# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 20:06:28 2021
#   Inital geometry file: a 85 line input string
#   Ligand name: (1R,3S)-N-[(2H-1,3-benzodioxol-5-yl)methyl]-3-methylcyclopentan-1-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CC[C@H](C1)NCc2ccc3OCOc3c2
#
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
 S4D  S4D  (1R,3S)-N-[(2H-1,3-benzodioxol-5-yl)methyl]-3-methylcyclopentan-1-amine  ligand  36  17  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_S4D
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
 S4D  C10   C  CR16  0  -0.329  -10.9365  92.3641  106.1698
 S4D  C13   C  CR16  0  -0.404   -8.8564  90.5362  106.7584
 S4D  C15   C  CH2   0   0.068   -8.4603  93.6936  108.3616
 S4D  C17   C  CH2   0  -0.444  -12.7233  86.1728  105.1412
 S4D  C01   C  CH3   0  -0.655  -14.3994  84.7356  103.8429
 S4D  C02   C  CH1   0  -0.235  -12.9842  85.2773  103.9340
 S4D  C03   C  CH2   0  -0.423  -12.5803  86.1925  102.7774
 S4D  C04   C  CH2   0  -0.455  -11.3348  86.9356  103.2830
 S4D  C05   C  CH1   0  -0.041  -11.3928  86.8621  104.8301
 S4D  C08   C  CR6   0   0.067   -9.9455  90.1444  105.9647
 S4D  C09   C  CR16  0  -0.307  -10.9615  91.0513  105.6859
 S4D  C11   C  CR56  0   0.282   -9.8575  92.7236  106.9393
 S4D  C12   C  CR56  0   0.313   -8.8415  91.8279  107.2242
 S4D  N06   N  NH1   0  -0.605  -11.3117  88.1724  105.4555
 S4D  O14   O  O     0  -0.489   -7.8989  92.4442  107.9821
 S4D  O16   O  O     0  -0.488   -9.5754  93.9224  107.5120
 S4D  H101  H  HCR6  0   0.269  -11.7312  93.0620  105.9422
 S4D  H131  H  HCR6  0   0.265   -8.0599  89.8415  106.9940
 S4D  H151  H  HCH2  0   0.230   -8.7908  93.6499  109.4057
 S4D  H152  H  HCH2  0   0.245   -7.7241  94.4854  108.2278
 S4D  H172  H  HCH2  0   0.233  -12.7093  85.6322  106.0904
 S4D  H171  H  HCH2  0   0.211  -13.5120  86.9326  105.2034
 S4D  H011  H  HCH3  0   0.223  -14.6452  84.1107  104.7034
 S4D  H013  H  HCH3  0   0.212  -15.1259  85.5508  103.8047
 S4D  H012  H  HCH3  0   0.223  -14.5350  84.1274  102.9466
 S4D  H021  H  HCH1  0   0.217  -12.2837  84.4335  103.9703
 S4D  H032  H  HCH2  0   0.228  -12.4082  85.6526  101.8444
 S4D  H031  H  HCH2  0   0.211  -13.3928  86.9027  102.5919
 S4D  H042  H  HCH2  0   0.226  -10.4229  86.4668  102.9105
 S4D  H041  H  HCH2  0   0.229  -11.3189  87.9731  102.9434
 S4D  H051  H  HCH1  0   0.197  -10.5755  86.2100  105.1790
 S4D  H071  H  HCH2  0   0.213   -9.2242  88.1312  105.8983
 S4D  H072  H  HCH2  0   0.243   -9.6815  88.7900  104.3432
 S4D  H091  H  HCR6  0   0.248  -11.8010  90.7297  105.0839
 S4D  H061  H  HNH1  0   0.342  -11.5782  88.0878  106.4301
 S4D  C07   C  CH2   0  -0.318   -9.9842  88.7492  105.3945

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
 S4D  C02  C01   single    1.518  0.020  1.518
 S4D  C03  C02   single    1.529  0.020  1.529
 S4D  C04  C03   single    1.536  0.020  1.536
 S4D  C05  C04   single    1.550  0.020  1.550
 S4D  C07  N06   single    1.449  0.020  1.449
 S4D  C08  C07   single    1.508  0.020  1.508
 S4D  C09  C08   aromatic  1.390  0.020  1.390
 S4D  C10  C09   aromatic  1.399  0.020  1.399
 S4D  C11  C10   aromatic  1.373  0.020  1.373
 S4D  C12  C11   aromatic  1.384  0.020  1.384
 S4D  C13  C12   aromatic  1.373  0.020  1.373
 S4D  O14  C12   single    1.357  0.020  1.357
 S4D  C15  O14   single    1.421  0.020  1.421
 S4D  O16  C15   single    1.420  0.020  1.420
 S4D  N06  C05   single    1.454  0.020  1.454
 S4D  C17  C05   single    1.530  0.020  1.530
 S4D  C02  C17   single    1.526  0.020  1.526
 S4D  C08  C13   aromatic  1.403  0.020  1.403
 S4D  C11  O16   single    1.358  0.020  1.358
 S4D  C10  H101  single    0.930  0.020  1.080
 S4D  C13  H131  single    0.930  0.020  1.080
 S4D  C15  H151  single    0.970  0.020  1.090
 S4D  C15  H152  single    0.970  0.020  1.090
 S4D  C17  H172  single    0.970  0.020  1.090
 S4D  C17  H171  single    0.970  0.020  1.090
 S4D  C01  H011  single    0.970  0.020  1.090
 S4D  C01  H013  single    0.970  0.020  1.090
 S4D  C01  H012  single    0.970  0.020  1.090
 S4D  C02  H021  single    0.970  0.020  1.090
 S4D  C03  H032  single    0.970  0.020  1.090
 S4D  C03  H031  single    0.970  0.020  1.090
 S4D  C04  H042  single    0.970  0.020  1.090
 S4D  C04  H041  single    0.970  0.020  1.090
 S4D  C05  H051  single    0.970  0.020  1.090
 S4D  C07  H071  single    0.970  0.020  1.090
 S4D  C07  H072  single    0.970  0.020  1.090
 S4D  C09  H091  single    0.930  0.020  1.080
 S4D  N06  H061  single    0.890  0.020  1.040

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
 S4D  H101  C10  C11   121.75  3.000
 S4D  H101  C10  C09   121.29  3.000
 S4D  C11   C10  C09   116.96  3.000
 S4D  H131  C13  C12   121.44  3.000
 S4D  H131  C13  C08   120.98  3.000
 S4D  C12   C13  C08   117.57  3.000
 S4D  H152  C15  H151  110.47  3.000
 S4D  H152  C15  O16   109.87  3.000
 S4D  H151  C15  O16   109.85  3.000
 S4D  H152  C15  O14   109.82  3.000
 S4D  H151  C15  O14   109.78  3.000
 S4D  O16   C15  O14   106.98  3.000
 S4D  H171  C17  H172  107.62  3.000
 S4D  H171  C17  C05   108.94  3.000
 S4D  H172  C17  C05   112.86  3.000
 S4D  H171  C17  C02   109.17  3.000
 S4D  H172  C17  C02   113.53  3.000
 S4D  C05   C17  C02   104.61  3.000
 S4D  H012  C01  H013  107.72  3.000
 S4D  H012  C01  H011  107.48  3.000
 S4D  H013  C01  H011  107.76  3.000
 S4D  H012  C01  C02   111.34  3.000
 S4D  H013  C01  C02   110.83  3.000
 S4D  H011  C01  C02   111.53  3.000
 S4D  H021  C02  C03   108.46  3.000
 S4D  H021  C02  C01   108.82  3.000
 S4D  C03   C02  C01   114.48  3.000
 S4D  H021  C02  C17   108.42  3.000
 S4D  C03   C02  C17   101.66  3.000
 S4D  C01   C02  C17   114.61  3.000
 S4D  H031  C03  H032  107.04  3.000
 S4D  H031  C03  C04   110.10  3.000
 S4D  H032  C03  C04   113.13  3.000
 S4D  H031  C03  C02   108.68  3.000
 S4D  H032  C03  C02   113.09  3.000
 S4D  C04   C03  C02   104.76  3.000
 S4D  H041  C04  H042  106.86  3.000
 S4D  H041  C04  C05   110.85  3.000
 S4D  H042  C04  C05   110.59  3.000
 S4D  H041  C04  C03   111.67  3.000
 S4D  H042  C04  C03   110.95  3.000
 S4D  C05   C04  C03   105.98  3.000
 S4D  H051  C05  N06   110.83  3.000
 S4D  H051  C05  C04   108.44  3.000
 S4D  N06   C05  C04   112.61  3.000
 S4D  H051  C05  C17   108.28  3.000
 S4D  N06   C05  C17   111.53  3.000
 S4D  C04   C05  C17   104.88  3.000
 S4D  C09   C08  C07   120.60  3.000
 S4D  C09   C08  C13   119.90  3.000
 S4D  C07   C08  C13   119.48  3.000
 S4D  H091  C09  C08   119.00  3.000
 S4D  H091  C09  C10   119.02  3.000
 S4D  C08   C09  C10   121.98  3.000
 S4D  O16   C11  C12   109.39  3.000
 S4D  O16   C11  C10   129.09  3.000
 S4D  C12   C11  C10   121.52  3.000
 S4D  O14   C12  C11   109.32  3.000
 S4D  O14   C12  C13   128.61  3.000
 S4D  C11   C12  C13   122.07  3.000
 S4D  H061  N06  C07   108.33  3.000
 S4D  H061  N06  C05   108.88  3.000
 S4D  C07   N06  C05   113.07  3.000
 S4D  C12   O14  C15   105.89  3.000
 S4D  C11   O16  C15   105.85  3.000
 S4D  H072  C07  H071  105.63  3.000
 S4D  H072  C07  N06   107.98  3.000
 S4D  H071  C07  N06   112.93  3.000
 S4D  H072  C07  C08   108.76  3.000
 S4D  H071  C07  C08   109.18  3.000
 S4D  N06   C07  C08   112.09  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
 S4D  CONST_01  C13   C08  C09  C10    0.00   0.0  0
 S4D  CONST_02  C13   C12  C11  C10    0.00   0.0  0
 S4D  CONST_03  C11   C10  C09  C08    0.00   0.0  0
 S4D  CONST_04  C11   C12  C13  C08    0.00   0.0  0
 S4D  CONST_05  C12   C13  C08  C09    0.00   0.0  0
 S4D  CONST_06  C12   C11  C10  C09    0.00   0.0  0
 S4D  CONST_07  C07   C08  C09  C10  180.00   0.0  0
 S4D  CONST_08  C12   C13  C08  C07  180.00   0.0  0
 S4D  CONST_09  H091  C09  C08  C13  180.00   0.0  0
 S4D  CONST_10  H101  C10  C09  C08  180.00   0.0  0
 S4D  CONST_11  H131  C13  C08  C09  180.00   0.0  0
 S4D  Var_01    C11   C12  O14  C15    9.77  30.0  1
 S4D  Var_02    C12   C11  O16  C15   -9.78  30.0  1
 S4D  Var_03    C05   C04  C03  C02  -21.77  30.0  1
 S4D  Var_04    O14   C15  O16  C11   15.61  30.0  1
 S4D  Var_05    O16   C15  O14  C12  -15.62  30.0  1
 S4D  Var_06    N06   C07  C08  C13  139.50  30.0  2
 S4D  Var_07    C08   C07  N06  C05  176.12  30.0  1

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
 S4D  chir_01  C02  C01  C03  C17  negativ
 S4D  chir_02  C05  N06  C04  C17  positiv

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
 S4D  plan-1  C10   0.020
 S4D  plan-1  C13   0.020
 S4D  plan-1  C08   0.020
 S4D  plan-1  C09   0.020
 S4D  plan-1  C11   0.020
 S4D  plan-1  C12   0.020
 S4D  plan-1  O14   0.020
 S4D  plan-1  O16   0.020
 S4D  plan-1  H101  0.020
 S4D  plan-1  H131  0.020
 S4D  plan-1  H091  0.020
 S4D  plan-1  C07   0.020

