# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 03:36:09 2021
#   Inital geometry file: a 147 line input string
#   Ligand name: 5-(5-aminopent-1-yn-1-yl)-7-{2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-7H-pyrrolo[2,3-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCC#Cc1cn([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)c3ncnc(N)c13
#
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
 0L4  0L4  5-(5-aminopent-1-yn-1-yl)-7-{2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-7H-pyrrolo[2,3-d]pyrimidin-4-amine  ligand  60  36  .  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_0L4
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
 0L4  O2A  O  O     0  -0.670  19.7488  -16.2138  -12.7325
 0L4  PA   P  P     0   1.490  19.1805  -16.5429  -11.4172
 0L4  O1A  O  OH1   0  -0.698  19.4463  -15.5896  -10.1880
 0L4  O3A  O  O2    0  -0.683  17.5453  -16.6233  -11.4746
 0L4  PB   P  P     0   1.483  16.6512  -16.6760  -12.8061
 0L4  O3B  O  O2    0  -0.687  16.7594  -15.1456  -13.3006
 0L4  PG   P  P     0   1.461  16.7640  -14.6895  -14.8751
 0L4  O2G  O  OH1   0  -0.721  18.2252  -15.0188  -15.3886
 0L4  O3T  O  OH1   0  -0.710  16.9069  -13.1218  -14.7436
 0L4  O1G  O  O     0  -0.684  15.6137  -15.2434  -15.6053
 0L4  O1B  O  OH1   0  -0.700  15.2317  -16.7897  -12.1272
 0L4  O2B  O  O     0  -0.677  17.0361  -17.6468  -13.8414
 0L4  O5'  O  O2    0  -0.572  19.5817  -17.9142  -10.7404
 0L4  C5'  C  CH2   0  -0.230  19.3883  -19.1644  -11.4243
 0L4  C4'  C  CH1   0   0.027  18.6132  -20.1299  -10.5656
 0L4  O4'  O  O2    0  -0.496  19.3690  -20.4946   -9.4201
 0L4  C1'  C  CH1   0   0.184  18.5201  -20.7969   -8.3442
 0L4  C2'  C  CH2   0  -0.539  17.0902  -20.6242   -8.8548
 0L4  C3'  C  CH1   0   0.015  17.2735  -19.6517  -10.0147
 0L4  O3'  O  OH1   0  -0.658  16.3056  -19.7075  -11.0234
 0L4  N9   N  NR5   0  -0.543  18.8484  -19.9119   -7.2343
 0L4  C8   C  CR15  0  -0.070  19.3593  -18.6431   -7.3067
 0L4  C7   C  CR5   0  -0.152  19.4902  -18.1219   -6.0442
 0L4  C5   C  CR56  0  -0.124  19.0208  -19.1358   -5.1482
 0L4  C6   C  CR6   0   0.408  18.8648  -19.2929   -3.7576
 0L4  N6   N  NH2   0  -0.827  19.1804  -18.3299   -2.8850
 0L4  N1   N  N     0  -0.473  18.3664  -20.4410   -3.2887
 0L4  C2   C  CR16  0   0.039  18.0342  -21.3950   -4.1556
 0L4  N3   N  N     0  -0.468  18.1289  -21.3722   -5.4706
 0L4  C4   C  CR56  0   0.511  18.6317  -20.2235   -5.9270
 0L4  C42  C  CSP   0   0.107  20.0087  -16.8476   -5.7147
 0L4  C43  C  CSP   0  -0.019  20.4523  -15.7624   -5.4266
 0L4  C44  C  CH2   0  -0.621  21.0140  -14.4493   -5.1364
 0L4  C45  C  CH2   0  -0.440  22.0396  -14.0039   -6.1831
 0L4  C46  C  CH2   0  -0.280  21.4451  -13.8727   -7.5761
 0L4  N47  N  NH2   0  -0.799  22.4585  -13.4437   -8.5283
 0L4  H1   H  HOH1  0   0.515  19.4841  -14.6488  -10.4110
 0L4  H2   H  HOH1  0   0.503  18.4490  -15.9592  -15.4305
 0L4  H3   H  HOH1  0   0.514  16.0683  -12.6406  -14.7712
 0L4  H4   H  HOH1  0   0.518  14.5568  -17.2273  -12.6656
 0L4  H5   H  HCH2  0   0.258  18.8512  -19.0357  -12.3668
 0L4  H6   H  HCH2  0   0.287  20.3729  -19.5670  -11.6625
 0L4  H7   H  HCH1  0   0.254  18.4362  -21.0140  -11.1953
 0L4  H8   H  HCH1  0   0.273  18.7012  -21.8125   -7.9875
 0L4  H9   H  HCH2  0   0.280  16.4091  -20.2741   -8.0801
 0L4  H10  H  HCH2  0   0.266  16.7208  -21.5806   -9.2317
 0L4  H11  H  HCH1  0   0.230  17.3681  -18.6332   -9.6182
 0L4  H12  H  HOH1  0   0.460  15.5077  -19.2748  -10.7055
 0L4  H13  H  HCR5  0   0.302  19.6190  -18.1868   -8.2461
 0L4  H14  H  HNH2  0   0.401  19.1273  -18.5152   -1.8980
 0L4  H15  H  HNH2  0   0.408  19.6459  -17.4891   -3.1810
 0L4  H16  H  HCR6  0   0.250  17.6345  -22.3043   -3.7190
 0L4  H17  H  HCH2  0   0.276  21.4829  -14.4701   -4.1497
 0L4  H18  H  HCH2  0   0.263  20.2062  -13.7135   -5.0741
 0L4  H19  H  HCH2  0   0.229  22.8742  -14.7085   -6.2061
 0L4  H20  H  HCH2  0   0.237  22.4452  -13.0394   -5.8646
 0L4  H21  H  HCH2  0   0.191  20.5725  -13.2037   -7.5281
 0L4  H22  H  HCH2  0   0.220  21.0674  -14.8466   -7.8973
 0L4  H23  H  HNH2  0   0.343  22.0573  -13.4045   -9.4565
 0L4  H24  H  HNH2  0   0.339  22.7401  -12.4944   -8.3155

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
 0L4  O1G  PG   double    1.471  0.020  1.471
 0L4  O2G  PG   single    1.583  0.020  1.583
 0L4  PG   O3T  single    1.580  0.020  1.580
 0L4  PG   O3B  single    1.639  0.020  1.639
 0L4  O2B  PB   double    1.471  0.020  1.471
 0L4  O2A  PA   double    1.470  0.020  1.470
 0L4  O3B  PB   single    1.612  0.020  1.612
 0L4  PB   O1B  single    1.578  0.020  1.578
 0L4  PB   O3A  single    1.605  0.020  1.605
 0L4  C5'  O5'  single    1.438  0.020  1.438
 0L4  C5'  C4'  single    1.507  0.020  1.507
 0L4  PA   O3A  single    1.638  0.020  1.638
 0L4  PA   O5'  single    1.581  0.020  1.581
 0L4  PA   O1A  single    1.578  0.020  1.578
 0L4  O3'  C3'  single    1.399  0.020  1.399
 0L4  C4'  C3'  single    1.525  0.020  1.525
 0L4  C4'  O4'  single    1.420  0.020  1.420
 0L4  C3'  C2'  single    1.525  0.020  1.525
 0L4  O4'  C1'  single    1.403  0.020  1.403
 0L4  N47  C46  single    1.455  0.020  1.455
 0L4  C2'  C1'  single    1.528  0.020  1.528
 0L4  C1'  N9   single    1.457  0.020  1.457
 0L4  C46  C45  single    1.520  0.020  1.520
 0L4  C8   N9   aromatic  1.370  0.020  1.370
 0L4  C8   C7   aromatic  1.372  0.020  1.372
 0L4  N9   C4   aromatic  1.361  0.020  1.361
 0L4  C45  C44  single    1.532  0.020  1.532
 0L4  C7   C42  single    1.415  0.020  1.415
 0L4  C7   C5   aromatic  1.432  0.020  1.432
 0L4  C4   N3   aromatic  1.334  0.020  1.334
 0L4  C4   C5   aromatic  1.393  0.020  1.393
 0L4  C42  C43  triple    1.207  0.020  1.207
 0L4  C43  C44  single    1.457  0.020  1.457
 0L4  N3   C2   aromatic  1.319  0.020  1.319
 0L4  C5   C6   aromatic  1.408  0.020  1.408
 0L4  C2   N1   aromatic  1.331  0.020  1.331
 0L4  C6   N1   aromatic  1.336  0.020  1.336
 0L4  C6   N6   single    1.337  0.020  1.337
 0L4  O1A  H1   single    0.850  0.020  0.980
 0L4  O2G  H2   single    0.850  0.020  0.980
 0L4  O3T  H3   single    0.850  0.020  0.980
 0L4  O1B  H4   single    0.850  0.020  0.980
 0L4  C5'  H5   single    0.970  0.020  1.090
 0L4  C5'  H6   single    0.970  0.020  1.090
 0L4  C4'  H7   single    0.970  0.020  1.090
 0L4  C1'  H8   single    0.970  0.020  1.090
 0L4  C2'  H9   single    0.970  0.020  1.090
 0L4  C2'  H10  single    0.970  0.020  1.090
 0L4  C3'  H11  single    0.970  0.020  1.090
 0L4  O3'  H12  single    0.850  0.020  0.980
 0L4  C8   H13  single    0.930  0.020  1.080
 0L4  N6   H14  single    0.860  0.020  1.020
 0L4  N6   H15  single    0.860  0.020  1.020
 0L4  C2   H16  single    0.930  0.020  1.080
 0L4  C44  H17  single    0.970  0.020  1.090
 0L4  C44  H18  single    0.970  0.020  1.090
 0L4  C45  H19  single    0.970  0.020  1.090
 0L4  C45  H20  single    0.970  0.020  1.090
 0L4  C46  H21  single    0.970  0.020  1.090
 0L4  C46  H22  single    0.970  0.020  1.090
 0L4  N47  H23  single    0.890  0.020  1.040
 0L4  N47  H24  single    0.890  0.020  1.040

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
 0L4  O5'  PA   O3A  103.05  3.000
 0L4  O5'  PA   O1A   98.50  3.000
 0L4  O3A  PA   O1A  103.00  3.000
 0L4  O1A  PA   O2A  119.77  3.000
 0L4  O5'  PA   O2A  118.63  3.000
 0L4  O3A  PA   O2A  111.44  3.000
 0L4  H1   O1A  PA   114.48  3.000
 0L4  PB   O3A  PA   125.93  3.000
 0L4  O2B  PB   O1B  119.40  3.000
 0L4  O1B  PB   O3B  105.12  3.000
 0L4  O2B  PB   O3B  113.15  3.000
 0L4  O1B  PB   O3A   98.43  3.000
 0L4  O3B  PB   O3A  100.72  3.000
 0L4  O2B  PB   O3A  117.39  3.000
 0L4  PG   O3B  PB   123.99  3.000
 0L4  O1G  PG   O3T  119.06  3.000
 0L4  O3T  PG   O2G   98.62  3.000
 0L4  O1G  PG   O2G  118.85  3.000
 0L4  O3T  PG   O3B  101.33  3.000
 0L4  O2G  PG   O3B  104.85  3.000
 0L4  O1G  PG   O3B  111.71  3.000
 0L4  H2   O2G  PG   115.44  3.000
 0L4  H3   O3T  PG   114.39  3.000
 0L4  H4   O1B  PB   114.87  3.000
 0L4  C5'  O5'  PA   121.08  3.000
 0L4  H6   C5'  H5   107.40  3.000
 0L4  H6   C5'  C4'  110.64  3.000
 0L4  H5   C5'  C4'  108.31  3.000
 0L4  H6   C5'  O5'  107.67  3.000
 0L4  H5   C5'  O5'  111.96  3.000
 0L4  C4'  C5'  O5'  110.81  3.000
 0L4  H7   C4'  C3'  108.51  3.000
 0L4  H7   C4'  O4'  109.94  3.000
 0L4  C3'  C4'  O4'  104.87  3.000
 0L4  H7   C4'  C5'  105.76  3.000
 0L4  O4'  C4'  C5'  110.52  3.000
 0L4  C3'  C4'  C5'  117.18  3.000
 0L4  C1'  O4'  C4'  110.60  3.000
 0L4  H8   C1'  N9   106.19  3.000
 0L4  H8   C1'  C2'  111.69  3.000
 0L4  N9   C1'  C2'  113.37  3.000
 0L4  H8   C1'  O4'  110.52  3.000
 0L4  N9   C1'  O4'  108.47  3.000
 0L4  C2'  C1'  O4'  106.59  3.000
 0L4  H10  C2'  H9   108.38  3.000
 0L4  H10  C2'  C3'  109.67  3.000
 0L4  H9   C2'  C3'  114.28  3.000
 0L4  H10  C2'  C1'  109.44  3.000
 0L4  H9   C2'  C1'  112.57  3.000
 0L4  C3'  C2'  C1'  102.34  3.000
 0L4  H11  C3'  O3'  110.93  3.000
 0L4  H11  C3'  C2'  109.12  3.000
 0L4  O3'  C3'  C2'  116.10  3.000
 0L4  H11  C3'  C4'  110.23  3.000
 0L4  C2'  C3'  C4'  100.39  3.000
 0L4  O3'  C3'  C4'  109.55  3.000
 0L4  H12  O3'  C3'  108.52  3.000
 0L4  C4   N9   C8   108.79  3.000
 0L4  C4   N9   C1'  123.83  3.000
 0L4  C8   N9   C1'  127.34  3.000
 0L4  H13  C8   C7   128.25  3.000
 0L4  H13  C8   N9   121.93  3.000
 0L4  C7   C8   N9   109.81  3.000
 0L4  C42  C7   C5   127.74  3.000
 0L4  C5   C7   C8   105.98  3.000
 0L4  C42  C7   C8   126.26  3.000
 0L4  C4   C5   C6   115.72  3.000
 0L4  C6   C5   C7   137.15  3.000
 0L4  C4   C5   C7   107.13  3.000
 0L4  N1   C6   N6   118.53  3.000
 0L4  N6   C6   C5   122.54  3.000
 0L4  N1   C6   C5   118.92  3.000
 0L4  H15  N6   H14  117.87  3.000
 0L4  H15  N6   C6   121.28  3.000
 0L4  H14  N6   C6   119.68  3.000
 0L4  C2   N1   C6   118.70  3.000
 0L4  H16  C2   N3   116.25  3.000
 0L4  H16  C2   N1   115.51  3.000
 0L4  N3   C2   N1   128.25  3.000
 0L4  C4   N3   C2   112.52  3.000
 0L4  N3   C4   C5   125.89  3.000
 0L4  C5   C4   N9   108.28  3.000
 0L4  N3   C4   N9   125.83  3.000
 0L4  C43  C42  C7   180.00  3.000
 0L4  C44  C43  C42  180.00  3.000
 0L4  H18  C44  H17  106.15  3.000
 0L4  H18  C44  C45  109.73  3.000
 0L4  H17  C44  C45  109.59  3.000
 0L4  H18  C44  C43  109.43  3.000
 0L4  H17  C44  C43  109.15  3.000
 0L4  C45  C44  C43  112.58  3.000
 0L4  H20  C45  H19  106.96  3.000
 0L4  H20  C45  C46  109.62  3.000
 0L4  H19  C45  C46  109.58  3.000
 0L4  H20  C45  C44  107.80  3.000
 0L4  H19  C45  C44  109.78  3.000
 0L4  C46  C45  C44  112.92  3.000
 0L4  H22  C46  H21  106.29  3.000
 0L4  H22  C46  N47  108.13  3.000
 0L4  H21  C46  N47  113.68  3.000
 0L4  H22  C46  C45  109.12  3.000
 0L4  H21  C46  C45  108.82  3.000
 0L4  N47  C46  C45  110.65  3.000
 0L4  H24  N47  H23  105.47  3.000
 0L4  H24  N47  C46  109.42  3.000
 0L4  H23  N47  C46  109.60  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
 0L4  CONST_01  C5   C7   C8   N9      0.00   0.0  0
 0L4  CONST_02  C2   N3   C4   N9    180.00   0.0  0
 0L4  CONST_03  C7   C5   C4   N9      0.00   0.0  0
 0L4  CONST_04  C6   C5   C4   N9    180.00   0.0  0
 0L4  CONST_05  N3   C4   N9   C8    180.00   0.0  0
 0L4  CONST_06  C5   C4   N9   C8      0.00   0.0  0
 0L4  CONST_07  C4   C5   C7   C8      0.00   0.0  0
 0L4  CONST_08  C6   C5   C7   C8    180.00   0.0  0
 0L4  CONST_09  C4   N9   C8   C7      0.00   0.0  0
 0L4  CONST_10  N3   C4   C5   C7    180.00   0.0  0
 0L4  CONST_11  N1   C6   C5   C7    180.00   0.0  0
 0L4  CONST_12  C2   N3   C4   C5      0.00   0.0  0
 0L4  CONST_13  C2   N1   C6   C5      0.00   0.0  0
 0L4  CONST_14  N3   C4   C5   C6      0.00   0.0  0
 0L4  CONST_15  N3   C2   N1   C6      0.00   0.0  0
 0L4  CONST_16  C4   N3   C2   N1      0.00   0.0  0
 0L4  CONST_17  C4   C5   C6   N1      0.00   0.0  0
 0L4  CONST_18  C7   C8   N9   C1'   180.00   0.0  0
 0L4  CONST_19  N3   C4   N9   C1'     0.00   0.0  0
 0L4  CONST_20  C5   C4   N9   C1'   180.00   0.0  0
 0L4  CONST_21  C42  C7   C8   N9    180.00   0.0  0
 0L4  CONST_22  N6   C6   C5   C7      0.00   0.0  0
 0L4  CONST_23  C42  C7   C5   C6      0.00   0.0  0
 0L4  CONST_24  C4   C5   C6   N6    180.00   0.0  0
 0L4  CONST_25  C2   N1   C6   N6    180.00   0.0  0
 0L4  CONST_26  C42  C7   C5   C4    180.00   0.0  0
 0L4  CONST_27  H13  C8   N9   C1'     0.00   0.0  0
 0L4  CONST_28  H16  C2   N1   C6    180.00   0.0  0
 0L4  CONST_29  H14  N6   C6   C5    180.00   0.0  0
 0L4  CONST_30  H15  N6   C6   C5      0.00   0.0  0
 0L4  Var_01    C4'  C5'  O5'  PA   -127.36  30.0  2
 0L4  Var_02    O2B  PB   O3A  PA     48.74  30.0  2
 0L4  Var_03    O1G  PG   O3B  PB     52.92  30.0  3
 0L4  Var_04    O5'  PA   O3A  PB   -115.19  30.0  2
 0L4  Var_05    C45  C44  C43  C42   -11.75  30.0  3
 0L4  Var_06    C46  C45  C44  C43    61.57  30.0  1
 0L4  Var_07    N47  C46  C45  C44   179.80  30.0  1
 0L4  Var_08    H23  N47  C46  C45   177.30  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
 0L4  chir_03  C4'  C5'  C3'  O4'  positiv
 0L4  chir_04  C1'  O4'  N9   C2'  negativ
 0L4  chir_05  C3'  O3'  C4'  C2'  positiv
 0L4  chir_06  PA   O3A  O5'  O1A  both
 0L4  chir_07  PB   O1B  O3B  O2B  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
 0L4  plan-1  C1'  0.020
 0L4  plan-1  N9   0.020
 0L4  plan-1  C8   0.020
 0L4  plan-1  C7   0.020
 0L4  plan-1  C5   0.020
 0L4  plan-1  C6   0.020
 0L4  plan-1  N6   0.020
 0L4  plan-1  N1   0.020
 0L4  plan-1  C2   0.020
 0L4  plan-1  N3   0.020
 0L4  plan-1  C4   0.020
 0L4  plan-1  C42  0.020
 0L4  plan-1  C43  0.020
 0L4  plan-1  H13  0.020
 0L4  plan-1  H16  0.020
 0L4  plan-2  C6   0.020
 0L4  plan-2  N6   0.020
 0L4  plan-2  H14  0.020
 0L4  plan-2  H15  0.020

