# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 15:52:57 2022
#   Inital geometry file: a 59 line input string
#   Ligand name: (2S)-2,6-diaminohexane-1,1-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCC[C@H](N)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
 LYK  LYK  (2S)-2,6-diaminohexane-1,1-diol  peptide  26  10  .  2016-04-26  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LYK
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
 LYK  C     C  CH1   0   0.289  5.2240  10.2141  15.6758
 LYK  N     N  NH2   0  -0.813  6.6671  11.7678  14.5241
 LYK  O     O  OH1   0  -0.665  4.0188   9.5145  15.5763
 LYK  CA    C  CH1   0  -0.136  5.4073  11.0452  14.4086
 LYK  CB    C  CH2   0  -0.404  5.4201  10.1594  13.1652
 LYK  CD    C  CH2   0  -0.420  5.3679  10.0690  10.6316
 LYK  CE    C  CH2   0  -0.270  5.5728  10.8318   9.3330
 LYK  CG    C  CH2   0  -0.436  5.5967  10.9340  11.8635
 LYK  NZ    N  NH2   0  -0.797  5.3027   9.9865   8.1782
 LYK  OXT   O  OH1   0  -0.671  5.2234  11.0974  16.7637
 LYK  H     H  HNH2  0   0.349  6.7891  12.3713  13.7216
 LYK  H2    H  HNH2  0   0.342  6.6293  12.3847  15.3250
 LYK  HO    H  HOH1  0   0.454  4.0313   8.7708  16.1870
 LYK  HA    H  HCH1  0   0.197  4.5370  11.7202  14.3280
 LYK  HB    H  HCH2  0   0.208  6.2188   9.4154  13.2606
 LYK  HBA   H  HCH2  0   0.222  4.4797   9.6072  13.1185
 LYK  HD    H  HCH2  0   0.212  4.3528   9.6607  10.6501
 LYK  HDA   H  HCH2  0   0.210  6.0467   9.2086  10.6579
 LYK  HE    H  HCH2  0   0.209  4.8792  11.6773   9.3055
 LYK  HEA   H  HCH2  0   0.185  6.5832  11.2665   9.3327
 LYK  HG    H  HCH2  0   0.211  4.8978  11.7784  11.8446
 LYK  HGA   H  HCH2  0   0.212  6.6009  11.3663  11.8121
 LYK  HNZ   H  HNH2  0   0.343  5.4159  10.5275   7.3303
 LYK  HNZA  H  HNH2  0   0.335  6.0034   9.2567   8.1282
 LYK  HXT   H  HOH1  0   0.454  5.4587  10.6194  17.5653
 LYK  H1    H  HCH1  0   0.182  6.0692   9.5145  15.7615

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
 LYK  CA   C     single  1.525  0.021  1.525
 LYK  C    O     single  1.231  0.020  1.231
 LYK  C    OXT   single  1.401  0.020  1.401
 LYK  CA   N     single  1.458  0.019  1.458
 LYK  N    H     single  0.860  0.020  0.860
 LYK  N    H2    single  0.890  0.020  1.040
 LYK  O    HO    single  0.850  0.020  0.980
 LYK  CB   CA    single  1.530  0.020  1.530
 LYK  CA   HA    single  0.970  0.020  0.970
 LYK  CG   CB    single  1.525  0.020  1.525
 LYK  CB   HB    single  0.970  0.020  1.090
 LYK  CB   HBA   single  0.970  0.020  1.090
 LYK  CE   CD    single  1.520  0.020  1.520
 LYK  CD   CG    single  1.522  0.020  1.522
 LYK  CD   HD    single  0.970  0.020  1.090
 LYK  CD   HDA   single  0.970  0.020  1.090
 LYK  NZ   CE    single  1.456  0.020  1.456
 LYK  CE   HE    single  0.970  0.020  1.090
 LYK  CE   HEA   single  0.970  0.020  1.090
 LYK  CG   HG    single  0.970  0.020  1.090
 LYK  CG   HGA   single  0.970  0.020  1.090
 LYK  NZ   HNZ   single  0.890  0.020  1.040
 LYK  NZ   HNZA  single  0.890  0.020  1.040
 LYK  OXT  HXT   single  0.850  0.020  0.980
 LYK  C    H1    single  0.970  0.020  1.090

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
 LYK  H1    C    OXT  109.91  3.000
 LYK  H1    C    CA   108.57  3.000
 LYK  OXT   C    CA   107.54  3.000
 LYK  H1    C    O    110.47  3.000
 LYK  OXT   C    O    111.75  3.000
 LYK  CA    C    O    120.80  1.700
 LYK  H2    N    H    105.59  3.000
 LYK  H2    N    CA   109.44  3.000
 LYK  H     N    CA   114.00  3.000
 LYK  HO    O    C    109.30  3.000
 LYK  HA    CA   CB   109.00  3.000
 LYK  HA    CA   N    110.00  3.000
 LYK  CB    CA   N    110.50  1.700
 LYK  HA    CA   C    109.00  3.000
 LYK  CB    CA   C    110.10  1.900
 LYK  N     CA   C    111.00  2.800
 LYK  HBA   CB   HB   106.76  3.000
 LYK  HBA   CB   CG   108.68  3.000
 LYK  HB    CB   CG   109.56  3.000
 LYK  HBA   CB   CA   108.73  3.000
 LYK  HB    CB   CA   109.22  3.000
 LYK  CG    CB   CA   113.67  3.000
 LYK  HDA   CD   HD   106.33  3.000
 LYK  HDA   CD   CG   109.48  3.000
 LYK  HD    CD   CG   109.74  3.000
 LYK  HDA   CD   CE   109.32  3.000
 LYK  HD    CD   CE   109.07  3.000
 LYK  CG    CD   CE   112.70  3.000
 LYK  HEA   CE   HE   106.08  3.000
 LYK  HEA   CE   NZ   113.55  3.000
 LYK  HE    CE   NZ   108.13  3.000
 LYK  HEA   CE   CD   108.80  3.000
 LYK  HE    CE   CD   108.90  3.000
 LYK  NZ    CE   CD   111.17  3.000
 LYK  HGA   CG   HG   106.25  3.000
 LYK  HGA   CG   CD   108.92  3.000
 LYK  HG    CG   CD   109.14  3.000
 LYK  HGA   CG   CB   110.30  3.000
 LYK  HG    CG   CB   109.40  3.000
 LYK  CD    CG   CB   112.62  3.000
 LYK  HNZA  NZ   HNZ  105.45  3.000
 LYK  HNZA  NZ   CE   109.21  3.000
 LYK  HNZ   NZ   CE   109.47  3.000
 LYK  HXT   OXT  C    109.48  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
 LYK  Var_01  CD   CG  CB  CA  -170.14  30.0  1
 LYK  Var_02  CE   CD  CG  CB  -178.76  30.0  1
 LYK  Var_03  NZ   CE  CD  CG  -178.11  30.0  1
 LYK  Var_04  HNZ  NZ  CE  CD   178.08  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
 LYK  chir_01  CA  C  N  CB  negativ

