# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun  4 11:59:41 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 3-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]-4-oxidanyl-cyclobut-3-ene-1,2-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[n+]1cn([C@@H]2O[C@H](CNC3=C(O)C(=O)C3=O)[C@@H](O)[C@H]2O)c4N=C(N)NC(=O)c14
#
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
 5PQ  5PQ  3-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]-4-oxidanyl-cyclobut-3-ene-1,2-dione  ligand  45  28  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_5PQ
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
 5PQ  C4   C  CR56  0   0.525   2.5780   0.1669  -0.1427
 5PQ  C5   C  CR56  0   0.081   2.7193   1.4455   0.3401
 5PQ  C6   C  CR6   0   0.565   3.9174   2.1771   0.0834
 5PQ  C8   C  CR15  0   0.262   0.7585   0.7296   0.9568
 5PQ  N1   N  NR16  0  -0.733   4.7917   1.3946  -0.6713
 5PQ  N3   N  N     0  -0.508   3.4471  -0.5328  -0.8591
 5PQ  O6   O  O     0  -0.439   4.2023   3.3041   0.4320
 5PQ  C2   C  CR6   0   0.733   4.5636   0.1209  -1.1121
 5PQ  N7   N  NR5   1  -0.473   1.5620   1.7635   1.0180
 5PQ  CAA  C  CH3   0  -0.524   1.2651   3.0232   1.6820
 5PQ  N9   N  NR5   0  -0.549   1.3374  -0.2615   0.2630
 5PQ  CAZ  C  CH1   0   0.208   0.7323  -1.5429  -0.0390
 5PQ  OAN  O  O2    0  -0.486  -0.4697  -1.3235  -0.7128
 5PQ  CAX  C  CH1   0  -0.037   0.3626  -2.3547   1.1972
 5PQ  OAH  O  OH1   0  -0.648   1.4912  -2.9865   1.7106
 5PQ  CAW  C  CH1   0  -0.046  -0.7015  -3.2834   0.6050
 5PQ  OAG  O  OH1   0  -0.663  -0.1074  -4.3185  -0.1314
 5PQ  CAY  C  CH1   0  -0.004  -1.4160  -2.3445  -0.3650
 5PQ  CAJ  C  CH2   0  -0.318  -2.6653  -1.7117   0.2288
 5PQ  NAL  N  NH1   0  -0.634  -3.3098  -0.8240  -0.7138
 5PQ  CAQ  C  C     0   0.245  -3.3258   0.4898  -0.6280
 5PQ  CAT  C  C     0   0.258  -2.8562   1.4832   0.3574
 5PQ  OAE  O  O     0  -0.424  -2.2700   1.4415   1.4153
 5PQ  CAS  C  C     0   0.230  -3.4247   2.5666  -0.5280
 5PQ  OAD  O  O     0  -0.425  -3.4962   3.7740  -0.4964
 5PQ  CAP  C  C     0   0.181  -3.8465   1.5060  -1.4252
 5PQ  OAF  O  OH1   0  -0.557  -4.4771   1.4372  -2.5705
 5PQ  H1   H  HCR5  0   0.365  -0.2279   0.6937   1.3920
 5PQ  H2   H  HNR6  0   0.440   5.6743   1.8335  -0.9056
 5PQ  H3   H  HNH2  0   0.427   6.3829  -0.0012  -2.0564
 5PQ  H4   H  HNH2  0   0.428   5.3716  -1.3915  -2.1748
 5PQ  H5   H  HCH3  0   0.289   1.3095   3.8326   0.9600
 5PQ  H6   H  HCH3  0   0.278   0.2666   2.9653   2.1029
 5PQ  H7   H  HCH3  0   0.289   1.9859   3.1945   2.4754
 5PQ  H8   H  HCH1  0   0.284   1.4653  -2.0775  -0.6519
 5PQ  H9   H  HCH1  0   0.256  -0.1144  -1.7003   1.9398
 5PQ  H10  H  HOH1  0   0.474   1.3187  -3.2473   2.6212
 5PQ  H11  H  HCH1  0   0.265  -1.3811  -3.6693   1.3758
 5PQ  H12  H  HOH1  0   0.454   0.5694  -4.7295   0.4195
 5PQ  H13  H  HCH1  0   0.276  -1.6949  -2.8862  -1.2741
 5PQ  H14  H  HCH2  0   0.286  -3.3632  -2.5079   0.4935
 5PQ  H15  H  HCH2  0   0.268  -2.4416  -1.1626   1.1427
 5PQ  H16  H  HNH1  0   0.419  -3.7365  -1.2511  -1.5234
 5PQ  H17  H  HOH1  0   0.503  -4.7138   2.3184  -2.8910
 5PQ  N2   N  NH2   0  -0.821   5.5219  -0.4629  -1.8182

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
 5PQ  OAE  CAT  double    1.210  0.020  1.210
 5PQ  NAL  CAQ  single    1.317  0.020  1.317
 5PQ  NAL  CAJ  single    1.446  0.020  1.446
 5PQ  N2   C2   single    1.326  0.020  1.326
 5PQ  N1   C2   single    1.367  0.020  1.367
 5PQ  N1   C6   single    1.395  0.020  1.395
 5PQ  O6   C6   double    1.214  0.020  1.214
 5PQ  C2   N3   double    1.318  0.020  1.318
 5PQ  CAT  CAQ  single    1.476  0.020  1.476
 5PQ  CAT  CAS  single    1.510  0.020  1.510
 5PQ  C6   C5   single    1.427  0.020  1.427
 5PQ  OAN  CAY  single    1.435  0.020  1.435
 5PQ  OAN  CAZ  single    1.395  0.020  1.395
 5PQ  N3   C4   single    1.326  0.020  1.326
 5PQ  CAQ  CAP  double    1.393  0.020  1.393
 5PQ  C5   C4   aromatic  1.374  0.020  1.374
 5PQ  C5   N7   aromatic  1.378  0.020  1.378
 5PQ  CAJ  CAY  single    1.521  0.020  1.521
 5PQ  C4   N9   aromatic  1.374  0.020  1.374
 5PQ  CAA  N7   single    1.455  0.020  1.455
 5PQ  N7   C8   aromatic  1.311  0.020  1.311
 5PQ  N9   C8   aromatic  1.341  0.020  1.341
 5PQ  N9   CAZ  single    1.449  0.020  1.449
 5PQ  CAY  CAW  single    1.527  0.020  1.527
 5PQ  CAZ  CAX  single    1.524  0.020  1.524
 5PQ  CAS  CAP  single    1.452  0.020  1.452
 5PQ  CAS  OAD  double    1.210  0.020  1.210
 5PQ  CAP  OAF  single    1.309  0.020  1.309
 5PQ  CAW  CAX  single    1.532  0.020  1.532
 5PQ  CAW  OAG  single    1.402  0.020  1.402
 5PQ  CAX  OAH  single    1.392  0.020  1.392
 5PQ  C8   H1   single    0.930  0.020  1.080
 5PQ  N1   H2   single    0.860  0.020  1.020
 5PQ  N2   H3   single    0.860  0.020  1.020
 5PQ  N2   H4   single    0.860  0.020  1.020
 5PQ  CAA  H5   single    0.970  0.020  1.090
 5PQ  CAA  H6   single    0.970  0.020  1.090
 5PQ  CAA  H7   single    0.970  0.020  1.090
 5PQ  CAZ  H8   single    0.970  0.020  1.090
 5PQ  CAX  H9   single    0.970  0.020  1.090
 5PQ  OAH  H10  single    0.850  0.020  0.980
 5PQ  CAW  H11  single    0.970  0.020  1.090
 5PQ  OAG  H12  single    0.850  0.020  0.980
 5PQ  CAY  H13  single    0.970  0.020  1.090
 5PQ  CAJ  H14  single    0.970  0.020  1.090
 5PQ  CAJ  H15  single    0.970  0.020  1.090
 5PQ  NAL  H16  single    0.860  0.020  1.020
 5PQ  OAF  H17  single    0.850  0.020  0.980

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
 5PQ  N9   C4   N3   125.94  3.000
 5PQ  N9   C4   C5   106.22  3.000
 5PQ  N3   C4   C5   127.84  3.000
 5PQ  N7   C5   C6   132.47  3.000
 5PQ  N7   C5   C4   107.52  3.000
 5PQ  C6   C5   C4   120.01  3.000
 5PQ  O6   C6   N1   121.95  3.000
 5PQ  O6   C6   C5   128.42  3.000
 5PQ  N1   C6   C5   109.63  3.000
 5PQ  H1   C8   N9   125.37  3.000
 5PQ  H1   C8   N7   124.60  3.000
 5PQ  N9   C8   N7   110.02  3.000
 5PQ  H2   N1   C2   118.32  3.000
 5PQ  H2   N1   C6   115.34  3.000
 5PQ  C2   N1   C6   126.33  3.000
 5PQ  C2   N3   C4   113.40  3.000
 5PQ  N3   C2   N2   119.74  3.000
 5PQ  N3   C2   N1   122.79  3.000
 5PQ  N2   C2   N1   117.48  3.000
 5PQ  CAA  N7   C8   125.40  3.000
 5PQ  C8   N7   C5   108.05  3.000
 5PQ  CAA  N7   C5   126.55  3.000
 5PQ  H7   CAA  H6   109.63  3.000
 5PQ  H7   CAA  H5   109.96  3.000
 5PQ  H6   CAA  H5   109.60  3.000
 5PQ  H7   CAA  N7   109.56  3.000
 5PQ  H6   CAA  N7   108.58  3.000
 5PQ  H5   CAA  N7   109.50  3.000
 5PQ  CAZ  N9   C8   125.53  3.000
 5PQ  CAZ  N9   C4   126.25  3.000
 5PQ  C8   N9   C4   108.19  3.000
 5PQ  H8   CAZ  CAX  110.87  3.000
 5PQ  H8   CAZ  OAN  112.53  3.000
 5PQ  CAX  CAZ  OAN  105.45  3.000
 5PQ  H8   CAZ  N9   105.60  3.000
 5PQ  CAX  CAZ  N9   113.78  3.000
 5PQ  OAN  CAZ  N9   108.75  3.000
 5PQ  CAY  OAN  CAZ  109.83  3.000
 5PQ  H9   CAX  CAW  108.72  3.000
 5PQ  H9   CAX  OAH  111.91  3.000
 5PQ  CAW  CAX  OAH  115.52  3.000
 5PQ  H9   CAX  CAZ  109.65  3.000
 5PQ  OAH  CAX  CAZ  110.13  3.000
 5PQ  CAW  CAX  CAZ  100.24  3.000
 5PQ  H10  OAH  CAX  109.06  3.000
 5PQ  H11  CAW  CAY  111.86  3.000
 5PQ  H11  CAW  OAG  111.81  3.000
 5PQ  CAY  CAW  OAG  108.57  3.000
 5PQ  H11  CAW  CAX  111.83  3.000
 5PQ  OAG  CAW  CAX  110.87  3.000
 5PQ  CAY  CAW  CAX  101.41  3.000
 5PQ  H12  OAG  CAW  108.17  3.000
 5PQ  H13  CAY  CAJ  108.71  3.000
 5PQ  H13  CAY  CAW  110.03  3.000
 5PQ  CAJ  CAY  CAW  113.08  3.000
 5PQ  H13  CAY  OAN  108.60  3.000
 5PQ  CAW  CAY  OAN  106.43  3.000
 5PQ  CAJ  CAY  OAN  109.89  3.000
 5PQ  H15  CAJ  H14  107.19  3.000
 5PQ  H15  CAJ  NAL  109.20  3.000
 5PQ  H14  CAJ  NAL  108.71  3.000
 5PQ  H15  CAJ  CAY  111.63  3.000
 5PQ  H14  CAJ  CAY  108.45  3.000
 5PQ  NAL  CAJ  CAY  111.52  3.000
 5PQ  H16  NAL  CAQ  117.98  3.000
 5PQ  H16  NAL  CAJ  116.82  3.000
 5PQ  CAQ  NAL  CAJ  125.12  3.000
 5PQ  CAP  CAQ  CAT   90.57  3.000
 5PQ  CAP  CAQ  NAL  134.05  3.000
 5PQ  CAT  CAQ  NAL  135.34  3.000
 5PQ  CAS  CAT  OAE  136.02  3.000
 5PQ  CAS  CAT  CAQ   88.38  3.000
 5PQ  OAE  CAT  CAQ  135.61  3.000
 5PQ  CAP  CAS  OAD  136.72  3.000
 5PQ  OAD  CAS  CAT  136.29  3.000
 5PQ  CAP  CAS  CAT   87.00  3.000
 5PQ  OAF  CAP  CAS  135.96  3.000
 5PQ  OAF  CAP  CAQ  129.98  3.000
 5PQ  CAS  CAP  CAQ   94.06  3.000
 5PQ  H17  OAF  CAP  111.10  3.000
 5PQ  H4   N2   H3   117.89  3.000
 5PQ  H4   N2   C2   119.16  3.000
 5PQ  H3   N2   C2   122.88  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
 5PQ  CONST_01  C8   N7   C5   C4      0.00   0.0  0
 5PQ  CONST_02  N7   C8   N9   C4      0.00   0.0  0
 5PQ  CONST_03  C8   N9   C4   C5      0.00   0.0  0
 5PQ  CONST_04  N9   C8   N7   C5      0.00   0.0  0
 5PQ  CONST_05  N9   C4   C5   N7      0.00   0.0  0
 5PQ  CONST_06  CAZ  N9   C4   C5    180.00   0.0  0
 5PQ  CONST_07  CAZ  N9   C4   N3      0.00   0.0  0
 5PQ  CONST_08  CAZ  N9   C8   N7    180.00   0.0  0
 5PQ  CONST_09  N1   C2   N3   C4      0.00   0.0  0
 5PQ  CONST_10  C2   N1   C6   C5      0.00   0.0  0
 5PQ  CONST_11  N3   C2   N1   C6      0.00   0.0  0
 5PQ  CONST_12  CAA  N7   C5   C4    180.00   0.0  0
 5PQ  CONST_13  CAA  N7   C5   C6      0.00   0.0  0
 5PQ  CONST_14  N9   C8   N7   CAA   180.00   0.0  0
 5PQ  CONST_15  N2   C2   N3   C4    180.00   0.0  0
 5PQ  CONST_16  N2   C2   N1   C6    180.00   0.0  0
 5PQ  CONST_17  C2   N1   C6   O6    180.00   0.0  0
 5PQ  CONST_18  H1   C8   N9   C4    180.00   0.0  0
 5PQ  CONST_19  H2   N1   C6   C5    180.00   0.0  0
 5PQ  CONST_20  H3   N2   C2   N1      0.00   0.0  0
 5PQ  CONST_21  H4   N2   C2   N1    180.00   0.0  0
 5PQ  Var_01    CAP  CAS  CAT  CAQ     0.20  30.0  1
 5PQ  Var_02    CAQ  NAL  CAJ  CAY  -108.34  30.0  1
 5PQ  Var_03    CAT  CAQ  NAL  CAJ    -4.73  30.0  2
 5PQ  Var_04    H5   CAA  N7   C5     59.16  30.0  2

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
 5PQ  chir_01  CAZ  OAN  N9   CAX  negativ
 5PQ  chir_02  CAX  OAH  CAZ  CAW  negativ
 5PQ  chir_03  CAW  OAG  CAX  CAY  negativ
 5PQ  chir_04  CAY  OAN  CAW  CAJ  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
 5PQ  plan-1  CAQ  0.020
 5PQ  plan-1  CAT  0.020
 5PQ  plan-1  OAE  0.020
 5PQ  plan-1  CAS  0.020
 5PQ  plan-2  C4   0.020
 5PQ  plan-2  C5   0.020
 5PQ  plan-2  C6   0.020
 5PQ  plan-2  C8   0.020
 5PQ  plan-2  N1   0.020
 5PQ  plan-2  N3   0.020
 5PQ  plan-2  O6   0.020
 5PQ  plan-2  C2   0.020
 5PQ  plan-2  N7   0.020
 5PQ  plan-2  CAA  0.020
 5PQ  plan-2  N9   0.020
 5PQ  plan-2  CAZ  0.020
 5PQ  plan-2  H1   0.020
 5PQ  plan-2  H2   0.020
 5PQ  plan-2  H3   0.020
 5PQ  plan-2  H4   0.020
 5PQ  plan-2  N2   0.020
 5PQ  plan-3  CAT  0.020
 5PQ  plan-3  CAS  0.020
 5PQ  plan-3  OAD  0.020
 5PQ  plan-3  CAP  0.020

