# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 20:13:30 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: N-{3-[(4S)-2-amino-1,4-dimethyl-6-oxo-1,4,5,6-tetrahydropyrimidin-4-yl]phenyl}-5-(2,2,2-trifluoroethoxy)pyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=N[C@@](C)(CC1=O)c2cccc(NC(=O)c3ccc(OCC(F)(F)F)cn3)c2)N
#
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
 WZV  WZV  N-{3-[(4S)-2-amino-1,4-dimethyl-6-oxo-1,4,5,6-tetrahydropyrimidin-4-yl]phenyl}-5-(2,2,2-trifluoroethoxy)pyridine-2-carboxamide  ligand  51  31  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_WZV
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
 WZV  F30   F  F     0  -0.304  -7.7832  -1.9101  -1.0248
 WZV  C28   C  CT    0   0.991  -7.1305  -2.2214   0.0986
 WZV  F31   F  F     0  -0.304  -7.8046  -1.6695   1.1114
 WZV  F29   F  F     0  -0.305  -7.1891  -3.5480   0.2469
 WZV  C27   C  CH2   0  -0.381  -5.6896  -1.7675   0.0630
 WZV  O26   O  O2    0  -0.466  -5.7227  -0.3699  -0.0932
 WZV  C18   C  CR6   0   0.336  -4.5624   0.3030  -0.1186
 WZV  C23   C  CR16  0  -0.173  -3.3026  -0.2920  -0.0375
 WZV  N22   N  N     0  -0.428  -2.1897   0.4216  -0.0568
 WZV  C19   C  CR16  0  -0.243  -4.6352   1.6882  -0.2335
 WZV  C20   C  CR16  0  -0.269  -3.4654   2.4176  -0.2534
 WZV  C21   C  CR6   0   0.098  -2.2541   1.7404  -0.1588
 WZV  C24   C  C     0   0.536  -0.9682   2.5088  -0.1656
 WZV  O25   O  O     0  -0.461  -0.9665   3.7253  -0.2585
 WZV  N13   N  NH1   0  -0.762   0.1272   1.7292  -0.0576
 WZV  C7    C  CR6   0   0.425   1.4745   2.0945  -0.0071
 WZV  C12   C  CR16  0  -0.453   2.3893   1.0510   0.1686
 WZV  C8    C  CR16  0  -0.336   1.9384   3.4029  -0.1222
 WZV  C9    C  CR16  0  -0.234   3.3063   3.6355  -0.0545
 WZV  C10   C  CR16  0  -0.321   4.2088   2.6017   0.1233
 WZV  C11   C  CR6   0   0.161   3.7520   1.2872   0.2356
 WZV  C1    C  CT    0  -0.017   4.7431   0.1460   0.4223
 WZV  C2    C  CH2   0  -0.575   5.7041   0.1259  -0.7700
 WZV  C3    C  C     0   0.557   6.5890  -1.0887  -0.7476
 WZV  O16   O  O     0  -0.456   7.7196  -1.0937  -1.1916
 WZV  C14   C  CH3   0  -0.631   5.5092   0.3604   1.7378
 WZV  N6    N  N     0  -0.454   4.0325  -1.1098   0.4771
 WZV  C5    C  C     0   0.640   4.6764  -2.1743   0.2092
 WZV  N15   N  NH2   0  -0.835   4.1023  -3.3984   0.3894
 WZV  N4    N  NT    0  -0.539   6.0139  -2.2142  -0.2153
 WZV  C17   C  CH3   0  -0.588   6.7796  -3.4509  -0.1520
 WZV  H271  H  HCH2  0   0.283  -5.1995  -2.0653   0.9958
 WZV  H272  H  HCH2  0   0.283  -5.1806  -2.2625  -0.7704
 WZV  H23   H  HCR6  0   0.295  -3.1823  -1.3656   0.0439
 WZV  H19   H  HCR6  0   0.292  -5.5978   2.1782  -0.3035
 WZV  H20   H  HCR6  0   0.283  -3.4938   3.4943  -0.3376
 WZV  H13   H  HNH1  0   0.417  -0.0675   0.7380   0.0131
 WZV  H12   H  HCR6  0   0.267   2.0312   0.0330   0.2571
 WZV  H8    H  HCR6  0   0.277   1.2611   4.2289  -0.2612
 WZV  H9    H  HCR6  0   0.254   3.6682   4.6518  -0.1449
 WZV  H10   H  HCR6  0   0.244   5.2670   2.8270   0.1714
 WZV  H21C  H  HCH2  0   0.292   5.1283   0.0974  -1.7024
 WZV  H22C  H  HCH2  0   0.276   6.3373   1.0115  -0.8124
 WZV  H141  H  HCH3  0   0.241   4.8173   0.3536   2.5798
 WZV  H142  H  HCH3  0   0.234   6.2468  -0.4275   1.9026
 WZV  H143  H  HCH3  0   0.230   6.0398   1.3128   1.7437
 WZV  H151  H  HNH2  0   0.392   3.1158  -3.3532   0.5902
 WZV  H152  H  HNH2  0   0.399   4.3383  -4.1362  -0.2561
 WZV  H171  H  HCH3  0   0.276   6.5340  -3.9896   0.7589
 WZV  H172  H  HCH3  0   0.270   6.5839  -4.0940  -1.0110
 WZV  H173  H  HCH3  0   0.286   7.8385  -3.2159  -0.1377

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
 WZV  F30  C28   single    1.336  0.020  1.336
 WZV  C28  F31   single    1.336  0.020  1.336
 WZV  C28  F29   single    1.336  0.020  1.336
 WZV  C28  C27   single    1.511  0.020  1.511
 WZV  C27  O26   single    1.407  0.020  1.407
 WZV  O26  C18   single    1.342  0.020  1.342
 WZV  C18  C23   aromatic  1.396  0.020  1.396
 WZV  C18  C19   aromatic  1.392  0.020  1.392
 WZV  C23  N22   aromatic  1.322  0.020  1.322
 WZV  N22  C21   aromatic  1.324  0.020  1.324
 WZV  C19  C20   aromatic  1.379  0.020  1.379
 WZV  C20  C21   aromatic  1.391  0.020  1.391
 WZV  C21  C24   single    1.498  0.020  1.498
 WZV  C24  O25   double    1.220  0.020  1.220
 WZV  C24  N13   single    1.349  0.020  1.349
 WZV  N13  C7    single    1.397  0.020  1.397
 WZV  C7   C12   aromatic  1.399  0.020  1.399
 WZV  C7   C8    aromatic  1.393  0.020  1.393
 WZV  C12  C11   aromatic  1.385  0.020  1.385
 WZV  C8   C9    aromatic  1.389  0.020  1.389
 WZV  C9   C10   aromatic  1.384  0.020  1.384
 WZV  C10  C11   aromatic  1.396  0.020  1.396
 WZV  C11  C1    single    1.523  0.020  1.523
 WZV  C1   C2    single    1.531  0.020  1.531
 WZV  C1   C14   single    1.537  0.020  1.537
 WZV  C1   N6    single    1.444  0.020  1.444
 WZV  C2   C3    single    1.503  0.020  1.503
 WZV  C3   O16   double    1.215  0.020  1.215
 WZV  C3   N4    single    1.371  0.020  1.371
 WZV  N6   C5    double    1.273  0.020  1.273
 WZV  C5   N15   single    1.364  0.020  1.364
 WZV  C5   N4    single    1.404  0.020  1.404
 WZV  N4   C17   single    1.456  0.020  1.456
 WZV  C27  H271  single    0.970  0.020  1.090
 WZV  C27  H272  single    0.970  0.020  1.090
 WZV  C23  H23   single    0.930  0.020  1.080
 WZV  C19  H19   single    0.930  0.020  1.080
 WZV  C20  H20   single    0.930  0.020  1.080
 WZV  N13  H13   single    0.860  0.020  1.020
 WZV  C12  H12   single    0.930  0.020  1.080
 WZV  C8   H8    single    0.930  0.020  1.080
 WZV  C9   H9    single    0.930  0.020  1.080
 WZV  C10  H10   single    0.930  0.020  1.080
 WZV  C2   H21C  single    0.970  0.020  1.090
 WZV  C2   H22C  single    0.970  0.020  1.090
 WZV  C14  H141  single    0.970  0.020  1.090
 WZV  C14  H142  single    0.970  0.020  1.090
 WZV  C14  H143  single    0.970  0.020  1.090
 WZV  N15  H151  single    0.890  0.020  1.040
 WZV  N15  H152  single    0.890  0.020  1.040
 WZV  C17  H171  single    0.970  0.020  1.090
 WZV  C17  H172  single    0.970  0.020  1.090
 WZV  C17  H173  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
 WZV  C27   C28  F29   110.04  3.000
 WZV  C27   C28  F31   112.01  3.000
 WZV  F29   C28  F31   107.69  3.000
 WZV  C27   C28  F30   112.09  3.000
 WZV  F29   C28  F30   107.65  3.000
 WZV  F31   C28  F30   107.14  3.000
 WZV  H272  C27  H271  108.50  3.000
 WZV  H272  C27  O26   112.06  3.000
 WZV  H271  C27  O26   112.04  3.000
 WZV  H272  C27  C28   108.99  3.000
 WZV  H271  C27  C28   108.97  3.000
 WZV  O26   C27  C28   106.18  3.000
 WZV  C18   O26  C27   118.69  3.000
 WZV  C19   C18  C23   118.44  3.000
 WZV  C19   C18  O26   117.10  3.000
 WZV  C23   C18  O26   124.46  3.000
 WZV  H23   C23  N22   116.26  3.000
 WZV  H23   C23  C18   121.81  3.000
 WZV  N22   C23  C18   121.93  3.000
 WZV  C21   N22  C23   119.84  3.000
 WZV  H19   C19  C20   120.94  3.000
 WZV  H19   C19  C18   120.15  3.000
 WZV  C20   C19  C18   118.90  3.000
 WZV  H20   C20  C21   120.89  3.000
 WZV  H20   C20  C19   120.40  3.000
 WZV  C21   C20  C19   118.71  3.000
 WZV  C24   C21  C20   119.83  3.000
 WZV  C24   C21  N22   118.00  3.000
 WZV  C20   C21  N22   122.17  3.000
 WZV  N13   C24  O25   125.53  3.000
 WZV  N13   C24  C21   113.60  3.000
 WZV  O25   C24  C21   120.87  3.000
 WZV  H13   N13  C7    116.04  3.000
 WZV  H13   N13  C24   114.53  3.000
 WZV  C7    N13  C24   129.43  3.000
 WZV  C8    C7   C12   119.56  3.000
 WZV  C8    C7   N13   124.32  3.000
 WZV  C12   C7   N13   116.12  3.000
 WZV  H12   C12  C11   118.81  3.000
 WZV  H12   C12  C7    119.69  3.000
 WZV  C11   C12  C7    121.49  3.000
 WZV  H8    C8   C9    119.80  3.000
 WZV  H8    C8   C7    121.44  3.000
 WZV  C9    C8   C7    118.76  3.000
 WZV  H9    C9   C10   119.61  3.000
 WZV  H9    C9   C8    118.83  3.000
 WZV  C10   C9   C8    121.56  3.000
 WZV  H10   C10  C11   120.80  3.000
 WZV  H10   C10  C9    119.17  3.000
 WZV  C11   C10  C9    120.03  3.000
 WZV  C1    C11  C10   120.16  3.000
 WZV  C1    C11  C12   121.23  3.000
 WZV  C10   C11  C12   118.60  3.000
 WZV  N6    C1   C14   109.52  3.000
 WZV  N6    C1   C2    109.08  3.000
 WZV  C14   C1   C2    110.81  3.000
 WZV  N6    C1   C11   109.64  3.000
 WZV  C14   C1   C11   108.95  3.000
 WZV  C2    C1   C11   108.83  3.000
 WZV  H22C  C2   H21C  107.05  3.000
 WZV  H22C  C2   C3    108.38  3.000
 WZV  H21C  C2   C3    107.52  3.000
 WZV  H22C  C2   C1    112.60  3.000
 WZV  H21C  C2   C1    109.45  3.000
 WZV  C3    C2   C1    111.62  3.000
 WZV  N4    C3   O16   121.93  3.000
 WZV  N4    C3   C2    114.96  3.000
 WZV  O16   C3   C2    123.09  3.000
 WZV  H143  C14  H142  107.51  3.000
 WZV  H143  C14  H141  108.08  3.000
 WZV  H142  C14  H141  107.92  3.000
 WZV  H143  C14  C1    111.66  3.000
 WZV  H142  C14  C1    111.42  3.000
 WZV  H141  C14  C1    110.11  3.000
 WZV  C5    N6   C1    118.06  3.000
 WZV  N4    C5   N15   114.55  3.000
 WZV  N4    C5   N6    124.72  3.000
 WZV  N15   C5   N6    120.65  3.000
 WZV  H152  N15  H151  112.93  3.000
 WZV  H152  N15  C5    118.26  3.000
 WZV  H151  N15  C5    113.46  3.000
 WZV  C17   N4   C5    120.80  3.000
 WZV  C17   N4   C3    119.56  3.000
 WZV  C5    N4   C3    119.58  3.000
 WZV  H173  C17  H172  108.26  3.000
 WZV  H173  C17  H171  108.49  3.000
 WZV  H172  C17  H171  109.11  3.000
 WZV  H173  C17  N4    109.26  3.000
 WZV  H172  C17  N4    111.85  3.000
 WZV  H171  C17  N4    109.80  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
 WZV  CONST_01  C21   N22  C23  C18    0.00   0.0  0
 WZV  CONST_02  C21   C20  C19  C18    0.00   0.0  0
 WZV  CONST_03  C20   C19  C18  C23    0.00   0.0  0
 WZV  CONST_04  C20   C21  N22  C23    0.00   0.0  0
 WZV  CONST_05  C19   C18  C23  N22    0.00   0.0  0
 WZV  CONST_06  C19   C20  C21  N22    0.00   0.0  0
 WZV  CONST_07  C10   C11  C12  C7     0.00   0.0  0
 WZV  CONST_08  C10   C9   C8   C7     0.00   0.0  0
 WZV  CONST_09  C9    C8   C7   C12    0.00   0.0  0
 WZV  CONST_10  C9    C10  C11  C12    0.00   0.0  0
 WZV  CONST_11  C11   C12  C7   C8     0.00   0.0  0
 WZV  CONST_12  C11   C10  C9   C8     0.00   0.0  0
 WZV  CONST_13  C1    C11  C12  C7   180.00   0.0  0
 WZV  CONST_14  C1    C11  C10  C9   180.00   0.0  0
 WZV  CONST_15  N4    C5   N6   C1     0.00   0.0  0
 WZV  CONST_16  C5    N4   C3   C2     0.00   0.0  0
 WZV  CONST_18  N22   C23  C18  O26  180.00   0.0  0
 WZV  CONST_19  C20   C19  C18  O26  180.00   0.0  0
 WZV  CONST_20  C24   C21  N22  C23  180.00   0.0  0
 WZV  CONST_21  C24   C21  C20  C19  180.00   0.0  0
 WZV  CONST_22  C11   C12  C7   N13  180.00   0.0  0
 WZV  CONST_23  C9    C8   C7   N13  180.00   0.0  0
 WZV  CONST_24  N15   C5   N6   C1   180.00   0.0  0
 WZV  CONST_25  C17   N4   C3   C2   180.00   0.0  0
 WZV  CONST_27  C5    N4   C3   O16  180.00   0.0  0
 WZV  CONST_29  H20   C20  C19  C18  180.00   0.0  0
 WZV  CONST_30  H19   C19  C18  C23  180.00   0.0  0
 WZV  CONST_31  H23   C23  C18  C19  180.00   0.0  0
 WZV  CONST_32  H9    C9   C8   C7   180.00   0.0  0
 WZV  CONST_33  H8    C8   C7   C12  180.00   0.0  0
 WZV  CONST_34  H10   C10  C11  C12  180.00   0.0  0
 WZV  CONST_35  H12   C12  C7   C8   180.00   0.0  0
 WZV  CONST_36  C7    N13  C24  C21  180.00   0.0  0
 WZV  CONST_37  C12   C7   N13  C24  180.00   0.0  0
 WZV  CONST_38  C8    C7   N13  C24    0.00   0.0  0
 WZV  CONST_39  C17   N4   C3   O16    0.00   0.0  0
 WZV  CONST_40  C17   N4   C5   N15    0.00   0.0  0
 WZV  CONST_41  H13   N13  C7   C12    0.00   0.0  0
 WZV  CONST_42  H151  N15  C5   N6     0.00   0.0  0
 WZV  CONST_44  C7    N13  C24  O25    0.00   0.0  0
 WZV  Var_01    H21C  C2   C3   N4   -87.45  30.0  1
 WZV  Var_02    C23   C18  O26  C27    1.88  30.0  2
 WZV  Var_03    O25   C24  C21  N22  179.93  30.0  2
 WZV  Var_04    H171  C17  N4   C3   143.76  30.0  3
 WZV  Var_05    H271  C27  O26  C18   59.33  30.0  2
 WZV  Var_06    O26   C27  C28  F30   60.28  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
 WZV  chir_01  C1  C2  C11  N6  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
 WZV  plan-1  O26   0.020
 WZV  plan-1  C18   0.020
 WZV  plan-1  C23   0.020
 WZV  plan-1  N22   0.020
 WZV  plan-1  C19   0.020
 WZV  plan-1  C20   0.020
 WZV  plan-1  C21   0.020
 WZV  plan-1  C24   0.020
 WZV  plan-1  H23   0.020
 WZV  plan-1  H19   0.020
 WZV  plan-1  H20   0.020
 WZV  plan-2  N13   0.020
 WZV  plan-2  C7    0.020
 WZV  plan-2  C12   0.020
 WZV  plan-2  C8    0.020
 WZV  plan-2  C9    0.020
 WZV  plan-2  C10   0.020
 WZV  plan-2  C11   0.020
 WZV  plan-2  C1    0.020
 WZV  plan-2  H12   0.020
 WZV  plan-2  H8    0.020
 WZV  plan-2  H9    0.020
 WZV  plan-2  H10   0.020
 WZV  plan-3  C21   0.020
 WZV  plan-3  C24   0.020
 WZV  plan-3  O25   0.020
 WZV  plan-3  N13   0.020
 WZV  plan-3  C7    0.020
 WZV  plan-3  H13   0.020
 WZV  plan-4  C1    0.020
 WZV  plan-4  C2    0.020
 WZV  plan-4  C3    0.020
 WZV  plan-4  O16   0.020
 WZV  plan-4  N6    0.020
 WZV  plan-4  C5    0.020
 WZV  plan-4  N15   0.020
 WZV  plan-4  N4    0.020
 WZV  plan-4  C17   0.020
 WZV  plan-4  H151  0.020
 WZV  plan-4  H152  0.020

