# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 11:41:24 2022
#   Inital geometry file: a 117 line input string
#   Ligand name: 2-[(1S)-1-amino-2-(1H-imidazol-5-yl)ethyl]-1-(carboxymethyl)-4-[(4-oxocyclohexa-2,5-dien-1-ylidene)methyl]-1H-imidazol-5-olate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1[nH]cnc1)c2nc(C=C3C=CC(=O)C=C3)c([O-])n2CC(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
 CR8  CR8  "2-[1-AMINO-2-(1H-IMIDAZOL-5-YL)ETHYL]-1-(CARBOXYMETHYL)-4-[(4-OXOCYCLOHEXA-2,5-DIEN-1-YLIDENE)METHYL]-1H-IMIDAZOL-5-OLATE"  L-peptide  41  26  .  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_CR8
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
 CR8  C1    C  CR6    0   0.332   2.7594  -2.5785  -1.3027
 CR8  C2    C  CR16   0  -0.412   1.5711  -2.0626  -0.6662
 CR8  C4    C  CR16   0  -0.435   3.4610  -1.6223  -2.1214
 CR8  C5    C  CR16   0  -0.269   3.0215  -0.3362  -2.2728
 CR8  C6    C  CR16   0  -0.294   1.1427  -0.7745  -0.8304
 CR8  C7    C  CR6    0   0.078   1.8501   0.1474  -1.6423
 CR8  C8    C  C1     0  -0.377   1.4720   1.5010  -1.8457
 CR8  C9    C  CR5    0   0.029   0.3978   2.2032  -1.3830
 CR8  C10   C  CR15   0   0.067  -0.4491   0.6159   3.9683
 CR8  O3    O  O      0  -0.578   3.1492  -3.7592  -1.1517
 CR8  N11   N  N      0  -0.450  -0.1508   1.8872   3.9126
 CR8  C12   C  CR5    0   0.491   0.1776   3.6191  -1.6668
 CR8  N13   N  NR5    0  -0.545  -1.0085   3.8922  -1.0166
 CR8  C14   C  CR5    0   0.548  -1.4166   2.7415  -0.3735
 CR8  N15   N  N      0  -0.471  -0.6355   1.7384  -0.5786
 CR8  C20   C  CH2    0  -0.509  -2.7446   1.4296   1.2881
 CR8  C21   C  CR5    0   0.333  -1.7131   1.4222   2.3598
 CR8  N22   N  NR15   0  -0.617  -1.3853   0.2908   3.0522
 CR8  C23   C  CR15   0  -0.294  -0.9348   2.4016   2.9130
 CR8  O25   O  OC    -1  -0.502   0.8360   4.4264  -2.3134
 CR8  N     N  NH2    0  -0.782  -3.8763   2.6306  -0.4846
 CR8  C16   C  CH1    0  -0.228  -2.7080   2.6638   0.3914
 CR8  C     C  C      0   0.419  -1.2730   5.9608   0.3924
 CR8  C17   C  CH2    0  -0.474  -1.5842   5.2065  -0.9194
 CR8  OXT   O  OC    -1  -0.613  -1.8026   7.0843   0.4741
 CR8  O19   O  O      0  -0.579  -0.5376   5.3991   1.2199
 CR8  H2    H  HCR6   0   0.220   1.0054  -2.7355  -0.0303
 CR8  H4    H  HCR6   0   0.220   4.3648  -1.9457  -2.6270
 CR8  H5    H  HCR6   0   0.236   3.5871   0.3440  -2.9024
 CR8  H6    H  HCR6   0   0.265   0.2453  -0.4405  -0.3250
 CR8  H8    H  H      0   0.244   2.1487   2.0810  -2.4686
 CR8  H10   H  HCR5   0   0.269  -0.0250  -0.1117   4.6434
 CR8  H201  H  HCH2   0   0.262  -3.7441   1.3837   1.7299
 CR8  H202  H  HCH2   0   0.248  -2.6381   0.5349   0.6687
 CR8  H22   H  HNR5   0   0.412  -1.7687  -0.6291   2.9017
 CR8  H23   H  HCR5   0   0.266  -0.8779   3.4386   2.6172
 CR8  H1    H  HNH2   0   0.348  -3.7652   1.8923  -1.1695
 CR8  H2A   H  HNH2   0   0.358  -3.9635   3.4920  -1.0080
 CR8  H16   H  HCH1   0   0.263  -2.7957   3.5545   1.0207
 CR8  H171  H  HCH2   0   0.253  -2.6654   5.1586  -1.0639
 CR8  H172  H  HCH2   0   0.269  -1.2013   5.7913  -1.7575

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
 CR8  C1   C2    single    1.443  0.020  1.443
 CR8  C1   C4    single    1.441  0.020  1.441
 CR8  C1   O3    double    1.253  0.020  1.253
 CR8  C2   C6    double    1.367  0.020  1.367
 CR8  C2   H2    single    0.930  0.020  1.080
 CR8  C4   C5    double    1.368  0.020  1.368
 CR8  C4   H4    single    0.930  0.020  1.080
 CR8  C5   C7    single    1.415  0.020  1.415
 CR8  C5   H5    single    0.930  0.020  1.080
 CR8  C6   C7    single    1.418  0.020  1.418
 CR8  C6   H6    single    0.930  0.020  1.080
 CR8  C7   C8    double    1.420  0.020  1.420
 CR8  C8   C9    single    1.364  0.020  1.364
 CR8  C8   H8    single    0.930  0.020  1.080
 CR8  C9   C12   aromatic  1.461  0.020  1.461
 CR8  C9   N15   aromatic  1.390  0.020  1.390
 CR8  C10  N11   aromatic  1.307  0.020  1.307
 CR8  C10  N22   aromatic  1.350  0.020  1.350
 CR8  C10  H10   single    0.930  0.020  1.080
 CR8  N11  C23   aromatic  1.371  0.020  1.371
 CR8  C12  N13   aromatic  1.380  0.020  1.380
 CR8  C12  O25   single    1.226  0.020  1.226
 CR8  N13  C14   aromatic  1.380  0.020  1.380
 CR8  N13  C17   single    1.438  0.020  1.438
 CR8  C14  N15   aromatic  1.288  0.020  1.288
 CR8  C14  C16   single    1.503  0.020  1.503
 CR8  C20  C21   single    1.488  0.020  1.488
 CR8  C20  C16   single    1.526  0.020  1.526
 CR8  C20  H201  single    0.970  0.020  1.090
 CR8  C20  H202  single    0.970  0.020  1.090
 CR8  C21  N22   aromatic  1.366  0.020  1.366
 CR8  C21  C23   aromatic  1.368  0.020  1.368
 CR8  N22  H22   single    0.860  0.020  1.020
 CR8  C23  H23   single    0.930  0.020  1.080
 CR8  N    C16   single    1.461  0.020  1.461
 CR8  N    H1    single    0.890  0.020  1.040
 CR8  N    H2A   single    0.890  0.020  1.040
 CR8  C16  H16   single    0.970  0.020  1.090
 CR8  C    C17   single    1.545  0.020  1.545
 CR8  C    O19   deloc     1.241  0.020  1.241
 CR8  C    OXT   deloc     1.245  0.020  1.245
 CR8  C17  H171  single    0.970  0.020  1.090
 CR8  C17  H172  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
 CR8  O3    C1   C4    122.85  3.000
 CR8  O3    C1   C2    122.68  3.000
 CR8  C4    C1   C2    114.47  3.000
 CR8  H2    C2   C6    119.42  3.000
 CR8  H2    C2   C1    117.78  3.000
 CR8  C6    C2   C1    122.80  3.000
 CR8  H4    C4   C5    119.77  3.000
 CR8  H4    C4   C1    118.20  3.000
 CR8  C5    C4   C1    122.03  3.000
 CR8  H5    C5   C7    118.38  3.000
 CR8  H5    C5   C4    119.07  3.000
 CR8  C7    C5   C4    122.55  3.000
 CR8  H6    C6   C7    118.71  3.000
 CR8  H6    C6   C2    119.62  3.000
 CR8  C7    C6   C2    121.67  3.000
 CR8  C8    C7   C6    124.68  3.000
 CR8  C8    C7   C5    118.83  3.000
 CR8  C6    C7   C5    116.48  3.000
 CR8  H8    C8   C9    114.19  3.000
 CR8  H8    C8   C7    115.13  3.000
 CR8  C9    C8   C7    130.68  3.000
 CR8  N15   C9   C12   108.94  3.000
 CR8  N15   C9   C8    127.56  3.000
 CR8  C12   C9   C8    123.49  3.000
 CR8  H10   C10  N22   122.32  3.000
 CR8  H10   C10  N11   126.35  3.000
 CR8  N22   C10  N11   111.33  3.000
 CR8  C23   N11  C10   105.40  3.000
 CR8  O25   C12  N13   125.43  3.000
 CR8  O25   C12  C9    131.28  3.000
 CR8  N13   C12  C9    103.29  3.000
 CR8  C17   N13  C14   127.74  3.000
 CR8  C17   N13  C12   123.84  3.000
 CR8  C14   N13  C12   107.99  3.000
 CR8  C16   C14  N15   124.19  3.000
 CR8  C16   C14  N13   122.31  3.000
 CR8  N15   C14  N13   113.32  3.000
 CR8  C14   N15  C9    106.42  3.000
 CR8  H202  C20  H201  106.47  3.000
 CR8  H202  C20  C16   109.06  3.000
 CR8  H201  C20  C16   107.05  3.000
 CR8  H202  C20  C21   109.67  3.000
 CR8  H201  C20  C21   110.03  3.000
 CR8  C16   C20  C21   114.25  3.000
 CR8  C23   C21  N22   104.56  3.000
 CR8  C23   C21  C20   133.03  3.000
 CR8  N22   C21  C20   122.39  3.000
 CR8  H22   N22  C21   126.07  3.000
 CR8  H22   N22  C10   125.81  3.000
 CR8  C21   N22  C10   108.11  3.000
 CR8  H23   C23  C21   127.36  3.000
 CR8  H23   C23  N11   122.01  3.000
 CR8  C21   C23  N11   110.59  3.000
 CR8  H2A   N    H1    106.27  3.000
 CR8  H2A   N    C16   111.10  3.000
 CR8  H1    N    C16   109.53  3.000
 CR8  H16   C16  N     107.42  3.000
 CR8  H16   C16  C20   108.57  3.000
 CR8  N     C16  C20   108.35  3.000
 CR8  H16   C16  C14   108.63  3.000
 CR8  N     C16  C14   112.53  3.000
 CR8  C20   C16  C14   111.19  3.000
 CR8  O19   C    OXT   128.07  3.000
 CR8  OXT   C    C17   114.25  3.000
 CR8  O19   C    C17   117.67  3.000
 CR8  H172  C17  H171  105.62  3.000
 CR8  H172  C17  C     108.65  3.000
 CR8  H171  C17  C     109.47  3.000
 CR8  H172  C17  N13   107.30  3.000
 CR8  H171  C17  N13   110.33  3.000
 CR8  C     C17  N13   115.02  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
 CR8  CONST_01  C14   N13  C12  C9      0.00   0.0  0
 CR8  CONST_02  N13   C14  N15  C9      0.00   0.0  0
 CR8  CONST_03  C21   C23  N11  C10     0.00   0.0  0
 CR8  CONST_04  C23   C21  N22  C10     0.00   0.0  0
 CR8  CONST_05  C21   N22  C10  N11     0.00   0.0  0
 CR8  CONST_06  N22   C21  C23  N11     0.00   0.0  0
 CR8  CONST_07  C14   N15  C9   C12     0.00   0.0  0
 CR8  CONST_08  N15   C14  N13  C12     0.00   0.0  0
 CR8  CONST_09  N15   C9   C12  N13     0.00   0.0  0
 CR8  CONST_10  C23   N11  C10  N22     0.00   0.0  0
 CR8  CONST_11  N13   C12  C9   C8    180.00   0.0  0
 CR8  CONST_12  C14   N15  C9   C8    180.00   0.0  0
 CR8  CONST_13  C17   N13  C12  C9    180.00   0.0  0
 CR8  CONST_14  C16   C14  N15  C9    180.00   0.0  0
 CR8  CONST_15  C20   C21  N22  C10   180.00   0.0  0
 CR8  CONST_16  C20   C21  C23  N11   180.00   0.0  0
 CR8  CONST_17  C16   C14  N13  C12   180.00   0.0  0
 CR8  CONST_18  O25   C12  N13  C14   180.00   0.0  0
 CR8  CONST_19  O25   C12  C9   N15   180.00   0.0  0
 CR8  CONST_20  C17   N13  C14  N15   180.00   0.0  0
 CR8  CONST_21  H23   C23  N11  C10   180.00   0.0  0
 CR8  CONST_22  H22   N22  C10  N11   180.00   0.0  0
 CR8  CONST_23  H10   C10  N22  C21   180.00   0.0  0
 CR8  CONST_24  H23   C23  C21  N22   180.00   0.0  0
 CR8  CONST_25  H10   C10  N11  C23   180.00   0.0  0
 CR8  CONST_26  H22   N22  C21  C23   180.00   0.0  0
 CR8  Var_01    C9    C8   C7   C5    178.78   0.0  2
 CR8  Var_02    C9    C8   C7   C6     -1.94   0.0  2
 CR8  Var_03    C12   C9   C8   C7    178.39  30.0  2
 CR8  Var_04    N15   C9   C8   C7     -0.77  30.0  2
 CR8  Var_05    C     C17  N13  C12   -96.72  30.0  2
 CR8  Var_06    C     C17  N13  C14    74.80  30.0  2
 CR8  Var_07    C16   C20  C21  N22  -164.44  30.0  3
 CR8  Var_08    C16   C20  C21  C23    17.57  30.0  3
 CR8  Var_09    H8    C8   C7   C5     -1.55   0.0  2
 CR8  Var_10    H8    C8   C7   C6    177.72   0.0  2
 CR8  Var_11    H8    C8   C9   C12    -1.28  30.0  1
 CR8  Var_12    H171  C17  N13  C12   138.86  30.0  2
 CR8  Var_13    H172  C17  N13  C12    24.27  30.0  2
 CR8  Var_14    H171  C17  N13  C14   -49.62  30.0  2
 CR8  Var_15    H172  C17  N13  C14  -164.21  30.0  2
 CR8  Var_16    H8    C8   C9   N15   179.56  30.0  1
 CR8  Var_17    H201  C20  C21  N22    75.13  30.0  3
 CR8  Var_18    H202  C20  C21  N22   -41.66  30.0  3
 CR8  Var_19    H201  C20  C21  C23  -102.87  30.0  3
 CR8  Var_20    H202  C20  C21  C23   140.34  30.0  3
 CR8  Var_21    O19   C    C17  N13     1.94  30.0  2
 CR8  Var_22    OXT   C    C17  N13  -178.48  30.0  2
 CR8  Var_23    H171  C17  C    OXT   -53.61  30.0  3
 CR8  Var_24    H172  C17  C    OXT    61.27  30.0  3
 CR8  Var_25    H171  C17  C    O19   126.80  30.0  3
 CR8  Var_26    H172  C17  C    O19  -118.32  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
 CR8  chir_01  C16  C14  C20  N  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
 CR8  plan-1  C8   0.020
 CR8  plan-1  C9   0.020
 CR8  plan-1  C12  0.020
 CR8  plan-1  N13  0.020
 CR8  plan-1  C14  0.020
 CR8  plan-1  N15  0.020
 CR8  plan-1  O25  0.020
 CR8  plan-1  C16  0.020
 CR8  plan-1  C17  0.020
 CR8  plan-2  C10  0.020
 CR8  plan-2  N11  0.020
 CR8  plan-2  C20  0.020
 CR8  plan-2  C21  0.020
 CR8  plan-2  N22  0.020
 CR8  plan-2  C23  0.020
 CR8  plan-2  H10  0.020
 CR8  plan-2  H22  0.020
 CR8  plan-2  H23  0.020
 CR8  plan-3  C1   0.020
 CR8  plan-3  C2   0.020
 CR8  plan-3  C4   0.020
 CR8  plan-3  C5   0.020
 CR8  plan-3  C6   0.020
 CR8  plan-3  C7   0.020
 CR8  plan-3  C8   0.020
 CR8  plan-3  C9   0.020
 CR8  plan-3  O3   0.020
 CR8  plan-3  H2   0.020
 CR8  plan-3  H4   0.020
 CR8  plan-3  H5   0.020
 CR8  plan-3  H6   0.020
 CR8  plan-3  H8   0.020
 CR8  plan-4  C    0.020
 CR8  plan-4  C17  0.020
 CR8  plan-4  OXT  0.020
 CR8  plan-4  O19  0.020

