# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 05:44:14 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: [(2~{S})-2-azanyl-3-oxidanylidene-propyl] [(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CO[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=O)NC2=O)C=O
#
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
 BQL  BQL  '[(2~{S})-2-azanyl-3-oxidanylidene-propyl] [(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate'  ligand  44  26  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BQL
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
 BQL  N    N  NH2   0  -0.776  -3.6648   1.8127  -1.4460
 BQL  CA   C  CH1   0  -0.238  -4.2204   0.6863  -0.7435
 BQL  C    C  C1    0   0.167  -5.6354   0.3026  -1.1259
 BQL  O    O  O     0  -0.365  -6.2982   0.8864  -1.9438
 BQL  CB   C  CH2   0  -0.178  -4.1818   0.8971   0.7679
 BQL  C1'  C  CR15  0   0.235   2.1942  -0.6786  -1.0111
 BQL  C2   C  CR6   0   0.813   2.2161   1.0349   0.7594
 BQL  C2'  C  CR15  0  -0.056   2.5720  -1.9365  -0.2303
 BQL  C3   C  CR15  0  -0.026   0.2757  -1.9607  -0.8005
 BQL  C3'  C  CR15  0  -0.039   1.4724  -2.8995  -0.7063
 BQL  C4   C  CR6   0   0.574   3.5438   3.0969   0.4627
 BQL  C5   C  CR16  0  -0.503   3.9752   2.5564  -0.8019
 BQL  C5'  C  CH2   0  -0.184  -0.5060  -1.9383   0.5015
 BQL  C6   C  CR16  0   0.099   3.5206   1.3601  -1.2019
 BQL  N1   N  NR6   0  -0.573   2.6637   0.5897  -0.4593
 BQL  N3   N  NR16  0  -0.730   2.6683   2.2578   1.1445
 BQL  O1   O  OH1   0  -0.666   1.7571  -3.3974  -1.9856
 BQL  O3   O  OH1   0  -0.655   3.8700  -2.3216  -0.5758
 BQL  O4   O  O     0  -0.451   3.8715   4.1643   0.9396
 BQL  O4'  O  O     0  -0.478   0.8061  -0.6756  -1.1214
 BQL  O5'  O  O2    0  -0.586  -1.3976  -0.8271   0.4617
 BQL  OP1  O  OH1   0  -0.771  -0.8741   0.4244   2.6358
 BQL  OP2  O  O     0  -0.712  -2.8437  -1.2091   2.5903
 BQL  OP3  O  O2    0  -0.570  -2.8449   1.0163   1.2493
 BQL  P    P  P     0   1.453  -2.0424  -0.2452   1.8083
 BQL  H1   H  HNH2  0   0.358  -3.5611   1.5931  -2.4280
 BQL  H2   H  HNH2  0   0.346  -4.2989   2.6015  -1.3994
 BQL  H4   H  HCH1  0   0.281  -3.6235  -0.2066  -0.9720
 BQL  H5   H  H     0   0.195  -6.0296  -0.5857  -0.5997
 BQL  H6   H  HCH2  0   0.262  -4.6840   1.8314   1.0246
 BQL  H7   H  HCH2  0   0.246  -4.7063   0.0889   1.2839
 BQL  H8   H  HCR5  0   0.261   2.6597  -0.7379  -2.0013
 BQL  H9   H  HCR5  0   0.267   2.4720  -1.7778   0.8466
 BQL  H10  H  HCR5  0   0.271  -0.3946  -2.2596  -1.6117
 BQL  H11  H  HCR5  0   0.256   1.3021  -3.7071   0.0181
 BQL  H12  H  HCR6  0   0.302   4.6536   3.1209  -1.4221
 BQL  H13  H  HCH2  0   0.259  -1.0676  -2.8719   0.5853
 BQL  H14  H  HCH2  0   0.237   0.1630  -1.8756   1.3627
 BQL  H15  H  HCR6  0   0.336   3.8151   0.9383  -2.1517
 BQL  H16  H  HNR6  0   0.435   2.3380   2.5772   2.0481
 BQL  H17  H  HOH1  0   0.451   2.6690  -3.7118  -1.9857
 BQL  H18  H  HOH1  0   0.471   4.2201  -2.8901   0.1170
 BQL  H19  H  HOH1  0   0.506   0.0064   0.5211   2.1959
 BQL  O2   O  O     0  -0.526   1.4702   0.3728   1.4662

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
 BQL  C5   C6   double  1.341  0.020  1.341
 BQL  C5   C4   single  1.441  0.020  1.441
 BQL  C6   N1   single  1.371  0.020  1.371
 BQL  O4   C4   double  1.214  0.020  1.214
 BQL  C4   N3   single  1.391  0.020  1.391
 BQL  N1   C1'  single  1.461  0.020  1.461
 BQL  N1   C2   single  1.373  0.020  1.373
 BQL  O3   C2'  single  1.397  0.020  1.397
 BQL  C1'  C2'  single  1.528  0.020  1.528
 BQL  C1'  O4'  single  1.392  0.020  1.392
 BQL  N3   C2   single  1.359  0.020  1.359
 BQL  C2'  C3'  single  1.537  0.020  1.537
 BQL  C2   O2   double  1.222  0.020  1.222
 BQL  O4'  C3   single  1.427  0.020  1.427
 BQL  O1   C3'  single  1.402  0.020  1.402
 BQL  C3'  C3   single  1.524  0.020  1.524
 BQL  C3   C5'  single  1.519  0.020  1.519
 BQL  N    CA   single  1.439  0.020  1.439
 BQL  O    C    double  1.204  0.020  1.204
 BQL  O5'  C5'  single  1.425  0.020  1.425
 BQL  O5'  P    single  1.602  0.020  1.602
 BQL  CA   C    single  1.515  0.020  1.515
 BQL  CA   CB   single  1.526  0.020  1.526
 BQL  OP2  P    double  1.477  0.020  1.477
 BQL  P    OP3  single  1.596  0.020  1.596
 BQL  P    OP1  single  1.581  0.020  1.581
 BQL  OP3  CB   single  1.426  0.020  1.426
 BQL  N    H1   single  0.890  0.020  1.040
 BQL  N    H2   single  0.890  0.020  1.040
 BQL  CA   H4   single  0.970  0.020  1.090
 BQL  C    H5   single  0.930  0.020  1.080
 BQL  CB   H6   single  0.970  0.020  1.090
 BQL  CB   H7   single  0.970  0.020  1.090
 BQL  C1'  H8   single  0.970  0.020  1.090
 BQL  C2'  H9   single  0.970  0.020  1.090
 BQL  C3   H10  single  0.970  0.020  1.090
 BQL  C3'  H11  single  0.970  0.020  1.090
 BQL  C5   H12  single  0.930  0.020  1.080
 BQL  C5'  H13  single  0.970  0.020  1.090
 BQL  C5'  H14  single  0.970  0.020  1.090
 BQL  C6   H15  single  0.930  0.020  1.080
 BQL  N3   H16  single  0.860  0.020  1.020
 BQL  O1   H17  single  0.850  0.020  0.980
 BQL  O3   H18  single  0.850  0.020  0.980
 BQL  OP1  H19  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
 BQL  H2   N    H1   106.13  3.000
 BQL  H2   N    CA   110.20  3.000
 BQL  H1   N    CA   110.09  3.000
 BQL  H4   CA   CB   107.73  3.000
 BQL  H4   CA   C    104.43  3.000
 BQL  CB   CA   C    107.97  3.000
 BQL  H4   CA   N    108.96  3.000
 BQL  CB   CA   N    111.44  3.000
 BQL  C    CA   N    115.82  3.000
 BQL  H5   C    O    121.12  3.000
 BQL  H5   C    CA   114.61  3.000
 BQL  O    C    CA   124.26  3.000
 BQL  H7   CB   H6   107.53  3.000
 BQL  H7   CB   OP3  110.63  3.000
 BQL  H6   CB   OP3  106.29  3.000
 BQL  H7   CB   CA   110.68  3.000
 BQL  H6   CB   CA   109.84  3.000
 BQL  OP3  CB   CA   111.69  3.000
 BQL  H8   C1'  O4'  110.61  3.000
 BQL  H8   C1'  N1   104.59  3.000
 BQL  O4'  C1'  N1   110.40  3.000
 BQL  H8   C1'  C2'  108.19  3.000
 BQL  O4'  C1'  C2'  106.78  3.000
 BQL  N1   C1'  C2'  116.25  3.000
 BQL  O2   C2   N3   121.76  3.000
 BQL  O2   C2   N1   122.46  3.000
 BQL  N3   C2   N1   115.77  3.000
 BQL  H9   C2'  O3   111.63  3.000
 BQL  H9   C2'  C3'  109.30  3.000
 BQL  O3   C2'  C3'  114.54  3.000
 BQL  H9   C2'  C1'  111.18  3.000
 BQL  C3'  C2'  C1'  100.41  3.000
 BQL  O3   C2'  C1'  109.28  3.000
 BQL  H10  C3   O4'  107.89  3.000
 BQL  H10  C3   C5'  108.93  3.000
 BQL  O4'  C3   C5'  111.77  3.000
 BQL  H10  C3   C3'  111.02  3.000
 BQL  C5'  C3   C3'  111.11  3.000
 BQL  O4'  C3   C3'  106.07  3.000
 BQL  H11  C3'  O1   111.85  3.000
 BQL  H11  C3'  C3   111.84  3.000
 BQL  O1   C3'  C3   108.77  3.000
 BQL  H11  C3'  C2'  111.56  3.000
 BQL  C3   C3'  C2'  101.24  3.000
 BQL  O1   C3'  C2'  111.09  3.000
 BQL  O4   C4   N3   120.50  3.000
 BQL  N3   C4   C5   113.09  3.000
 BQL  O4   C4   C5   126.41  3.000
 BQL  H12  C5   C6   120.57  3.000
 BQL  H12  C5   C4   119.76  3.000
 BQL  C6   C5   C4   119.66  3.000
 BQL  H14  C5'  H13  107.66  3.000
 BQL  H14  C5'  O5'  111.12  3.000
 BQL  H13  C5'  O5'  110.29  3.000
 BQL  H14  C5'  C3   111.19  3.000
 BQL  H13  C5'  C3   108.52  3.000
 BQL  O5'  C5'  C3   108.03  3.000
 BQL  H15  C6   N1   115.30  3.000
 BQL  H15  C6   C5   121.21  3.000
 BQL  N1   C6   C5   123.49  3.000
 BQL  C6   N1   C2   120.17  3.000
 BQL  C2   N1   C1'  120.81  3.000
 BQL  C6   N1   C1'  118.96  3.000
 BQL  H16  N3   C4   116.86  3.000
 BQL  H16  N3   C2   115.31  3.000
 BQL  C4   N3   C2   127.81  3.000
 BQL  H17  O1   C3'  107.92  3.000
 BQL  H18  O3   C2'  108.83  3.000
 BQL  C3   O4'  C1'  110.54  3.000
 BQL  P    O5'  C5'  120.75  3.000
 BQL  H19  OP1  P    117.82  3.000
 BQL  P    OP3  CB   121.57  3.000
 BQL  OP3  P    OP2  115.36  3.000
 BQL  OP3  P    OP1  102.71  3.000
 BQL  OP2  P    OP1  113.59  3.000
 BQL  OP1  P    O5'  107.24  3.000
 BQL  OP3  P    O5'  101.24  3.000
 BQL  OP2  P    O5'  115.22  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
 BQL  CONST_01  N3   C2   N1   C1'  180.00   0.0  0
 BQL  CONST_02  C5   C4   N3   C2     0.00   0.0  0
 BQL  CONST_03  N1   C2   N3   C4     0.00   0.0  0
 BQL  CONST_04  N3   C2   N1   C6     0.00   0.0  0
 BQL  CONST_05  O2   C2   N1   C1'    0.00   0.0  0
 BQL  CONST_06  O4   C4   N3   C2   180.00   0.0  0
 BQL  CONST_07  O2   C2   N3   C4   180.00   0.0  0
 BQL  CONST_08  O2   C2   N1   C6   180.00   0.0  0
 BQL  CONST_09  H16  N3   C4   C5   180.00   0.0  0
 BQL  Var_01    O5'  P    OP3  CB    87.33  30.0  1
 BQL  Var_02    H13  C5'  O5'  P     80.12  30.0  3
 BQL  Var_03    H6   CB   OP3  P    146.09  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
 BQL  chir_01  CA   N    C    CB   positiv
 BQL  chir_02  C1'  N1   C2'  O4'  negativ
 BQL  chir_03  C2'  O3   C3'  C1'  positiv
 BQL  chir_04  C3   O4'  C3'  C5'  negativ
 BQL  chir_05  C3'  O1   C3   C2'  positiv
 BQL  chir_06  P    OP2  OP3  OP1  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
 BQL  plan-1  C1'  0.020
 BQL  plan-1  C2   0.020
 BQL  plan-1  C4   0.020
 BQL  plan-1  C5   0.020
 BQL  plan-1  C6   0.020
 BQL  plan-1  N1   0.020
 BQL  plan-1  N3   0.020
 BQL  plan-1  O4   0.020
 BQL  plan-1  H12  0.020
 BQL  plan-1  H15  0.020
 BQL  plan-1  H16  0.020
 BQL  plan-1  O2   0.020
 BQL  plan-2  CA   0.020
 BQL  plan-2  C    0.020
 BQL  plan-2  O    0.020
 BQL  plan-2  H5   0.020

