# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 08:24:19 2021
#   Inital geometry file: a 156 line input string
#   Ligand name: 2-amino-5-(5-aminopent-1-yn-1-yl)-7-{2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one
#   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)c3N=C(N)NC(=O)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
 0L7  0L7  2-amino-5-(5-aminopent-1-yn-1-yl)-7-{2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one  ligand  61  37  .  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_0L7
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
 0L7  O6   O  O     0  -0.469  19.2280  -17.7452   -3.0723
 0L7  C6   C  CR6   0   0.482  18.9805  -18.6379   -3.8696
 0L7  N1   N  NR16  0  -0.722  18.4758  -19.8593   -3.4118
 0L7  C2   C  CR6   0   0.678  18.1458  -20.9283   -4.1930
 0L7  N2   N  NH2   0  -0.832  17.7079  -22.0308   -3.5611
 0L7  N3   N  N     0  -0.521  18.2737  -20.9232   -5.4933
 0L7  C5   C  CR56  0  -0.229  19.1326  -18.6337   -5.2846
 0L7  C4   C  CR56  0   0.535  18.7706  -19.7762   -5.9881
 0L7  C7   C  CR5   0  -0.159  19.5841  -17.6703   -6.2444
 0L7  C32  C  CSP   0   0.129  20.0600  -16.3608   -5.9984
 0L7  C33  C  CSP   0  -0.018  20.4598  -15.2469   -5.7661
 0L7  C34  C  CH2   0  -0.598  20.8600  -13.8798   -5.4611
 0L7  C35  C  CH2   0  -0.463  20.3699  -13.4105   -4.0838
 0L7  C36  C  CH2   0  -0.273  21.2512  -13.8477   -2.9225
 0L7  N37  N  NH2   0  -0.806  21.5758  -15.2624   -2.9691
 0L7  C8   C  CR15  0  -0.102  19.4723  -18.2727   -7.4693
 0L7  N9   N  NR5   0  -0.541  18.9871  -19.5504   -7.3077
 0L7  C1'  C  CH1   0   0.184  18.6424  -20.5005   -8.3578
 0L7  C2'  C  CH2   0  -0.538  17.1972  -20.3690   -8.8372
 0L7  C3'  C  CH1   0   0.014  17.3403  -19.4403  -10.0379
 0L7  O3'  O  OH1   0  -0.658  16.3439  -19.5324  -11.0149
 0L7  O4'  O  O2    0  -0.496  19.4570  -20.2510   -9.4745
 0L7  C4'  C  CH1   0   0.027  18.6646  -19.9368  -10.6100
 0L7  C5'  C  CH2   0  -0.234  19.4090  -19.0074  -11.5337
 0L7  O5'  O  O2    0  -0.564  19.6479  -17.7406  -10.8921
 0L7  PA   P  P     0   1.533  19.1793  -16.3604  -11.4779
 0L7  O1A  O  OH1   0  -0.686  19.4160  -15.4606  -10.2129
 0L7  O2A  O  O     0  -0.706  19.7716  -15.9402  -12.7726
 0L7  O3A  O  O2    0  -0.685  17.5659  -16.4749  -11.5921
 0L7  PB   P  P     0   1.488  16.6944  -16.5608  -12.9554
 0L7  O1B  O  O     0  -0.661  17.1174  -17.5914  -13.9092
 0L7  O2B  O  OH1   0  -0.698  15.2733  -16.6357  -12.2790
 0L7  O3B  O  O2    0  -0.696  16.7828  -15.0503  -13.4907
 0L7  PG   P  P     0   1.450  17.4804  -14.4163  -14.8397
 0L7  O3G  O  O     0  -0.684  17.2704  -15.2472  -16.0343
 0L7  O2G  O  OH1   0  -0.715  16.8524  -12.9612  -14.8509
 0L7  O1G  O  OH1   0  -0.760  18.9484  -14.0879  -14.3834
 0L7  H1   H  HNR6  0   0.423  18.3530  -19.9371   -2.4105
 0L7  H2   H  HNH2  0   0.409  17.3008  -22.7522   -4.1321
 0L7  H3   H  HNH2  0   0.412  17.3599  -21.9721   -2.6185
 0L7  H4   H  HCH2  0   0.256  21.9477  -13.7797   -5.5252
 0L7  H5   H  HCH2  0   0.264  20.4504  -13.2229   -6.2332
 0L7  H6   H  HCH2  0   0.242  20.3277  -12.3193   -4.0804
 0L7  H7   H  HCH2  0   0.229  19.3440  -13.7566   -3.9325
 0L7  H8   H  HCH2  0   0.205  22.1886  -13.2839   -2.9678
 0L7  H9   H  HCH2  0   0.197  20.7549  -13.5334   -1.9929
 0L7  H10  H  HNH2  0   0.341  22.0194  -15.5356   -2.1016
 0L7  H11  H  HNH2  0   0.350  20.7373  -15.8243   -3.0510
 0L7  H13  H  HCR5  0   0.298  19.7298  -17.8787   -8.4356
 0L7  H14  H  HCH1  0   0.272  18.8462  -21.4938   -7.9543
 0L7  H15  H  HCH2  0   0.280  16.5309  -19.9972   -8.0598
 0L7  H16  H  HCH2  0   0.265  16.8317  -21.3442   -9.1672
 0L7  H17  H  HCH1  0   0.228  17.4433  -18.4093   -9.6780
 0L7  H18  H  HOH1  0   0.461  15.5691  -19.0509  -10.7104
 0L7  H19  H  HCH1  0   0.255  18.4697  -20.8464  -11.1964
 0L7  H20  H  HCH2  0   0.265  18.8360  -18.8956  -12.4558
 0L7  H21  H  HCH2  0   0.290  20.3814  -19.4220  -11.7973
 0L7  H22  H  HOH1  0   0.520  19.4913  -14.5093  -10.3761
 0L7  H23  H  HOH1  0   0.520  14.5629  -16.9403  -12.8623
 0L7  H24  H  HOH1  0   0.508  16.0840  -12.8705  -15.4310
 0L7  H25  H  HOH1  0   0.499  19.3800  -14.7741  -13.8037

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
 0L7  O3G  PG   double    1.470  0.020  1.470
 0L7  O1G  PG   single    1.572  0.020  1.572
 0L7  PG   O2G  single    1.585  0.020  1.585
 0L7  PG   O3B  single    1.646  0.020  1.646
 0L7  O1B  PB   double    1.467  0.020  1.467
 0L7  O2A  PA   double    1.484  0.020  1.484
 0L7  O3B  PB   single    1.605  0.020  1.605
 0L7  PB   O2B  single    1.576  0.020  1.576
 0L7  PB   O3A  single    1.620  0.020  1.620
 0L7  C5'  O5'  single    1.440  0.020  1.440
 0L7  C5'  C4'  single    1.507  0.020  1.507
 0L7  PA   O3A  single    1.621  0.020  1.621
 0L7  PA   O5'  single    1.571  0.020  1.571
 0L7  PA   O1A  single    1.570  0.020  1.570
 0L7  O3'  C3'  single    1.398  0.020  1.398
 0L7  C4'  C3'  single    1.526  0.020  1.526
 0L7  C4'  O4'  single    1.420  0.020  1.420
 0L7  C3'  C2'  single    1.525  0.020  1.525
 0L7  O4'  C1'  single    1.405  0.020  1.405
 0L7  C2'  C1'  single    1.528  0.020  1.528
 0L7  C1'  N9   single    1.457  0.020  1.457
 0L7  C8   N9   aromatic  1.376  0.020  1.376
 0L7  C8   C7   aromatic  1.370  0.020  1.370
 0L7  N9   C4   aromatic  1.356  0.020  1.356
 0L7  C7   C32  single    1.415  0.020  1.415
 0L7  C7   C5   aromatic  1.433  0.020  1.433
 0L7  C32  C33  triple    1.206  0.020  1.206
 0L7  C4   N3   single    1.344  0.020  1.344
 0L7  C4   C5   aromatic  1.390  0.020  1.390
 0L7  C33  C34  single    1.457  0.020  1.457
 0L7  C34  C35  single    1.535  0.020  1.535
 0L7  N3   C2   double    1.307  0.020  1.307
 0L7  C5   C6   single    1.423  0.020  1.423
 0L7  C35  C36  single    1.522  0.020  1.522
 0L7  C2   N2   single    1.344  0.020  1.344
 0L7  C2   N1   single    1.364  0.020  1.364
 0L7  C6   N1   single    1.399  0.020  1.399
 0L7  C6   O6   double    1.222  0.020  1.222
 0L7  C36  N37  single    1.452  0.020  1.452
 0L7  N1   H1   single    0.860  0.020  1.020
 0L7  N2   H2   single    0.890  0.020  1.040
 0L7  N2   H3   single    0.890  0.020  1.040
 0L7  C34  H4   single    0.970  0.020  1.090
 0L7  C34  H5   single    0.970  0.020  1.090
 0L7  C35  H6   single    0.970  0.020  1.090
 0L7  C35  H7   single    0.970  0.020  1.090
 0L7  C36  H8   single    0.970  0.020  1.090
 0L7  C36  H9   single    0.970  0.020  1.090
 0L7  N37  H10  single    0.890  0.020  1.040
 0L7  N37  H11  single    0.890  0.020  1.040
 0L7  C8   H13  single    0.930  0.020  1.080
 0L7  C1'  H14  single    0.970  0.020  1.090
 0L7  C2'  H15  single    0.970  0.020  1.090
 0L7  C2'  H16  single    0.970  0.020  1.090
 0L7  C3'  H17  single    0.970  0.020  1.090
 0L7  O3'  H18  single    0.850  0.020  0.980
 0L7  C4'  H19  single    0.970  0.020  1.090
 0L7  C5'  H20  single    0.970  0.020  1.090
 0L7  C5'  H21  single    0.970  0.020  1.090
 0L7  O1A  H22  single    0.850  0.020  0.980
 0L7  O2B  H23  single    0.850  0.020  0.980
 0L7  O2G  H24  single    0.850  0.020  0.980
 0L7  O1G  H25  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
 0L7  C5   C6   N1   111.50  3.000
 0L7  N1   C6   O6   119.83  3.000
 0L7  C5   C6   O6   128.67  3.000
 0L7  H1   N1   C2   118.49  3.000
 0L7  H1   N1   C6   115.77  3.000
 0L7  C2   N1   C6   125.74  3.000
 0L7  N3   C2   N2   120.19  3.000
 0L7  N2   C2   N1   116.89  3.000
 0L7  N3   C2   N1   122.89  3.000
 0L7  H3   N2   H2   115.69  3.000
 0L7  H3   N2   C2   120.34  3.000
 0L7  H2   N2   C2   116.94  3.000
 0L7  C4   N3   C2   113.94  3.000
 0L7  C7   C5   C4   107.20  3.000
 0L7  C4   C5   C6   118.23  3.000
 0L7  C7   C5   C6   134.56  3.000
 0L7  N9   C4   C5   108.31  3.000
 0L7  C5   C4   N3   127.69  3.000
 0L7  N9   C4   N3   123.99  3.000
 0L7  C8   C7   C32  126.16  3.000
 0L7  C32  C7   C5   127.72  3.000
 0L7  C8   C7   C5   106.11  3.000
 0L7  C33  C32  C7   180.00  3.000
 0L7  C34  C33  C32  180.00  3.000
 0L7  H5   C34  H4   106.03  3.000
 0L7  H5   C34  C35  109.28  3.000
 0L7  H4   C34  C35  109.99  3.000
 0L7  H5   C34  C33  108.24  3.000
 0L7  H4   C34  C33  110.28  3.000
 0L7  C35  C34  C33  112.77  3.000
 0L7  H7   C35  H6   106.24  3.000
 0L7  H7   C35  C36  110.29  3.000
 0L7  H6   C35  C36  107.88  3.000
 0L7  H7   C35  C34  109.08  3.000
 0L7  H6   C35  C34  108.70  3.000
 0L7  C36  C35  C34  114.31  3.000
 0L7  H9   C36  H8   105.92  3.000
 0L7  H9   C36  N37  113.98  3.000
 0L7  H8   C36  N37  108.00  3.000
 0L7  H9   C36  C35  107.55  3.000
 0L7  H8   C36  C35  108.44  3.000
 0L7  N37  C36  C35  112.63  3.000
 0L7  H11  N37  H10  106.41  3.000
 0L7  H11  N37  C36  110.98  3.000
 0L7  H10  N37  C36  109.49  3.000
 0L7  H13  C8   N9   122.03  3.000
 0L7  H13  C8   C7   128.55  3.000
 0L7  N9   C8   C7   109.40  3.000
 0L7  C1'  N9   C8   127.16  3.000
 0L7  C8   N9   C4   108.97  3.000
 0L7  C1'  N9   C4   123.70  3.000
 0L7  H14  C1'  O4'  110.33  3.000
 0L7  H14  C1'  C2'  111.77  3.000
 0L7  O4'  C1'  C2'  106.48  3.000
 0L7  H14  C1'  N9   106.43  3.000
 0L7  C2'  C1'  N9   113.17  3.000
 0L7  O4'  C1'  N9   108.65  3.000
 0L7  H16  C2'  H15  108.40  3.000
 0L7  H16  C2'  C3'  109.71  3.000
 0L7  H15  C2'  C3'  114.30  3.000
 0L7  H16  C2'  C1'  109.53  3.000
 0L7  H15  C2'  C1'  112.58  3.000
 0L7  C3'  C2'  C1'  102.17  3.000
 0L7  H17  C3'  C4'  110.33  3.000
 0L7  H17  C3'  O3'  110.98  3.000
 0L7  C4'  C3'  O3'  109.58  3.000
 0L7  H17  C3'  C2'  108.84  3.000
 0L7  C4'  C3'  C2'  100.28  3.000
 0L7  O3'  C3'  C2'  116.31  3.000
 0L7  H18  O3'  C3'  108.66  3.000
 0L7  C4'  O4'  C1'  110.58  3.000
 0L7  H19  C4'  C5'  105.71  3.000
 0L7  H19  C4'  O4'  110.02  3.000
 0L7  C5'  C4'  O4'  110.55  3.000
 0L7  H19  C4'  C3'  108.38  3.000
 0L7  O4'  C4'  C3'  104.87  3.000
 0L7  C5'  C4'  C3'  117.26  3.000
 0L7  H21  C5'  H20  107.65  3.000
 0L7  H21  C5'  O5'  107.12  3.000
 0L7  H20  C5'  O5'  111.93  3.000
 0L7  H21  C5'  C4'  110.76  3.000
 0L7  H20  C5'  C4'  108.77  3.000
 0L7  O5'  C5'  C4'  110.57  3.000
 0L7  PA   O5'  C5'  123.87  3.000
 0L7  O3A  PA   O2A  110.83  3.000
 0L7  O3A  PA   O1A  104.31  3.000
 0L7  O2A  PA   O1A  118.70  3.000
 0L7  O1A  PA   O5'   99.10  3.000
 0L7  O3A  PA   O5'  105.13  3.000
 0L7  O2A  PA   O5'  117.06  3.000
 0L7  H22  O1A  PA   116.04  3.000
 0L7  PB   O3A  PA   126.74  3.000
 0L7  O3B  PB   O2B  103.74  3.000
 0L7  O2B  PB   O1B  120.39  3.000
 0L7  O3B  PB   O1B  115.38  3.000
 0L7  O2B  PB   O3A   97.26  3.000
 0L7  O3B  PB   O3A  101.60  3.000
 0L7  O1B  PB   O3A  115.42  3.000
 0L7  H23  O2B  PB   114.71  3.000
 0L7  PG   O3B  PB   131.24  3.000
 0L7  O1G  PG   O2G  100.38  3.000
 0L7  O2G  PG   O3G  117.16  3.000
 0L7  O1G  PG   O3G  119.16  3.000
 0L7  O2G  PG   O3B  101.04  3.000
 0L7  O1G  PG   O3B  103.79  3.000
 0L7  O3G  PG   O3B  112.82  3.000
 0L7  H24  O2G  PG   113.90  3.000
 0L7  H25  O1G  PG   115.43  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
 0L7  CONST_01  N9   C8   C7   C5      0.00   0.0  0
 0L7  CONST_02  C8   N9   C4   C5      0.00   0.0  0
 0L7  CONST_03  C7   C8   N9   C4      0.00   0.0  0
 0L7  CONST_04  C8   C7   C5   C4      0.00   0.0  0
 0L7  CONST_05  N9   C4   C5   C7      0.00   0.0  0
 0L7  CONST_06  C1'  N9   C4   N3      0.00   0.0  0
 0L7  CONST_07  C1'  N9   C4   C5    180.00   0.0  0
 0L7  CONST_08  C1'  N9   C8   C7    180.00   0.0  0
 0L7  CONST_09  N3   C2   N1   C6      0.00   0.0  0
 0L7  CONST_10  C4   N3   C2   N1      0.00   0.0  0
 0L7  CONST_11  C5   C6   N1   C2      0.00   0.0  0
 0L7  CONST_12  C32  C7   C5   C6      0.00   0.0  0
 0L7  CONST_13  C32  C7   C5   C4    180.00   0.0  0
 0L7  CONST_14  N9   C8   C7   C32   180.00   0.0  0
 0L7  CONST_15  C2   N1   C6   O6    180.00   0.0  0
 0L7  CONST_16  N2   C2   N1   C6    180.00   0.0  0
 0L7  CONST_17  C4   N3   C2   N2    180.00   0.0  0
 0L7  CONST_18  H13  C8   C7   C5    180.00   0.0  0
 0L7  CONST_19  H1   N1   C2   N3    180.00   0.0  0
 0L7  CONST_20  H2   N2   C2   N1    180.00   0.0  0
 0L7  Var_01    C35  C34  C33  C32    48.87  30.0  3
 0L7  Var_02    C36  C35  C34  C33    82.47  30.0  3
 0L7  Var_03    N37  C36  C35  C34   -48.59  30.0  3
 0L7  Var_04    O2A  PA   O5'  C5'   -63.76  30.0  1
 0L7  Var_05    O1B  PB   O3A  PA     51.72  30.0  2
 0L7  Var_06    O3G  PG   O3B  PB     40.83  30.0  2
 0L7  Var_07    H10  N37  C36  C35  -170.10  30.0  3
 0L7  Var_08    H20  C5'  O5'  PA     -1.90  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
 0L7  chir_01  C1'  O4'  C2'  N9   positiv
 0L7  chir_02  C3'  O3'  C4'  C2'  positiv
 0L7  chir_03  C4'  O4'  C3'  C5'  negativ
 0L7  chir_04  PA   O3A  O5'  O1A  both
 0L7  chir_05  PB   O2B  O3B  O1B  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
 0L7  plan-1  O6   0.020
 0L7  plan-1  C6   0.020
 0L7  plan-1  N1   0.020
 0L7  plan-1  C2   0.020
 0L7  plan-1  N2   0.020
 0L7  plan-1  N3   0.020
 0L7  plan-1  C5   0.020
 0L7  plan-1  C4   0.020
 0L7  plan-1  C7   0.020
 0L7  plan-1  C32  0.020
 0L7  plan-1  C33  0.020
 0L7  plan-1  C8   0.020
 0L7  plan-1  N9   0.020
 0L7  plan-1  C1'  0.020
 0L7  plan-1  H1   0.020
 0L7  plan-1  H2   0.020
 0L7  plan-1  H3   0.020
 0L7  plan-1  H13  0.020

