# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 06:11:15 2021
#   Inital geometry file: a 123 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC2=C(N[C@H]3N2[C@@H]4O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@]3(O)[C@H]4O)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
 2X3  2X3  'None                     '  ligand  48  32  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2X3
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
 2X3  C2   C  CR6   0   0.686   -3.6364  114.8769  127.2309
 2X3  C4   C  CR56  0   0.432   -5.7117  115.3051  126.5483
 2X3  C5   C  CR56  0  -0.001   -5.6260  116.6497  126.7610
 2X3  C6   C  CR6   0   0.496   -4.4257  117.1984  127.2635
 2X3  C8   C  CR15  0   0.022   -7.7076  116.2621  125.9272
 2X3  O6   O  O     0  -0.495   -4.1781  118.3670  127.5384
 2X3  OBD  O  OH1   0  -0.764  -15.1408  112.9195  121.7412
 2X3  PBC  P  P     0   1.464  -14.9163  113.6638  120.3795
 2X3  OBE  O  O     0  -0.677  -14.3684  112.9306  119.2288
 2X3  OBF  O  OH1   0  -0.724  -16.3273  114.3598  120.1942
 2X3  OAZ  O  O2    0  -0.699  -13.8718  114.8882  120.7252
 2X3  PAY  P  P     0   1.511  -13.7368  116.0386  121.8159
 2X3  OBA  O  O     0  -0.641  -13.4180  117.3634  121.2816
 2X3  OBB  O  OH1   0  -0.733  -15.0372  115.8327  122.6890
 2X3  OAV  O  O2    0  -0.689  -12.5085  115.5009  122.7351
 2X3  PAU  P  P     0   1.530  -12.4100  114.2209  123.7065
 2X3  OAW  O  O     0  -0.697  -13.0002  112.9759  123.1587
 2X3  OAX  O  OH1   0  -0.720  -13.0662  114.8155  125.0172
 2X3  CAR  C  CH2   0  -0.218  -10.0148  115.0856  124.4781
 2X3  CAP  C  CH1   0   0.011   -9.7534  114.8183  125.9414
 2X3  OAO  O  O2    0  -0.485   -8.9077  113.6844  126.1284
 2X3  CAN  C  CH1   0   0.075   -7.8228  114.1286  126.9080
 2X3  N9   N  NR5   0  -0.480   -6.9769  114.9767  126.0691
 2X3  N3   N  N     0  -0.503   -4.7705  114.3868  126.7822
 2X3  N2   N  NH2   0  -0.830   -2.5991  114.0582  127.4555
 2X3  N1   N  NR16  0  -0.715   -3.4515  116.2041  127.4419
 2X3  N7   N  NR15  0  -0.661   -6.8664  117.2909  126.5420
 2X3  CAL  C  CT    0   0.127   -9.0076  115.9551  126.6849
 2X3  OAS  O  OH1   0  -0.653   -9.7461  117.0996  126.9054
 2X3  CAM  C  CH1   0   0.006   -8.4488  115.1372  127.8672
 2X3  OAQ  O  OH1   0  -0.661   -9.4117  114.5579  128.6929
 2X3  H2   H  HCR5  0   0.278   -7.8864  116.5087  124.8759
 2X3  H3   H  HOH1  0   0.505  -14.3303  112.8216  122.3207
 2X3  H4   H  HOH1  0   0.507  -16.5479  114.5694  119.2761
 2X3  H5   H  HOH1  0   0.519  -15.2650  116.5637  123.2829
 2X3  H6   H  HOH1  0   0.517  -13.3353  114.1611  125.6788
 2X3  H7   H  HCH2  0   0.279   -9.1020  115.0538  123.8857
 2X3  H8   H  HCH2  0   0.266  -10.4621  116.0748  124.3561
 2X3  H9   H  HCH1  0   0.260  -10.7116  114.6391  126.4456
 2X3  H10  H  HCH1  0   0.287   -7.2770  113.2824  127.3206
 2X3  H11  H  HNH2  0   0.412   -2.7743  113.0679  127.4373
 2X3  H12  H  HNH2  0   0.415   -1.8003  114.3633  127.9851
 2X3  H13  H  HNR5  0   0.377   -6.7942  118.1028  125.9442
 2X3  H15  H  HOH1  0   0.459  -10.5225  116.8849  127.4350
 2X3  H16  H  HCH1  0   0.271   -7.6954  115.6924  128.4374
 2X3  H17  H  HOH1  0   0.464   -9.6405  115.1859  129.3848
 2X3  H18  H  HNR6  0   0.425   -2.5537  116.5243  127.7820
 2X3  OAT  O  O2    0  -0.556  -10.8605  114.0569  123.9223

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
 2X3  C2   N2   single  1.340  0.020  1.340
 2X3  C4   N3   single  1.336  0.020  1.336
 2X3  C5   C4   double  1.364  0.020  1.364
 2X3  C5   C6   single  1.412  0.020  1.412
 2X3  C6   N1   single  1.403  0.020  1.403
 2X3  C8   N7   single  1.464  0.020  1.464
 2X3  C8   N9   single  1.485  0.020  1.485
 2X3  C8   CAL  single  1.536  0.020  1.536
 2X3  C8   H2   single  0.970  0.020  1.090
 2X3  O6   C6   double  1.226  0.020  1.226
 2X3  OBD  H3   single  0.850  0.020  0.980
 2X3  PBC  OBD  single  1.568  0.020  1.568
 2X3  PBC  OBF  single  1.584  0.020  1.584
 2X3  PBC  OAZ  single  1.646  0.020  1.646
 2X3  OBE  PBC  double  1.470  0.020  1.470
 2X3  OBF  H4   single  0.850  0.020  0.980
 2X3  OAZ  PAY  single  1.591  0.020  1.591
 2X3  PAY  OBA  double  1.464  0.020  1.464
 2X3  PAY  OAV  single  1.626  0.020  1.626
 2X3  PAY  OBB  single  1.580  0.020  1.580
 2X3  OBB  H5   single  0.850  0.020  0.980
 2X3  PAU  OAV  single  1.610  0.020  1.610
 2X3  PAU  OAT  single  1.573  0.020  1.573
 2X3  PAU  OAX  single  1.582  0.020  1.582
 2X3  OAW  PAU  double  1.483  0.020  1.483
 2X3  OAX  H6   single  0.850  0.020  0.980
 2X3  OAT  CAR  single  1.443  0.020  1.443
 2X3  CAR  CAP  single  1.510  0.020  1.510
 2X3  CAR  H7   single  0.970  0.020  1.090
 2X3  CAR  H8   single  0.970  0.020  1.090
 2X3  CAP  OAO  single  1.427  0.020  1.427
 2X3  CAP  CAL  single  1.550  0.020  1.550
 2X3  CAP  H9   single  0.970  0.020  1.090
 2X3  OAO  CAN  single  1.408  0.020  1.408
 2X3  CAN  CAM  single  1.526  0.020  1.526
 2X3  CAN  H10  single  0.970  0.020  1.090
 2X3  N9   C4   single  1.392  0.020  1.392
 2X3  N9   CAN  single  1.462  0.020  1.462
 2X3  N3   C2   double  1.314  0.020  1.314
 2X3  N2   H11  single  0.890  0.020  1.040
 2X3  N2   H12  single  0.890  0.020  1.040
 2X3  N1   C2   single  1.357  0.020  1.357
 2X3  N7   C5   single  1.413  0.020  1.413
 2X3  N7   H13  single  0.890  0.020  1.040
 2X3  CAL  OAS  single  1.380  0.020  1.380
 2X3  CAL  CAM  single  1.542  0.020  1.542
 2X3  OAS  H15  single  0.850  0.020  0.980
 2X3  CAM  OAQ  single  1.394  0.020  1.394
 2X3  CAM  H16  single  0.970  0.020  1.090
 2X3  OAQ  H17  single  0.850  0.020  0.980
 2X3  N1   H18  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
 2X3  N1   C2   N2   117.78  3.000
 2X3  N1   C2   N3   122.38  3.000
 2X3  N2   C2   N3   119.81  3.000
 2X3  N3   C4   N9   122.58  3.000
 2X3  N9   C4   C5   110.08  3.000
 2X3  N3   C4   C5   127.31  3.000
 2X3  N7   C5   C6   128.66  3.000
 2X3  N7   C5   C4   111.58  3.000
 2X3  C6   C5   C4   119.47  3.000
 2X3  N1   C6   O6   120.44  3.000
 2X3  O6   C6   C5   128.46  3.000
 2X3  N1   C6   C5   111.09  3.000
 2X3  H2   C8   CAL  112.37  3.000
 2X3  H2   C8   N7   109.80  3.000
 2X3  CAL  C8   N7   114.81  3.000
 2X3  H2   C8   N9   111.54  3.000
 2X3  CAL  C8   N9   101.32  3.000
 2X3  N7   C8   N9   106.58  3.000
 2X3  H3   OBD  PBC  115.66  3.000
 2X3  OAZ  PBC  OBF  105.25  3.000
 2X3  OAZ  PBC  OBE  107.39  3.000
 2X3  OBF  PBC  OBE  117.35  3.000
 2X3  OBE  PBC  OBD  119.75  3.000
 2X3  OAZ  PBC  OBD  105.16  3.000
 2X3  OBF  PBC  OBD  100.52  3.000
 2X3  H4   OBF  PBC  114.16  3.000
 2X3  PAY  OAZ  PBC  137.36  3.000
 2X3  OAV  PAY  OBB  105.44  3.000
 2X3  OBB  PAY  OBA  119.93  3.000
 2X3  OAV  PAY  OBA  109.95  3.000
 2X3  OBB  PAY  OAZ  102.41  3.000
 2X3  OAV  PAY  OAZ  102.28  3.000
 2X3  OBA  PAY  OAZ  115.01  3.000
 2X3  H5   OBB  PAY  115.72  3.000
 2X3  PAU  OAV  PAY  130.57  3.000
 2X3  OAT  PAU  OAX  109.52  3.000
 2X3  OAX  PAU  OAW  117.17  3.000
 2X3  OAT  PAU  OAW  110.80  3.000
 2X3  OAW  PAU  OAV  114.86  3.000
 2X3  OAX  PAU  OAV  100.12  3.000
 2X3  OAT  PAU  OAV  103.05  3.000
 2X3  H6   OAX  PAU  115.30  3.000
 2X3  H8   CAR  H7   108.00  3.000
 2X3  H8   CAR  CAP  109.84  3.000
 2X3  H7   CAR  CAP  112.14  3.000
 2X3  H8   CAR  OAT  111.25  3.000
 2X3  H7   CAR  OAT  105.13  3.000
 2X3  CAP  CAR  OAT  110.39  3.000
 2X3  H9   CAP  CAL  108.64  3.000
 2X3  H9   CAP  OAO  109.12  3.000
 2X3  CAL  CAP  OAO  103.58  3.000
 2X3  H9   CAP  CAR  108.84  3.000
 2X3  CAL  CAP  CAR  114.73  3.000
 2X3  OAO  CAP  CAR  111.73  3.000
 2X3  CAN  OAO  CAP  106.18  3.000
 2X3  H10  CAN  CAM  118.77  3.000
 2X3  H10  CAN  N9   112.23  3.000
 2X3  CAM  CAN  N9   102.39  3.000
 2X3  N9   CAN  OAO  108.12  3.000
 2X3  H10  CAN  OAO  110.56  3.000
 2X3  CAM  CAN  OAO  103.91  3.000
 2X3  CAN  N9   C8   105.79  3.000
 2X3  CAN  N9   C4   117.71  3.000
 2X3  C8   N9   C4   106.01  3.000
 2X3  C4   N3   C2   114.30  3.000
 2X3  H12  N2   H11  116.52  3.000
 2X3  H12  N2   C2   121.17  3.000
 2X3  H11  N2   C2   117.62  3.000
 2X3  H18  N1   C6   115.75  3.000
 2X3  H18  N1   C2   118.86  3.000
 2X3  C6   N1   C2   125.37  3.000
 2X3  H13  N7   C8   110.92  3.000
 2X3  H13  N7   C5   113.17  3.000
 2X3  C8   N7   C5   104.51  3.000
 2X3  CAM  CAL  OAS  120.75  3.000
 2X3  CAM  CAL  CAP   98.81  3.000
 2X3  OAS  CAL  CAP  115.32  3.000
 2X3  CAM  CAL  C8   100.23  3.000
 2X3  OAS  CAL  C8   111.48  3.000
 2X3  CAP  CAL  C8   108.50  3.000
 2X3  H15  OAS  CAL  109.52  3.000
 2X3  H16  CAM  OAQ  112.15  3.000
 2X3  H16  CAM  CAL  112.28  3.000
 2X3  OAQ  CAM  CAL  115.08  3.000
 2X3  H16  CAM  CAN  112.33  3.000
 2X3  OAQ  CAM  CAN  112.39  3.000
 2X3  CAL  CAM  CAN   90.99  3.000
 2X3  H17  OAQ  CAM  108.60  3.000
 2X3  CAR  OAT  PAU  123.77  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
 2X3  CONST_01  C5   C4   N3   C2      0.00   0.0  0
 2X3  CONST_02  N9   C4   N3   C2    180.00   0.0  0
 2X3  CONST_03  C5   C6   N1   C2      0.00   0.0  0
 2X3  CONST_04  N1   C2   N3   C4      0.00   0.0  0
 2X3  CONST_05  C8   N9   C4   C5      0.00   0.0  0
 2X3  CONST_07  N3   C2   N1   C6      0.00   0.0  0
 2X3  CONST_08  N3   C4   N9   C8    180.00   0.0  0
 2X3  CONST_10  O6   C6   N1   C2    180.00   0.0  0
 2X3  CONST_11  N2   C2   N3   C4    180.00   0.0  0
 2X3  CONST_12  N2   C2   N1   C6    180.00   0.0  0
 2X3  CONST_13  H18  N1   C6   C5    180.00   0.0  0
 2X3  CONST_14  H11  N2   C2   N3      0.00   0.0  0
 2X3  CONST_15  H12  N2   C2   N3    180.00   0.0  0
 2X3  Var_01    CAP  CAR  OAT  PAU    99.46  30.0  3
 2X3  Var_02    OBA  PAY  OAZ  PBC  -133.66  30.0  3
 2X3  Var_03    OAT  PAU  OAV  PAY   163.46  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
 2X3  chir_01  C8   N7   N9   CAL  negativ
 2X3  chir_04  CAP  OAO  CAR  CAL  positiv
 2X3  chir_05  CAN  OAO  N9   CAM  negativ
 2X3  chir_06  CAL  CAM  CAP  C8   positiv
 2X3  chir_07  CAM  OAQ  CAN  CAL  negativ
 2X3  chir_08  PAY  OBA  OAV  OBB  both
 2X3  chir_09  PAU  OAT  OAX  OAW  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
 2X3  plan-1  C2   0.020
 2X3  plan-1  C4   0.020
 2X3  plan-1  C5   0.020
 2X3  plan-1  C6   0.020
 2X3  plan-1  C8   0.020
 2X3  plan-1  O6   0.020
 2X3  plan-1  CAN  0.020
 2X3  plan-1  N9   0.020
 2X3  plan-1  N3   0.020
 2X3  plan-1  N2   0.020
 2X3  plan-1  N1   0.020
 2X3  plan-1  N7   0.020
 2X3  plan-1  H11  0.020
 2X3  plan-1  H12  0.020
 2X3  plan-1  H13  0.020
 2X3  plan-1  H18  0.020

