# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 21:28:52 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: (3S)-3,7-diaminoheptanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCC[C@H](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
 B3K  B3K  '(3S)-3,7-diaminoheptanoic acid'  L-peptide  27  11  .  2022-03-15  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_B3K
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
 B3K  N     N  NH2   0  -0.785   0.4400  -3.3295  -0.8482
 B3K  CB    C  CH1   0  -0.080   0.8049  -2.0269  -0.3085
 B3K  CG    C  CH2   0  -0.413   2.2727  -1.7355  -0.6130
 B3K  CD    C  CH2   0  -0.412   3.2439  -2.7407  -0.0088
 B3K  CE    C  CH2   0  -0.438   4.6993  -2.4149  -0.3226
 B3K  CF    C  CH2   0  -0.284   5.6764  -3.4312   0.2610
 B3K  NZ    N  NH2   0  -0.791   7.0853  -3.1781  -0.0048
 B3K  CA    C  CH2   0  -0.595  -0.0988  -0.9043  -0.8331
 B3K  C     C  C     0   0.547   0.0201   0.3985  -0.0920
 B3K  O     O  O     0  -0.448   0.4455   0.5225   1.0304
 B3K  OXT   O  OH1   0  -0.595  -0.4419   1.4230  -0.8035
 B3K  H     H  HNH2  0   0.335   0.5019  -3.3086  -1.8603
 B3K  H2    H  HNH2  0   0.345  -0.5300  -3.5289  -0.6356
 B3K  HB    H  HCH1  0   0.224   0.6838  -2.0860   0.7776
 B3K  HG2   H  HCH2  0   0.209   2.4066  -1.7015  -1.7015
 B3K  HG3   H  HCH2  0   0.224   2.5235  -0.7362  -0.2466
 B3K  HD2   H  HCH2  0   0.216   3.0043  -3.7423  -0.3734
 B3K  HD3   H  HCH2  0   0.206   3.1042  -2.7703   1.0779
 B3K  HE2   H  HCH2  0   0.207   4.8382  -2.3674  -1.4090
 B3K  HE3   H  HCH2  0   0.207   4.9474  -1.4192   0.0623
 B3K  HF1   H  HCH2  0   0.211   5.5378  -3.4834   1.3453
 B3K  HF2   H  HCH2  0   0.210   5.4302  -4.4263  -0.1213
 B3K  HNZ1  H  HNH2  0   0.337   7.3350  -2.2665   0.3602
 B3K  HNZ2  H  HNH2  0   0.336   7.2279  -3.1142  -1.0059
 B3K  HA1   H  HCH2  0   0.262   0.0766  -0.7413  -1.9004
 B3K  HA2   H  HCH2  0   0.289  -1.1481  -1.2102  -0.7452
 B3K  HXT   H  HOH1  0   0.477  -0.3929   2.2362  -0.2785

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
 B3K  N    CB    single  1.456  0.020  1.456
 B3K  N    H     single  0.860  0.020  0.860
 B3K  N    H2    single  0.890  0.020  1.040
 B3K  CB   CG    single  1.527  0.020  1.527
 B3K  CB   CA    single  1.530  0.020  1.530
 B3K  CB   HB    single  0.970  0.020  1.090
 B3K  CG   CD    single  1.523  0.020  1.523
 B3K  CG   HG2   single  0.970  0.020  1.090
 B3K  CG   HG3   single  0.970  0.020  1.090
 B3K  CD   CE    single  1.524  0.020  1.524
 B3K  CD   HD2   single  0.970  0.020  1.090
 B3K  CD   HD3   single  0.970  0.020  1.090
 B3K  CE   CF    single  1.526  0.020  1.526
 B3K  CE   HE2   single  0.970  0.020  1.090
 B3K  CE   HE3   single  0.970  0.020  1.090
 B3K  CF   NZ    single  1.456  0.020  1.456
 B3K  CF   HF1   single  0.970  0.020  1.090
 B3K  CF   HF2   single  0.970  0.020  1.090
 B3K  NZ   HNZ1  single  0.890  0.020  1.040
 B3K  NZ   HNZ2  single  0.890  0.020  1.040
 B3K  CA   C     single  1.525  0.021  1.525
 B3K  CA   HA1   single  0.970  0.020  1.090
 B3K  CA   HA2   single  0.970  0.020  1.090
 B3K  C    OXT   single  1.330  0.020  1.330
 B3K  C    O     double  1.231  0.020  1.231
 B3K  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
 B3K  H2    N    H     105.78  3.000
 B3K  H2    N    CB    109.77  3.000
 B3K  H     N    CB    109.64  3.000
 B3K  HB    CB   CA    108.29  3.000
 B3K  HB    CB   CG    108.33  3.000
 B3K  CA    CB   CG    111.01  3.000
 B3K  HB    CB   N     106.96  3.000
 B3K  CA    CB   N     110.50  1.700
 B3K  CG    CB   N     109.73  3.000
 B3K  HG3   CG   HG2   106.03  3.000
 B3K  HG3   CG   CD    108.91  3.000
 B3K  HG2   CG   CD    109.65  3.000
 B3K  HG3   CG   CB    109.15  3.000
 B3K  HG2   CG   CB    108.72  3.000
 B3K  CD    CG   CB    114.08  3.000
 B3K  HD3   CD   HD2   106.15  3.000
 B3K  HD3   CD   CE    109.37  3.000
 B3K  HD2   CD   CE    109.68  3.000
 B3K  HD3   CD   CG    109.26  3.000
 B3K  HD2   CD   CG    109.44  3.000
 B3K  CE    CD   CG    112.72  3.000
 B3K  HE3   CE   HE2   106.26  3.000
 B3K  HE3   CE   CF    109.02  3.000
 B3K  HE2   CE   CF    109.07  3.000
 B3K  HE3   CE   CD    109.76  3.000
 B3K  HE2   CE   CD    109.53  3.000
 B3K  CF    CE   CD    112.98  3.000
 B3K  HF2   CF   HF1   105.92  3.000
 B3K  HF2   CF   NZ    108.18  3.000
 B3K  HF1   CF   NZ    108.17  3.000
 B3K  HF2   CF   CE    109.15  3.000
 B3K  HF1   CF   CE    109.25  3.000
 B3K  NZ    CF   CE    115.73  3.000
 B3K  HNZ2  NZ   HNZ1  105.34  3.000
 B3K  HNZ2  NZ   CF    109.12  3.000
 B3K  HNZ1  NZ   CF    109.21  3.000
 B3K  HA2   CA   HA1   105.86  3.000
 B3K  HA2   CA   C     106.14  3.000
 B3K  HA1   CA   C     109.82  3.000
 B3K  HA2   CA   CB    109.41  3.000
 B3K  HA1   CA   CB    110.38  3.000
 B3K  C     CA   CB    110.10  1.900
 B3K  OXT   C    O     122.74  3.000
 B3K  O     C    CA    120.80  1.700
 B3K  OXT   C    CA    112.11  3.000
 B3K  HXT   OXT  C     109.82  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
 B3K  CONST_01  HXT   OXT  C   CA   180.00   0.0  0
 B3K  Var_01    CE    CD   CG  CB  -179.56  30.0  3
 B3K  Var_02    OXT   C    CA  CB   160.65  30.0  3
 B3K  Var_03    CF    CE   CD  CG  -179.07  30.0  3
 B3K  Var_04    NZ    CF   CE  CD   179.92  30.0  3
 B3K  Var_05    HNZ1  NZ   CF  CE    58.34  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
 B3K  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
 B3K  plan-1  CA   0.020
 B3K  plan-1  C    0.020
 B3K  plan-1  O    0.020
 B3K  plan-1  OXT  0.020
 B3K  plan-1  HXT  0.020

