# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 13:21:35 2022
#   Inital geometry file: a 60 line input string
#   Ligand name: (2S)-2-aminoheptanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC[C@H](N)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
 AHP  AHP  '(2S)-2-aminoheptanoic acid'  L-peptide  24  10  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_AHP
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
 AHP  N    N  NH2    0  -0.815   3.6130  17.5689  7.9173
 AHP  CA   C  CH1    0  -0.186   4.3053  16.6827  6.9927
 AHP  C    C  C      0   0.397   5.5645  17.3646  6.4061
 AHP  O    O  O      0  -0.613   6.4161  16.5990  5.9111
 AHP  OXT  O  OC    -1  -0.603   5.6137  18.6113  6.4449
 AHP  CB   C  CH2    0  -0.449   3.4522  16.0983  5.8494
 AHP  CG   C  CH2    0  -0.436   3.0602  17.0285  4.6985
 AHP  CD   C  CH2    0  -0.422   2.0876  18.1855  4.9502
 AHP  CE   C  CH2    0  -0.420   0.6164  17.8084  5.1400
 AHP  CZ   C  CH3    0  -0.673   0.2235  17.2860  6.5165
 AHP  H    H  HNH2   0   0.333   2.6442  17.2944  8.0154
 AHP  H2   H  HNH2   0   0.332   3.6221  18.5056  7.5365
 AHP  HA   H  HCH1   0   0.197   4.6544  15.8143  7.5660
 AHP  HB2  H  HCH2   0   0.212   4.0263  15.2757  5.4135
 AHP  HB3  H  HCH2   0   0.216   2.5632  15.6283  6.2795
 AHP  HG2  H  HCH2   0   0.217   3.9764  17.4435  4.2678
 AHP  HG3  H  HCH2   0   0.209   2.6286  16.4090  3.9044
 AHP  HD2  H  HCH2   0   0.204   2.4226  18.8028  5.7866
 AHP  HD3  H  HCH2   0   0.217   2.1440  18.8341  4.0710
 AHP  HE2  H  HCH2   0   0.215   0.0106  18.6952  4.9328
 AHP  HE3  H  HCH2   0   0.207   0.3360  17.0753  4.3767
 AHP  HZ1  H  HCH3   0   0.226  -0.8544  17.1272  6.5757
 AHP  HZ2  H  HCH3   0   0.223   0.7019  16.3376  6.7583
 AHP  HZ3  H  HCH3   0   0.213   0.4900  17.9999  7.2986

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
 AHP  N   CA   single  1.458  0.019  1.458
 AHP  N   H    single  0.860  0.020  0.860
 AHP  N   H2   single  0.890  0.020  1.040
 AHP  CA  C    single  1.525  0.021  1.525
 AHP  CA  CB   single  1.521  0.033  1.521
 AHP  CA  HA   single  0.970  0.020  0.970
 AHP  C   O    deloc   1.231  0.020  1.231
 AHP  C   OXT  deloc   1.248  0.020  1.248
 AHP  CB  CG   single  1.531  0.020  1.531
 AHP  CB  HB2  single  0.970  0.020  1.090
 AHP  CB  HB3  single  0.970  0.020  1.090
 AHP  CG  CD   single  1.532  0.020  1.532
 AHP  CG  HG2  single  0.970  0.020  1.090
 AHP  CG  HG3  single  0.970  0.020  1.090
 AHP  CD  CE   single  1.531  0.020  1.531
 AHP  CD  HD2  single  0.970  0.020  1.090
 AHP  CD  HD3  single  0.970  0.020  1.090
 AHP  CE  CZ   single  1.524  0.020  1.524
 AHP  CE  HE2  single  0.970  0.020  1.090
 AHP  CE  HE3  single  0.970  0.020  1.090
 AHP  CZ  HZ1  single  0.970  0.020  1.090
 AHP  CZ  HZ2  single  0.970  0.020  1.090
 AHP  CZ  HZ3  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
 AHP  H2   N   H    107.24  3.000
 AHP  H2   N   CA   108.69  3.000
 AHP  H    N   CA   114.00  3.000
 AHP  HA   CA  CB   109.00  3.000
 AHP  HA   CA  C    109.00  3.000
 AHP  CB   CA  C    110.50  1.500
 AHP  HA   CA  N    110.00  3.000
 AHP  CB   CA  N    110.40  1.500
 AHP  C    CA  N    111.00  2.800
 AHP  OXT  C   O    126.75  3.000
 AHP  OXT  C   CA   117.42  3.000
 AHP  O    C   CA   120.80  1.700
 AHP  HB3  CB  HB2  105.08  3.000
 AHP  HB3  CB  CG   110.40  3.000
 AHP  HB2  CB  CG   106.97  3.000
 AHP  HB3  CB  CA   108.73  3.000
 AHP  HB2  CB  CA   106.87  3.000
 AHP  CG   CB  CA   117.96  3.000
 AHP  HG3  CG  HG2  105.01  3.000
 AHP  HG3  CG  CD   107.21  3.000
 AHP  HG2  CG  CD   108.05  3.000
 AHP  HG3  CG  CB   107.58  3.000
 AHP  HG2  CG  CB   108.18  3.000
 AHP  CD   CG  CB   119.86  3.000
 AHP  HD3  CD  HD2  105.34  3.000
 AHP  HD3  CD  CE   107.17  3.000
 AHP  HD2  CD  CE   109.82  3.000
 AHP  HD3  CD  CG   106.43  3.000
 AHP  HD2  CD  CG   110.98  3.000
 AHP  CE   CD  CG   116.39  3.000
 AHP  HE3  CE  HE2  105.60  3.000
 AHP  HE3  CE  CZ   109.52  3.000
 AHP  HE2  CE  CZ   107.83  3.000
 AHP  HE3  CE  CD   108.95  3.000
 AHP  HE2  CE  CD   108.01  3.000
 AHP  CZ   CE  CD   116.38  3.000
 AHP  HZ3  CZ  HZ2  107.64  3.000
 AHP  HZ3  CZ  HZ1  107.30  3.000
 AHP  HZ2  CZ  HZ1  107.16  3.000
 AHP  HZ3  CZ  CE   111.09  3.000
 AHP  HZ2  CZ  CE   112.69  3.000
 AHP  HZ1  CZ  CE   110.71  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
 AHP  Var_01  CD   CG  CB  CA  -67.73  30.0  3
 AHP  Var_02  CE   CD  CG  CB  -73.70  30.0  3
 AHP  Var_03  CZ   CE  CD  CG   79.64  30.0  3
 AHP  Var_04  HZ1  CZ  CE  CD  175.17  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
 AHP  chir_01  CA  N  C  CB  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
 AHP  plan-1  CA   0.020
 AHP  plan-1  C    0.020
 AHP  plan-1  O    0.020
 AHP  plan-1  OXT  0.020

