# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 07:56:24 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 5'-O-[(S)-[(2-aminobenzoyl)oxy](hydroxy)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccccc1C(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34
#
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
 3UK  3UK  5'-O-[(S)-[(2-aminobenzoyl)oxy](hydroxy)phosphoryl]adenosine  ligand  51  32  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3UK
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
 3UK  C10  C  CH1   0   0.212  -2.8512   1.2447  -0.6537
 3UK  C15  C  CR56  0   0.493  -3.8849  -1.0244  -0.4604
 3UK  C17  C  CR16  0   0.047  -5.2786  -2.1932  -1.6882
 3UK  C21  C  CH1   0  -0.050  -3.1891   2.4637   0.2022
 3UK  C26  C  CR6   0  -0.189   4.5515  -1.2061  -0.0891
 3UK  C28  C  CR16  0  -0.280   3.9841  -2.9105  -1.7254
 3UK  O01  O  O     0  -0.444   4.8462   0.5744   1.4684
 3UK  C02  C  C     0   0.640   4.1853  -0.0001   0.6361
 3UK  O03  O  O2    0  -0.591   2.9598   0.4794   0.2868
 3UK  P04  P  P     0   1.474   2.3070   1.7754   1.0287
 3UK  O05  O  O     0  -0.681   2.0994   1.6689   2.4790
 3UK  O06  O  O2    0  -0.574   1.0102   1.8179   0.1078
 3UK  C07  C  CH2   0  -0.178  -0.0525   2.7228   0.4254
 3UK  C08  C  CH1   0  -0.043  -1.0344   2.6974  -0.7266
 3UK  O09  O  O2    0  -0.485  -1.4892   1.3662  -0.9654
 3UK  N11  N  NR5   0  -0.542  -3.0833  -0.0166  -0.0028
 3UK  C12  C  CR15  0   0.117  -2.5157  -0.4777   1.1560
 3UK  N13  N  N     0  -0.447  -2.8935  -1.6786   1.4735
 3UK  C14  C  CR56  0  -0.011  -3.7573  -2.0414   0.4712
 3UK  N16  N  N     0  -0.457  -4.6329  -1.0468  -1.5601
 3UK  N18  N  N     0  -0.475  -5.2567  -3.2490  -0.8796
 3UK  C19  C  CR6   0   0.462  -4.4995  -3.2110   0.2230
 3UK  N20  N  NH2   0  -0.816  -4.4742  -4.2688   1.0334
 3UK  O22  O  OH1   0  -0.651  -4.5547   2.7334   0.1258
 3UK  C23  C  CH1   0  -0.034  -2.2793   3.5243  -0.4255
 3UK  O24  O  OH1   0  -0.664  -2.8064   3.9891  -1.6382
 3UK  O25  O  OH1   0  -0.728   3.1993   3.0326   0.6546
 3UK  C27  C  CR16  0  -0.265   3.6637  -1.7766  -1.0213
 3UK  C29  C  CR16  0  -0.234   5.2317  -3.5076  -1.5078
 3UK  C30  C  CR16  0  -0.335   6.1211  -2.9791  -0.6070
 3UK  C31  C  CR6   0   0.376   5.8146  -1.8175   0.1371
 3UK  N32  N  NH2   0  -0.861   6.7194  -1.3657   1.0248
 3UK  H1   H  HCH1  0   0.265  -3.4716   1.2360  -1.5561
 3UK  H2   H  HCR6  0   0.253  -5.9091  -2.2907  -2.5652
 3UK  H3   H  HCH1  0   0.250  -2.8691   2.2913   1.2384
 3UK  H4   H  HCR6  0   0.257   3.2870  -3.3324  -2.4353
 3UK  H5   H  HCH2  0   0.246  -0.5217   2.4250   1.3670
 3UK  H6   H  HCH2  0   0.263   0.3248   3.7420   0.5440
 3UK  H7   H  HCH1  0   0.277  -0.5330   3.0642  -1.6270
 3UK  H8   H  HCR5  0   0.290  -1.8198   0.1179   1.7277
 3UK  H9   H  HNH2  0   0.412  -3.9222  -4.2699   1.8728
 3UK  H10  H  HNH2  0   0.405  -5.0195  -5.0857   0.8182
 3UK  H11  H  HOH1  0   0.471  -4.8005   3.3045   0.8607
 3UK  H12  H  HCH1  0   0.260  -2.0696   4.3459   0.2720
 3UK  H13  H  HOH1  0   0.452  -3.7264   4.2369  -1.4886
 3UK  H14  H  HOH1  0   0.505   3.3190   3.2185  -0.2874
 3UK  H15  H  HCR6  0   0.267   2.7017  -1.3133  -1.1897
 3UK  H16  H  HCR6  0   0.266   5.5058  -4.4007  -2.0549
 3UK  H17  H  HCR6  0   0.268   7.0830  -3.4527  -0.4526
 3UK  H18  H  HNH2  0   0.400   7.6347  -1.7799   1.0464
 3UK  H19  H  HNH2  0   0.408   6.5950  -0.4854   1.4914

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
 3UK  O24  C23  single    1.402  0.020  1.402
 3UK  N32  C31  single    1.346  0.020  1.346
 3UK  C30  C31  aromatic  1.413  0.020  1.413
 3UK  C30  C29  aromatic  1.372  0.020  1.372
 3UK  O05  P04  double    1.469  0.020  1.469
 3UK  C31  C26  aromatic  1.421  0.020  1.421
 3UK  C29  C28  aromatic  1.400  0.020  1.400
 3UK  C23  C08  single    1.525  0.020  1.525
 3UK  C23  C21  single    1.532  0.020  1.532
 3UK  C07  C08  single    1.514  0.020  1.514
 3UK  C07  O06  single    1.431  0.020  1.431
 3UK  O03  P04  single    1.630  0.020  1.630
 3UK  O03  C02  single    1.361  0.020  1.361
 3UK  P04  O06  single    1.591  0.020  1.591
 3UK  P04  O25  single    1.586  0.020  1.586
 3UK  C26  C02  single    1.454  0.020  1.454
 3UK  C26  C27  aromatic  1.408  0.020  1.408
 3UK  C28  C27  aromatic  1.373  0.020  1.373
 3UK  C08  O09  single    1.427  0.020  1.427
 3UK  C21  O22  single    1.394  0.020  1.394
 3UK  C21  C10  single    1.527  0.020  1.527
 3UK  C02  O01  double    1.208  0.020  1.208
 3UK  O09  C10  single    1.402  0.020  1.402
 3UK  C10  N11  single    1.438  0.020  1.438
 3UK  C12  N11  aromatic  1.370  0.020  1.370
 3UK  C12  N13  aromatic  1.298  0.020  1.298
 3UK  N11  C15  aromatic  1.367  0.020  1.367
 3UK  N13  C14  aromatic  1.372  0.020  1.372
 3UK  C15  C14  aromatic  1.385  0.020  1.385
 3UK  C15  N16  aromatic  1.330  0.020  1.330
 3UK  C14  C19  aromatic  1.407  0.020  1.407
 3UK  N16  C17  aromatic  1.322  0.020  1.322
 3UK  C19  N20  single    1.333  0.020  1.333
 3UK  C19  N18  aromatic  1.338  0.020  1.338
 3UK  C17  N18  aromatic  1.330  0.020  1.330
 3UK  C10  H1   single    0.970  0.020  1.090
 3UK  C17  H2   single    0.930  0.020  1.080
 3UK  C21  H3   single    0.970  0.020  1.090
 3UK  C28  H4   single    0.930  0.020  1.080
 3UK  C07  H5   single    0.970  0.020  1.090
 3UK  C07  H6   single    0.970  0.020  1.090
 3UK  C08  H7   single    0.970  0.020  1.090
 3UK  C12  H8   single    0.930  0.020  1.080
 3UK  N20  H9   single    0.860  0.020  1.020
 3UK  N20  H10  single    0.860  0.020  1.020
 3UK  O22  H11  single    0.850  0.020  0.980
 3UK  C23  H12  single    0.970  0.020  1.090
 3UK  O24  H13  single    0.850  0.020  0.980
 3UK  O25  H14  single    0.850  0.020  0.980
 3UK  C27  H15  single    0.930  0.020  1.080
 3UK  C29  H16  single    0.930  0.020  1.080
 3UK  C30  H17  single    0.930  0.020  1.080
 3UK  N32  H18  single    0.860  0.020  1.020
 3UK  N32  H19  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
 3UK  H1   C10  N11  105.93  3.000
 3UK  H1   C10  O09  111.58  3.000
 3UK  N11  C10  O09  109.47  3.000
 3UK  H1   C10  C21  110.05  3.000
 3UK  N11  C10  C21  114.24  3.000
 3UK  O09  C10  C21  105.68  3.000
 3UK  N16  C15  C14  126.55  3.000
 3UK  N16  C15  N11  128.24  3.000
 3UK  C14  C15  N11  105.20  3.000
 3UK  H2   C17  N18  115.45  3.000
 3UK  H2   C17  N16  116.12  3.000
 3UK  N18  C17  N16  128.43  3.000
 3UK  H3   C21  C23  108.80  3.000
 3UK  H3   C21  O22  111.57  3.000
 3UK  C23  C21  O22  115.17  3.000
 3UK  H3   C21  C10  109.82  3.000
 3UK  O22  C21  C10  109.90  3.000
 3UK  C23  C21  C10  101.04  3.000
 3UK  C31  C26  C27  119.43  3.000
 3UK  C27  C26  C02  120.49  3.000
 3UK  C31  C26  C02  120.08  3.000
 3UK  H4   C28  C29  120.69  3.000
 3UK  H4   C28  C27  120.59  3.000
 3UK  C29  C28  C27  118.72  3.000
 3UK  O03  C02  O01  120.11  3.000
 3UK  O01  C02  C26  126.88  3.000
 3UK  O03  C02  C26  113.01  3.000
 3UK  P04  O03  C02  121.59  3.000
 3UK  O25  P04  O06  107.51  3.000
 3UK  O25  P04  O05  111.70  3.000
 3UK  O06  P04  O05  117.27  3.000
 3UK  O25  P04  O03  107.31  3.000
 3UK  O06  P04  O03   94.83  3.000
 3UK  O05  P04  O03  116.64  3.000
 3UK  C07  O06  P04  119.57  3.000
 3UK  H6   C07  H5   107.98  3.000
 3UK  H6   C07  C08  108.79  3.000
 3UK  H5   C07  C08  111.87  3.000
 3UK  H6   C07  O06  110.93  3.000
 3UK  H5   C07  O06  109.72  3.000
 3UK  C08  C07  O06  107.58  3.000
 3UK  H7   C08  C23  110.79  3.000
 3UK  H7   C08  O09  108.74  3.000
 3UK  C23  C08  O09  106.19  3.000
 3UK  H7   C08  C07  108.87  3.000
 3UK  O09  C08  C07  110.47  3.000
 3UK  C23  C08  C07  111.73  3.000
 3UK  C08  O09  C10  110.68  3.000
 3UK  C12  N11  C15  106.14  3.000
 3UK  C15  N11  C10  126.15  3.000
 3UK  C12  N11  C10  127.67  3.000
 3UK  H8   C12  N13  124.63  3.000
 3UK  H8   C12  N11  121.94  3.000
 3UK  N13  C12  N11  113.42  3.000
 3UK  C14  N13  C12  104.43  3.000
 3UK  C19  C14  N13  132.90  3.000
 3UK  C19  C14  C15  116.29  3.000
 3UK  N13  C14  C15  110.81  3.000
 3UK  C17  N16  C15  111.67  3.000
 3UK  C19  N18  C17  119.19  3.000
 3UK  N20  C19  N18  119.29  3.000
 3UK  N18  C19  C14  117.87  3.000
 3UK  N20  C19  C14  122.85  3.000
 3UK  H10  N20  H9   118.42  3.000
 3UK  H10  N20  C19  120.29  3.000
 3UK  H9   N20  C19  121.29  3.000
 3UK  H11  O22  C21  108.85  3.000
 3UK  H12  C23  O24  111.92  3.000
 3UK  H12  C23  C08  112.05  3.000
 3UK  O24  C23  C08  108.42  3.000
 3UK  H12  C23  C21  111.79  3.000
 3UK  C08  C23  C21  100.97  3.000
 3UK  O24  C23  C21  111.15  3.000
 3UK  H13  O24  C23  108.04  3.000
 3UK  H14  O25  P04  116.83  3.000
 3UK  H15  C27  C28  118.81  3.000
 3UK  H15  C27  C26  119.38  3.000
 3UK  C28  C27  C26  121.81  3.000
 3UK  H16  C29  C30  119.05  3.000
 3UK  H16  C29  C28  119.92  3.000
 3UK  C30  C29  C28  121.03  3.000
 3UK  H17  C30  C31  118.48  3.000
 3UK  H17  C30  C29  120.06  3.000
 3UK  C31  C30  C29  121.45  3.000
 3UK  N32  C31  C30  118.52  3.000
 3UK  C30  C31  C26  117.55  3.000
 3UK  N32  C31  C26  123.92  3.000
 3UK  H19  N32  H18  117.67  3.000
 3UK  H19  N32  C31  121.17  3.000
 3UK  H18  N32  C31  119.22  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
 3UK  CONST_01  N13  C12  N11  C15    0.00   0.0  0
 3UK  CONST_02  C12  N13  C14  C15    0.00   0.0  0
 3UK  CONST_03  N18  C19  C14  C15    0.00   0.0  0
 3UK  CONST_04  N18  C17  N16  C15    0.00   0.0  0
 3UK  CONST_05  N11  C15  N16  C17  180.00   0.0  0
 3UK  CONST_06  C14  C15  N16  C17    0.00   0.0  0
 3UK  CONST_07  C14  C19  N18  C17    0.00   0.0  0
 3UK  CONST_08  C29  C30  C31  C26    0.00   0.0  0
 3UK  CONST_09  C29  C28  C27  C26    0.00   0.0  0
 3UK  CONST_10  C31  C30  C29  C28    0.00   0.0  0
 3UK  CONST_11  C31  C26  C27  C28    0.00   0.0  0
 3UK  CONST_12  C14  N13  C12  N11    0.00   0.0  0
 3UK  CONST_13  N13  C14  C15  N11    0.00   0.0  0
 3UK  CONST_14  C19  C14  C15  N11  180.00   0.0  0
 3UK  CONST_15  C14  C15  N11  C12    0.00   0.0  0
 3UK  CONST_16  N16  C15  N11  C12  180.00   0.0  0
 3UK  CONST_17  C19  C14  N13  C12  180.00   0.0  0
 3UK  CONST_18  N16  C15  C14  N13  180.00   0.0  0
 3UK  CONST_19  N18  C19  C14  N13  180.00   0.0  0
 3UK  CONST_20  C19  C14  C15  N16    0.00   0.0  0
 3UK  CONST_21  C19  N18  C17  N16    0.00   0.0  0
 3UK  CONST_22  C30  C31  C26  C27    0.00   0.0  0
 3UK  CONST_23  C30  C29  C28  C27    0.00   0.0  0
 3UK  CONST_24  N13  C12  N11  C10  180.00   0.0  0
 3UK  CONST_25  C14  C15  N11  C10  180.00   0.0  0
 3UK  CONST_26  N16  C15  N11  C10    0.00   0.0  0
 3UK  CONST_27  N20  C19  C14  C15  180.00   0.0  0
 3UK  CONST_28  N20  C19  N18  C17  180.00   0.0  0
 3UK  CONST_29  C02  C26  C27  C28  180.00   0.0  0
 3UK  CONST_30  C30  C31  C26  C02  180.00   0.0  0
 3UK  CONST_31  N20  C19  C14  N13    0.00   0.0  0
 3UK  CONST_32  N32  C31  C26  C27  180.00   0.0  0
 3UK  CONST_33  N32  C31  C30  C29  180.00   0.0  0
 3UK  CONST_34  H8   C12  N11  C10    0.00   0.0  0
 3UK  CONST_35  H2   C17  N16  C15  180.00   0.0  0
 3UK  CONST_36  H17  C30  C31  C26  180.00   0.0  0
 3UK  CONST_37  H4   C28  C27  C26  180.00   0.0  0
 3UK  CONST_38  H16  C29  C28  C27  180.00   0.0  0
 3UK  CONST_39  H15  C27  C28  C29  180.00   0.0  0
 3UK  CONST_40  H18  N32  C31  C26  180.00   0.0  0
 3UK  CONST_41  H19  N32  C31  C26    0.00   0.0  0
 3UK  CONST_42  H9   N20  C19  C14    0.00   0.0  0
 3UK  CONST_43  H10  N20  C19  C14  180.00   0.0  0
 3UK  Var_01    C31  C26  C02  O01   -1.14  30.0  2
 3UK  Var_02    C08  C07  O06  P04  171.29  30.0  2
 3UK  Var_03    O05  P04  O03  C02  -59.49  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
 3UK  chir_01  C10  C21  O09  N11  negativ
 3UK  chir_02  C21  O22  C23  C10  positiv
 3UK  chir_04  C08  C23  C07  O09  negativ
 3UK  chir_05  C23  O24  C21  C08  negativ
 3UK  chir_06  P04  O03  O06  O25  both

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
 3UK  plan-1  C26  0.020
 3UK  plan-1  C28  0.020
 3UK  plan-1  C02  0.020
 3UK  plan-1  C27  0.020
 3UK  plan-1  C29  0.020
 3UK  plan-1  C30  0.020
 3UK  plan-1  C31  0.020
 3UK  plan-1  N32  0.020
 3UK  plan-1  H4   0.020
 3UK  plan-1  H15  0.020
 3UK  plan-1  H16  0.020
 3UK  plan-1  H17  0.020
 3UK  plan-2  C10  0.020
 3UK  plan-2  C15  0.020
 3UK  plan-2  C17  0.020
 3UK  plan-2  N11  0.020
 3UK  plan-2  C12  0.020
 3UK  plan-2  N13  0.020
 3UK  plan-2  C14  0.020
 3UK  plan-2  N16  0.020
 3UK  plan-2  N18  0.020
 3UK  plan-2  C19  0.020
 3UK  plan-2  N20  0.020
 3UK  plan-2  H2   0.020
 3UK  plan-2  H8   0.020
 3UK  plan-3  C19  0.020
 3UK  plan-3  N20  0.020
 3UK  plan-3  H9   0.020
 3UK  plan-3  H10  0.020
 3UK  plan-4  C31  0.020
 3UK  plan-4  N32  0.020
 3UK  plan-4  H18  0.020
 3UK  plan-4  H19  0.020
 3UK  plan-5  C26  0.020
 3UK  plan-5  O01  0.020
 3UK  plan-5  C02  0.020
 3UK  plan-5  O03  0.020

