# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 06:14:26 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: (phenylmethyl) ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1C[C@H](NC(=O)OCc2ccccc2)C(=O)N1
#
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
 JP5  JP5  '(phenylmethyl) ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamate'  ligand  30  18  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JP5
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
 JP5  O    O  O     0  -0.408   2.6082  -1.7413   1.1407
 JP5  C    C  CR5   0   0.574   3.1204  -0.7874   0.6156
 JP5  ND2  N  NR15  0  -0.678   4.3651  -0.2841   0.8900
 JP5  CG   C  CR5   0   0.549   4.6466   0.9078   0.2602
 JP5  OD1  O  O     0  -0.419   5.6907   1.5018   0.3498
 JP5  CB   C  CH2   0  -0.602   3.4134   1.3189  -0.5063
 JP5  CA   C  CR15  0  -0.228   2.5237   0.0787  -0.4910
 JP5  N    N  NH1   0  -0.657   1.1309   0.3359  -0.3061
 JP5  CAI  C  C     0   0.766   0.1798  -0.4478  -0.8624
 JP5  OAK  O  O     0  -0.511   0.3884  -1.3340  -1.6630
 JP5  OAJ  O  O2    0  -0.477  -1.0302  -0.0935  -0.4300
 JP5  CAL  C  CH2   0  -0.243  -2.1483  -0.8196  -0.9607
 JP5  CAM  C  CR6   0   0.075  -3.3766  -0.2682  -0.3042
 JP5  CAN  C  CR16  0  -0.287  -3.7901  -0.7511   0.9347
 JP5  CAO  C  CR16  0  -0.242  -4.9128  -0.2246   1.5575
 JP5  CAP  C  CR16  0  -0.261  -5.6336   0.7935   0.9455
 JP5  CAQ  C  CR16  0  -0.242  -5.2283   1.2804  -0.2902
 JP5  CAR  C  CR16  0  -0.292  -4.1037   0.7516  -0.9099
 JP5  H1   H  HNR5  0   0.428   5.0070  -0.7234   1.5385
 JP5  H2   H  HCH2  0   0.313   2.9501   2.1547   0.0254
 JP5  H3   H  HCH2  0   0.312   3.6679   1.6645  -1.5062
 JP5  H4   H  HCR5  0   0.331   2.6545  -0.4778  -1.4224
 JP5  H5   H  HNH1  0   0.409   0.8602   0.9800   0.4219
 JP5  H6   H  HCH2  0   0.251  -2.1957  -0.6921  -2.0439
 JP5  H7   H  HCH2  0   0.251  -2.0369  -1.8844  -0.7471
 JP5  H8   H  HCR6  0   0.255  -3.2325  -1.5475   1.4136
 JP5  H9   H  HCR6  0   0.259  -5.2259  -0.6100   2.5190
 JP5  H10  H  HCR6  0   0.259  -6.5103   1.2038   1.4298
 JP5  H11  H  HCR6  0   0.259  -5.7887   2.0701  -0.7734
 JP5  H12  H  HCR6  0   0.256  -3.7938   1.1327  -1.8758

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
 JP5  O    C    double    1.203  0.020  1.203
 JP5  C    ND2  single    1.370  0.020  1.370
 JP5  C    CA   single    1.527  0.020  1.527
 JP5  ND2  CG   single    1.377  0.020  1.377
 JP5  OAK  CAI  double    1.212  0.020  1.212
 JP5  CA   N    single    1.428  0.020  1.428
 JP5  CA   CB   single    1.526  0.020  1.526
 JP5  CG   OD1  double    1.205  0.020  1.205
 JP5  CG   CB   single    1.509  0.020  1.509
 JP5  CAI  OAJ  single    1.333  0.020  1.333
 JP5  CAI  N    single    1.352  0.020  1.352
 JP5  CAL  OAJ  single    1.435  0.020  1.435
 JP5  CAL  CAM  single    1.498  0.020  1.498
 JP5  CAN  CAM  aromatic  1.393  0.020  1.393
 JP5  CAN  CAO  aromatic  1.388  0.020  1.388
 JP5  CAM  CAR  aromatic  1.391  0.020  1.391
 JP5  CAO  CAP  aromatic  1.389  0.020  1.389
 JP5  CAR  CAQ  aromatic  1.389  0.020  1.389
 JP5  CAP  CAQ  aromatic  1.389  0.020  1.389
 JP5  ND2  H1   single    0.860  0.020  1.020
 JP5  CB   H2   single    0.970  0.020  1.090
 JP5  CB   H3   single    0.970  0.020  1.090
 JP5  CA   H4   single    0.970  0.020  1.090
 JP5  N    H5   single    0.860  0.020  1.020
 JP5  CAL  H6   single    0.970  0.020  1.090
 JP5  CAL  H7   single    0.970  0.020  1.090
 JP5  CAN  H8   single    0.930  0.020  1.080
 JP5  CAO  H9   single    0.930  0.020  1.080
 JP5  CAP  H10  single    0.930  0.020  1.080
 JP5  CAQ  H11  single    0.930  0.020  1.080
 JP5  CAR  H12  single    0.930  0.020  1.080

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
 JP5  CA   C    ND2  106.97  3.000
 JP5  CA   C    O    126.84  3.000
 JP5  ND2  C    O    126.19  3.000
 JP5  H1   ND2  CG   122.60  3.000
 JP5  H1   ND2  C    123.00  3.000
 JP5  CG   ND2  C    114.33  3.000
 JP5  CB   CG   OD1  127.72  3.000
 JP5  CB   CG   ND2  107.52  3.000
 JP5  OD1  CG   ND2  124.75  3.000
 JP5  H3   CB   H2   107.64  3.000
 JP5  H3   CB   CA   113.80  3.000
 JP5  H2   CB   CA   111.66  3.000
 JP5  H3   CB   CG   111.23  3.000
 JP5  H2   CB   CG   107.90  3.000
 JP5  CA   CB   CG   104.47  3.000
 JP5  H4   CA   N    108.59  3.000
 JP5  H4   CA   CB   109.60  3.000
 JP5  N    CA   CB   115.05  3.000
 JP5  H4   CA   C    106.39  3.000
 JP5  CB   CA   C    103.91  3.000
 JP5  N    CA   C    112.92  3.000
 JP5  H5   N    CAI  118.56  3.000
 JP5  H5   N    CA   118.03  3.000
 JP5  CAI  N    CA   121.89  3.000
 JP5  OAJ  CAI  OAK  124.38  3.000
 JP5  OAJ  CAI  N    110.55  3.000
 JP5  OAK  CAI  N    125.05  3.000
 JP5  CAL  OAJ  CAI  116.93  3.000
 JP5  H7   CAL  H6   108.21  3.000
 JP5  H7   CAL  CAM  110.91  3.000
 JP5  H6   CAL  CAM  110.87  3.000
 JP5  H7   CAL  OAJ  109.98  3.000
 JP5  H6   CAL  OAJ  109.98  3.000
 JP5  CAM  CAL  OAJ  106.89  3.000
 JP5  CAR  CAM  CAN  119.10  3.000
 JP5  CAR  CAM  CAL  120.50  3.000
 JP5  CAN  CAM  CAL  120.38  3.000
 JP5  H8   CAN  CAO  119.79  3.000
 JP5  H8   CAN  CAM  119.69  3.000
 JP5  CAO  CAN  CAM  120.53  3.000
 JP5  H9   CAO  CAP  120.15  3.000
 JP5  H9   CAO  CAN  119.85  3.000
 JP5  CAP  CAO  CAN  120.01  3.000
 JP5  H10  CAP  CAQ  120.12  3.000
 JP5  H10  CAP  CAO  120.06  3.000
 JP5  CAQ  CAP  CAO  119.83  3.000
 JP5  H11  CAQ  CAR  119.87  3.000
 JP5  H11  CAQ  CAP  120.13  3.000
 JP5  CAR  CAQ  CAP  120.00  3.000
 JP5  H12  CAR  CAQ  119.70  3.000
 JP5  H12  CAR  CAM  119.76  3.000
 JP5  CAQ  CAR  CAM  120.53  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
 JP5  CONST_01  CAP  CAO  CAN  CAM    0.00   0.0  0
 JP5  CONST_02  CAP  CAQ  CAR  CAM    0.00   0.0  0
 JP5  CONST_03  CAQ  CAR  CAM  CAN    0.00   0.0  0
 JP5  CONST_04  CAQ  CAP  CAO  CAN    0.00   0.0  0
 JP5  CONST_05  CAR  CAM  CAN  CAO    0.00   0.0  0
 JP5  CONST_06  CAR  CAQ  CAP  CAO    0.00   0.0  0
 JP5  CONST_07  CA   C    ND2  CG     0.00   0.0  0
 JP5  CONST_08  CAO  CAN  CAM  CAL  180.00   0.0  0
 JP5  CONST_09  CAQ  CAR  CAM  CAL  180.00   0.0  0
 JP5  CONST_10  CG   ND2  C    O    180.00   0.0  0
 JP5  CONST_11  H9   CAO  CAN  CAM  180.00   0.0  0
 JP5  CONST_12  H11  CAQ  CAR  CAM  180.00   0.0  0
 JP5  CONST_13  H12  CAR  CAM  CAN  180.00   0.0  0
 JP5  CONST_14  H10  CAP  CAO  CAN  180.00   0.0  0
 JP5  CONST_15  H8   CAN  CAO  CAP  180.00   0.0  0
 JP5  CONST_16  H1   ND2  C    CA   180.00   0.0  0
 JP5  Var_01    CB   CG   ND2  C      2.77  30.0  1
 JP5  Var_02    CA   CB   CG   ND2  -12.30  30.0  1
 JP5  Var_03    CAN  CAM  CAL  OAJ  -85.20  30.0  2
 JP5  Var_04    OAK  CAI  N    CA    -8.01  30.0  1
 JP5  Var_05    CAM  CAL  OAJ  CAI  178.56  30.0  1

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
 JP5  chir_01  CA  C  N  CB  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
 JP5  plan-1  CAL  0.020
 JP5  plan-1  CAM  0.020
 JP5  plan-1  CAN  0.020
 JP5  plan-1  CAO  0.020
 JP5  plan-1  CAP  0.020
 JP5  plan-1  CAQ  0.020
 JP5  plan-1  CAR  0.020
 JP5  plan-1  H8   0.020
 JP5  plan-1  H9   0.020
 JP5  plan-1  H10  0.020
 JP5  plan-1  H11  0.020
 JP5  plan-1  H12  0.020
 JP5  plan-2  O    0.020
 JP5  plan-2  C    0.020
 JP5  plan-2  ND2  0.020
 JP5  plan-2  CG   0.020
 JP5  plan-2  CA   0.020
 JP5  plan-2  H1   0.020
 JP5  plan-3  ND2  0.020
 JP5  plan-3  CG   0.020
 JP5  plan-3  OD1  0.020
 JP5  plan-3  CB   0.020
 JP5  plan-4  N    0.020
 JP5  plan-4  CAI  0.020
 JP5  plan-4  OAK  0.020
 JP5  plan-4  OAJ  0.020

