# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 06:45:16 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: N-{4-[(R)-methylsulfinyl]butyl}thioformamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S@@](=O)CCCCNC=S
#
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
 LE3  LE3  N-{4-[(R)-methylsulfinyl]butyl}thioformamide  ligand  23  10  .  2022-07-25  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_LE3
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
 LE3  C     C  C1    0  -0.105   4.1791   0.6244  -0.1990
 LE3  N     N  NH1   0  -0.505   2.9205   1.0023  -0.2152
 LE3  S     S  S1    0  -0.377   4.7325  -0.9050   0.1098
 LE3  C1    C  CH2   0  -0.233   1.7957   0.1249   0.0368
 LE3  C2    C  CH2   0  -0.471   0.4857   0.8878  -0.0611
 LE3  C3    C  CH2   0  -0.427  -0.7048  -0.0269   0.1953
 LE3  C4    C  CH2   0  -0.605  -2.0171   0.7323   0.0931
 LE3  S5    S  S3    0   0.723  -3.4079  -0.3828   0.4332
 LE3  O5A   O  O     0  -0.793  -3.4034  -1.4274  -0.6608
 LE3  C5B   C  CH3   0  -0.803  -4.7362   0.7715   0.0451
 LE3  H1    H  HCH2  0   0.248   1.8180  -0.6977  -0.6833
 LE3  H1A   H  HCH2  0   0.248   1.9084  -0.3237   1.0277
 LE3  H2    H  HCH2  0   0.244   0.4834   1.7086   0.6625
 LE3  H2A   H  HCH2  0   0.244   0.3972   1.3379  -1.0543
 LE3  H3    H  HCH2  0   0.244  -0.7019  -0.8474  -0.5265
 LE3  H3A   H  HCH2  0   0.244  -0.6145  -0.4758   1.1888
 LE3  H4    H  HCH2  0   0.279  -2.0707   1.5370   0.8298
 LE3  H4A   H  HCH2  0   0.283  -2.1587   1.1576  -0.9037
 LE3  H5B   H  HCH3  0   0.281  -4.6164   1.1495  -0.9695
 LE3  H5BA  H  HCH3  0   0.291  -5.6768   0.2305   0.1315
 LE3  H5BB  H  HCH3  0   0.277  -4.7268   1.5919   0.7606
 LE3  H12   H  H     0   0.291   4.8685   1.4372  -0.4155
 LE3  H13   H  HNH1  0   0.421   2.7263   1.9714  -0.4215

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
 LE3  C    N     single  1.314  0.020  1.314
 LE3  S    C     double  1.656  0.020  1.656
 LE3  C1   N     single  1.449  0.020  1.449
 LE3  C1   C2    single  1.519  0.020  1.519
 LE3  C1   H1    single  0.970  0.020  1.090
 LE3  C1   H1A   single  0.970  0.020  1.090
 LE3  C2   C3    single  1.523  0.020  1.523
 LE3  C2   H2    single  0.970  0.020  1.090
 LE3  C2   H2A   single  0.970  0.020  1.090
 LE3  C3   C4    single  1.520  0.020  1.520
 LE3  C3   H3    single  0.970  0.020  1.090
 LE3  C3   H3A   single  0.970  0.020  1.090
 LE3  C4   H4    single  0.970  0.020  1.090
 LE3  C4   H4A   single  0.970  0.020  1.090
 LE3  S5   C4    single  1.815  0.020  1.815
 LE3  S5   O5A   double  1.513  0.020  1.513
 LE3  S5   C5B   single  1.802  0.020  1.802
 LE3  C5B  H5B   single  0.970  0.020  1.090
 LE3  C5B  H5BA  single  0.970  0.020  1.090
 LE3  C5B  H5BB  single  0.970  0.020  1.090
 LE3  C    H12   single  0.930  0.020  1.080
 LE3  N    H13   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
 LE3  H12   C    S     121.04  3.000
 LE3  H12   C    N     112.93  3.000
 LE3  S     C    N     126.02  3.000
 LE3  H13   N    C1    117.88  3.000
 LE3  H13   N    C     117.56  3.000
 LE3  C1    N    C     124.56  3.000
 LE3  H1A   C1   H1    106.62  3.000
 LE3  H1A   C1   C2    110.69  3.000
 LE3  H1    C1   C2    110.67  3.000
 LE3  H1A   C1   N     109.03  3.000
 LE3  H1    C1   N     108.99  3.000
 LE3  C2    C1   N     110.74  3.000
 LE3  H2A   C2   H2    106.95  3.000
 LE3  H2A   C2   C3    109.67  3.000
 LE3  H2    C2   C3    109.72  3.000
 LE3  H2A   C2   C1    109.57  3.000
 LE3  H2    C2   C1    109.63  3.000
 LE3  C3    C2   C1    111.20  3.000
 LE3  H3A   C3   H3    106.96  3.000
 LE3  H3A   C3   C4    109.72  3.000
 LE3  H3    C3   C4    109.45  3.000
 LE3  H3A   C3   C2    109.56  3.000
 LE3  H3    C3   C2    109.73  3.000
 LE3  C4    C3   C2    111.32  3.000
 LE3  H4A   C4   H4    108.79  3.000
 LE3  H4A   C4   S5    108.10  3.000
 LE3  H4    C4   S5    106.78  3.000
 LE3  S5    C4   C3    110.01  3.000
 LE3  H4A   C4   C3    111.57  3.000
 LE3  H4    C4   C3    111.42  3.000
 LE3  C5B   S5   O5A   106.79  3.000
 LE3  C5B   S5   C4     97.52  3.000
 LE3  O5A   S5   C4    106.65  3.000
 LE3  H5BB  C5B  H5BA  109.26  3.000
 LE3  H5BB  C5B  H5B   110.48  3.000
 LE3  H5BA  C5B  H5B   109.97  3.000
 LE3  H5BB  C5B  S5    109.56  3.000
 LE3  H5BA  C5B  S5    107.54  3.000
 LE3  H5B   C5B  S5    109.99  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
 LE3  Var_01  C2   C1   N   C   -180.00  30.0  1
 LE3  Var_02  C3   C2   C1  N    179.72  30.0  3
 LE3  Var_03  C1   N    C   S     -0.12  30.0  2
 LE3  Var_04  C4   C3   C2  C1  -179.80  30.0  3
 LE3  Var_05  S5   C4   C3  C2  -179.00  30.0  3
 LE3  Var_06  O5A  S5   C4  C3   -63.83  30.0  1
 LE3  Var_07  H5B  C5B  S5  C4    56.31  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
 LE3  plan-1  C    0.020
 LE3  plan-1  N    0.020
 LE3  plan-1  S    0.020
 LE3  plan-1  H12  0.020
 LE3  plan-2  C4   0.020
 LE3  plan-2  S5   0.020
 LE3  plan-2  O5A  0.020
 LE3  plan-2  C5B  0.020

