# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 06:57:36 2021
#   Inital geometry file: a 61 line input string
#   Ligand name: 6,7-dimethyl-2-sulfanylidene-1~{H}-pteridin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc2NC(=S)NC(=O)c2nc1C
#
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
 KD8  KD8  6,7-dimethyl-2-sulfanylidene-1~{H}-pteridin-4-one  ligand  22  14  .  2022-07-25  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_KD8
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
 KD8  N1   N  NR16  0  -0.675  -21.4825  2.7055  20.8343
 KD8  N3   N  NR16  0  -0.675  -23.4191  1.4884  20.7435
 KD8  C4   C  CR6   0   0.554  -24.1586  2.3378  21.5518
 KD8  C6   C  CR6   0   0.186  -23.2823  5.4397  23.1912
 KD8  C7   C  CR6   0   0.234  -21.9207  5.5765  22.7988
 KD8  C2   C  CR6   0   0.364  -22.1186  1.6157  20.3621
 KD8  C4A  C  CR66  0  -0.005  -23.3978  3.4996  22.0175
 KD8  C8A  C  CR66  0   0.531  -22.0736  3.6443  21.6396
 KD8  CAK  C  CH3   0  -0.744  -23.9413  6.4698  24.0475
 KD8  CAL  C  CH3   0  -0.747  -21.1157  6.7485  23.2419
 KD8  N5   N  N     0  -0.369  -23.9860  4.4045  22.7938
 KD8  N8   N  N     0  -0.406  -21.3396  4.6770  22.0316
 KD8  O4   O  O     0  -0.413  -25.3137  2.1065  21.8195
 KD8  S2   S  S1    0  -0.309  -21.3766  0.5025  19.3842
 KD8  H1   H  HNR6  0   0.438  -20.5143  2.8394  20.5728
 KD8  H2   H  HNR6  0   0.439  -23.9013  0.6723  20.3871
 KD8  H3   H  HCH3  0   0.268  -24.9502  6.1566  24.3042
 KD8  H4   H  HCH3  0   0.259  -23.3855  6.6425  24.9701
 KD8  H5   H  HCH3  0   0.262  -24.0009  7.4289  23.5290
 KD8  H6   H  HCH3  0   0.272  -20.0902  6.6656  22.8918
 KD8  H7   H  HCH3  0   0.269  -21.5421  7.6773  22.8578
 KD8  H8   H  HCH3  0   0.267  -21.1102  6.8310  24.3300

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
 KD8  S2   C2   double    1.657  0.020  1.657
 KD8  C2   N3   single    1.361  0.020  1.361
 KD8  C2   N1   single    1.347  0.020  1.347
 KD8  N3   C4   single    1.386  0.020  1.386
 KD8  N1   C8A  single    1.371  0.020  1.371
 KD8  C4   O4   double    1.208  0.020  1.208
 KD8  C4   C4A  single    1.465  0.020  1.465
 KD8  C8A  C4A  aromatic  1.385  0.020  1.385
 KD8  C8A  N8   aromatic  1.326  0.020  1.326
 KD8  C4A  N5   aromatic  1.329  0.020  1.329
 KD8  N8   C7   aromatic  1.317  0.020  1.317
 KD8  N5   C6   aromatic  1.313  0.020  1.313
 KD8  C7   C6   aromatic  1.424  0.020  1.424
 KD8  C7   CAL  single    1.489  0.020  1.489
 KD8  C6   CAK  single    1.493  0.020  1.493
 KD8  N1   H1   single    0.860  0.020  1.020
 KD8  N3   H2   single    0.860  0.020  1.020
 KD8  CAK  H3   single    0.970  0.020  1.090
 KD8  CAK  H4   single    0.970  0.020  1.090
 KD8  CAK  H5   single    0.970  0.020  1.090
 KD8  CAL  H6   single    0.970  0.020  1.090
 KD8  CAL  H7   single    0.970  0.020  1.090
 KD8  CAL  H8   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
 KD8  H1   N1   C8A  118.28  3.000
 KD8  H1   N1   C2   117.92  3.000
 KD8  C8A  N1   C2   123.80  3.000
 KD8  H2   N3   C2   115.57  3.000
 KD8  H2   N3   C4   116.42  3.000
 KD8  C2   N3   C4   128.00  3.000
 KD8  O4   C4   C4A  125.31  3.000
 KD8  C4A  C4   N3   113.22  3.000
 KD8  O4   C4   N3   121.46  3.000
 KD8  N5   C6   CAK  118.75  3.000
 KD8  CAK  C6   C7   120.93  3.000
 KD8  N5   C6   C7   120.32  3.000
 KD8  N8   C7   CAL  118.18  3.000
 KD8  CAL  C7   C6   120.70  3.000
 KD8  N8   C7   C6   121.12  3.000
 KD8  S2   C2   N3   122.03  3.000
 KD8  N3   C2   N1   115.37  3.000
 KD8  S2   C2   N1   122.60  3.000
 KD8  N5   C4A  C8A  120.76  3.000
 KD8  N5   C4A  C4   119.72  3.000
 KD8  C8A  C4A  C4   119.53  3.000
 KD8  N8   C8A  C4A  122.01  3.000
 KD8  N8   C8A  N1   117.92  3.000
 KD8  C4A  C8A  N1   120.07  3.000
 KD8  H5   CAK  H4   106.88  3.000
 KD8  H5   CAK  H3   108.33  3.000
 KD8  H4   CAK  H3   108.59  3.000
 KD8  H5   CAK  C6   110.97  3.000
 KD8  H4   CAK  C6   111.68  3.000
 KD8  H3   CAK  C6   110.26  3.000
 KD8  H8   CAL  H7   106.77  3.000
 KD8  H8   CAL  H6   108.80  3.000
 KD8  H7   CAL  H6   108.67  3.000
 KD8  H8   CAL  C7   111.03  3.000
 KD8  H7   CAL  C7   110.71  3.000
 KD8  H6   CAL  C7   110.74  3.000
 KD8  C4A  N5   C6   118.43  3.000
 KD8  C8A  N8   C7   117.37  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
 KD8  CONST_01  C8A  C4A  N5   C6      0.00   0.0  0
 KD8  CONST_02  C8A  N8   C7   C6      0.00   0.0  0
 KD8  CONST_03  C4A  C8A  N8   C7      0.00   0.0  0
 KD8  CONST_04  C4A  N5   C6   C7      0.00   0.0  0
 KD8  CONST_05  N8   C8A  C4A  N5      0.00   0.0  0
 KD8  CONST_06  N8   C7   C6   N5      0.00   0.0  0
 KD8  CONST_07  C4   N3   C2   N1      0.00   0.0  0
 KD8  CONST_08  C8A  N1   C2   N3      0.00   0.0  0
 KD8  CONST_09  C4A  C4   N3   C2      0.00   0.0  0
 KD8  CONST_10  CAK  C6   N5   C4A   180.00   0.0  0
 KD8  CONST_11  CAL  C7   N8   C8A   180.00   0.0  0
 KD8  CONST_12  N8   C7   C6   CAK   180.00   0.0  0
 KD8  CONST_13  N5   C6   C7   CAL   180.00   0.0  0
 KD8  CONST_14  S2   C2   N3   C4    180.00   0.0  0
 KD8  CONST_15  O4   C4   N3   C2    180.00   0.0  0
 KD8  CONST_16  S2   C2   N1   C8A   180.00   0.0  0
 KD8  CONST_17  H2   N3   C2   N1    180.00   0.0  0
 KD8  CONST_18  H1   N1   C2   N3    180.00   0.0  0
 KD8  Var_01    H6   CAL  C7   C6    177.22  30.0  2
 KD8  Var_02    H3   CAK  C6   C7   -175.64  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
 KD8  plan-1  N1   0.020
 KD8  plan-1  N3   0.020
 KD8  plan-1  C4   0.020
 KD8  plan-1  C6   0.020
 KD8  plan-1  C7   0.020
 KD8  plan-1  C2   0.020
 KD8  plan-1  C4A  0.020
 KD8  plan-1  C8A  0.020
 KD8  plan-1  CAK  0.020
 KD8  plan-1  CAL  0.020
 KD8  plan-1  N5   0.020
 KD8  plan-1  N8   0.020
 KD8  plan-1  O4   0.020
 KD8  plan-1  S2   0.020
 KD8  plan-1  H1   0.020
 KD8  plan-1  H2   0.020

