# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 15:26:12 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  27  13  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (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   0.546   3.7368  -0.4241  -0.1165
 API  C2    C  CH1   0  -0.217   2.5508   0.3036   0.4827
 API  C3    C  CH2   0  -0.438   1.2553  -0.2487  -0.1445
 API  C4    C  CH2   0  -0.433  -0.0001   0.3764   0.4495
 API  C5    C  CH2   0  -0.438  -1.2642  -0.2427  -0.1329
 API  C6    C  CH1   0  -0.216  -2.5509   0.3282   0.4953
 API  C7    C  C     0   0.546  -3.7449  -0.4089  -0.0762
 API  O1    O  O     0  -0.439   4.5310   0.0638  -0.8797
 API  O2    O  OH1   0  -0.595   3.7866  -1.6936   0.2730
 API  O3    O  O     0  -0.439  -4.5335   0.0585  -0.8578
 API  O4    O  OH1   0  -0.595  -3.8072  -1.6623   0.3608
 API  N2    N  NH2   0  -0.785   2.7542   1.7302   0.3514
 API  N6    N  NH2   0  -0.785  -2.7497   1.7522   0.3322
 API  H2    H  HCH1  0   0.270   2.5300   0.0684   1.5523
 API  H31   H  HCH2  0   0.232   1.2768  -0.0744  -1.2258
 API  H32   H  HCH2  0   0.237   1.2106  -1.3316  -0.0038
 API  H41   H  HCH2  0   0.228   0.0039   0.2382   1.5365
 API  H42   H  HCH2  0   0.217   0.0009   1.4539   0.2682
 API  H51   H  HCH2  0   0.232  -1.2896  -0.0789  -1.2158
 API  H52   H  HCH2  0   0.237  -1.2285  -1.3248   0.0172
 API  H6    H  HCH1  0   0.269  -2.5179   0.1183   1.5696
 API  HO2   H  HOH1  0   0.481   4.5240  -2.1459  -0.1629
 API  HO4   H  HOH1  0   0.481  -4.5467  -2.1251  -0.0604
 API  HN21  H  HNH2  0   0.344   2.6437   2.0149  -0.6148
 API  HN22  H  HNH2  0   0.359   2.0392   2.2199   0.8725
 API  HN61  H  HNH2  0   0.359  -2.0340   2.2517   0.8428
 API  HN62  H  HNH2  0   0.344  -2.6392   2.0157  -0.6399

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  1.515  0.020  1.515
 API  C1  O1    double  1.205  0.020  1.205
 API  C1  O2    single  1.329  0.020  1.329
 API  C2  C3    single  1.542  0.020  1.542
 API  C2  N2    single  1.447  0.020  1.447
 API  C2  H2    single  0.970  0.020  1.090
 API  C3  C4    single  1.523  0.020  1.523
 API  C3  H31   single  0.970  0.020  1.090
 API  C3  H32   single  0.970  0.020  1.090
 API  C4  C5    single  1.523  0.020  1.523
 API  C4  H41   single  0.970  0.020  1.090
 API  C4  H42   single  0.970  0.020  1.090
 API  C5  C6    single  1.541  0.020  1.541
 API  C5  H51   single  0.970  0.020  1.090
 API  C5  H52   single  0.970  0.020  1.090
 API  C6  C7    single  1.515  0.020  1.515
 API  C6  N6    single  1.447  0.020  1.447
 API  C6  H6    single  0.970  0.020  1.090
 API  C7  O3    double  1.205  0.020  1.205
 API  C7  O4    single  1.329  0.020  1.329
 API  O2  HO2   single  0.850  0.020  0.980
 API  O4  HO4   single  0.850  0.020  0.980
 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    123.23  3.000
 API  O2    C1  C2    111.85  3.000
 API  O1    C1  C2    124.90  3.000
 API  H2    C2  N2    107.63  3.000
 API  H2    C2  C3    107.72  3.000
 API  N2    C2  C3    115.75  3.000
 API  H2    C2  C1    107.34  3.000
 API  N2    C2  C1    109.12  3.000
 API  C3    C2  C1    108.96  3.000
 API  H32   C3  H31   106.59  3.000
 API  H32   C3  C4    108.83  3.000
 API  H31   C3  C4    109.62  3.000
 API  H32   C3  C2    109.69  3.000
 API  H31   C3  C2    109.15  3.000
 API  C4    C3  C2    112.77  3.000
 API  H42   C4  H41   106.80  3.000
 API  H42   C4  C5    109.76  3.000
 API  H41   C4  C5    109.34  3.000
 API  H42   C4  C3    109.83  3.000
 API  H41   C4  C3    109.40  3.000
 API  C5    C4  C3    111.60  3.000
 API  H52   C5  H51   106.53  3.000
 API  H52   C5  C6    109.75  3.000
 API  H51   C5  C6    109.15  3.000
 API  H52   C5  C4    108.83  3.000
 API  H51   C5  C4    109.66  3.000
 API  C6    C5  C4    112.73  3.000
 API  H6    C6  N6    107.65  3.000
 API  H6    C6  C7    107.48  3.000
 API  N6    C6  C7    109.15  3.000
 API  H6    C6  C5    107.68  3.000
 API  N6    C6  C5    115.67  3.000
 API  C7    C6  C5    108.91  3.000
 API  O4    C7  O3    123.27  3.000
 API  O4    C7  C6    111.83  3.000
 API  O3    C7  C6    124.88  3.000
 API  HO2   O2  C1    110.03  3.000
 API  HO4   O4  C7    110.08  3.000
 API  HN22  N2  HN21  106.16  3.000
 API  HN22  N2  C2    109.34  3.000
 API  HN21  N2  C2    110.38  3.000
 API  HN62  N6  HN61  106.19  3.000
 API  HN62  N6  C6    110.43  3.000
 API  HN61  N6  C6    109.39  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  CONST_01  HO2  O2  C1  C2   180.00   0.0  0
 API  CONST_02  HO4  O4  C7  C6   180.00   0.0  0
 API  Var_01    C5   C4  C3  C2  -176.84  30.0  3
 API  Var_02    C6   C5  C4  C3   177.50  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-1  HO2  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
 API  plan-2  HO4  0.020

