# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Sep 30 19:35:00 2022
#   Inital geometry file: a 129 line input string
#   Ligand name: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2~{S},3~{S})-2-azanyl-3-methyl-pentanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](C)[C@H](N)C(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
#
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
 GV6  GV6  "[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2S,3S)-2-azanyl-3-methyl-pentanoate"  ligand  56  31  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GV6
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
 GV6  N1   N  N     0  -0.471   8.3733  7.5543  32.8431
 GV6  C2   C  CR16  0   0.045   7.3891  7.3107  33.7041
 GV6  N3   N  N     0  -0.455   7.4620  7.1614  35.0153
 GV6  C4   C  CR56  0   0.489   8.7113  7.2865  35.4557
 GV6  C5   C  CR56  0  -0.010   9.8351  7.5409  34.6861
 GV6  C6   C  CR6   0   0.457   9.6243  7.6764  33.3014
 GV6  N7   N  NR5   0  -0.542   9.1702  7.1938  36.7394
 GV6  C8   C  CR15  0   0.107  10.5239  7.4002  36.6776
 GV6  N9   N  N     0  -0.447  10.9579  7.6103  35.4712
 GV6  C10  C  CH1   0   0.204   8.3708  6.9526  37.9106
 GV6  C11  C  CH1   0  -0.009   8.7533  5.6875  38.6769
 GV6  C12  C  CH1   0  -0.063   8.2502  6.0247  40.0814
 GV6  C13  C  CH1   0  -0.019   8.5187  7.5392  40.1540
 GV6  O14  O  O2    0  -0.490   8.5310  8.0134  38.8097
 GV6  N15  N  NH2   0  -0.816  10.6156  7.9079  32.4390
 GV6  C16  C  CH2   0  -0.217   9.7906  7.9475  40.8601
 GV6  O17  O  O2    0  -0.587  10.9108  7.3383  40.2094
 GV6  P18  P  P     0   1.498  12.3316  7.1197  40.8834
 GV6  O19  O  O     0  -0.662  13.3296  6.6629  39.9091
 GV6  O20  O  O2    0  -0.574  12.0653  6.1409  42.1702
 GV6  O21  O  OH1   0  -0.650   8.1776  4.5847  38.0524
 GV6  O22  O  OH1   0  -0.663   6.8786  5.7327  40.1352
 GV6  O23  O  OH1   0  -0.724  12.6512  8.4066  41.7584
 GV6  C24  C  C     0   0.602  11.6967  4.8495  41.9986
 GV6  C25  C  CH1   0  -0.187  11.6010  4.0507  43.2831
 GV6  O26  O  O     0  -0.409  11.4763  4.3936  40.9118
 GV6  N27  N  NH2   0  -0.799  12.0905  4.7880  44.4253
 GV6  C28  C  CH1   0  -0.258  10.1371  3.5912  43.4801
 GV6  C29  C  CH2   0  -0.423   9.1997  4.7544  43.8147
 GV6  C30  C  CH3   0  -0.669   7.7253  4.3881  43.7046
 GV6  C31  C  CH3   0  -0.671  10.0661  2.4828  44.5271
 GV6  H1   H  HCR6  0   0.250   6.3995  7.2243  33.2680
 GV6  H2   H  HCR5  0   0.297  11.1413  7.3867  37.5634
 GV6  H3   H  HCH1  0   0.260   7.3357  6.8740  37.5587
 GV6  H4   H  HCH1  0   0.251   9.8451  5.6017  38.7207
 GV6  H5   H  HCH1  0   0.260   8.8028  5.4818  40.8568
 GV6  H6   H  HCH1  0   0.269   7.7044  8.0291  40.7011
 GV6  H7   H  HNH2  0   0.402  10.4131  8.0582  31.4655
 GV6  H8   H  HNH2  0   0.410  11.5542  8.0682  32.7603
 GV6  H9   H  HCH2  0   0.271   9.9058  9.0327  40.8311
 GV6  H10  H  HCH2  0   0.258   9.7188  7.6410  41.9070
 GV6  H11  H  HOH1  0   0.461   8.5703  3.7828  38.4111
 GV6  H12  H  HOH1  0   0.457   6.5588  5.9318  41.0215
 GV6  H13  H  HOH1  0   0.508  13.0474  9.1406  41.2664
 GV6  H14  H  HCH1  0   0.269  12.1821  3.1399  43.0674
 GV6  H15  H  HNH2  0   0.360  11.9308  4.2453  45.2640
 GV6  H16  H  HNH2  0   0.357  13.0939  4.9076  44.3651
 GV6  H18  H  HCH1  0   0.241   9.8210  3.1576  42.5256
 GV6  H19  H  HCH2  0   0.231   9.3951  5.5952  43.1431
 GV6  H20  H  HCH2  0   0.226   9.4164  5.1231  44.8202
 GV6  H21  H  HCH3  0   0.231   7.0956  5.2534  43.9140
 GV6  H22  H  HCH3  0   0.219   7.4815  4.0383  42.6992
 GV6  H23  H  HCH3  0   0.226   7.4417  3.6031  44.4058
 GV6  H24  H  HCH3  0   0.236  10.7622  1.6756  44.2947
 GV6  H25  H  HCH3  0   0.221  10.2956  2.8492  45.5300
 GV6  H26  H  HCH3  0   0.244   9.0679  2.0482  44.5678

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
 GV6  N15  C6   single    1.334  0.020  1.334
 GV6  N1   C6   aromatic  1.338  0.020  1.338
 GV6  N1   C2   aromatic  1.330  0.020  1.330
 GV6  C6   C5   aromatic  1.407  0.020  1.407
 GV6  C2   N3   aromatic  1.322  0.020  1.322
 GV6  C5   C4   aromatic  1.386  0.020  1.386
 GV6  C5   N9   aromatic  1.372  0.020  1.372
 GV6  N3   C4   aromatic  1.331  0.020  1.331
 GV6  C4   N7   aromatic  1.366  0.020  1.366
 GV6  N9   C8   aromatic  1.299  0.020  1.299
 GV6  C8   N7   aromatic  1.371  0.020  1.371
 GV6  N7   C10  single    1.438  0.020  1.438
 GV6  C10  C11  single    1.528  0.020  1.528
 GV6  C10  O14  single    1.400  0.020  1.400
 GV6  O21  C11  single    1.392  0.020  1.392
 GV6  C11  C12  single    1.530  0.020  1.530
 GV6  O14  C13  single    1.426  0.020  1.426
 GV6  O22  C12  single    1.403  0.020  1.403
 GV6  O19  P18  double    1.468  0.020  1.468
 GV6  C12  C13  single    1.540  0.020  1.540
 GV6  C13  C16  single    1.511  0.020  1.511
 GV6  O17  P18  single    1.588  0.020  1.588
 GV6  O17  C16  single    1.432  0.020  1.432
 GV6  P18  O23  single    1.589  0.020  1.589
 GV6  P18  O20  single    1.639  0.020  1.639
 GV6  O26  C24  double    1.199  0.020  1.199
 GV6  O20  C24  single    1.354  0.020  1.354
 GV6  C24  C25  single    1.516  0.020  1.516
 GV6  C29  C30  single    1.523  0.020  1.523
 GV6  C29  C28  single    1.531  0.020  1.531
 GV6  C25  C28  single    1.547  0.020  1.547
 GV6  C25  N27  single    1.445  0.020  1.445
 GV6  C28  C31  single    1.526  0.020  1.526
 GV6  C2   H1   single    0.930  0.020  1.080
 GV6  C8   H2   single    0.930  0.020  1.080
 GV6  C10  H3   single    0.970  0.020  1.090
 GV6  C11  H4   single    0.970  0.020  1.090
 GV6  C12  H5   single    0.970  0.020  1.090
 GV6  C13  H6   single    0.970  0.020  1.090
 GV6  N15  H7   single    0.860  0.020  1.020
 GV6  N15  H8   single    0.860  0.020  1.020
 GV6  C16  H9   single    0.970  0.020  1.090
 GV6  C16  H10  single    0.970  0.020  1.090
 GV6  O21  H11  single    0.850  0.020  0.980
 GV6  O22  H12  single    0.850  0.020  0.980
 GV6  O23  H13  single    0.850  0.020  0.980
 GV6  C25  H14  single    0.970  0.020  1.090
 GV6  N27  H15  single    0.890  0.020  1.040
 GV6  N27  H16  single    0.890  0.020  1.040
 GV6  C28  H18  single    0.970  0.020  1.090
 GV6  C29  H19  single    0.970  0.020  1.090
 GV6  C29  H20  single    0.970  0.020  1.090
 GV6  C30  H21  single    0.970  0.020  1.090
 GV6  C30  H22  single    0.970  0.020  1.090
 GV6  C30  H23  single    0.970  0.020  1.090
 GV6  C31  H24  single    0.970  0.020  1.090
 GV6  C31  H25  single    0.970  0.020  1.090
 GV6  C31  H26  single    0.970  0.020  1.090

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
 GV6  C6   N1   C2   119.13  3.000
 GV6  H1   C2   N3   116.11  3.000
 GV6  H1   C2   N1   115.42  3.000
 GV6  N3   C2   N1   128.46  3.000
 GV6  C4   N3   C2   111.69  3.000
 GV6  N7   C4   C5   105.18  3.000
 GV6  N7   C4   N3   128.31  3.000
 GV6  C5   C4   N3   126.51  3.000
 GV6  N9   C5   C6   132.92  3.000
 GV6  N9   C5   C4   110.81  3.000
 GV6  C6   C5   C4   116.28  3.000
 GV6  N15  C6   C5   122.78  3.000
 GV6  C5   C6   N1   117.93  3.000
 GV6  N15  C6   N1   119.29  3.000
 GV6  C10  N7   C8   127.65  3.000
 GV6  C10  N7   C4   126.14  3.000
 GV6  C8   N7   C4   106.20  3.000
 GV6  H2   C8   N9   124.94  3.000
 GV6  H2   C8   N7   121.72  3.000
 GV6  N9   C8   N7   113.34  3.000
 GV6  C8   N9   C5   104.47  3.000
 GV6  H3   C10  O14  111.63  3.000
 GV6  H3   C10  C11  109.76  3.000
 GV6  O14  C10  C11  106.06  3.000
 GV6  H3   C10  N7   105.99  3.000
 GV6  O14  C10  N7   109.41  3.000
 GV6  C11  C10  N7   114.09  3.000
 GV6  H4   C11  O21  111.58  3.000
 GV6  H4   C11  C12  107.95  3.000
 GV6  O21  C11  C12  116.78  3.000
 GV6  H4   C11  C10  109.53  3.000
 GV6  C12  C11  C10  101.29  3.000
 GV6  O21  C11  C10  109.12  3.000
 GV6  H5   C12  O22  111.26  3.000
 GV6  H5   C12  C13  111.47  3.000
 GV6  O22  C12  C13  111.92  3.000
 GV6  H5   C12  C11  112.00  3.000
 GV6  C13  C12  C11  101.70  3.000
 GV6  O22  C12  C11  108.10  3.000
 GV6  H6   C13  C16  105.74  3.000
 GV6  H6   C13  O14  109.16  3.000
 GV6  C16  C13  O14  110.09  3.000
 GV6  H6   C13  C12  109.48  3.000
 GV6  C16  C13  C12  115.76  3.000
 GV6  O14  C13  C12  106.51  3.000
 GV6  C13  O14  C10  110.65  3.000
 GV6  H8   N15  H7   118.28  3.000
 GV6  H8   N15  C6   121.00  3.000
 GV6  H7   N15  C6   120.13  3.000
 GV6  H10  C16  H9   108.13  3.000
 GV6  H10  C16  O17  111.55  3.000
 GV6  H9   C16  O17  109.17  3.000
 GV6  H10  C16  C13  108.45  3.000
 GV6  H9   C16  C13  110.19  3.000
 GV6  O17  C16  C13  109.34  3.000
 GV6  P18  O17  C16  124.46  3.000
 GV6  O23  P18  O20   94.82  3.000
 GV6  O20  P18  O19  116.48  3.000
 GV6  O23  P18  O19  118.75  3.000
 GV6  O20  P18  O17  105.68  3.000
 GV6  O23  P18  O17  107.60  3.000
 GV6  O19  P18  O17  111.69  3.000
 GV6  C24  O20  P18  120.96  3.000
 GV6  H11  O21  C11  108.92  3.000
 GV6  H12  O22  C12  108.47  3.000
 GV6  H13  O23  P18  114.61  3.000
 GV6  O26  C24  C25  123.80  3.000
 GV6  C25  C24  O20  114.36  3.000
 GV6  O26  C24  O20  121.85  3.000
 GV6  H14  C25  C28  106.17  3.000
 GV6  H14  C25  N27  113.45  3.000
 GV6  C28  C25  N27  111.81  3.000
 GV6  H14  C25  C24  103.68  3.000
 GV6  N27  C25  C24  112.31  3.000
 GV6  C28  C25  C24  108.92  3.000
 GV6  H16  N27  H15  105.61  3.000
 GV6  H16  N27  C25  110.43  3.000
 GV6  H15  N27  C25  109.15  3.000
 GV6  H18  C28  C31  107.27  3.000
 GV6  H18  C28  C29  108.34  3.000
 GV6  C31  C28  C29  111.92  3.000
 GV6  H18  C28  C25  106.25  3.000
 GV6  C31  C28  C25  110.31  3.000
 GV6  C29  C28  C25  112.43  3.000
 GV6  H20  C29  H19  105.68  3.000
 GV6  H20  C29  C30  109.86  3.000
 GV6  H19  C29  C30  108.26  3.000
 GV6  H20  C29  C28  109.64  3.000
 GV6  H19  C29  C28  109.91  3.000
 GV6  C30  C29  C28  113.22  3.000
 GV6  H23  C30  H22  107.66  3.000
 GV6  H23  C30  H21  107.32  3.000
 GV6  H22  C30  H21  107.58  3.000
 GV6  H23  C30  C29  112.24  3.000
 GV6  H22  C30  C29  111.08  3.000
 GV6  H21  C30  C29  110.75  3.000
 GV6  H26  C31  H25  106.98  3.000
 GV6  H26  C31  H24  107.30  3.000
 GV6  H25  C31  H24  108.05  3.000
 GV6  H26  C31  C28  110.97  3.000
 GV6  H25  C31  C28  112.12  3.000
 GV6  H24  C31  C28  111.19  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
 GV6  CONST_01  C4   C5   C6   N1      0.00   0.0  0
 GV6  CONST_02  N9   C5   C6   N1    180.00   0.0  0
 GV6  CONST_03  C4   N3   C2   N1      0.00   0.0  0
 GV6  CONST_04  C5   C6   N1   C2      0.00   0.0  0
 GV6  CONST_05  C5   C4   N3   C2      0.00   0.0  0
 GV6  CONST_06  N7   C4   N3   C2    180.00   0.0  0
 GV6  CONST_07  C6   N1   C2   N3      0.00   0.0  0
 GV6  CONST_08  C6   C5   C4   N3      0.00   0.0  0
 GV6  CONST_09  N9   C5   C4   N3    180.00   0.0  0
 GV6  CONST_10  C8   N7   C4   N3    180.00   0.0  0
 GV6  CONST_11  C8   N9   C5   C4      0.00   0.0  0
 GV6  CONST_12  N9   C8   N7   C4      0.00   0.0  0
 GV6  CONST_13  C8   N7   C4   C5      0.00   0.0  0
 GV6  CONST_14  N7   C8   N9   C5      0.00   0.0  0
 GV6  CONST_15  N7   C4   C5   C6    180.00   0.0  0
 GV6  CONST_16  C8   N9   C5   C6    180.00   0.0  0
 GV6  CONST_17  N9   C5   C4   N7      0.00   0.0  0
 GV6  CONST_18  C10  N7   C4   N3      0.00   0.0  0
 GV6  CONST_19  C10  N7   C4   C5    180.00   0.0  0
 GV6  CONST_20  C10  N7   C8   N9    180.00   0.0  0
 GV6  CONST_21  N15  C6   N1   C2    180.00   0.0  0
 GV6  CONST_22  N15  C6   C5   C4    180.00   0.0  0
 GV6  CONST_23  N15  C6   C5   N9      0.00   0.0  0
 GV6  CONST_24  H1   C2   N3   C4    180.00   0.0  0
 GV6  CONST_25  H2   C8   N7   C4    180.00   0.0  0
 GV6  CONST_26  H2   C8   N9   C5    180.00   0.0  0
 GV6  CONST_27  H1   C2   N1   C6    180.00   0.0  0
 GV6  CONST_28  H2   C8   N7   C10     0.00   0.0  0
 GV6  CONST_29  H7   N15  C6   N1      0.00   0.0  0
 GV6  CONST_30  H8   N15  C6   N1    180.00   0.0  0
 GV6  CONST_31  H7   N15  C6   C5    180.00   0.0  0
 GV6  CONST_32  H8   N15  C6   C5      0.00   0.0  0
 GV6  Var_01    P18  O17  C16  C13  -159.15  30.0  1
 GV6  Var_02    O19  P18  O17  C16  -171.24  30.0  3
 GV6  Var_03    O23  P18  O17  C16   -39.24  30.0  3
 GV6  Var_04    O20  P18  O17  C16    61.17  30.0  3
 GV6  Var_05    C24  O20  P18  O17    68.31  30.0  3
 GV6  Var_06    O26  C24  O20  P18    -4.38  30.0  3
 GV6  Var_07    C25  C24  O20  P18   175.23  30.0  3
 GV6  Var_08    C24  O20  P18  O19   -56.35  30.0  3
 GV6  Var_09    C24  O20  P18  O23   178.11  30.0  3
 GV6  Var_10    H9   C16  O17  P18    80.23  30.0  3
 GV6  Var_11    H10  C16  O17  P18   -39.20  30.0  3
 GV6  Var_12    H21  C30  C29  C28  -177.85  30.0  3
 GV6  Var_13    H22  C30  C29  C28   -58.36  30.0  3
 GV6  Var_14    H23  C30  C29  C28    62.22  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
 GV6  chir_01  C10  N7   C11  O14  negativ
 GV6  chir_02  C11  O21  C12  C10  positiv
 GV6  chir_03  C12  O22  C13  C11  positiv
 GV6  chir_04  C13  O14  C12  C16  negativ
 GV6  chir_06  C25  C24  C28  N27  positiv
 GV6  chir_07  C28  C29  C25  C31  negativ
 GV6  chir_08  P18  O17  O23  O20  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
 GV6  plan-1  N1   0.020
 GV6  plan-1  C2   0.020
 GV6  plan-1  N3   0.020
 GV6  plan-1  C4   0.020
 GV6  plan-1  C5   0.020
 GV6  plan-1  C6   0.020
 GV6  plan-1  N7   0.020
 GV6  plan-1  C8   0.020
 GV6  plan-1  N9   0.020
 GV6  plan-1  C10  0.020
 GV6  plan-1  N15  0.020
 GV6  plan-1  H1   0.020
 GV6  plan-1  H2   0.020
 GV6  plan-2  C6   0.020
 GV6  plan-2  N15  0.020
 GV6  plan-2  H7   0.020
 GV6  plan-2  H8   0.020
 GV6  plan-3  O20  0.020
 GV6  plan-3  C24  0.020
 GV6  plan-3  C25  0.020
 GV6  plan-3  O26  0.020

