# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 08:40:15 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  26  11  .  2022-03-15  2022-07-24
;
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  -0.790   0.4579  -3.3846  -0.8236
 B3K  CB    C  CH1    0  -0.072   0.8015  -2.0650  -0.2928
 B3K  CG    C  CH2    0  -0.409   2.2640  -1.7565  -0.6020
 B3K  CD    C  CH2    0  -0.410   3.2566  -2.7571  -0.0250
 B3K  CE    C  CH2    0  -0.436   4.7047  -2.4063  -0.3455
 B3K  CF    C  CH2    0  -0.284   5.7027  -3.4141   0.2169
 B3K  NZ    N  NH2    0  -0.792   7.1056  -3.1360  -0.0566
 B3K  CA    C  CH2    0  -0.577  -0.1149  -0.9511  -0.8019
 B3K  C     C  C      0   0.403   0.0299   0.4112  -0.1019
 B3K  O     O  O      0  -0.616   0.3520   0.3990   1.1047
 B3K  OXT   O  OC    -1  -0.625  -0.2246   1.4258  -0.7839
 B3K  H     H  HNH2   0   0.326   0.5116  -3.3566  -1.8367
 B3K  H2    H  HNH2   0   0.336  -0.5146  -3.5811  -0.6168
 B3K  HB    H  HCH1   0   0.199   0.6920  -2.1205   0.7946
 B3K  HG2   H  HCH2   0   0.196   2.3920  -1.6995  -1.6911
 B3K  HG3   H  HCH2   0   0.217   2.4975  -0.7605  -0.2164
 B3K  HD2   H  HCH2   0   0.211   3.0284  -3.7566  -0.4033
 B3K  HD3   H  HCH2   0   0.200   3.1274  -2.8079   1.0624
 B3K  HE2   H  HCH2   0   0.205   4.8343  -2.3427  -1.4323
 B3K  HE3   H  HCH2   0   0.205   4.9412  -1.4116   0.0496
 B3K  HF1   H  HCH2   0   0.210   5.5738  -3.4821   1.3016
 B3K  HF2   H  HCH2   0   0.209   5.4688  -4.4085  -0.1756
 B3K  HNZ1  H  HNH2   0   0.336   7.3431  -2.2250   0.3177
 B3K  HNZ2  H  HNH2   0   0.336   7.2387  -3.0567  -1.0579
 B3K  HA1   H  HCH2   0   0.196   0.0197  -0.8333  -1.8829
 B3K  HA2   H  HCH2   0   0.225  -1.1565  -1.2708  -0.6645

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  1.463  0.020  1.463
 B3K  N   H     single  0.860  0.020  0.860
 B3K  N   H2    single  0.890  0.020  1.040
 B3K  CB  CG    single  1.526  0.020  1.526
 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   deloc   1.249  0.020  1.249
 B3K  C   O     deloc   1.231  0.020  1.231

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     105.06  3.000
 B3K  H2    N   CB    109.03  3.000
 B3K  H     N   CB    108.96  3.000
 B3K  HB    CB  CA    107.92  3.000
 B3K  HB    CB  CG    107.90  3.000
 B3K  CA    CB  CG    111.07  3.000
 B3K  HB    CB  N     106.93  3.000
 B3K  CA    CB  N     110.50  1.700
 B3K  CG    CB  N     109.50  3.000
 B3K  HG3   CG  HG2   106.12  3.000
 B3K  HG3   CG  CD    109.01  3.000
 B3K  HG2   CG  CD    109.51  3.000
 B3K  HG3   CG  CB    108.50  3.000
 B3K  HG2   CG  CB    108.85  3.000
 B3K  CD    CG  CB    114.52  3.000
 B3K  HD3   CD  HD2   106.05  3.000
 B3K  HD3   CD  CE    109.34  3.000
 B3K  HD2   CD  CE    109.64  3.000
 B3K  HD3   CD  CG    109.24  3.000
 B3K  HD2   CD  CG    109.49  3.000
 B3K  CE    CD  CG    112.85  3.000
 B3K  HE3   CE  HE2   106.21  3.000
 B3K  HE3   CE  CF    108.99  3.000
 B3K  HE2   CE  CF    109.05  3.000
 B3K  HE3   CE  CD    109.77  3.000
 B3K  HE2   CE  CD    109.52  3.000
 B3K  CF    CE  CD    113.08  3.000
 B3K  HF2   CF  HF1   105.90  3.000
 B3K  HF2   CF  NZ    108.18  3.000
 B3K  HF1   CF  NZ    108.15  3.000
 B3K  HF2   CF  CE    109.16  3.000
 B3K  HF1   CF  CE    109.22  3.000
 B3K  NZ    CF  CE    115.77  3.000
 B3K  HNZ2  NZ  HNZ1  105.30  3.000
 B3K  HNZ2  NZ  CF    109.10  3.000
 B3K  HNZ1  NZ  CF    109.16  3.000
 B3K  HA2   CA  HA1   105.74  3.000
 B3K  HA2   CA  C     106.87  3.000
 B3K  HA1   CA  C     110.00  3.000
 B3K  HA2   CA  CB    108.34  3.000
 B3K  HA1   CA  CB    109.46  3.000
 B3K  C     CA  CB    110.10  1.900
 B3K  OXT   C   O     126.03  3.000
 B3K  O     C   CA    120.80  1.700
 B3K  OXT   C   CA    116.86  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  Var_01  CE    CD  CG  CB  -179.48  30.0  3
 B3K  Var_02  OXT   C   CA  CB   150.46  30.0  3
 B3K  Var_03  CF    CE  CD  CG  -179.35  30.0  3
 B3K  Var_04  NZ    CF  CE  CD   179.93  30.0  3
 B3K  Var_05  HNZ1  NZ  CF  CE    58.29  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

