# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 23:31:11 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 5-(2-ethoxyethyl)-5-[4-(4-fluorophenoxy)phenoxy]pyrimidine-2,4,6(1H,3H,5H)-trione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOCCC1(Oc2ccc(Oc3ccc(F)cc3)cc2)C(=O)NC(=O)NC1=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
 PFD  PFD  5-(2-ethoxyethyl)-5-[4-(4-fluorophenoxy)phenoxy]pyrimidine-2,4,6(1H,3H,5H)-trione  ligand  48  29  .  2021-08-19  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PFD
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
 PFD  F29   F  F     0  -0.316   2.6059   0.7701  -7.9095
 PFD  C28   C  CR6   0   0.520   1.7806   0.4377  -6.9035
 PFD  C26   C  CR16  0  -0.402   1.3686   1.4214  -6.0236
 PFD  C24   C  CR16  0  -0.288   0.5151   1.0784  -4.9868
 PFD  C27   C  CR16  0  -0.406   1.3682  -0.8739  -6.7801
 PFD  C25   C  CR16  0  -0.307   0.5219  -1.2139  -5.7333
 PFD  C23   C  CR6   0   0.311   0.0957  -0.2389  -4.8446
 PFD  O22   O  O2    0  -0.512  -0.7846  -0.5972  -3.8584
 PFD  C20   C  CR6   0   0.337  -0.4502  -0.3585  -2.5550
 PFD  C16   C  CR16  0  -0.311   0.8626  -0.3614  -2.0962
 PFD  C12   C  CR16  0  -0.340   1.1214  -0.1600  -0.7521
 PFD  C17   C  CR16  0  -0.326  -1.4882  -0.1529  -1.6617
 PFD  C13   C  CR16  0  -0.337  -1.2275   0.0427  -0.3116
 PFD  C6    C  CR6   0   0.372   0.0820   0.0421   0.1493
 PFD  O2    O  O2    0  -0.482   0.4657   0.2287   1.4444
 PFD  C1    C  CT    0  -0.041  -0.4713   0.3796   2.4552
 PFD  C5    C  CH2   0  -0.496   0.3106   0.5571   3.7776
 PFD  C11   C  CH2   0  -0.123   1.2934  -0.5634   4.0893
 PFD  O15   O  O2    0  -0.488   1.9148  -0.2221   5.3017
 PFD  C19   C  CH2   0  -0.144   2.8876  -1.1621   5.7040
 PFD  C21   C  CH3   0  -0.689   3.4733  -0.7320   7.0296
 PFD  C4    C  C     0   0.563  -1.2623   1.6778   2.2798
 PFD  O10   O  O     0  -0.382  -0.7913   2.6424   1.7371
 PFD  N9    N  NH1   0  -0.703  -2.4967   1.6876   2.8682
 PFD  C14   C  C     0   0.705  -3.1936   0.5968   3.3426
 PFD  O18   O  O     0  -0.424  -4.2763   0.7013   3.8585
 PFD  N7    N  NH1   0  -0.702  -2.5851  -0.6254   3.1509
 PFD  C3    C  C     0   0.562  -1.3589  -0.8561   2.5884
 PFD  O8    O  O     0  -0.382  -0.9801  -1.9584   2.2895
 PFD  H26   H  HCR6  0   0.287   1.7019   2.4435  -6.1459
 PFD  H24   H  HCR6  0   0.289   0.1792   1.8411  -4.2958
 PFD  H27   H  HCR6  0   0.287   1.7038  -1.6255  -7.4821
 PFD  H25   H  HCR6  0   0.282   0.1921  -2.2377  -5.6145
 PFD  H16   H  HCR6  0   0.285   1.6920  -0.5251  -2.7718
 PFD  H12   H  HCR6  0   0.277   2.1439  -0.1642  -0.3965
 PFD  H17   H  HCR6  0   0.279  -2.5121  -0.1473  -2.0121
 PFD  H13   H  HCR6  0   0.274  -2.0850   0.1973   0.3300
 PFD  H51   H  HCH2  0   0.275  -0.4014   0.6569   4.6005
 PFD  H52   H  HCH2  0   0.290   0.8578   1.5009   3.7116
 PFD  H111  H  HCH2  0   0.216   2.0331  -0.6600   3.2855
 PFD  H112  H  HCH2  0   0.213   0.7833  -1.5302   4.1790
 PFD  H191  H  HCH2  0   0.200   3.6800  -1.2384   4.9470
 PFD  H192  H  HCH2  0   0.200   2.4396  -2.1610   5.7942
 PFD  H211  H  HCH3  0   0.232   4.2377  -1.4428   7.3427
 PFD  H212  H  HCH3  0   0.229   3.9417   0.2503   6.9572
 PFD  H213  H  HCH3  0   0.229   2.7117  -0.6942   7.8088
 PFD  HN9   H  HNH1  0   0.444  -2.9852   2.5750   2.9151
 PFD  HN7   H  HNH1  0   0.443  -3.1468  -1.4362   3.3862

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
 PFD  F29  C28   single    1.343  0.020  1.343
 PFD  C28  C26   aromatic  1.383  0.020  1.383
 PFD  C28  C27   aromatic  1.380  0.020  1.380
 PFD  C26  C24   aromatic  1.386  0.020  1.386
 PFD  C26  H26   single    0.930  0.020  1.080
 PFD  C24  C23   aromatic  1.390  0.020  1.390
 PFD  C24  H24   single    0.930  0.020  1.080
 PFD  C27  C25   aromatic  1.388  0.020  1.388
 PFD  C27  H27   single    0.930  0.020  1.080
 PFD  C25  C23   aromatic  1.386  0.020  1.386
 PFD  C25  H25   single    0.930  0.020  1.080
 PFD  C23  O22   single    1.370  0.020  1.370
 PFD  O22  C20   single    1.367  0.020  1.367
 PFD  C20  C16   aromatic  1.391  0.020  1.391
 PFD  C20  C17   aromatic  1.385  0.020  1.385
 PFD  C16  C12   aromatic  1.384  0.020  1.384
 PFD  C16  H16   single    0.930  0.020  1.080
 PFD  C12  C6    aromatic  1.391  0.020  1.391
 PFD  C12  H12   single    0.930  0.020  1.080
 PFD  C17  C13   aromatic  1.389  0.020  1.389
 PFD  C17  H17   single    0.930  0.020  1.080
 PFD  C13  C6    aromatic  1.388  0.020  1.388
 PFD  C13  H13   single    0.930  0.020  1.080
 PFD  C6   O2    single    1.364  0.020  1.364
 PFD  O2   C1    single    1.387  0.020  1.387
 PFD  C1   C5    single    1.546  0.020  1.546
 PFD  C1   C4    single    1.530  0.020  1.530
 PFD  C1   C3    single    1.527  0.020  1.527
 PFD  C5   C11   single    1.523  0.020  1.523
 PFD  C5   H51   single    0.970  0.020  1.090
 PFD  C5   H52   single    0.970  0.020  1.090
 PFD  C11  O15   single    1.404  0.020  1.404
 PFD  C11  H111  single    0.970  0.020  1.090
 PFD  C11  H112  single    0.970  0.020  1.090
 PFD  O15  C19   single    1.411  0.020  1.411
 PFD  C19  C21   single    1.512  0.020  1.512
 PFD  C19  H191  single    0.970  0.020  1.090
 PFD  C19  H192  single    0.970  0.020  1.090
 PFD  C21  H211  single    0.970  0.020  1.090
 PFD  C21  H212  single    0.970  0.020  1.090
 PFD  C21  H213  single    0.970  0.020  1.090
 PFD  C4   O10   double    1.203  0.020  1.203
 PFD  C4   N9    single    1.368  0.020  1.368
 PFD  N9   C14   single    1.379  0.020  1.379
 PFD  N9   HN9   single    0.860  0.020  1.020
 PFD  C14  O18   double    1.204  0.020  1.204
 PFD  C14  N7    single    1.379  0.020  1.379
 PFD  N7   C3    single    1.369  0.020  1.369
 PFD  N7   HN7   single    0.860  0.020  1.020
 PFD  C3   O8    double    1.203  0.020  1.203

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
 PFD  C27   C28  C26   122.01  3.000
 PFD  C27   C28  F29   119.06  3.000
 PFD  C26   C28  F29   118.93  3.000
 PFD  H26   C26  C24   120.53  3.000
 PFD  H26   C26  C28   120.56  3.000
 PFD  C24   C26  C28   118.91  3.000
 PFD  H24   C24  C23   120.58  3.000
 PFD  H24   C24  C26   119.62  3.000
 PFD  C23   C24  C26   119.80  3.000
 PFD  H27   C27  C25   120.55  3.000
 PFD  H27   C27  C28   120.62  3.000
 PFD  C25   C27  C28   118.83  3.000
 PFD  H25   C25  C23   120.08  3.000
 PFD  H25   C25  C27   120.01  3.000
 PFD  C23   C25  C27   119.90  3.000
 PFD  O22   C23  C25   118.37  3.000
 PFD  O22   C23  C24   121.04  3.000
 PFD  C25   C23  C24   120.54  3.000
 PFD  C20   O22  C23   118.93  3.000
 PFD  C17   C20  C16   119.68  3.000
 PFD  C17   C20  O22   117.24  3.000
 PFD  C16   C20  O22   123.04  3.000
 PFD  H16   C16  C12   119.02  3.000
 PFD  H16   C16  C20   121.19  3.000
 PFD  C12   C16  C20   119.79  3.000
 PFD  H12   C12  C6    119.57  3.000
 PFD  H12   C12  C16   119.69  3.000
 PFD  C6    C12  C16   120.74  3.000
 PFD  H17   C17  C13   119.45  3.000
 PFD  H17   C17  C20   120.07  3.000
 PFD  C13   C17  C20   120.48  3.000
 PFD  H13   C13  C6    123.42  3.000
 PFD  H13   C13  C17   116.60  3.000
 PFD  C6    C13  C17   119.98  3.000
 PFD  O2    C6   C13   125.50  3.000
 PFD  O2    C6   C12   115.17  3.000
 PFD  C13   C6   C12   119.33  3.000
 PFD  C1    O2   C6    121.14  3.000
 PFD  C3    C1   C4    113.33  3.000
 PFD  C3    C1   C5    108.19  3.000
 PFD  C4    C1   C5    105.19  3.000
 PFD  C3    C1   O2    111.61  3.000
 PFD  C4    C1   O2    110.98  3.000
 PFD  C5    C1   O2    107.11  3.000
 PFD  H52   C5   H51   107.02  3.000
 PFD  H52   C5   C11   108.94  3.000
 PFD  H51   C5   C11   109.48  3.000
 PFD  H52   C5   C1    107.50  3.000
 PFD  H51   C5   C1    108.97  3.000
 PFD  C11   C5   C1    114.65  3.000
 PFD  H112  C11  H111  107.21  3.000
 PFD  H112  C11  O15   110.45  3.000
 PFD  H111  C11  O15   110.83  3.000
 PFD  H112  C11  C5    111.42  3.000
 PFD  H111  C11  C5    110.50  3.000
 PFD  O15   C11  C5    106.47  3.000
 PFD  C19   O15  C11   112.91  3.000
 PFD  H192  C19  H191  106.72  3.000
 PFD  H192  C19  C21   110.16  3.000
 PFD  H191  C19  C21   110.15  3.000
 PFD  H192  C19  O15   110.36  3.000
 PFD  H191  C19  O15   110.31  3.000
 PFD  C21   C19  O15   109.12  3.000
 PFD  H213  C21  H212  108.44  3.000
 PFD  H213  C21  H211  107.89  3.000
 PFD  H212  C21  H211  107.78  3.000
 PFD  H213  C21  C19   111.46  3.000
 PFD  H212  C21  C19   111.37  3.000
 PFD  H211  C21  C19   109.76  3.000
 PFD  N9    C4   O10   122.81  3.000
 PFD  N9    C4   C1    115.05  3.000
 PFD  O10   C4   C1    121.98  3.000
 PFD  HN9   N9   C14   115.66  3.000
 PFD  HN9   N9   C4    117.45  3.000
 PFD  C14   N9   C4    126.78  3.000
 PFD  N7    C14  O18   122.24  3.000
 PFD  N7    C14  N9    115.50  3.000
 PFD  O18   C14  N9    122.24  3.000
 PFD  HN7   N7   C3    117.19  3.000
 PFD  HN7   N7   C14   115.60  3.000
 PFD  C3    N7   C14   127.01  3.000
 PFD  O8    C3   N7    122.58  3.000
 PFD  O8    C3   C1    122.46  3.000
 PFD  N7    C3   C1    114.84  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
 PFD  CONST_01  C23   C24  C26  C28     0.00   0.0  0
 PFD  CONST_02  C23   C25  C27  C28     0.00   0.0  0
 PFD  CONST_03  C25   C27  C28  C26     0.00   0.0  0
 PFD  CONST_04  C25   C23  C24  C26     0.00   0.0  0
 PFD  CONST_05  C27   C28  C26  C24     0.00   0.0  0
 PFD  CONST_06  C27   C25  C23  C24     0.00   0.0  0
 PFD  CONST_07  C6    C12  C16  C20     0.00   0.0  0
 PFD  CONST_08  C6    C13  C17  C20     0.00   0.0  0
 PFD  CONST_09  C13   C17  C20  C16     0.00   0.0  0
 PFD  CONST_10  C13   C6   C12  C16     0.00   0.0  0
 PFD  CONST_11  C17   C20  C16  C12     0.00   0.0  0
 PFD  CONST_12  C17   C13  C6   C12     0.00   0.0  0
 PFD  CONST_13  C14   N9   C4   C1      0.00   0.0  0
 PFD  CONST_14  N7    C14  N9   C4      0.00   0.0  0
 PFD  CONST_15  C3    N7   C14  N9      0.00   0.0  0
 PFD  CONST_16  C24   C26  C28  F29   180.00   0.0  0
 PFD  CONST_17  C25   C27  C28  F29   180.00   0.0  0
 PFD  CONST_18  O22   C23  C24  C26   180.00   0.0  0
 PFD  CONST_19  O22   C23  C25  C27   180.00   0.0  0
 PFD  CONST_20  C12   C16  C20  O22   180.00   0.0  0
 PFD  CONST_21  C13   C17  C20  O22   180.00   0.0  0
 PFD  CONST_22  O2    C6   C12  C16   180.00   0.0  0
 PFD  CONST_23  O2    C6   C13  C17   180.00   0.0  0
 PFD  CONST_24  O18   C14  N9   C4    180.00   0.0  0
 PFD  CONST_25  C14   N9   C4   O10   180.00   0.0  0
 PFD  CONST_26  C3    N7   C14  O18   180.00   0.0  0
 PFD  CONST_27  H24   C24  C26  C28   180.00   0.0  0
 PFD  CONST_28  H25   C25  C27  C28   180.00   0.0  0
 PFD  CONST_29  H27   C27  C28  C26   180.00   0.0  0
 PFD  CONST_30  H26   C26  C28  C27   180.00   0.0  0
 PFD  CONST_31  H12   C12  C16  C20   180.00   0.0  0
 PFD  CONST_32  H13   C13  C17  C20   180.00   0.0  0
 PFD  CONST_33  H17   C17  C20  C16   180.00   0.0  0
 PFD  CONST_34  H16   C16  C20  C17   180.00   0.0  0
 PFD  CONST_35  HN9   N9   C4   C1    180.00   0.0  0
 PFD  CONST_36  HN7   N7   C14  N9    180.00   0.0  0
 PFD  Var_01    C16   C20  O22  C23   -30.45  30.0  2
 PFD  Var_02    O8    C3   N7   C14  -169.42  30.0  1
 PFD  Var_03    O15   C11  C5   C1    179.17  30.0  3
 PFD  Var_04    C21   C19  O15  C11  -178.53  30.0  3
 PFD  Var_05    H211  C21  C19  O15  -179.11  30.0  3

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
 PFD  chir_01  C1  C5  C4  C3  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
 PFD  plan-1  F29  0.020
 PFD  plan-1  C28  0.020
 PFD  plan-1  C26  0.020
 PFD  plan-1  C24  0.020
 PFD  plan-1  C27  0.020
 PFD  plan-1  C25  0.020
 PFD  plan-1  C23  0.020
 PFD  plan-1  O22  0.020
 PFD  plan-1  H26  0.020
 PFD  plan-1  H24  0.020
 PFD  plan-1  H27  0.020
 PFD  plan-1  H25  0.020
 PFD  plan-2  O22  0.020
 PFD  plan-2  C20  0.020
 PFD  plan-2  C16  0.020
 PFD  plan-2  C12  0.020
 PFD  plan-2  C17  0.020
 PFD  plan-2  C13  0.020
 PFD  plan-2  C6   0.020
 PFD  plan-2  O2   0.020
 PFD  plan-2  H16  0.020
 PFD  plan-2  H12  0.020
 PFD  plan-2  H17  0.020
 PFD  plan-2  H13  0.020
 PFD  plan-3  C1   0.020
 PFD  plan-3  N7   0.020
 PFD  plan-3  C3   0.020
 PFD  plan-3  O8   0.020
 PFD  plan-4  C1   0.020
 PFD  plan-4  C4   0.020
 PFD  plan-4  O10  0.020
 PFD  plan-4  N9   0.020
 PFD  plan-4  C14  0.020
 PFD  plan-4  O18  0.020
 PFD  plan-4  N7   0.020
 PFD  plan-4  C3   0.020
 PFD  plan-4  HN9  0.020
 PFD  plan-4  HN7  0.020

