# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 00:12:16 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  25  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  -0.374  -0.0336   0.3771  -1.1517
 AMH  C2   C  CH2    0  -0.406  -1.3563  -0.0216  -0.5076
 AMH  C3   C  CH2    0  -0.417  -1.4220   0.3934   0.9587
 AMH  C4   C  CH1    0  -0.238  -0.2592  -0.1717   1.7708
 AMH  C5   C  CH2    0  -0.401   1.0679   0.2205   1.1272
 AMH  C6   C  CH2    0  -0.417   1.1376  -0.1835  -0.3416
 AMH  C7   C  CH2    0  -0.259  -0.3575   0.2642   3.2278
 AMH  C8   C  C      0   0.424   0.0814  -0.0024  -2.6424
 AMH  N    N  NH2    0  -0.798   0.6847  -0.3341   4.0502
 AMH  O1   O  O      0  -0.605  -0.9141  -0.5114  -3.1967
 AMH  O2   O  OC    -1  -0.625   1.1775   0.2407  -3.1921
 AMH  H1   H  HCH1   0   0.204   0.0431   1.4742  -1.0990
 AMH  H21  H  HCH2   0   0.194  -1.4842  -1.1074  -0.5795
 AMH  H22  H  HCH2   0   0.211  -2.1915   0.4200  -1.0549
 AMH  H31  H  HCH2   0   0.215  -2.3722   0.0683   1.3942
 AMH  H32  H  HCH2   0   0.198  -1.4102   1.4884   1.0318
 AMH  H4   H  HCH1   0   0.199  -0.3393  -1.2689   1.7388
 AMH  H51  H  HCH2   0   0.193   1.1899   1.3086   1.2089
 AMH  H52  H  HCH2   0   0.219   1.8976  -0.2247   1.6804
 AMH  H61  H  HCH2   0   0.196   1.1386  -1.2783  -0.4165
 AMH  H62  H  HCH2   0   0.216   2.0808   0.1544  -0.7743
 AMH  H71  H  HCH2   0   0.191  -1.3732   0.0414   3.5893
 AMH  H72  H  HCH2   0   0.202  -0.2489   1.3530   3.2781
 AMH  HN1  H  HNH2   0   0.344   0.5738  -0.0268   5.0083
 AMH  HN2  H  HNH2   0   0.334   0.5510  -1.3381   4.0714

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  1.524  0.020  1.524
 AMH  C1  C6   single  1.530  0.020  1.530
 AMH  C1  C8   single  1.543  0.020  1.543
 AMH  C1  H1   single  0.970  0.020  1.090
 AMH  C2  C3   single  1.525  0.020  1.525
 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  1.525  0.020  1.525
 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   deloc   1.248  0.020  1.248
 AMH  C8  O2   deloc   1.250  0.020  1.250
 AMH  N   HN1  single  0.890  0.020  1.040
 AMH  N   HN2  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
 AMH  H1   C1  C8   106.63  3.000
 AMH  H1   C1  C6   106.64  3.000
 AMH  C8   C1  C6   111.37  3.000
 AMH  H1   C1  C2   107.51  3.000
 AMH  C8   C1  C2   114.13  3.000
 AMH  C6   C1  C2   110.16  3.000
 AMH  H22  C2  H21  106.18  3.000
 AMH  H22  C2  C3   109.81  3.000
 AMH  H21  C2  C3   109.13  3.000
 AMH  H22  C2  C1   110.25  3.000
 AMH  H21  C2  C1   109.44  3.000
 AMH  C3   C2  C1   111.87  3.000
 AMH  H32  C3  H31  106.21  3.000
 AMH  H32  C3  C4   109.00  3.000
 AMH  H31  C3  C4   109.85  3.000
 AMH  H32  C3  C2   109.58  3.000
 AMH  H31  C3  C2   109.82  3.000
 AMH  C4   C3  C2   112.20  3.000
 AMH  H4   C4  C7   107.95  3.000
 AMH  H4   C4  C5   107.89  3.000
 AMH  C7   C4  C5   112.69  3.000
 AMH  H4   C4  C3   107.34  3.000
 AMH  C7   C4  C3   110.70  3.000
 AMH  C5   C4  C3   110.05  3.000
 AMH  H52  C5  H51  106.37  3.000
 AMH  H52  C5  C6   110.20  3.000
 AMH  H51  C5  C6   109.22  3.000
 AMH  H52  C5  C4   110.01  3.000
 AMH  H51  C5  C4   108.66  3.000
 AMH  C6   C5  C4   112.20  3.000
 AMH  H62  C6  H61  106.32  3.000
 AMH  H62  C6  C5   109.83  3.000
 AMH  H61  C6  C5   109.27  3.000
 AMH  H62  C6  C1   109.76  3.000
 AMH  H61  C6  C1   109.28  3.000
 AMH  C5   C6  C1   112.20  3.000
 AMH  H72  C7  H71  106.11  3.000
 AMH  H72  C7  N    108.15  3.000
 AMH  H71  C7  N    113.06  3.000
 AMH  H72  C7  C4   108.77  3.000
 AMH  H71  C7  C4   108.40  3.000
 AMH  N    C7  C4   112.10  3.000
 AMH  O2   C8  O1   125.69  3.000
 AMH  O2   C8  C1   116.26  3.000
 AMH  O1   C8  C1   118.04  3.000
 AMH  HN2  N   HN1  105.46  3.000
 AMH  HN2  N   C7   108.94  3.000
 AMH  HN1  N   C7   109.35  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  Var_01  C4   C3  C2  C1   -56.04  30.0  1
 AMH  Var_02  C4   C5  C6  C1    55.07  30.0  1
 AMH  Var_03  HN1  N   C7  C4  -179.31  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

