# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 14:19:49 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: 2-hydroxyethyl (4R)-4-(4-cyanophenyl)-6-methyl-2-oxo-1-[3-(trifluoromethyl)phenyl]-1,2,3,4-tetrahydropyrimidine-5-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C([C@H](NC(=O)N1c2cccc(c2)C(F)(F)F)c3ccc(cc3)C#N)C(=O)OCCO
#
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
 2HY  2HY  '2-hydroxyethyl (4R)-4-(4-cyanophenyl)-6-methyl-2-oxo-1-[3-(trifluoromethyl)phenyl]-1,2,3,4-tetrahydropyrimidine-5-carboxylate'  ligand  50  32  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2HY
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
 2HY  C1    C  C     0   0.698   0.6616   0.6677  -1.4683
 2HY  F1    F  F     0  -0.309   6.5225   0.6324  -1.1237
 2HY  N1    N  NT    0  -0.679   1.0534   0.2060  -0.2066
 2HY  O1    O  O     0  -0.469   1.3816   1.4025  -2.1118
 2HY  C2    C  CH1   0  -0.212  -1.5183  -0.4663  -1.0941
 2HY  F2    F  F     0  -0.301   5.8241  -1.3012  -0.4911
 2HY  N2    N  NH1   0  -0.634  -0.5263   0.2129  -1.8936
 2HY  O2    O  O     0  -0.444  -1.1797  -3.1553   1.4039
 2HY  C3    C  C     0  -0.201  -0.8402  -1.1997   0.0384
 2HY  F3    F  F     0  -0.305   6.8931  -0.0360   0.8844
 2HY  N3    N  NS    0  -0.232  -6.3536   3.9698   0.9852
 2HY  O3    O  O2    0  -0.462  -2.8449  -2.3070   0.1957
 2HY  C4    C  C     0   0.389   0.3870  -0.8145   0.4615
 2HY  C5    C  CR6   0   0.295   2.3047   0.7093   0.2602
 2HY  C6    C  CR16  0  -0.247   3.4864   0.0998  -0.1289
 2HY  C7    C  CR6   0  -0.185   4.6944   0.5883   0.3436
 2HY  C8    C  CR16  0  -0.244   4.7214   1.6900   1.1906
 2HY  C9    C  CR16  0  -0.222   3.5362   2.2992   1.5655
 2HY  C10   C  CR16  0  -0.223   2.3253   1.8090   1.1004
 2HY  C11   C  CT    0   1.060   5.9841  -0.0359  -0.0954
 2HY  C13   C  CR6   0   0.224  -2.5876   0.4994  -0.6056
 2HY  C14   C  CR16  0  -0.287  -3.9034   0.3558  -1.0282
 2HY  C15   C  CR16  0  -0.218  -4.8794   1.2472  -0.6193
 2HY  C16   C  CR6   0   0.011  -4.5408   2.2991   0.2283
 2HY  C17   C  CR16  0  -0.210  -3.2245   2.4483   0.6645
 2HY  C18   C  CR16  0  -0.270  -2.2613   1.5509   0.2463
 2HY  C19   C  CSP   0   0.042  -5.5422   3.2239   0.6497
 2HY  C20   C  C     0   0.596  -1.5864  -2.3144   0.6362
 2HY  C21   C  CH2   0  -0.170  -3.7181  -3.3474   0.6112
 2HY  C22   C  CH2   0  -0.183  -5.1120  -2.9921   0.1630
 2HY  C23   C  CH3   0  -0.747   1.1230  -1.3899   1.6277
 2HY  O33   O  OH1   0  -0.628  -5.1577  -2.9495  -1.2415
 2HY  H2    H  HCH1  0   0.294  -2.0012  -1.1865  -1.7560
 2HY  HN2   H  HNH1  0   0.390  -0.8043   0.5286  -2.8085
 2HY  H6    H  HCR6  0   0.261   3.4494  -0.7501  -0.7968
 2HY  H8    H  HCR6  0   0.256   5.6605   2.0743   1.5647
 2HY  H9    H  HCR6  0   0.243   3.5550   3.1552   2.2253
 2HY  H10   H  HCR6  0   0.237   1.3941   2.2768   1.3931
 2HY  H14   H  HCR6  0   0.258  -4.1732  -0.4764  -1.6658
 2HY  H15   H  HCR6  0   0.242  -5.9013   1.1307  -0.9541
 2HY  H17   H  HCR6  0   0.248  -2.9639   3.2629   1.3265
 2HY  H18   H  HCR6  0   0.244  -1.2447   1.6743   0.5974
 2HY  H21   H  HCH2  0   0.233  -3.4026  -4.3004   0.1782
 2HY  H21A  H  HCH2  0   0.224  -3.7079  -3.4527   1.6983
 2HY  H22   H  HCH2  0   0.199  -5.7837  -3.7580   0.5732
 2HY  H22A  H  HCH2  0   0.199  -5.4019  -2.0341   0.6150
 2HY  H23   H  HCH3  0   0.253   1.5011  -0.5975   2.2719
 2HY  H23A  H  HCH3  0   0.293   0.4966  -2.0465   2.2141
 2HY  H23B  H  HCH3  0   0.264   1.9880  -1.9599   1.2841
 2HY  HO33  H  HOH1  0   0.431  -6.0689  -2.8224  -1.5129

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
 2HY  C1   N1    single    1.399  0.020  1.399
 2HY  C1   O1    double    1.213  0.020  1.213
 2HY  C1   N2    single    1.341  0.020  1.341
 2HY  F1   C11   single    1.339  0.020  1.339
 2HY  N1   C4    single    1.390  0.020  1.390
 2HY  N1   C5    single    1.427  0.020  1.427
 2HY  C2   N2    single    1.444  0.020  1.444
 2HY  C2   C3    single    1.510  0.020  1.510
 2HY  C2   C13   single    1.521  0.020  1.521
 2HY  F2   C11   single    1.335  0.020  1.335
 2HY  O2   C20   double    1.209  0.020  1.209
 2HY  C3   C4    double    1.354  0.020  1.354
 2HY  C3   C20   single    1.469  0.020  1.469
 2HY  F3   C11   single    1.337  0.020  1.337
 2HY  N3   C19   triple    1.152  0.020  1.152
 2HY  O3   C20   single    1.333  0.020  1.333
 2HY  O3   C21   single    1.420  0.020  1.420
 2HY  C4   C23   single    1.494  0.020  1.494
 2HY  C5   C6    aromatic  1.385  0.020  1.385
 2HY  C5   C10   aromatic  1.384  0.020  1.384
 2HY  C6   C7    aromatic  1.386  0.020  1.386
 2HY  C7   C8    aromatic  1.390  0.020  1.390
 2HY  C7   C11   single    1.499  0.020  1.499
 2HY  C8   C9    aromatic  1.384  0.020  1.384
 2HY  C9   C10   aromatic  1.387  0.020  1.387
 2HY  C13  C14   aromatic  1.389  0.020  1.389
 2HY  C13  C18   aromatic  1.392  0.020  1.392
 2HY  C14  C15   aromatic  1.384  0.020  1.384
 2HY  C15  C16   aromatic  1.393  0.020  1.393
 2HY  C16  C17   aromatic  1.395  0.020  1.395
 2HY  C16  C19   single    1.427  0.020  1.427
 2HY  C17  C18   aromatic  1.381  0.020  1.381
 2HY  C21  C22   single    1.507  0.020  1.507
 2HY  C22  O33   single    1.406  0.020  1.406
 2HY  C2   H2    single    0.970  0.020  1.090
 2HY  N2   HN2   single    0.860  0.020  1.020
 2HY  C6   H6    single    0.930  0.020  1.080
 2HY  C8   H8    single    0.930  0.020  1.080
 2HY  C9   H9    single    0.930  0.020  1.080
 2HY  C10  H10   single    0.930  0.020  1.080
 2HY  C14  H14   single    0.930  0.020  1.080
 2HY  C15  H15   single    0.930  0.020  1.080
 2HY  C17  H17   single    0.930  0.020  1.080
 2HY  C18  H18   single    0.930  0.020  1.080
 2HY  C21  H21   single    0.970  0.020  1.090
 2HY  C21  H21A  single    0.970  0.020  1.090
 2HY  C22  H22   single    0.970  0.020  1.090
 2HY  C22  H22A  single    0.970  0.020  1.090
 2HY  C23  H23   single    0.970  0.020  1.090
 2HY  C23  H23A  single    0.970  0.020  1.090
 2HY  C23  H23B  single    0.970  0.020  1.090
 2HY  O33  HO33  single    0.850  0.020  0.980

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
 2HY  N2    C1   O1    124.25  3.000
 2HY  N2    C1   N1    114.96  3.000
 2HY  O1    C1   N1    120.78  3.000
 2HY  C5    N1   C4    121.47  3.000
 2HY  C5    N1   C1    115.08  3.000
 2HY  C4    N1   C1    122.78  3.000
 2HY  H2    C2   C13   107.63  3.000
 2HY  H2    C2   C3    109.46  3.000
 2HY  C13   C2   C3    112.52  3.000
 2HY  H2    C2   N2    106.19  3.000
 2HY  C13   C2   N2    111.23  3.000
 2HY  C3    C2   N2    109.58  3.000
 2HY  HN2   N2   C2    117.44  3.000
 2HY  HN2   N2   C1    115.24  3.000
 2HY  C2    N2   C1    126.33  3.000
 2HY  C20   C3   C4    123.32  3.000
 2HY  C20   C3   C2    116.47  3.000
 2HY  C4    C3   C2    120.21  3.000
 2HY  C21   O3   C20   118.66  3.000
 2HY  C23   C4   C3    125.50  3.000
 2HY  C23   C4   N1    114.95  3.000
 2HY  C3    C4   N1    119.55  3.000
 2HY  C10   C5   C6    120.49  3.000
 2HY  C10   C5   N1    119.45  3.000
 2HY  C6    C5   N1    120.06  3.000
 2HY  H6    C6   C7    121.15  3.000
 2HY  H6    C6   C5    119.34  3.000
 2HY  C7    C6   C5    119.51  3.000
 2HY  C11   C7   C8    119.47  3.000
 2HY  C11   C7   C6    120.23  3.000
 2HY  C8    C7   C6    120.26  3.000
 2HY  H8    C8   C9    119.56  3.000
 2HY  H8    C8   C7    120.62  3.000
 2HY  C9    C8   C7    119.82  3.000
 2HY  H9    C9   C10   119.99  3.000
 2HY  H9    C9   C8    119.93  3.000
 2HY  C10   C9   C8    120.08  3.000
 2HY  H10   C10  C9    120.52  3.000
 2HY  H10   C10  C5    119.65  3.000
 2HY  C9    C10  C5    119.83  3.000
 2HY  C7    C11  F3    111.75  3.000
 2HY  C7    C11  F2    112.23  3.000
 2HY  F3    C11  F2    107.38  3.000
 2HY  C7    C11  F1    111.29  3.000
 2HY  F3    C11  F1    106.83  3.000
 2HY  F2    C11  F1    107.07  3.000
 2HY  C18   C13  C14   119.09  3.000
 2HY  C18   C13  C2    120.75  3.000
 2HY  C14   C13  C2    120.15  3.000
 2HY  H14   C14  C15   119.57  3.000
 2HY  H14   C14  C13   119.65  3.000
 2HY  C15   C14  C13   120.76  3.000
 2HY  H15   C15  C16   119.96  3.000
 2HY  H15   C15  C14   120.37  3.000
 2HY  C16   C15  C14   119.67  3.000
 2HY  C19   C16  C17   120.05  3.000
 2HY  C19   C16  C15   119.91  3.000
 2HY  C17   C16  C15   120.04  3.000
 2HY  H17   C17  C18   120.44  3.000
 2HY  H17   C17  C16   119.96  3.000
 2HY  C18   C17  C16   119.59  3.000
 2HY  H18   C18  C17   118.85  3.000
 2HY  H18   C18  C13   120.31  3.000
 2HY  C17   C18  C13   120.84  3.000
 2HY  C16   C19  N3    180.00  3.000
 2HY  O3    C20  C3    109.93  3.000
 2HY  O3    C20  O2    122.08  3.000
 2HY  C3    C20  O2    127.98  3.000
 2HY  H21A  C21  H21   107.90  3.000
 2HY  H21A  C21  C22   109.11  3.000
 2HY  H21   C21  C22   110.78  3.000
 2HY  H21A  C21  O3    110.85  3.000
 2HY  H21   C21  O3    110.20  3.000
 2HY  C22   C21  O3    108.00  3.000
 2HY  H22A  C22  H22   107.05  3.000
 2HY  H22A  C22  O33   112.09  3.000
 2HY  H22   C22  O33   111.98  3.000
 2HY  H22A  C22  C21   109.12  3.000
 2HY  H22   C22  C21   106.87  3.000
 2HY  O33   C22  C21   109.54  3.000
 2HY  H23B  C23  H23A  108.24  3.000
 2HY  H23B  C23  H23   106.92  3.000
 2HY  H23A  C23  H23   108.81  3.000
 2HY  H23B  C23  C4    110.23  3.000
 2HY  H23A  C23  C4    111.84  3.000
 2HY  H23   C23  C4    110.64  3.000
 2HY  HO33  O33  C22   108.52  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
 2HY  CONST_01  C8   C7   C6   C5     0.00   0.0  0
 2HY  CONST_02  C8   C9   C10  C5     0.00   0.0  0
 2HY  CONST_03  C9   C10  C5   C6     0.00   0.0  0
 2HY  CONST_04  C9   C8   C7   C6     0.00   0.0  0
 2HY  CONST_05  C10  C5   C6   C7     0.00   0.0  0
 2HY  CONST_06  C10  C9   C8   C7     0.00   0.0  0
 2HY  CONST_07  C16  C15  C14  C13    0.00   0.0  0
 2HY  CONST_08  C16  C17  C18  C13    0.00   0.0  0
 2HY  CONST_09  C17  C18  C13  C14    0.00   0.0  0
 2HY  CONST_10  C17  C16  C15  C14    0.00   0.0  0
 2HY  CONST_11  C18  C13  C14  C15    0.00   0.0  0
 2HY  CONST_12  C18  C17  C16  C15    0.00   0.0  0
 2HY  CONST_13  C7   C6   C5   N1   180.00   0.0  0
 2HY  CONST_14  C9   C10  C5   N1   180.00   0.0  0
 2HY  CONST_15  C15  C14  C13  C2   180.00   0.0  0
 2HY  CONST_16  C17  C18  C13  C2   180.00   0.0  0
 2HY  CONST_17  C2   N2   C1   N1     0.00   0.0  0
 2HY  CONST_18  C4   N1   C1   N2     0.00   0.0  0
 2HY  CONST_19  C5   N1   C1   N2   180.00   0.0  0
 2HY  CONST_20  C11  C7   C6   C5   180.00   0.0  0
 2HY  CONST_21  C11  C7   C8   C9   180.00   0.0  0
 2HY  CONST_22  C19  C16  C15  C14  180.00   0.0  0
 2HY  CONST_23  C19  C16  C17  C18  180.00   0.0  0
 2HY  CONST_24  C4   N1   C1   O1   180.00   0.0  0
 2HY  CONST_25  C5   N1   C1   O1     0.00   0.0  0
 2HY  CONST_26  C2   N2   C1   O1   180.00   0.0  0
 2HY  CONST_27  H6   C6   C5   N1     0.00   0.0  0
 2HY  CONST_28  H10  C10  C5   N1     0.00   0.0  0
 2HY  CONST_29  H14  C14  C13  C2     0.00   0.0  0
 2HY  CONST_30  H18  C18  C13  C2     0.00   0.0  0
 2HY  CONST_31  H9   C9   C10  C5   180.00   0.0  0
 2HY  CONST_32  H8   C8   C7   C6   180.00   0.0  0
 2HY  CONST_33  H15  C15  C14  C13  180.00   0.0  0
 2HY  CONST_34  H17  C17  C18  C13  180.00   0.0  0
 2HY  CONST_35  HN2  N2   C1   N1   180.00   0.0  0
 2HY  Var_01    C3   C4   N1   C1   -14.36  30.0  1
 2HY  Var_02    C6   C5   N1   C1   -84.02  30.0  2
 2HY  Var_03    C2   C3   C4   N1    -3.96  30.0  1
 2HY  Var_04    C6   C7   C11  F1    95.83  30.0  3
 2HY  Var_05    O2   C20  C3   C2   168.22  30.0  2
 2HY  Var_06    H23  C23  C4   N1    48.24  30.0  3
 2HY  Var_07    O33  C22  C21  O3    63.66  30.0  3
 2HY  Var_08    C22  C21  O3   C20  171.13  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
 2HY  chir_01  C2  N2  C3  C13  negativ

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
 2HY  plan-1  N1   0.020
 2HY  plan-1  C5   0.020
 2HY  plan-1  C6   0.020
 2HY  plan-1  C7   0.020
 2HY  plan-1  C8   0.020
 2HY  plan-1  C9   0.020
 2HY  plan-1  C10  0.020
 2HY  plan-1  C11  0.020
 2HY  plan-1  H6   0.020
 2HY  plan-1  H8   0.020
 2HY  plan-1  H9   0.020
 2HY  plan-1  H10  0.020
 2HY  plan-2  C2   0.020
 2HY  plan-2  N3   0.020
 2HY  plan-2  C13  0.020
 2HY  plan-2  C14  0.020
 2HY  plan-2  C15  0.020
 2HY  plan-2  C16  0.020
 2HY  plan-2  C17  0.020
 2HY  plan-2  C18  0.020
 2HY  plan-2  C19  0.020
 2HY  plan-2  H14  0.020
 2HY  plan-2  H15  0.020
 2HY  plan-2  H17  0.020
 2HY  plan-2  H18  0.020
 2HY  plan-3  C1   0.020
 2HY  plan-3  N1   0.020
 2HY  plan-3  O1   0.020
 2HY  plan-3  C2   0.020
 2HY  plan-3  N2   0.020
 2HY  plan-3  C4   0.020
 2HY  plan-3  C5   0.020
 2HY  plan-3  HN2  0.020
 2HY  plan-4  O2   0.020
 2HY  plan-4  C3   0.020
 2HY  plan-4  O3   0.020
 2HY  plan-4  C20  0.020

