# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 10:54:42 2021
#   Inital geometry file: a 117 line input string
#   Ligand name: [(2~{R},3~{S})-3-azanyl-4-oxidanylidene-butan-2-yl] [(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: C[C@@H](O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=O)NC2=O)[C@H](N)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
 BQO  BQO  '[(2~{R},3~{S})-3-azanyl-4-oxidanylidene-butan-2-yl] [(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  47  27  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_BQO
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
 BQO  N1   N  NR6   0  -0.565  108.7691  88.0239  67.3004
 BQO  C1   C  CH2   0  -0.184  105.1204  86.6109  69.2227
 BQO  O1   O  OH1   0  -0.662  109.2929  87.1691  70.7245
 BQO  CA   C  CH1   0  -0.199  103.6760  85.7780  64.2376
 BQO  C    C  C1    0   0.169  104.0344  85.7840  62.7740
 BQO  O    O  O     0  -0.368  103.5253  85.0660  61.9521
 BQO  CB   C  CH1   0   0.045  104.9324  85.5612  65.0925
 BQO  CG2  C  CH3   0  -0.697  106.0370  86.5715  64.8698
 BQO  C1'  C  CH1   0   0.162  108.5820  87.1665  68.4657
 BQO  C2   C  CR6   0   0.741  109.9525  87.9350  66.5898
 BQO  C2'  C  CH1   0  -0.039  108.5563  87.9240  69.8033
 BQO  C3   C  CH1   0   0.002  106.5965  86.6077  69.5336
 BQO  C3'  C  CH1   0  -0.034  107.0617  87.9183  70.1642
 BQO  C4   C  CR6   0   0.568  109.0985  89.6991  65.0699
 BQO  C5   C  CR16  0  -0.499  107.9034  89.7319  65.8770
 BQO  C6   C  CR16  0   0.105  107.7946  88.9073  66.9288
 BQO  N3   N  NR16  0  -0.734  110.0346  88.7763  65.5124
 BQO  O2   O  O     0  -0.473  110.8525  87.1790  66.8875
 BQO  O3'  O  OH1   0  -0.654  106.8150  87.9157  71.5396
 BQO  O4   O  O     0  -0.458  109.3196  90.3850  64.0904
 BQO  O4'  O  O2    0  -0.486  107.3502  86.5040  68.3390
 BQO  OP1  O  O2    0  -0.605  104.4950  85.6614  66.4627
 BQO  OP2  O  O     0  -0.700  106.0727  83.7915  67.3276
 BQO  OP3  O  OH1   0  -0.726  103.5097  83.6120  67.6398
 BQO  P    P  P     0   1.463  104.8142  84.5302  67.5441
 BQO  H1   H  HCH2  0   0.245  104.8980  87.3241  68.4247
 BQO  H2   H  HCH2  0   0.269  104.5807  86.9272  70.1151
 BQO  H3   H  HOH1  0   0.453  108.9403  87.3524  71.6044
 BQO  H8   H  H     0   0.210  104.7837  86.5370  62.4805
 BQO  H9   H  HCH1  0   0.252  105.3056  84.5523  64.8945
 BQO  H10  H  HCH3  0   0.258  106.8262  86.4243  65.6052
 BQO  H11  H  HCH3  0   0.242  106.4860  86.4518  63.8848
 BQO  H12  H  HCH3  0   0.238  105.6712  87.5953  64.9568
 BQO  H13  H  HCH1  0   0.289  109.4087  86.4566  68.4609
 BQO  H14  H  HCH1  0   0.261  108.9565  88.9401  69.6990
 BQO  H15  H  HCH1  0   0.257  106.8269  85.7751  70.2122
 BQO  H16  H  HCH1  0   0.250  106.5613  88.7641  69.6757
 BQO  H17  H  HCR6  0   0.296  107.1026  90.4095  65.6260
 BQO  H18  H  HCR6  0   0.317  106.9000  88.9123  67.5327
 BQO  H19  H  HNR6  0   0.429  110.8997  88.7193  64.9886
 BQO  H20  H  HOH1  0   0.472  106.7486  88.8251  71.8478
 BQO  H21  H  HOH1  0   0.498  103.6160  82.7481  67.2210
 BQO  O5'  O  O2    0  -0.576  104.6026  85.3198  68.9087
 BQO  H7   H  HCH1  0   0.257  103.3311  86.8107  64.4338
 BQO  N    N  NH2   0  -0.802  102.7004  84.7558  64.5257
 BQO  H4   H  HNH2  0   0.358  102.2755  84.9276  65.4258
 BQO  H5   H  HNH2  0   0.356  101.9509  84.7813  63.8469

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
 BQO  O    C    double  1.204  0.020  1.204
 BQO  C    CA   single  1.507  0.020  1.507
 BQO  N    CA   single  1.442  0.020  1.442
 BQO  CA   CB   single  1.535  0.020  1.535
 BQO  O4   C4   double  1.216  0.020  1.216
 BQO  CB   CG2  single  1.513  0.020  1.513
 BQO  CB   OP1  single  1.442  0.020  1.442
 BQO  C4   C5   single  1.442  0.020  1.442
 BQO  C4   N3   single  1.387  0.020  1.387
 BQO  C5   C6   double  1.341  0.020  1.341
 BQO  OP1  P    single  1.597  0.020  1.597
 BQO  OP2  P    double  1.475  0.020  1.475
 BQO  N3   C2   single  1.369  0.020  1.369
 BQO  C6   N1   single  1.367  0.020  1.367
 BQO  P    OP3  single  1.598  0.020  1.598
 BQO  P    O5'  single  1.591  0.020  1.591
 BQO  C2   N1   single  1.383  0.020  1.383
 BQO  C2   O2   double  1.212  0.020  1.212
 BQO  N1   C1'  single  1.459  0.020  1.459
 BQO  O4'  C1'  single  1.404  0.020  1.404
 BQO  O4'  C3   single  1.416  0.020  1.416
 BQO  C1   O5'  single  1.426  0.020  1.426
 BQO  C1   C3   single  1.509  0.020  1.509
 BQO  C1'  C2'  single  1.537  0.020  1.537
 BQO  C3   C3'  single  1.527  0.020  1.527
 BQO  C2'  C3'  single  1.538  0.020  1.538
 BQO  C2'  O1   single  1.400  0.020  1.400
 BQO  C3'  O3'  single  1.397  0.020  1.397
 BQO  C1   H1   single  0.970  0.020  1.090
 BQO  C1   H2   single  0.970  0.020  1.090
 BQO  O1   H3   single  0.850  0.020  0.980
 BQO  N    H4   single  0.890  0.020  1.040
 BQO  N    H5   single  0.890  0.020  1.040
 BQO  CA   H7   single  0.970  0.020  1.090
 BQO  C    H8   single  0.930  0.020  1.080
 BQO  CB   H9   single  0.970  0.020  1.090
 BQO  CG2  H10  single  0.970  0.020  1.090
 BQO  CG2  H11  single  0.970  0.020  1.090
 BQO  CG2  H12  single  0.970  0.020  1.090
 BQO  C1'  H13  single  0.970  0.020  1.090
 BQO  C2'  H14  single  0.970  0.020  1.090
 BQO  C3   H15  single  0.970  0.020  1.090
 BQO  C3'  H16  single  0.970  0.020  1.090
 BQO  C5   H17  single  0.930  0.020  1.080
 BQO  C6   H18  single  0.930  0.020  1.080
 BQO  N3   H19  single  0.860  0.020  1.020
 BQO  O3'  H20  single  0.850  0.020  0.980
 BQO  OP3  H21  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
 BQO  C6   N1   C2   120.78  3.000
 BQO  C2   N1   C1'  118.84  3.000
 BQO  C6   N1   C1'  120.38  3.000
 BQO  H2   C1   H1   107.92  3.000
 BQO  H2   C1   O5'  105.27  3.000
 BQO  H1   C1   O5'  110.86  3.000
 BQO  H2   C1   C3   108.45  3.000
 BQO  H1   C1   C3   110.54  3.000
 BQO  O5'  C1   C3   113.50  3.000
 BQO  H3   O1   C2'  107.76  3.000
 BQO  H7   CA   CB   106.75  3.000
 BQO  H7   CA   C    104.04  3.000
 BQO  CB   CA   C    110.29  3.000
 BQO  H7   CA   N    114.54  3.000
 BQO  CB   CA   N    110.02  3.000
 BQO  C    CA   N    110.96  3.000
 BQO  H8   C    O    120.87  3.000
 BQO  H8   C    CA   115.03  3.000
 BQO  O    C    CA   124.05  3.000
 BQO  H9   CB   OP1  109.86  3.000
 BQO  H9   CB   CG2  109.88  3.000
 BQO  OP1  CB   CG2  108.35  3.000
 BQO  H9   CB   CA   107.99  3.000
 BQO  OP1  CB   CA   105.73  3.000
 BQO  CG2  CB   CA   114.91  3.000
 BQO  H12  CG2  H11  108.28  3.000
 BQO  H12  CG2  H10  108.43  3.000
 BQO  H11  CG2  H10  107.29  3.000
 BQO  H12  CG2  CB   111.72  3.000
 BQO  H11  CG2  CB   111.14  3.000
 BQO  H10  CG2  CB   109.84  3.000
 BQO  H13  C1'  O4'  110.96  3.000
 BQO  H13  C1'  C2'  109.73  3.000
 BQO  O4'  C1'  C2'  107.23  3.000
 BQO  H13  C1'  N1   106.38  3.000
 BQO  C2'  C1'  N1   114.05  3.000
 BQO  O4'  C1'  N1   108.52  3.000
 BQO  O2   C2   N3   122.13  3.000
 BQO  O2   C2   N1   123.29  3.000
 BQO  N3   C2   N1   114.58  3.000
 BQO  H14  C2'  C3'  112.36  3.000
 BQO  H14  C2'  C1'  111.57  3.000
 BQO  C3'  C2'  C1'  102.63  3.000
 BQO  H14  C2'  O1   111.71  3.000
 BQO  C3'  C2'  O1   110.79  3.000
 BQO  C1'  C2'  O1   107.33  3.000
 BQO  H15  C3   O4'  110.73  3.000
 BQO  H15  C3   C3'  109.36  3.000
 BQO  O4'  C3   C3'  104.42  3.000
 BQO  H15  C3   C1   109.52  3.000
 BQO  C3'  C3   C1   112.42  3.000
 BQO  O4'  C3   C1   110.31  3.000
 BQO  H16  C3'  O3'  111.04  3.000
 BQO  H16  C3'  C3   109.80  3.000
 BQO  O3'  C3'  C3   110.56  3.000
 BQO  H16  C3'  C2'  109.62  3.000
 BQO  O3'  C3'  C2'  113.75  3.000
 BQO  C3   C3'  C2'  101.68  3.000
 BQO  O4   C4   N3   120.63  3.000
 BQO  N3   C4   C5   113.31  3.000
 BQO  O4   C4   C5   126.06  3.000
 BQO  H17  C5   C6   120.58  3.000
 BQO  H17  C5   C4   119.94  3.000
 BQO  C6   C5   C4   119.48  3.000
 BQO  H18  C6   C5   120.22  3.000
 BQO  H18  C6   N1   116.21  3.000
 BQO  C5   C6   N1   123.57  3.000
 BQO  H19  N3   C4   116.67  3.000
 BQO  H19  N3   C2   115.05  3.000
 BQO  C4   N3   C2   128.27  3.000
 BQO  H20  O3'  C3'  109.00  3.000
 BQO  C3   O4'  C1'  110.86  3.000
 BQO  P    OP1  CB   122.25  3.000
 BQO  H21  OP3  P    113.46  3.000
 BQO  OP3  P    OP2  114.67  3.000
 BQO  OP3  P    OP1  106.52  3.000
 BQO  OP2  P    OP1  115.20  3.000
 BQO  OP3  P    O5'   97.20  3.000
 BQO  OP2  P    O5'  119.20  3.000
 BQO  OP1  P    O5'  101.69  3.000
 BQO  P    O5'  C1   126.16  3.000
 BQO  H5   N    H4   106.37  3.000
 BQO  H5   N    CA   110.45  3.000
 BQO  H4   N    CA   110.00  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
 BQO  CONST_01  C4   N3  C2   N1     0.00   0.0  0
 BQO  CONST_02  N3   C2  N1   C1'  180.00   0.0  0
 BQO  CONST_03  C5   C4  N3   C2     0.00   0.0  0
 BQO  CONST_04  N3   C2  N1   C6     0.00   0.0  0
 BQO  CONST_05  O2   C2  N1   C1'    0.00   0.0  0
 BQO  CONST_06  O4   C4  N3   C2   180.00   0.0  0
 BQO  CONST_07  O2   C2  N3   C4   180.00   0.0  0
 BQO  CONST_08  O2   C2  N1   C6   180.00   0.0  0
 BQO  CONST_09  H19  N3  C2   N1   180.00   0.0  0
 BQO  Var_01    OP1  P   O5'  C1   -47.01  30.0  1
 BQO  Var_02    H1   C1  O5'  P     49.95  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
 BQO  chir_01  CA   C    N    CB   negativ
 BQO  chir_02  CB   OP1  CA   CG2  negativ
 BQO  chir_03  C1'  N1   O4'  C2'  positiv
 BQO  chir_04  C2'  O1   C1'  C3'  negativ
 BQO  chir_05  C3   O4'  C3'  C1   negativ
 BQO  chir_06  C3'  O3'  C3   C2'  positiv
 BQO  chir_07  P    OP2  OP3  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
 BQO  plan-1  N1   0.020
 BQO  plan-1  C1'  0.020
 BQO  plan-1  C2   0.020
 BQO  plan-1  C4   0.020
 BQO  plan-1  C5   0.020
 BQO  plan-1  C6   0.020
 BQO  plan-1  N3   0.020
 BQO  plan-1  O2   0.020
 BQO  plan-1  O4   0.020
 BQO  plan-1  H17  0.020
 BQO  plan-1  H18  0.020
 BQO  plan-1  H19  0.020
 BQO  plan-2  CA   0.020
 BQO  plan-2  C    0.020
 BQO  plan-2  O    0.020
 BQO  plan-2  H8   0.020

