# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 20:07:51 2021
#   Inital geometry file: a 57 line input string
#   Ligand name: ~{N}-[[(3~{S})-oxolan-3-yl]methyl]cyclopropanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1C[C@@H](CNC2CC2)CO1
#
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
 S8V  S8V  ~{N}-[[(3~{S})-oxolan-3-yl]methyl]cyclopropanamine  ligand  25  10  .  2022-07-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_S8V
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
 S8V  C4   C  CR15  0  -0.281  38.5908   4.4168  73.6164
 S8V  C5   C  CH2   0  -0.497  38.3358   4.7811  72.1391
 S8V  C6   C  CH2   0  -0.171  39.7326   5.0741  71.5731
 S8V  C7   C  CH2   0  -0.184  40.0713   4.7781  73.7815
 S8V  C    C  CH2   0  -0.265  38.3043   2.9426  73.8785
 S8V  O    O  O     0  -0.491  40.6533   4.5597  72.5152
 S8V  C1   C  CH1   0  -0.090  38.0991   1.2355  75.5597
 S8V  C2   C  CH2   0  -0.523  38.8389   0.5018  76.6241
 S8V  C3   C  CH2   0  -0.504  39.0229   0.1100  75.1818
 S8V  H1   H  HCR5  0   0.243  37.9732   5.0153  74.2896
 S8V  H2   H  HCH2  0   0.249  37.6800   5.6456  72.0416
 S8V  H3   H  HCH2  0   0.229  39.9193   4.5972  70.6100
 S8V  H4   H  HCH2  0   0.228  40.6065   4.1699  74.5144
 S8V  H5   H  HCH2  0   0.210  40.1744   5.8289  74.0868
 S8V  H6   H  HNH1  0   0.342  39.3454   2.8113  75.6254
 S8V  H8   H  HCH2  0   0.227  37.2787   2.7281  73.5628
 S8V  H9   H  HCH2  0   0.196  38.9564   2.3250  73.2393
 S8V  H10  H  HCH1  0   0.247  37.0368   1.0223  75.4789
 S8V  H11  H  HCH2  0   0.252  38.2846  -0.1610  77.2761
 S8V  H12  H  HCH2  0   0.249  39.6614   1.0125  77.1126
 S8V  H13  H  HCH2  0   0.243  38.5983  -0.8264  74.8422
 S8V  H14  H  HCH2  0   0.244  39.9645   0.3717  74.7127
 S8V  H15  H  HCH2  0   0.242  37.8582   3.9549  71.6092
 S8V  H16  H  HCH2  0   0.203  39.8759   6.1550  71.4463
 S8V  N    N  NH1   0  -0.599  38.4128   2.6062  75.2862

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
 S8V  C6  C5   single  1.535  0.020  1.535
 S8V  C6  O    single  1.414  0.020  1.414
 S8V  C5  C4   single  1.543  0.020  1.543
 S8V  O   C7   single  1.411  0.020  1.411
 S8V  C4  C7   single  1.533  0.020  1.533
 S8V  C4  C    single  1.524  0.020  1.524
 S8V  C   N    single  1.451  0.020  1.451
 S8V  C3  C1   single  1.504  0.020  1.504
 S8V  C3  C2   single  1.506  0.020  1.506
 S8V  N   C1   single  1.432  0.020  1.432
 S8V  C1  C2   single  1.490  0.020  1.490
 S8V  C4  H1   single  0.970  0.020  1.090
 S8V  C5  H2   single  0.970  0.020  1.090
 S8V  C6  H3   single  0.970  0.020  1.090
 S8V  C7  H4   single  0.970  0.020  1.090
 S8V  C7  H5   single  0.970  0.020  1.090
 S8V  N   H6   single  0.890  0.020  1.040
 S8V  C   H8   single  0.970  0.020  1.090
 S8V  C   H9   single  0.970  0.020  1.090
 S8V  C1  H10  single  0.970  0.020  1.090
 S8V  C2  H11  single  0.970  0.020  1.090
 S8V  C2  H12  single  0.970  0.020  1.090
 S8V  C3  H13  single  0.970  0.020  1.090
 S8V  C3  H14  single  0.970  0.020  1.090
 S8V  C5  H15  single  0.970  0.020  1.090
 S8V  C6  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
 S8V  H1   C4  C    108.52  3.000
 S8V  H1   C4  C7   110.53  3.000
 S8V  C    C4  C7   113.01  3.000
 S8V  H1   C4  C5   111.55  3.000
 S8V  C    C4  C5   111.22  3.000
 S8V  C7   C4  C5   101.95  3.000
 S8V  H15  C5  H2   107.08  3.000
 S8V  H15  C5  C6   111.32  3.000
 S8V  H2   C5  C6   111.30  3.000
 S8V  H15  C5  C4   111.00  3.000
 S8V  H2   C5  C4   111.87  3.000
 S8V  C6   C5  C4   104.34  3.000
 S8V  H16  C6  H3   107.83  3.000
 S8V  H16  C6  O    110.50  3.000
 S8V  H3   C6  O    108.52  3.000
 S8V  H16  C6  C5   110.44  3.000
 S8V  H3   C6  C5   113.44  3.000
 S8V  O    C6  C5   106.10  3.000
 S8V  H5   C7  H4   107.45  3.000
 S8V  H5   C7  O    111.02  3.000
 S8V  H4   C7  O    108.30  3.000
 S8V  H5   C7  C4   110.23  3.000
 S8V  H4   C7  C4   114.47  3.000
 S8V  O    C7  C4   105.39  3.000
 S8V  H9   C   H8   106.10  3.000
 S8V  H9   C   N    112.85  3.000
 S8V  H8   C   N    107.72  3.000
 S8V  H9   C   C4   109.32  3.000
 S8V  H8   C   C4   108.43  3.000
 S8V  N    C   C4   112.14  3.000
 S8V  C7   O   C6   105.85  3.000
 S8V  H10  C1  C3   115.78  3.000
 S8V  H10  C1  C2   116.24  3.000
 S8V  C3   C1  C2    60.39  3.000
 S8V  H10  C1  N    112.81  3.000
 S8V  C2   C1  N    119.93  3.000
 S8V  C3   C1  N    122.24  3.000
 S8V  H12  C2  H11  113.92  3.000
 S8V  H12  C2  C3   117.47  3.000
 S8V  H11  C2  C3   118.69  3.000
 S8V  H12  C2  C1   117.81  3.000
 S8V  H11  C2  C1   118.53  3.000
 S8V  C3   C2  C1    60.29  3.000
 S8V  H14  C3  H13  114.44  3.000
 S8V  H14  C3  C2   117.24  3.000
 S8V  H13  C3  C2   118.52  3.000
 S8V  H14  C3  C1   117.49  3.000
 S8V  H13  C3  C1   119.01  3.000
 S8V  C2   C3  C1    59.32  3.000
 S8V  H6   N   C1   109.35  3.000
 S8V  H6   N   C    110.27  3.000
 S8V  C1   N   C    112.99  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
 S8V  Var_01  O    C6  C5  C4   14.77  30.0  1
 S8V  Var_02  C2   C3  C1  N   108.67  30.0  1
 S8V  Var_03  H11  C2  C3  C1  108.34  30.0  1
 S8V  Var_04  C1   N   C   C4  177.84  30.0  3
 S8V  Var_05  C3   C1  N   C    72.61  30.0  3

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
 S8V  chir_01  C4  C5  C7  C   positiv
 S8V  chir_02  C1  C3  N   C2  both

