# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 00:51:11 2021
#   Inital geometry file: a 95 line input string
#   Ligand name: 1-[(1~{R},2~{R},4~{S})-2-bicyclo[2.2.1]heptanyl]-3-(2-pyridin-2-ylethyl)thiourea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: S=C(NCCc1ccccn1)N[C@@H]2C[C@H]3CC[C@@H]2C3
#
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
 SVM  SVM  1-[(1~{R},2~{R},4~{S})-2-bicyclo[2.2.1]heptanyl]-3-(2-pyridin-2-ylethyl)thiourea  ligand  40  19  .  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_SVM
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
 SVM  N1   N  N     0  -0.417  51.2664  120.1647  31.2605
 SVM  C4   C  CR16  0  -0.345  51.6790  117.9345  31.9888
 SVM  C5   C  CR16  0  -0.151  53.0215  118.0558  31.6670
 SVM  C6   C  CR16  0  -0.330  53.4746  119.2540  31.1365
 SVM  C7   C  CR16  0  -0.082  52.5527  120.2736  30.9529
 SVM  C8   C  CH1   0  -0.027  43.9598  120.2234  31.8627
 SVM  C10  C  CH1   0  -0.255  41.5923  119.7648  31.6255
 SVM  C13  C  CH1   0  -0.250  43.3088  120.7674  30.5772
 SVM  N    N  NH1   0  -0.623  47.1267  118.5969  31.0642
 SVM  C    C  C     0   0.427  46.2907  119.6232  31.2883
 SVM  C1   C  CH2   0  -0.273  48.5409  118.7224  30.8060
 SVM  C11  C  CH2   0  -0.437  41.2199  121.2514  31.6994
 SVM  C12  C  CH2   0  -0.447  42.4130  121.9435  30.9891
 SVM  C14  C  CH2   0  -0.441  42.2784  119.6818  30.2580
 SVM  C3   C  CR6   0   0.246  50.8280  119.0163  31.7747
 SVM  C9   C  CH2   0  -0.468  42.7743  119.5188  32.5726
 SVM  N2   N  NH1   0  -0.638  45.0357  119.2858  31.6131
 SVM  S    S  S1    0  -0.446  46.7884  121.2311  31.1628
 SVM  H1   H  HCR6  0   0.264  51.2908  117.0139  32.4048
 SVM  H2   H  HCR6  0   0.272  53.7025  117.2307  31.8303
 SVM  H3   H  HCR6  0   0.268  54.5129  119.4000  30.8724
 SVM  H4   H  HCR6  0   0.260  52.8702  121.2254  30.5407
 SVM  H5   H  HCH1  0   0.252  44.3670  121.0422  32.4580
 SVM  H6   H  HCH1  0   0.228  40.7549  119.0863  31.7901
 SVM  H7   H  HCH1  0   0.230  44.0382  121.0082  29.8050
 SVM  H8   H  HNH1  0   0.399  46.7849  117.6612  31.2261
 SVM  H9   H  HCH2  0   0.260  48.8556  117.8095  30.2997
 SVM  H10  H  HCH2  0   0.248  48.7072  119.5565  30.1253
 SVM  H11  H  HCH2  0   0.227  41.0851  121.5879  32.7293
 SVM  H12  H  HCH2  0   0.233  40.2829  121.4461  31.1741
 SVM  H13  H  HCH2  0   0.229  42.9396  122.6487  31.6359
 SVM  H14  H  HCH2  0   0.236  42.0805  122.4988  30.1106
 SVM  H15  H  HCH2  0   0.235  41.6195  119.9417  29.4261
 SVM  H16  H  HCH2  0   0.231  42.7210  118.7038  30.0506
 SVM  H17  H  HCH2  0   0.252  49.0296  119.8469  32.5620
 SVM  H18  H  HCH2  0   0.245  49.1757  118.0978  32.7701
 SVM  H19  H  HCH2  0   0.244  42.9618  118.4476  32.6862
 SVM  H20  H  HCH2  0   0.246  42.6009  119.9146  33.5742
 SVM  H21  H  HNH1  0   0.393  44.8050  118.3037  31.6541
 SVM  C2   C  CH2   0  -0.495  49.3630  118.9247  32.0824

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
 SVM  C13  C12  single    1.535  0.020  1.535
 SVM  C13  C14  single    1.530  0.020  1.530
 SVM  C13  C8   single    1.540  0.020  1.540
 SVM  C12  C11  single    1.551  0.020  1.551
 SVM  C14  C10  single    1.532  0.020  1.532
 SVM  C1   N    single    1.443  0.020  1.443
 SVM  C1   C2   single    1.532  0.020  1.532
 SVM  C5   C4   aromatic  1.386  0.020  1.386
 SVM  C5   C6   aromatic  1.387  0.020  1.387
 SVM  N    C    single    1.343  0.020  1.343
 SVM  C4   C3   aromatic  1.393  0.020  1.393
 SVM  C    S    double    1.688  0.020  1.688
 SVM  C    N2   single    1.340  0.020  1.340
 SVM  N2   C8   single    1.449  0.020  1.449
 SVM  C8   C9   single    1.551  0.020  1.551
 SVM  C11  C10  single    1.534  0.020  1.534
 SVM  C6   C7   aromatic  1.387  0.020  1.387
 SVM  C3   C2   single    1.500  0.020  1.500
 SVM  C3   N1   aromatic  1.332  0.020  1.332
 SVM  C10  C9   single    1.535  0.020  1.535
 SVM  C7   N1   aromatic  1.327  0.020  1.327
 SVM  C4   H1   single    0.930  0.020  1.080
 SVM  C5   H2   single    0.930  0.020  1.080
 SVM  C6   H3   single    0.930  0.020  1.080
 SVM  C7   H4   single    0.930  0.020  1.080
 SVM  C8   H5   single    0.970  0.020  1.090
 SVM  C10  H6   single    0.970  0.020  1.090
 SVM  C13  H7   single    0.970  0.020  1.090
 SVM  N    H8   single    0.860  0.020  1.020
 SVM  C1   H9   single    0.970  0.020  1.090
 SVM  C1   H10  single    0.970  0.020  1.090
 SVM  C11  H11  single    0.970  0.020  1.090
 SVM  C11  H12  single    0.970  0.020  1.090
 SVM  C12  H13  single    0.970  0.020  1.090
 SVM  C12  H14  single    0.970  0.020  1.090
 SVM  C14  H15  single    0.970  0.020  1.090
 SVM  C14  H16  single    0.970  0.020  1.090
 SVM  C2   H17  single    0.970  0.020  1.090
 SVM  C2   H18  single    0.970  0.020  1.090
 SVM  C9   H19  single    0.970  0.020  1.090
 SVM  C9   H20  single    0.970  0.020  1.090
 SVM  N2   H21  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
 SVM  C3   N1   C7   118.62  3.000
 SVM  H1   C4   C3   120.04  3.000
 SVM  H1   C4   C5   120.74  3.000
 SVM  C3   C4   C5   119.22  3.000
 SVM  H2   C5   C6   120.73  3.000
 SVM  H2   C5   C4   120.52  3.000
 SVM  C6   C5   C4   118.75  3.000
 SVM  H3   C6   C7   120.45  3.000
 SVM  H3   C6   C5   121.60  3.000
 SVM  C7   C6   C5   117.95  3.000
 SVM  H4   C7   C6   120.06  3.000
 SVM  H4   C7   N1   116.34  3.000
 SVM  C6   C7   N1   123.60  3.000
 SVM  H5   C8   N2   107.61  3.000
 SVM  H5   C8   C9   112.11  3.000
 SVM  N2   C8   C9   110.64  3.000
 SVM  H5   C8   C13  110.37  3.000
 SVM  C9   C8   C13  102.67  3.000
 SVM  N2   C8   C13  113.49  3.000
 SVM  H6   C10  C9   113.50  3.000
 SVM  H6   C10  C14  116.42  3.000
 SVM  C9   C10  C14  101.38  3.000
 SVM  H6   C10  C11  114.15  3.000
 SVM  C9   C10  C11  108.21  3.000
 SVM  C14  C10  C11  101.78  3.000
 SVM  H7   C13  C14  117.37  3.000
 SVM  H7   C13  C12  114.32  3.000
 SVM  C14  C13  C12  101.92  3.000
 SVM  H7   C13  C8   112.76  3.000
 SVM  C14  C13  C8   102.01  3.000
 SVM  C12  C13  C8   107.06  3.000
 SVM  H8   N    C1   116.18  3.000
 SVM  H8   N    C    118.10  3.000
 SVM  C1   N    C    125.01  3.000
 SVM  S    C    N2   122.29  3.000
 SVM  N2   C    N    115.56  3.000
 SVM  S    C    N    122.15  3.000
 SVM  H10  C1   H9   107.87  3.000
 SVM  H10  C1   C2   109.73  3.000
 SVM  H9   C1   C2   110.04  3.000
 SVM  H10  C1   N    109.14  3.000
 SVM  H9   C1   N    107.05  3.000
 SVM  C2   C1   N    112.86  3.000
 SVM  H12  C11  H11  107.04  3.000
 SVM  H12  C11  C12  111.11  3.000
 SVM  H11  C11  C12  112.91  3.000
 SVM  H12  C11  C10  110.98  3.000
 SVM  H11  C11  C10  111.96  3.000
 SVM  C12  C11  C10  102.91  3.000
 SVM  H14  C12  H13  107.17  3.000
 SVM  H14  C12  C11  111.18  3.000
 SVM  H13  C12  C11  112.81  3.000
 SVM  H14  C12  C13  110.60  3.000
 SVM  H13  C12  C13  111.85  3.000
 SVM  C11  C12  C13  103.29  3.000
 SVM  H16  C14  H15  108.21  3.000
 SVM  H16  C14  C13  113.68  3.000
 SVM  H15  C14  C13  113.33  3.000
 SVM  H16  C14  C10  113.52  3.000
 SVM  H15  C14  C10  113.36  3.000
 SVM  C13  C14  C10   94.41  3.000
 SVM  C2   C3   C4   121.19  3.000
 SVM  C2   C3   N1   116.94  3.000
 SVM  C4   C3   N1   121.85  3.000
 SVM  H20  C9   H19  106.70  3.000
 SVM  H20  C9   C10  112.71  3.000
 SVM  H19  C9   C10  110.68  3.000
 SVM  H20  C9   C8   112.14  3.000
 SVM  H19  C9   C8   111.20  3.000
 SVM  C10  C9   C8   103.50  3.000
 SVM  H21  N2   C    117.96  3.000
 SVM  H21  N2   C8   116.93  3.000
 SVM  C    N2   C8   125.07  3.000
 SVM  H18  C2   H17  108.10  3.000
 SVM  H18  C2   C3   110.06  3.000
 SVM  H17  C2   C3   109.68  3.000
 SVM  H18  C2   C1   109.44  3.000
 SVM  H17  C2   C1   108.29  3.000
 SVM  C3   C2   C1   111.19  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
 SVM  CONST_01  C5   C4   C3   N1     0.00   0.0  0
 SVM  CONST_02  C5   C6   C7   N1     0.00   0.0  0
 SVM  CONST_03  C7   C6   C5   C4     0.00   0.0  0
 SVM  CONST_04  C7   N1   C3   C4     0.00   0.0  0
 SVM  CONST_05  C3   C4   C5   C6     0.00   0.0  0
 SVM  CONST_06  C3   N1   C7   C6     0.00   0.0  0
 SVM  CONST_07  C2   C3   C4   C5   180.00   0.0  0
 SVM  CONST_08  C2   C3   N1   C7   180.00   0.0  0
 SVM  CONST_09  H1   C4   C3   N1   180.00   0.0  0
 SVM  CONST_10  H3   C6   C7   N1   180.00   0.0  0
 SVM  CONST_11  H4   C7   C6   C5   180.00   0.0  0
 SVM  CONST_12  H2   C5   C6   C7   180.00   0.0  0
 SVM  CONST_13  N    C    N2   C8   180.00   0.0  0
 SVM  CONST_14  S    C    N2   C8     0.00   0.0  0
 SVM  CONST_15  S    C    N    C1     0.00   0.0  0
 SVM  CONST_16  N2   C    N    C1   180.00   0.0  0
 SVM  CONST_17  H21  N2   C    N      0.00   0.0  0
 SVM  CONST_18  H8   N    C    N2     0.00   0.0  0
 SVM  Var_01    C13  C12  C11  C10    0.86  30.0  1
 SVM  Var_02    C1   C2   C3   N1    76.44  30.0  2
 SVM  Var_03    C3   C2   C1   N    178.59  30.0  3
 SVM  Var_04    C2   C1   N    C     80.18  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
 SVM  chir_01  C8   C13  N2   C9   positiv
 SVM  chir_02  C10  C9   C11  C14  negativ
 SVM  chir_03  C13  C8   C14  C12  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
 SVM  plan-1  N1   0.020
 SVM  plan-1  C4   0.020
 SVM  plan-1  C5   0.020
 SVM  plan-1  C6   0.020
 SVM  plan-1  C7   0.020
 SVM  plan-1  C3   0.020
 SVM  plan-1  H1   0.020
 SVM  plan-1  H2   0.020
 SVM  plan-1  H3   0.020
 SVM  plan-1  H4   0.020
 SVM  plan-1  C2   0.020
 SVM  plan-2  C8   0.020
 SVM  plan-2  N    0.020
 SVM  plan-2  C    0.020
 SVM  plan-2  C1   0.020
 SVM  plan-2  N2   0.020
 SVM  plan-2  S    0.020
 SVM  plan-2  H8   0.020
 SVM  plan-2  H21  0.020

