# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 07:23:03 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: (3S)-3-amino-6-[(diaminomethylidene)amino]hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCN=C(N)N)CC(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
 HR7  HR7  '(3S)-3-amino-6-[(diaminomethylidene)amino]hexanoic acid'  L-peptide  29  13  .  2022-03-18  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HR7
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
 HR7  N     N  NH2   0  -0.787   1.2577   0.8230  -1.1788
 HR7  CB    C  CH1   0  -0.092   1.4802   0.1027   0.0655
 HR7  CG    C  CH2   0  -0.410   0.2944  -0.8201   0.3419
 HR7  CD    C  CH2   0  -0.433  -1.0247  -0.0864   0.5380
 HR7  CE    C  CH2   0  -0.326  -2.2090  -1.0469   0.6565
 HR7  NZ    N  N     0  -0.485  -3.4579  -0.3833   0.9430
 HR7  CH    C  C     0   0.544  -4.1631   0.0509  -0.0337
 HR7  NH2   N  NH2   0  -0.830  -5.4183   0.5655   0.2122
 HR7  NH1   N  NH2   0  -0.833  -3.8502  -0.0423  -1.3674
 HR7  O     O  O     0  -0.448   4.0875   1.3101   0.1355
 HR7  CA    C  CH2   0  -0.583   2.7759  -0.7125   0.0954
 HR7  OXT   O  OH1   0  -0.595   5.0941  -0.6310  -0.2868
 HR7  HN1   H  HNH2  0   0.346   1.9949   1.4977  -1.3363
 HR7  HN2   H  HNH2  0   0.334   1.2875   0.1770  -1.9595
 HR7  HB    H  HCH1  0   0.226   1.5260   0.8470   0.8672
 HR7  HG2   H  HCH2  0   0.211   0.2022  -1.5336  -0.4869
 HR7  HG3   H  HCH2  0   0.221   0.5075  -1.4216   1.2311
 HR7  HA    H  HCH2  0   0.282   2.8514  -1.2707   1.0361
 HR7  HA2   H  HCH2  0   0.268   2.7671  -1.4683  -0.6962
 HR7  HD2   H  HCH2  0   0.214  -0.9736   0.5295   1.4416
 HR7  HD3   H  HCH2  0   0.214  -1.1784   0.6063  -0.2940
 HR7  HE2   H  HCH2  0   0.188  -2.2497  -1.6692  -0.2512
 HR7  HE3   H  HCH2  0   0.213  -2.0018  -1.7433   1.4760
 HR7  HH11  H  HNH2  0   0.394  -2.8754  -0.0583  -1.6135
 HR7  HH12  H  HNH2  0   0.388  -4.4086   0.4848  -2.0182
 HR7  HH21  H  HNH2  0   0.374  -5.5886   0.7415   1.1892
 HR7  HH22  H  HNH2  0   0.379  -5.7122   1.3344  -0.3700
 HR7  HXT   H  HOH1  0   0.478   5.8862  -0.0738  -0.3200
 HR7  C     C  C     0   0.549   4.0264   0.1143  -0.0194

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
 HR7  N    CB    single  1.455  0.020  1.455
 HR7  CB   CG    single  1.528  0.020  1.528
 HR7  CB   CA    single  1.530  0.020  1.530
 HR7  CG   CD    single  1.522  0.020  1.522
 HR7  CD   CE    single  1.529  0.020  1.529
 HR7  CE   NZ    single  1.443  0.020  1.443
 HR7  NZ   CH    double  1.281  0.020  1.281
 HR7  CH   NH1   single  1.373  0.020  1.373
 HR7  CH   NH2   single  1.379  0.020  1.379
 HR7  CA   C     single  1.525  0.021  1.525
 HR7  C    O     double  1.231  0.020  1.231
 HR7  C    OXT   single  1.329  0.020  1.329
 HR7  N    HN1   single  0.890  0.020  1.040
 HR7  N    HN2   single  0.890  0.020  1.040
 HR7  CB   HB    single  0.970  0.020  1.090
 HR7  CG   HG2   single  0.970  0.020  1.090
 HR7  CG   HG3   single  0.970  0.020  1.090
 HR7  CA   HA    single  0.970  0.020  0.970
 HR7  CA   HA2   single  0.970  0.020  1.090
 HR7  CD   HD2   single  0.970  0.020  1.090
 HR7  CD   HD3   single  0.970  0.020  1.090
 HR7  CE   HE2   single  0.970  0.020  1.090
 HR7  CE   HE3   single  0.970  0.020  1.090
 HR7  NH1  HH11  single  0.890  0.020  1.040
 HR7  NH1  HH12  single  0.890  0.020  1.040
 HR7  NH2  HH21  single  0.890  0.020  1.040
 HR7  NH2  HH22  single  0.890  0.020  1.040
 HR7  OXT  HXT   single  0.850  0.020  0.980

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
 HR7  HN2   N    HN1   106.48  3.000
 HR7  HN2   N    CB    109.80  3.000
 HR7  HN1   N    CB    110.61  3.000
 HR7  HB    CB   CA    108.19  3.000
 HR7  HB    CB   CG    108.09  3.000
 HR7  CA    CB   CG    109.38  3.000
 HR7  HB    CB   N     107.22  3.000
 HR7  CA    CB   N     110.50  1.700
 HR7  CG    CB   N     109.58  3.000
 HR7  HG3   CG   HG2   105.81  3.000
 HR7  HG3   CG   CD    109.21  3.000
 HR7  HG2   CG   CD    109.75  3.000
 HR7  HG3   CG   CB    109.13  3.000
 HR7  HG2   CG   CB    108.74  3.000
 HR7  CD    CG   CB    113.88  3.000
 HR7  HD3   CD   HD2   106.15  3.000
 HR7  HD3   CD   CE    110.36  3.000
 HR7  HD2   CD   CE    108.99  3.000
 HR7  HD3   CD   CG    109.22  3.000
 HR7  HD2   CD   CG    109.70  3.000
 HR7  CE    CD   CG    112.23  3.000
 HR7  HE3   CE   HE2   105.33  3.000
 HR7  HE3   CE   NZ    107.92  3.000
 HR7  HE2   CE   NZ    113.05  3.000
 HR7  HE3   CE   CD    108.11  3.000
 HR7  HE2   CE   CD    108.64  3.000
 HR7  NZ    CE   CD    113.38  3.000
 HR7  CH    NZ   CE    118.76  3.000
 HR7  NH1   CH   NH2   113.96  3.000
 HR7  NH2   CH   NZ    119.47  3.000
 HR7  NH1   CH   NZ    126.32  3.000
 HR7  HH22  NH2  HH21  112.17  3.000
 HR7  HH22  NH2  CH    116.56  3.000
 HR7  HH21  NH2  CH    113.09  3.000
 HR7  HH12  NH1  HH11  112.83  3.000
 HR7  HH12  NH1  CH    117.77  3.000
 HR7  HH11  NH1  CH    117.37  3.000
 HR7  HA2   CA   HA    105.63  3.000
 HR7  HA2   CA   C     109.35  3.000
 HR7  HA    CA   C     109.00  3.000
 HR7  HA2   CA   CB    110.28  3.000
 HR7  HA    CA   CB    109.00  3.000
 HR7  C     CA   CB    110.10  1.900
 HR7  HXT   OXT  C     109.94  3.000
 HR7  OXT   C    CA    112.02  3.000
 HR7  OXT   C    O     122.72  3.000
 HR7  CA    C    O     120.80  1.700

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
 HR7  CONST_01  NH1   CH   NZ  CE    0.00   0.0  0
 HR7  CONST_02  NH2   CH   NZ  CE  180.00   0.0  0
 HR7  CONST_04  HH12  NH1  CH  NZ  180.00   0.0  0
 HR7  CONST_05  HH21  NH2  CH  NZ    0.00   0.0  0
 HR7  CONST_07  HXT   OXT  C   O     0.00   0.0  0
 HR7  Var_01    CE    CD   CG  CB  173.63  30.0  3
 HR7  Var_02    O     C    CA  CB   15.42  30.0  3
 HR7  Var_03    NZ    CE   CD  CG  175.63  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
 HR7  chir_01  CB  N  CG  CA  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
 HR7  plan-1  CE    0.020
 HR7  plan-1  NZ    0.020
 HR7  plan-1  CH    0.020
 HR7  plan-1  NH2   0.020
 HR7  plan-1  NH1   0.020
 HR7  plan-1  HH11  0.020
 HR7  plan-1  HH12  0.020
 HR7  plan-1  HH21  0.020
 HR7  plan-1  HH22  0.020
 HR7  plan-2  O     0.020
 HR7  plan-2  CA    0.020
 HR7  plan-2  OXT   0.020
 HR7  plan-2  HXT   0.020
 HR7  plan-2  C     0.020

