# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 05:31:47 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: (2R,6S)-2,6-diaminoheptanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCC[C@@H](N)C(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
 API  API  '(2R,6S)-2,6-diaminoheptanedioic acid'  L-peptide  25  13  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT (side chain)
;

data_comp_API
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
 API  C1    C  C      0   0.403   3.7559  -0.4634  -0.1579
 API  C2    C  CH1    0  -0.197   2.5697   0.2819   0.4896
 API  C3    C  CH2    0  -0.423   1.2698  -0.2498  -0.1390
 API  C4    C  CH2    0  -0.430  -0.0037   0.3253   0.4698
 API  C5    C  CH2    0  -0.421  -1.2679  -0.2607  -0.1493
 API  C6    C  CH1    0  -0.203  -2.5751   0.2553   0.4772
 API  C7    C  C      0   0.403  -3.7578  -0.5032  -0.1635
 API  O1    O  O      0  -0.611   4.3503   0.1164  -1.0894
 API  O2    O  OC    -1  -0.622   3.9919  -1.6112   0.2706
 API  O3    O  O      0  -0.608  -4.4564   0.1142  -0.9917
 API  O4    O  OC    -1  -0.623  -3.8914  -1.6973   0.1749
 API  N2    N  NH2    0  -0.804   2.7567   1.7210   0.3836
 API  N6    N  NH2    0  -0.802  -2.7735   1.6930   0.3827
 API  H2    H  HCH1   0   0.195   2.5450   0.0220   1.5550
 API  H31   H  HCH2   0   0.204   1.2832  -0.0424  -1.2159
 API  H32   H  HCH2   0   0.209   1.2492  -1.3392  -0.0350
 API  H41   H  HCH2   0   0.209  -0.0079   0.1388   1.5502
 API  H42   H  HCH2   0   0.194  -0.0077   1.4135   0.3465
 API  H51   H  HCH2   0   0.204  -1.2758  -0.0478  -1.2255
 API  H52   H  HCH2   0   0.209  -1.2372  -1.3494  -0.0496
 API  H6    H  HCH1   0   0.198  -2.5460  -0.0096   1.5418
 API  HN21  H  HNH2   0   0.325   2.9657   1.9429  -0.5817
 API  HN22  H  HNH2   0   0.333   1.8999   2.2073   0.6161
 API  HN61  H  HNH2   0   0.333  -1.9201   2.1826   0.6202
 API  HN62  H  HNH2   0   0.325  -2.9861   1.9267  -0.5788

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
 API  C1  C2    single  1.543  0.020  1.543
 API  C1  O1    deloc   1.248  0.020  1.248
 API  C1  O2    deloc   1.248  0.020  1.248
 API  C2  C3    single  1.539  0.020  1.539
 API  C2  N2    single  1.455  0.020  1.455
 API  C2  H2    single  0.970  0.020  1.090
 API  C3  C4    single  1.524  0.020  1.524
 API  C3  H31   single  0.970  0.020  1.090
 API  C3  H32   single  0.970  0.020  1.090
 API  C4  C5    single  1.525  0.020  1.525
 API  C4  H41   single  0.970  0.020  1.090
 API  C4  H42   single  0.970  0.020  1.090
 API  C5  C6    single  1.539  0.020  1.539
 API  C5  H51   single  0.970  0.020  1.090
 API  C5  H52   single  0.970  0.020  1.090
 API  C6  C7    single  1.544  0.020  1.544
 API  C6  N6    single  1.454  0.020  1.454
 API  C6  H6    single  0.970  0.020  1.090
 API  C7  O3    deloc   1.247  0.020  1.247
 API  C7  O4    deloc   1.248  0.020  1.248
 API  N2  HN21  single  0.890  0.020  1.040
 API  N2  HN22  single  0.890  0.020  1.040
 API  N6  HN61  single  0.890  0.020  1.040
 API  N6  HN62  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
 API  O2    C1  O1    126.43  3.000
 API  O2    C1  C2    116.45  3.000
 API  O1    C1  C2    117.06  3.000
 API  H2    C2  N2    107.94  3.000
 API  H2    C2  C3    107.21  3.000
 API  N2    C2  C3    114.87  3.000
 API  H2    C2  C1    108.08  3.000
 API  N2    C2  C1    110.38  3.000
 API  C3    C2  C1    108.12  3.000
 API  H32   C3  H31   106.36  3.000
 API  H32   C3  C4    108.78  3.000
 API  H31   C3  C4    109.34  3.000
 API  H32   C3  C2    108.73  3.000
 API  H31   C3  C2    108.99  3.000
 API  C4    C3  C2    114.35  3.000
 API  H42   C4  H41   106.26  3.000
 API  H42   C4  C5    109.46  3.000
 API  H41   C4  C5    109.36  3.000
 API  H42   C4  C3    109.45  3.000
 API  H41   C4  C3    109.43  3.000
 API  C5    C4  C3    112.68  3.000
 API  H52   C5  H51   106.43  3.000
 API  H52   C5  C6    108.69  3.000
 API  H51   C5  C6    109.16  3.000
 API  H52   C5  C4    108.80  3.000
 API  H51   C5  C4    109.25  3.000
 API  C6    C5  C4    114.21  3.000
 API  H6    C6  N6    107.77  3.000
 API  H6    C6  C7    107.71  3.000
 API  N6    C6  C7    110.74  3.000
 API  H6    C6  C5    106.95  3.000
 API  N6    C6  C5    114.89  3.000
 API  C7    C6  C5    108.48  3.000
 API  O4    C7  O3    126.42  3.000
 API  O4    C7  C6    116.06  3.000
 API  O3    C7  C6    117.48  3.000
 API  HN22  N2  HN21  106.77  3.000
 API  HN22  N2  C2    110.46  3.000
 API  HN21  N2  C2    108.23  3.000
 API  HN62  N6  HN61  106.75  3.000
 API  HN62  N6  C6    108.58  3.000
 API  HN61  N6  C6    110.36  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
 API  Var_01  C5  C4  C3  C2  -178.12  30.0  3
 API  Var_02  C6  C5  C4  C3   177.75  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
 API  chir_01  C2  C1  C3  N2  positiv
 API  chir_02  C6  N6  C5  C7  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
 API  plan-1  C1  0.020
 API  plan-1  C2  0.020
 API  plan-1  O1  0.020
 API  plan-1  O2  0.020
 API  plan-2  C6  0.020
 API  plan-2  C7  0.020
 API  plan-2  O3  0.020
 API  plan-2  O4  0.020

