# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 16:46:16 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: trans-4-(aminomethyl)cyclohexanecarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@@H]1CC[C@H](CC1)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
 AMH  AMH  'trans-4-(aminomethyl)cyclohexanecarboxylic acid'  ligand  26  11  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_AMH
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
 AMH  C1   C  CH1   0  -0.380  -0.0649   0.3552  -1.1633
 AMH  C2   C  CH2   0  -0.418  -1.3858  -0.0416  -0.5137
 AMH  C3   C  CH2   0  -0.424  -1.4244   0.3795   0.9506
 AMH  C4   C  CH1   0  -0.241  -0.2548  -0.1956   1.7455
 AMH  C5   C  CH2   0  -0.408   1.0672   0.1842   1.0852
 AMH  C6   C  CH2   0  -0.427   1.1221  -0.2304  -0.3808
 AMH  C7   C  CH2   0  -0.262  -0.3254   0.2455   3.2026
 AMH  C8   C  C     0   0.563   0.0002  -0.0630  -2.6102
 AMH  N    N  NH2   0  -0.797   0.7277  -0.3592   4.0052
 AMH  O1   O  O     0  -0.443  -0.7700  -0.8158  -3.1545
 AMH  O2   O  OH1   0  -0.598   1.0334   0.4860  -3.2433
 AMH  H1   H  HCH1  0   0.264   0.0295   1.4481  -1.1334
 AMH  H21  H  HCH2  0   0.220  -1.5161  -1.1258  -0.5821
 AMH  H22  H  HCH2  0   0.237  -2.2227   0.4090  -1.0518
 AMH  H31  H  HCH2  0   0.229  -2.3712   0.0594   1.3942
 AMH  H32  H  HCH2  0   0.210  -1.4054   1.4738   1.0201
 AMH  H4   H  HCH1  0   0.208  -0.3446  -1.2917   1.7173
 AMH  H51  H  HCH2  0   0.206   1.2033   1.2704   1.1584
 AMH  H52  H  HCH2  0   0.234   1.8993  -0.2693   1.6256
 AMH  H61  H  HCH2  0   0.224   1.0992  -1.3229  -0.4561
 AMH  H62  H  HCH2  0   0.244   2.0668   0.0959  -0.8194
 AMH  H71  H  HCH2  0   0.195  -1.3362   0.0313   3.5814
 AMH  H72  H  HCH2  0   0.206  -0.2066   1.3331   3.2486
 AMH  HN1  H  HNH2  0   0.346   0.6604  -0.0205   4.9566
 AMH  HN2  H  HNH2  0   0.335   0.5679  -1.3579   4.0617
 AMH  HO2  H  HOH1  0   0.478   1.0626   0.1746  -4.1602

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
 AMH  C1  C2   single  1.525  0.020  1.525
 AMH  C1  C6   single  1.538  0.020  1.538
 AMH  C1  C8   single  1.508  0.020  1.508
 AMH  C1  H1   single  0.970  0.020  1.090
 AMH  C2  C3   single  1.524  0.020  1.524
 AMH  C2  H21  single  0.970  0.020  1.090
 AMH  C2  H22  single  0.970  0.020  1.090
 AMH  C3  C4   single  1.527  0.020  1.527
 AMH  C3  H31  single  0.970  0.020  1.090
 AMH  C3  H32  single  0.970  0.020  1.090
 AMH  C4  C5   single  1.526  0.020  1.526
 AMH  C4  C7   single  1.524  0.020  1.524
 AMH  C4  H4   single  0.970  0.020  1.090
 AMH  C5  C6   single  1.524  0.020  1.524
 AMH  C5  H51  single  0.970  0.020  1.090
 AMH  C5  H52  single  0.970  0.020  1.090
 AMH  C6  H61  single  0.970  0.020  1.090
 AMH  C6  H62  single  0.970  0.020  1.090
 AMH  C7  N    single  1.456  0.020  1.456
 AMH  C7  H71  single  0.970  0.020  1.090
 AMH  C7  H72  single  0.970  0.020  1.090
 AMH  C8  O1   double  1.207  0.020  1.207
 AMH  C8  O2   single  1.330  0.020  1.330
 AMH  N   HN1  single  0.890  0.020  1.040
 AMH  N   HN2  single  0.890  0.020  1.040
 AMH  O2  HO2  single  0.850  0.020  0.980

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
 AMH  H1   C1  C8   107.38  3.000
 AMH  H1   C1  C6   107.40  3.000
 AMH  C8   C1  C6   110.45  3.000
 AMH  H1   C1  C2   108.79  3.000
 AMH  C8   C1  C2   111.97  3.000
 AMH  C6   C1  C2   110.67  3.000
 AMH  H22  C2  H21  106.66  3.000
 AMH  H22  C2  C3   109.87  3.000
 AMH  H21  C2  C3   109.32  3.000
 AMH  H22  C2  C1   110.28  3.000
 AMH  H21  C2  C1   109.54  3.000
 AMH  C3   C2  C1   111.06  3.000
 AMH  H32  C3  H31  106.34  3.000
 AMH  H32  C3  C4   109.25  3.000
 AMH  H31  C3  C4   109.99  3.000
 AMH  H32  C3  C2   109.64  3.000
 AMH  H31  C3  C2   109.31  3.000
 AMH  C4   C3  C2   112.13  3.000
 AMH  H4   C4  C7   108.00  3.000
 AMH  H4   C4  C5   107.92  3.000
 AMH  C7   C4  C5   112.45  3.000
 AMH  H4   C4  C3   107.42  3.000
 AMH  C7   C4  C3   110.69  3.000
 AMH  C5   C4  C3   110.16  3.000
 AMH  H52  C5  H51  106.49  3.000
 AMH  H52  C5  C6   109.62  3.000
 AMH  H51  C5  C6   109.21  3.000
 AMH  H52  C5  C4   110.06  3.000
 AMH  H51  C5  C4   108.97  3.000
 AMH  C6   C5  C4   112.32  3.000
 AMH  H62  C6  H61  106.78  3.000
 AMH  H62  C6  C5   109.65  3.000
 AMH  H61  C6  C5   109.67  3.000
 AMH  H62  C6  C1   110.48  3.000
 AMH  H61  C6  C1   109.19  3.000
 AMH  C5   C6  C1   110.97  3.000
 AMH  H72  C7  H71  106.18  3.000
 AMH  H72  C7  N    108.11  3.000
 AMH  H71  C7  N    113.20  3.000
 AMH  H72  C7  C4   108.82  3.000
 AMH  H71  C7  C4   108.38  3.000
 AMH  N    C7  C4   111.92  3.000
 AMH  O2   C8  O1   122.58  3.000
 AMH  O2   C8  C1   112.08  3.000
 AMH  O1   C8  C1   125.34  3.000
 AMH  HN2  N   HN1  105.48  3.000
 AMH  HN2  N   C7   109.04  3.000
 AMH  HN1  N   C7   109.34  3.000
 AMH  HO2  O2  C8   109.95  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
 AMH  CONST_01  HO2  O2  C8  C1  180.00   0.0  0
 AMH  Var_01    C4   C3  C2  C1  -56.33  30.0  1
 AMH  Var_02    C4   C5  C6  C1   55.45  30.0  1
 AMH  Var_03    HN1  N   C7  C4  178.42  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
 AMH  chir_01  C1  C2  C6  C8  negativ
 AMH  chir_02  C4  C3  C5  C7  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
 AMH  plan-1  C1   0.020
 AMH  plan-1  C8   0.020
 AMH  plan-1  O1   0.020
 AMH  plan-1  O2   0.020
 AMH  plan-1  HO2  0.020

