# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 06:09:25 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: (2S)-2-[(1S,2S)-2-aminocyclohexyl]butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H]([C@@H]1CCCC[C@@H]1N)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
 GM8  GM8  '(2S)-2-[(1S,2S)-2-aminocyclohexyl]butanoic acid'  ligand  31  13  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GM8
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
 GM8  O     O  O      0  -0.612  -2.1427  -1.1518   1.0460
 GM8  C     C  C      0   0.419  -1.7569  -0.9145  -0.1169
 GM8  CA    C  CH1    0  -0.317  -1.0054   0.4127  -0.3462
 GM8  CZ    C  CH2    0  -0.414  -1.8175   1.5810   0.2176
 GM8  CQ    C  CH3    0  -0.668  -3.1721   1.7583  -0.4556
 GM8  CB    C  CH1    0  -0.191   0.4142   0.3692   0.2615
 GM8  CG    C  CH1    0  -0.099   1.1338  -0.9741   0.0468
 GM8  N     N  NH2    0  -0.814   1.2451  -1.2730  -1.3777
 GM8  CD1   C  CH2    0  -0.435   2.5248  -0.9457   0.6808
 GM8  CE1   C  CH2    0  -0.417   3.3856   0.1995   0.1630
 GM8  CE2   C  CH2    0  -0.429   2.6726   1.5305   0.3634
 GM8  CD2   C  CH2    0  -0.412   1.2812   1.5182  -0.2627
 GM8  OXT   O  OC    -1  -0.618  -1.9194  -1.6648  -1.1063
 GM8  HG    H  HCH1   0   0.185  -0.8991   0.5656  -1.4275
 GM8  HZ1   H  HCH2   0   0.203  -1.9574   1.4272   1.2908
 GM8  HZ2   H  HCH2   0   0.211  -1.2543   2.5116   0.1148
 GM8  HQ3   H  HCH3   0   0.211  -3.0623   1.9196  -1.5300
 GM8  HQ2   H  HCH3   0   0.218  -3.8119   0.8855  -0.3169
 GM8  HQ1   H  HCH3   0   0.221  -3.7058   2.6192  -0.0493
 GM8  HB    H  HCH1   0   0.193   0.3086   0.4905   1.3488
 GM8  HA    H  HCH1   0   0.203   0.5602  -1.7460   0.5812
 GM8  H2    H  HNH2   0   0.331   1.7713  -2.1315  -1.4917
 GM8  H3    H  HNH2   0   0.342   0.3166  -1.4716  -1.7342
 GM8  HD12  H  HCH2   0   0.211   2.4070  -0.8495   1.7654
 GM8  HD11  H  HCH2   0   0.218   3.0195  -1.9079   0.5118
 GM8  HE12  H  HCH2   0   0.216   4.3521   0.2040   0.6739
 GM8  HE11  H  HCH2   0   0.207   3.5938   0.0516  -0.9000
 GM8  HE22  H  HCH2   0   0.201   2.5834   1.7338   1.4367
 GM8  HE21  H  HCH2   0   0.218   3.2644   2.3485  -0.0566
 GM8  HD21  H  HCH2   0   0.203   1.3731   1.4228  -1.3489
 GM8  HD22  H  HCH2   0   0.219   0.7973   2.4787  -0.0741

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
 GM8  C    O     deloc   1.248  0.020  1.248
 GM8  C    CA    single  1.542  0.020  1.542
 GM8  CQ   CZ    single  1.523  0.020  1.523
 GM8  N    CG    single  1.460  0.020  1.460
 GM8  CA   CZ    single  1.530  0.020  1.530
 GM8  CA   CB    single  1.545  0.020  1.545
 GM8  CG   CB    single  1.539  0.020  1.539
 GM8  CG   CD1   single  1.529  0.020  1.529
 GM8  CB   CD2   single  1.532  0.020  1.532
 GM8  CD1  CE1   single  1.523  0.020  1.523
 GM8  CD2  CE2   single  1.526  0.020  1.526
 GM8  CE1  CE2   single  1.523  0.020  1.523
 GM8  C    OXT   deloc   1.252  0.020  1.252
 GM8  CA   HG    single  0.970  0.020  1.090
 GM8  CZ   HZ1   single  0.970  0.020  1.090
 GM8  CZ   HZ2   single  0.970  0.020  1.090
 GM8  CQ   HQ3   single  0.970  0.020  1.090
 GM8  CQ   HQ2   single  0.970  0.020  1.090
 GM8  CQ   HQ1   single  0.970  0.020  1.090
 GM8  CB   HB    single  0.970  0.020  1.090
 GM8  CG   HA    single  0.970  0.020  1.090
 GM8  N    H2    single  0.890  0.020  1.040
 GM8  N    H3    single  0.890  0.020  1.040
 GM8  CD1  HD12  single  0.970  0.020  1.090
 GM8  CD1  HD11  single  0.970  0.020  1.090
 GM8  CE1  HE12  single  0.970  0.020  1.090
 GM8  CE1  HE11  single  0.970  0.020  1.090
 GM8  CE2  HE22  single  0.970  0.020  1.090
 GM8  CE2  HE21  single  0.970  0.020  1.090
 GM8  CD2  HD21  single  0.970  0.020  1.090
 GM8  CD2  HD22  single  0.970  0.020  1.090

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
 GM8  OXT   C    CA    117.47  3.000
 GM8  OXT   C    O     125.60  3.000
 GM8  CA    C    O     116.92  3.000
 GM8  HG    CA   CB    107.62  3.000
 GM8  HG    CA   CZ    107.94  3.000
 GM8  CB    CA   CZ    111.36  3.000
 GM8  HG    CA   C     108.28  3.000
 GM8  CB    CA   C     111.41  3.000
 GM8  CZ    CA   C     110.09  3.000
 GM8  HZ2   CZ   HZ1   106.14  3.000
 GM8  HZ2   CZ   CQ    108.53  3.000
 GM8  HZ1   CZ   CQ    109.67  3.000
 GM8  HZ2   CZ   CA    110.00  3.000
 GM8  HZ1   CZ   CA    108.80  3.000
 GM8  CQ    CZ   CA    113.45  3.000
 GM8  HQ1   CQ   HQ2   107.27  3.000
 GM8  HQ1   CQ   HQ3   107.39  3.000
 GM8  HQ2   CQ   HQ3   107.59  3.000
 GM8  HQ1   CQ   CZ    111.24  3.000
 GM8  HQ2   CQ   CZ    111.85  3.000
 GM8  HQ3   CQ   CZ    111.27  3.000
 GM8  HB    CB   CD2   108.07  3.000
 GM8  HB    CB   CG    106.22  3.000
 GM8  CD2   CB   CG    110.02  3.000
 GM8  HB    CB   CA    107.32  3.000
 GM8  CD2   CB   CA    111.37  3.000
 GM8  CG    CB   CA    113.54  3.000
 GM8  HA    CG   CD1   106.61  3.000
 GM8  HA    CG   N     111.72  3.000
 GM8  CD1   CG   N     109.82  3.000
 GM8  HA    CG   CB    107.51  3.000
 GM8  CD1   CG   CB    110.57  3.000
 GM8  N     CG   CB    110.52  3.000
 GM8  H3    N    H2    105.66  3.000
 GM8  H3    N    CG    108.26  3.000
 GM8  H2    N    CG    108.83  3.000
 GM8  HD11  CD1  HD12  106.17  3.000
 GM8  HD11  CD1  CE1   110.66  3.000
 GM8  HD12  CD1  CE1   109.35  3.000
 GM8  HD11  CD1  CG    109.31  3.000
 GM8  HD12  CD1  CG    108.32  3.000
 GM8  CE1   CD1  CG    112.77  3.000
 GM8  HE11  CE1  HE12  106.66  3.000
 GM8  HE11  CE1  CE2   109.59  3.000
 GM8  HE12  CE1  CE2   110.41  3.000
 GM8  HE11  CE1  CD1   109.66  3.000
 GM8  HE12  CE1  CD1   110.10  3.000
 GM8  CE2   CE1  CD1   110.35  3.000
 GM8  HE21  CE2  HE22  106.35  3.000
 GM8  HE21  CE2  CD2   109.99  3.000
 GM8  HE22  CE2  CD2   109.21  3.000
 GM8  HE21  CE2  CE1   110.47  3.000
 GM8  HE22  CE2  CE1   109.21  3.000
 GM8  CD2   CE2  CE1   111.46  3.000
 GM8  HD22  CD2  HD21  106.58  3.000
 GM8  HD22  CD2  CE2   109.04  3.000
 GM8  HD21  CD2  CE2   109.35  3.000
 GM8  HD22  CD2  CB    110.48  3.000
 GM8  HD21  CD2  CB    108.77  3.000
 GM8  CE2   CD2  CB    112.44  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
 GM8  Var_01  CE1  CE2  CD2  CB    55.67  30.0  1
 GM8  Var_02  CD2  CE2  CE1  CD1  -54.31  30.0  1
 GM8  Var_03  HQ3  CQ   CZ   CA   -58.44  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
 GM8  chir_01  CA  C    CZ   CB  negativ
 GM8  chir_02  CB  CD2  CG   CA  positiv
 GM8  chir_03  CG  N    CD1  CB  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
 GM8  plan-1  O    0.020
 GM8  plan-1  C    0.020
 GM8  plan-1  CA   0.020
 GM8  plan-1  OXT  0.020

