# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 03:08:21 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: (2~{S})-2-azanyl-6-[(~{E})-[5-(hydroxymethyl)-2-methyl-3-oxidanyl-pyridin-4-yl]methylideneamino]hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO)c(C=NCCCC[C@H](N)C(O)=O)c1O
#
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
 JLP  JLP  '(2~{S})-2-azanyl-6-[(~{E})-[5-(hydroxymethyl)-2-methyl-3-oxidanyl-pyridin-4-yl]methylideneamino]hexanoic acid'  L-peptide  41  21  .  2022-07-25  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_JLP
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
 JLP  N    N  NH2    0  -0.786  -5.8883   0.3303  -1.3790
 JLP  CA   C  CH1    0  -0.213  -5.4340  -0.3744  -0.1888
 JLP  CB   C  CH2    0  -0.416  -4.0199   0.0759   0.1857
 JLP  CG   C  CH2    0  -0.410  -2.9833  -0.1548  -0.9058
 JLP  CD   C  CH2    0  -0.431  -1.5833   0.2520  -0.4643
 JLP  CE   C  CH2    0  -0.286  -0.5341  -0.0211  -1.5370
 JLP  NZ   N  N      0  -0.451   0.7732   0.3833  -1.0787
 JLP  C4A  C  C1     0   0.050   1.6507  -0.5033  -0.8362
 JLP  C4   C  CR6    0  -0.022   2.9690  -0.1428  -0.3160
 JLP  C3   C  CR6    0   0.297   3.2779   1.2023  -0.0736
 JLP  O3   O  OH1    0  -0.629   2.4156   2.1873  -0.2980
 JLP  C5   C  CR6    0  -0.085   3.9443  -1.1172  -0.0416
 JLP  C5A  C  CH2    0  -0.222   3.6754  -2.5876  -0.2741
 JLP  OP4  O  OH1    0  -0.651   4.7038  -3.4305   0.1694
 JLP  C6   C  CR16   0  -0.153   5.1624  -0.6823   0.4427
 JLP  N1   N  N      0  -0.399   5.4501   0.6010   0.6692
 JLP  C2   C  CR6    0   0.125   4.5513   1.5340   0.4286
 JLP  C2A  C  CH3    0  -0.721   4.9015   2.9640   0.6993
 JLP  C    C  C      0   0.384  -6.3564  -0.2461   1.0499
 JLP  O    O  O      0  -0.608  -7.2606   0.6122   1.0130
 JLP  O1   O  OC    -1  -0.625  -6.1004  -1.0104   2.0046
 JLP  H1   H  HNH2   0   0.333  -6.7784  -0.0610  -1.6634
 JLP  H2   H  HNH2   0   0.321  -6.1117   1.2819  -1.1094
 JLP  H4   H  HCH1   0   0.206  -5.3782  -1.4401  -0.4437
 JLP  H5   H  HCH2   0   0.204  -4.0384   1.1409   0.4495
 JLP  H6   H  HCH2   0   0.216  -3.7140  -0.4563   1.0896
 JLP  H7   H  HCH2   0   0.206  -2.9835  -1.2151  -1.1819
 JLP  H8   H  HCH2   0   0.217  -3.2673   0.3952  -1.8062
 JLP  H9   H  HCH2   0   0.223  -1.5660   1.3148  -0.2057
 JLP  H10  H  HCH2   0   0.220  -1.3082  -0.2945   0.4433
 JLP  H11  H  HCH2   0   0.212  -0.5484  -1.0834  -1.8104
 JLP  H12  H  HCH2   0   0.242  -0.7758   0.5526  -2.4355
 JLP  H13  H  H      0   0.252   1.4342  -1.5595  -1.0092
 JLP  H14  H  HOH1   0   0.469   1.5745   1.7732  -0.6491
 JLP  H15  H  HCH2   0   0.229   2.7176  -2.8615   0.1843
 JLP  H16  H  HCH2   0   0.252   3.5657  -2.7657  -1.3472
 JLP  H17  H  HOH1   0   0.456   4.6981  -3.4380   1.1319
 JLP  H18  H  HCR6   0   0.251   5.9521  -1.3893   0.6623
 JLP  H19  H  HCH3   0   0.247   4.8062   3.5807  -0.1961
 JLP  H20  H  HCH3   0   0.247   4.2466   3.4004   1.4557
 JLP  H21  H  HCH3   0   0.247   5.9273   3.0341   1.0549

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
 JLP  C2A  C2   single    1.497  0.020  1.497
 JLP  O3   C3   single    1.328  0.020  1.328
 JLP  C3   C2   aromatic  1.408  0.020  1.408
 JLP  C3   C4   aromatic  1.401  0.020  1.401
 JLP  C2   N1   aromatic  1.318  0.020  1.318
 JLP  NZ   CE   single    1.443  0.020  1.443
 JLP  NZ   C4A  double    1.271  0.020  1.271
 JLP  CE   CD   single    1.525  0.020  1.525
 JLP  N1   C6   aromatic  1.335  0.020  1.335
 JLP  C4   C4A  single    1.462  0.020  1.462
 JLP  C4   C5   aromatic  1.406  0.020  1.406
 JLP  CD   CG   single    1.523  0.020  1.523
 JLP  C6   C5   aromatic  1.381  0.020  1.381
 JLP  C5   C5A  single    1.513  0.020  1.513
 JLP  CG   CB   single    1.523  0.020  1.523
 JLP  C5A  OP4  single    1.402  0.020  1.402
 JLP  CB   CA   single    1.530  0.020  1.530
 JLP  CA   N    single    1.458  0.019  1.458
 JLP  CA   C    single    1.525  0.021  1.525
 JLP  C    O    deloc     1.231  0.020  1.231
 JLP  C    O1   deloc     1.249  0.020  1.249
 JLP  N    H1   single    0.890  0.020  1.040
 JLP  N    H2   single    0.890  0.020  1.040
 JLP  CA   H4   single    0.970  0.020  1.090
 JLP  CB   H5   single    0.970  0.020  1.090
 JLP  CB   H6   single    0.970  0.020  1.090
 JLP  CG   H7   single    0.970  0.020  1.090
 JLP  CG   H8   single    0.970  0.020  1.090
 JLP  CD   H9   single    0.970  0.020  1.090
 JLP  CD   H10  single    0.970  0.020  1.090
 JLP  CE   H11  single    0.970  0.020  1.090
 JLP  CE   H12  single    0.970  0.020  1.090
 JLP  C4A  H13  single    0.930  0.020  1.080
 JLP  O3   H14  single    0.850  0.020  0.980
 JLP  C5A  H15  single    0.970  0.020  1.090
 JLP  C5A  H16  single    0.970  0.020  1.090
 JLP  OP4  H17  single    0.850  0.020  0.980
 JLP  C6   H18  single    0.930  0.020  1.080
 JLP  C2A  H19  single    0.970  0.020  1.090
 JLP  C2A  H20  single    0.970  0.020  1.090
 JLP  C2A  H21  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
 JLP  H2   N    H1   104.09  3.000
 JLP  H2   N    CA   107.80  3.000
 JLP  H1   N    CA   108.47  3.000
 JLP  H4   CA   C    107.24  3.000
 JLP  H4   CA   CB   107.19  3.000
 JLP  C    CA   CB   110.10  1.900
 JLP  H4   CA   N    107.23  3.000
 JLP  C    CA   N    111.00  2.800
 JLP  CB   CA   N    110.50  1.700
 JLP  H6   CB   H5   106.17  3.000
 JLP  H6   CB   CG   109.18  3.000
 JLP  H5   CB   CG   109.31  3.000
 JLP  H6   CB   CA   108.53  3.000
 JLP  H5   CB   CA   109.20  3.000
 JLP  CG   CB   CA   114.14  3.000
 JLP  H8   CG   H7   106.23  3.000
 JLP  H8   CG   CD   110.08  3.000
 JLP  H7   CG   CD   109.37  3.000
 JLP  H8   CG   CB   109.72  3.000
 JLP  H7   CG   CB   109.09  3.000
 JLP  CD   CG   CB   112.17  3.000
 JLP  H10  CD   H9   106.56  3.000
 JLP  H10  CD   CE   108.72  3.000
 JLP  H9   CD   CE   109.23  3.000
 JLP  H10  CD   CG   109.76  3.000
 JLP  H9   CD   CG   110.03  3.000
 JLP  CE   CD   CG   112.37  3.000
 JLP  H12  CE   H11  107.48  3.000
 JLP  H12  CE   NZ   108.32  3.000
 JLP  H11  CE   NZ   111.25  3.000
 JLP  H12  CE   CD   109.39  3.000
 JLP  H11  CE   CD   109.86  3.000
 JLP  NZ   CE   CD   110.47  3.000
 JLP  C4A  NZ   CE   119.38  3.000
 JLP  H13  C4A  C4   118.27  3.000
 JLP  H13  C4A  NZ   120.51  3.000
 JLP  C4   C4A  NZ   121.22  3.000
 JLP  C5   C4   C3   118.60  3.000
 JLP  C5   C4   C4A  121.60  3.000
 JLP  C3   C4   C4A  119.80  3.000
 JLP  C2   C3   O3   118.20  3.000
 JLP  C2   C3   C4   119.15  3.000
 JLP  O3   C3   C4   122.66  3.000
 JLP  H14  O3   C3   107.33  3.000
 JLP  C6   C5   C5A  121.11  3.000
 JLP  C5A  C5   C4   121.36  3.000
 JLP  C6   C5   C4   117.52  3.000
 JLP  H16  C5A  H15  106.38  3.000
 JLP  H16  C5A  OP4  106.63  3.000
 JLP  H15  C5A  OP4  111.00  3.000
 JLP  H16  C5A  C5   109.09  3.000
 JLP  H15  C5A  C5   109.50  3.000
 JLP  OP4  C5A  C5   113.92  3.000
 JLP  H17  OP4  C5A  108.46  3.000
 JLP  H18  C6   N1   115.87  3.000
 JLP  H18  C6   C5   120.59  3.000
 JLP  N1   C6   C5   123.54  3.000
 JLP  C2   N1   C6   120.18  3.000
 JLP  C2A  C2   N1   118.93  3.000
 JLP  N1   C2   C3   121.00  3.000
 JLP  C2A  C2   C3   120.07  3.000
 JLP  H21  C2A  H20  108.27  3.000
 JLP  H21  C2A  H19  108.31  3.000
 JLP  H20  C2A  H19  106.87  3.000
 JLP  H21  C2A  C2   109.95  3.000
 JLP  H20  C2A  C2   111.52  3.000
 JLP  H19  C2A  C2   111.78  3.000
 JLP  O1   C    O    126.30  3.000
 JLP  O1   C    CA   115.98  3.000
 JLP  O    C    CA   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
 JLP  CONST_01  N1   C2   C3   C4      0.00   0.0  0
 JLP  CONST_02  N1   C6   C5   C4      0.00   0.0  0
 JLP  CONST_03  C6   N1   C2   C3      0.00   0.0  0
 JLP  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 JLP  CONST_05  C2   C3   C4   C5      0.00   0.0  0
 JLP  CONST_06  C2   N1   C6   C5      0.00   0.0  0
 JLP  CONST_07  C2   C3   C4   C4A   180.00   0.0  0
 JLP  CONST_08  C6   C5   C4   C4A   180.00   0.0  0
 JLP  CONST_09  C2A  C2   C3   C4    180.00   0.0  0
 JLP  CONST_10  C5A  C5   C4   C3    180.00   0.0  0
 JLP  CONST_11  N1   C2   C3   O3    180.00   0.0  0
 JLP  CONST_12  C5   C4   C3   O3    180.00   0.0  0
 JLP  CONST_13  N1   C6   C5   C5A   180.00   0.0  0
 JLP  CONST_14  C2A  C2   N1   C6    180.00   0.0  0
 JLP  CONST_15  H18  C6   C5   C4    180.00   0.0  0
 JLP  Var_01    C3   C4   C4A  NZ      0.19  30.0  2
 JLP  Var_02    OP4  C5A  C5   C4   -174.25  30.0  2
 JLP  Var_03    H19  C2A  C2   C3    -58.13  30.0  2
 JLP  Var_04    C4   C4A  NZ   CE   -177.36   0.0  2
 JLP  Var_05    CD   CG   CB   CA   -177.49  30.0  1
 JLP  Var_06    CE   CD   CG   CB    178.06  30.0  2
 JLP  Var_07    NZ   CE   CD   CG    179.78  30.0  2

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
 JLP  chir_01  CA  CB  N  C  positiv

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
 JLP  plan-1  C4A  0.020
 JLP  plan-1  C4   0.020
 JLP  plan-1  C3   0.020
 JLP  plan-1  O3   0.020
 JLP  plan-1  C5   0.020
 JLP  plan-1  C5A  0.020
 JLP  plan-1  C6   0.020
 JLP  plan-1  N1   0.020
 JLP  plan-1  C2   0.020
 JLP  plan-1  C2A  0.020
 JLP  plan-1  H18  0.020
 JLP  plan-2  CA   0.020
 JLP  plan-2  C    0.020
 JLP  plan-2  O    0.020
 JLP  plan-2  O1   0.020
 JLP  plan-3  CE   0.020
 JLP  plan-3  NZ   0.020
 JLP  plan-3  C4A  0.020
 JLP  plan-3  C4   0.020
 JLP  plan-3  H13  0.020

