# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 06:33:06 2021
#   Inital geometry file: a 50 line input string
#   Ligand name: 2-sulfanylidene-1,7-dihydropyrrolo[2,3-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC(=S)Nc2[nH]ccc12
#
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
 KBQ  KBQ  2-sulfanylidene-1,7-dihydropyrrolo[2,3-d]pyrimidin-4-one  ligand  16  11  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KBQ
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
 KBQ  N1  N  NR16  0  -0.681  -68.4717  90.1831  160.9261
 KBQ  N3  N  NR16  0  -0.671  -70.4243  88.9820  160.9371
 KBQ  C4  C  CR56  0   0.648  -69.7764  88.0078  161.6364
 KBQ  C5  C  CR56  0  -0.178  -68.4484  88.0929  162.0053
 KBQ  C6  C  CR6   0   0.530  -67.7003  89.2552  161.6431
 KBQ  C7  C  CR15  0  -0.391  -68.1419  86.8956  162.7137
 KBQ  C8  C  CR15  0  -0.024  -69.2856  86.1565  162.7368
 KBQ  C2  C  CR6   0   0.361  -69.7771  90.1046  160.5614
 KBQ  N9  N  NR15  0  -0.652  -70.2797  86.8476  162.0740
 KBQ  O6  O  O     0  -0.450  -66.5331  89.4923  161.8864
 KBQ  S2  S  S1    0  -0.355  -70.5330  91.3171  159.7044
 KBQ  H1  H  HNR6  0   0.430  -67.9941  91.0268  160.6350
 KBQ  H2  H  HNR6  0   0.442  -71.3966  88.8887  160.6780
 KBQ  H3  H  HCR5  0   0.265  -67.1952  86.6223  163.1494
 KBQ  H4  H  HCR5  0   0.294  -69.4912  85.1912  163.1665
 KBQ  H5  H  HNR5  0   0.432  -71.2270  86.5248  161.9511

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
 KBQ  S2  C2  double    1.666  0.020  1.666
 KBQ  C2  N1  single    1.358  0.020  1.358
 KBQ  C2  N3  single    1.349  0.020  1.349
 KBQ  N1  C6  single    1.404  0.020  1.404
 KBQ  N3  C4  single    1.363  0.020  1.363
 KBQ  C6  O6  double    1.216  0.020  1.216
 KBQ  C6  C5  single    1.429  0.020  1.429
 KBQ  C4  C5  aromatic  1.381  0.020  1.381
 KBQ  C4  N9  aromatic  1.338  0.020  1.338
 KBQ  C5  C7  aromatic  1.425  0.020  1.425
 KBQ  N9  C8  aromatic  1.380  0.020  1.380
 KBQ  C7  C8  aromatic  1.362  0.020  1.362
 KBQ  N1  H1  single    0.860  0.020  1.020
 KBQ  N3  H2  single    0.860  0.020  1.020
 KBQ  C7  H3  single    0.930  0.020  1.080
 KBQ  C8  H4  single    0.930  0.020  1.080
 KBQ  N9  H5  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
 KBQ  H1  N1  C2  115.12  3.000
 KBQ  H1  N1  C6  116.02  3.000
 KBQ  C2  N1  C6  128.86  3.000
 KBQ  H2  N3  C2  117.84  3.000
 KBQ  H2  N3  C4  121.52  3.000
 KBQ  C2  N3  C4  120.63  3.000
 KBQ  N9  C4  C5  109.13  3.000
 KBQ  N9  C4  N3  127.49  3.000
 KBQ  C5  C4  N3  123.38  3.000
 KBQ  C7  C5  C6  134.19  3.000
 KBQ  C7  C5  C4  106.74  3.000
 KBQ  C6  C5  C4  119.07  3.000
 KBQ  O6  C6  C5  127.64  3.000
 KBQ  C5  C6  N1  112.30  3.000
 KBQ  O6  C6  N1  120.06  3.000
 KBQ  H3  C7  C8  126.40  3.000
 KBQ  H3  C7  C5  127.11  3.000
 KBQ  C8  C7  C5  106.49  3.000
 KBQ  H4  C8  N9  120.21  3.000
 KBQ  H4  C8  C7  130.83  3.000
 KBQ  N9  C8  C7  108.96  3.000
 KBQ  S2  C2  N3  122.08  3.000
 KBQ  N3  C2  N1  115.76  3.000
 KBQ  S2  C2  N1  122.16  3.000
 KBQ  H5  N9  C8  125.09  3.000
 KBQ  H5  N9  C4  126.23  3.000
 KBQ  C8  N9  C4  108.68  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
 KBQ  CONST_01  C8  C7  C5  C4    0.00  0.0  0
 KBQ  CONST_02  C7  C8  N9  C4    0.00  0.0  0
 KBQ  CONST_03  C8  N9  C4  C5    0.00  0.0  0
 KBQ  CONST_04  N9  C8  C7  C5    0.00  0.0  0
 KBQ  CONST_05  N9  C4  C5  C7    0.00  0.0  0
 KBQ  CONST_06  C4  N3  C2  N1    0.00  0.0  0
 KBQ  CONST_07  C6  N1  C2  N3    0.00  0.0  0
 KBQ  CONST_08  C2  N1  C6  C5    0.00  0.0  0
 KBQ  CONST_09  S2  C2  N3  C4  180.00  0.0  0
 KBQ  CONST_10  S2  C2  N1  C6  180.00  0.0  0
 KBQ  CONST_11  O6  C6  N1  C2  180.00  0.0  0
 KBQ  CONST_12  H5  N9  C4  N3    0.00  0.0  0
 KBQ  CONST_13  H3  C7  C5  C4  180.00  0.0  0
 KBQ  CONST_14  H4  C8  N9  C4  180.00  0.0  0
 KBQ  CONST_15  H2  N3  C2  N1  180.00  0.0  0
 KBQ  CONST_16  H1  N1  C2  N3  180.00  0.0  0

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
 KBQ  plan-1  N1  0.020
 KBQ  plan-1  N3  0.020
 KBQ  plan-1  C4  0.020
 KBQ  plan-1  C5  0.020
 KBQ  plan-1  C6  0.020
 KBQ  plan-1  C7  0.020
 KBQ  plan-1  C8  0.020
 KBQ  plan-1  C2  0.020
 KBQ  plan-1  N9  0.020
 KBQ  plan-1  O6  0.020
 KBQ  plan-1  S2  0.020
 KBQ  plan-1  H1  0.020
 KBQ  plan-1  H2  0.020
 KBQ  plan-1  H3  0.020
 KBQ  plan-1  H4  0.020
 KBQ  plan-1  H5  0.020

