# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 06:00:24 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: (6R)-2-amino-6-[2-(3'-methoxybiphenyl-3-yl)ethyl]-3,6-dimethyl-5,6-dihydropyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(c1)c2cccc(CC[C@]3(C)CC(=O)N(C)C(=N3)N)c2
#
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
 C27  C27  (6R)-2-amino-6-[2-(3'-methoxybiphenyl-3-yl)ethyl]-3,6-dimethyl-5,6-dihydropyrimidin-4(3H)-one  ligand  51  26  .  2021-08-07  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_C27
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
 C27  C1    C  CH3   0  -0.437   7.7370  -1.2642   1.1776
 C27  O2    O  O2    0  -0.473   6.6300  -0.3873   1.2397
 C27  C3    C  CR6   0   0.405   5.5590  -0.6486   0.4660
 C27  C4    C  CR16  0  -0.395   5.4716  -1.7214  -0.4176
 C27  C5    C  CR16  0  -0.227   4.3060  -1.8962  -1.1554
 C27  C6    C  CR16  0  -0.334   3.2368  -1.0282  -1.0284
 C27  C7    C  CR6   0   0.101   3.3204   0.0528  -0.1452
 C27  C8    C  CR16  0  -0.412   4.4834   0.2316   0.5943
 C27  C9    C  CR6   0   0.108   2.1867   0.9897   0.0041
 C27  C10   C  CR16  0  -0.329   2.3997   2.3598   0.1603
 C27  C11   C  CR16  0  -0.224   1.3228   3.2227   0.2959
 C27  C12   C  CR16  0  -0.327   0.0240   2.7324   0.2828
 C27  C13   C  CR6   0   0.179  -0.2139   1.3688   0.1347
 C27  C14   C  CH2   0  -0.546  -1.6137   0.8211   0.0951
 C27  C15   C  CH2   0  -0.373  -2.1328   0.7412  -1.3408
 C27  C16   C  CT    0   0.026  -3.5131   0.0871  -1.5430
 C27  C17   C  CH3   0  -0.637  -3.8317   0.1420  -3.0371
 C27  C18   C  CH2   0  -0.578  -4.6176   0.8279  -0.7881
 C27  C19   C  C     0   0.547  -4.7065   0.4859   0.6698
 C27  O20   O  O     0  -0.460  -5.0975   1.2763   1.5074
 C27  N21   N  NT    0  -0.534  -4.3860  -0.8102   0.9836
 C27  C22   C  CH3   0  -0.575  -4.5699  -1.2884   2.3454
 C27  C23   C  C     0   0.609  -3.8628  -1.6650  -0.0038
 C27  N24   N  N     0  -0.447  -3.4520  -1.3035  -1.1516
 C27  N25   N  NH2   0  -0.839  -3.8591  -2.9911   0.3333
 C27  C26   C  CR16  0  -0.379   0.8756   0.5153  -0.0069
 C27  H1C1  H  HCH3  0   0.260   8.4690  -0.8901   1.8891
 C27  H1C2  H  HCH3  0   0.228   7.4648  -2.2857   1.4561
 C27  H1C3  H  HCH3  0   0.228   8.1908  -1.2802   0.1833
 C27  H4    H  HCR6  0   0.279   6.2846  -2.4227  -0.5454
 C27  H8    H  HCR6  0   0.258   4.5606   1.0481   1.3026
 C27  H5    H  HCR6  0   0.260   4.2435  -2.7268  -1.8463
 C27  H6    H  HCR6  0   0.250   2.3468  -1.1761  -1.6265
 C27  H10   H  HCR6  0   0.252   3.4078   2.7554   0.1577
 C27  H26   H  HCR6  0   0.244   0.6988  -0.5503  -0.1051
 C27  H11   H  HCR6  0   0.255   1.4973   4.2850   0.4085
 C27  H12   H  HCR6  0   0.247  -0.8118   3.4138   0.3912
 C27  H141  H  HCH2  0   0.246  -1.6149  -0.1736   0.5467
 C27  H142  H  HCH2  0   0.246  -2.2610   1.4566   0.7043
 C27  H151  H  HCH2  0   0.227  -2.1662   1.7504  -1.7635
 C27  H152  H  HCH2  0   0.234  -1.4122   0.1768  -1.9403
 C27  H171  H  HCH3  0   0.230  -3.0613  -0.3699  -3.6155
 C27  H172  H  HCH3  0   0.229  -4.7885  -0.3394  -3.2452
 C27  H173  H  HCH3  0   0.221  -3.8892   1.1745  -3.3865
 C27  H181  H  HCH2  0   0.274  -4.5271   1.9096  -0.8932
 C27  H182  H  HCH2  0   0.288  -5.5888   0.5508  -1.2169
 C27  H221  H  HCH3  0   0.281  -4.9790  -0.4867   2.9487
 C27  H222  H  HCH3  0   0.260  -5.2661  -2.1252   2.3743
 C27  H223  H  HCH3  0   0.259  -3.6209  -1.5935   2.7871
 C27  H251  H  HNH2  0   0.406  -3.7160  -3.2520   1.2949
 C27  H252  H  HNH2  0   0.389  -3.3203  -3.5571  -0.3029

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
 C27  C1   O2    single    1.414  0.020  1.414
 C27  O2   C3    single    1.347  0.020  1.347
 C27  C3   C4    aromatic  1.393  0.020  1.393
 C27  C3   C8    aromatic  1.396  0.020  1.396
 C27  C4   C5    aromatic  1.391  0.020  1.391
 C27  C5   C6    aromatic  1.383  0.020  1.383
 C27  C6   C7    aromatic  1.398  0.020  1.398
 C27  C7   C8    aromatic  1.390  0.020  1.390
 C27  C7   C9    single    1.478  0.020  1.478
 C27  C9   C10   aromatic  1.395  0.020  1.395
 C27  C9   C26   aromatic  1.394  0.020  1.394
 C27  C10  C11   aromatic  1.387  0.020  1.387
 C27  C11  C12   aromatic  1.388  0.020  1.388
 C27  C12  C13   aromatic  1.392  0.020  1.392
 C27  C13  C14   single    1.504  0.020  1.504
 C27  C13  C26   aromatic  1.391  0.020  1.391
 C27  C14  C15   single    1.529  0.020  1.529
 C27  C15  C16   single    1.541  0.020  1.541
 C27  C16  C17   single    1.529  0.020  1.529
 C27  C16  C18   single    1.529  0.020  1.529
 C27  C16  N24   single    1.446  0.020  1.446
 C27  C18  C19   single    1.500  0.020  1.500
 C27  C19  O20   double    1.216  0.020  1.216
 C27  C19  N21   single    1.372  0.020  1.372
 C27  N21  C22   single    1.455  0.020  1.455
 C27  N21  C23   single    1.407  0.020  1.407
 C27  C23  N24   double    1.272  0.020  1.272
 C27  C23  N25   single    1.368  0.020  1.368
 C27  C1   H1C1  single    0.970  0.020  1.090
 C27  C1   H1C2  single    0.970  0.020  1.090
 C27  C1   H1C3  single    0.970  0.020  1.090
 C27  C4   H4    single    0.930  0.020  1.080
 C27  C8   H8    single    0.930  0.020  1.080
 C27  C5   H5    single    0.930  0.020  1.080
 C27  C6   H6    single    0.930  0.020  1.080
 C27  C10  H10   single    0.930  0.020  1.080
 C27  C26  H26   single    0.930  0.020  1.080
 C27  C11  H11   single    0.930  0.020  1.080
 C27  C12  H12   single    0.930  0.020  1.080
 C27  C14  H141  single    0.970  0.020  1.090
 C27  C14  H142  single    0.970  0.020  1.090
 C27  C15  H151  single    0.970  0.020  1.090
 C27  C15  H152  single    0.970  0.020  1.090
 C27  C17  H171  single    0.970  0.020  1.090
 C27  C17  H172  single    0.970  0.020  1.090
 C27  C17  H173  single    0.970  0.020  1.090
 C27  C18  H181  single    0.970  0.020  1.090
 C27  C18  H182  single    0.970  0.020  1.090
 C27  C22  H221  single    0.970  0.020  1.090
 C27  C22  H222  single    0.970  0.020  1.090
 C27  C22  H223  single    0.970  0.020  1.090
 C27  N25  H251  single    0.890  0.020  1.040
 C27  N25  H252  single    0.890  0.020  1.040

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
 C27  H1C3  C1   H1C2  108.75  3.000
 C27  H1C3  C1   H1C1  108.71  3.000
 C27  H1C2  C1   H1C1  108.81  3.000
 C27  H1C3  C1   O2    111.97  3.000
 C27  H1C2  C1   O2    111.93  3.000
 C27  H1C1  C1   O2    106.56  3.000
 C27  C3    O2   C1    118.50  3.000
 C27  C8    C3   C4    119.72  3.000
 C27  C8    C3   O2    115.95  3.000
 C27  C4    C3   O2    124.32  3.000
 C27  H4    C4   C5    119.08  3.000
 C27  H4    C4   C3    121.83  3.000
 C27  C5    C4   C3    119.09  3.000
 C27  H5    C5   C6    119.72  3.000
 C27  H5    C5   C4    118.92  3.000
 C27  C6    C5   C4    121.36  3.000
 C27  H6    C6   C7    120.25  3.000
 C27  H6    C6   C5    119.94  3.000
 C27  C7    C6   C5    119.80  3.000
 C27  C9    C7   C8    120.43  3.000
 C27  C9    C7   C6    120.52  3.000
 C27  C8    C7   C6    119.05  3.000
 C27  H8    C8   C7    120.29  3.000
 C27  H8    C8   C3    118.71  3.000
 C27  C7    C8   C3    120.98  3.000
 C27  C26   C9   C10   118.58  3.000
 C27  C26   C9   C7    120.31  3.000
 C27  C10   C9   C7    121.10  3.000
 C27  H10   C10  C11   119.73  3.000
 C27  H10   C10  C9    120.03  3.000
 C27  C11   C10  C9    120.23  3.000
 C27  H11   C11  C12   119.89  3.000
 C27  H11   C11  C10   119.72  3.000
 C27  C12   C11  C10   120.39  3.000
 C27  H12   C12  C13   119.65  3.000
 C27  H12   C12  C11   119.90  3.000
 C27  C13   C12  C11   120.45  3.000
 C27  C26   C13  C14   120.19  3.000
 C27  C26   C13  C12   118.55  3.000
 C27  C14   C13  C12   121.24  3.000
 C27  H142  C14  H141  107.36  3.000
 C27  H142  C14  C15   110.66  3.000
 C27  H141  C14  C15   109.90  3.000
 C27  H142  C14  C13   108.96  3.000
 C27  H141  C14  C13   108.77  3.000
 C27  C15   C14  C13   111.09  3.000
 C27  H152  C15  H151  106.50  3.000
 C27  H152  C15  C16   107.40  3.000
 C27  H151  C15  C16   108.27  3.000
 C27  H152  C15  C14   108.54  3.000
 C27  H151  C15  C14   108.95  3.000
 C27  C16   C15  C14   116.72  3.000
 C27  N24   C16  C18   111.27  3.000
 C27  N24   C16  C17   107.93  3.000
 C27  C18   C16  C17   108.33  3.000
 C27  N24   C16  C15   109.57  3.000
 C27  C18   C16  C15   112.13  3.000
 C27  C17   C16  C15   107.44  3.000
 C27  H173  C17  H172  108.07  3.000
 C27  H173  C17  H171  108.14  3.000
 C27  H172  C17  H171  108.13  3.000
 C27  H173  C17  C16   110.96  3.000
 C27  H172  C17  C16   110.69  3.000
 C27  H171  C17  C16   110.74  3.000
 C27  H182  C18  H181  106.63  3.000
 C27  H182  C18  C19   105.65  3.000
 C27  H181  C18  C19   108.95  3.000
 C27  H182  C18  C16   108.91  3.000
 C27  H181  C18  C16   111.90  3.000
 C27  C19   C18  C16   114.34  3.000
 C27  N21   C19  O20   122.12  3.000
 C27  N21   C19  C18   115.08  3.000
 C27  O20   C19  C18   122.70  3.000
 C27  C23   N21  C22   120.28  3.000
 C27  C23   N21  C19   120.03  3.000
 C27  C22   N21  C19   119.69  3.000
 C27  H223  C22  H222  109.31  3.000
 C27  H223  C22  H221  108.07  3.000
 C27  H222  C22  H221  108.20  3.000
 C27  H223  C22  N21   111.17  3.000
 C27  H222  C22  N21   110.99  3.000
 C27  H221  C22  N21   109.00  3.000
 C27  N25   C23  N24   119.81  3.000
 C27  N25   C23  N21   114.64  3.000
 C27  N24   C23  N21   125.51  3.000
 C27  C23   N24  C16   120.28  3.000
 C27  H252  N25  H251  112.43  3.000
 C27  H252  N25  C23   112.97  3.000
 C27  H251  N25  C23   119.14  3.000
 C27  H26   C26  C13   118.97  3.000
 C27  H26   C26  C9    119.22  3.000
 C27  C13   C26  C9    121.80  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
 C27  CONST_01  C6    C5   C4   C3      0.00   0.0  0
 C27  CONST_02  C6    C7   C8   C3      0.00   0.0  0
 C27  CONST_03  C9    C7   C8   C3    180.00   0.0  0
 C27  CONST_04  C7    C8   C3   C4      0.00   0.0  0
 C27  CONST_05  C7    C6   C5   C4      0.00   0.0  0
 C27  CONST_06  C8    C3   C4   C5      0.00   0.0  0
 C27  CONST_07  C8    C7   C6   C5      0.00   0.0  0
 C27  CONST_08  C9    C7   C6   C5    180.00   0.0  0
 C27  CONST_11  C11   C10  C9   C7    180.00   0.0  0
 C27  CONST_12  C13   C26  C9   C7    180.00   0.0  0
 C27  CONST_15  C12   C11  C10  C9      0.00   0.0  0
 C27  CONST_16  C12   C13  C26  C9      0.00   0.0  0
 C27  CONST_17  C13   C26  C9   C10     0.00   0.0  0
 C27  CONST_18  C13   C12  C11  C10     0.00   0.0  0
 C27  CONST_19  C26   C9   C10  C11     0.00   0.0  0
 C27  CONST_20  C26   C13  C12  C11     0.00   0.0  0
 C27  CONST_21  N21   C23  N24  C16     0.00   0.0  0
 C27  CONST_22  C23   N21  C19  C18     0.00   0.0  0
 C27  CONST_23  N24   C23  N21  C19     0.00   0.0  0
 C27  CONST_24  C5    C4   C3   O2    180.00   0.0  0
 C27  CONST_25  C7    C8   C3   O2    180.00   0.0  0
 C27  CONST_26  C14   C13  C26  C9    180.00   0.0  0
 C27  CONST_27  C14   C13  C12  C11   180.00   0.0  0
 C27  CONST_28  N25   C23  N24  C16   180.00   0.0  0
 C27  CONST_29  C22   N21  C19  C18   180.00   0.0  0
 C27  CONST_30  N25   C23  N21  C19   180.00   0.0  0
 C27  CONST_31  C23   N21  C19  O20   180.00   0.0  0
 C27  CONST_32  N24   C23  N21  C22   180.00   0.0  0
 C27  CONST_33  H5    C5   C4   C3    180.00   0.0  0
 C27  CONST_34  H8    C8   C3   C4    180.00   0.0  0
 C27  CONST_35  H6    C6   C5   C4    180.00   0.0  0
 C27  CONST_36  H4    C4   C5   C6    180.00   0.0  0
 C27  CONST_37  H10   C10  C9   C7      0.00   0.0  0
 C27  CONST_38  H26   C26  C9   C7      0.00   0.0  0
 C27  CONST_39  H11   C11  C10  C9    180.00   0.0  0
 C27  CONST_40  H12   C12  C11  C10   180.00   0.0  0
 C27  CONST_41  C22   N21  C19  O20     0.00   0.0  0
 C27  CONST_42  N25   C23  N21  C22     0.00   0.0  0
 C27  CONST_44  H252  N25  C23  N21   180.00   0.0  0
 C27  Var_01    H181  C18  C19  N21  -159.49  30.0  1
 C27  Var_02    C4    C3   O2   C1     -1.11  30.0  2
 C27  Var_03    C15   C14  C13  C12    91.61  30.0  2
 C27  Var_04    C16   C15  C14  C13   175.04  30.0  3
 C27  Var_05    H221  C22  N21  C19     0.92  30.0  3
 C27  Var_06    H1C1  C1   O2   C3   -178.56  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
 C27  chir_01  C16  C17  C18  N24  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
 C27  plan-1  O2    0.020
 C27  plan-1  C3    0.020
 C27  plan-1  C4    0.020
 C27  plan-1  C5    0.020
 C27  plan-1  C6    0.020
 C27  plan-1  C7    0.020
 C27  plan-1  C8    0.020
 C27  plan-1  C9    0.020
 C27  plan-1  H4    0.020
 C27  plan-1  H8    0.020
 C27  plan-1  H5    0.020
 C27  plan-1  H6    0.020
 C27  plan-2  C7    0.020
 C27  plan-2  C9    0.020
 C27  plan-2  C10   0.020
 C27  plan-2  C11   0.020
 C27  plan-2  C12   0.020
 C27  plan-2  C13   0.020
 C27  plan-2  C14   0.020
 C27  plan-2  C26   0.020
 C27  plan-2  H10   0.020
 C27  plan-2  H26   0.020
 C27  plan-2  H11   0.020
 C27  plan-2  H12   0.020
 C27  plan-3  C16   0.020
 C27  plan-3  C18   0.020
 C27  plan-3  C19   0.020
 C27  plan-3  O20   0.020
 C27  plan-3  N21   0.020
 C27  plan-3  C22   0.020
 C27  plan-3  C23   0.020
 C27  plan-3  N24   0.020
 C27  plan-3  N25   0.020
 C27  plan-3  H251  0.020
 C27  plan-3  H252  0.020

