# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 23:40:13 2022
#   Inital geometry file: a 132 line input string
#   Ligand name: (2~{S},3~{R})-2-[2-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]ethanoylamino]-3-oxidanyl-butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@H](NC(=O)C[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=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
 QCB  QCB  '(2~{S},3~{R})-2-[2-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]ethanoylamino]-3-oxidanyl-butanoic acid'  ligand  54  33  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_QCB
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
 QCB  N1   N  N      0  -0.472  38.6392  -20.7303  -15.9932
 QCB  C2   C  CR16   0   0.045  37.5968  -20.1142  -16.5435
 QCB  N3   N  N      0  -0.454  37.4669  -19.6639  -17.7792
 QCB  C4   C  CR56   0   0.488  38.5581  -19.8954  -18.5041
 QCB  C5   C  CR56   0  -0.009  39.7167  -20.5222  -18.0737
 QCB  C6   C  CR6    0   0.457  39.7301  -20.9543  -16.7347
 QCB  CX   C  C      0   0.458  34.8593  -22.7521  -22.8899
 QCB  OX   O  O      0  -0.570  34.5388  -21.6820  -22.3572
 QCB  CAX  C  CH1    0  -0.247  34.4712  -22.9680  -24.3787
 QCB  CBX  C  CH1    0   0.041  34.0998  -24.4287  -24.6664
 QCB  CGX  C  CH3    0  -0.672  33.6611  -24.6453  -26.1019
 QCB  OGX  O  OH1    0  -0.703  35.1822  -25.2838  -24.3797
 QCB  NX   N  NH1    0  -0.623  35.5750  -22.5591  -25.2248
 QCB  CCA  C  C      0   0.523  35.6984  -21.3409  -25.7751
 QCB  CP2  C  CH2    0  -0.869  36.9789  -21.1173  -26.5507
 QCB  OCA  O  O      0  -0.508  34.8410  -20.4678  -25.6929
 QCB  P1   P  P      0   1.273  38.5291  -21.6207  -25.6914
 QCB  OP3  O  O      0  -0.779  39.6925  -20.9795  -26.3882
 QCB  OP1  O  OP    -1  -0.777  38.4755  -23.1056  -25.4425
 QCB  O5'  O  O2     0  -0.615  38.3207  -20.9452  -24.1969
 QCB  C5'  C  CH2    0  -0.158  38.4019  -19.5507  -24.0205
 QCB  C4'  C  CR15   0  -0.025  37.3767  -19.1309  -22.9865
 QCB  C3'  C  CR15   0  -0.043  37.4705  -17.6486  -22.6325
 QCB  O3'  O  OH1    0  -0.662  36.1809  -17.1835  -22.3285
 QCB  C2'  C  CR15   0  -0.027  38.3622  -17.6863  -21.3936
 QCB  O2'  O  OH1    0  -0.653  38.2160  -16.5311  -20.6290
 QCB  C1'  C  CR15   0   0.196  37.8534  -18.9646  -20.7199
 QCB  O4'  O  O      0  -0.485  37.5832  -19.8516  -21.7680
 QCB  N9   N  NR5    0  -0.544  38.7876  -19.5774  -19.8132
 QCB  C8   C  CR15   0   0.111  40.0464  -20.0351  -20.1014
 QCB  N7   N  N      0  -0.446  40.6345  -20.6005  -19.0907
 QCB  N6   N  NH2    0  -0.816  40.7807  -21.5622  -16.1801
 QCB  H1   H  HCR6   0   0.250  36.7449  -19.9649  -15.8884
 QCB  H2   H  HCH1   0   0.232  33.6141  -22.3378  -24.6181
 QCB  H3   H  HCH1   0   0.186  33.2385  -24.6587  -24.0165
 QCB  H4   H  HCH3   0   0.219  32.8117  -24.0049  -26.3433
 QCB  H5   H  HCH3   0   0.220  34.4632  -24.4214  -26.8065
 QCB  H6   H  HCH3   0   0.229  33.3515  -25.6794  -26.2598
 QCB  H7   H  HOH1   0   0.434  35.5072  -24.9366  -23.5162
 QCB  H8   H  HNH1   0   0.384  36.3881  -23.1652  -25.2626
 QCB  H9   H  HCH2   0   0.282  36.9417  -21.6933  -27.4811
 QCB  H10  H  HCH2   0   0.267  37.0266  -20.0664  -26.8372
 QCB  H12  H  HCH2   0   0.221  39.4118  -19.2657  -23.7009
 QCB  H13  H  HCH2   0   0.218  38.1904  -18.9967  -24.9424
 QCB  H14  H  HCR5   0   0.249  36.3766  -19.3643  -23.3669
 QCB  H15  H  HCR5   0   0.254  37.9297  -17.0653  -23.4414
 QCB  H16  H  HOH1   0   0.452  36.2527  -16.2883  -21.9802
 QCB  H17  H  HCR5   0   0.245  39.4020  -17.8334  -21.7179
 QCB  H18  H  HOH1   0   0.465  38.8815  -16.5227  -19.9335
 QCB  H19  H  HCR5   0   0.253  36.9583  -18.7414  -20.1285
 QCB  H20  H  HCR5   0   0.300  40.4761  -19.9267  -21.0865
 QCB  H21  H  HNH2   0   0.402  40.7200  -21.9145  -15.2402
 QCB  H22  H  HNH2   0   0.410  41.5852  -21.8102  -16.7289
 QCB  OXT  O  OC    -1  -0.606  35.5027  -23.6908  -22.3479

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
 QCB  CGX  CBX  single    1.517  0.020  1.517
 QCB  CBX  OGX  single    1.409  0.020  1.409
 QCB  CBX  CAX  single    1.534  0.020  1.534
 QCB  NX   CAX  single    1.450  0.020  1.450
 QCB  NX   CCA  single    1.342  0.020  1.342
 QCB  CAX  CX   single    1.554  0.020  1.554
 QCB  CCA  CP2  single    1.514  0.020  1.514
 QCB  CCA  OCA  double    1.227  0.020  1.227
 QCB  CP2  P1   single    1.843  0.020  1.843
 QCB  CX   OX   deloc     1.238  0.020  1.238
 QCB  CX   OXT  deloc     1.261  0.020  1.261
 QCB  OP3  P1   deloc     1.500  0.020  1.500
 QCB  P1   OP1  deloc     1.507  0.020  1.507
 QCB  P1   O5'  single    1.653  0.020  1.653
 QCB  C5'  O5'  single    1.408  0.020  1.408
 QCB  C5'  C4'  single    1.515  0.020  1.515
 QCB  C3'  C4'  single    1.527  0.020  1.527
 QCB  C3'  O3'  single    1.404  0.020  1.404
 QCB  C3'  C2'  single    1.527  0.020  1.527
 QCB  C4'  O4'  single    1.431  0.020  1.431
 QCB  C2'  O2'  single    1.393  0.020  1.393
 QCB  C2'  C1'  single    1.532  0.020  1.532
 QCB  O4'  C1'  single    1.399  0.020  1.399
 QCB  C1'  N9   single    1.439  0.020  1.439
 QCB  C8   N9   aromatic  1.370  0.020  1.370
 QCB  C8   N7   aromatic  1.299  0.020  1.299
 QCB  N9   C4   aromatic  1.367  0.020  1.367
 QCB  N7   C5   aromatic  1.372  0.020  1.372
 QCB  C4   C5   aromatic  1.386  0.020  1.386
 QCB  C4   N3   aromatic  1.330  0.020  1.330
 QCB  C5   C6   aromatic  1.407  0.020  1.407
 QCB  N3   C2   aromatic  1.322  0.020  1.322
 QCB  C6   N6   single    1.334  0.020  1.334
 QCB  C6   N1   aromatic  1.338  0.020  1.338
 QCB  C2   N1   aromatic  1.330  0.020  1.330
 QCB  C2   H1   single    0.930  0.020  1.080
 QCB  CAX  H2   single    0.970  0.020  1.090
 QCB  CBX  H3   single    0.970  0.020  1.090
 QCB  CGX  H4   single    0.970  0.020  1.090
 QCB  CGX  H5   single    0.970  0.020  1.090
 QCB  CGX  H6   single    0.970  0.020  1.090
 QCB  OGX  H7   single    0.850  0.020  0.980
 QCB  NX   H8   single    0.860  0.020  1.020
 QCB  CP2  H9   single    0.970  0.020  1.090
 QCB  CP2  H10  single    0.970  0.020  1.090
 QCB  C5'  H12  single    0.970  0.020  1.090
 QCB  C5'  H13  single    0.970  0.020  1.090
 QCB  C4'  H14  single    0.970  0.020  1.090
 QCB  C3'  H15  single    0.970  0.020  1.090
 QCB  O3'  H16  single    0.850  0.020  0.980
 QCB  C2'  H17  single    0.970  0.020  1.090
 QCB  O2'  H18  single    0.850  0.020  0.980
 QCB  C1'  H19  single    0.970  0.020  1.090
 QCB  C8   H20  single    0.930  0.020  1.080
 QCB  N6   H21  single    0.860  0.020  1.020
 QCB  N6   H22  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
 QCB  C6   N1   C2   119.16  3.000
 QCB  H1   C2   N3   116.14  3.000
 QCB  H1   C2   N1   115.42  3.000
 QCB  N3   C2   N1   128.44  3.000
 QCB  C4   N3   C2   111.69  3.000
 QCB  N9   C4   C5   105.21  3.000
 QCB  C5   C4   N3   126.53  3.000
 QCB  N9   C4   N3   128.26  3.000
 QCB  N7   C5   C6   132.95  3.000
 QCB  C6   C5   C4   116.26  3.000
 QCB  N7   C5   C4   110.78  3.000
 QCB  N6   C6   C5   122.88  3.000
 QCB  N6   C6   N1   119.20  3.000
 QCB  C5   C6   N1   117.92  3.000
 QCB  OXT  CX   CAX  115.85  3.000
 QCB  OXT  CX   OX   126.23  3.000
 QCB  CAX  CX   OX   117.90  3.000
 QCB  H2   CAX  NX   107.90  3.000
 QCB  H2   CAX  CBX  108.59  3.000
 QCB  NX   CAX  CBX  110.09  3.000
 QCB  H2   CAX  CX   109.05  3.000
 QCB  NX   CAX  CX   109.26  3.000
 QCB  CBX  CAX  CX   111.87  3.000
 QCB  H3   CBX  OGX  110.69  3.000
 QCB  H3   CBX  CGX  107.58  3.000
 QCB  OGX  CBX  CGX  109.16  3.000
 QCB  H3   CBX  CAX  106.08  3.000
 QCB  OGX  CBX  CAX  110.71  3.000
 QCB  CGX  CBX  CAX  112.55  3.000
 QCB  H6   CGX  H5   108.04  3.000
 QCB  H6   CGX  H4   107.67  3.000
 QCB  H5   CGX  H4   108.01  3.000
 QCB  H6   CGX  CBX  110.76  3.000
 QCB  H5   CGX  CBX  111.68  3.000
 QCB  H4   CGX  CBX  110.54  3.000
 QCB  H7   OGX  CBX  102.58  3.000
 QCB  H8   NX   CCA  116.94  3.000
 QCB  H8   NX   CAX  117.60  3.000
 QCB  CCA  NX   CAX  124.42  3.000
 QCB  OCA  CCA  CP2  121.37  3.000
 QCB  OCA  CCA  NX   123.66  3.000
 QCB  CP2  CCA  NX   114.96  3.000
 QCB  H10  CP2  H9   106.58  3.000
 QCB  H10  CP2  P1   110.42  3.000
 QCB  H9   CP2  P1   106.33  3.000
 QCB  H10  CP2  CCA  108.31  3.000
 QCB  H9   CP2  CCA  109.21  3.000
 QCB  P1   CP2  CCA  115.62  3.000
 QCB  O5'  P1   OP1  104.42  3.000
 QCB  O5'  P1   OP3  110.06  3.000
 QCB  OP1  P1   OP3  121.71  3.000
 QCB  O5'  P1   CP2  101.76  3.000
 QCB  OP1  P1   CP2  108.44  3.000
 QCB  OP3  P1   CP2  108.61  3.000
 QCB  C5'  O5'  P1   120.71  3.000
 QCB  H13  C5'  H12  106.94  3.000
 QCB  H13  C5'  C4'  107.65  3.000
 QCB  H12  C5'  C4'  110.61  3.000
 QCB  H13  C5'  O5'  112.59  3.000
 QCB  H12  C5'  O5'  110.30  3.000
 QCB  C4'  C5'  O5'  108.71  3.000
 QCB  H14  C4'  O4'  108.68  3.000
 QCB  H14  C4'  C3'  110.09  3.000
 QCB  O4'  C4'  C3'  106.42  3.000
 QCB  H14  C4'  C5'  108.77  3.000
 QCB  O4'  C4'  C5'  110.12  3.000
 QCB  C3'  C4'  C5'  112.68  3.000
 QCB  H15  C3'  C2'  111.51  3.000
 QCB  H15  C3'  O3'  111.57  3.000
 QCB  C2'  C3'  O3'  111.64  3.000
 QCB  H15  C3'  C4'  111.76  3.000
 QCB  C2'  C3'  C4'  101.54  3.000
 QCB  O3'  C3'  C4'  108.38  3.000
 QCB  H16  O3'  C3'  108.52  3.000
 QCB  H17  C2'  C1'  109.41  3.000
 QCB  H17  C2'  O2'  111.85  3.000
 QCB  C1'  C2'  O2'  114.56  3.000
 QCB  H17  C2'  C3'  108.44  3.000
 QCB  C1'  C2'  C3'  100.57  3.000
 QCB  O2'  C2'  C3'  111.32  3.000
 QCB  H18  O2'  C2'  109.35  3.000
 QCB  H19  C1'  N9   106.09  3.000
 QCB  H19  C1'  O4'  112.06  3.000
 QCB  N9   C1'  O4'  109.11  3.000
 QCB  H19  C1'  C2'  109.79  3.000
 QCB  N9   C1'  C2'  114.64  3.000
 QCB  O4'  C1'  C2'  105.28  3.000
 QCB  C1'  O4'  C4'  110.28  3.000
 QCB  C8   N9   C1'  127.32  3.000
 QCB  C8   N9   C4   106.14  3.000
 QCB  C1'  N9   C4   126.42  3.000
 QCB  H20  C8   N7   124.98  3.000
 QCB  H20  C8   N9   121.59  3.000
 QCB  N7   C8   N9   113.44  3.000
 QCB  C8   N7   C5   104.42  3.000
 QCB  H22  N6   H21  118.18  3.000
 QCB  H22  N6   C6   121.04  3.000
 QCB  H21  N6   C6   120.04  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
 QCB  CONST_01  N7   C5   C6   N1    180.00   0.0  0
 QCB  CONST_02  C4   C5   C6   N1      0.00   0.0  0
 QCB  CONST_03  C4   N3   C2   N1      0.00   0.0  0
 QCB  CONST_04  N9   C4   N3   C2    180.00   0.0  0
 QCB  CONST_05  C5   C4   N3   C2      0.00   0.0  0
 QCB  CONST_06  C5   C6   N1   C2      0.00   0.0  0
 QCB  CONST_07  C8   N9   C4   N3    180.00   0.0  0
 QCB  CONST_08  N7   C5   C4   N3    180.00   0.0  0
 QCB  CONST_09  C6   C5   C4   N3      0.00   0.0  0
 QCB  CONST_10  C6   N1   C2   N3      0.00   0.0  0
 QCB  CONST_11  N7   C8   N9   C4      0.00   0.0  0
 QCB  CONST_12  C8   N7   C5   C4      0.00   0.0  0
 QCB  CONST_13  N9   C8   N7   C5      0.00   0.0  0
 QCB  CONST_14  C8   N9   C4   C5      0.00   0.0  0
 QCB  CONST_15  C8   N7   C5   C6    180.00   0.0  0
 QCB  CONST_16  N9   C4   C5   C6    180.00   0.0  0
 QCB  CONST_17  N7   C5   C4   N9      0.00   0.0  0
 QCB  CONST_18  C1'  N9   C4   N3      0.00   0.0  0
 QCB  CONST_19  C1'  N9   C4   C5    180.00   0.0  0
 QCB  CONST_20  N7   C8   N9   C1'   180.00   0.0  0
 QCB  CONST_21  N6   C6   N1   C2    180.00   0.0  0
 QCB  CONST_22  N6   C6   C5   C4    180.00   0.0  0
 QCB  CONST_23  N6   C6   C5   N7      0.00   0.0  0
 QCB  CONST_24  H20  C8   N9   C4    180.00   0.0  0
 QCB  CONST_25  H1   C2   N3   C4    180.00   0.0  0
 QCB  CONST_26  H21  N6   C6   N1      0.00   0.0  0
 QCB  CONST_27  H22  N6   C6   N1    180.00   0.0  0
 QCB  CONST_28  CP2  CCA  NX   CAX   180.00   0.0  0
 QCB  CONST_29  OCA  CCA  NX   CAX     0.00   0.0  0
 QCB  CONST_30  H8   NX   CCA  CP2     0.00   0.0  0
 QCB  Var_01    C4'  C5'  O5'  P1    143.13  30.0  1
 QCB  Var_02    P1   CP2  CCA  NX    -48.27  30.0  3
 QCB  Var_03    OP3  P1   CP2  CCA  -163.48  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
 QCB  chir_01  CAX  CBX  NX   CX   positiv
 QCB  chir_02  CBX  OGX  CAX  CGX  negativ
 QCB  chir_04  C4'  C5'  C3'  O4'  positiv
 QCB  chir_05  C3'  O3'  C2'  C4'  negativ
 QCB  chir_06  C2'  O2'  C1'  C3'  negativ
 QCB  chir_07  C1'  O4'  N9   C2'  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
 QCB  plan-1  N1   0.020
 QCB  plan-1  C2   0.020
 QCB  plan-1  N3   0.020
 QCB  plan-1  C4   0.020
 QCB  plan-1  C5   0.020
 QCB  plan-1  C6   0.020
 QCB  plan-1  C1'  0.020
 QCB  plan-1  N9   0.020
 QCB  plan-1  C8   0.020
 QCB  plan-1  N7   0.020
 QCB  plan-1  N6   0.020
 QCB  plan-1  H1   0.020
 QCB  plan-1  H20  0.020
 QCB  plan-2  C6   0.020
 QCB  plan-2  N6   0.020
 QCB  plan-2  H21  0.020
 QCB  plan-2  H22  0.020
 QCB  plan-3  CAX  0.020
 QCB  plan-3  NX   0.020
 QCB  plan-3  CCA  0.020
 QCB  plan-3  CP2  0.020
 QCB  plan-3  OCA  0.020
 QCB  plan-3  H8   0.020
 QCB  plan-4  CX   0.020
 QCB  plan-4  OX   0.020
 QCB  plan-4  CAX  0.020
 QCB  plan-4  OXT  0.020

