# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 02:00:46 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: ~{N}-[(3~{R})-1,1-bis(oxidanylidene)thian-3-yl]-2-methyl-pyridin-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncccc1N[C@@H]2CCC[S](=O)(=O)C2
#
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
 6RR  6RR  ~{N}-[(3~{R})-1,1-bis(oxidanylidene)thian-3-yl]-2-methyl-pyridin-3-amine  ligand  32  16  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_6RR
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
 6RR  O10  O  OS    0  -0.685  -3.0696   0.7828  -1.4180
 6RR  C15  C  CR16  0  -0.118   4.5757   0.9435  -0.3677
 6RR  C14  C  CR16  0  -0.316   3.4814   1.7240  -0.6869
 6RR  C12  C  CH2   0  -0.624  -1.5162  -1.0442  -0.3115
 6RR  C02  C  CR6   0   0.171   3.2501  -0.8588   0.1527
 6RR  C03  C  CR6   0   0.278   2.0682  -0.1405  -0.1449
 6RR  N04  N  NH1   0  -0.694   0.8482  -0.7762  -0.0487
 6RR  C05  C  CH1   0  -0.107  -0.3993  -0.0457  -0.0059
 6RR  C06  C  CH2   0  -0.442  -0.6268   0.6647   1.3327
 6RR  C07  C  CH2   0  -0.467  -1.9290   1.4576   1.3955
 6RR  C08  C  CH2   0  -0.608  -3.1625   0.5832   1.2149
 6RR  S09  S  S     0   1.212  -3.1125  -0.2391  -0.3690
 6RR  O11  O  OS    0  -0.678  -4.1593  -1.2579  -0.4396
 6RR  C13  C  CR16  0  -0.243   2.2116   1.1791  -0.5706
 6RR  N16  N  N     0  -0.408   4.4513  -0.3165   0.0403
 6RR  H2   H  HCR6  0   0.264   3.6113   2.7460  -1.0166
 6RR  H3   H  HCH2  0   0.332  -1.3769  -1.5197  -1.2849
 6RR  H4   H  HCH2  0   0.303  -1.5822  -1.8209   0.4549
 6RR  H5   H  HCH3  0   0.251   2.6758  -2.9169  -0.1399
 6RR  H6   H  HCH3  0   0.263   4.1724  -2.6816   0.7674
 6RR  H7   H  HCH3  0   0.248   2.6153  -2.3936   1.5376
 6RR  H8   H  HNH1  0   0.388   0.8480  -1.5925   0.5454
 6RR  H9   H  HCH1  0   0.267  -0.3924   0.6916  -0.8126
 6RR  H10  H  HCH2  0   0.239  -0.6130  -0.0845   2.1313
 6RR  H11  H  HCH2  0   0.278  -2.0087   1.9434   2.3688
 6RR  H12  H  HCH2  0   0.300  -3.2216  -0.1972   1.9762
 6RR  H13  H  HCH2  0   0.324  -4.0904   1.1587   1.2300
 6RR  H14  H  HCR6  0   0.273   1.3508   1.7864  -0.8176
 6RR  H15  H  HCH2  0   0.264   0.2074   1.3433   1.5217
 6RR  H16  H  HCH2  0   0.255  -1.9286   2.2568   0.6508
 6RR  H1   H  HCR6  0   0.250   5.5832   1.3364  -0.4403
 6RR  C01  C  CH3   0  -0.765   3.1725  -2.2868   0.6023

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
 6RR  O11  S09  double    1.462  0.020  1.462
 6RR  S09  C08  single    1.785  0.020  1.785
 6RR  S09  C12  single    1.789  0.020  1.789
 6RR  S09  O10  double    1.465  0.020  1.465
 6RR  C08  C07  single    1.523  0.020  1.523
 6RR  C12  C05  single    1.529  0.020  1.529
 6RR  C07  C06  single    1.526  0.020  1.526
 6RR  C05  N04  single    1.446  0.020  1.446
 6RR  C05  C06  single    1.532  0.020  1.532
 6RR  C13  C14  aromatic  1.387  0.020  1.387
 6RR  C13  C03  aromatic  1.394  0.020  1.394
 6RR  C14  C15  aromatic  1.382  0.020  1.382
 6RR  N04  C03  single    1.379  0.020  1.379
 6RR  C15  N16  aromatic  1.330  0.020  1.330
 6RR  C03  C02  aromatic  1.415  0.020  1.415
 6RR  N16  C02  aromatic  1.323  0.020  1.323
 6RR  C02  C01  single    1.499  0.020  1.499
 6RR  C15  H1   single    0.930  0.020  1.080
 6RR  C14  H2   single    0.930  0.020  1.080
 6RR  C12  H3   single    0.970  0.020  1.090
 6RR  C12  H4   single    0.970  0.020  1.090
 6RR  C01  H5   single    0.970  0.020  1.090
 6RR  C01  H6   single    0.970  0.020  1.090
 6RR  C01  H7   single    0.970  0.020  1.090
 6RR  N04  H8   single    0.890  0.020  1.040
 6RR  C05  H9   single    0.970  0.020  1.090
 6RR  C06  H10  single    0.970  0.020  1.090
 6RR  C07  H11  single    0.970  0.020  1.090
 6RR  C08  H12  single    0.970  0.020  1.090
 6RR  C08  H13  single    0.970  0.020  1.090
 6RR  C13  H14  single    0.930  0.020  1.080
 6RR  C06  H15  single    0.970  0.020  1.090
 6RR  C07  H16  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
 6RR  H1   C15  N16  116.80  3.000
 6RR  H1   C15  C14  121.06  3.000
 6RR  N16  C15  C14  122.14  3.000
 6RR  H2   C14  C13  120.45  3.000
 6RR  H2   C14  C15  120.60  3.000
 6RR  C13  C14  C15  118.94  3.000
 6RR  H4   C12  H3   108.85  3.000
 6RR  H4   C12  S09  106.76  3.000
 6RR  H3   C12  S09  106.32  3.000
 6RR  H4   C12  C05  111.59  3.000
 6RR  H3   C12  C05  111.67  3.000
 6RR  S09  C12  C05  111.37  3.000
 6RR  N16  C02  C03  122.18  3.000
 6RR  N16  C02  C01  117.58  3.000
 6RR  C03  C02  C01  120.23  3.000
 6RR  C13  C03  N04  123.27  3.000
 6RR  N04  C03  C02  119.36  3.000
 6RR  C13  C03  C02  117.32  3.000
 6RR  H8   N04  C05  113.01  3.000
 6RR  H8   N04  C03  114.45  3.000
 6RR  C05  N04  C03  122.16  3.000
 6RR  H9   C05  C06  109.45  3.000
 6RR  H9   C05  N04  108.27  3.000
 6RR  C06  C05  N04  112.83  3.000
 6RR  H9   C05  C12  107.32  3.000
 6RR  C06  C05  C12  111.65  3.000
 6RR  N04  C05  C12  107.12  3.000
 6RR  H15  C06  H10  106.81  3.000
 6RR  H15  C06  C07  108.79  3.000
 6RR  H10  C06  C07  109.65  3.000
 6RR  H15  C06  C05  109.02  3.000
 6RR  H10  C06  C05  108.54  3.000
 6RR  C07  C06  C05  113.80  3.000
 6RR  H16  C07  H11  106.41  3.000
 6RR  H16  C07  C08  109.85  3.000
 6RR  H11  C07  C08  107.61  3.000
 6RR  H16  C07  C06  110.59  3.000
 6RR  H11  C07  C06  109.30  3.000
 6RR  C08  C07  C06  112.83  3.000
 6RR  H13  C08  H12  108.72  3.000
 6RR  H13  C08  S09  106.19  3.000
 6RR  H12  C08  S09  106.91  3.000
 6RR  H13  C08  C07  112.58  3.000
 6RR  H12  C08  C07  111.81  3.000
 6RR  S09  C08  C07  110.31  3.000
 6RR  O11  S09  C08  110.10  3.000
 6RR  C08  S09  C12  101.76  3.000
 6RR  O11  S09  C12  109.08  3.000
 6RR  C12  S09  O10  108.11  3.000
 6RR  C08  S09  O10  108.35  3.000
 6RR  O11  S09  O10  118.18  3.000
 6RR  H14  C13  C03  121.28  3.000
 6RR  H14  C13  C14  119.26  3.000
 6RR  C03  C13  C14  119.46  3.000
 6RR  C02  N16  C15  119.95  3.000
 6RR  H7   C01  H6   107.64  3.000
 6RR  H7   C01  H5   107.03  3.000
 6RR  H6   C01  H5   108.16  3.000
 6RR  H7   C01  C02  112.07  3.000
 6RR  H6   C01  C02  110.10  3.000
 6RR  H5   C01  C02  111.65  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
 6RR  CONST_01  C03  C13  C14  C15    0.00   0.0  0
 6RR  CONST_02  C03  C02  N16  C15    0.00   0.0  0
 6RR  CONST_03  C02  C03  C13  C14    0.00   0.0  0
 6RR  CONST_04  C02  N16  C15  C14    0.00   0.0  0
 6RR  CONST_05  N16  C15  C14  C13    0.00   0.0  0
 6RR  CONST_06  N16  C02  C03  C13    0.00   0.0  0
 6RR  CONST_07  C01  C02  N16  C15  180.00   0.0  0
 6RR  CONST_08  N04  C03  C13  C14  180.00   0.0  0
 6RR  CONST_09  C13  C03  C02  C01  180.00   0.0  0
 6RR  CONST_10  N16  C02  C03  N04  180.00   0.0  0
 6RR  CONST_13  H14  C13  C14  C15  180.00   0.0  0
 6RR  CONST_14  H1   C15  N16  C02  180.00   0.0  0
 6RR  CONST_15  H2   C14  C13  C03  180.00   0.0  0
 6RR  Var_01    C07  C08  S09  C12   54.06  30.0  1
 6RR  Var_02    C08  S09  C12  C05  -54.31  30.0  1
 6RR  Var_03    C08  C07  C06  C05   61.20  30.0  1
 6RR  Var_04    S09  C08  C07  C06  -59.83  30.0  1
 6RR  Var_05    H5   C01  C02  C03   58.83  30.0  2

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
 6RR  chir_01  C05  C12  N04  C06  positiv

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
 6RR  plan-1  C15  0.020
 6RR  plan-1  C14  0.020
 6RR  plan-1  C02  0.020
 6RR  plan-1  C03  0.020
 6RR  plan-1  N04  0.020
 6RR  plan-1  C13  0.020
 6RR  plan-1  N16  0.020
 6RR  plan-1  H2   0.020
 6RR  plan-1  H14  0.020
 6RR  plan-1  H1   0.020
 6RR  plan-1  C01  0.020
 6RR  plan-2  C03  0.020
 6RR  plan-2  N04  0.020
 6RR  plan-2  C05  0.020
 6RR  plan-2  H8   0.020

