# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 06:43:52 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: [(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(1H-indol-3-ylmethylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@H](N)C1=N\C(=C/c2c[nH]c3ccccc23)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
 NYC  NYC  '[(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(1H-indol-3-ylmethylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid'  L-peptide  42  25  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NYC
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
 NYC  C25   C  CH3    0  -0.697  -4.3580   2.9997  -0.3817
 NYC  C23   C  CH1    0   0.006  -3.2309   1.9879  -0.5164
 NYC  O24   O  OH1    0  -0.656  -2.2469   2.4095  -1.4315
 NYC  C22   C  CH1    0  -0.241  -2.6085   1.6487   0.8660
 NYC  N26   N  NH2    0  -0.791  -1.9188   2.7378   1.5257
 NYC  C14   C  CR5    0   0.565  -1.6598   0.5043   0.7031
 NYC  N13   N  N      0  -0.489  -0.3871   0.6547   0.5609
 NYC  C12   C  CR5    0   0.068   0.1313  -0.6182   0.3692
 NYC  C11   C  C1     0  -0.418   1.4285  -0.9454   0.1847
 NYC  C7    C  CR5    0   0.022   2.5537  -0.0655   0.1549
 NYC  C8    C  CR15   0  -0.036   2.5721   1.3096   0.3080
 NYC  N9    N  NR15   0  -0.674   3.8401   1.7623   0.2203
 NYC  C6    C  CR56   0   0.356   4.7013   0.7165   0.0084
 NYC  C5    C  CR16   0  -0.295   6.0850   0.7080  -0.1420
 NYC  C4    C  CR16   0  -0.283   6.6916  -0.5170  -0.3457
 NYC  C3    C  CR16   0  -0.261   5.9399  -1.7011  -0.3984
 NYC  C2    C  CR16   0  -0.373   4.5663  -1.6836  -0.2468
 NYC  C1    C  CR56   0   0.050   3.9272  -0.4583  -0.0395
 NYC  C16   C  CR5    0   0.524  -0.9713  -1.5937   0.4074
 NYC  O17   O  O      0  -0.469  -0.9695  -2.8062   0.2950
 NYC  N15   N  NR5    0  -0.541  -2.0766  -0.8077   0.6464
 NYC  C18   C  CH2    0  -0.473  -3.4090  -1.3467   0.7274
 NYC  C     C  C      0   0.422  -4.0367  -1.6993  -0.6406
 NYC  O     O  O      0  -0.586  -3.4133  -1.3662  -1.6600
 NYC  OXT   O  OC    -1  -0.612  -5.1335  -2.2823  -0.5623
 NYC  H251  H  HCH3   0   0.248  -4.8094   3.1991  -1.3537
 NYC  H252  H  HCH3   0   0.234  -5.1407   2.6266   0.2799
 NYC  H253  H  HCH3   0   0.219  -4.0079   3.9532   0.0209
 NYC  H23   H  HCH1   0   0.249  -3.6379   1.0672  -0.9393
 NYC  H24   H  HOH1   0   0.437  -1.9158   3.2700  -1.1535
 NYC  H22   H  HCH1   0   0.259  -3.4343   1.3369   1.5143
 NYC  H261  H  HNH2   0   0.349  -1.0938   3.0099   1.0071
 NYC  H262  H  HNH2   0   0.357  -2.5182   3.5483   1.6044
 NYC  H11   H  H      0   0.259   1.6352  -2.0017   0.0448
 NYC  H8    H  HCR5   0   0.299   1.7478   1.9830   0.4734
 NYC  HN9   H  HNR5   0   0.420   4.1061   2.7308   0.2991
 NYC  H5    H  HCR6   0   0.265   6.6643   1.6214  -0.1011
 NYC  H4    H  HCR6   0   0.254   7.7659  -0.5639  -0.4654
 NYC  H3    H  HCR6   0   0.252   6.4479  -2.6426  -0.5622
 NYC  H2    H  HCR6   0   0.246   4.0014  -2.6071  -0.2890
 NYC  H181  H  HCH2   0   0.267  -3.3815  -2.2407   1.3532
 NYC  H182  H  HCH2   0   0.267  -4.0505  -0.6357   1.2499

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
 NYC  C25  C23   single    1.521  0.020  1.521
 NYC  C25  H251  single    0.970  0.020  1.090
 NYC  C25  H252  single    0.970  0.020  1.090
 NYC  C25  H253  single    0.970  0.020  1.090
 NYC  C23  O24   single    1.408  0.020  1.408
 NYC  C23  C22   single    1.554  0.020  1.554
 NYC  C23  H23   single    0.970  0.020  1.090
 NYC  O24  H24   single    0.850  0.020  0.980
 NYC  C22  N26   single    1.448  0.020  1.448
 NYC  C22  C14   single    1.495  0.020  1.495
 NYC  C22  H22   single    0.970  0.020  1.090
 NYC  N26  H261  single    0.890  0.020  1.040
 NYC  N26  H262  single    0.890  0.020  1.040
 NYC  C14  N13   double    1.289  0.020  1.289
 NYC  C14  N15   single    1.378  0.020  1.378
 NYC  N13  C12   single    1.388  0.020  1.388
 NYC  C12  C11   double    1.350  0.020  1.350
 NYC  C12  C16   single    1.473  0.020  1.473
 NYC  C11  C7    single    1.429  0.020  1.429
 NYC  C11  H11   single    0.930  0.020  1.080
 NYC  C7   C8    aromatic  1.384  0.020  1.384
 NYC  C7   C1    aromatic  1.442  0.020  1.442
 NYC  C8   N9    aromatic  1.349  0.020  1.349
 NYC  C8   H8    single    0.930  0.020  1.080
 NYC  N9   C6    aromatic  1.371  0.020  1.371
 NYC  N9   HN9   single    0.860  0.020  1.020
 NYC  C6   C5    aromatic  1.392  0.020  1.392
 NYC  C6   C1    aromatic  1.408  0.020  1.408
 NYC  C5   C4    aromatic  1.382  0.020  1.382
 NYC  C5   H5    single    0.930  0.020  1.080
 NYC  C4   C3    aromatic  1.404  0.020  1.404
 NYC  C4   H4    single    0.930  0.020  1.080
 NYC  C3   C2    aromatic  1.382  0.020  1.382
 NYC  C3   H3    single    0.930  0.020  1.080
 NYC  C2   C1    aromatic  1.397  0.020  1.397
 NYC  C2   H2    single    0.930  0.020  1.080
 NYC  C16  O17   double    1.218  0.020  1.218
 NYC  C16  N15   single    1.377  0.020  1.377
 NYC  N15  C18   single    1.440  0.020  1.440
 NYC  C18  C     single    1.546  0.020  1.546
 NYC  C18  H181  single    0.970  0.020  1.090
 NYC  C18  H182  single    0.970  0.020  1.090
 NYC  C    O     deloc     1.241  0.020  1.241
 NYC  C    OXT   deloc     1.245  0.020  1.245

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
 NYC  H253  C25  H252  107.76  3.000
 NYC  H253  C25  H251  107.55  3.000
 NYC  H252  C25  H251  107.83  3.000
 NYC  H253  C25  C23   112.07  3.000
 NYC  H252  C25  C23   110.98  3.000
 NYC  H251  C25  C23   110.46  3.000
 NYC  H23   C23  C22   108.05  3.000
 NYC  H23   C23  O24   105.15  3.000
 NYC  C22   C23  O24   111.33  3.000
 NYC  H23   C23  C25   108.60  3.000
 NYC  C22   C23  C25   111.31  3.000
 NYC  O24   C23  C25   112.10  3.000
 NYC  H24   O24  C23   108.67  3.000
 NYC  H22   C22  C14   108.96  3.000
 NYC  H22   C22  N26   107.67  3.000
 NYC  C14   C22  N26   108.84  3.000
 NYC  H22   C22  C23   106.67  3.000
 NYC  C14   C22  C23   108.92  3.000
 NYC  N26   C22  C23   115.59  3.000
 NYC  H262  N26  H261  107.92  3.000
 NYC  H262  N26  C22   110.85  3.000
 NYC  H261  N26  C22   110.92  3.000
 NYC  N15   C14  N13   113.90  3.000
 NYC  N15   C14  C22   122.77  3.000
 NYC  N13   C14  C22   123.29  3.000
 NYC  C12   N13  C14   106.08  3.000
 NYC  C16   C12  C11   124.21  3.000
 NYC  C16   C12  N13   108.92  3.000
 NYC  C11   C12  N13   126.87  3.000
 NYC  H11   C11  C7    116.53  3.000
 NYC  H11   C11  C12   115.87  3.000
 NYC  C7    C11  C12   127.60  3.000
 NYC  C1    C7   C8    105.84  3.000
 NYC  C1    C7   C11   125.83  3.000
 NYC  C8    C7   C11   128.33  3.000
 NYC  H8    C8   N9    121.29  3.000
 NYC  H8    C8   C7    128.91  3.000
 NYC  N9    C8   C7    109.80  3.000
 NYC  HN9   N9   C6    125.41  3.000
 NYC  HN9   N9   C8    124.44  3.000
 NYC  C6    N9   C8    110.15  3.000
 NYC  C1    C6   C5    122.54  3.000
 NYC  C1    C6   N9    107.24  3.000
 NYC  C5    C6   N9    130.22  3.000
 NYC  H5    C5   C4    121.24  3.000
 NYC  H5    C5   C6    121.52  3.000
 NYC  C4    C5   C6    117.24  3.000
 NYC  H4    C4   C3    119.40  3.000
 NYC  H4    C4   C5    119.38  3.000
 NYC  C3    C4   C5    121.22  3.000
 NYC  H3    C3   C2    119.61  3.000
 NYC  H3    C3   C4    119.22  3.000
 NYC  C2    C3   C4    121.16  3.000
 NYC  H2    C2   C1    120.98  3.000
 NYC  H2    C2   C3    120.21  3.000
 NYC  C1    C2   C3    118.81  3.000
 NYC  C2    C1   C6    119.03  3.000
 NYC  C2    C1   C7    134.00  3.000
 NYC  C6    C1   C7    106.97  3.000
 NYC  N15   C16  O17   125.83  3.000
 NYC  N15   C16  C12   103.15  3.000
 NYC  O17   C16  C12   131.00  3.000
 NYC  C18   N15  C16   122.61  3.000
 NYC  C18   N15  C14   129.36  3.000
 NYC  C16   N15  C14   107.93  3.000
 NYC  H182  C18  H181  105.90  3.000
 NYC  H182  C18  C     109.50  3.000
 NYC  H181  C18  C     109.31  3.000
 NYC  H182  C18  N15   109.10  3.000
 NYC  H181  C18  N15   108.39  3.000
 NYC  C     C18  N15   114.29  3.000
 NYC  OXT   C    O     128.34  3.000
 NYC  OXT   C    C18   114.14  3.000
 NYC  O     C    C18   117.51  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
 NYC  CONST_01  C6   N9   C8   C7     0.00   0.0  0
 NYC  CONST_02  N9   C6   C1   C7     0.00   0.0  0
 NYC  CONST_03  C5   C6   C1   C7   180.00   0.0  0
 NYC  CONST_04  C3   C2   C1   C7   180.00   0.0  0
 NYC  CONST_05  C6   C1   C7   C8     0.00   0.0  0
 NYC  CONST_06  C2   C1   C7   C8   180.00   0.0  0
 NYC  CONST_07  C5   C6   N9   C8   180.00   0.0  0
 NYC  CONST_08  C1   C6   N9   C8     0.00   0.0  0
 NYC  CONST_09  C1   C7   C8   N9     0.00   0.0  0
 NYC  CONST_10  C4   C5   C6   N9   180.00   0.0  0
 NYC  CONST_11  C2   C1   C6   N9   180.00   0.0  0
 NYC  CONST_12  C3   C4   C5   C6     0.00   0.0  0
 NYC  CONST_13  C3   C2   C1   C6     0.00   0.0  0
 NYC  CONST_14  C2   C1   C6   C5     0.00   0.0  0
 NYC  CONST_15  C2   C3   C4   C5     0.00   0.0  0
 NYC  CONST_16  C1   C6   C5   C4     0.00   0.0  0
 NYC  CONST_17  C1   C2   C3   C4     0.00   0.0  0
 NYC  CONST_18  C16  C12  N13  C14    0.00   0.0  0
 NYC  CONST_19  C12  C16  N15  C14    0.00   0.0  0
 NYC  CONST_20  C16  N15  C14  N13    0.00   0.0  0
 NYC  CONST_21  N15  C16  C12  N13    0.00   0.0  0
 NYC  CONST_22  N15  C14  N13  C12    0.00   0.0  0
 NYC  CONST_23  N9   C8   C7   C11  180.00   0.0  0
 NYC  CONST_24  C6   C1   C7   C11  180.00   0.0  0
 NYC  CONST_25  C2   C1   C7   C11    0.00   0.0  0
 NYC  CONST_26  C12  N13  C14  C22  180.00   0.0  0
 NYC  CONST_27  C16  N15  C14  C22  180.00   0.0  0
 NYC  CONST_28  O17  C16  N15  C14  180.00   0.0  0
 NYC  CONST_29  C18  N15  C14  N13  180.00   0.0  0
 NYC  CONST_30  C18  N15  C16  C12  180.00   0.0  0
 NYC  CONST_31  HN9  N9   C8   C7   180.00   0.0  0
 NYC  CONST_32  H2   C2   C1   C7     0.00   0.0  0
 NYC  CONST_33  H5   C5   C6   N9     0.00   0.0  0
 NYC  CONST_34  H8   C8   N9   C6   180.00   0.0  0
 NYC  CONST_35  H4   C4   C5   C6   180.00   0.0  0
 NYC  CONST_36  H3   C3   C4   C5   180.00   0.0  0
 NYC  CONST_37  C18  N15  C14  C22    0.00   0.0  0
 NYC  CONST_38  C18  N15  C16  O17    0.00   0.0  0
 NYC  Var_01    C7   C11  C12  N13    0.50  30.0  2
 NYC  Var_02    C8   C7   C11  C12    0.07  30.0  2
 NYC  Var_03    C    C18  N15  C14   99.44  30.0  3
 NYC  Var_04    O    C    C18  N15   -7.23  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
 NYC  chir_01  C23  C25  O24  C22  negativ
 NYC  chir_02  C22  N26  C23  C14  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
 NYC  plan-1  C22  0.020
 NYC  plan-1  C14  0.020
 NYC  plan-1  N13  0.020
 NYC  plan-1  C12  0.020
 NYC  plan-1  C11  0.020
 NYC  plan-1  C16  0.020
 NYC  plan-1  O17  0.020
 NYC  plan-1  N15  0.020
 NYC  plan-1  C18  0.020
 NYC  plan-2  C11  0.020
 NYC  plan-2  C7   0.020
 NYC  plan-2  C8   0.020
 NYC  plan-2  N9   0.020
 NYC  plan-2  C6   0.020
 NYC  plan-2  C5   0.020
 NYC  plan-2  C4   0.020
 NYC  plan-2  C3   0.020
 NYC  plan-2  C2   0.020
 NYC  plan-2  C1   0.020
 NYC  plan-2  H8   0.020
 NYC  plan-2  HN9  0.020
 NYC  plan-2  H5   0.020
 NYC  plan-2  H4   0.020
 NYC  plan-2  H3   0.020
 NYC  plan-2  H2   0.020
 NYC  plan-3  C18  0.020
 NYC  plan-3  C    0.020
 NYC  plan-3  O    0.020
 NYC  plan-3  OXT  0.020

