# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 23:43:34 2021
#   Inital geometry file: a 139 line input string
#   Ligand name: 5'-O-[(S)-{[(S)-[2-(acetylamino)ethoxy](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]guanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)NCCO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3C(=O)NC(=Nc23)N
#
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
 Y9Z  Y9Z  5'-O-[(S)-{[(S)-[2-(acetylamino)ethoxy](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]guanosine  ligand  56  34  .  2021-08-25  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Y9Z
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
 Y9Z  N    N  NR16  0  -0.728  39.5087  33.8253  11.8532
 Y9Z  C    C  CR6   0   0.505  40.6165  34.6196  11.5310
 Y9Z  O    O  O     0  -0.473  40.5172  35.5239  10.7189
 Y9Z  P    P  P     0   1.505  47.9121  33.3700  14.6129
 Y9Z  P1   P  P     0   1.459  50.1348  34.5831  15.9976
 Y9Z  C1   C  CR6   0   0.695  39.4925  32.7885  12.7416
 Y9Z  N1   N  NH2   0  -0.832  38.3175  32.1780  12.9438
 Y9Z  O1   O  OH1   0  -0.652  43.8551  30.0445  13.3483
 Y9Z  C2   C  CR56  0   0.511  41.6421  33.1318  13.1328
 Y9Z  N2   N  N     0  -0.513  40.5535  32.4024  13.4070
 Y9Z  O2   O  OH1   0  -0.665  44.2524  29.5289  15.9652
 Y9Z  C3   C  CR56  0  -0.098  41.7630  34.1999  12.2644
 Y9Z  N3   N  N     0  -0.441  43.0464  34.6842  12.2660
 Y9Z  O3   O  O2    0  -0.578  46.4255  33.2054  15.1364
 Y9Z  C4   C  CR15  0   0.094  43.6838  33.9304  13.1052
 Y9Z  N4   N  NR5   0  -0.541  42.8835  32.9617  13.6669
 Y9Z  O4   O  O2    0  -0.688  48.5487  34.3039  15.7672
 Y9Z  C5   C  CH1   0   0.202  43.2650  31.9647  14.6308
 Y9Z  N5   N  NH1   0  -0.594  52.6362  34.3950  19.0672
 Y9Z  O5   O  O2    0  -0.583  50.4634  33.5824  17.1988
 Y9Z  C6   C  CH1   0  -0.006  44.3889  31.0472  14.1514
 Y9Z  O6   O  O     0  -0.561  51.6915  36.3775  18.5135
 Y9Z  C7   C  CH1   0  -0.049  45.0089  30.6044  15.4771
 Y9Z  O7   O  OH1   0  -0.758  50.0582  36.0147  16.6266
 Y9Z  C8   C  CH1   0  -0.016  44.8381  31.8642  16.3433
 Y9Z  O8   O  O     0  -0.699  50.9448  34.3904  14.7808
 Y9Z  C9   C  CH2   0  -0.209  46.0567  32.7527  16.4432
 Y9Z  O9   O  O     0  -0.668  47.9409  33.8957  13.2426
 Y9Z  C10  C  CH2   0  -0.187  51.7350  32.9284  17.2844
 Y9Z  O10  O  OH1   0  -0.741  48.6694  31.9987  14.8946
 Y9Z  C11  C  CH2   0  -0.361  52.8365  33.8682  17.7363
 Y9Z  O11  O  O2    0  -0.493  43.7458  32.5929  15.7873
 Y9Z  C12  C  C     0   0.582  52.1118  35.5802  19.3653
 Y9Z  C13  C  CH3   0  -0.766  52.0789  35.9474  20.8204
 Y9Z  H1   H  HNR6  0   0.426  38.6506  34.0550  11.3681
 Y9Z  H2   H  HNH2  0   0.414  38.3188  31.3213  13.4708
 Y9Z  H3   H  HNH2  0   0.416  37.5383  32.3258  12.3252
 Y9Z  H4   H  HOH1  0   0.464  44.5765  29.5805  12.9126
 Y9Z  H5   H  HOH1  0   0.458  44.6323  29.2470  16.8033
 Y9Z  H6   H  HCR5  0   0.287  44.7271  34.0310  13.3628
 Y9Z  H7   H  HCH1  0   0.263  42.3641  31.3768  14.8384
 Y9Z  H8   H  HNH1  0   0.420  52.9466  33.8171  19.8322
 Y9Z  H9   H  HCH1  0   0.244  45.1310  31.6427  13.6082
 Y9Z  H10  H  HCH1  0   0.247  46.0668  30.3336  15.3692
 Y9Z  H11  H  HOH1  0   0.510  50.7369  36.1825  17.3634
 Y9Z  H12  H  HCH1  0   0.270  44.5923  31.5734  17.3712
 Y9Z  H13  H  HCH2  0   0.254  46.8603  32.1890  16.9226
 Y9Z  H14  H  HCH2  0   0.273  45.8406  33.6256  17.0607
 Y9Z  H15  H  HCH2  0   0.256  52.0086  32.4860  16.3251
 Y9Z  H16  H  HCH2  0   0.265  51.6032  32.1226  18.0045
 Y9Z  H17  H  HOH1  0   0.509  48.7763  31.4326  14.1173
 Y9Z  H18  H  HCH2  0   0.291  53.7697  33.3044  17.7365
 Y9Z  H19  H  HCH2  0   0.268  52.9716  34.6899  17.0315
 Y9Z  H20  H  HCH3  0   0.275  51.0589  36.2032  21.1044
 Y9Z  H21  H  HCH3  0   0.258  52.4364  35.1545  21.4739
 Y9Z  H22  H  HCH3  0   0.278  52.6949  36.8325  20.9799

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
 Y9Z  O    C    double    1.219  0.020  1.219
 Y9Z  C    N    single    1.401  0.020  1.401
 Y9Z  C    C3   single    1.424  0.020  1.424
 Y9Z  N    C1   single    1.365  0.020  1.365
 Y9Z  C3   N3   aromatic  1.372  0.020  1.372
 Y9Z  C3   C2   aromatic  1.382  0.020  1.382
 Y9Z  N3   C4   aromatic  1.296  0.020  1.296
 Y9Z  C1   N1   single    1.339  0.020  1.339
 Y9Z  C1   N2   double    1.311  0.020  1.311
 Y9Z  C4   N4   aromatic  1.376  0.020  1.376
 Y9Z  C2   N2   single    1.339  0.020  1.339
 Y9Z  C2   N4   aromatic  1.362  0.020  1.362
 Y9Z  O1   C6   single    1.391  0.020  1.391
 Y9Z  O9   P    double    1.468  0.020  1.468
 Y9Z  N4   C5   single    1.438  0.020  1.438
 Y9Z  C6   C5   single    1.528  0.020  1.528
 Y9Z  C6   C7   single    1.529  0.020  1.529
 Y9Z  C5   O11  single    1.401  0.020  1.401
 Y9Z  P    O3   single    1.585  0.020  1.585
 Y9Z  P    O10  single    1.592  0.020  1.592
 Y9Z  P    O4   single    1.615  0.020  1.615
 Y9Z  O3   C9   single    1.431  0.020  1.431
 Y9Z  O8   P1   double    1.474  0.020  1.474
 Y9Z  C7   O2   single    1.403  0.020  1.403
 Y9Z  C7   C8   single    1.538  0.020  1.538
 Y9Z  O11  C8   single    1.426  0.020  1.426
 Y9Z  O4   P1   single    1.627  0.020  1.627
 Y9Z  P1   O7   single    1.566  0.020  1.566
 Y9Z  P1   O5   single    1.598  0.020  1.598
 Y9Z  C8   C9   single    1.511  0.020  1.511
 Y9Z  C11  C10  single    1.517  0.020  1.517
 Y9Z  C11  N5   single    1.445  0.020  1.445
 Y9Z  O5   C10  single    1.432  0.020  1.432
 Y9Z  N5   C12  single    1.330  0.020  1.330
 Y9Z  O6   C12  double    1.240  0.020  1.240
 Y9Z  C12  C13  single    1.501  0.020  1.501
 Y9Z  N    H1   single    0.860  0.020  1.020
 Y9Z  N1   H2   single    0.890  0.020  1.040
 Y9Z  N1   H3   single    0.890  0.020  1.040
 Y9Z  O1   H4   single    0.850  0.020  0.980
 Y9Z  O2   H5   single    0.850  0.020  0.980
 Y9Z  C4   H6   single    0.930  0.020  1.080
 Y9Z  C5   H7   single    0.970  0.020  1.090
 Y9Z  N5   H8   single    0.860  0.020  1.020
 Y9Z  C6   H9   single    0.970  0.020  1.090
 Y9Z  C7   H10  single    0.970  0.020  1.090
 Y9Z  O7   H11  single    0.850  0.020  0.980
 Y9Z  C8   H12  single    0.970  0.020  1.090
 Y9Z  C9   H13  single    0.970  0.020  1.090
 Y9Z  C9   H14  single    0.970  0.020  1.090
 Y9Z  C10  H15  single    0.970  0.020  1.090
 Y9Z  C10  H16  single    0.970  0.020  1.090
 Y9Z  O10  H17  single    0.850  0.020  0.980
 Y9Z  C11  H18  single    0.970  0.020  1.090
 Y9Z  C11  H19  single    0.970  0.020  1.090
 Y9Z  C13  H20  single    0.970  0.020  1.090
 Y9Z  C13  H21  single    0.970  0.020  1.090
 Y9Z  C13  H22  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
 Y9Z  H1   N    C1   118.30  3.000
 Y9Z  H1   N    C    115.57  3.000
 Y9Z  C1   N    C    126.13  3.000
 Y9Z  C3   C    O    128.83  3.000
 Y9Z  C3   C    N    110.55  3.000
 Y9Z  O    C    N    120.62  3.000
 Y9Z  O10  P    O9   117.67  3.000
 Y9Z  O10  P    O4   100.61  3.000
 Y9Z  O9   P    O4   116.89  3.000
 Y9Z  O4   P    O3   101.17  3.000
 Y9Z  O10  P    O3   107.36  3.000
 Y9Z  O9   P    O3   111.35  3.000
 Y9Z  O8   P1   O7   118.56  3.000
 Y9Z  O7   P1   O5   106.31  3.000
 Y9Z  O8   P1   O5   115.19  3.000
 Y9Z  O5   P1   O4   101.51  3.000
 Y9Z  O7   P1   O4    99.56  3.000
 Y9Z  O8   P1   O4   113.34  3.000
 Y9Z  N2   C1   N1   119.95  3.000
 Y9Z  N2   C1   N    122.99  3.000
 Y9Z  N1   C1   N    117.05  3.000
 Y9Z  H3   N1   H2   116.64  3.000
 Y9Z  H3   N1   C1   121.31  3.000
 Y9Z  H2   N1   C1   117.79  3.000
 Y9Z  H4   O1   C6   108.75  3.000
 Y9Z  N4   C2   C3   105.26  3.000
 Y9Z  N4   C2   N2   126.35  3.000
 Y9Z  C3   C2   N2   128.39  3.000
 Y9Z  C2   N2   C1   113.19  3.000
 Y9Z  H5   O2   C7   108.35  3.000
 Y9Z  N3   C3   C2   110.73  3.000
 Y9Z  C2   C3   C    118.75  3.000
 Y9Z  N3   C3   C    130.52  3.000
 Y9Z  C4   N3   C3   104.81  3.000
 Y9Z  C9   O3   P    125.19  3.000
 Y9Z  H6   C4   N4   122.02  3.000
 Y9Z  H6   C4   N3   125.16  3.000
 Y9Z  N4   C4   N3   112.81  3.000
 Y9Z  C5   N4   C4   127.39  3.000
 Y9Z  C5   N4   C2   126.23  3.000
 Y9Z  C4   N4   C2   106.38  3.000
 Y9Z  P1   O4   P    125.78  3.000
 Y9Z  H7   C5   O11  111.49  3.000
 Y9Z  H7   C5   C6   110.00  3.000
 Y9Z  O11  C5   C6   106.01  3.000
 Y9Z  H7   C5   N4   106.31  3.000
 Y9Z  O11  C5   N4   109.48  3.000
 Y9Z  C6   C5   N4   113.65  3.000
 Y9Z  H8   N5   C12  117.53  3.000
 Y9Z  H8   N5   C11  116.57  3.000
 Y9Z  C12  N5   C11  125.87  3.000
 Y9Z  C10  O5   P1   120.90  3.000
 Y9Z  H9   C6   C7   108.21  3.000
 Y9Z  H9   C6   C5   109.11  3.000
 Y9Z  C7   C6   C5   101.54  3.000
 Y9Z  H9   C6   O1   111.44  3.000
 Y9Z  C7   C6   O1   116.58  3.000
 Y9Z  C5   C6   O1   109.37  3.000
 Y9Z  H10  C7   C8   111.37  3.000
 Y9Z  H10  C7   C6   112.15  3.000
 Y9Z  C8   C7   C6   101.89  3.000
 Y9Z  H10  C7   O2   111.40  3.000
 Y9Z  C8   C7   O2   111.85  3.000
 Y9Z  C6   C7   O2   107.76  3.000
 Y9Z  H11  O7   P1   114.19  3.000
 Y9Z  H12  C8   O11  109.23  3.000
 Y9Z  H12  C8   C9   105.95  3.000
 Y9Z  O11  C8   C9   110.06  3.000
 Y9Z  H12  C8   C7   109.61  3.000
 Y9Z  C9   C8   C7   115.41  3.000
 Y9Z  O11  C8   C7   106.50  3.000
 Y9Z  H14  C9   H13  108.07  3.000
 Y9Z  H14  C9   C8   110.38  3.000
 Y9Z  H13  C9   C8   108.59  3.000
 Y9Z  H14  C9   O3   108.35  3.000
 Y9Z  H13  C9   O3   111.98  3.000
 Y9Z  C8   C9   O3   109.47  3.000
 Y9Z  H16  C10  H15  108.16  3.000
 Y9Z  H16  C10  C11  110.45  3.000
 Y9Z  H15  C10  C11  109.33  3.000
 Y9Z  H16  C10  O5   105.67  3.000
 Y9Z  H15  C10  O5   110.80  3.000
 Y9Z  C11  C10  O5   112.31  3.000
 Y9Z  H17  O10  P    114.48  3.000
 Y9Z  H19  C11  H18  106.47  3.000
 Y9Z  H19  C11  C10  111.35  3.000
 Y9Z  H18  C11  C10  107.53  3.000
 Y9Z  H19  C11  N5   109.73  3.000
 Y9Z  H18  C11  N5   107.88  3.000
 Y9Z  C10  C11  N5   113.55  3.000
 Y9Z  C8   O11  C5   110.83  3.000
 Y9Z  C13  C12  O6   120.07  3.000
 Y9Z  C13  C12  N5   116.36  3.000
 Y9Z  O6   C12  N5   123.55  3.000
 Y9Z  H22  C13  H21  108.56  3.000
 Y9Z  H22  C13  H20  107.48  3.000
 Y9Z  H21  C13  H20  108.80  3.000
 Y9Z  H22  C13  C12  109.15  3.000
 Y9Z  H21  C13  C12  113.38  3.000
 Y9Z  H20  C13  C12  109.31  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
 Y9Z  CONST_01  C4   N3   C3   C2      0.00   0.0  0
 Y9Z  CONST_02  N3   C4   N4   C2      0.00   0.0  0
 Y9Z  CONST_03  N4   C4   N3   C3      0.00   0.0  0
 Y9Z  CONST_04  C4   N4   C2   C3      0.00   0.0  0
 Y9Z  CONST_05  N4   C2   C3   N3      0.00   0.0  0
 Y9Z  CONST_06  C5   N4   C2   N2      0.00   0.0  0
 Y9Z  CONST_07  C5   N4   C2   C3    180.00   0.0  0
 Y9Z  CONST_08  C5   N4   C4   N3    180.00   0.0  0
 Y9Z  CONST_09  C2   N2   C1   N       0.00   0.0  0
 Y9Z  CONST_10  N2   C1   N    C       0.00   0.0  0
 Y9Z  CONST_11  C3   C    N    C1      0.00   0.0  0
 Y9Z  CONST_12  N1   C1   N    C     180.00   0.0  0
 Y9Z  CONST_13  C1   N    C    O     180.00   0.0  0
 Y9Z  CONST_14  C2   N2   C1   N1    180.00   0.0  0
 Y9Z  CONST_15  H6   C4   N4   C2    180.00   0.0  0
 Y9Z  CONST_16  H1   N    C1   N2    180.00   0.0  0
 Y9Z  CONST_17  H2   N1   C1   N     180.00   0.0  0
 Y9Z  CONST_18  H3   N1   C1   N       0.00   0.0  0
 Y9Z  CONST_19  C11  N5   C12  O6      0.00   0.0  0
 Y9Z  CONST_20  C13  C12  N5   C11   180.00   0.0  0
 Y9Z  CONST_21  H8   N5   C12  O6    180.00   0.0  0
 Y9Z  Var_01    C8   C9   O3   P    -141.56  30.0  3
 Y9Z  Var_02    O8   P1   O4   P      24.02  30.0  3
 Y9Z  Var_03    O9   P    O4   P1    -72.90  30.0  1
 Y9Z  Var_04    C11  C10  O5   P1     74.69  30.0  3
 Y9Z  Var_05    O5   C10  C11  N5     62.92  30.0  3
 Y9Z  Var_06    C12  N5   C11  C10   -97.62  30.0  3
 Y9Z  Var_07    H20  C13  C12  N5   -125.42  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
 Y9Z  chir_03  C5  N4   C6   O11  negativ
 Y9Z  chir_04  C6  O1   C7   C5   positiv
 Y9Z  chir_05  C7  O2   C8   C6   positiv
 Y9Z  chir_06  C8  O11  C7   C9   negativ
 Y9Z  chir_07  P   O3   O10  O4   both
 Y9Z  chir_08  P1  O4   O7   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
 Y9Z  plan-1  N    0.020
 Y9Z  plan-1  C    0.020
 Y9Z  plan-1  O    0.020
 Y9Z  plan-1  C1   0.020
 Y9Z  plan-1  N1   0.020
 Y9Z  plan-1  C2   0.020
 Y9Z  plan-1  N2   0.020
 Y9Z  plan-1  C3   0.020
 Y9Z  plan-1  N3   0.020
 Y9Z  plan-1  C4   0.020
 Y9Z  plan-1  N4   0.020
 Y9Z  plan-1  C5   0.020
 Y9Z  plan-1  H1   0.020
 Y9Z  plan-1  H2   0.020
 Y9Z  plan-1  H3   0.020
 Y9Z  plan-1  H6   0.020
 Y9Z  plan-2  N5   0.020
 Y9Z  plan-2  O6   0.020
 Y9Z  plan-2  C11  0.020
 Y9Z  plan-2  C12  0.020
 Y9Z  plan-2  C13  0.020
 Y9Z  plan-2  H8   0.020

