# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 15:29:14 2022
#   Inital geometry file: a 119 line input string
#   Ligand name: 5'-O-[(S)-[(3S)-3-carboxypyrrolidin-1-yl](hydroxy)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)N4CC[C@@H](C4)C(O)=O)[C@@H](O)[C@H]3O
#
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
 V2J  V2J  5'-O-[(S)-[(3S)-3-carboxypyrrolidin-1-yl](hydroxy)phosphoryl]adenosine  ligand  49  30  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_V2J
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
 V2J  C4   C  CR56   0   0.478  37.3885  -20.5327  -21.1204
 V2J  C5   C  CR56   0  -0.005  37.0476  -20.1254  -22.4026
 V2J  C6   C  CR6    0   0.452  36.9350  -18.7394  -22.6159
 V2J  C8   C  CR15   0   0.108  37.1258  -22.2259  -22.4771
 V2J  N1   N  N      0  -0.469  37.1570  -17.9247  -21.5803
 V2J  C2   C  CR16   0   0.041  37.4693  -18.4549  -20.4003
 V2J  O2A  O  O      0  -0.798  38.6600  -19.5076  -15.0597
 V2J  PA   P  P      0   1.323  39.5082  -20.5417  -15.7417
 V2J  O1A  O  OP    -1  -0.805  40.0946  -21.6978  -14.9794
 V2J  N    N  NR5    0  -0.607  40.7333  -19.7772  -16.5949
 V2J  CA   C  CH2    0  -0.247  41.8833  -20.5198  -17.1069
 V2J  CD   C  CH2    0  -0.260  40.5023  -18.5674  -17.3709
 V2J  CG   C  CH2    0  -0.448  41.8486  -18.3194  -18.0368
 V2J  CB   C  CR15   0  -0.412  42.3544  -19.7270  -18.3369
 V2J  C    C  C      0   0.477  41.8228  -20.3329  -19.6500
 V2J  OX   O  O      0  -0.636  42.1225  -21.5493  -19.8257
 V2J  O    O  OC    -1  -0.560  41.1762  -19.6254  -20.4324
 V2J  C5'  C  CH2    0  -0.175  37.7104  -22.2248  -16.7772
 V2J  C4'  C  CR15   0  -0.004  37.7309  -23.2349  -17.9096
 V2J  C3'  C  CR15   0  -0.057  39.1438  -23.5889  -18.4070
 V2J  O3'  O  OH1    0  -0.671  39.2551  -24.9367  -18.8015
 V2J  C2'  C  CR15   0  -0.022  39.2457  -22.7196  -19.6636
 V2J  O2'  O  OH1    0  -0.708  40.1880  -23.0784  -20.6093
 V2J  C1'  C  CR15   0   0.230  37.8211  -22.8646  -20.1872
 V2J  O4'  O  O      0  -0.500  37.0089  -22.7545  -19.0564
 V2J  N9   N  NR5    0  -0.544  37.4354  -21.8998  -21.1848
 V2J  N3   N  N      0  -0.451  37.6021  -19.7290  -20.0807
 V2J  N6   N  NH2    0  -0.817  36.6050  -18.2191  -23.8012
 V2J  N7   N  N      0  -0.452  36.8886  -21.2007  -23.2371
 V2J  H1   H  HCR5   0   0.296  37.0949  -23.2586  -22.7943
 V2J  H2   H  HCR6   0   0.248  37.6372  -17.7429  -19.5988
 V2J  H4   H  HCH2   0   0.223  41.6390  -21.5500  -17.3724
 V2J  H5   H  HCH2   0   0.204  42.6756  -20.5699  -16.3522
 V2J  H6   H  HCH2   0   0.215  40.1934  -17.7369  -16.7333
 V2J  H7   H  HCH2   0   0.200  39.7249  -18.6995  -18.1341
 V2J  H8   H  HCH2   0   0.221  42.5223  -17.8242  -17.3323
 V2J  H9   H  HCH2   0   0.229  41.7709  -17.6891  -18.9210
 V2J  H10  H  HCR5   0   0.247  43.4472  -19.7537  -18.3953
 V2J  H12  H  HCH2   0   0.216  36.6874  -21.8486  -16.6499
 V2J  H13  H  HCH2   0   0.203  37.9619  -22.7734  -15.8635
 V2J  H14  H  HCR5   0   0.239  37.2219  -24.1349  -17.5422
 V2J  H15  H  HCR5   0   0.239  39.9049  -23.3331  -17.6598
 V2J  H16  H  HOH1   0   0.449  39.1344  -25.4899  -18.0235
 V2J  H17  H  HCR5   0   0.240  39.3749  -21.6858  -19.3247
 V2J  H18  H  HOH1   0   0.453  40.9864  -22.5077  -20.4292
 V2J  H19  H  HCR5   0   0.237  37.7058  -23.8410  -20.6768
 V2J  H20  H  HNH2   0   0.401  36.6251  -17.2225  -23.9346
 V2J  H21  H  HNH2   0   0.408  36.5330  -18.8028  -24.6161
 V2J  O5'  O  O2     0  -0.630  38.6095  -21.1693  -17.0049

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
 V2J  N6   C6   single    1.336  0.020  1.336
 V2J  C6   C5   aromatic  1.407  0.020  1.407
 V2J  C6   N1   aromatic  1.336  0.020  1.336
 V2J  N7   C5   aromatic  1.370  0.020  1.370
 V2J  N7   C8   aromatic  1.298  0.020  1.298
 V2J  C5   C4   aromatic  1.388  0.020  1.388
 V2J  N1   C2   aromatic  1.331  0.020  1.331
 V2J  C8   N9   aromatic  1.368  0.020  1.368
 V2J  O2'  C2'  single    1.382  0.020  1.382
 V2J  C4   N9   aromatic  1.369  0.020  1.369
 V2J  C4   N3   aromatic  1.331  0.020  1.331
 V2J  N9   C1'  single    1.440  0.020  1.440
 V2J  C2   N3   aromatic  1.320  0.020  1.320
 V2J  C2'  C1'  single    1.525  0.020  1.525
 V2J  C2'  C3'  single    1.531  0.020  1.531
 V2J  C1'  O4'  single    1.397  0.020  1.397
 V2J  OX   C    deloc     1.265  0.020  1.265
 V2J  O    C    deloc     1.237  0.020  1.237
 V2J  C    CB   single    1.541  0.020  1.541
 V2J  O3'  C3'  single    1.409  0.020  1.409
 V2J  C3'  C4'  single    1.539  0.020  1.539
 V2J  O4'  C4'  single    1.438  0.020  1.438
 V2J  C4'  C5'  single    1.518  0.020  1.518
 V2J  CB   CG   single    1.526  0.020  1.526
 V2J  CB   CA   single    1.537  0.020  1.537
 V2J  CG   CD   single    1.522  0.020  1.522
 V2J  CD   N    single    1.456  0.020  1.456
 V2J  O5'  C5'  single    1.405  0.020  1.405
 V2J  O5'  PA   single    1.673  0.020  1.673
 V2J  CA   N    single    1.462  0.020  1.462
 V2J  N    PA   single    1.677  0.020  1.677
 V2J  PA   O2A  deloc     1.501  0.020  1.501
 V2J  PA   O1A  deloc     1.504  0.020  1.504
 V2J  C8   H1   single    0.930  0.020  1.080
 V2J  C2   H2   single    0.930  0.020  1.080
 V2J  CA   H4   single    0.970  0.020  1.090
 V2J  CA   H5   single    0.970  0.020  1.090
 V2J  CD   H6   single    0.970  0.020  1.090
 V2J  CD   H7   single    0.970  0.020  1.090
 V2J  CG   H8   single    0.970  0.020  1.090
 V2J  CG   H9   single    0.970  0.020  1.090
 V2J  CB   H10  single    0.970  0.020  1.090
 V2J  C5'  H12  single    0.970  0.020  1.090
 V2J  C5'  H13  single    0.970  0.020  1.090
 V2J  C4'  H14  single    0.970  0.020  1.090
 V2J  C3'  H15  single    0.970  0.020  1.090
 V2J  O3'  H16  single    0.850  0.020  0.980
 V2J  C2'  H17  single    0.970  0.020  1.090
 V2J  O2'  H18  single    0.850  0.020  0.980
 V2J  C1'  H19  single    0.970  0.020  1.090
 V2J  N6   H20  single    0.860  0.020  1.020
 V2J  N6   H21  single    0.860  0.020  1.020

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
 V2J  N3   C4   N9   129.34  3.000
 V2J  N3   C4   C5   125.71  3.000
 V2J  N9   C4   C5   104.94  3.000
 V2J  N7   C5   C6   132.18  3.000
 V2J  N7   C5   C4   111.15  3.000
 V2J  C6   C5   C4   116.67  3.000
 V2J  N6   C6   N1   119.42  3.000
 V2J  N1   C6   C5   118.03  3.000
 V2J  N6   C6   C5   122.55  3.000
 V2J  H1   C8   N7   125.29  3.000
 V2J  H1   C8   N9   120.75  3.000
 V2J  N7   C8   N9   113.96  3.000
 V2J  C2   N1   C6   118.90  3.000
 V2J  H2   C2   N3   116.03  3.000
 V2J  H2   C2   N1   115.46  3.000
 V2J  N3   C2   N1   128.51  3.000
 V2J  O5'  PA   N    100.33  3.000
 V2J  N    PA   O1A  108.87  3.000
 V2J  O5'  PA   O1A  107.69  3.000
 V2J  O1A  PA   O2A  121.30  3.000
 V2J  N    PA   O2A  109.26  3.000
 V2J  O5'  PA   O2A  107.33  3.000
 V2J  CD   N    CA   111.13  3.000
 V2J  CA   N    PA   121.42  3.000
 V2J  CD   N    PA   122.28  3.000
 V2J  H5   CA   H4   106.64  3.000
 V2J  H5   CA   CB   110.69  3.000
 V2J  H4   CA   CB   111.15  3.000
 V2J  H5   CA   N    110.55  3.000
 V2J  H4   CA   N    112.87  3.000
 V2J  CB   CA   N    105.03  3.000
 V2J  H7   CD   H6   107.29  3.000
 V2J  H7   CD   CG   109.99  3.000
 V2J  H6   CD   CG   112.45  3.000
 V2J  H7   CD   N    112.53  3.000
 V2J  H6   CD   N    111.46  3.000
 V2J  CG   CD   N    103.19  3.000
 V2J  H9   CG   H8   107.76  3.000
 V2J  H9   CG   CB   113.46  3.000
 V2J  H8   CG   CB   109.90  3.000
 V2J  H9   CG   CD   112.74  3.000
 V2J  H8   CG   CD   109.69  3.000
 V2J  CB   CG   CD   103.24  3.000
 V2J  H10  CB   C    106.82  3.000
 V2J  H10  CB   CG   111.35  3.000
 V2J  C    CB   CG   114.59  3.000
 V2J  H10  CB   CA   109.64  3.000
 V2J  CG   CB   CA   102.52  3.000
 V2J  C    CB   CA   111.92  3.000
 V2J  O    C    OX   125.86  3.000
 V2J  O    C    CB   119.63  3.000
 V2J  OX   C    CB   114.50  3.000
 V2J  H13  C5'  H12  106.79  3.000
 V2J  H13  C5'  C4'  106.62  3.000
 V2J  H12  C5'  C4'  109.11  3.000
 V2J  H13  C5'  O5'  111.38  3.000
 V2J  H12  C5'  O5'  110.97  3.000
 V2J  C4'  C5'  O5'  111.75  3.000
 V2J  H14  C4'  O4'  107.96  3.000
 V2J  H14  C4'  C3'  110.21  3.000
 V2J  O4'  C4'  C3'  106.26  3.000
 V2J  H14  C4'  C5'  106.85  3.000
 V2J  O4'  C4'  C5'  111.47  3.000
 V2J  C3'  C4'  C5'  113.99  3.000
 V2J  H15  C3'  C2'  112.37  3.000
 V2J  H15  C3'  O3'  111.04  3.000
 V2J  C2'  C3'  O3'  107.94  3.000
 V2J  H15  C3'  C4'  111.30  3.000
 V2J  O3'  C3'  C4'  112.52  3.000
 V2J  C2'  C3'  C4'  101.28  3.000
 V2J  H16  O3'  C3'  108.28  3.000
 V2J  H17  C2'  C1'  107.83  3.000
 V2J  H17  C2'  O2'  112.09  3.000
 V2J  C1'  C2'  O2'  112.17  3.000
 V2J  H17  C2'  C3'  106.83  3.000
 V2J  C1'  C2'  C3'   99.54  3.000
 V2J  O2'  C2'  C3'  117.35  3.000
 V2J  H18  O2'  C2'  105.88  3.000
 V2J  H19  C1'  N9   104.99  3.000
 V2J  H19  C1'  O4'  111.72  3.000
 V2J  N9   C1'  O4'  110.62  3.000
 V2J  H19  C1'  C2'  109.62  3.000
 V2J  O4'  C1'  C2'  104.94  3.000
 V2J  N9   C1'  C2'  115.11  3.000
 V2J  C1'  O4'  C4'  109.12  3.000
 V2J  C1'  N9   C8   123.71  3.000
 V2J  C1'  N9   C4   130.19  3.000
 V2J  C8   N9   C4   105.94  3.000
 V2J  C2   N3   C4   112.17  3.000
 V2J  H21  N6   H20  118.00  3.000
 V2J  H21  N6   C6   120.73  3.000
 V2J  H20  N6   C6   119.92  3.000
 V2J  C8   N7   C5   104.01  3.000
 V2J  C5'  O5'  PA   120.22  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
 V2J  CONST_01  N1   C6   C5   C4      0.00   0.0  0
 V2J  CONST_02  C8   N7   C5   C4      0.00   0.0  0
 V2J  CONST_03  N7   C8   N9   C4      0.00   0.0  0
 V2J  CONST_04  N1   C2   N3   C4      0.00   0.0  0
 V2J  CONST_05  C2   N1   C6   C5      0.00   0.0  0
 V2J  CONST_06  N9   C8   N7   C5      0.00   0.0  0
 V2J  CONST_07  C8   N9   C4   C5      0.00   0.0  0
 V2J  CONST_08  C2   N3   C4   C5      0.00   0.0  0
 V2J  CONST_09  C8   N7   C5   C6    180.00   0.0  0
 V2J  CONST_10  N9   C4   C5   C6    180.00   0.0  0
 V2J  CONST_11  N3   C4   C5   C6      0.00   0.0  0
 V2J  CONST_12  N3   C2   N1   C6      0.00   0.0  0
 V2J  CONST_13  N3   C4   N9   C8    180.00   0.0  0
 V2J  CONST_14  N7   C5   C6   N1    180.00   0.0  0
 V2J  CONST_15  N9   C4   N3   C2    180.00   0.0  0
 V2J  CONST_16  N7   C5   C4   N9      0.00   0.0  0
 V2J  CONST_17  N7   C5   C4   N3    180.00   0.0  0
 V2J  CONST_18  C1'  N9   C4   C5    180.00   0.0  0
 V2J  CONST_19  N7   C8   N9   C1'   180.00   0.0  0
 V2J  CONST_20  N3   C4   N9   C1'     0.00   0.0  0
 V2J  CONST_21  N6   C6   C5   C4    180.00   0.0  0
 V2J  CONST_22  N6   C6   N1   C2    180.00   0.0  0
 V2J  CONST_23  N7   C5   C6   N6      0.00   0.0  0
 V2J  CONST_24  H1   C8   N9   C4    180.00   0.0  0
 V2J  CONST_25  H2   C2   N3   C4    180.00   0.0  0
 V2J  CONST_26  H20  N6   C6   C5    180.00   0.0  0
 V2J  CONST_27  H21  N6   C6   C5      0.00   0.0  0
 V2J  Var_01    CB   CG   CD   N      35.99  30.0  1
 V2J  Var_02    CG   CD   N    CA    -20.87  30.0  1
 V2J  Var_03    CB   CA   N    CD     -2.64  30.0  1
 V2J  Var_04    CD   N    PA   O2A   -41.68  30.0  2
 V2J  Var_05    C4'  C5'  O5'  PA   -140.53  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
 V2J  chir_02  CB   C    CG   CA   negativ
 V2J  chir_03  C4'  O4'  C3'  C5'  negativ
 V2J  chir_04  C3'  O3'  C4'  C2'  positiv
 V2J  chir_05  C2'  O2'  C3'  C1'  positiv
 V2J  chir_06  C1'  O4'  N9   C2'  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
 V2J  plan-1  C6   0.020
 V2J  plan-1  N6   0.020
 V2J  plan-1  H20  0.020
 V2J  plan-1  H21  0.020
 V2J  plan-2  C4   0.020
 V2J  plan-2  C5   0.020
 V2J  plan-2  C6   0.020
 V2J  plan-2  C8   0.020
 V2J  plan-2  N1   0.020
 V2J  plan-2  C2   0.020
 V2J  plan-2  C1'  0.020
 V2J  plan-2  N9   0.020
 V2J  plan-2  N3   0.020
 V2J  plan-2  N6   0.020
 V2J  plan-2  N7   0.020
 V2J  plan-2  H1   0.020
 V2J  plan-2  H2   0.020
 V2J  plan-3  CB   0.020
 V2J  plan-3  C    0.020
 V2J  plan-3  OX   0.020
 V2J  plan-3  O    0.020

