# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 19:07:49 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: 3-(2-methoxyethyl)-2-thioxo-1,2,3,7-tetrahydro-6H-purin-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCN1C(=S)NC(=O)c2[nH]cnc12
#
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
 PVW  PVW  3-(2-methoxyethyl)-2-thioxo-1,2,3,7-tetrahydro-6H-purin-6-one  ligand  25  15  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PVW
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
 PVW  C1    C  CH3   0  -0.395  -3.2078  -1.3468   1.8479
 PVW  O2    O  O2    0  -0.472  -2.5788  -0.7347   0.7510
 PVW  C3    C  CH2   0  -0.146  -2.0732  -1.6628  -0.1665
 PVW  C4    C  CH2   0  -0.355  -1.3341  -0.9269  -1.2661
 PVW  N5    N  NR6   0  -0.527  -0.2697  -0.0786  -0.7381
 PVW  C6    C  CR56  0   0.443   0.8886  -0.6758  -0.3064
 PVW  C7    C  CR56  0   0.140   1.9172   0.0281   0.2668
 PVW  C8    C  CR6   0   0.535   1.8601   1.4372   0.4547
 PVW  O9    O  O     0  -0.448   2.6965   2.1682   0.9459
 PVW  N10   N  NR16  0  -0.695   0.6470   1.9255  -0.0274
 PVW  C11   C  CR6   0   0.392  -0.4019   1.2641  -0.6055
 PVW  S12   S  S1    0  -0.349  -1.7225   2.1446  -1.1192
 PVW  N13   N  NR15  0  -0.624   2.8708  -0.9102   0.5437
 PVW  C14   C  CR15  0   0.140   2.3834  -2.0875   0.1377
 PVW  N15   N  N     0  -0.462   1.1767  -1.9871  -0.3876
 PVW  H11C  H  HCH3  0   0.234  -3.5690  -0.5598   2.5088
 PVW  H12C  H  HCH3  0   0.205  -4.0631  -1.9622   1.5441
 PVW  H13C  H  HCH3  0   0.204  -2.5190  -1.9850   2.4143
 PVW  H31C  H  HCH2  0   0.213  -1.4033  -2.3802   0.3258
 PVW  H32C  H  HCH2  0   0.223  -2.8745  -2.2494  -0.6383
 PVW  HA1   H  HCH2  0   0.283  -0.8889  -1.6503  -1.9474
 PVW  HB2   H  HCH2  0   0.281  -2.0090  -0.2929  -1.8339
 PVW  H13   H  HNR5  0   0.440   3.7681  -0.7533   0.9779
 PVW  H10   H  HNR6  0   0.433   0.5140   2.9261   0.0515
 PVW  H14   H  HCR5  0   0.307   2.9386  -3.0061   0.2414

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
 PVW  C1   O2    single    1.405  0.020  1.405
 PVW  O2   C3    single    1.400  0.020  1.400
 PVW  C3   C4    single    1.516  0.020  1.516
 PVW  C4   N5    single    1.460  0.020  1.460
 PVW  N5   C6    single    1.373  0.020  1.373
 PVW  N5   C11   single    1.356  0.020  1.356
 PVW  C6   C7    aromatic  1.372  0.020  1.372
 PVW  C6   N15   aromatic  1.345  0.020  1.345
 PVW  C7   C8    single    1.423  0.020  1.423
 PVW  C7   N13   aromatic  1.366  0.020  1.366
 PVW  C8   O9    double    1.215  0.020  1.215
 PVW  C8   N10   single    1.394  0.020  1.394
 PVW  N10  C11   single    1.368  0.020  1.368
 PVW  C11  S12   double    1.668  0.020  1.668
 PVW  N13  C14   aromatic  1.337  0.020  1.337
 PVW  C14  N15   aromatic  1.320  0.020  1.320
 PVW  C1   H11C  single    0.970  0.020  1.090
 PVW  C1   H12C  single    0.970  0.020  1.090
 PVW  C1   H13C  single    0.970  0.020  1.090
 PVW  C3   H31C  single    0.970  0.020  1.090
 PVW  C3   H32C  single    0.970  0.020  1.090
 PVW  C4   HA1   single    0.970  0.020  1.090
 PVW  C4   HB2   single    0.970  0.020  1.090
 PVW  N13  H13   single    0.860  0.020  1.020
 PVW  N10  H10   single    0.860  0.020  1.020
 PVW  C14  H14   single    0.930  0.020  1.080

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
 PVW  H13C  C1   H12C  107.85  3.000
 PVW  H13C  C1   H11C  108.38  3.000
 PVW  H12C  C1   H11C  108.36  3.000
 PVW  H13C  C1   O2    112.06  3.000
 PVW  H12C  C1   O2    112.17  3.000
 PVW  H11C  C1   O2    107.90  3.000
 PVW  C3    O2   C1    112.62  3.000
 PVW  H32C  C3   H31C  106.77  3.000
 PVW  H32C  C3   C4    107.65  3.000
 PVW  H31C  C3   C4    110.18  3.000
 PVW  H32C  C3   O2    111.83  3.000
 PVW  H31C  C3   O2    111.08  3.000
 PVW  C4    C3   O2    109.26  3.000
 PVW  HB2   C4   HA1   108.35  3.000
 PVW  HB2   C4   N5    107.63  3.000
 PVW  HA1   C4   N5    108.31  3.000
 PVW  HB2   C4   C3    111.08  3.000
 PVW  HA1   C4   C3    109.31  3.000
 PVW  N5    C4   C3    112.04  3.000
 PVW  C11   N5   C6    118.85  3.000
 PVW  C11   N5   C4    122.66  3.000
 PVW  C6    N5   C4    118.43  3.000
 PVW  N15   C6   C7    111.39  3.000
 PVW  N15   C6   N5    125.87  3.000
 PVW  C7    C6   N5    122.73  3.000
 PVW  N13   C7   C8    132.96  3.000
 PVW  N13   C7   C6    104.81  3.000
 PVW  C8    C7   C6    122.22  3.000
 PVW  N10   C8   O9    121.90  3.000
 PVW  N10   C8   C7    109.65  3.000
 PVW  O9    C8   C7    128.45  3.000
 PVW  H10   N10  C11   114.20  3.000
 PVW  H10   N10  C8    115.70  3.000
 PVW  C11   N10  C8    130.10  3.000
 PVW  S12   C11  N10   118.81  3.000
 PVW  S12   C11  N5    124.74  3.000
 PVW  N10   C11  N5    116.44  3.000
 PVW  H13   N13  C14   126.27  3.000
 PVW  H13   N13  C7    126.95  3.000
 PVW  C14   N13  C7    106.78  3.000
 PVW  H14   C14  N15   125.02  3.000
 PVW  H14   C14  N13   122.22  3.000
 PVW  N15   C14  N13   112.76  3.000
 PVW  C14   N15  C6    104.24  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
 PVW  CONST_01  C14   N13  C7   C6      0.00   0.0  0
 PVW  CONST_02  N13   C14  N15  C6      0.00   0.0  0
 PVW  CONST_03  C14   N15  C6   C7      0.00   0.0  0
 PVW  CONST_04  N15   C14  N13  C7      0.00   0.0  0
 PVW  CONST_05  N15   C6   C7   N13     0.00   0.0  0
 PVW  CONST_06  C8    N10  C11  N5      0.00   0.0  0
 PVW  CONST_07  N10   C11  N5   C6      0.00   0.0  0
 PVW  CONST_08  C11   N10  C8   C7      0.00   0.0  0
 PVW  CONST_09  N10   C11  N5   C4    180.00   0.0  0
 PVW  CONST_10  S12   C11  N5   C6    180.00   0.0  0
 PVW  CONST_11  S12   C11  N10  C8    180.00   0.0  0
 PVW  CONST_12  C11   N10  C8   O9    180.00   0.0  0
 PVW  CONST_13  H13   N13  C7   C6    180.00   0.0  0
 PVW  CONST_14  H14   C14  N15  C6    180.00   0.0  0
 PVW  CONST_15  H10   N10  C11  N5    180.00   0.0  0
 PVW  CONST_16  S12   C11  N5   C4      0.00   0.0  0
 PVW  Var_01    C6    N5   C4   C3     75.32  30.0  3
 PVW  Var_02    N5    C4   C3   O2     56.51  30.0  3
 PVW  Var_03    C4    C3   O2   C1   -176.27  30.0  3
 PVW  Var_04    H11C  C1   O2   C3    179.94  30.0  3

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
 PVW  plan-1  C4   0.020
 PVW  plan-1  N5   0.020
 PVW  plan-1  C6   0.020
 PVW  plan-1  C7   0.020
 PVW  plan-1  C8   0.020
 PVW  plan-1  O9   0.020
 PVW  plan-1  N10  0.020
 PVW  plan-1  C11  0.020
 PVW  plan-1  S12  0.020
 PVW  plan-1  N13  0.020
 PVW  plan-1  C14  0.020
 PVW  plan-1  N15  0.020
 PVW  plan-1  H13  0.020
 PVW  plan-1  H10  0.020
 PVW  plan-1  H14  0.020

