# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 04:05:04 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 2-amino-6-(2-phenylethyl)pyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=CC(=O)N1)CCc2ccccc2
#
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
 V15  V15  2-amino-6-(2-phenylethyl)pyrimidin-4(3H)-one  ligand  29  16  .  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_V15
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
 V15  N1    N  NR16  0  -0.706  -3.8368  -0.0552   0.0905
 V15  C2    C  CR6   0   0.686  -3.0310  -1.1457   0.1076
 V15  C3    C  CR6   0   0.550  -3.3897   1.2334  -0.1901
 V15  C4    C  CR16  0  -0.534  -1.9883   1.2925  -0.4578
 V15  C5    C  CR6   0   0.313  -1.2399   0.1492  -0.4175
 V15  N6    N  N     0  -0.513  -1.7444  -1.0719  -0.1355
 V15  C8    C  CR16  0  -0.310   3.2407   1.1057   0.4436
 V15  C9    C  CR16  0  -0.240   4.6006   1.1285   0.1632
 V15  C10   C  CR16  0  -0.273   5.2557  -0.0386  -0.2083
 V15  C11   C  CR16  0  -0.240   4.5412  -1.2265  -0.2964
 V15  C12   C  CR16  0  -0.309   3.1815  -1.2437  -0.0151
 V15  N14   N  NH2   0  -0.828  -3.5935  -2.3267   0.3698
 V15  C15   C  CH2   0  -0.491   0.2377   0.1846  -0.6641
 V15  C7    C  CR6   0   0.129   2.5136  -0.0797   0.3594
 V15  C16   C  CH2   0  -0.510   1.0333  -0.0962   0.6187
 V15  O15   O  O     0  -0.500  -4.1853   2.1645  -0.1864
 V15  H1    H  HNR6  0   0.420  -4.8247  -0.1635   0.2820
 V15  H141  H  HNH2  0   0.417  -4.5631  -2.4202   0.6167
 V15  H142  H  HNH2  0   0.414  -3.0081  -3.1412   0.4366
 V15  H4    H  HCR6  0   0.260  -1.5418   2.2483  -0.6920
 V15  H151  H  HCH2  0   0.256   0.4892  -0.5692  -1.4150
 V15  H152  H  HCH2  0   0.254   0.5264   1.1565  -1.0678
 V15  H9    H  HCR6  0   0.253   5.1502   2.0584   0.2375
 V15  H10   H  HCR6  0   0.253   6.3165  -0.0230  -0.4227
 V15  H11   H  HCR6  0   0.253   5.0434  -2.1424  -0.5810
 V15  H12   H  HCR6  0   0.246   2.6306  -2.1751  -0.0821
 V15  H161  H  HCH2  0   0.252   0.7779   0.6554   1.3697
 V15  H162  H  HCH2  0   0.252   0.7353  -1.0667   1.0205
 V15  H8    H  HCR6  0   0.246   2.7385   2.0205   0.7372

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
 V15  N1   C2    single    1.356  0.020  1.356
 V15  N1   C3    single    1.393  0.020  1.393
 V15  N1   H1    single    0.860  0.020  1.020
 V15  C2   N6    double    1.311  0.020  1.311
 V15  C2   N14   single    1.334  0.020  1.334
 V15  C3   C4    single    1.428  0.020  1.428
 V15  C3   O15   double    1.225  0.020  1.225
 V15  C4   C5    double    1.367  0.020  1.367
 V15  C4   H4    single    0.930  0.020  1.080
 V15  C5   N6    single    1.351  0.020  1.351
 V15  C5   C15   single    1.498  0.020  1.498
 V15  C8   C9    aromatic  1.389  0.020  1.389
 V15  C8   C7    aromatic  1.393  0.020  1.393
 V15  C8   H8    single    0.930  0.020  1.080
 V15  C9   C10   aromatic  1.389  0.020  1.389
 V15  C9   H9    single    0.930  0.020  1.080
 V15  C10  C11   aromatic  1.389  0.020  1.389
 V15  C10  H10   single    0.930  0.020  1.080
 V15  C11  C12   aromatic  1.389  0.020  1.389
 V15  C11  H11   single    0.930  0.020  1.080
 V15  C12  C7    aromatic  1.393  0.020  1.393
 V15  C12  H12   single    0.930  0.020  1.080
 V15  N14  H141  single    0.860  0.020  1.020
 V15  N14  H142  single    0.860  0.020  1.020
 V15  C15  C16   single    1.535  0.020  1.535
 V15  C15  H151  single    0.970  0.020  1.090
 V15  C15  H152  single    0.970  0.020  1.090
 V15  C7   C16   single    1.503  0.020  1.503
 V15  C16  H161  single    0.970  0.020  1.090
 V15  C16  H162  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
 V15  H1    N1   C3    116.78  3.000
 V15  H1    N1   C2    119.45  3.000
 V15  C3    N1   C2    123.77  3.000
 V15  N14   C2   N6    119.99  3.000
 V15  N14   C2   N1    117.64  3.000
 V15  N6    C2   N1    122.37  3.000
 V15  O15   C3   C4    127.35  3.000
 V15  O15   C3   N1    119.62  3.000
 V15  C4    C3   N1    113.03  3.000
 V15  H4    C4   C5    121.32  3.000
 V15  H4    C4   C3    118.86  3.000
 V15  C5    C4   C3    119.81  3.000
 V15  C15   C5   N6    115.09  3.000
 V15  C15   C5   C4    121.01  3.000
 V15  N6    C5   C4    123.89  3.000
 V15  C5    N6   C2    117.12  3.000
 V15  H8    C8   C7    119.51  3.000
 V15  H8    C8   C9    119.63  3.000
 V15  C7    C8   C9    120.85  3.000
 V15  H9    C9   C10   120.04  3.000
 V15  H9    C9   C8    119.82  3.000
 V15  C10   C9   C8    120.14  3.000
 V15  H10   C10  C11   120.26  3.000
 V15  H10   C10  C9    120.20  3.000
 V15  C11   C10  C9    119.54  3.000
 V15  H11   C11  C12   119.81  3.000
 V15  H11   C11  C10   120.10  3.000
 V15  C12   C11  C10   120.09  3.000
 V15  H12   C12  C7    119.38  3.000
 V15  H12   C12  C11   119.71  3.000
 V15  C7    C12  C11   120.91  3.000
 V15  H142  N14  H141  118.04  3.000
 V15  H142  N14  C2    119.01  3.000
 V15  H141  N14  C2    122.51  3.000
 V15  H152  C15  H151  107.40  3.000
 V15  H152  C15  C16   109.56  3.000
 V15  H151  C15  C16   109.18  3.000
 V15  H152  C15  C5    110.05  3.000
 V15  H151  C15  C5    108.88  3.000
 V15  C16   C15  C5    111.66  3.000
 V15  C16   C7   C12   120.63  3.000
 V15  C16   C7   C8    120.86  3.000
 V15  C12   C7   C8    118.48  3.000
 V15  H162  C16  H161  107.14  3.000
 V15  H162  C16  C7    110.01  3.000
 V15  H161  C16  C7    109.96  3.000
 V15  H162  C16  C15   109.18  3.000
 V15  H161  C16  C15   109.10  3.000
 V15  C7    C16  C15   111.36  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
 V15  CONST_01  C11   C10  C9   C8     0.00   0.0  0
 V15  CONST_02  C11   C12  C7   C8     0.00   0.0  0
 V15  CONST_03  C12   C7   C8   C9     0.00   0.0  0
 V15  CONST_04  C12   C11  C10  C9     0.00   0.0  0
 V15  CONST_05  C7    C8   C9   C10    0.00   0.0  0
 V15  CONST_06  C7    C12  C11  C10    0.00   0.0  0
 V15  CONST_07  C5    N6   C2   N1     0.00   0.0  0
 V15  CONST_08  C4    C3   N1   C2     0.00   0.0  0
 V15  CONST_09  N6    C2   N1   C3     0.00   0.0  0
 V15  CONST_10  C16   C7   C8   C9   180.00   0.0  0
 V15  CONST_11  C16   C7   C12  C11  180.00   0.0  0
 V15  CONST_12  O15   C3   N1   C2   180.00   0.0  0
 V15  CONST_13  N14   C2   N1   C3   180.00   0.0  0
 V15  CONST_14  N14   C2   N6   C5   180.00   0.0  0
 V15  CONST_15  H10   C10  C9   C8   180.00   0.0  0
 V15  CONST_16  H12   C12  C7   C8   180.00   0.0  0
 V15  CONST_17  H11   C11  C10  C9   180.00   0.0  0
 V15  CONST_18  H8    C8   C9   C10  180.00   0.0  0
 V15  CONST_19  H9    C9   C10  C11  180.00   0.0  0
 V15  CONST_20  H1    N1   C3   C4   180.00   0.0  0
 V15  CONST_21  H141  N14  C2   N1     0.00   0.0  0
 V15  CONST_22  H142  N14  C2   N1   180.00   0.0  0
 V15  Var_01    C16   C15  C5   C4   109.90  30.0  3
 V15  Var_02    C7    C16  C15  C5   179.13  30.0  3
 V15  Var_03    C15   C16  C7   C8    88.46  30.0  2

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
 V15  plan-1  N1    0.020
 V15  plan-1  C2    0.020
 V15  plan-1  C3    0.020
 V15  plan-1  C4    0.020
 V15  plan-1  C5    0.020
 V15  plan-1  N6    0.020
 V15  plan-1  N14   0.020
 V15  plan-1  C15   0.020
 V15  plan-1  O15   0.020
 V15  plan-1  H1    0.020
 V15  plan-1  H141  0.020
 V15  plan-1  H142  0.020
 V15  plan-1  H4    0.020
 V15  plan-2  C8    0.020
 V15  plan-2  C9    0.020
 V15  plan-2  C10   0.020
 V15  plan-2  C11   0.020
 V15  plan-2  C12   0.020
 V15  plan-2  C7    0.020
 V15  plan-2  C16   0.020
 V15  plan-2  H9    0.020
 V15  plan-2  H10   0.020
 V15  plan-2  H11   0.020
 V15  plan-2  H12   0.020
 V15  plan-2  H8    0.020

