGJ  CONST_48  C26   C25  C24  O23  180.00   0.0  0
 PGJ  CONST_49  C28   C29  C24  O23  180.00   0.0  0
 PGJ  CONST_50  O34   C29  C24  C25  180.00   0.0  0
 PGJ  CONST_51  O34   C29  C28  C27  180.00   0.0  0
 PGJ  CONST_52  O47   C4   C5   C35    0.00   0.0  0
 PGJ  CONST_53  F45   C38  C37  C36  180.00   0.0  0
 PGJ  CONST_54  F45   C38  C39  C40  180.00   0.0  0
 PGJ  CONST_55  H18   C18  C17  C1     0.00   0.0  0
 PGJ  CONST_56  H36   C36  C35  C5     0.00   0.0  0
 PGJ  CONST_57  H40   C40  C35  C5     0.00   0.0  0
 PGJ  CONST_58  H19   C19  C18  C17  180.00   0.0  0
 PGJ  CONST_59  H26   C26  C25  C24  180.00   0.0  0
 PGJ  CONST_60  H28   C28  C29  C24  180.00   0.0  0
 PGJ  CONST_61  H27   C27  C26  C25  180.00   0.0  0
 PGJ  CONST_62  H25   C25  C26  C27  180.00   0.0  0
 PGJ  CONST_63  H37   C37  C36  C35  180.00   0.0  0
 PGJ  CONST_64  H39   C39  C40  C35  180.00   0.0  0
 PGJ  Var_01    C25   C24  O23  C21   94.04  30.0  2
 PGJ  Var_02    O7    C6   N2   C1   -69.51  30.0  2
 PGJ  Var_03    C11   C10  O7   C6   168.07  30.0  3
 PGJ  Var_04    H111  C11  C10  O7   179.41  30.0  3

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
 PGJ  plan-1  C1   0.020
 PGJ  plan-1  N2   0.020
 PGJ  plan-1  O3   0.020
 PGJ  plan-1  C4   0.020
 PGJ  plan-1  C5   0.020
 PGJ  plan-1  C6   0.020
 PGJ  plan-1  C17  0.020
 PGJ  plan-1  C35  0.020
 PGJ  plan-1  O47  0.020
 PGJ  plan-2  C1   0.020
 PGJ  plan-2  C17  0.020
 PGJ  plan-2  C18  0.020
 PGJ  plan-2  C19  0.020
 PGJ  plan-2  N20  0.020
 PGJ  plan-2  C21  0.020
 PGJ  plan-2  N22  0.020
 PGJ  plan-2  O23  0.020
 PGJ  plan-2  H18  0.020
 PGJ  plan-2  H19  0.020
 PGJ  plan-3  O23  0.020
 PGJ  plan-3  C24  0.020
 PGJ  plan-3  C25  0.020
 PGJ  plan-3  C26  0.020
 PGJ  plan-3  C27  0.020
 PGJ  plan-3  C28  0.020
 PGJ  plan-3  C29  0.020
 PGJ  plan-3  O34  0.020
 PGJ  plan-3  H25  0.020
 PGJ  plan-3  H26  0.020
 PGJ  plan-3  H27  0.020
 PGJ  plan-3  H28  0.020
 PGJ  plan-4  C5   0.020
 PGJ  plan-4  C35  0.020
 PGJ  plan-4  C36  0.020
 PGJ  plan-4  C37  0.020
 PGJ  plan-4  C38  0.020
 PGJ  plan-4  C39  0.020
 PGJ  plan-4  C40  0.020
 PGJ  plan-4  F45  0.020
 PGJ  plan-4  H36  0.020
 PGJ  plan-4  H37  0.020
 PGJ  plan-4  H39  0.020
 PGJ  plan-4  H40  0.020

