# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 03:20:33 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 5-[5-(hydroxymethyl)-1H-imidazol-2-yl]-L-norvaline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCc1[nH]c(CO)cn1)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
 OJY  OJY  5-[5-(hydroxymethyl)-1H-imidazol-2-yl]-L-norvaline  L-peptide  29  15  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT (side chain)
;

data_comp_OJY
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
 OJY  C11  C  CH2    0  -0.520  -0.2902  -1.1113  -0.7094
 OJY  C14  C  CR5    0   0.258  -3.7015  -0.0263  -0.0703
 OJY  C10  C  CH2    0  -0.431   0.6367  -0.1668   0.0603
 OJY  C12  C  CR5    0   0.428  -1.7233  -0.9721  -0.3288
 OJY  C15  C  CR15   0  -0.266  -3.7029  -1.2991   0.4214
 OJY  C06  C  C      0   0.404   4.5133   0.1676   0.0306
 OJY  O07  O  O      0  -0.607   5.1212   0.9631  -0.7119
 OJY  C08  C  CH1    0  -0.209   3.0744   0.5401   0.4497
 OJY  C09  C  CH2    0  -0.427   2.0954  -0.3475  -0.3378
 OJY  N13  N  NR15   0  -0.646  -2.4326   0.1634  -0.5427
 OJY  N16  N  N      0  -0.459  -2.4685  -1.8747   0.2560
 OJY  O18  O  OH1    0  -0.664  -5.9170   0.5076   0.4540
 OJY  N19  N  NH2    0  -0.796   2.8484   1.9700   0.3155
 OJY  H1   H  HCH2   0   0.248  -0.1724  -0.9365  -1.7837
 OJY  H2   H  HCH2   0   0.250   0.0015  -2.1468  -0.5263
 OJY  H3   H  HCH2   0   0.210   0.3244   0.8666  -0.1192
 OJY  H4   H  HCH2   0   0.228   0.5219  -0.3445   1.1343
 OJY  H7   H  HCR5   0   0.245  -4.5189  -1.8325   0.8833
 OJY  H17  H  HCH1   0   0.202   2.9611   0.2847   1.5105
 OJY  H18  H  HCH2   0   0.215   2.3769  -1.3938  -0.1891
 OJY  H19  H  HCH2   0   0.209   2.2074  -0.1414  -1.4095
 OJY  H20  H  HNR5   0   0.412  -2.0864   1.0010  -0.9842
 OJY  H22  H  HOH1   0   0.463  -6.6189   1.1555   0.3475
 OJY  H23  H  HNH2   0   0.325   3.0468   2.2467  -0.6379
 OJY  H8   H  HNH2   0   0.333   1.8749   2.1895   0.4852
 OJY  H5   H  HCH2   0   0.219  -4.4064   1.9352   0.3507
 OJY  H6   H  HCH2   0   0.221  -4.9282   1.2924  -1.1991
 OJY  C17  C  CH2    0  -0.223  -4.7571   1.0210  -0.1483
 OJY  OXT  O  OC    -1  -0.623   4.9353  -0.9325   0.4430

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
 OJY  C11  C12  single    1.489  0.020  1.489
 OJY  C11  C10  single    1.531  0.020  1.531
 OJY  C14  C17  single    1.489  0.020  1.489
 OJY  C14  N13  aromatic  1.367  0.020  1.367
 OJY  C14  C15  aromatic  1.364  0.020  1.364
 OJY  C10  C09  single    1.523  0.020  1.523
 OJY  C12  N13  aromatic  1.356  0.020  1.356
 OJY  C12  N16  aromatic  1.308  0.020  1.308
 OJY  C17  O18  single    1.404  0.020  1.404
 OJY  C15  N16  aromatic  1.372  0.020  1.372
 OJY  C06  O07  deloc     1.246  0.020  1.246
 OJY  C06  C08  single    1.544  0.020  1.544
 OJY  C08  N19  single    1.454  0.020  1.454
 OJY  C08  C09  single    1.538  0.020  1.538
 OJY  C11  H1   single    0.970  0.020  1.090
 OJY  C11  H2   single    0.970  0.020  1.090
 OJY  C10  H3   single    0.970  0.020  1.090
 OJY  C10  H4   single    0.970  0.020  1.090
 OJY  C17  H5   single    0.970  0.020  1.090
 OJY  C17  H6   single    0.970  0.020  1.090
 OJY  C15  H7   single    0.930  0.020  1.080
 OJY  C08  H17  single    0.970  0.020  1.090
 OJY  C09  H18  single    0.970  0.020  1.090
 OJY  C09  H19  single    0.970  0.020  1.090
 OJY  N13  H20  single    0.860  0.020  1.020
 OJY  O18  H22  single    0.850  0.020  0.980
 OJY  N19  H23  single    0.890  0.020  1.040
 OJY  C06  OXT  deloc     1.248  0.020  1.248
 OJY  N19  H8   single    0.890  0.020  1.040

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
 OJY  H2   C11  H1   106.70  3.000
 OJY  H2   C11  C12  107.64  3.000
 OJY  H1   C11  C12  109.85  3.000
 OJY  H2   C11  C10  109.82  3.000
 OJY  H1   C11  C10  109.25  3.000
 OJY  C12  C11  C10  113.36  3.000
 OJY  N13  C14  C15  104.77  3.000
 OJY  C15  C14  C17  132.40  3.000
 OJY  N13  C14  C17  122.84  3.000
 OJY  H4   C10  H3   106.52  3.000
 OJY  H4   C10  C09  109.74  3.000
 OJY  H3   C10  C09  110.03  3.000
 OJY  H4   C10  C11  109.25  3.000
 OJY  H3   C10  C11  109.10  3.000
 OJY  C09  C10  C11  112.05  3.000
 OJY  N16  C12  N13  110.51  3.000
 OJY  N16  C12  C11  126.71  3.000
 OJY  N13  C12  C11  122.78  3.000
 OJY  H7   C15  N16  121.65  3.000
 OJY  H7   C15  C14  128.05  3.000
 OJY  N16  C15  C14  110.30  3.000
 OJY  OXT  C06  C08  115.97  3.000
 OJY  OXT  C06  O07  126.46  3.000
 OJY  C08  C06  O07  117.53  3.000
 OJY  H17  C08  N19  107.59  3.000
 OJY  H17  C08  C09  107.16  3.000
 OJY  N19  C08  C09  114.91  3.000
 OJY  H17  C08  C06  107.61  3.000
 OJY  C09  C08  C06  108.35  3.000
 OJY  N19  C08  C06  110.91  3.000
 OJY  H19  C09  H18  106.63  3.000
 OJY  H19  C09  C08  109.07  3.000
 OJY  H18  C09  C08  108.58  3.000
 OJY  H19  C09  C10  109.32  3.000
 OJY  H18  C09  C10  108.94  3.000
 OJY  C08  C09  C10  114.04  3.000
 OJY  H20  N13  C12  125.82  3.000
 OJY  H20  N13  C14  125.82  3.000
 OJY  C12  N13  C14  108.35  3.000
 OJY  C15  N16  C12  106.07  3.000
 OJY  H22  O18  C17  108.01  3.000
 OJY  H8   N19  H23  106.68  3.000
 OJY  H8   N19  C08  110.32  3.000
 OJY  H23  N19  C08  108.98  3.000
 OJY  H6   C17  H5   106.17  3.000
 OJY  H6   C17  O18  111.84  3.000
 OJY  H5   C17  O18  111.90  3.000
 OJY  H6   C17  C14  109.53  3.000
 OJY  H5   C17  C14  109.57  3.000
 OJY  O18  C17  C14  107.82  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
 OJY  CONST_01  N16  C12  N13  C14     0.00   0.0  0
 OJY  CONST_02  C12  N16  C15  C14     0.00   0.0  0
 OJY  CONST_03  C15  C14  N13  C12     0.00   0.0  0
 OJY  CONST_04  N13  C12  N16  C15     0.00   0.0  0
 OJY  CONST_05  N16  C15  C14  N13     0.00   0.0  0
 OJY  CONST_06  C14  N13  C12  C11   180.00   0.0  0
 OJY  CONST_07  C15  N16  C12  C11   180.00   0.0  0
 OJY  CONST_08  C17  C14  N13  C12   180.00   0.0  0
 OJY  CONST_09  N16  C15  C14  C17   180.00   0.0  0
 OJY  CONST_10  H7   C15  N16  C12   180.00   0.0  0
 OJY  CONST_11  H20  N13  C14  C15   180.00   0.0  0
 OJY  Var_01    N13  C12  C11  C10    64.26  30.0  2
 OJY  Var_02    O18  C17  C14  C15     1.76  30.0  2
 OJY  Var_03    C09  C10  C11  C12   179.20  30.0  3
 OJY  Var_04    C08  C09  C10  C11  -177.65  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
 OJY  chir_01  C08  C06  N19  C09  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
 OJY  plan-1  C11  0.020
 OJY  plan-1  C14  0.020
 OJY  plan-1  C12  0.020
 OJY  plan-1  C15  0.020
 OJY  plan-1  N13  0.020
 OJY  plan-1  N16  0.020
 OJY  plan-1  H7   0.020
 OJY  plan-1  H20  0.020
 OJY  plan-1  C17  0.020
 OJY  plan-2  C06  0.020
 OJY  plan-2  O07  0.020
 OJY  plan-2  C08  0.020
 OJY  plan-2  OXT  0.020

