# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 16:20:08 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: [1-(aminomethyl)cyclohexyl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC1(CCCCC1)CC(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
 GBN  GBN  '[1-(aminomethyl)cyclohexyl]acetic acid'  ligand  28  12  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GBN
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
 GBN  N1    N  NH2    0  -0.802   0.8567   2.7819   0.2327
 GBN  C2    C  CH2    0  -0.263   1.0269   1.6362  -0.6502
 GBN  C3    C  CH2    0  -0.579  -1.2824   0.7901  -0.3308
 GBN  C1R   C  CT     0  -0.068   0.2003   0.4017  -0.2345
 GBN  C2R   C  CH2    0  -0.415   0.5246  -0.7333  -1.2213
 GBN  C3R   C  CH2    0  -0.440   1.9425  -1.2868  -1.0873
 GBN  C4R   C  CH2    0  -0.422   2.2428  -1.7069   0.3474
 GBN  C5R   C  CH2    0  -0.441   1.9884  -0.5618   1.3224
 GBN  C6R   C  CH2    0  -0.400   0.5624  -0.0331   1.1918
 GBN  C     C  C      0   0.417  -2.4123  -0.2198  -0.0287
 GBN  OA    O  OC    -1  -0.633  -3.5630   0.2665  -0.0925
 GBN  OB    O  O      0  -0.592  -2.1458  -1.4059   0.2498
 GBN  HN11  H  HNH2   0   0.344   1.5312   3.4932  -0.0175
 GBN  HN12  H  HNH2   0   0.338  -0.0482   3.2059   0.0769
 GBN  H21   H  HCH2   0   0.187   0.7777   1.8638  -1.6994
 GBN  H22   H  HCH2   0   0.220   2.0894   1.3858  -0.6445
 GBN  H31   H  HCH2   0   0.218  -1.4696   1.6421   0.3329
 GBN  H32   H  HCH2   0   0.218  -1.4694   1.1737  -1.3433
 GBN  H2R1  H  HCH2   0   0.230  -0.1868  -1.5425  -1.0545
 GBN  H2R2  H  HCH2   0   0.199   0.3570  -0.3800  -2.2460
 GBN  H3R1  H  HCH2   0   0.219   2.0647  -2.1380  -1.7628
 GBN  H3R2  H  HCH2   0   0.205   2.6794  -0.5441  -1.4089
 GBN  H4R1  H  HCH2   0   0.201   1.6024  -2.5539   0.6191
 GBN  H4R2  H  HCH2   0   0.216   3.2742  -2.0603   0.4317
 GBN  H5R1  H  HCH2   0   0.217   2.1598  -0.8995   2.3487
 GBN  H5R2  H  HCH2   0   0.205   2.7139   0.2392   1.1458
 GBN  H6R1  H  HCH2   0   0.204   0.4119   0.8054   1.8765
 GBN  H6R2  H  HCH2   0   0.218  -0.1294  -0.8214   1.4947

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
 GBN  N1   C2    single  1.456  0.020  1.456
 GBN  N1   HN11  single  0.890  0.020  1.040
 GBN  N1   HN12  single  0.890  0.020  1.040
 GBN  C2   C1R   single  1.543  0.020  1.543
 GBN  C2   H21   single  0.970  0.020  1.090
 GBN  C2   H22   single  0.970  0.020  1.090
 GBN  C3   C1R   single  1.536  0.020  1.536
 GBN  C3   C     single  1.545  0.020  1.545
 GBN  C3   H31   single  0.970  0.020  1.090
 GBN  C3   H32   single  0.970  0.020  1.090
 GBN  C1R  C2R   single  1.539  0.020  1.539
 GBN  C1R  C6R   single  1.534  0.020  1.534
 GBN  C2R  C3R   single  1.528  0.020  1.528
 GBN  C2R  H2R1  single  0.970  0.020  1.090
 GBN  C2R  H2R2  single  0.970  0.020  1.090
 GBN  C3R  C4R   single  1.525  0.020  1.525
 GBN  C3R  H3R1  single  0.970  0.020  1.090
 GBN  C3R  H3R2  single  0.970  0.020  1.090
 GBN  C4R  C5R   single  1.525  0.020  1.525
 GBN  C4R  H4R1  single  0.970  0.020  1.090
 GBN  C4R  H4R2  single  0.970  0.020  1.090
 GBN  C5R  C6R   single  1.526  0.020  1.526
 GBN  C5R  H5R1  single  0.970  0.020  1.090
 GBN  C5R  H5R2  single  0.970  0.020  1.090
 GBN  C6R  H6R1  single  0.970  0.020  1.090
 GBN  C6R  H6R2  single  0.970  0.020  1.090
 GBN  C    OA    deloc   1.251  0.020  1.251
 GBN  C    OB    deloc   1.247  0.020  1.247

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
 GBN  HN12  N1   HN11  105.28  3.000
 GBN  HN12  N1   C2    109.94  3.000
 GBN  HN11  N1   C2    108.98  3.000
 GBN  H22   C2   H21   105.81  3.000
 GBN  H22   C2   C1R   109.66  3.000
 GBN  H21   C2   C1R   107.49  3.000
 GBN  H22   C2   N1    106.92  3.000
 GBN  H21   C2   N1    112.85  3.000
 GBN  C1R   C2   N1    113.80  3.000
 GBN  H32   C3   H31   104.92  3.000
 GBN  H32   C3   C     106.49  3.000
 GBN  H31   C3   C     105.35  3.000
 GBN  H32   C3   C1R   108.09  3.000
 GBN  H31   C3   C1R   108.88  3.000
 GBN  C     C3   C1R   121.90  3.000
 GBN  C6R   C1R  C2R   109.72  3.000
 GBN  C6R   C1R  C3    110.97  3.000
 GBN  C2R   C1R  C3    110.48  3.000
 GBN  C6R   C1R  C2    110.53  3.000
 GBN  C2R   C1R  C2    107.73  3.000
 GBN  C3    C1R  C2    107.33  3.000
 GBN  H2R2  C2R  H2R1  106.40  3.000
 GBN  H2R2  C2R  C3R   109.90  3.000
 GBN  H2R1  C2R  C3R   108.86  3.000
 GBN  H2R2  C2R  C1R   109.23  3.000
 GBN  H2R1  C2R  C1R   108.17  3.000
 GBN  C3R   C2R  C1R   113.99  3.000
 GBN  H3R2  C3R  H3R1  105.75  3.000
 GBN  H3R2  C3R  C4R   109.32  3.000
 GBN  H3R1  C3R  C4R   110.16  3.000
 GBN  H3R2  C3R  C2R   110.69  3.000
 GBN  H3R1  C3R  C2R   109.36  3.000
 GBN  C4R   C3R  C2R   111.41  3.000
 GBN  H4R2  C4R  H4R1  106.39  3.000
 GBN  H4R2  C4R  C5R   110.53  3.000
 GBN  H4R1  C4R  C5R   108.92  3.000
 GBN  H4R2  C4R  C3R   110.32  3.000
 GBN  H4R1  C4R  C3R   109.33  3.000
 GBN  C5R   C4R  C3R   111.21  3.000
 GBN  H5R2  C5R  H5R1  105.86  3.000
 GBN  H5R2  C5R  C6R   110.60  3.000
 GBN  H5R1  C5R  C6R   109.49  3.000
 GBN  H5R2  C5R  C4R   109.60  3.000
 GBN  H5R1  C5R  C4R   109.99  3.000
 GBN  C6R   C5R  C4R   111.17  3.000
 GBN  H6R2  C6R  H6R1  107.03  3.000
 GBN  H6R2  C6R  C5R   108.55  3.000
 GBN  H6R1  C6R  C5R   109.92  3.000
 GBN  H6R2  C6R  C1R   108.24  3.000
 GBN  H6R1  C6R  C1R   109.42  3.000
 GBN  C5R   C6R  C1R   113.46  3.000
 GBN  OB    C    OA    125.29  3.000
 GBN  OB    C    C3    120.59  3.000
 GBN  OA    C    C3    114.12  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
 GBN  Var_01  C4R   C3R  C2R  C1R   53.40  30.0  1
 GBN  Var_02  C4R   C5R  C6R  C1R  -55.39  30.0  1
 GBN  Var_03  C5R   C4R  C3R  C2R  -54.61  30.0  1
 GBN  Var_04  C6R   C5R  C4R  C3R   55.65  30.0  1
 GBN  Var_05  OA    C    C3   C1R  176.90  30.0  3
 GBN  Var_06  HN11  N1   C2   C1R  171.28  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
 GBN  chir_01  C1R  C3  C2R  C6R  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
 GBN  plan-1  C3  0.020
 GBN  plan-1  C   0.020
 GBN  plan-1  OA  0.020
 GBN  plan-1  OB  0.020

