# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 18:22:46 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: 4-methyl-7,8-dihydro-5H-thiopyrano[4,3-d]pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc(N)nc2CCSCc12
#
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
 MO8  MO8  4-methyl-7,8-dihydro-5H-thiopyrano[4,3-d]pyrimidin-2-amine  ligand  23  12  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MO8
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
 MO8  N11   N  NH2   0  -0.826   3.5466  -1.1477  -0.2168
 MO8  C9    C  CR6   0   0.518   2.3170  -0.5988  -0.0875
 MO8  N8    N  N     0  -0.474   2.2529   0.7333  -0.0059
 MO8  C7    C  CR6   0   0.276   1.0477   1.2749   0.0561
 MO8  C12   C  CH3   0  -0.754   0.9824   2.7667   0.1562
 MO8  C2    C  CR6   0  -0.033  -0.1239   0.5038   0.0312
 MO8  N10   N  N     0  -0.484   1.2736  -1.4203  -0.0763
 MO8  C3    C  CR6   0   0.283   0.0618  -0.8754  -0.0122
 MO8  C4    C  CH2   0  -0.484  -1.0671  -1.8702  -0.0014
 MO8  C5    C  CH2   0  -0.585  -2.4021  -1.3184   0.4544
 MO8  S6    S  S2    0  -0.011  -2.8336   0.1596  -0.4941
 MO8  C1    C  CH2   0  -0.655  -1.4646   1.1823   0.0958
 MO8  HN11  H  HNH2  0   0.391   4.3440  -0.5805   0.0136
 MO8  HN1A  H  HNH2  0   0.390   3.6426  -2.1360  -0.0588
 MO8  H12   H  HCH3  0   0.260   0.4962   3.1970  -0.7218
 MO8  H12A  H  HCH3  0   0.256   0.4011   3.0809   1.0251
 MO8  H12B  H  HCH3  0   0.261   1.9819   3.1870   0.2359
 MO8  H4    H  HCH2  0   0.268  -1.1660  -2.2815  -1.0100
 MO8  H4A   H  HCH2  0   0.265  -0.7725  -2.7047   0.6400
 MO8  H5    H  HCH2  0   0.292  -3.1935  -2.0503   0.2966
 MO8  H5A   H  HCH2  0   0.274  -2.3900  -1.0701   1.5176
 MO8  H1    H  HCH2  0   0.283  -1.6823   1.5151   1.1149
 MO8  H1A   H  HCH2  0   0.289  -1.4714   2.0737  -0.5340

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
 MO8  N11  C9    single    1.353  0.020  1.353
 MO8  N11  HN11  single    0.890  0.020  1.040
 MO8  N11  HN1A  single    0.890  0.020  1.040
 MO8  N10  C9    aromatic  1.328  0.020  1.328
 MO8  C9   N8    aromatic  1.336  0.020  1.336
 MO8  N8   C7    aromatic  1.323  0.020  1.323
 MO8  C2   C7    aromatic  1.403  0.020  1.403
 MO8  C7   C12   single    1.497  0.020  1.497
 MO8  C12  H12   single    0.970  0.020  1.090
 MO8  C12  H12A  single    0.970  0.020  1.090
 MO8  C12  H12B  single    0.970  0.020  1.090
 MO8  C3   C2    aromatic  1.392  0.020  1.392
 MO8  C2   C1    single    1.504  0.020  1.504
 MO8  N10  C3    aromatic  1.330  0.020  1.330
 MO8  C4   C3    single    1.505  0.020  1.505
 MO8  C5   C4    single    1.515  0.020  1.515
 MO8  C4   H4    single    0.970  0.020  1.090
 MO8  C4   H4A   single    0.970  0.020  1.090
 MO8  C5   S6    single    1.808  0.020  1.808
 MO8  C5   H5    single    0.970  0.020  1.090
 MO8  C5   H5A   single    0.970  0.020  1.090
 MO8  S6   C1    single    1.808  0.020  1.808
 MO8  C1   H1    single    0.970  0.020  1.090
 MO8  C1   H1A   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
 MO8  HN1A  N11  HN11  116.28  3.000
 MO8  HN1A  N11  C9    118.08  3.000
 MO8  HN11  N11  C9    118.04  3.000
 MO8  N10   C9   N8    125.35  3.000
 MO8  N8    C9   N11   117.00  3.000
 MO8  N10   C9   N11   117.64  3.000
 MO8  C7    N8   C9    117.05  3.000
 MO8  C2    C7   C12   120.84  3.000
 MO8  C12   C7   N8    116.81  3.000
 MO8  C2    C7   N8    122.35  3.000
 MO8  H12B  C12  H12A  108.66  3.000
 MO8  H12B  C12  H12   108.42  3.000
 MO8  H12A  C12  H12   106.83  3.000
 MO8  H12B  C12  C7    110.50  3.000
 MO8  H12A  C12  C7    111.31  3.000
 MO8  H12   C12  C7    111.01  3.000
 MO8  C1    C2   C3    124.55  3.000
 MO8  C1    C2   C7    119.72  3.000
 MO8  C3    C2   C7    115.70  3.000
 MO8  C3    N10  C9    117.57  3.000
 MO8  C4    C3   N10   114.40  3.000
 MO8  C4    C3   C2    123.69  3.000
 MO8  N10   C3   C2    121.92  3.000
 MO8  H4A   C4   H4    106.17  3.000
 MO8  H4A   C4   C5    109.82  3.000
 MO8  H4    C4   C5    109.56  3.000
 MO8  H4A   C4   C3    107.86  3.000
 MO8  H4    C4   C3    108.05  3.000
 MO8  C5    C4   C3    114.99  3.000
 MO8  H5A   C5   H5    107.58  3.000
 MO8  H5A   C5   S6    109.12  3.000
 MO8  H5    C5   S6    107.45  3.000
 MO8  H5A   C5   C4    111.47  3.000
 MO8  H5    C5   C4    110.60  3.000
 MO8  S6    C5   C4    110.50  3.000
 MO8  C1    S6   C5     96.35  3.000
 MO8  H1A   C1   H1    106.72  3.000
 MO8  H1A   C1   S6    105.61  3.000
 MO8  H1    C1   S6    108.99  3.000
 MO8  H1A   C1   C2    110.44  3.000
 MO8  H1    C1   C2    110.77  3.000
 MO8  S6    C1   C2    113.94  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
 MO8  CONST_01  C2    C3   N10  C9     0.00   0.0  0
 MO8  CONST_02  C2    C7   N8   C9     0.00   0.0  0
 MO8  CONST_03  C3    N10  C9   N8     0.00   0.0  0
 MO8  CONST_04  C3    C2   C7   N8     0.00   0.0  0
 MO8  CONST_05  N10   C9   N8   C7     0.00   0.0  0
 MO8  CONST_06  N10   C3   C2   C7     0.00   0.0  0
 MO8  CONST_07  C3    N10  C9   N11  180.00   0.0  0
 MO8  CONST_08  C7    N8   C9   N11  180.00   0.0  0
 MO8  CONST_09  C12   C7   N8   C9   180.00   0.0  0
 MO8  CONST_10  C3    C2   C7   C12  180.00   0.0  0
 MO8  CONST_11  C1    C2   C7   C12    0.00   0.0  0
 MO8  CONST_13  HN1A  N11  C9   N8   180.00   0.0  0
 MO8  Var_01    S6    C1   C2   C7   160.47  30.0  1
 MO8  Var_02    C5    C4   C3   C2   -16.77  30.0  1
 MO8  Var_03    S6    C5   C4   C3    52.82  30.0  1
 MO8  Var_04    H12   C12  C7   N8   116.18  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
 MO8  plan-1  N11   0.020
 MO8  plan-1  C9    0.020
 MO8  plan-1  HN11  0.020
 MO8  plan-1  HN1A  0.020
 MO8  plan-2  N11   0.020
 MO8  plan-2  C9    0.020
 MO8  plan-2  N8    0.020
 MO8  plan-2  C7    0.020
 MO8  plan-2  C12   0.020
 MO8  plan-2  C2    0.020
 MO8  plan-2  N10   0.020
 MO8  plan-2  C3    0.020
 MO8  plan-2  C4    0.020
 MO8  plan-2  C1    0.020

