# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun  4 13:50:43 2020
#   Inital geometry file: a 46 line input string
#   Ligand name: (~{R})-azanyl(pyridin-3-yl)methanethiol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](S)c1cccnc1
#
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
 M58  M58  (~{R})-azanyl(pyridin-3-yl)methanethiol  ligand  17  9  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_M58
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
 M58  C02  C  CH1   0  -0.285  -1.2896  -0.2473   0.7128
 M58  C04  C  CR6   0   0.040   0.1737  -0.1394   0.3589
 M58  C05  C  CR16  0  -0.164   0.8554   1.0682   0.4907
 M58  C06  C  CR16  0  -0.321   2.2010   1.1275   0.1805
 M58  C07  C  CR16  0  -0.070   2.8290  -0.0267  -0.2693
 M58  C09  C  CR16  0  -0.096   0.9078  -1.2359  -0.0792
 M58  N01  N  NH2   0  -0.760  -1.7894  -1.5773   0.5833
 M58  N08  N  N     0  -0.401   2.1991  -1.1848  -0.3969
 M58  S03  S  S2    0  -0.256  -2.2682   1.0520  -0.2025
 M58  H1   H  HCH1  0   0.306  -1.4183   0.0656   1.7512
 M58  H2   H  HCR6  0   0.267   0.3342   1.9556   0.8275
 M58  H3   H  HCR6  0   0.271   2.7567   2.0501   0.2778
 M58  H4   H  HCR6  0   0.264   3.8809  -0.0104  -0.5329
 M58  H5   H  HCR6  0   0.260   0.4355  -2.2062  -0.1745
 M58  H6   H  HNH2  0   0.371  -2.7266  -1.6361   0.9571
 M58  H7   H  HNH2  0   0.358  -1.8434  -1.8605  -0.3873
 M58  H9   H  HSH1  0   0.217  -1.9387   0.6468  -1.4354

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
 M58  N01  C02  single    1.427  0.020  1.427
 M58  C06  C07  aromatic  1.389  0.020  1.389
 M58  C06  C05  aromatic  1.382  0.020  1.382
 M58  C07  N08  aromatic  1.324  0.020  1.324
 M58  C05  C04  aromatic  1.393  0.020  1.393
 M58  N08  C09  aromatic  1.331  0.020  1.331
 M58  C04  C09  aromatic  1.390  0.020  1.390
 M58  C04  C02  single    1.509  0.020  1.509
 M58  C02  S03  single    1.866  0.020  1.866
 M58  C02  H1   single    0.970  0.020  1.090
 M58  C05  H2   single    0.930  0.020  1.080
 M58  C06  H3   single    0.930  0.020  1.080
 M58  C07  H4   single    0.930  0.020  1.080
 M58  C09  H5   single    0.930  0.020  1.080
 M58  N01  H6   single    0.890  0.020  1.040
 M58  N01  H7   single    0.890  0.020  1.040
 M58  S03  H9   single    1.200  0.020  1.300

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
 M58  H1   C02  S03  101.83  3.000
 M58  H1   C02  N01  108.19  3.000
 M58  S03  C02  N01  114.88  3.000
 M58  H1   C02  C04  108.46  3.000
 M58  S03  C02  C04  110.09  3.000
 M58  N01  C02  C04  112.65  3.000
 M58  C09  C04  C05  117.07  3.000
 M58  C09  C04  C02  121.96  3.000
 M58  C05  C04  C02  120.95  3.000
 M58  H2   C05  C06  120.21  3.000
 M58  H2   C05  C04  120.29  3.000
 M58  C06  C05  C04  119.50  3.000
 M58  H3   C06  C07  120.38  3.000
 M58  H3   C06  C05  121.11  3.000
 M58  C07  C06  C05  118.50  3.000
 M58  H4   C07  N08  116.80  3.000
 M58  H4   C07  C06  120.32  3.000
 M58  N08  C07  C06  122.88  3.000
 M58  H5   C09  N08  115.88  3.000
 M58  H5   C09  C04  120.25  3.000
 M58  N08  C09  C04  123.87  3.000
 M58  H7   N01  H6   106.79  3.000
 M58  H7   N01  C02  111.50  3.000
 M58  H6   N01  C02  110.22  3.000
 M58  C09  N08  C07  118.16  3.000
 M58  H9   S03  C02   96.42  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
 M58  CONST_01  C07  C06  C05  C04    0.00  0.0  0
 M58  CONST_02  C07  N08  C09  C04    0.00  0.0  0
 M58  CONST_03  N08  C07  C06  C05    0.00  0.0  0
 M58  CONST_04  N08  C09  C04  C05    0.00  0.0  0
 M58  CONST_05  C09  N08  C07  C06    0.00  0.0  0
 M58  CONST_06  C09  C04  C05  C06    0.00  0.0  0
 M58  CONST_07  C06  C05  C04  C02  180.00  0.0  0
 M58  CONST_08  N08  C09  C04  C02  180.00  0.0  0
 M58  CONST_09  H3   C06  C05  C04  180.00  0.0  0
 M58  CONST_10  H4   C07  C06  C05  180.00  0.0  0
 M58  CONST_11  H5   C09  C04  C05  180.00  0.0  0
 M58  CONST_12  H2   C05  C06  C07  180.00  0.0  0

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 M58  chir_01  C02  N01  C04  S03  negativ

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
 M58  plan-1  C02  0.020
 M58  plan-1  C04  0.020
 M58  plan-1  C05  0.020
 M58  plan-1  C06  0.020
 M58  plan-1  C07  0.020
 M58  plan-1  C09  0.020
 M58  plan-1  N08  0.020
 M58  plan-1  H2   0.020
 M58  plan-1  H3   0.020
 M58  plan-1  H4   0.020
 M58  plan-1  H5   0.020

