# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 10:35:05 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: 2-methyl-3,5,7,8-tetrahydro-4H-thiopyrano[4,3-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=NC2=C(CSCC2)C(=O)N1
#
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
 DRL  DRL  2-methyl-3,5,7,8-tetrahydro-4H-thiopyrano[4,3-d]pyrimidin-4-one  ligand  22  12  .  2021-08-08  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DRL
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
 DRL  C1A   C  CH3   0  -0.747   3.6629   1.2226   0.1306
 DRL  C1I   C  CR6   0   0.459   2.2865   0.6589   0.0420
 DRL  N1G   N  N     0  -0.468   1.2483   1.4282   0.0354
 DRL  C1J   C  CR6   0   0.267   0.0106   0.8517  -0.0383
 DRL  C1D   C  CH2   0  -0.483  -1.1069   1.8544  -0.0579
 DRL  C1C   C  CH2   0  -0.585  -2.4472   1.3093  -0.5052
 DRL  S1H   S  S2    0  -0.013  -2.8836  -0.1710   0.4380
 DRL  C1E   C  CH2   0  -0.630  -1.5094  -1.1907  -0.1385
 DRL  C1K   C  CR6   0  -0.128  -0.1800  -0.4986  -0.0807
 DRL  C1L   C  CR6   0   0.548   0.9767  -1.3623  -0.1035
 DRL  O1B   O  O     0  -0.479   0.9521  -2.5830  -0.1788
 DRL  N1F   N  NR16  0  -0.667   2.1791  -0.6854  -0.0304
 DRL  H1A   H  HCH3  0   0.272   3.6217   2.3075   0.1368
 DRL  H1AA  H  HCH3  0   0.274   4.1578   0.8832   1.0417
 DRL  H1AB  H  HCH3  0   0.273   4.2710   0.8955  -0.7137
 DRL  H1D   H  HCH2  0   0.270  -1.1947   2.2861   0.9436
 DRL  H1DA  H  HCH2  0   0.268  -0.8063   2.6753  -0.7147
 DRL  H1C   H  HCH2  0   0.293  -3.2340   2.0446  -0.3415
 DRL  H1CA  H  HCH2  0   0.275  -2.4401   1.0651  -1.5693
 DRL  H1E   H  HCH2  0   0.291  -1.4952  -2.0760   0.4990
 DRL  H1EA  H  HCH2  0   0.285  -1.7146  -1.5392  -1.1544
 DRL  HN1F  H  HNR6  0   0.427   3.0212  -1.2481  -0.0390

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
 DRL  C1A  C1I   single  1.490  0.020  1.490
 DRL  C1I  N1G   double  1.292  0.020  1.292
 DRL  C1I  N1F   single  1.351  0.020  1.351
 DRL  N1G  C1J   single  1.367  0.020  1.367
 DRL  C1J  C1D   single  1.501  0.020  1.501
 DRL  C1J  C1K   double  1.364  0.020  1.364
 DRL  C1D  C1C   single  1.514  0.020  1.514
 DRL  C1C  S1H   single  1.809  0.020  1.809
 DRL  S1H  C1E   single  1.806  0.020  1.806
 DRL  C1E  C1K   single  1.500  0.020  1.500
 DRL  C1K  C1L   single  1.444  0.020  1.444
 DRL  C1L  O1B   double  1.223  0.020  1.223
 DRL  C1L  N1F   single  1.382  0.020  1.382
 DRL  C1A  H1A   single  0.970  0.020  1.090
 DRL  C1A  H1AA  single  0.970  0.020  1.090
 DRL  C1A  H1AB  single  0.970  0.020  1.090
 DRL  C1D  H1D   single  0.970  0.020  1.090
 DRL  C1D  H1DA  single  0.970  0.020  1.090
 DRL  C1C  H1C   single  0.970  0.020  1.090
 DRL  C1C  H1CA  single  0.970  0.020  1.090
 DRL  C1E  H1E   single  0.970  0.020  1.090
 DRL  C1E  H1EA  single  0.970  0.020  1.090
 DRL  N1F  HN1F  single  0.860  0.020  1.020

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
 DRL  H1AB  C1A  H1AA  107.47  3.000
 DRL  H1AB  C1A  H1A   108.98  3.000
 DRL  H1AA  C1A  H1A   108.86  3.000
 DRL  H1AB  C1A  C1I   110.83  3.000
 DRL  H1AA  C1A  C1I   110.55  3.000
 DRL  H1A   C1A  C1I   110.08  3.000
 DRL  N1F   C1I  N1G   121.90  3.000
 DRL  N1F   C1I  C1A   116.95  3.000
 DRL  N1G   C1I  C1A   121.15  3.000
 DRL  C1J   N1G  C1I   118.46  3.000
 DRL  C1K   C1J  C1D   123.82  3.000
 DRL  C1K   C1J  N1G   123.05  3.000
 DRL  C1D   C1J  N1G   113.13  3.000
 DRL  H1DA  C1D  H1D   106.00  3.000
 DRL  H1DA  C1D  C1C   109.64  3.000
 DRL  H1D   C1D  C1C   109.96  3.000
 DRL  H1DA  C1D  C1J   107.73  3.000
 DRL  H1D   C1D  C1J   108.14  3.000
 DRL  C1C   C1D  C1J   114.97  3.000
 DRL  H1CA  C1C  H1C   107.59  3.000
 DRL  H1CA  C1C  S1H   109.07  3.000
 DRL  H1C   C1C  S1H   107.45  3.000
 DRL  H1CA  C1C  C1D   111.26  3.000
 DRL  H1C   C1C  C1D   110.60  3.000
 DRL  S1H   C1C  C1D   110.73  3.000
 DRL  C1E   S1H  C1C    96.44  3.000
 DRL  H1EA  C1E  H1E   106.66  3.000
 DRL  H1EA  C1E  C1K   110.44  3.000
 DRL  H1E   C1E  C1K   109.89  3.000
 DRL  H1EA  C1E  S1H   109.50  3.000
 DRL  H1E   C1E  S1H   106.36  3.000
 DRL  C1K   C1E  S1H   113.68  3.000
 DRL  C1L   C1K  C1E   115.69  3.000
 DRL  C1L   C1K  C1J   118.73  3.000
 DRL  C1E   C1K  C1J   125.57  3.000
 DRL  N1F   C1L  O1B   120.64  3.000
 DRL  N1F   C1L  C1K   113.78  3.000
 DRL  O1B   C1L  C1K   125.58  3.000
 DRL  HN1F  N1F  C1L   116.80  3.000
 DRL  HN1F  N1F  C1I   119.17  3.000
 DRL  C1L   N1F  C1I   124.03  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
 DRL  CONST_01  C1K   C1L  N1F  C1I    0.00   0.0  0
 DRL  CONST_02  C1L   N1F  C1I  N1G    0.00   0.0  0
 DRL  CONST_03  N1F   C1I  N1G  C1J    0.00   0.0  0
 DRL  CONST_04  C1J   N1G  C1I  C1A  180.00   0.0  0
 DRL  CONST_05  C1L   N1F  C1I  C1A  180.00   0.0  0
 DRL  CONST_06  O1B   C1L  N1F  C1I  180.00   0.0  0
 DRL  CONST_07  HN1F  N1F  C1I  N1G  180.00   0.0  0
 DRL  Var_01    C1C   C1D  C1J  N1G  164.39  30.0  1
 DRL  Var_02    S1H   C1C  C1D  C1J   51.89  30.0  1
 DRL  Var_03    S1H   C1E  C1K  C1J  -20.85  30.0  1
 DRL  Var_04    C1K   C1E  S1H  C1C   47.36  30.0  1
 DRL  Var_05    H1A   C1A  C1I  N1G   -2.61  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
 DRL  plan-1  C1A   0.020
 DRL  plan-1  C1I   0.020
 DRL  plan-1  N1G   0.020
 DRL  plan-1  C1J   0.020
 DRL  plan-1  C1D   0.020
 DRL  plan-1  C1E   0.020
 DRL  plan-1  C1K   0.020
 DRL  plan-1  C1L   0.020
 DRL  plan-1  O1B   0.020
 DRL  plan-1  N1F   0.020
 DRL  plan-1  HN1F  0.020

