# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 01:23:52 2022
#   Inital geometry file: a 63 line input string
#   Ligand name: (2S)-2-aminoheptanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCC(O)=O)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
 NPI  NPI  '(2S)-2-aminoheptanedioic acid'  L-peptide  23  12  .  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_NPI
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
 NPI  CA   C  CH1    0  -0.191  13.3199  4.5468   1.3137
 NPI  CB   C  CH2    0  -0.410  13.5392  5.6696   0.2958
 NPI  C4   C  CH2    0  -0.411  13.9193  5.2100  -1.1061
 NPI  C5   C  CH2    0  -0.400  13.9653  6.3578  -2.1073
 NPI  C6   C  CH2    0  -0.571  14.2987  5.9008  -3.5187
 NPI  C    C  C      0   0.384  14.6308  3.7538   1.5216
 NPI  O    O  O      0  -0.613  14.7825  2.7097   0.8544
 NPI  OXT  O  OC    -1  -0.611  15.4485  4.2449   2.3297
 NPI  N    N  NH2    0  -0.794  12.7774  5.1318   2.5393
 NPI  C7   C  C      0   0.405  14.3589  7.0068  -4.5911
 NPI  O71  O  O      0  -0.624  14.3025  6.6226  -5.7784
 NPI  O72  O  OC    -1  -0.608  14.4809  8.1856  -4.1999
 NPI  HA   H  HCH1   0   0.191  12.5606  3.8716   0.9043
 NPI  H31  H  HCH2   0   0.203  12.6136  6.2524   0.2405
 NPI  H32  H  HCH2   0   0.197  14.3059  6.3532   0.6797
 NPI  H41  H  HCH2   0   0.205  14.8889  4.7044  -1.0913
 NPI  H42  H  HCH2   0   0.194  13.1966  4.4594  -1.4465
 NPI  H51  H  HCH2   0   0.194  12.9984  6.8724  -2.1067
 NPI  H52  H  HCH2   0   0.197  14.6975  7.0997  -1.7764
 NPI  H61  H  HCH2   0   0.213  15.2695  5.3881  -3.5122
 NPI  H62  H  HCH2   0   0.202  13.5806  5.1382  -3.8384
 NPI  H    H  HNH2   0   0.330  12.5137  4.3814   3.1680
 NPI  H2   H  HNH2   0   0.320  13.5474  5.5955   3.0108

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
 NPI  CA  CB   single  1.521  0.033  1.521
 NPI  CA  C    single  1.525  0.021  1.525
 NPI  CA  N    single  1.458  0.019  1.458
 NPI  CA  HA   single  0.970  0.020  0.970
 NPI  CB  C4   single  1.523  0.020  1.523
 NPI  CB  H31  single  0.970  0.020  1.090
 NPI  CB  H32  single  0.970  0.020  1.090
 NPI  C4  C5   single  1.524  0.020  1.524
 NPI  C4  H41  single  0.970  0.020  1.090
 NPI  C4  H42  single  0.970  0.020  1.090
 NPI  C5  C6   single  1.520  0.020  1.520
 NPI  C5  H51  single  0.970  0.020  1.090
 NPI  C5  H52  single  0.970  0.020  1.090
 NPI  C6  C7   single  1.542  0.020  1.542
 NPI  C6  H61  single  0.970  0.020  1.090
 NPI  C6  H62  single  0.970  0.020  1.090
 NPI  C   O    deloc   1.231  0.020  1.231
 NPI  C   OXT  deloc   1.250  0.020  1.250
 NPI  N   H    single  0.860  0.020  0.860
 NPI  N   H2   single  0.890  0.020  1.040
 NPI  C7  O71  deloc   1.249  0.020  1.249
 NPI  C7  O72  deloc   1.248  0.020  1.248

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
 NPI  HA   CA  N    110.00  3.000
 NPI  HA   CA  C    109.00  3.000
 NPI  N    CA  C    111.00  2.800
 NPI  HA   CA  CB   109.00  3.000
 NPI  N    CA  CB   110.40  1.500
 NPI  C    CA  CB   110.50  1.500
 NPI  H32  CB  H31  106.07  3.000
 NPI  H32  CB  C4   109.62  3.000
 NPI  H31  CB  C4   108.96  3.000
 NPI  H32  CB  CA   108.94  3.000
 NPI  H31  CB  CA   107.62  3.000
 NPI  C4   CB  CA   115.23  3.000
 NPI  H42  C4  H41  105.79  3.000
 NPI  H42  C4  C5   109.37  3.000
 NPI  H41  C4  C5   109.29  3.000
 NPI  H42  C4  CB   109.14  3.000
 NPI  H41  C4  CB   110.38  3.000
 NPI  C5   C4  CB   112.64  3.000
 NPI  H52  C5  H51  105.79  3.000
 NPI  H52  C5  C6   109.75  3.000
 NPI  H51  C5  C6   109.59  3.000
 NPI  H52  C5  C4   109.42  3.000
 NPI  H51  C5  C4   109.08  3.000
 NPI  C6   C5  C4   112.97  3.000
 NPI  H62  C6  H61  104.85  3.000
 NPI  H62  C6  C7   108.79  3.000
 NPI  H61  C6  C7   107.73  3.000
 NPI  H62  C6  C5   109.66  3.000
 NPI  H61  C6  C5   109.19  3.000
 NPI  C7   C6  C5   116.02  3.000
 NPI  OXT  C   O    126.48  3.000
 NPI  OXT  C   CA   116.10  3.000
 NPI  O    C   CA   120.80  1.700
 NPI  H2   N   H    104.32  3.000
 NPI  H2   N   CA   106.90  3.000
 NPI  H    N   CA   114.00  3.000
 NPI  O72  C7  O71  126.37  3.000
 NPI  O72  C7  C6   117.60  3.000
 NPI  O71  C7  C6   116.02  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
 NPI  Var_01  C5   C4  CB  CA   173.36  30.0  3
 NPI  Var_02  C6   C5  C4  CB  -178.09  30.0  3
 NPI  Var_03  C7   C6  C5  C4   179.80  30.0  3
 NPI  Var_04  O71  C7  C6  C5  -163.02  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
 NPI  chir_01  CA  CB  C  N  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
 NPI  plan-1  CA   0.020
 NPI  plan-1  C    0.020
 NPI  plan-1  O    0.020
 NPI  plan-1  OXT  0.020
 NPI  plan-2  C6   0.020
 NPI  plan-2  C7   0.020
 NPI  plan-2  O71  0.020
 NPI  plan-2  O72  0.020

