# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 06:24:37 2022
#   Inital geometry file: a 75 line input string
#   Ligand name: 2,2,5,5-tetramethyl-3,4-bis(sulfanylmethyl)-2,5-dihydro-1H-pyrrol-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)N([O])C(C)(C)C(=C1CS)CS
#
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
 RXR  RXR  2,2,5,5-tetramethyl-3,4-bis(sulfanylmethyl)-2,5-dihydro-1H-pyrrol-1-ol  ligand  32  14  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RXR
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
 RXR  N1    N  NR5   0  -0.032  44.0724   -6.3164   0.9973
 RXR  O1    O  O     0  -0.451  44.9202   -5.8178   1.7764
 RXR  C2    C  CR5   0   0.033  44.1087   -7.7267   0.5922
 RXR  C3    C  CR5   0   0.114  42.9120   -7.7731  -0.3197
 RXR  C4    C  CR5   0   0.110  42.3375   -6.5788  -0.4615
 RXR  C5    C  CR5   0   0.036  43.0303   -5.5124   0.3451
 RXR  C6    C  CH3   0  -0.633  43.6634   -4.4284  -0.5274
 RXR  C7    C  CH3   0  -0.639  42.1127   -4.8875   1.3951
 RXR  C8    C  CH3   0  -0.633  45.4090   -8.0264  -0.1566
 RXR  C9    C  CH3   0  -0.634  43.9719   -8.6394   1.8086
 RXR  SD    S  S2    0  -0.230  41.0654   -9.7223   0.0203
 RXR  CE    C  CH2   0  -0.653  42.4546   -9.0389  -0.9620
 RXR  C10   C  CH2   0  -0.650  41.1498   -6.2819  -1.3143
 RXR  S10   S  S2    0  -0.231  41.7074   -6.0769  -3.0488
 RXR  H6    H  HCH3  0   0.236  42.8930   -3.8575  -1.0448
 RXR  H6A   H  HCH3  0   0.244  44.2391   -3.7354   0.0864
 RXR  H6B   H  HCH3  0   0.237  44.3242   -4.8621  -1.2781
 RXR  H7    H  HCH3  0   0.234  41.3443   -4.2788   0.9178
 RXR  H7A   H  HCH3  0   0.240  41.6191   -5.6508   1.9973
 RXR  H7B   H  HCH3  0   0.248  42.6809   -4.2344   2.0584
 RXR  H8    H  HCH3  0   0.236  45.4095   -9.0536  -0.5213
 RXR  H8A   H  HCH3  0   0.238  45.5341   -7.3615  -1.0114
 RXR  H8B   H  HCH3  0   0.246  46.2682   -7.9104   0.5048
 RXR  H9    H  HCH3  0   0.236  43.9625   -9.6841   1.4976
 RXR  H9A   H  HCH3  0   0.244  44.8183   -8.5006   2.4812
 RXR  H9B   H  HCH3  0   0.238  43.0518   -8.4400   2.3580
 RXR  HSD   H  HSH1  0   0.225  40.8456  -10.8132  -0.7243
 RXR  HE    H  HCH2  0   0.291  42.1140   -8.8567  -1.9808
 RXR  HEA   H  HCH2  0   0.292  43.2550   -9.7770  -1.0007
 RXR  H10   H  HCH2  0   0.290  40.4270   -7.0956  -1.2676
 RXR  H10A  H  HCH2  0   0.291  40.6531   -5.3680  -0.9917
 RXR  HS10  H  HSH1  0   0.226  40.5054   -5.8404  -3.5886

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
 RXR  N1   O1    single  1.255  0.020  1.255
 RXR  N1   C2    single  1.468  0.020  1.468
 RXR  N1   C5    single  1.469  0.020  1.469
 RXR  C2   C3    single  1.505  0.020  1.505
 RXR  C2   C8    single  1.530  0.020  1.530
 RXR  C2   C9    single  1.527  0.020  1.527
 RXR  C3   C4    double  1.333  0.020  1.333
 RXR  C3   CE    single  1.491  0.020  1.491
 RXR  C4   C5    single  1.506  0.020  1.506
 RXR  C4   C10   single  1.492  0.020  1.492
 RXR  C5   C6    single  1.529  0.020  1.529
 RXR  C5   C7    single  1.528  0.020  1.528
 RXR  C6   H6    single  0.970  0.020  1.090
 RXR  C6   H6A   single  0.970  0.020  1.090
 RXR  C6   H6B   single  0.970  0.020  1.090
 RXR  C7   H7    single  0.970  0.020  1.090
 RXR  C7   H7A   single  0.970  0.020  1.090
 RXR  C7   H7B   single  0.970  0.020  1.090
 RXR  C8   H8    single  0.970  0.020  1.090
 RXR  C8   H8A   single  0.970  0.020  1.090
 RXR  C8   H8B   single  0.970  0.020  1.090
 RXR  C9   H9    single  0.970  0.020  1.090
 RXR  C9   H9A   single  0.970  0.020  1.090
 RXR  C9   H9B   single  0.970  0.020  1.090
 RXR  SD   CE    single  1.834  0.020  1.834
 RXR  SD   HSD   single  1.200  0.020  1.300
 RXR  CE   HE    single  0.970  0.020  1.090
 RXR  CE   HEA   single  0.970  0.020  1.090
 RXR  C10  S10   single  1.833  0.020  1.833
 RXR  C10  H10   single  0.970  0.020  1.090
 RXR  C10  H10A  single  0.970  0.020  1.090
 RXR  S10  HS10  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
 RXR  C5    N1   C2   114.89  3.000
 RXR  C5    N1   O1   122.52  3.000
 RXR  C2    N1   O1   122.44  3.000
 RXR  C9    C2   C8   110.42  3.000
 RXR  C9    C2   C3   113.14  3.000
 RXR  C8    C2   C3   111.90  3.000
 RXR  C9    C2   N1   110.63  3.000
 RXR  C8    C2   N1   110.14  3.000
 RXR  C3    C2   N1   100.20  3.000
 RXR  CE    C3   C4   125.63  3.000
 RXR  CE    C3   C2   122.06  3.000
 RXR  C4    C3   C2   112.30  3.000
 RXR  C10   C4   C5   122.10  3.000
 RXR  C10   C4   C3   125.61  3.000
 RXR  C5    C4   C3   112.29  3.000
 RXR  C7    C5   C6   110.54  3.000
 RXR  C7    C5   C4   112.42  3.000
 RXR  C6    C5   C4   112.77  3.000
 RXR  C7    C5   N1   110.17  3.000
 RXR  C6    C5   N1   110.35  3.000
 RXR  C4    C5   N1   100.17  3.000
 RXR  H6B   C6   H6A  108.70  3.000
 RXR  H6B   C6   H6   108.06  3.000
 RXR  H6A   C6   H6   107.92  3.000
 RXR  H6B   C6   C5   111.22  3.000
 RXR  H6A   C6   C5   110.37  3.000
 RXR  H6    C6   C5   110.47  3.000
 RXR  H7B   C7   H7A  108.61  3.000
 RXR  H7B   C7   H7   107.40  3.000
 RXR  H7A   C7   H7   108.27  3.000
 RXR  H7B   C7   C5   110.49  3.000
 RXR  H7A   C7   C5   111.41  3.000
 RXR  H7    C7   C5   110.53  3.000
 RXR  H8B   C8   H8A  108.68  3.000
 RXR  H8B   C8   H8   107.63  3.000
 RXR  H8A   C8   H8   108.21  3.000
 RXR  H8B   C8   C2   110.60  3.000
 RXR  H8A   C8   C2   111.21  3.000
 RXR  H8    C8   C2   110.41  3.000
 RXR  H9B   C9   H9A  108.73  3.000
 RXR  H9B   C9   H9   108.17  3.000
 RXR  H9A   C9   H9   107.74  3.000
 RXR  H9B   C9   C2   111.58  3.000
 RXR  H9A   C9   C2   110.24  3.000
 RXR  H9    C9   C2   110.27  3.000
 RXR  HSD   SD   CE    97.48  3.000
 RXR  HEA   CE   HE   108.04  3.000
 RXR  HEA   CE   SD   108.86  3.000
 RXR  HE    CE   SD   109.05  3.000
 RXR  HEA   CE   C3   111.41  3.000
 RXR  HE    CE   C3   110.89  3.000
 RXR  SD    CE   C3   108.55  3.000
 RXR  H10A  C10  H10  108.15  3.000
 RXR  H10A  C10  S10  108.97  3.000
 RXR  H10   C10  S10  109.02  3.000
 RXR  H10A  C10  C4   111.15  3.000
 RXR  H10   C10  C4   110.80  3.000
 RXR  S10   C10  C4   108.72  3.000
 RXR  HS10  S10  C10   97.37  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
 RXR  Var_01  C4   C3   C2  N1     2.77  30.0  1
 RXR  Var_02  C3   C4   C5  N1    -1.52  30.0  1
 RXR  Var_03  C4   C5   N1  C2     3.49  30.0  1
 RXR  Var_04  C5   C4   C3  C2    -0.83  30.0  1
 RXR  Var_05  C5   N1   C2  C3    -3.91  30.0  1
 RXR  Var_06  SD   CE   C3  C2    98.62  30.0  3
 RXR  Var_07  S10  C10  C4  C3   -81.25  30.0  3
 RXR  Var_08  H8   C8   C2  N1  -175.97  30.0  3
 RXR  Var_09  H9   C9   C2  N1   177.92  30.0  3
 RXR  Var_10  H6   C6   C5  N1   177.63  30.0  3
 RXR  Var_11  H7   C7   C5  N1   179.28  30.0  3

