# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 02:09:31 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: N-({(1R,2R)-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
 JAI  JAI  N-({(1R,2R)-3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl}acetyl)-L-isoleucine  ligand  52  23  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_JAI
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
 JAI  C     C  C     0   0.542  -3.2841  -0.6661   1.3373
 JAI  N     N  NH1   0  -0.643  -1.6996   0.8184   0.2585
 JAI  O1    O  O     0  -0.432  -2.7826  -1.6854   0.9397
 JAI  O2    O  OH1   0  -0.588  -4.1486  -0.6157   2.3417
 JAI  CA    C  CH1   0  -0.121  -3.0572   0.7065   0.7227
 JAI  CB    C  CH1   0  -0.296  -4.0312   0.9827  -0.4438
 JAI  C01   C  CH3   0  -0.654   5.3198   3.5893   1.0968
 JAI  C02   C  CH2   0  -0.492   4.7301   2.7759  -0.0549
 JAI  C03   C  C1    0  -0.209   5.5135   1.5250  -0.3120
 JAI  C04   C  C1    0  -0.212   5.1477   0.2803  -0.0094
 JAI  C05   C  CH2   0  -0.507   3.8530  -0.1078   0.6422
 JAI  C06   C  CH1   0  -0.348   2.7562  -0.5154  -0.3443
 JAI  C07   C  C     0   0.421   2.9495  -1.8790  -0.9798
 JAI  C09   C  CH2   0  -0.564   1.6012  -2.5513  -1.1270
 JAI  C10   C  CH2   0  -0.460   0.5863  -1.4770  -0.7543
 JAI  C11   C  CH1   0  -0.246   1.3414  -0.5860   0.2395
 JAI  C13   C  C     0   0.559  -0.6534   0.6610   1.0856
 JAI  O14   O  O     0  -0.497  -0.8035   0.3972   2.2712
 JAI  CG1   C  CH2   0  -0.415  -5.4614   1.2001   0.0570
 JAI  CG2   C  CH3   0  -0.666  -3.9674  -0.0716  -1.5463
 JAI  HN    H  HNH1  0   0.404  -1.5343   1.0449  -0.7086
 JAI  HO2   H  HOH1  0   0.481  -4.3143  -1.5082   2.6817
 JAI  HA    H  HCH1  0   0.282  -3.2412   1.4634   1.4918
 JAI  HB    H  HCH1  0   0.254  -3.6892   1.9379  -0.8609
 JAI  H01   H  HCH3  0   0.222   5.3001   3.0184   2.0262
 JAI  H01A  H  HCH3  0   0.223   6.3575   3.8610   0.8971
 JAI  H01B  H  HCH3  0   0.229   4.7601   4.5115   1.2570
 JAI  H02   H  HCH2  0   0.224   3.6829   2.5478   0.1550
 JAI  H02A  H  HCH2  0   0.236   4.7295   3.3892  -0.9602
 JAI  H03   H  H     0   0.231   6.4874   1.6713  -0.7717
 JAI  H04   H  H     0   0.234   5.8264  -0.5280  -0.2571
 JAI  H05   H  HCH2  0   0.250   4.0192  -0.9277   1.3462
 JAI  H05A  H  HCH2  0   0.246   3.4757   0.7245   1.2403
 JAI  H06   H  HCH1  0   0.283   2.7410   0.2026  -1.1797
 JAI  H09   H  HCH2  0   0.279   1.4712  -2.9817  -2.1209
 JAI  H09A  H  HCH2  0   0.278   1.5718  -3.3822  -0.4139
 JAI  H10   H  HCH2  0   0.231   0.3169  -0.8914  -1.6389
 JAI  H10A  H  HCH2  0   0.262  -0.3375  -1.8809  -0.3421
 JAI  H11   H  HCH1  0   0.252   1.3940  -1.1020   1.2061
 JAI  H12   H  HCH2  0   0.271   1.3350   1.3927   1.1087
 JAI  H12A  H  HCH2  0   0.253   0.6524   1.3099  -0.5103
 JAI  HD1   H  HCH3  0   0.221  -5.9596   2.8087  -1.3101
 JAI  HD1A  H  HCH3  0   0.225  -6.4814   1.2229  -1.8714
 JAI  HD1B  H  HCH3  0   0.235  -7.3582   2.0267  -0.5784
 JAI  HG1   H  HCH2  0   0.224  -5.8983   0.2487   0.3723
 JAI  HG1A  H  HCH2  0   0.229  -5.4370   1.8382   0.9446
 JAI  HG2   H  HCH3  0   0.243  -4.4959   0.2748  -2.4336
 JAI  HG2A  H  HCH3  0   0.231  -2.9464  -0.2977  -1.8555
 JAI  HG2B  H  HCH3  0   0.228  -4.4317  -1.0079  -1.2344
 JAI  CD1   C  CH3   0  -0.670  -6.3633   1.8476  -0.9861
 JAI  C12   C  CH2   0  -0.567   0.7097   0.7869   0.4484
 JAI  O3    O  O     0  -0.398   4.0100  -2.3619  -1.2955

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
 JAI  O1   C     double  1.204  0.020  1.204
 JAI  C    O2    single  1.326  0.020  1.326
 JAI  C    CA    single  1.521  0.020  1.521
 JAI  CA   N     single  1.439  0.020  1.439
 JAI  C13  N     single  1.343  0.020  1.343
 JAI  N    HN    single  0.860  0.020  1.020
 JAI  O2   HO2   single  0.850  0.020  0.980
 JAI  C07  O3    double  1.207  0.020  1.207
 JAI  CA   CB    single  1.545  0.020  1.545
 JAI  CA   HA    single  0.970  0.020  1.090
 JAI  CG2  CB    single  1.527  0.020  1.527
 JAI  CB   CG1   single  1.531  0.020  1.531
 JAI  CB   HB    single  0.970  0.020  1.090
 JAI  C01  C02   single  1.528  0.020  1.528
 JAI  C01  H01   single  0.970  0.020  1.090
 JAI  C01  H01A  single  0.970  0.020  1.090
 JAI  C01  H01B  single  0.970  0.020  1.090
 JAI  C02  C03   single  1.498  0.020  1.498
 JAI  C02  H02   single  0.970  0.020  1.090
 JAI  C02  H02A  single  0.970  0.020  1.090
 JAI  C03  C04   double  1.332  0.020  1.332
 JAI  C03  H03   single  0.930  0.020  1.080
 JAI  C05  C04   single  1.500  0.020  1.500
 JAI  C04  H04   single  0.930  0.020  1.080
 JAI  C05  C06   single  1.530  0.020  1.530
 JAI  C05  H05   single  0.970  0.020  1.090
 JAI  C05  H05A  single  0.970  0.020  1.090
 JAI  C11  C06   single  1.532  0.020  1.532
 JAI  C06  C07   single  1.517  0.020  1.517
 JAI  C06  H06   single  0.970  0.020  1.090
 JAI  C07  C09   single  1.514  0.020  1.514
 JAI  C10  C09   single  1.524  0.020  1.524
 JAI  C09  H09   single  0.970  0.020  1.090
 JAI  C09  H09A  single  0.970  0.020  1.090
 JAI  C11  C10   single  1.534  0.020  1.534
 JAI  C10  H10   single  0.970  0.020  1.090
 JAI  C10  H10A  single  0.970  0.020  1.090
 JAI  C11  C12   single  1.526  0.020  1.526
 JAI  C11  H11   single  0.970  0.020  1.090
 JAI  C13  C12   single  1.510  0.020  1.510
 JAI  C12  H12   single  0.970  0.020  1.090
 JAI  C12  H12A  single  0.970  0.020  1.090
 JAI  O14  C13   double  1.224  0.020  1.224
 JAI  CD1  CG1   single  1.523  0.020  1.523
 JAI  CD1  HD1   single  0.970  0.020  1.090
 JAI  CD1  HD1A  single  0.970  0.020  1.090
 JAI  CD1  HD1B  single  0.970  0.020  1.090
 JAI  CG1  HG1   single  0.970  0.020  1.090
 JAI  CG1  HG1A  single  0.970  0.020  1.090
 JAI  CG2  HG2   single  0.970  0.020  1.090
 JAI  CG2  HG2A  single  0.970  0.020  1.090
 JAI  CG2  HG2B  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
 JAI  CA    C    O2    111.65  3.000
 JAI  CA    C    O1    124.66  3.000
 JAI  O2    C    O1    123.64  3.000
 JAI  HN    N    C13   119.34  3.000
 JAI  HN    N    CA    118.83  3.000
 JAI  C13   N    CA    121.81  3.000
 JAI  HO2   O2   C     110.01  3.000
 JAI  HA    CA   CB    107.52  3.000
 JAI  HA    CA   N     109.36  3.000
 JAI  CB    CA   N     109.71  3.000
 JAI  HA    CA   C     108.36  3.000
 JAI  CB    CA   C     111.86  3.000
 JAI  N     CA   C     109.95  3.000
 JAI  HB    CB   CG2   108.28  3.000
 JAI  HB    CB   CG1   106.97  3.000
 JAI  CG2   CB   CG1   111.92  3.000
 JAI  HB    CB   CA    104.26  3.000
 JAI  CG1   CB   CA    111.55  3.000
 JAI  CG2   CB   CA    113.30  3.000
 JAI  H01B  C01  H01A  107.72  3.000
 JAI  H01B  C01  H01   107.95  3.000
 JAI  H01A  C01  H01   107.66  3.000
 JAI  H01B  C01  C02   111.26  3.000
 JAI  H01A  C01  C02   111.20  3.000
 JAI  H01   C01  C02   110.88  3.000
 JAI  H02A  C02  H02   106.01  3.000
 JAI  H02A  C02  C03   109.05  3.000
 JAI  H02   C02  C03   111.10  3.000
 JAI  H02A  C02  C01   109.00  3.000
 JAI  H02   C02  C01   109.66  3.000
 JAI  C03   C02  C01   111.83  3.000
 JAI  H03   C03  C04   117.90  3.000
 JAI  H03   C03  C02   115.39  3.000
 JAI  C04   C03  C02   126.69  3.000
 JAI  H04   C04  C05   116.52  3.000
 JAI  H04   C04  C03   118.22  3.000
 JAI  C05   C04  C03   125.26  3.000
 JAI  H05A  C05  H05   105.75  3.000
 JAI  H05A  C05  C06   107.96  3.000
 JAI  H05   C05  C06   108.92  3.000
 JAI  H05A  C05  C04   109.81  3.000
 JAI  H05   C05  C04   110.02  3.000
 JAI  C06   C05  C04   114.04  3.000
 JAI  H06   C06  C11   107.83  3.000
 JAI  H06   C06  C07   105.66  3.000
 JAI  C11   C06  C07   103.64  3.000
 JAI  H06   C06  C05   108.97  3.000
 JAI  C07   C06  C05   114.72  3.000
 JAI  C11   C06  C05   115.37  3.000
 JAI  C09   C07  C06   109.06  3.000
 JAI  C09   C07  O3    125.40  3.000
 JAI  C06   C07  O3    125.53  3.000
 JAI  H09A  C09  H09   106.90  3.000
 JAI  H09A  C09  C10   110.95  3.000
 JAI  H09   C09  C10   114.93  3.000
 JAI  H09A  C09  C07   107.31  3.000
 JAI  H09   C09  C07   111.72  3.000
 JAI  C10   C09  C07   104.85  3.000
 JAI  H10A  C10  H10   107.19  3.000
 JAI  H10A  C10  C11   112.81  3.000
 JAI  H10   C10  C11   109.52  3.000
 JAI  H10A  C10  C09   113.32  3.000
 JAI  H10   C10  C09   110.08  3.000
 JAI  C11   C10  C09   103.89  3.000
 JAI  H11   C11  C12   108.81  3.000
 JAI  H11   C11  C10   108.75  3.000
 JAI  C12   C11  C10   114.06  3.000
 JAI  H11   C11  C06   108.25  3.000
 JAI  C12   C11  C06   113.14  3.000
 JAI  C10   C11  C06   103.56  3.000
 JAI  O14   C13  C12   122.51  3.000
 JAI  O14   C13  N     121.76  3.000
 JAI  C12   C13  N     115.70  3.000
 JAI  HG1A  CG1  HG1   106.42  3.000
 JAI  HG1A  CG1  CD1   108.72  3.000
 JAI  HG1   CG1  CD1   109.31  3.000
 JAI  HG1A  CG1  CB    109.13  3.000
 JAI  HG1   CG1  CB    110.13  3.000
 JAI  CD1   CG1  CB    112.92  3.000
 JAI  HG2B  CG2  HG2A  107.56  3.000
 JAI  HG2B  CG2  HG2   107.42  3.000
 JAI  HG2A  CG2  HG2   106.82  3.000
 JAI  HG2B  CG2  CB    111.62  3.000
 JAI  HG2A  CG2  CB    112.77  3.000
 JAI  HG2   CG2  CB    110.39  3.000
 JAI  HD1B  CD1  HD1A  107.40  3.000
 JAI  HD1B  CD1  HD1   107.69  3.000
 JAI  HD1A  CD1  HD1   107.67  3.000
 JAI  HD1B  CD1  CG1   110.74  3.000
 JAI  HD1A  CD1  CG1   112.13  3.000
 JAI  HD1   CD1  CG1   111.01  3.000
 JAI  H12A  C12  H12   107.13  3.000
 JAI  H12A  C12  C13   111.25  3.000
 JAI  H12   C12  C13   107.93  3.000
 JAI  H12A  C12  C11   109.39  3.000
 JAI  H12   C12  C11   110.17  3.000
 JAI  C13   C12  C11   110.89  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
 JAI  CONST_01  C12  C13  N    CA    180.00   0.0  0
 JAI  CONST_02  O14  C13  N    CA      0.00   0.0  0
 JAI  CONST_03  HN   N    C13  C12     0.00   0.0  0
 JAI  CONST_04  HO2  O2   C    O1      0.00   0.0  0
 JAI  Var_01    C10  C09  C07  C06     8.05  30.0  1
 JAI  Var_02    C11  C10  C09  C07   -28.94  30.0  1
 JAI  Var_03    C11  C12  C13  N    -102.98  30.0  3
 JAI  Var_04    C06  C05  C04  C03    94.93  30.0  1
 JAI  Var_05    C05  C04  C03  C02     0.77   0.0  2
 JAI  Var_06    C04  C03  C02  C01   106.37  30.0  3
 JAI  Var_07    HD1  CD1  CG1  CB    -57.88  30.0  3
 JAI  Var_08    H01  C01  C02  C03   -61.50  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
 JAI  chir_01  CA   C    N    CB   negativ
 JAI  chir_02  CB   CA   CG2  CG1  negativ
 JAI  chir_03  C06  C05  C11  C07  positiv
 JAI  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
 JAI  plan-1  N    0.020
 JAI  plan-1  CA   0.020
 JAI  plan-1  C13  0.020
 JAI  plan-1  O14  0.020
 JAI  plan-1  HN   0.020
 JAI  plan-1  C12  0.020
 JAI  plan-2  C06  0.020
 JAI  plan-2  C07  0.020
 JAI  plan-2  C09  0.020
 JAI  plan-2  O3   0.020
 JAI  plan-3  C    0.020
 JAI  plan-3  O1   0.020
 JAI  plan-3  O2   0.020
 JAI  plan-3  CA   0.020
 JAI  plan-3  HO2  0.020
 JAI  plan-4  C02  0.020
 JAI  plan-4  C03  0.020
 JAI  plan-4  C04  0.020
 JAI  plan-4  C05  0.020
 JAI  plan-4  H03  0.020
 JAI  plan-4  H04  0.020

