# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 18:48:11 2022
#   Inital geometry file: a 117 line input string
#   Ligand name: 2-[(4~{Z})-2-[(1~{S})-1-azanyl-3-methyl-butyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N)C1=N\C(=C/c2ccc(O)cc2)C(=O)N1CC(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
 VYA  VYA  "2-[(4~{Z})-2-[(1~{S})-1-azanyl-3-methyl-butyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic acid"  L-peptide  44  24  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VYA
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
 VYA  C2   C  CR16   0  -0.361   4.5430  -1.0462  -0.8193
 VYA  C4   C  CR16   0  -0.331   5.7101   0.7999   0.2010
 VYA  C5   C  CR16   0  -0.287   4.4964   1.3486   0.5625
 VYA  C6   C  CR16   0  -0.301   3.3341  -0.4883  -0.4519
 VYA  C3   C  CH3    0  -0.649  -3.4349  -4.0904   1.5834
 VYA  C10  C  CH3    0  -0.665  -4.5257  -2.7644  -0.2445
 VYA  C20  C  CH2    0  -0.421  -2.2532  -2.0939   0.6612
 VYA  C16  C  CH1    0  -0.230  -1.8865  -1.2004  -0.5418
 VYA  N    N  NH2    0  -0.784  -1.2503  -1.8858  -1.6490
 VYA  C14  C  CR5    0   0.583  -0.9828  -0.1135  -0.0547
 VYA  N15  N  N      0  -0.494   0.3018  -0.1586  -0.1525
 VYA  N13  N  NR5    0  -0.540  -1.4579   0.9730   0.6467
 VYA  C17  C  CH2    0  -0.485  -2.8225   1.4311   0.6852
 VYA  C    C  C      0   0.419  -3.3034   2.0278  -0.6589
 VYA  O19  O  O      0  -0.587  -2.4980   2.0095  -1.6032
 VYA  C12  C  CR5    0   0.523  -0.3799   1.7611   0.9789
 VYA  O25  O  O      0  -0.457  -0.4234   2.8368   1.5438
 VYA  C9   C  CR5    0   0.089   0.7765   0.9810   0.4824
 VYA  C7   C  CR6    0   0.131   3.2800   0.7257   0.2482
 VYA  C1   C  CR6    0   0.359   5.7420  -0.4075  -0.4962
 VYA  O3   O  OH1    0  -0.621   6.9418  -0.9062  -0.8306
 VYA  OXT  O  OC    -1  -0.608  -4.4680   2.4638  -0.6432
 VYA  H1   H  HCR6   0   0.275   4.5566  -1.9849  -1.3621
 VYA  H2   H  HCR6   0   0.269   6.6360   1.3015   0.4522
 VYA  H3   H  HCR6   0   0.260   4.4879   2.2871   1.1042
 VYA  H4   H  HCR6   0   0.279   2.4157  -0.9972  -0.7083
 VYA  H5   H  H      0   0.262   2.1788   2.3080   1.1972
 VYA  H6   H  HCH3   0   0.227  -4.0674  -4.9520   1.3642
 VYA  H7   H  HCH3   0   0.226  -2.4969  -4.4635   1.9977
 VYA  H8   H  HCH3   0   0.215  -3.9318  -3.5038   2.3597
 VYA  H9   H  HCH1   0   0.215  -2.7134  -3.8934  -0.4098
 VYA  H10  H  HCH3   0   0.229  -4.4093  -2.2688  -1.2097
 VYA  H11  H  HCH3   0   0.233  -5.2113  -3.5994  -0.3994
 VYA  H12  H  HCH3   0   0.217  -5.0129  -2.0603   0.4350
 VYA  H13  H  HCH2   0   0.224  -2.7103  -1.4859   1.4507
 VYA  H14  H  HCH2   0   0.238  -1.3249  -2.4942   1.0827
 VYA  H15  H  HCH1   0   0.262  -2.7979  -0.7357  -0.9259
 VYA  H16  H  HNH2   0   0.345  -0.4085  -2.3488  -1.3276
 VYA  H17  H  HNH2   0   0.356  -1.8634  -2.6146  -1.9905
 VYA  H19  H  HCH2   0   0.263  -3.4811   0.6145   0.9872
 VYA  H20  H  HCH2   0   0.276  -2.8999   2.1848   1.4696
 VYA  H21  H  HOH1   0   0.479   6.8444  -1.7392  -1.3061
 VYA  C8   C  C1     0  -0.394   2.0534   1.3719   0.6615
 VYA  C21  C  CH1    0  -0.243  -3.1995  -3.2501   0.3321

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
 VYA  N    C16  single    1.449  0.020  1.449
 VYA  C17  N13  single    1.440  0.020  1.440
 VYA  C17  C    single    1.547  0.020  1.547
 VYA  O19  C    deloc     1.241  0.020  1.241
 VYA  O25  C12  double    1.216  0.020  1.216
 VYA  N13  C12  single    1.376  0.020  1.376
 VYA  N13  C14  single    1.378  0.020  1.378
 VYA  C16  C14  single    1.495  0.020  1.495
 VYA  C16  C20  single    1.543  0.020  1.543
 VYA  C12  C9   single    1.481  0.020  1.481
 VYA  C14  N15  double    1.289  0.020  1.289
 VYA  C21  C10  single    1.526  0.020  1.526
 VYA  C21  C20  single    1.530  0.020  1.530
 VYA  C21  C3   single    1.526  0.020  1.526
 VYA  N15  C9   single    1.388  0.020  1.388
 VYA  C9   C8   double    1.347  0.020  1.347
 VYA  C8   C7   single    1.447  0.020  1.447
 VYA  C6   C7   aromatic  1.402  0.020  1.402
 VYA  C6   C2   aromatic  1.381  0.020  1.381
 VYA  C7   C5   aromatic  1.402  0.020  1.402
 VYA  C2   C1   aromatic  1.396  0.020  1.396
 VYA  C5   C4   aromatic  1.380  0.020  1.380
 VYA  C1   C4   aromatic  1.395  0.020  1.395
 VYA  C1   O3   single    1.342  0.020  1.342
 VYA  C    OXT  deloc     1.244  0.020  1.244
 VYA  C2   H1   single    0.930  0.020  1.080
 VYA  C4   H2   single    0.930  0.020  1.080
 VYA  C5   H3   single    0.930  0.020  1.080
 VYA  C6   H4   single    0.930  0.020  1.080
 VYA  C8   H5   single    0.930  0.020  1.080
 VYA  C3   H6   single    0.970  0.020  1.090
 VYA  C3   H7   single    0.970  0.020  1.090
 VYA  C3   H8   single    0.970  0.020  1.090
 VYA  C21  H9   single    0.970  0.020  1.090
 VYA  C10  H10  single    0.970  0.020  1.090
 VYA  C10  H11  single    0.970  0.020  1.090
 VYA  C10  H12  single    0.970  0.020  1.090
 VYA  C20  H13  single    0.970  0.020  1.090
 VYA  C20  H14  single    0.970  0.020  1.090
 VYA  C16  H15  single    0.970  0.020  1.090
 VYA  N    H16  single    0.890  0.020  1.040
 VYA  N    H17  single    0.890  0.020  1.040
 VYA  C17  H19  single    0.970  0.020  1.090
 VYA  C17  H20  single    0.970  0.020  1.090
 VYA  O3   H21  single    0.850  0.020  0.980

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
 VYA  H1   C2   C1   120.06  3.000
 VYA  H1   C2   C6   119.59  3.000
 VYA  C1   C2   C6   120.35  3.000
 VYA  H2   C4   C1   119.84  3.000
 VYA  H2   C4   C5   120.47  3.000
 VYA  C1   C4   C5   119.69  3.000
 VYA  H3   C5   C7   119.34  3.000
 VYA  H3   C5   C4   118.82  3.000
 VYA  C7   C5   C4   121.84  3.000
 VYA  H4   C6   C7   119.56  3.000
 VYA  H4   C6   C2   119.37  3.000
 VYA  C7   C6   C2   121.08  3.000
 VYA  H8   C3   H7   107.74  3.000
 VYA  H8   C3   H6   107.64  3.000
 VYA  H7   C3   H6   107.74  3.000
 VYA  H8   C3   C21  110.93  3.000
 VYA  H7   C3   C21  111.54  3.000
 VYA  H6   C3   C21  111.08  3.000
 VYA  H12  C10  H11  107.52  3.000
 VYA  H12  C10  H10  107.74  3.000
 VYA  H11  C10  H10  106.80  3.000
 VYA  H12  C10  C21  110.95  3.000
 VYA  H11  C10  C21  110.87  3.000
 VYA  H10  C10  C21  112.72  3.000
 VYA  H14  C20  H13  106.19  3.000
 VYA  H14  C20  C16  108.08  3.000
 VYA  H13  C20  C16  109.85  3.000
 VYA  H14  C20  C21  109.32  3.000
 VYA  H13  C20  C21  108.43  3.000
 VYA  C16  C20  C21  114.65  3.000
 VYA  H15  C16  C14  108.02  3.000
 VYA  H15  C16  N    107.38  3.000
 VYA  C14  C16  N    109.11  3.000
 VYA  H15  C16  C20  108.79  3.000
 VYA  C14  C16  C20  108.10  3.000
 VYA  N    C16  C20  115.23  3.000
 VYA  H17  N    H16  106.34  3.000
 VYA  H17  N    C16  109.42  3.000
 VYA  H16  N    C16  109.79  3.000
 VYA  N13  C14  N15  114.20  3.000
 VYA  N15  C14  C16  123.51  3.000
 VYA  N13  C14  C16  122.06  3.000
 VYA  C9   N15  C14  106.10  3.000
 VYA  C12  N13  C17  123.63  3.000
 VYA  C12  N13  C14  107.72  3.000
 VYA  C17  N13  C14  126.25  3.000
 VYA  H20  C17  H19  105.97  3.000
 VYA  H20  C17  C    109.65  3.000
 VYA  H19  C17  C    109.95  3.000
 VYA  H20  C17  N13  107.84  3.000
 VYA  H19  C17  N13  109.95  3.000
 VYA  C    C17  N13  113.20  3.000
 VYA  OXT  C    O19  128.49  3.000
 VYA  OXT  C    C17  114.54  3.000
 VYA  O19  C    C17  116.97  3.000
 VYA  C9   C12  O25  130.54  3.000
 VYA  C9   C12  N13  103.25  3.000
 VYA  O25  C12  N13  126.21  3.000
 VYA  C12  C9   N15  108.59  3.000
 VYA  N15  C9   C8   128.54  3.000
 VYA  C12  C9   C8   122.87  3.000
 VYA  C8   C7   C6   124.19  3.000
 VYA  C6   C7   C5   117.58  3.000
 VYA  C8   C7   C5   118.23  3.000
 VYA  O3   C1   C4   117.83  3.000
 VYA  O3   C1   C2   122.69  3.000
 VYA  C4   C1   C2   119.47  3.000
 VYA  H21  O3   C1   110.72  3.000
 VYA  H5   C8   C7   115.35  3.000
 VYA  H5   C8   C9   115.16  3.000
 VYA  C7   C8   C9   129.50  3.000
 VYA  H9   C21  C20  108.36  3.000
 VYA  H9   C21  C10  108.46  3.000
 VYA  C20  C21  C10  112.24  3.000
 VYA  H9   C21  C3   107.48  3.000
 VYA  C20  C21  C3   109.59  3.000
 VYA  C10  C21  C3   110.56  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
 VYA  CONST_01  C5   C7   C6   C2      0.00   0.0  0
 VYA  CONST_02  C5   C4   C1   C2      0.00   0.0  0
 VYA  CONST_03  C6   C7   C5   C4      0.00   0.0  0
 VYA  CONST_04  C6   C2   C1   C4      0.00   0.0  0
 VYA  CONST_05  C1   C2   C6   C7      0.00   0.0  0
 VYA  CONST_06  C1   C4   C5   C7      0.00   0.0  0
 VYA  CONST_07  C9   C12  N13  C14     0.00   0.0  0
 VYA  CONST_08  C12  C9   N15  C14     0.00   0.0  0
 VYA  CONST_09  C12  N13  C14  N15     0.00   0.0  0
 VYA  CONST_10  N13  C12  C9   N15     0.00   0.0  0
 VYA  CONST_11  C9   N15  C14  N13     0.00   0.0  0
 VYA  CONST_12  C8   C7   C6   C2    180.00   0.0  0
 VYA  CONST_13  C8   C7   C5   C4    180.00   0.0  0
 VYA  CONST_14  O3   C1   C4   C5    180.00   0.0  0
 VYA  CONST_15  O3   C1   C2   C6    180.00   0.0  0
 VYA  CONST_16  C12  N13  C14  C16   180.00   0.0  0
 VYA  CONST_17  C9   N15  C14  C16   180.00   0.0  0
 VYA  CONST_18  O25  C12  N13  C14   180.00   0.0  0
 VYA  CONST_19  C17  N13  C14  N15   180.00   0.0  0
 VYA  CONST_20  C9   C12  N13  C17   180.00   0.0  0
 VYA  CONST_21  H2   C4   C1   C2    180.00   0.0  0
 VYA  CONST_22  H1   C2   C1   C4    180.00   0.0  0
 VYA  CONST_23  H4   C6   C7   C5    180.00   0.0  0
 VYA  CONST_24  H3   C5   C7   C6    180.00   0.0  0
 VYA  CONST_25  H1   C2   C6   C7    180.00   0.0  0
 VYA  CONST_26  H2   C4   C5   C7    180.00   0.0  0
 VYA  CONST_27  H4   C6   C2   C1    180.00   0.0  0
 VYA  CONST_28  H3   C5   C4   C1    180.00   0.0  0
 VYA  CONST_30  O25  C12  N13  C17     0.00   0.0  0
 VYA  Var_01    C7   C8   C9   N15     0.06   0.0  2
 VYA  Var_02    C7   C8   C9   C12   179.64   0.0  2
 VYA  Var_03    C9   C8   C7   C5   -179.99  30.0  2
 VYA  Var_04    C9   C8   C7   C6      0.12  30.0  2
 VYA  Var_05    C    C17  N13  C14   -69.15  30.0  2
 VYA  Var_06    C12  N13  C17  C      91.06  30.0  3
 VYA  Var_07    H5   C8   C9   N15  -179.75   0.0  2
 VYA  Var_08    H5   C8   C9   C12    -0.17   0.0  2
 VYA  Var_09    H5   C8   C7   C5     -0.18  30.0  2
 VYA  Var_10    H5   C8   C7   C6    179.92  30.0  2
 VYA  Var_11    H19  C17  N13  C14    54.26  30.0  2
 VYA  Var_12    H20  C17  N13  C14   169.37  30.0  2
 VYA  Var_13    H19  C17  N13  C12  -145.53  30.0  2
 VYA  Var_14    H20  C17  N13  C12   -30.42  30.0  2
 VYA  Var_15    O19  C    C17  N13     2.04  30.0  3
 VYA  Var_16    OXT  C    C17  N13  -178.19  30.0  3
 VYA  Var_17    C16  C20  C21  C3    177.51  30.0  3
 VYA  Var_18    C16  C20  C21  C10   -59.24  30.0  3
 VYA  Var_19    H10  C10  C21  C3   -172.62  30.0  3
 VYA  Var_20    H11  C10  C21  C3    -52.96  30.0  3
 VYA  Var_21    H12  C10  C21  C3     66.45  30.0  3
 VYA  Var_22    H13  C20  C21  C3    -59.35  30.0  3
 VYA  Var_23    H14  C20  C21  C3     56.00  30.0  3
 VYA  Var_24    H13  C20  C21  C10    63.89  30.0  3
 VYA  Var_25    H14  C20  C21  C10   179.25  30.0  3
 VYA  Var_26    H6   C3   C21  C10    58.62  30.0  3
 VYA  Var_27    H7   C3   C21  C10   178.83  30.0  3
 VYA  Var_28    H8   C3   C21  C10   -61.06  30.0  3
 VYA  Var_29    H10  C10  C21  C20    64.68  30.0  3
 VYA  Var_30    H11  C10  C21  C20  -175.66  30.0  3
 VYA  Var_31    H12  C10  C21  C20   -56.25  30.0  3
 VYA  Var_32    H6   C3   C21  C20  -177.15  30.0  3
 VYA  Var_33    H7   C3   C21  C20   -56.94  30.0  3
 VYA  Var_34    H8   C3   C21  C20    63.17  30.0  3
 VYA  Var_35    H9   C21  C20  C16    60.50  30.0  2
 VYA  Var_36    H19  C17  C    O19  -121.37  30.0  3
 VYA  Var_37    H20  C17  C    O19   122.50  30.0  3
 VYA  Var_38    H19  C17  C    OXT    58.41  30.0  3
 VYA  Var_39    H20  C17  C    OXT   -57.72  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
 VYA  chir_01  C16  N  C14  C20  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
 VYA  plan-1  C16  0.020
 VYA  plan-1  C14  0.020
 VYA  plan-1  N15  0.020
 VYA  plan-1  N13  0.020
 VYA  plan-1  C17  0.020
 VYA  plan-1  C12  0.020
 VYA  plan-1  O25  0.020
 VYA  plan-1  C9   0.020
 VYA  plan-1  C7   0.020
 VYA  plan-1  H5   0.020
 VYA  plan-1  C8   0.020
 VYA  plan-2  C2   0.020
 VYA  plan-2  C4   0.020
 VYA  plan-2  C5   0.020
 VYA  plan-2  C6   0.020
 VYA  plan-2  C7   0.020
 VYA  plan-2  C1   0.020
 VYA  plan-2  O3   0.020
 VYA  plan-2  H1   0.020
 VYA  plan-2  H2   0.020
 VYA  plan-2  H3   0.020
 VYA  plan-2  H4   0.020
 VYA  plan-2  C8   0.020
 VYA  plan-3  C17  0.020
 VYA  plan-3  C    0.020
 VYA  plan-3  O19  0.020
 VYA  plan-3  OXT  0.020

