# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 20 03:36:30 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  30  15  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (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  -0.523  -0.2742  -1.0883  -0.7594
 OJY  C14  C  CR5   0   0.258  -3.6751   0.0140  -0.0978
 OJY  C10  C  CH2   0  -0.433   0.6611  -0.1666   0.0271
 OJY  C12  C  CR5   0   0.428  -1.7041  -0.9414  -0.3700
 OJY  C15  C  CR15  0  -0.265  -3.6781  -1.2577   0.3974
 OJY  C06  C  C     0   0.546   4.5011   0.2112  -0.0025
 OJY  O07  O  O     0  -0.440   5.1790   0.9368  -0.6849
 OJY  C08  C  CH1   0  -0.215   3.0831   0.5163   0.4349
 OJY  C09  C  CH2   0  -0.441   2.1150  -0.3657  -0.3784
 OJY  N13  N  NR15  0  -0.645  -2.4097   0.1964  -0.5820
 OJY  N16  N  N     0  -0.457  -2.4481  -1.8395   0.2225
 OJY  O18  O  OH1   0  -0.664  -5.9142   0.5235   0.3441
 OJY  N19  N  NH2   0  -0.786   2.8605   1.9432   0.3452
 OJY  H1   H  HCH2  0   0.252  -0.1580  -0.8942  -1.8302
 OJY  H2   H  HCH2  0   0.254   0.0077  -2.1297  -0.5960
 OJY  H3   H  HCH2  0   0.223   0.3681   0.8740  -0.1371
 OJY  H4   H  HCH2  0   0.238   0.5453  -0.3613   1.0975
 OJY  H7   H  HCR5  0   0.246  -4.4934  -1.7871   0.8650
 OJY  H17  H  HCH1  0   0.269   2.9927   0.2309   1.4880
 OJY  H18  H  HCH2  0   0.239   2.3806  -1.4179  -0.2467
 OJY  H19  H  HCH2  0   0.234   2.2329  -0.1405  -1.4441
 OJY  H20  H  HNR5  0   0.412  -2.0632   1.0316  -1.0281
 OJY  H22  H  HOH1  0   0.463  -6.5769   1.2194   0.3607
 OJY  H23  H  HNH2  0   0.345   2.8216   2.2356  -0.6242
 OJY  HXT  H  HOH1  0   0.481   5.7975  -1.1670   0.0871
 OJY  H8   H  HNH2  0   0.359   1.9615   2.1717   0.7485
 OJY  C17  C  CH2   0  -0.223  -4.7229   1.0701  -0.1594
 OJY  OXT  O  OH1   0  -0.594   4.9082  -0.9793   0.4235
 OJY  H5   H  HCH2  0   0.222  -4.3972   1.9446   0.4208
 OJY  H6   H  HCH2  0   0.219  -4.8358   1.4159  -1.1965

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  1.365  0.020  1.365
 OJY  C10  C09  single    1.522  0.020  1.522
 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  double    1.205  0.020  1.205
 OJY  C06  C08  single    1.515  0.020  1.515
 OJY  C08  N19  single    1.447  0.020  1.447
 OJY  C08  C09  single    1.542  0.020  1.542
 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  single    1.328  0.020  1.328
 OJY  OXT  HXT  single    0.850  0.020  0.980
 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   106.76  3.000
 OJY  H2   C11  C12  107.64  3.000
 OJY  H1   C11  C12  109.89  3.000
 OJY  H2   C11  C10  109.87  3.000
 OJY  H1   C11  C10  109.33  3.000
 OJY  C12  C11  C10  113.14  3.000
 OJY  N13  C14  C15  104.77  3.000
 OJY  C15  C14  C17  132.41  3.000
 OJY  N13  C14  C17  122.82  3.000
 OJY  H4   C10  H3   106.73  3.000
 OJY  H4   C10  C09  109.77  3.000
 OJY  H3   C10  C09  109.90  3.000
 OJY  H4   C10  C11  109.32  3.000
 OJY  H3   C10  C11  109.40  3.000
 OJY  C09  C10  C11  111.59  3.000
 OJY  N16  C12  N13  110.55  3.000
 OJY  N16  C12  C11  126.64  3.000
 OJY  N13  C12  C11  122.80  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  112.01  3.000
 OJY  OXT  C06  O07  123.29  3.000
 OJY  C08  C06  O07  124.67  3.000
 OJY  H17  C08  N19  107.70  3.000
 OJY  H17  C08  C09  107.84  3.000
 OJY  N19  C08  C09  115.78  3.000
 OJY  H17  C08  C06  107.60  3.000
 OJY  C09  C08  C06  108.68  3.000
 OJY  N19  C08  C06  108.95  3.000
 OJY  H19  C09  H18  106.80  3.000
 OJY  H19  C09  C08  109.15  3.000
 OJY  H18  C09  C08  109.55  3.000
 OJY  H19  C09  C10  109.57  3.000
 OJY  H18  C09  C10  109.01  3.000
 OJY  C08  C09  C10  112.60  3.000
 OJY  H20  N13  C12  125.84  3.000
 OJY  H20  N13  C14  125.83  3.000
 OJY  C12  N13  C14  108.33  3.000
 OJY  C15  N16  C12  106.05  3.000
 OJY  H22  O18  C17  108.02  3.000
 OJY  H8   N19  H23  106.40  3.000
 OJY  H8   N19  C08  109.56  3.000
 OJY  H23  N19  C08  110.47  3.000
 OJY  H6   C17  H5   106.16  3.000
 OJY  H6   C17  O18  111.95  3.000
 OJY  H5   C17  O18  111.83  3.000
 OJY  H6   C17  C14  109.54  3.000
 OJY  H5   C17  C14  109.52  3.000
 OJY  O18  C17  C14  107.82  3.000
 OJY  HXT  OXT  C06  110.09  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  CONST_12  HXT  OXT  C06  O07     0.00   0.0  0
 OJY  Var_01    N13  C12  C11  C10    65.55  30.0  2
 OJY  Var_02    O18  C17  C14  C15    -4.02  30.0  2
 OJY  Var_03    C09  C10  C11  C12   178.84  30.0  3
 OJY  Var_04    C08  C09  C10  C11  -177.98  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  HXT  0.020
 OJY  plan-2  OXT  0.020

