# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 16:53:42 2021
#   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  64  37  .  2022-07-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  CR56  0   0.491  -3.6438  -2.6633   -9.9923
 N37  C2   C  CR16  0   0.046  -5.6977  -3.0775  -10.6457
 N37  C3   C  CR6   0   0.460  -4.6149  -1.3507  -11.7136
 N37  C4   C  CR56  0  -0.012  -3.5039  -1.6197  -10.8931
 N37  C5   C  CR15  0   0.110  -1.6702  -1.7299   -9.8533
 N37  C6   C  CH1   0   0.203  -2.0953  -3.6713   -8.3028
 N37  C7   C  CH1   0  -0.008  -0.9279  -4.5784   -8.6844
 N37  C8   C  CH1   0  -0.041  -0.3978  -4.9648   -7.3068
 N37  C9   C  CH1   0  -0.016  -0.5460  -3.6339   -6.5598
 N37  C10  C  CH2   0  -0.463   0.6594  -2.7059   -6.6654
 N37  C11  C  CH1   0  -0.450   1.9152  -3.1952   -5.9220
 N37  C12  C  CH2   0  -0.413   1.7052  -3.3167   -4.4048
 N37  C13  C  CH2   0  -0.436   2.9509  -3.7915   -3.6698
 N37  C14  C  CH1   0  -0.210   2.6992  -3.9938   -2.1710
 N37  C15  C  C     0   0.527   3.9135  -4.6920   -1.5629
 N37  C16  C  CSP   0   0.191   3.0173  -2.2845   -6.2205
 N37  C17  C  CSP   0   0.099   3.9116  -1.5111   -6.4552
 N37  C18  C  CR6   0  -0.126   4.9719  -0.5966   -6.7254
 N37  C19  C  CR16  0  -0.299   6.2413  -0.8012   -6.1795
 N37  C20  C  CR16  0  -0.236   7.2679   0.0871   -6.4560
 N37  C21  C  CR16  0  -0.269   7.0451   1.1823   -7.2761
 N37  C22  C  CR6   0  -0.028   5.7794   1.4103   -7.8112
 N37  C23  C  CR16  0  -0.336   4.7507   0.5159   -7.5405
 N37  C24  C  C     0   0.484   5.5880   2.6054   -8.6937
 N37  N1   N  NR5   0  -0.539  -2.4508  -2.7259   -9.3300
 N37  N2   N  N     0  -0.456  -4.7209  -3.4267   -9.8266
 N37  N3   N  N     0  -0.475  -5.7060  -2.1097  -11.5585
 N37  N4   N  NH2   0  -0.816  -4.6215  -0.3760  -12.6235
 N37  N5   N  N     0  -0.449  -2.2621  -1.0470  -10.7865
 N37  N6   N  NH2   0  -0.781   2.2802  -2.7573   -1.5566
 N37  N7   N  NH2   0  -0.810   4.3370   3.0801   -8.7834
 N37  O1   O  O2    0  -0.495  -1.6826  -2.9878   -7.1535
 N37  O2   O  OH1   0  -0.652  -1.3819  -5.6087   -9.4994
 N37  O3   O  OH1   0  -0.667  -1.2373  -5.9648   -6.7920
 N37  O4   O  OH1   0  -0.584   4.4883  -4.0106   -0.5827
 N37  O5   O  O     0  -0.454   4.3099  -5.7701   -1.9365
 N37  O6   O  O     0  -0.478   6.5330   3.1009   -9.2912
 N37  H1   H  HCR6  0   0.252  -6.6139  -3.6530  -10.5681
 N37  H2   H  HCR5  0   0.295  -0.6678  -1.5440   -9.4976
 N37  H3   H  HCH1  0   0.262  -2.9945  -4.2693   -8.1184
 N37  H4   H  HCH1  0   0.241  -0.1568  -3.9774   -9.1861
 N37  H5   H  HCH1  0   0.257   0.6468  -5.2966   -7.3469
 N37  H6   H  HCH1  0   0.259  -0.7847  -3.8141   -5.5073
 N37  H7   H  HCH2  0   0.248   0.9190  -2.5515   -7.7171
 N37  H8   H  HCH2  0   0.260   0.3776  -1.7274   -6.2682
 N37  H9   H  HCH1  0   0.275   2.1946  -4.1827   -6.3090
 N37  H10  H  HCH2  0   0.238   1.3716  -2.3562   -4.0083
 N37  H11  H  HCH2  0   0.237   0.9020  -4.0341   -4.2178
 N37  H12  H  HCH2  0   0.243   3.2902  -4.7323   -4.1083
 N37  H13  H  HCH2  0   0.242   3.7643  -3.0704   -3.8011
 N37  H14  H  HCH1  0   0.275   1.8811  -4.7159   -2.0656
 N37  H15  H  HCR6  0   0.265   6.4190  -1.6588   -5.5442
 N37  H16  H  HCR6  0   0.269   8.2490  -0.0769   -6.0308
 N37  H17  H  HCR6  0   0.268   7.8533   1.8675   -7.4932
 N37  H18  H  HCR6  0   0.264   3.7668   0.6496   -7.9720
 N37  H19  H  HNH2  0   0.404  -5.4265  -0.2335  -13.2084
 N37  H20  H  HNH2  0   0.412  -3.8033   0.1812  -12.7950
 N37  H21  H  HNH2  0   0.356   2.0632  -2.8900   -0.5777
 N37  H22  H  HNH2  0   0.346   3.0177  -2.0654   -1.6024
 N37  H24  H  HNH2  0   0.407   4.1565   3.8999   -9.3400
 N37  H25  H  HNH2  0   0.414   3.5997   2.7793   -8.1699
 N37  H26  H  HOH1  0   0.464  -0.6235  -6.0968   -9.8345
 N37  H27  H  HOH1  0   0.456  -0.9457  -6.1812   -5.9008
 N37  H28  H  HOH1  0   0.481   5.2447  -4.5083   -0.2363

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    1.333  0.020  1.333
 N37  N5   C5   aromatic  1.299  0.020  1.299
 N37  N5   C4   aromatic  1.372  0.020  1.372
 N37  C3   C4   aromatic  1.407  0.020  1.407
 N37  C3   N3   aromatic  1.338  0.020  1.338
 N37  C5   N1   aromatic  1.369  0.020  1.369
 N37  C4   C1   aromatic  1.386  0.020  1.386
 N37  N3   C2   aromatic  1.330  0.020  1.330
 N37  N1   C1   aromatic  1.366  0.020  1.366
 N37  N1   C6   single    1.441  0.020  1.441
 N37  C1   N2   aromatic  1.331  0.020  1.331
 N37  O2   C7   single    1.390  0.020  1.390
 N37  C7   C6   single    1.527  0.020  1.527
 N37  C7   C8   single    1.526  0.020  1.526
 N37  C2   N2   aromatic  1.322  0.020  1.322
 N37  C6   O1   single    1.399  0.020  1.399
 N37  C8   C9   single    1.533  0.020  1.533
 N37  C8   O3   single    1.403  0.020  1.403
 N37  O6   C24  double    1.223  0.020  1.223
 N37  O1   C9   single    1.436  0.020  1.436
 N37  N7   C24  single    1.341  0.020  1.341
 N37  C24  C22  single    1.498  0.020  1.498
 N37  C10  C9   single    1.525  0.020  1.525
 N37  C10  C11  single    1.539  0.020  1.539
 N37  C23  C22  aromatic  1.390  0.020  1.390
 N37  C23  C18  aromatic  1.397  0.020  1.397
 N37  C22  C21  aromatic  1.393  0.020  1.393
 N37  C11  C16  single    1.460  0.020  1.460
 N37  C11  C12  single    1.536  0.020  1.536
 N37  C16  C17  triple    1.205  0.020  1.205
 N37  C17  C18  single    1.426  0.020  1.426
 N37  C18  C19  aromatic  1.397  0.020  1.397
 N37  C21  C20  aromatic  1.386  0.020  1.386
 N37  C19  C20  aromatic  1.385  0.020  1.385
 N37  C12  C13  single    1.522  0.020  1.522
 N37  C13  C14  single    1.533  0.020  1.533
 N37  C14  N6   single    1.443  0.020  1.443
 N37  C14  C15  single    1.527  0.020  1.527
 N37  O5   C15  double    1.208  0.020  1.208
 N37  C15  O4   single    1.325  0.020  1.325
 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
 N37  O4   H28  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   128.34  3.000
 N37  N2   C1   C4   126.49  3.000
 N37  N1   C1   C4   105.16  3.000
 N37  H1   C2   N3   115.46  3.000
 N37  H1   C2   N2   116.08  3.000
 N37  N3   C2   N2   128.46  3.000
 N37  N4   C3   N3   119.32  3.000
 N37  N3   C3   C4   117.89  3.000
 N37  N4   C3   C4   122.79  3.000
 N37  N5   C4   C3   132.87  3.000
 N37  C3   C4   C1   116.32  3.000
 N37  N5   C4   C1   110.81  3.000
 N37  H2   C5   N5   124.69  3.000
 N37  H2   C5   N1   121.90  3.000
 N37  N5   C5   N1   113.40  3.000
 N37  H3   C6   O1   111.75  3.000
 N37  H3   C6   N1   106.00  3.000
 N37  O1   C6   N1   109.74  3.000
 N37  H3   C6   C7   110.20  3.000
 N37  O1   C6   C7   105.66  3.000
 N37  N1   C6   C7   113.60  3.000
 N37  H4   C7   O2   111.53  3.000
 N37  H4   C7   C8   107.88  3.000
 N37  O2   C7   C8   117.08  3.000
 N37  H4   C7   C6   109.01  3.000
 N37  C8   C7   C6   100.97  3.000
 N37  O2   C7   C6   109.71  3.000
 N37  H5   C8   O3   111.57  3.000
 N37  H5   C8   C9   111.87  3.000
 N37  O3   C8   C9   112.45  3.000
 N37  H5   C8   C7   111.99  3.000
 N37  O3   C8   C7   107.68  3.000
 N37  C9   C8   C7   100.75  3.000
 N37  H6   C9   O1   107.41  3.000
 N37  H6   C9   C10  109.83  3.000
 N37  O1   C9   C10  108.86  3.000
 N37  H6   C9   C8   110.29  3.000
 N37  C10  C9   C8   114.71  3.000
 N37  O1   C9   C8   105.40  3.000
 N37  H8   C10  H7   106.50  3.000
 N37  H8   C10  C11  108.63  3.000
 N37  H7   C10  C11  108.39  3.000
 N37  H8   C10  C9   108.42  3.000
 N37  H7   C10  C9   109.88  3.000
 N37  C11  C10  C9   114.71  3.000
 N37  H9   C11  C16  107.28  3.000
 N37  H9   C11  C12  108.18  3.000
 N37  C16  C11  C12  110.75  3.000
 N37  H9   C11  C10  108.88  3.000
 N37  C12  C11  C10  112.99  3.000
 N37  C16  C11  C10  108.59  3.000
 N37  H11  C12  H10  106.91  3.000
 N37  H11  C12  C13  108.30  3.000
 N37  H10  C12  C13  110.44  3.000
 N37  H11  C12  C11  108.74  3.000
 N37  H10  C12  C11  109.32  3.000
 N37  C13  C12  C11  112.93  3.000
 N37  H13  C13  H12  106.77  3.000
 N37  H13  C13  C14  109.03  3.000
 N37  H12  C13  C14  109.26  3.000
 N37  H13  C13  C12  110.16  3.000
 N37  H12  C13  C12  109.21  3.000
 N37  C14  C13  C12  112.26  3.000
 N37  H14  C14  N6   107.87  3.000
 N37  H14  C14  C15  104.71  3.000
 N37  N6   C14  C15  116.95  3.000
 N37  H14  C14  C13  107.66  3.000
 N37  C15  C14  C13  108.60  3.000
 N37  N6   C14  C13  110.54  3.000
 N37  O5   C15  O4   123.05  3.000
 N37  O4   C15  C14  113.86  3.000
 N37  O5   C15  C14  123.09  3.000
 N37  C17  C16  C11  180.00  3.000
 N37  C18  C17  C16  180.00  3.000
 N37  C23  C18  C19  119.25  3.000
 N37  C19  C18  C17  120.51  3.000
 N37  C23  C18  C17  120.24  3.000
 N37  H15  C19  C20  120.25  3.000
 N37  H15  C19  C18  119.66  3.000
 N37  C20  C19  C18  120.10  3.000
 N37  H16  C20  C21  119.87  3.000
 N37  H16  C20  C19  119.76  3.000
 N37  C21  C20  C19  120.37  3.000
 N37  H17  C21  C22  119.88  3.000
 N37  H17  C21  C20  119.95  3.000
 N37  C22  C21  C20  120.17  3.000
 N37  C24  C22  C23  122.25  3.000
 N37  C23  C22  C21  119.50  3.000
 N37  C24  C22  C21  118.23  3.000
 N37  H18  C23  C22  121.04  3.000
 N37  H18  C23  C18  118.35  3.000
 N37  C22  C23  C18  120.60  3.000
 N37  O6   C24  N7   123.00  3.000
 N37  N7   C24  C22  116.17  3.000
 N37  O6   C24  C22  120.82  3.000
 N37  C6   N1   C5   127.53  3.000
 N37  C6   N1   C1   126.25  3.000
 N37  C5   N1   C1   106.21  3.000
 N37  C2   N2   C1   111.69  3.000
 N37  C3   N3   C2   119.15  3.000
 N37  H20  N4   H19  118.31  3.000
 N37  H20  N4   C3   121.19  3.000
 N37  H19  N4   C3   120.30  3.000
 N37  C5   N5   C4   104.41  3.000
 N37  H22  N6   H21  106.85  3.000
 N37  H22  N6   C14  110.78  3.000
 N37  H21  N6   C14  111.22  3.000
 N37  H25  N7   H24  116.70  3.000
 N37  H25  N7   C24  122.51  3.000
 N37  H24  N7   C24  119.49  3.000
 N37  C9   O1   C6   110.69  3.000
 N37  H26  O2   C7   108.83  3.000
 N37  H27  O3   C8   108.58  3.000
 N37  H28  O4   C15  109.80  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    180.00   0.0  0
 N37  CONST_41  H20  N4   C3   C4      0.00   0.0  0
 N37  CONST_42  H24  N7   C24  C22   180.00   0.0  0
 N37  CONST_43  H25  N7   C24  C22     0.00   0.0  0
 N37  CONST_44  H28  O4   C15  C14   180.00   0.0  0
 N37  Var_01    O6   C24  C22  C21    24.12  30.0  2
 N37  Var_02    C14  C13  C12  C11  -176.32  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
 N37  plan-5  H28  0.020

