# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun 11 03:24:13 2020
#   Inital geometry file: a 157 line input string
#   Ligand name: 9-{9-amino-6-[(3-carbamoylphenyl)ethynyl]-5,6,7,8,9-pentadeoxy-D-glycero-alpha-L-talo-decofuranuronosyl}-9H-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC[C@@H](C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C#Cc4cccc(c4)C(N)=O)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
 N37  N37  9-{9-amino-6-[(3-carbamoylphenyl)ethynyl]-5,6,7,8,9-pentadeoxy-D-glycero-alpha-L-talo-decofuranuronosyl}-9H-purin-6-amine  ligand  63  37  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_N37
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
 N37  C1   C  CR5    0   0.486  -4.4027  -1.5639   0.4394
 N37  C2   C  C1     0   0.039  -5.9876  -3.0784   0.5349
 N37  C3   C  C      0   0.457  -6.6564  -0.8833   0.7218
 N37  C4   C  CR5    0  -0.002  -5.3026  -0.5211   0.5927
 N37  C5   C  CR15   0   0.106  -3.3986   0.3755   0.4253
 N37  C6   C  CH1    0   0.174  -1.9205  -1.6853   0.1448
 N37  C7   C  CH1    0  -0.044  -1.7581  -2.1601  -1.2985
 N37  C8   C  CH1    0  -0.027  -1.0491  -0.9517  -1.9189
 N37  C9   C  CH1    0   0.041  -0.1287  -0.5156  -0.7810
 N37  C10  C  CH2    0  -0.458   0.2428   0.9503  -0.8143
 N37  C11  C  CH1    0  -0.438   1.0601   1.4354   0.3918
 N37  C12  C  CH2    0  -0.399   1.4889   2.9058   0.2467
 N37  C13  C  CH2    0  -0.441   0.3195   3.8750   0.1467
 N37  C14  C  CH1    0  -0.214   0.7522   5.3442   0.1712
 N37  C15  C  C      0   0.385  -0.4652   6.2460  -0.1590
 N37  C16  C  CSP    0   0.194   2.2364   0.5959   0.5975
 N37  C17  C  CSP    0   0.085   3.2218  -0.0834   0.7450
 N37  C18  C  C      0  -0.125   4.3897  -0.8833   0.9187
 N37  C19  C  C1     0  -0.297   5.0580  -0.9089   2.1464
 N37  C20  C  C1     0  -0.235   6.1906  -1.6894   2.3036
 N37  C21  C  C1     0  -0.283   6.6788  -2.4406   1.2440
 N37  C22  C  C      0  -0.028   6.0262  -2.4195   0.0130
 N37  C23  C  C1     0  -0.326   4.8776  -1.6520  -0.1381
 N37  C24  C  C      0   0.488   6.4880  -3.2231  -1.1642
 N37  N1   N  NR5    0  -0.534  -3.1798  -0.9713   0.3313
 N37  N2   N  N      0  -0.459  -4.6902  -2.8640   0.4029
 N37  N3   N  N      0  -0.474  -6.9623  -2.1853   0.6866
 N37  N4   N  NH2    0  -0.816  -7.6308   0.0129   0.8846
 N37  N5   N  N      0  -0.451  -4.6532   0.6847   0.5821
 N37  N6   N  NH2    0  -0.784   1.4312   5.6455   1.4218
 N37  N7   N  NH2    0  -0.813   7.7815  -3.5741  -1.1722
 N37  O1   O  O2     0  -0.500  -0.8612  -0.8194   0.4100
 N37  O2   O  OH1    0  -0.665  -0.9219  -3.2840  -1.2867
 N37  O3   O  OH1    0  -0.657  -0.2975  -1.2557  -3.0589
 N37  O4   O  OC    -1  -0.624  -0.9426   6.1191  -1.3066
 N37  O5   O  O      0  -0.606  -0.8788   7.0105   0.7338
 N37  O6   O  O      0  -0.479   5.7106  -3.5325  -2.0566
 N37  H1   H  H      0   0.252  -6.3051  -4.1155   0.5167
 N37  H2   H  HCR5   0   0.288  -2.5937   1.0915   0.3801
 N37  H3   H  HCH1   0   0.283  -1.9203  -2.5241   0.8462
 N37  H4   H  HCH1   0   0.259  -2.7251  -2.3765  -1.7686
 N37  H5   H  HCH1   0   0.243  -1.7881  -0.1651  -2.1194
 N37  H6   H  HCH1   0   0.245   0.7817  -1.1271  -0.7993
 N37  H7   H  HCH2   0   0.252   0.8134   1.1266  -1.7308
 N37  H8   H  HCH2   0   0.246  -0.6642   1.5553  -0.8884
 N37  H9   H  HCH1   0   0.271   0.4329   1.3584   1.2876
 N37  H10  H  HCH2   0   0.239   2.1023   3.1746   1.1078
 N37  H11  H  HCH2   0   0.219   2.1285   3.0030  -0.6364
 N37  H12  H  HCH2   0   0.230  -0.2416   3.7026  -0.7727
 N37  H13  H  HCH2   0   0.209  -0.3791   3.6944   0.9745
 N37  H14  H  HCH1   0   0.210   1.4818   5.4810  -0.6369
 N37  H15  H  H      0   0.265   4.6847  -0.3184   2.9725
 N37  H16  H  H      0   0.270   6.6958  -1.7177   3.2595
 N37  H17  H  H      0   0.265   7.5555  -3.0551   1.4015
 N37  H18  H  H      0   0.263   4.3592  -1.6384  -1.0875
 N37  H19  H  HNH2   0   0.411  -7.4377   0.9984   0.8522
 N37  H20  H  HNH2   0   0.403  -8.5916  -0.2824   0.9073
 N37  H21  H  HNH2   0   0.335   1.8066   6.5849   1.3680
 N37  H22  H  HNH2   0   0.323   0.7299   5.6993   2.1524
 N37  H24  H  HNH2   0   0.414   8.4482  -3.2141  -0.5122
 N37  H25  H  HNH2   0   0.407   8.1483  -4.1005  -1.9484
 N37  H26  H  HOH1   0   0.452  -0.4339  -3.2967  -2.1195
 N37  H27  H  HOH1   0   0.469  -0.8772  -1.2446  -3.8273

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
 N37  N4   C3   single    1.334  0.020  1.334
 N37  N5   C5   aromatic  1.302  0.020  1.302
 N37  N5   C4   aromatic  1.370  0.020  1.370
 N37  C3   C4   aromatic  1.407  0.020  1.407
 N37  C3   N3   aromatic  1.338  0.020  1.338
 N37  C5   N1   aromatic  1.368  0.020  1.368
 N37  C4   C1   aromatic  1.386  0.020  1.386
 N37  N3   C2   aromatic  1.331  0.020  1.331
 N37  N1   C1   aromatic  1.363  0.020  1.363
 N37  N1   C6   single    1.460  0.020  1.460
 N37  C1   N2   aromatic  1.332  0.020  1.332
 N37  O2   C7   single    1.401  0.020  1.401
 N37  C7   C6   single    1.528  0.020  1.528
 N37  C7   C8   single    1.532  0.020  1.532
 N37  C2   N2   aromatic  1.322  0.020  1.322
 N37  C6   O1   single    1.394  0.020  1.394
 N37  C8   C9   single    1.527  0.020  1.527
 N37  C8   O3   single    1.399  0.020  1.399
 N37  O6   C24  double    1.223  0.020  1.223
 N37  O1   C9   single    1.431  0.020  1.431
 N37  N7   C24  single    1.340  0.020  1.340
 N37  C24  C22  single    1.498  0.020  1.498
 N37  C10  C9   single    1.513  0.020  1.513
 N37  C10  C11  single    1.536  0.020  1.536
 N37  C23  C22  aromatic  1.390  0.020  1.390
 N37  C23  C18  aromatic  1.395  0.020  1.395
 N37  C22  C21  aromatic  1.393  0.020  1.393
 N37  C11  C16  single    1.460  0.020  1.460
 N37  C11  C12  single    1.538  0.020  1.538
 N37  C16  C17  triple    1.206  0.020  1.206
 N37  C17  C18  single    1.426  0.020  1.426
 N37  C18  C19  aromatic  1.398  0.020  1.398
 N37  C21  C20  aromatic  1.388  0.020  1.388
 N37  C19  C20  aromatic  1.384  0.020  1.384
 N37  C12  C13  single    1.522  0.020  1.522
 N37  C13  C14  single    1.532  0.020  1.532
 N37  C14  N6   single    1.455  0.020  1.455
 N37  C14  C15  single    1.551  0.020  1.551
 N37  O5   C15  deloc     1.246  0.020  1.246
 N37  C15  O4   deloc     1.249  0.020  1.249
 N37  C2   H1   single    0.930  0.020  1.080
 N37  C5   H2   single    0.930  0.020  1.080
 N37  C6   H3   single    0.970  0.020  1.090
 N37  C7   H4   single    0.970  0.020  1.090
 N37  C8   H5   single    0.970  0.020  1.090
 N37  C9   H6   single    0.970  0.020  1.090
 N37  C10  H7   single    0.970  0.020  1.090
 N37  C10  H8   single    0.970  0.020  1.090
 N37  C11  H9   single    0.970  0.020  1.090
 N37  C12  H10  single    0.970  0.020  1.090
 N37  C12  H11  single    0.970  0.020  1.090
 N37  C13  H12  single    0.970  0.020  1.090
 N37  C13  H13  single    0.970  0.020  1.090
 N37  C14  H14  single    0.970  0.020  1.090
 N37  C19  H15  single    0.930  0.020  1.080
 N37  C20  H16  single    0.930  0.020  1.080
 N37  C21  H17  single    0.930  0.020  1.080
 N37  C23  H18  single    0.930  0.020  1.080
 N37  N4   H19  single    0.860  0.020  1.020
 N37  N4   H20  single    0.860  0.020  1.020
 N37  N6   H21  single    0.890  0.020  1.040
 N37  N6   H22  single    0.890  0.020  1.040
 N37  N7   H24  single    0.860  0.020  1.020
 N37  N7   H25  single    0.860  0.020  1.020
 N37  O2   H26  single    0.850  0.020  0.980
 N37  O3   H27  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
 N37  N2   C1   N1   128.00  3.000
 N37  N2   C1   C4   126.68  3.000
 N37  N1   C1   C4   105.32  3.000
 N37  H1   C2   N3   115.42  3.000
 N37  H1   C2   N2   116.15  3.000
 N37  N3   C2   N2   128.43  3.000
 N37  N4   C3   N3   119.35  3.000
 N37  N3   C3   C4   117.90  3.000
 N37  N4   C3   C4   122.75  3.000
 N37  N5   C4   C3   133.11  3.000
 N37  C3   C4   C1   116.17  3.000
 N37  N5   C4   C1   110.72  3.000
 N37  H2   C5   N5   124.53  3.000
 N37  H2   C5   N1   122.11  3.000
 N37  N5   C5   N1   113.35  3.000
 N37  H3   C6   O1   110.76  3.000
 N37  H3   C6   N1   107.07  3.000
 N37  O1   C6   N1   109.12  3.000
 N37  H3   C6   C7   111.56  3.000
 N37  O1   C6   C7   106.98  3.000
 N37  N1   C6   C7   111.37  3.000
 N37  H4   C7   O2   111.81  3.000
 N37  H4   C7   C8   112.96  3.000
 N37  O2   C7   C8   111.10  3.000
 N37  H4   C7   C6   111.86  3.000
 N37  C8   C7   C6   100.75  3.000
 N37  O2   C7   C6   107.75  3.000
 N37  H5   C8   O3   111.63  3.000
 N37  H5   C8   C9   109.71  3.000
 N37  O3   C8   C9   110.21  3.000
 N37  H5   C8   C7   109.12  3.000
 N37  O3   C8   C7   114.03  3.000
 N37  C9   C8   C7   101.67  3.000
 N37  H6   C9   O1   108.69  3.000
 N37  H6   C9   C10  109.64  3.000
 N37  O1   C9   C10  110.48  3.000
 N37  H6   C9   C8   109.18  3.000
 N37  C10  C9   C8   114.10  3.000
 N37  O1   C9   C8   104.54  3.000
 N37  H8   C10  H7   106.67  3.000
 N37  H8   C10  C11  108.67  3.000
 N37  H7   C10  C11  109.24  3.000
 N37  H8   C10  C9   109.52  3.000
 N37  H7   C10  C9   107.62  3.000
 N37  C11  C10  C9   114.81  3.000
 N37  H9   C11  C16  107.79  3.000
 N37  H9   C11  C12  107.67  3.000
 N37  C16  C11  C12  109.78  3.000
 N37  H9   C11  C10  108.37  3.000
 N37  C12  C11  C10  112.10  3.000
 N37  C16  C11  C10  110.97  3.000
 N37  H11  C12  H10  106.64  3.000
 N37  H11  C12  C13  109.83  3.000
 N37  H10  C12  C13  109.08  3.000
 N37  H11  C12  C11  108.89  3.000
 N37  H10  C12  C11  108.53  3.000
 N37  C13  C12  C11  113.62  3.000
 N37  H13  C13  H12  106.38  3.000
 N37  H13  C13  C14  108.99  3.000
 N37  H12  C13  C14  108.08  3.000
 N37  H13  C13  C12  109.54  3.000
 N37  H12  C13  C12  110.48  3.000
 N37  C14  C13  C12  113.12  3.000
 N37  H14  C14  N6   107.27  3.000
 N37  H14  C14  C15  107.02  3.000
 N37  N6   C14  C15  115.41  3.000
 N37  H14  C14  C13  107.20  3.000
 N37  C15  C14  C13  109.43  3.000
 N37  N6   C14  C13  110.14  3.000
 N37  O5   C15  O4   126.41  3.000
 N37  O4   C15  C14  115.89  3.000
 N37  O5   C15  C14  117.70  3.000
 N37  C17  C16  C11  180.00  3.000
 N37  C18  C17  C16  180.00  3.000
 N37  C23  C18  C19  119.21  3.000
 N37  C19  C18  C17  120.57  3.000
 N37  C23  C18  C17  120.22  3.000
 N37  H15  C19  C20  120.21  3.000
 N37  H15  C19  C18  119.71  3.000
 N37  C20  C19  C18  120.07  3.000
 N37  H16  C20  C21  119.76  3.000
 N37  H16  C20  C19  119.82  3.000
 N37  C21  C20  C19  120.42  3.000
 N37  H17  C21  C22  121.11  3.000
 N37  H17  C21  C20  118.77  3.000
 N37  C22  C21  C20  120.11  3.000
 N37  C24  C22  C23  117.74  3.000
 N37  C23  C22  C21  119.44  3.000
 N37  C24  C22  C21  122.80  3.000
 N37  H18  C23  C22  119.90  3.000
 N37  H18  C23  C18  119.36  3.000
 N37  C22  C23  C18  120.74  3.000
 N37  O6   C24  N7   122.86  3.000
 N37  N7   C24  C22  116.27  3.000
 N37  O6   C24  C22  120.87  3.000
 N37  C6   N1   C5   128.94  3.000
 N37  C6   N1   C1   124.86  3.000
 N37  C5   N1   C1   106.20  3.000
 N37  C2   N2   C1   111.56  3.000
 N37  C3   N3   C2   119.26  3.000
 N37  H20  N4   H19  118.20  3.000
 N37  H20  N4   C3   120.23  3.000
 N37  H19  N4   C3   120.98  3.000
 N37  C5   N5   C4   104.41  3.000
 N37  H22  N6   H21  104.20  3.000
 N37  H22  N6   C14  107.91  3.000
 N37  H21  N6   C14  108.63  3.000
 N37  H25  N7   H24  116.86  3.000
 N37  H25  N7   C24  119.54  3.000
 N37  H24  N7   C24  122.86  3.000
 N37  C9   O1   C6   111.27  3.000
 N37  H26  O2   C7   107.76  3.000
 N37  H27  O3   C8   108.94  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
 N37  CONST_01  C5   N5   C4   C1     0.00   0.0  0
 N37  CONST_02  N3   C3   C4   C1     0.00   0.0  0
 N37  CONST_03  N5   C5   N1   C1     0.00   0.0  0
 N37  CONST_04  N3   C2   N2   C1     0.00   0.0  0
 N37  CONST_05  C4   C3   N3   C2     0.00   0.0  0
 N37  CONST_06  C4   C1   N2   C2     0.00   0.0  0
 N37  CONST_07  N1   C1   N2   C2   180.00   0.0  0
 N37  CONST_08  C5   N5   C4   C3   180.00   0.0  0
 N37  CONST_09  N1   C1   C4   C3   180.00   0.0  0
 N37  CONST_10  N2   C1   C4   C3     0.00   0.0  0
 N37  CONST_11  N2   C2   N3   C3     0.00   0.0  0
 N37  CONST_12  N1   C5   N5   C4     0.00   0.0  0
 N37  CONST_13  C5   N1   C1   C4     0.00   0.0  0
 N37  CONST_14  N2   C1   N1   C5   180.00   0.0  0
 N37  CONST_15  C21  C22  C23  C18    0.00   0.0  0
 N37  CONST_16  C21  C20  C19  C18    0.00   0.0  0
 N37  CONST_17  C22  C23  C18  C19    0.00   0.0  0
 N37  CONST_18  C22  C21  C20  C19    0.00   0.0  0
 N37  CONST_19  C23  C22  C21  C20    0.00   0.0  0
 N37  CONST_20  C23  C18  C19  C20    0.00   0.0  0
 N37  CONST_21  N5   C4   C1   N1     0.00   0.0  0
 N37  CONST_22  N5   C4   C1   N2   180.00   0.0  0
 N37  CONST_23  N5   C4   C3   N3   180.00   0.0  0
 N37  CONST_24  C6   N1   C1   C4   180.00   0.0  0
 N37  CONST_25  N5   C5   N1   C6   180.00   0.0  0
 N37  CONST_26  N2   C1   N1   C6     0.00   0.0  0
 N37  CONST_27  N4   C3   C4   C1   180.00   0.0  0
 N37  CONST_28  N4   C3   N3   C2   180.00   0.0  0
 N37  CONST_29  C22  C23  C18  C17  180.00   0.0  0
 N37  CONST_30  C20  C19  C18  C17  180.00   0.0  0
 N37  CONST_31  C24  C22  C23  C18  180.00   0.0  0
 N37  CONST_32  C24  C22  C21  C20  180.00   0.0  0
 N37  CONST_33  N5   C4   C3   N4     0.00   0.0  0
 N37  CONST_34  H2   C5   N1   C1   180.00   0.0  0
 N37  CONST_35  H1   C2   N2   C1   180.00   0.0  0
 N37  CONST_36  H16  C20  C19  C18  180.00   0.0  0
 N37  CONST_37  H18  C23  C18  C19  180.00   0.0  0
 N37  CONST_38  H17  C21  C20  C19  180.00   0.0  0
 N37  CONST_39  H15  C19  C20  C21  180.00   0.0  0
 N37  CONST_40  H19  N4   C3   C4     0.00   0.0  0
 N37  CONST_41  H20  N4   C3   C4   180.00   0.0  0
 N37  CONST_42  H24  N7   C24  C22    0.00   0.0  0
 N37  CONST_43  H25  N7   C24  C22  180.00   0.0  0
 N37  Var_01    O6   C24  C22  C21  156.23  30.0  2
 N37  Var_02    C14  C13  C12  C11  173.13  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
 N37  chir_01  C6   N1   C7   O1   negativ
 N37  chir_02  C7   O2   C8   C6   positiv
 N37  chir_03  C8   O3   C9   C7   positiv
 N37  chir_04  C9   O1   C10  C8   positiv
 N37  chir_05  C11  C10  C16  C12  negativ
 N37  chir_06  C14  N6   C13  C15  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
 N37  plan-1  C16  0.020
 N37  plan-1  C17  0.020
 N37  plan-1  C18  0.020
 N37  plan-1  C19  0.020
 N37  plan-1  C20  0.020
 N37  plan-1  C21  0.020
 N37  plan-1  C22  0.020
 N37  plan-1  C23  0.020
 N37  plan-1  C24  0.020
 N37  plan-1  H15  0.020
 N37  plan-1  H16  0.020
 N37  plan-1  H17  0.020
 N37  plan-1  H18  0.020
 N37  plan-2  C1   0.020
 N37  plan-2  C2   0.020
 N37  plan-2  C3   0.020
 N37  plan-2  C4   0.020
 N37  plan-2  C5   0.020
 N37  plan-2  C6   0.020
 N37  plan-2  N1   0.020
 N37  plan-2  N2   0.020
 N37  plan-2  N3   0.020
 N37  plan-2  N4   0.020
 N37  plan-2  N5   0.020
 N37  plan-2  H1   0.020
 N37  plan-2  H2   0.020
 N37  plan-3  C3   0.020
 N37  plan-3  N4   0.020
 N37  plan-3  H19  0.020
 N37  plan-3  H20  0.020
 N37  plan-4  C22  0.020
 N37  plan-4  C24  0.020
 N37  plan-4  N7   0.020
 N37  plan-4  O6   0.020
 N37  plan-4  H24  0.020
 N37  plan-4  H25  0.020
 N37  plan-5  C14  0.020
 N37  plan-5  C15  0.020
 N37  plan-5  O4   0.020
 N37  plan-5  O5   0.020

