# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 13:04:19 2021
#   Inital geometry file: a 149 line input string
#   Ligand name: a 2 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccccc1C(=O)O[C@H]2C[C@@H](O[C@@H]2CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)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
 DOT  DOT  '3'-O-[(2-aminophenyl)carbonyl]-2'-deoxyadenosine 5'-(tetrahydrogen triphosphate)'  ligand  60  39  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DOT
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
 DOT  PG    P  P     0   1.480  35.8404  73.1479  43.9108
 DOT  O1G   O  OH1   0  -0.727  37.1732  73.5090  43.1438
 DOT  O2G   O  O     0  -0.668  35.2216  74.2965  44.5796
 DOT  O3G   O  OH1   0  -0.741  36.2255  71.8759  44.7846
 DOT  PB    P  P     0   1.506  34.8975  71.2120  41.8851
 DOT  O1B   O  O     0  -0.637  34.1886  71.4010  40.6208
 DOT  O2B   O  OH1   0  -0.767  36.4330  70.8421  41.8681
 DOT  O3B   O  O2    0  -0.679  34.8310  72.5527  42.7760
 DOT  PA    P  P     0   1.537  34.8008  68.9300  43.7536
 DOT  O1A   O  O     0  -0.680  36.2431  68.7352  43.4994
 DOT  O2A   O  OH1   0  -0.710  34.4904  69.3398  45.2450
 DOT  O3A   O  O2    0  -0.709  34.1760  70.1175  42.8442
 DOT  O5'   O  O2    0  -0.567  33.9374  67.6688  43.3784
 DOT  C5B   C  CH2   0  -0.219  32.5060  67.5739  43.4058
 DOT  C4B   C  CH1   0  -0.063  32.0786  66.2614  42.7830
 DOT  O4'   O  O2    0  -0.484  32.3957  66.1721  41.4027
 DOT  C3B   C  CH1   0   0.008  32.7350  65.0265  43.4028
 DOT  O3'   O  O2    0  -0.479  31.8953  63.8834  43.2379
 DOT  C2B   C  CH2   0  -0.552  33.9636  64.8139  42.5320
 DOT  C1B   C  CH1   0   0.227  33.6054  65.5025  41.2054
 DOT  N9    N  NR5   0  -0.535  34.6171  66.4731  40.7882
 DOT  C8    C  CR15  0   0.091  34.3940  67.7539  40.3669
 DOT  N7    N  N     0  -0.450  35.4879  68.4129  40.1151
 DOT  C5    C  CR56  0   0.006  36.4894  67.5191  40.3756
 DOT  C6    C  CR6   0   0.455  37.8901  67.6234  40.3374
 DOT  N6    N  NH2   0  -0.818  38.5169  68.7575  40.0137
 DOT  N1    N  N     0  -0.475  38.6089  66.5440  40.6619
 DOT  C2    C  CR16  0   0.039  37.9743  65.4287  41.0165
 DOT  N3    N  N     0  -0.460  36.6737  65.2163  41.1100
 DOT  C4    C  CR56  0   0.487  35.9703  66.3017  40.7870
 DOT  C'    C  C     0   0.636  30.8642  63.7344  44.0711
 DOT  O1'   O  O     0  -0.473  30.6248  64.5479  44.9412
 DOT  C1'   C  CR6   0  -0.191  30.0874  62.5181  43.8098
 DOT  C2'   C  CR6   0   0.357  28.9445  62.2124  44.5933
 DOT  N2'   N  NH2   0  -0.864  28.5259  62.9598  45.6384
 DOT  C3'   C  CR16  0  -0.334  28.2235  61.0414  44.2742
 DOT  C4'   C  CR16  0  -0.238  28.6141  60.2149  43.2491
 DOT  C5'   C  CR16  0  -0.281  29.7457  60.5093  42.4828
 DOT  C6'   C  CR16  0  -0.275  30.4599  61.6490  42.7700
 DOT  HOG1  H  HOH1  0   0.503  37.6537  72.7952  42.7006
 DOT  HOG3  H  HOH1  0   0.511  35.6957  71.7553  45.5855
 DOT  HOB2  H  HOH1  0   0.508  36.6736  70.0099  42.3472
 DOT  HOA2  H  HOH1  0   0.514  33.5795  69.5483  45.4975
 DOT  H5'1  H  HCH2  0   0.281  32.0615  68.4043  42.8540
 DOT  H5'2  H  HCH2  0   0.274  32.1483  67.6073  44.4375
 DOT  H4B   H  HCH1  0   0.303  30.9897  66.2398  42.8694
 DOT  H3B   H  HCH1  0   0.291  32.9881  65.1604  44.4554
 DOT  H2'1  H  HCH2  0   0.294  34.1861  63.7580  42.3926
 DOT  H2'2  H  HCH2  0   0.291  34.8318  65.2670  43.0027
 DOT  H1'   H  HCH1  0   0.284  33.4742  64.7853  40.3928
 DOT  H8    H  HCR5  0   0.295  33.3994  68.1557  40.2586
 DOT  HN61  H  HNH2  0   0.408  38.0012  69.5524  39.6795
 DOT  HN62  H  HNH2  0   0.402  39.5185  68.7734  39.9280
 DOT  H2    H  HCR6  0   0.251  38.6144  64.5876  41.2612
 DOT  H2B   H  HNH2  0   0.403  28.9159  63.8728  45.7904
 DOT  H2D   H  HNH2  0   0.393  27.6129  62.7818  46.0193
 DOT  H3'   H  HCR6  0   0.264  27.3443  60.7983  44.8591
 DOT  H4'   H  HCR6  0   0.263  28.0333  59.3260  43.0374
 DOT  H5'   H  HCR6  0   0.253  30.0548  59.8565  41.6785
 DOT  H6'   H  HCR6  0   0.262  31.3324  61.8792  42.1749

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
 DOT  PG   O1G   single    1.580  0.020  1.580
 DOT  PG   O2G   double    1.466  0.020  1.466
 DOT  PG   O3G   single    1.591  0.020  1.591
 DOT  PG   O3B   single    1.631  0.020  1.631
 DOT  O1G  HOG1  single    0.850  0.020  0.980
 DOT  O3G  HOG3  single    0.850  0.020  0.980
 DOT  PB   O1B   double    1.462  0.020  1.462
 DOT  PB   O2B   single    1.579  0.020  1.579
 DOT  PB   O3B   single    1.611  0.020  1.611
 DOT  PB   O3A   single    1.624  0.020  1.624
 DOT  O2B  HOB2  single    0.850  0.020  0.980
 DOT  PA   O1A   double    1.477  0.020  1.477
 DOT  PA   O2A   single    1.577  0.020  1.577
 DOT  PA   O3A   single    1.621  0.020  1.621
 DOT  PA   O5'   single    1.574  0.020  1.574
 DOT  O2A  HOA2  single    0.850  0.020  0.980
 DOT  O5'  C5B   single    1.435  0.020  1.435
 DOT  C5B  C4B   single    1.514  0.020  1.514
 DOT  C5B  H5'1  single    0.970  0.020  1.090
 DOT  C5B  H5'2  single    0.970  0.020  1.090
 DOT  C4B  O4'   single    1.419  0.020  1.419
 DOT  C4B  C3B   single    1.530  0.020  1.530
 DOT  C4B  H4B   single    0.970  0.020  1.090
 DOT  O4'  C1B   single    1.397  0.020  1.397
 DOT  C3B  O3'   single    1.428  0.020  1.428
 DOT  C3B  C2B   single    1.521  0.020  1.521
 DOT  C3B  H3B   single    0.970  0.020  1.090
 DOT  O3'  C'    single    1.334  0.020  1.334
 DOT  C2B  C1B   single    1.537  0.020  1.537
 DOT  C2B  H2'1  single    0.970  0.020  1.090
 DOT  C2B  H2'2  single    0.970  0.020  1.090
 DOT  C1B  N9    single    1.463  0.020  1.463
 DOT  C1B  H1'   single    0.970  0.020  1.090
 DOT  N9   C8    aromatic  1.367  0.020  1.367
 DOT  N9   C4    aromatic  1.364  0.020  1.364
 DOT  C8   N7    aromatic  1.302  0.020  1.302
 DOT  C8   H8    single    0.930  0.020  1.080
 DOT  N7   C5    aromatic  1.367  0.020  1.367
 DOT  C5   C6    aromatic  1.405  0.020  1.405
 DOT  C5   C4    aromatic  1.386  0.020  1.386
 DOT  C6   N6    single    1.336  0.020  1.336
 DOT  C6   N1    aromatic  1.337  0.020  1.337
 DOT  N6   HN61  single    0.860  0.020  1.020
 DOT  N6   HN62  single    0.860  0.020  1.020
 DOT  N1   C2    aromatic  1.331  0.020  1.331
 DOT  C2   N3    aromatic  1.321  0.020  1.321
 DOT  C2   H2    single    0.930  0.020  1.080
 DOT  N3   C4    aromatic  1.333  0.020  1.333
 DOT  C'   O1'   double    1.215  0.020  1.215
 DOT  C'   C1'   single    1.467  0.020  1.467
 DOT  C1'  C2'   aromatic  1.419  0.020  1.419
 DOT  C1'  C6'   aromatic  1.405  0.020  1.405
 DOT  C2'  N2'   single    1.351  0.020  1.351
 DOT  C2'  C3'   aromatic  1.412  0.020  1.412
 DOT  N2'  H2B   single    0.890  0.020  1.040
 DOT  N2'  H2D   single    0.890  0.020  1.040
 DOT  C3'  C4'   aromatic  1.373  0.020  1.373
 DOT  C3'  H3'   single    0.930  0.020  1.080
 DOT  C4'  C5'   aromatic  1.398  0.020  1.398
 DOT  C4'  H4'   single    0.930  0.020  1.080
 DOT  C5'  C6'   aromatic  1.375  0.020  1.375
 DOT  C5'  H5'   single    0.930  0.020  1.080
 DOT  C6'  H6'   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
 DOT  O3B   PG   O3G   103.90  3.000
 DOT  O3B   PG   O2G   110.00  3.000
 DOT  O3G   PG   O2G   118.56  3.000
 DOT  O3B   PG   O1G   105.53  3.000
 DOT  O3G   PG   O1G   104.20  3.000
 DOT  O2G   PG   O1G   113.48  3.000
 DOT  HOG1  O1G  PG    118.21  3.000
 DOT  HOG3  O3G  PG    114.94  3.000
 DOT  O3A   PB   O3B   102.46  3.000
 DOT  O3A   PB   O2B   106.28  3.000
 DOT  O3B   PB   O2B   103.94  3.000
 DOT  O3A   PB   O1B   112.48  3.000
 DOT  O3B   PB   O1B   110.53  3.000
 DOT  O2B   PB   O1B   119.50  3.000
 DOT  HOB2  O2B  PB    115.34  3.000
 DOT  PB    O3B  PG    131.51  3.000
 DOT  O5'   PA   O3A   103.99  3.000
 DOT  O5'   PA   O2A   109.00  3.000
 DOT  O3A   PA   O2A   105.32  3.000
 DOT  O5'   PA   O1A   112.88  3.000
 DOT  O3A   PA   O1A   112.11  3.000
 DOT  O2A   PA   O1A   112.89  3.000
 DOT  HOA2  O2A  PA    119.19  3.000
 DOT  PA    O3A  PB    130.82  3.000
 DOT  C5B   O5'  PA    126.57  3.000
 DOT  H5'2  C5B  H5'1  108.71  3.000
 DOT  H5'2  C5B  C4B   108.81  3.000
 DOT  H5'1  C5B  C4B   109.66  3.000
 DOT  H5'2  C5B  O5'   110.04  3.000
 DOT  H5'1  C5B  O5'   110.26  3.000
 DOT  C4B   C5B  O5'   109.33  3.000
 DOT  H4B   C4B  C3B   112.31  3.000
 DOT  H4B   C4B  O4'   107.36  3.000
 DOT  C3B   C4B  O4'   104.32  3.000
 DOT  H4B   C4B  C5B   105.42  3.000
 DOT  C3B   C4B  C5B   114.33  3.000
 DOT  O4'   C4B  C5B   113.05  3.000
 DOT  C1B   O4'  C4B   111.17  3.000
 DOT  H3B   C3B  C2B   112.47  3.000
 DOT  H3B   C3B  O3'   110.25  3.000
 DOT  C2B   C3B  O3'   107.28  3.000
 DOT  H3B   C3B  C4B   113.04  3.000
 DOT  C2B   C3B  C4B   103.15  3.000
 DOT  O3'   C3B  C4B   110.31  3.000
 DOT  C'    O3'  C3B   118.15  3.000
 DOT  H2'2  C2B  H2'1  107.26  3.000
 DOT  H2'2  C2B  C1B   111.92  3.000
 DOT  H2'1  C2B  C1B   111.83  3.000
 DOT  H2'2  C2B  C3B   109.83  3.000
 DOT  H2'1  C2B  C3B   111.97  3.000
 DOT  C1B   C2B  C3B   104.08  3.000
 DOT  H1'   C1B  N9    107.86  3.000
 DOT  H1'   C1B  C2B   112.10  3.000
 DOT  N9    C1B  C2B   112.47  3.000
 DOT  H1'   C1B  O4'   108.42  3.000
 DOT  N9    C1B  O4'   108.74  3.000
 DOT  C2B   C1B  O4'   107.14  3.000
 DOT  C4    N9   C8    106.23  3.000
 DOT  C4    N9   C1B   127.09  3.000
 DOT  C8    N9   C1B   126.64  3.000
 DOT  H8    C8   N7    124.56  3.000
 DOT  H8    C8   N9    122.06  3.000
 DOT  N7    C8   N9    113.38  3.000
 DOT  C5    N7   C8    104.35  3.000
 DOT  C4    C5   C6    116.53  3.000
 DOT  C4    C5   N7    110.87  3.000
 DOT  C6    C5   N7    132.57  3.000
 DOT  N1    C6   N6    119.48  3.000
 DOT  N1    C6   C5    118.00  3.000
 DOT  N6    C6   C5    122.51  3.000
 DOT  HN62  N6   HN61  118.06  3.000
 DOT  HN62  N6   C6    120.11  3.000
 DOT  HN61  N6   C6    120.77  3.000
 DOT  C2    N1   C6    119.00  3.000
 DOT  H2    C2   N3    116.11  3.000
 DOT  H2    C2   N1    115.36  3.000
 DOT  N3    C2   N1    128.53  3.000
 DOT  C4    N3   C2    111.80  3.000
 DOT  N3    C4   C5    126.12  3.000
 DOT  N3    C4   N9    128.72  3.000
 DOT  C5    C4   N9    105.16  3.000
 DOT  C1'   C'   O1'   125.34  3.000
 DOT  C1'   C'   O3'   113.00  3.000
 DOT  O1'   C'   O3'   121.66  3.000
 DOT  C6'   C1'  C2'   119.27  3.000
 DOT  C6'   C1'  C'    120.28  3.000
 DOT  C2'   C1'  C'    120.45  3.000
 DOT  C3'   C2'  N2'   118.38  3.000
 DOT  C3'   C2'  C1'   117.72  3.000
 DOT  N2'   C2'  C1'   123.88  3.000
 DOT  H2D   N2'  H2B   117.15  3.000
 DOT  H2D   N2'  C2'   118.46  3.000
 DOT  H2B   N2'  C2'   119.97  3.000
 DOT  H3'   C3'  C4'   119.91  3.000
 DOT  H3'   C3'  C2'   118.58  3.000
 DOT  C4'   C3'  C2'   121.51  3.000
 DOT  H4'   C4'  C5'   119.99  3.000
 DOT  H4'   C4'  C3'   119.17  3.000
 DOT  C5'   C4'  C3'   120.84  3.000
 DOT  H5'   C5'  C6'   120.48  3.000
 DOT  H5'   C5'  C4'   120.80  3.000
 DOT  C6'   C5'  C4'   118.71  3.000
 DOT  H6'   C6'  C5'   118.73  3.000
 DOT  H6'   C6'  C1'   119.32  3.000
 DOT  C5'   C6'  C1'   121.95  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
 DOT  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 DOT  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 DOT  CONST_03  C6    C5   C4   N9    180.00   0.0  0
 DOT  CONST_04  C2    N3   C4   N9    180.00   0.0  0
 DOT  CONST_05  C5    C4   N9   C8      0.00   0.0  0
 DOT  CONST_06  N3    C4   N9   C8    180.00   0.0  0
 DOT  CONST_07  C6    C5   N7   C8    180.00   0.0  0
 DOT  CONST_08  C4    C5   N7   C8      0.00   0.0  0
 DOT  CONST_09  C4    N9   C8   N7      0.00   0.0  0
 DOT  CONST_10  N1    C6   C5   N7    180.00   0.0  0
 DOT  CONST_11  N3    C4   C5   N7    180.00   0.0  0
 DOT  CONST_12  C2    N1   C6   C5      0.00   0.0  0
 DOT  CONST_13  C2    N3   C4   C5      0.00   0.0  0
 DOT  CONST_14  N3    C4   C5   C6      0.00   0.0  0
 DOT  CONST_15  N3    C2   N1   C6      0.00   0.0  0
 DOT  CONST_16  C4    C5   C6   N1      0.00   0.0  0
 DOT  CONST_17  C4    N3   C2   N1      0.00   0.0  0
 DOT  CONST_18  C4'   C3'  C2'  C1'     0.00   0.0  0
 DOT  CONST_19  C4'   C5'  C6'  C1'     0.00   0.0  0
 DOT  CONST_20  C5'   C6'  C1'  C2'     0.00   0.0  0
 DOT  CONST_21  C5'   C4'  C3'  C2'     0.00   0.0  0
 DOT  CONST_22  C6'   C1'  C2'  C3'     0.00   0.0  0
 DOT  CONST_23  C6'   C5'  C4'  C3'     0.00   0.0  0
 DOT  CONST_24  N7    C8   N9   C1B   180.00   0.0  0
 DOT  CONST_25  C5    C4   N9   C1B   180.00   0.0  0
 DOT  CONST_26  N3    C4   N9   C1B     0.00   0.0  0
 DOT  CONST_27  N6    C6   C5   N7      0.00   0.0  0
 DOT  CONST_28  C4    C5   C6   N6    180.00   0.0  0
 DOT  CONST_29  C2    N1   C6   N6    180.00   0.0  0
 DOT  CONST_30  C3'   C2'  C1'  C'    180.00   0.0  0
 DOT  CONST_31  C5'   C6'  C1'  C'    180.00   0.0  0
 DOT  CONST_32  C6'   C1'  C2'  N2'   180.00   0.0  0
 DOT  CONST_33  C4'   C3'  C2'  N2'   180.00   0.0  0
 DOT  CONST_34  H8    C8   N9   C1B     0.00   0.0  0
 DOT  CONST_35  H2    C2   N1   C6    180.00   0.0  0
 DOT  CONST_36  H3'   C3'  C2'  C1'   180.00   0.0  0
 DOT  CONST_37  H5'   C5'  C6'  C1'   180.00   0.0  0
 DOT  CONST_38  H6'   C6'  C1'  C2'   180.00   0.0  0
 DOT  CONST_39  H4'   C4'  C3'  C2'   180.00   0.0  0
 DOT  CONST_40  HN61  N6   C6   C5      0.00   0.0  0
 DOT  CONST_41  HN62  N6   C6   C5    180.00   0.0  0
 DOT  CONST_42  H2B   N2'  C2'  C1'     0.00   0.0  0
 DOT  CONST_43  H2D   N2'  C2'  C1'   180.00   0.0  0
 DOT  Var_01    C1'   C'   O3'  C3B  -179.41  30.0  3
 DOT  Var_02    C2'   C1'  C'   O3'  -179.20  30.0  2
 DOT  Var_03    C4B   C5B  O5'  PA    171.85  30.0  3
 DOT  Var_04    O1B   PB   O3B  PG   -152.53  30.0  2
 DOT  Var_05    O1A   PA   O3A  PB     -9.05  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
 DOT  chir_03  C4B  C5B  O4'  C3B  negativ
 DOT  chir_04  C3B  O3'  C2B  C4B  negativ
 DOT  chir_05  C1B  O4'  N9   C2B  negativ
 DOT  chir_06  PB   O2B  O3B  O3A  both
 DOT  chir_07  PA   O2A  O3A  O5'  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
 DOT  plan-1  C'    0.020
 DOT  plan-1  C1'   0.020
 DOT  plan-1  C2'   0.020
 DOT  plan-1  N2'   0.020
 DOT  plan-1  C3'   0.020
 DOT  plan-1  C4'   0.020
 DOT  plan-1  C5'   0.020
 DOT  plan-1  C6'   0.020
 DOT  plan-1  H3'   0.020
 DOT  plan-1  H4'   0.020
 DOT  plan-1  H5'   0.020
 DOT  plan-1  H6'   0.020
 DOT  plan-2  C1B   0.020
 DOT  plan-2  N9    0.020
 DOT  plan-2  C8    0.020
 DOT  plan-2  N7    0.020
 DOT  plan-2  C5    0.020
 DOT  plan-2  C6    0.020
 DOT  plan-2  N6    0.020
 DOT  plan-2  N1    0.020
 DOT  plan-2  C2    0.020
 DOT  plan-2  N3    0.020
 DOT  plan-2  C4    0.020
 DOT  plan-2  H8    0.020
 DOT  plan-2  H2    0.020
 DOT  plan-3  C6    0.020
 DOT  plan-3  N6    0.020
 DOT  plan-3  HN61  0.020
 DOT  plan-3  HN62  0.020
 DOT  plan-4  C2'   0.020
 DOT  plan-4  N2'   0.020
 DOT  plan-4  H2B   0.020
 DOT  plan-4  H2D   0.020
 DOT  plan-5  O3'   0.020
 DOT  plan-5  C'    0.020
 DOT  plan-5  O1'   0.020
 DOT  plan-5  C1'   0.020

