# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:41:52 2022
#   Inital geometry file: a 50 line input string
#   Ligand name: (1~{S},2~{R})-2-azanylcyclopentane-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1CCC[C@@H]1C(O)=O
#
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
 9FB  9FB  '(1~{S},2~{R})-2-azanylcyclopentane-1-carboxylic acid'  ligand  19  9  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_9FB
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
 9FB  C64  C  C      0   0.417   7.0286  23.6185  -22.9850
 9FB  O16  O  O      0  -0.610   5.9096  23.5417  -23.5391
 9FB  C63  C  CH1    0  -0.367   8.2565  23.7519  -23.9007
 9FB  C66  C  CH2    0  -0.418   9.5520  23.1240  -23.3675
 9FB  C62  C  CH2    0  -0.434  10.4356  22.8776  -24.6092
 9FB  C65  C  CH1    0  -0.093   8.1261  23.1790  -25.3139
 9FB  C61  C  CH2    0  -0.438   9.5638  23.2527  -25.8213
 9FB  N13  N  NH2    0  -0.807   7.7028  21.7853  -25.2531
 9FB  O1   O  OC    -1  -0.603   7.2418  23.6342  -21.7555
 9FB  H1   H  HCH1   0   0.221   8.4317  24.8310  -24.0238
 9FB  H2   H  HCH2   0   0.208   9.3317  22.1807  -22.8660
 9FB  H3   H  HCH2   0   0.209  10.0421  23.7626  -22.6323
 9FB  H4   H  HCH2   0   0.215  10.7479  21.8338  -24.6603
 9FB  H5   H  HCH2   0   0.214  11.3503  23.4721  -24.5852
 9FB  H6   H  HCH1   0   0.191   7.4618  23.7990  -25.9318
 9FB  H7   H  HCH2   0   0.219   9.7374  22.6128  -26.6901
 9FB  H8   H  HCH2   0   0.213   9.7755  24.2776  -26.1371
 9FB  H9   H  HNH2   0   0.335   6.7516  21.7571  -24.9079
 9FB  H10  H  HNH2   0   0.330   7.6758  21.4016  -26.1900

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
 9FB  C61  C65  single  1.526  0.020  1.526
 9FB  C61  C62  single  1.539  0.020  1.539
 9FB  N13  C65  single  1.458  0.020  1.458
 9FB  C65  C63  single  1.531  0.020  1.531
 9FB  C62  C66  single  1.544  0.020  1.544
 9FB  C63  C66  single  1.535  0.020  1.535
 9FB  C63  C64  single  1.538  0.020  1.538
 9FB  O16  C64  deloc   1.251  0.020  1.251
 9FB  C64  O1   deloc   1.248  0.020  1.248
 9FB  C63  H1   single  0.970  0.020  1.090
 9FB  C66  H2   single  0.970  0.020  1.090
 9FB  C66  H3   single  0.970  0.020  1.090
 9FB  C62  H4   single  0.970  0.020  1.090
 9FB  C62  H5   single  0.970  0.020  1.090
 9FB  C65  H6   single  0.970  0.020  1.090
 9FB  C61  H7   single  0.970  0.020  1.090
 9FB  C61  H8   single  0.970  0.020  1.090
 9FB  N13  H9   single  0.890  0.020  1.040
 9FB  N13  H10  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
 9FB  O1   C64  C63  116.69  3.000
 9FB  O1   C64  O16  126.15  3.000
 9FB  C63  C64  O16  117.12  3.000
 9FB  H1   C63  C65  106.10  3.000
 9FB  H1   C63  C66  107.80  3.000
 9FB  C65  C63  C66  103.86  3.000
 9FB  H1   C63  C64  106.19  3.000
 9FB  C66  C63  C64  115.57  3.000
 9FB  C65  C63  C64  116.70  3.000
 9FB  H3   C66  H2   106.70  3.000
 9FB  H3   C66  C62  112.25  3.000
 9FB  H2   C66  C62  110.33  3.000
 9FB  H3   C66  C63  111.96  3.000
 9FB  H2   C66  C63  110.06  3.000
 9FB  C62  C66  C63  105.60  3.000
 9FB  H5   C62  H4   106.40  3.000
 9FB  H5   C62  C61  111.06  3.000
 9FB  H4   C62  C61  111.00  3.000
 9FB  H5   C62  C66  112.03  3.000
 9FB  H4   C62  C66  110.75  3.000
 9FB  C61  C62  C66  105.68  3.000
 9FB  H6   C65  N13  112.79  3.000
 9FB  H6   C65  C61  110.81  3.000
 9FB  N13  C65  C61  109.48  3.000
 9FB  H6   C65  C63  111.07  3.000
 9FB  N13  C65  C63  110.12  3.000
 9FB  C61  C65  C63  102.04  3.000
 9FB  H8   C61  H7   106.77  3.000
 9FB  H8   C61  C65  108.88  3.000
 9FB  H7   C61  C65  112.68  3.000
 9FB  H8   C61  C62  110.26  3.000
 9FB  H7   C61  C62  113.16  3.000
 9FB  C65  C61  C62  105.07  3.000
 9FB  H10  N13  H9   106.26  3.000
 9FB  H10  N13  C65  109.35  3.000
 9FB  H9   N13  C65  108.28  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
 9FB  Var_01  C61  C62  C66  C63   -5.09  30.0  1
 9FB  Var_02  C65  C61  C62  C66  -20.81  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
 9FB  chir_01  C63  C65  C66  C64  positiv
 9FB  chir_02  C65  N13  C63  C61  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
 9FB  plan-1  C64  0.020
 9FB  plan-1  O16  0.020
 9FB  plan-1  C63  0.020
 9FB  plan-1  O1   0.020

