# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 02:58:56 2022
#   Inital geometry file: a 124 line input string
#   Ligand name: N-({(1R,2S)-3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl}acetyl)-L-isoleucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC\C=C/C[C@H]1[C@H](CCC1=O)CC(=O)N[C@@H]([C@@H](C)CC)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
 7JA  7JA  N-({(1R,2S)-3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl}acetyl)-L-isoleucine  L-peptide  51  23  .  2012-08-28  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_7JA
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
 7JA  C     C  C      0   0.409   1.4456   1.9636  50.2834
 7JA  N     N  NH1    0  -0.640   1.3501   3.1417  48.0825
 7JA  O     O  O      0  -0.601   1.4666   0.8229  50.7864
 7JA  CA    C  CH1    0  -0.124   1.9501   2.0475  48.8167
 7JA  CB    C  CH1    0  -0.274   3.4848   2.1719  48.7265
 7JA  C01   C  CH3    0  -0.655  -3.2422   8.4721  42.8525
 7JA  C02   C  CH2    0  -0.493  -3.1669   7.3514  43.8877
 7JA  C03   C  C1     0  -0.200  -1.7965   6.7550  43.9625
 7JA  C04   C  C1     0  -0.223  -0.9882   6.7310  45.0207
 7JA  C05   C  CH2    0  -0.517  -1.3040   7.2993  46.3765
 7JA  C06   C  CH1    0  -0.356  -2.1779   6.3764  47.2568
 7JA  C07   C  C      0   0.413  -2.6912   7.1856  48.4407
 7JA  O08   O  O      0  -0.395  -3.5242   8.0569  48.3719
 7JA  C09   C  CH2    0  -0.570  -1.9872   6.7386  49.7039
 7JA  C10   C  CH2    0  -0.456  -0.8799   5.8111  49.2186
 7JA  C11   C  CH1    0  -0.234  -1.4571   5.2014  47.9351
 7JA  C12   C  CH2    0  -0.572  -0.4304   4.4505  47.0978
 7JA  O14   O  O      0  -0.511  -0.7443   2.3119  48.1249
 7JA  CG1   C  CH2    0  -0.405   4.1879   0.8665  49.1068
 7JA  CG2   C  CH3    0  -0.664   4.0383   3.3558  49.5192
 7JA  OXT   O  OC    -1  -0.597   1.0992   3.0241  50.8366
 7JA  HN    H  HNH1   0   0.389   1.9208   3.9342  47.8378
 7JA  HA    H  HCH1   0   0.222   1.6715   1.1154  48.3144
 7JA  HB    H  HCH1   0   0.219   3.7057   2.3485  47.6649
 7JA  H01   H  HCH3   0   0.229  -4.2560   8.8652  42.7719
 7JA  H01A  H  HCH3   0   0.223  -2.5825   9.2978  43.1210
 7JA  H02   H  HCH2   0   0.231  -3.4889   7.7265  44.8610
 7JA  H03   H  H      0   0.230  -1.4334   6.3110  43.0389
 7JA  H04   H  H      0   0.237  -0.0171   6.2630  44.9025
 7JA  H05   H  HCH2   0   0.255  -0.3734   7.5383  46.8983
 7JA  H05A  H  HCH2   0   0.258  -1.8336   8.2475  46.2557
 7JA  H06   H  HCH1   0   0.281  -3.0272   6.0401  46.6554
 7JA  H09   H  HCH2   0   0.274  -1.6517   7.5916  50.2956
 7JA  H09A  H  HCH2   0   0.275  -2.7141   6.1944  50.3170
 7JA  H10   H  HCH2   0   0.231   0.0227   6.3826  48.9848
 7JA  H10A  H  HCH2   0   0.254  -0.6003   5.0528  49.9491
 7JA  H11   H  HCH1   0   0.247  -2.2334   4.4848  48.2248
 7JA  H12   H  HCH2   0   0.264  -0.8795   4.1380  46.1516
 7JA  H12A  H  HCH2   0   0.246   0.4088   5.1055  46.8515
 7JA  HD1   H  HCH3   0   0.227   6.0980  -0.1406  48.9372
 7JA  HD1A  H  HCH3   0   0.214   5.8020   1.0364  47.6624
 7JA  HG1   H  HCH2   0   0.215   4.0818   0.6887  50.1789
 7JA  HG2   H  HCH3   0   0.228   5.0921   3.5150  49.2924
 7JA  HG2A  H  HCH3   0   0.222   3.5234   4.2908  49.2929
 7JA  HG2B  H  HCH3   0   0.220   3.9530   3.1894  50.5941
 7JA  H26   H  HCH3   0   0.221  -2.9443   8.1169  41.8648
 7JA  H27   H  HCH2   0   0.234  -3.8798   6.5673  43.6131
 7JA  H28   H  HCH3   0   0.220   6.2479   1.5741  49.2788
 7JA  H29   H  HCH2   0   0.214   3.6801   0.0358  48.6087
 7JA  CD1   C  CH3    0  -0.668   5.6633   0.8373  48.7269
 7JA  C13   C  C      0   0.555   0.0404   3.2036  47.8192

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
 7JA  C    OXT   deloc   1.245  0.020  1.245
 7JA  N    CA    single  1.458  0.019  1.458
 7JA  N    HN    single  0.860  0.020  1.020
 7JA  O    C     deloc   1.231  0.020  1.231
 7JA  CA   C     single  1.525  0.021  1.525
 7JA  CA   CB    single  1.540  0.027  1.540
 7JA  CA   HA    single  0.970  0.020  0.970
 7JA  CB   CG1   single  1.531  0.020  1.531
 7JA  CB   CG2   single  1.529  0.020  1.529
 7JA  CB   HB    single  0.970  0.020  1.090
 7JA  C01  C02   single  1.528  0.020  1.528
 7JA  C01  H01   single  0.970  0.020  1.090
 7JA  C01  H01A  single  0.970  0.020  1.090
 7JA  C02  C03   single  1.496  0.020  1.496
 7JA  C02  H02   single  0.970  0.020  1.090
 7JA  C03  C04   double  1.332  0.020  1.332
 7JA  C03  H03   single  0.930  0.020  1.080
 7JA  C04  C05   single  1.504  0.020  1.504
 7JA  C04  H04   single  0.930  0.020  1.080
 7JA  C05  C06   single  1.546  0.020  1.546
 7JA  C05  H05   single  0.970  0.020  1.090
 7JA  C05  H05A  single  0.970  0.020  1.090
 7JA  C06  C11   single  1.536  0.020  1.536
 7JA  C06  C07   single  1.523  0.020  1.523
 7JA  C06  H06   single  0.970  0.020  1.090
 7JA  C07  O08   double  1.207  0.020  1.207
 7JA  C07  C09   single  1.514  0.020  1.514
 7JA  C09  H09   single  0.970  0.020  1.090
 7JA  C09  H09A  single  0.970  0.020  1.090
 7JA  C10  C09   single  1.524  0.020  1.524
 7JA  C10  H10   single  0.970  0.020  1.090
 7JA  C10  H10A  single  0.970  0.020  1.090
 7JA  C11  C10   single  1.534  0.020  1.534
 7JA  C11  H11   single  0.970  0.020  1.090
 7JA  C12  C11   single  1.523  0.020  1.523
 7JA  C12  C13   single  1.516  0.020  1.516
 7JA  C12  H12   single  0.970  0.020  1.090
 7JA  C12  H12A  single  0.970  0.020  1.090
 7JA  C13  N     single  1.337  0.020  1.337
 7JA  O14  C13   double  1.227  0.020  1.227
 7JA  CD1  HD1   single  0.970  0.020  1.090
 7JA  CD1  HD1A  single  0.970  0.020  1.090
 7JA  CG1  CD1   single  1.524  0.020  1.524
 7JA  CG1  HG1   single  0.970  0.020  1.090
 7JA  CG2  HG2   single  0.970  0.020  1.090
 7JA  CG2  HG2A  single  0.970  0.020  1.090
 7JA  CG2  HG2B  single  0.970  0.020  1.090
 7JA  C01  H26   single  0.970  0.020  1.090
 7JA  C02  H27   single  0.970  0.020  1.090
 7JA  CD1  H28   single  0.970  0.020  1.090
 7JA  CG1  H29   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
 7JA  OXT   C    CA    117.63  3.000
 7JA  CA    C    O     120.80  1.700
 7JA  OXT   C    O     127.20  3.000
 7JA  HN    N    C13   118.09  3.000
 7JA  C13   N    CA    122.73  3.000
 7JA  HN    N    CA    118.90  3.000
 7JA  HA    CA   CB    109.00  3.000
 7JA  HA    CA   N     110.00  3.000
 7JA  CB    CA   N     111.50  1.700
 7JA  HA    CA   C     109.00  3.000
 7JA  CB    CA   C     111.60  2.000
 7JA  N     CA   C     111.00  2.800
 7JA  HB    CB   CG2   107.69  3.000
 7JA  HB    CB   CG1   106.55  3.000
 7JA  CG2   CB   CG1   111.43  3.000
 7JA  HB    CB   CA    105.64  3.000
 7JA  CG2   CB   CA    113.11  3.000
 7JA  CG1   CB   CA    111.94  3.000
 7JA  H26   C01  H01A  107.71  3.000
 7JA  H26   C01  H01   107.71  3.000
 7JA  H01A  C01  H01   107.92  3.000
 7JA  H26   C01  C02   111.17  3.000
 7JA  H01A  C01  C02   111.03  3.000
 7JA  H01   C01  C02   111.13  3.000
 7JA  H27   C02  H02   106.12  3.000
 7JA  H27   C02  C03   108.87  3.000
 7JA  H02   C02  C03   111.25  3.000
 7JA  H27   C02  C01   108.87  3.000
 7JA  H02   C02  C01   109.73  3.000
 7JA  C03   C02  C01   111.81  3.000
 7JA  H03   C03  C04   117.71  3.000
 7JA  H03   C03  C02   115.22  3.000
 7JA  C04   C03  C02   127.07  3.000
 7JA  H04   C04  C05   116.71  3.000
 7JA  H04   C04  C03   117.68  3.000
 7JA  C05   C04  C03   125.60  3.000
 7JA  H05A  C05  H05   106.00  3.000
 7JA  H05A  C05  C06   107.87  3.000
 7JA  H05   C05  C06   109.86  3.000
 7JA  H05A  C05  C04   109.28  3.000
 7JA  H05   C05  C04   109.53  3.000
 7JA  C06   C05  C04   113.98  3.000
 7JA  H06   C06  C11   111.83  3.000
 7JA  H06   C06  C07   109.22  3.000
 7JA  C11   C06  C07   102.78  3.000
 7JA  H06   C06  C05   108.03  3.000
 7JA  C07   C06  C05   108.42  3.000
 7JA  C11   C06  C05   116.27  3.000
 7JA  C09   C07  O08   125.56  3.000
 7JA  C09   C07  C06   109.58  3.000
 7JA  O08   C07  C06   124.86  3.000
 7JA  H09A  C09  H09   106.79  3.000
 7JA  H09A  C09  C10   110.98  3.000
 7JA  H09   C09  C10   115.16  3.000
 7JA  C10   C09  C07   104.59  3.000
 7JA  H09A  C09  C07   107.77  3.000
 7JA  H09   C09  C07   111.39  3.000
 7JA  H10A  C10  H10   107.18  3.000
 7JA  H10A  C10  C11   112.40  3.000
 7JA  H10   C10  C11   109.84  3.000
 7JA  C11   C10  C09   103.59  3.000
 7JA  H10A  C10  C09   113.36  3.000
 7JA  H10   C10  C09   110.48  3.000
 7JA  H11   C11  C12   107.50  3.000
 7JA  C12   C11  C10   113.73  3.000
 7JA  H11   C11  C10   107.78  3.000
 7JA  C12   C11  C06   116.79  3.000
 7JA  H11   C11  C06   106.53  3.000
 7JA  C10   C11  C06   104.01  3.000
 7JA  H12A  C12  H12   106.97  3.000
 7JA  H12A  C12  C13   111.21  3.000
 7JA  H12   C12  C13   107.73  3.000
 7JA  H12A  C12  C11   110.25  3.000
 7JA  H12   C12  C11   109.88  3.000
 7JA  C13   C12  C11   110.70  3.000
 7JA  H29   CG1  HG1   106.17  3.000
 7JA  H29   CG1  CD1   108.76  3.000
 7JA  HG1   CG1  CD1   109.62  3.000
 7JA  H29   CG1  CB    108.74  3.000
 7JA  HG1   CG1  CB    109.77  3.000
 7JA  CD1   CG1  CB    113.52  3.000
 7JA  HG2B  CG2  HG2A  107.35  3.000
 7JA  HG2B  CG2  HG2   107.64  3.000
 7JA  HG2A  CG2  HG2   106.74  3.000
 7JA  HG2B  CG2  CB    111.37  3.000
 7JA  HG2A  CG2  CB    112.66  3.000
 7JA  HG2   CG2  CB    110.82  3.000
 7JA  H28   CD1  HD1A  107.59  3.000
 7JA  H28   CD1  HD1   107.13  3.000
 7JA  HD1A  CD1  HD1   107.51  3.000
 7JA  H28   CD1  CG1   112.33  3.000
 7JA  HD1A  CD1  CG1   111.26  3.000
 7JA  HD1   CD1  CG1   110.79  3.000
 7JA  O14   C13  C12   121.20  3.000
 7JA  O14   C13  N     122.95  3.000
 7JA  C12   C13  N     115.85  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
 7JA  CONST_01  C12  C13  N    CA    180.00   0.0  0
 7JA  CONST_02  O14  C13  N    CA      0.00   0.0  0
 7JA  CONST_03  HN   N    C13  C12     0.00   0.0  0
 7JA  Var_01    C10  C09  C07  C06     9.14  30.0  1
 7JA  Var_02    C11  C10  C09  C07   -29.93  30.0  1
 7JA  Var_03    C11  C12  C13  N    -119.98  30.0  1
 7JA  Var_04    C06  C05  C04  C03    80.97  30.0  3
 7JA  Var_05    C05  C04  C03  C02     0.53   0.0  2
 7JA  Var_06    C04  C03  C02  C01   118.87  30.0  3
 7JA  Var_07    HD1  CD1  CG1  CB   -175.03  30.0  3
 7JA  Var_08    H01  C01  C02  C03   177.19  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
 7JA  chir_01  CA   N    C    CB   positiv
 7JA  chir_02  CB   CA   CG1  CG2  positiv
 7JA  chir_03  C06  C05  C11  C07  negativ
 7JA  chir_04  C11  C06  C10  C12  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
 7JA  plan-1  N    0.020
 7JA  plan-1  CA   0.020
 7JA  plan-1  C12  0.020
 7JA  plan-1  O14  0.020
 7JA  plan-1  HN   0.020
 7JA  plan-1  C13  0.020
 7JA  plan-2  C06  0.020
 7JA  plan-2  C07  0.020
 7JA  plan-2  O08  0.020
 7JA  plan-2  C09  0.020
 7JA  plan-3  C    0.020
 7JA  plan-3  O    0.020
 7JA  plan-3  CA   0.020
 7JA  plan-3  OXT  0.020
 7JA  plan-4  C02  0.020
 7JA  plan-4  C03  0.020
 7JA  plan-4  C04  0.020
 7JA  plan-4  C05  0.020
 7JA  plan-4  H03  0.020
 7JA  plan-4  H04  0.020

