# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 16:13:10 2022
#   Inital geometry file: a 87 line input string
#   Ligand name: (2~{S},4~{S},6~{S})-2-azanyl-4-methyl-6-oxidanyl-8-oxidanylidene-decanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)C[C@@H](O)C[C@@H](C)C[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
 BZK  BZK  '(2~{S},4~{S},6~{S})-2-azanyl-4-methyl-6-oxidanyl-8-oxidanylidene-decanoic acid'  L-peptide  36  16  .  2019-03-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_BZK
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
 BZK  N    N  NH2    0  -0.814  20.4042   8.5178  12.3411
 BZK  CA   C  CH1    0  -0.236  21.4399   9.0036  13.2442
 BZK  CB   C  CH2    0  -0.389  20.8271   9.8867  14.3314
 BZK  C    C  C      0   0.419  22.2402   7.8187  13.8478
 BZK  O    O  O      0  -0.606  22.9250   8.0670  14.8595
 BZK  CG1  C  CH1    0  -0.230  20.0052  11.0723  13.8195
 BZK  CGB  C  CH3    0  -0.664  20.8129  11.9627  12.8773
 BZK  CD   C  CH2    0  -0.422  19.4789  11.9337  14.9741
 BZK  CE   C  CH1    0   0.066  18.6517  11.2180  16.0335
 BZK  OE   O  OH1    0  -0.673  17.5470  10.6178  15.3856
 BZK  CZ   C  CH2    0  -0.597  18.1733  12.1963  17.1086
 BZK  CH   C  C      0   0.402  19.2586  12.7414  18.0073
 BZK  OH   O  O      0  -0.405  20.2676  12.1158  18.2476
 BZK  CI   C  CH2    0  -0.556  18.9906  14.0972  18.6060
 BZK  CK   C  CH3    0  -0.660  20.0167  14.5639  19.6216
 BZK  H1   H  HNH2   0   0.329  20.2037   9.2139  11.6348
 BZK  H2   H  HNH2   0   0.331  20.7700   7.7070  11.8594
 BZK  HA   H  HCH1   0   0.195  22.1949   9.6058  12.7087
 BZK  HB2  H  HCH2   0   0.207  20.1922   9.2548  14.9601
 BZK  HB1  H  HCH2   0   0.196  21.6272  10.2650  14.9734
 BZK  HG1  H  HCH1   0   0.210  19.1457  10.6871  13.2620
 BZK  H4   H  HCH3   0   0.222  20.2354  12.8374  12.5717
 BZK  HGB  H  HCH3   0   0.210  21.7239  12.3212  13.3635
 BZK  H5   H  HCH3   0   0.227  21.1107  11.4398  11.9671
 BZK  HD2  H  HCH2   0   0.221  20.3344  12.4033  15.4699
 BZK  HD1  H  HCH2   0   0.217  18.8785  12.7536  14.5628
 BZK  HE   H  HCH1   0   0.206  19.2699  10.4532  16.5176
 BZK  HOE  H  HOH1   0   0.445  17.0866  10.0607  16.0207
 BZK  HZ2  H  HCH2   0   0.253  17.6135  13.0203  16.6564
 BZK  HZ1  H  HCH2   0   0.282  17.4638  11.6901  17.7777
 BZK  HI1  H  HCH2   0   0.267  18.9178  14.8032  17.7709
 BZK  HI2  H  HCH2   0   0.263  17.9843  14.0787  19.0380
 BZK  HK2  H  HCH3   0   0.234  19.7459  15.5458  20.0077
 BZK  HK1  H  HCH3   0   0.227  20.0812  13.8818  20.4691
 BZK  HK3  H  HCH3   0   0.228  21.0099  14.6445  19.1811
 BZK  OXT  O  OC    -1  -0.604  22.1665   6.7250  13.2507

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
 BZK  N    CA   single  1.458  0.019  1.458
 BZK  CGB  CG1  single  1.527  0.020  1.527
 BZK  CA   C    single  1.525  0.021  1.525
 BZK  CA   CB   single  1.521  0.033  1.521
 BZK  CG1  CB   single  1.531  0.020  1.531
 BZK  CG1  CD   single  1.534  0.020  1.534
 BZK  C    O    deloc   1.231  0.020  1.231
 BZK  CD   CE   single  1.523  0.020  1.523
 BZK  OE   CE   single  1.414  0.020  1.414
 BZK  CE   CZ   single  1.530  0.020  1.530
 BZK  CZ   CH   single  1.511  0.020  1.511
 BZK  OH   CH   double  1.211  0.020  1.211
 BZK  CH   CI   single  1.506  0.020  1.506
 BZK  CI   CK   single  1.517  0.020  1.517
 BZK  N    H1   single  0.890  0.020  1.040
 BZK  N    H2   single  0.890  0.020  1.040
 BZK  CA   HA   single  0.970  0.020  0.970
 BZK  CB   HB2  single  0.970  0.020  1.090
 BZK  CB   HB1  single  0.970  0.020  1.090
 BZK  CG1  HG1  single  0.970  0.020  1.090
 BZK  CGB  H4   single  0.970  0.020  1.090
 BZK  CGB  HGB  single  0.970  0.020  1.090
 BZK  CGB  H5   single  0.970  0.020  1.090
 BZK  CD   HD2  single  0.970  0.020  1.090
 BZK  CD   HD1  single  0.970  0.020  1.090
 BZK  CE   HE   single  0.970  0.020  1.090
 BZK  OE   HOE  single  0.850  0.020  0.980
 BZK  CZ   HZ2  single  0.970  0.020  1.090
 BZK  CZ   HZ1  single  0.970  0.020  1.090
 BZK  CI   HI1  single  0.970  0.020  1.090
 BZK  CI   HI2  single  0.970  0.020  1.090
 BZK  CK   HK2  single  0.970  0.020  1.090
 BZK  CK   HK1  single  0.970  0.020  1.090
 BZK  CK   HK3  single  0.970  0.020  1.090
 BZK  C    OXT  deloc   1.248  0.020  1.248

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
 BZK  H2   N    H1   106.90  3.000
 BZK  H2   N    CA   107.77  3.000
 BZK  H1   N    CA   110.13  3.000
 BZK  HA   CA   C    110.00  3.000
 BZK  HA   CA   CB   109.00  3.000
 BZK  C    CA   CB   110.50  1.500
 BZK  HA   CA   N    110.00  3.000
 BZK  CB   CA   N    110.40  1.500
 BZK  C    CA   N    111.00  2.800
 BZK  HB1  CB   HB2  106.68  3.000
 BZK  HB1  CB   CG1  108.74  3.000
 BZK  HB2  CB   CG1  109.14  3.000
 BZK  HB1  CB   CA   108.91  3.000
 BZK  HB2  CB   CA   107.91  3.000
 BZK  CG1  CB   CA   115.14  3.000
 BZK  OXT  C    O    126.52  3.000
 BZK  OXT  C    CA   120.80  1.700
 BZK  O    C    CA   120.80  1.700
 BZK  HG1  CG1  CD   108.16  3.000
 BZK  HG1  CG1  CGB  107.83  3.000
 BZK  CD   CG1  CGB  108.57  3.000
 BZK  HG1  CG1  CB   108.63  3.000
 BZK  CD   CG1  CB   111.57  3.000
 BZK  CGB  CG1  CB   111.95  3.000
 BZK  H5   CGB  HGB  107.51  3.000
 BZK  H5   CGB  H4   107.15  3.000
 BZK  HGB  CGB  H4   107.61  3.000
 BZK  H5   CGB  CG1  112.31  3.000
 BZK  HGB  CGB  CG1  110.95  3.000
 BZK  H4   CGB  CG1  111.09  3.000
 BZK  HD1  CD   HD2  106.09  3.000
 BZK  HD1  CD   CE   108.37  3.000
 BZK  HD2  CD   CE   108.12  3.000
 BZK  HD1  CD   CG1  109.00  3.000
 BZK  HD2  CD   CG1  108.28  3.000
 BZK  CE   CD   CG1  116.50  3.000
 BZK  HE   CE   CZ   108.18  3.000
 BZK  HE   CE   OE   110.29  3.000
 BZK  CZ   CE   OE   110.43  3.000
 BZK  HE   CE   CD   109.20  3.000
 BZK  CZ   CE   CD   110.98  3.000
 BZK  OE   CE   CD   107.76  3.000
 BZK  HOE  OE   CE   108.48  3.000
 BZK  HZ1  CZ   HZ2  105.56  3.000
 BZK  HZ1  CZ   CH   105.54  3.000
 BZK  HZ2  CZ   CH   109.98  3.000
 BZK  HZ1  CZ   CE   109.58  3.000
 BZK  HZ2  CZ   CE   110.55  3.000
 BZK  CH   CZ   CE   115.09  3.000
 BZK  CI   CH   OH   122.29  3.000
 BZK  CI   CH   CZ   115.68  3.000
 BZK  OH   CH   CZ   122.01  3.000
 BZK  HI2  CI   HI1  104.50  3.000
 BZK  HI2  CI   CK   111.26  3.000
 BZK  HI1  CI   CK   110.91  3.000
 BZK  HI2  CI   CH   107.76  3.000
 BZK  HI1  CI   CH   106.78  3.000
 BZK  CK   CI   CH   115.00  3.000
 BZK  HK3  CK   HK1  107.87  3.000
 BZK  HK3  CK   HK2  107.65  3.000
 BZK  HK1  CK   HK2  107.65  3.000
 BZK  HK3  CK   CI   111.63  3.000
 BZK  HK1  CK   CI   111.60  3.000
 BZK  HK2  CK   CI   110.26  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
 BZK  Var_01  OH   CH  CZ  CE   -28.34  30.0  3
 BZK  Var_02  CK   CI  CH  CZ   173.65  30.0  3
 BZK  Var_03  HK2  CK  CI  CH  -179.67  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
 BZK  chir_01  CA   N    C   CB  positiv
 BZK  chir_02  CG1  CGB  CB  CD  negativ
 BZK  chir_03  CE   OE   CD  CZ  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
 BZK  plan-1  CZ   0.020
 BZK  plan-1  CH   0.020
 BZK  plan-1  OH   0.020
 BZK  plan-1  CI   0.020
 BZK  plan-2  CA   0.020
 BZK  plan-2  C    0.020
 BZK  plan-2  O    0.020
 BZK  plan-2  OXT  0.020

