# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 17:48:23 2021
#   Inital geometry file: a 71 line input string
#   Ligand name: 2-methyl-2-{[(3-methylthiophen-2-yl)methyl]amino}propan-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccsc1CNC(C)(C)CO
#
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
 RX7  RX7  2-methyl-2-{[(3-methylthiophen-2-yl)methyl]amino}propan-1-ol  ligand  30  13  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_RX7
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
 RX7  C4   C  CR5   0  -0.238  19.9195  -2.0950  10.4381
 RX7  C5   C  CH2   0  -0.337  20.5674  -0.7536  10.2798
 RX7  C6   C  CT    0   0.050  22.5667   0.3410   9.2928
 RX7  C7   C  CH3   0  -0.669  23.0880   0.8370  10.6413
 RX7  C8   C  CH3   0  -0.661  21.7972   1.4702   8.5933
 RX7  N    N  NH1   0  -0.583  21.7754  -0.8756   9.4837
 RX7  C    C  CH3   0  -0.743  21.6271  -3.1609  11.9719
 RX7  O    O  OH1   0  -0.675  23.3747  -0.5431   7.2044
 RX7  C1   C  CR5   0   0.157  20.3739  -3.1690  11.1526
 RX7  C2   C  CR15  0  -0.212  19.5011  -4.2912  11.0403
 RX7  C3   C  CR15  0  -0.474  18.4191  -4.0574  10.2486
 RX7  C9   C  CH2   0  -0.121  23.7869  -0.0560   8.4624
 RX7  S    S  S2    0   0.196  18.4451  -2.4629   9.6271
 RX7  H1   H  HCH2  0   0.245  20.8312  -0.3807  11.2717
 RX7  H2   H  HCH2  0   0.221  19.8356  -0.0406   9.8746
 RX7  H3   H  HCH3  0   0.235  22.2948   1.2627  11.2569
 RX7  H4   H  HCH3  0   0.234  23.5535   0.0253  11.2027
 RX7  H5   H  HCH3  0   0.232  23.8319   1.6212  10.4949
 RX7  H6   H  HCH3  0   0.228  20.9340   1.7868   9.1814
 RX7  H7   H  HCH3  0   0.222  22.4305   2.3491   8.4564
 RX7  H8   H  HCH3  0   0.229  21.4332   1.1631   7.6120
 RX7  H9   H  HNH1  0   0.337  21.5266  -1.2495   8.5757
 RX7  H11  H  HCH3  0   0.242  21.4393  -2.8036  12.9868
 RX7  H12  H  HCH3  0   0.242  22.0476  -4.1630  12.0563
 RX7  H13  H  HCH3  0   0.249  22.3802  -2.5134  11.5247
 RX7  H14  H  HOH1  0   0.456  24.1480  -0.8788   6.7432
 RX7  H15  H  HCR5  0   0.257  19.6809  -5.2371  11.5342
 RX7  H16  H  HCR5  0   0.289  17.6160  -4.7341  10.0007
 RX7  H17  H  HCH2  0   0.201  24.3503  -0.8171   9.0184
 RX7  H18  H  HCH2  0   0.189  24.4392   0.8211   8.3544

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
 RX7  O   C9   single    1.411  0.020  1.411
 RX7  C9  C6   single    1.528  0.020  1.528
 RX7  C8  C6   single    1.535  0.020  1.535
 RX7  C6  N    single    1.464  0.020  1.464
 RX7  C6  C7   single    1.529  0.020  1.529
 RX7  S   C3   aromatic  1.711  0.020  1.711
 RX7  S   C4   aromatic  1.722  0.020  1.722
 RX7  N   C5   single    1.452  0.020  1.452
 RX7  C3  C2   aromatic  1.361  0.020  1.361
 RX7  C5  C4   single    1.498  0.020  1.498
 RX7  C4  C1   aromatic  1.368  0.020  1.368
 RX7  C2  C1   aromatic  1.426  0.020  1.426
 RX7  C1  C    single    1.497  0.020  1.497
 RX7  C5  H1   single    0.970  0.020  1.090
 RX7  C5  H2   single    0.970  0.020  1.090
 RX7  C7  H3   single    0.970  0.020  1.090
 RX7  C7  H4   single    0.970  0.020  1.090
 RX7  C7  H5   single    0.970  0.020  1.090
 RX7  C8  H6   single    0.970  0.020  1.090
 RX7  C8  H7   single    0.970  0.020  1.090
 RX7  C8  H8   single    0.970  0.020  1.090
 RX7  N   H9   single    0.890  0.020  1.040
 RX7  C   H11  single    0.970  0.020  1.090
 RX7  C   H12  single    0.970  0.020  1.090
 RX7  C   H13  single    0.970  0.020  1.090
 RX7  O   H14  single    0.850  0.020  0.980
 RX7  C2  H15  single    0.930  0.020  1.080
 RX7  C3  H16  single    0.930  0.020  1.080
 RX7  C9  H17  single    0.970  0.020  1.090
 RX7  C9  H18  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
 RX7  S    C4  C1   111.26  3.000
 RX7  C1   C4  C5   127.93  3.000
 RX7  S    C4  C5   120.78  3.000
 RX7  H2   C5  H1   105.91  3.000
 RX7  H2   C5  N    113.98  3.000
 RX7  H1   C5  N    109.01  3.000
 RX7  H2   C5  C4   109.38  3.000
 RX7  H1   C5  C4   108.32  3.000
 RX7  N    C5  C4   110.03  3.000
 RX7  C9   C6  N    106.65  3.000
 RX7  N    C6  C8   113.57  3.000
 RX7  C9   C6  C8   110.10  3.000
 RX7  N    C6  C7   109.82  3.000
 RX7  C8   C6  C7   109.53  3.000
 RX7  C9   C6  C7   106.94  3.000
 RX7  H5   C7  H4   108.24  3.000
 RX7  H5   C7  H3   106.93  3.000
 RX7  H4   C7  H3   108.08  3.000
 RX7  H5   C7  C6   110.33  3.000
 RX7  H4   C7  C6   110.97  3.000
 RX7  H3   C7  C6   112.12  3.000
 RX7  H8   C8  H7   107.90  3.000
 RX7  H8   C8  H6   107.61  3.000
 RX7  H7   C8  H6   107.03  3.000
 RX7  H8   C8  C6   111.72  3.000
 RX7  H7   C8  C6   111.01  3.000
 RX7  H6   C8  C6   111.36  3.000
 RX7  H9   N   C6   108.83  3.000
 RX7  H9   N   C5   108.55  3.000
 RX7  C6   N   C5   116.83  3.000
 RX7  H13  C   H12  108.15  3.000
 RX7  H13  C   H11  107.81  3.000
 RX7  H12  C   H11  107.17  3.000
 RX7  H13  C   C1   110.93  3.000
 RX7  H12  C   C1   111.12  3.000
 RX7  H11  C   C1   111.49  3.000
 RX7  H14  O   C9   108.27  3.000
 RX7  C2   C1  C    124.02  3.000
 RX7  C    C1  C4   124.04  3.000
 RX7  C2   C1  C4   111.93  3.000
 RX7  H15  C2  C3   123.22  3.000
 RX7  H15  C2  C1   123.38  3.000
 RX7  C3   C2  C1   113.40  3.000
 RX7  H16  C3  S    120.81  3.000
 RX7  H16  C3  C2   128.14  3.000
 RX7  S    C3  C2   111.05  3.000
 RX7  H18  C9  H17  107.37  3.000
 RX7  H18  C9  O    111.20  3.000
 RX7  H17  C9  O    111.23  3.000
 RX7  H18  C9  C6   108.68  3.000
 RX7  H17  C9  C6   108.33  3.000
 RX7  O    C9  C6   109.93  3.000
 RX7  C3   S   C4    92.35  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
 RX7  CONST_01  C2   C3  S   C4     0.00   0.0  0
 RX7  CONST_02  C3   C2  C1  C4     0.00   0.0  0
 RX7  CONST_03  C3   S   C4  C1     0.00   0.0  0
 RX7  CONST_04  S    C3  C2  C1     0.00   0.0  0
 RX7  CONST_05  S    C4  C1  C2     0.00   0.0  0
 RX7  CONST_06  C3   S   C4  C5   180.00   0.0  0
 RX7  CONST_07  C2   C1  C4  C5   180.00   0.0  0
 RX7  CONST_08  S    C4  C1  C    180.00   0.0  0
 RX7  CONST_09  C3   C2  C1  C    180.00   0.0  0
 RX7  CONST_10  H16  C3  S   C4   180.00   0.0  0
 RX7  CONST_11  H15  C2  C1  C4   180.00   0.0  0
 RX7  Var_01    S    C4  C5  N   -108.85  30.0  2
 RX7  Var_02    H11  C   C1  C4    87.50  30.0  2
 RX7  Var_03    C6   N   C5  C4  -176.97  30.0  1
 RX7  Var_04    C9   C6  N   C5   178.59  30.0  2
 RX7  Var_05    O    C9  C6  C7   179.19  30.0  3
 RX7  Var_06    H6   C8  C6  C7   -61.30  30.0  3
 RX7  Var_07    H3   C7  C6  C8    53.41  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
 RX7  plan-1  C4   0.020
 RX7  plan-1  C5   0.020
 RX7  plan-1  C    0.020
 RX7  plan-1  C1   0.020
 RX7  plan-1  C2   0.020
 RX7  plan-1  C3   0.020
 RX7  plan-1  S    0.020
 RX7  plan-1  H15  0.020
 RX7  plan-1  H16  0.020

