# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 13:23:03 2022
#   Inital geometry file: a 56 line input string
#   Ligand name: (1S,3S,4S)-3-amino-4-(fluoromethyl)cyclopentane-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1C[C@H](C[C@@H]1CF)C(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
 I2V  I2V  "(1S,3S,4S)-3-amino-4-(fluoromethyl)cyclopentane-1-carboxylic acid"  ligand  22  11  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_I2V
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
 I2V  C10  C  CH2    0  -0.425  -6.7575  -60.4380  -24.1352
 I2V  C20  C  CH2    0   0.009  -6.6187  -59.1454  -26.3229
 I2V  C01  C  CH2    0  -0.429  -4.9131  -61.9925  -24.5572
 I2V  C02  C  CR15   0  -0.373  -6.0397  -61.6731  -23.5554
 I2V  C03  C  C      0   0.410  -5.5404  -61.5478  -22.0982
 I2V  C06  C  CR15   0  -0.065  -5.2852  -61.2485  -25.8349
 I2V  C08  C  CR15   0  -0.312  -5.8780  -59.9487  -25.2862
 I2V  F21  F  F      0  -0.386  -7.2468  -58.0471  -25.7274
 I2V  N07  N  NH2    0  -0.802  -4.1392  -61.0425  -26.7068
 I2V  O04  O  O      0  -0.614  -4.6939  -62.3946  -21.7425
 I2V  O05  O  OC    -1  -0.599  -6.0336  -60.6535  -21.3822
 I2V  H1   H  HCH2   0   0.230  -6.9200  -59.6725  -23.3792
 I2V  H2   H  HCH2   0   0.208  -7.7432  -60.7131  -24.5237
 I2V  H3   H  HCH2   0   0.191  -7.3946  -59.7541  -26.7955
 I2V  H4   H  HCH2   0   0.207  -5.9532  -58.7607  -27.0996
 I2V  H5   H  HCH2   0   0.221  -4.7777  -63.0628  -24.7239
 I2V  H6   H  HCH2   0   0.208  -3.9546  -61.6010  -24.2036
 I2V  H7   H  HCR5   0   0.229  -6.7451  -62.5124  -23.5489
 I2V  H8   H  HCR5   0   0.187  -6.1013  -61.8002  -26.3335
 I2V  H9   H  HCR5   0   0.223  -5.0451  -59.3531  -24.8914
 I2V  H10  H  HNH2   0   0.342  -3.7436  -61.9432  -26.9494
 I2V  H11  H  HNH2   0   0.340  -4.4416  -60.6443  -27.5879

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
 I2V  C20  F21  single  1.398  0.020  1.398
 I2V  C20  C08  single  1.506  0.020  1.506
 I2V  N07  C06  single  1.455  0.020  1.455
 I2V  C06  C08  single  1.530  0.020  1.530
 I2V  C06  C01  single  1.525  0.020  1.525
 I2V  C08  C10  single  1.529  0.020  1.529
 I2V  C01  C02  single  1.541  0.020  1.541
 I2V  C10  C02  single  1.542  0.020  1.542
 I2V  C02  C03  single  1.545  0.020  1.545
 I2V  C03  O04  deloc   1.249  0.020  1.249
 I2V  C03  O05  deloc   1.247  0.020  1.247
 I2V  C10  H1   single  0.970  0.020  1.090
 I2V  C10  H2   single  0.970  0.020  1.090
 I2V  C20  H3   single  0.970  0.020  1.090
 I2V  C20  H4   single  0.970  0.020  1.090
 I2V  C01  H5   single  0.970  0.020  1.090
 I2V  C01  H6   single  0.970  0.020  1.090
 I2V  C02  H7   single  0.970  0.020  1.090
 I2V  C06  H8   single  0.970  0.020  1.090
 I2V  C08  H9   single  0.970  0.020  1.090
 I2V  N07  H10  single  0.890  0.020  1.040
 I2V  N07  H11  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
 I2V  H2   C10  H1   106.79  3.000
 I2V  H2   C10  C08  109.35  3.000
 I2V  H1   C10  C08  112.57  3.000
 I2V  H2   C10  C02  110.57  3.000
 I2V  H1   C10  C02  111.83  3.000
 I2V  C08  C10  C02  105.76  3.000
 I2V  H4   C20  H3   108.72  3.000
 I2V  H4   C20  F21  107.44  3.000
 I2V  H3   C20  F21  107.61  3.000
 I2V  H4   C20  C08  112.17  3.000
 I2V  H3   C20  C08  110.45  3.000
 I2V  F21  C20  C08  110.28  3.000
 I2V  H6   C01  H5   106.95  3.000
 I2V  H6   C01  C06  108.06  3.000
 I2V  H5   C01  C06  112.38  3.000
 I2V  H6   C01  C02  110.87  3.000
 I2V  H5   C01  C02  113.15  3.000
 I2V  C06  C01  C02  105.38  3.000
 I2V  H7   C02  C03  105.33  3.000
 I2V  H7   C02  C01  108.39  3.000
 I2V  C03  C02  C01  113.17  3.000
 I2V  H7   C02  C10  108.42  3.000
 I2V  C03  C02  C10  116.11  3.000
 I2V  C01  C02  C10  105.19  3.000
 I2V  O05  C03  O04  126.20  3.000
 I2V  O05  C03  C02  118.14  3.000
 I2V  O04  C03  C02  115.63  3.000
 I2V  H8   C06  N07  112.48  3.000
 I2V  H8   C06  C08  107.45  3.000
 I2V  N07  C06  C08  113.56  3.000
 I2V  H8   C06  C01  108.36  3.000
 I2V  C08  C06  C01  102.04  3.000
 I2V  N07  C06  C01  112.29  3.000
 I2V  H9   C08  C06  107.22  3.000
 I2V  H9   C08  C20  109.35  3.000
 I2V  C06  C08  C20  113.37  3.000
 I2V  H9   C08  C10  109.85  3.000
 I2V  C06  C08  C10  102.76  3.000
 I2V  C20  C08  C10  113.95  3.000
 I2V  H11  N07  H10  104.94  3.000
 I2V  H11  N07  C06  109.99  3.000
 I2V  H10  N07  C06  108.97  3.000

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
 I2V  chir_01  C02  C01  C10  C03  positiv
 I2V  chir_02  C06  N07  C01  C08  negativ
 I2V  chir_03  C08  C10  C06  C20  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
 I2V  plan-1  C02  0.020
 I2V  plan-1  C03  0.020
 I2V  plan-1  O04  0.020
 I2V  plan-1  O05  0.020

