# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 20:00:48 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (1R,2S)-2-phenylcyclopropanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1C[C@H]1c2ccccc2
#
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
 GJZ  GJZ  (1R,2S)-2-phenylcyclopropanamine  ligand  21  10  .  2022-09-22  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_GJZ
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
 GJZ  N1    N  NH2   0  -0.794   3.3564   0.4920   0.8437
 GJZ  C2    C  CH1   0  -0.405   1.1940   0.2847  -0.4587
 GJZ  C3    C  CH1   0  -0.071   2.2267  -0.3038   0.4575
 GJZ  C4    C  CH2   0  -0.492   2.0462  -0.8809  -0.9100
 GJZ  C5    C  CR6   0   0.231  -0.2590   0.1397  -0.2040
 GJZ  C6    C  CR16  0  -0.329  -1.1108   1.2184  -0.4416
 GJZ  C7    C  CR16  0  -0.356  -0.8191  -1.0485   0.2691
 GJZ  C8    C  CR16  0  -0.239  -2.4772   1.1179  -0.2150
 GJZ  C9    C  CR16  0  -0.236  -2.1836  -1.1513   0.4971
 GJZ  C10   C  CR16  0  -0.278  -3.0211  -0.0690   0.2558
 GJZ  HN1   H  HNH2  0   0.349   4.1846  -0.0893   0.8890
 GJZ  HN1A  H  HNH2  0   0.348   3.5470   1.1951   0.1408
 GJZ  H3    H  HCH1  0   0.247   1.8333  -0.9018   1.2752
 GJZ  H4    H  HCH2  0   0.248   1.5653  -1.8474  -1.0079
 GJZ  H4A   H  HCH2  0   0.260   2.8019  -0.6792  -1.6596
 GJZ  H6    H  HCR6  0   0.248  -0.6986   2.1501  -0.8112
 GJZ  H7    H  HCR6  0   0.247  -0.1899  -1.9100   0.4607
 GJZ  H8    H  HCR6  0   0.253  -3.1172   1.9692  -0.4097
 GJZ  H9    H  HCR6  0   0.254  -2.5947  -2.0837   0.8623
 GJZ  H10   H  HCR6  0   0.253  -4.0858  -0.1518   0.4313
 GJZ  H2    H  HCH1  0   0.263   1.4671   1.2435  -0.8901

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
 GJZ  N1   C3    single    1.435  0.020  1.435
 GJZ  C2   C3    single    1.501  0.020  1.501
 GJZ  C2   C4    single    1.513  0.020  1.513
 GJZ  C2   C5    single    1.482  0.020  1.482
 GJZ  C3   C4    single    1.495  0.020  1.495
 GJZ  C5   C6    aromatic  1.395  0.020  1.395
 GJZ  C5   C7    aromatic  1.396  0.020  1.396
 GJZ  C6   C8    aromatic  1.389  0.020  1.389
 GJZ  C7   C9    aromatic  1.387  0.020  1.387
 GJZ  C8   C10   aromatic  1.388  0.020  1.388
 GJZ  C9   C10   aromatic  1.390  0.020  1.390
 GJZ  N1   HN1   single    0.890  0.020  1.040
 GJZ  N1   HN1A  single    0.890  0.020  1.040
 GJZ  C2   H2    single    0.970  0.020  1.090
 GJZ  C3   H3    single    0.970  0.020  1.090
 GJZ  C4   H4    single    0.970  0.020  1.090
 GJZ  C4   H4A   single    0.970  0.020  1.090
 GJZ  C6   H6    single    0.930  0.020  1.080
 GJZ  C7   H7    single    0.930  0.020  1.080
 GJZ  C8   H8    single    0.930  0.020  1.080
 GJZ  C9   H9    single    0.930  0.020  1.080
 GJZ  C10  H10   single    0.930  0.020  1.080

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
 GJZ  HN1A  N1   HN1  106.00  3.000
 GJZ  HN1A  N1   C3   110.28  3.000
 GJZ  HN1   N1   C3   109.73  3.000
 GJZ  H2    C2   C5   113.64  3.000
 GJZ  H2    C2   C4   114.83  3.000
 GJZ  C5    C2   C4   121.88  3.000
 GJZ  H2    C2   C3   114.55  3.000
 GJZ  C5    C2   C3   122.09  3.000
 GJZ  C4    C2   C3    59.49  3.000
 GJZ  H3    C3   C4   115.60  3.000
 GJZ  H3    C3   C2   115.22  3.000
 GJZ  C4    C3   C2    60.66  3.000
 GJZ  H3    C3   N1   112.81  3.000
 GJZ  C4    C3   N1   123.73  3.000
 GJZ  C2    C3   N1   119.25  3.000
 GJZ  H4A   C4   H4   114.39  3.000
 GJZ  H4A   C4   C3   118.47  3.000
 GJZ  H4    C4   C3   118.71  3.000
 GJZ  H4A   C4   C2   117.12  3.000
 GJZ  H4    C4   C2   117.65  3.000
 GJZ  C3    C4   C2    59.85  3.000
 GJZ  C7    C5   C6   118.09  3.000
 GJZ  C7    C5   C2   122.33  3.000
 GJZ  C6    C5   C2   119.59  3.000
 GJZ  H6    C6   C8   119.48  3.000
 GJZ  H6    C6   C5   119.38  3.000
 GJZ  C8    C6   C5   121.14  3.000
 GJZ  H7    C7   C9   118.89  3.000
 GJZ  H7    C7   C5   120.23  3.000
 GJZ  C9    C7   C5   120.89  3.000
 GJZ  H8    C8   C10  120.12  3.000
 GJZ  H8    C8   C6   119.69  3.000
 GJZ  C10   C8   C6   120.19  3.000
 GJZ  H9    C9   C10  120.04  3.000
 GJZ  H9    C9   C7   119.53  3.000
 GJZ  C10   C9   C7   120.43  3.000
 GJZ  H10   C10  C9   120.34  3.000
 GJZ  H10   C10  C8   120.40  3.000
 GJZ  C9    C10  C8   119.26  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
 GJZ  CONST_01  C10  C8   C6  C5     0.00   0.0  0
 GJZ  CONST_02  C10  C9   C7  C5     0.00   0.0  0
 GJZ  CONST_03  C9   C7   C5  C6     0.00   0.0  0
 GJZ  CONST_04  C9   C10  C8  C6     0.00   0.0  0
 GJZ  CONST_05  C8   C6   C5  C7     0.00   0.0  0
 GJZ  CONST_06  C8   C10  C9  C7     0.00   0.0  0
 GJZ  CONST_07  C8   C6   C5  C2   180.00   0.0  0
 GJZ  CONST_08  C9   C7   C5  C2   180.00   0.0  0
 GJZ  CONST_09  H6   C6   C5  C2     0.00   0.0  0
 GJZ  CONST_10  H7   C7   C5  C2     0.00   0.0  0
 GJZ  CONST_11  H8   C8   C6  C5   180.00   0.0  0
 GJZ  CONST_12  H9   C9   C7  C5   180.00   0.0  0
 GJZ  CONST_13  H10  C10  C8  C6   180.00   0.0  0
 GJZ  Var_01    C6   C5   C2  C3   140.10  30.0  2
 GJZ  Var_02    C5   C2   C4  C3  -111.08  30.0  1
 GJZ  Var_03    HN1  N1   C3  C2  -142.33  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
 GJZ  chir_01  C2  C3  C4  C5  both
 GJZ  chir_02  C3  N1  C2  C4  both

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
 GJZ  plan-1  C2   0.020
 GJZ  plan-1  C5   0.020
 GJZ  plan-1  C6   0.020
 GJZ  plan-1  C7   0.020
 GJZ  plan-1  C8   0.020
 GJZ  plan-1  C9   0.020
 GJZ  plan-1  C10  0.020
 GJZ  plan-1  H6   0.020
 GJZ  plan-1  H7   0.020
 GJZ  plan-1  H8   0.020
 GJZ  plan-1  H9   0.020
 GJZ  plan-1  H10  0.020

