# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jun 10 01:29:59 2020
#   Inital geometry file: a 150 line input string
#   Ligand name: [(2~{R},5~{S})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-(phenylmethyl)azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](C[C@@H](CC[C@H]([NH3+])C(O)=O)[NH2+]Cc4ccccc4)[C@@H](O)[C@H]3O
#
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
 76O  76O  '[(2~{R},5~{S})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-(phenylmethyl)azanium'  ligand  64  34  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_76O
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
 76O  C2   C  CR6    0   0.465   5.1278   1.3503   0.6856
 76O  C6   C  CR56   0   0.503   3.5474  -0.1559  -0.2383
 76O  C8   C  CR15   0   0.106   2.6094  -0.9140   1.5890
 76O  C10  C  CR56   0  -0.004   4.0966   0.4150   0.8961
 76O  C11  C  CR15   0   0.187   1.6904  -1.7755  -0.6050
 76O  C13  C  CR15   0   0.068  -0.6095  -2.0863  -0.2201
 76O  C14  C  CH2    0  -0.509  -1.7123  -1.3749   0.5416
 76O  C15  C  CH1    0  -0.112  -2.2440  -0.1349  -0.1731
 76O  C16  C  CH2    0  -0.447  -3.5802   0.3635   0.3591
 76O  C25  C  CR6    0   0.088  -0.1151   2.9894  -0.8090
 76O  C26  C  CR16   0  -0.294   1.1573   2.6803  -1.2850
 76O  C27  C  CR16   0  -0.234   2.2267   3.5210  -1.0145
 76O  C28  C  CR16   0  -0.254   2.0317   4.6781  -0.2712
 76O  C31  C  CR15   0  -0.023   0.1280  -3.1589   0.5726
 76O  N1   N  NH2    0  -0.814   5.7456   1.9796   1.6833
 76O  N3   N  N      0  -0.471   5.4898   1.6069  -0.5772
 76O  C4   C  CR16   0   0.036   4.8664   0.9816  -1.5717
 76O  N5   N  N      0  -0.458   3.8889   0.0937  -1.4987
 76O  N7   N  NR5    0  -0.543   2.5924  -1.0218   0.2213
 76O  N9   N  N      0  -0.440   3.4943  -0.0730   2.0282
 76O  O12  O  O      0  -0.536   0.4168  -1.1576  -0.5722
 76O  C17  C  CH2    0  -0.467  -4.7099  -0.6246   0.0781
 76O  C18  C  CH1    0  -0.265  -6.0893  -0.0175   0.2474
 76O  N19  N  NT3    1  -0.796  -6.3325   0.4233   1.6500
 76O  C20  C  C      0   0.474  -7.2542  -0.9711  -0.1462
 76O  O21  O  OC    -1  -0.568  -7.0939  -1.6186  -1.1855
 76O  O22  O  O      0  -0.591  -8.2389  -0.9478   0.6177
 76O  N23  N  NT2    1  -0.691  -1.2105   0.9516  -0.0380
 76O  C29  C  CR16   0  -0.239   0.7646   4.9941   0.2001
 76O  C30  C  CR16   0  -0.283  -0.3047   4.1503  -0.0660
 76O  O32  O  OH1    0  -0.655  -0.5899  -4.3561   0.5505
 76O  C33  C  CR15   0  -0.062   1.4746  -3.2290  -0.1667
 76O  O34  O  OH1    0  -0.661   1.3587  -4.0011  -1.3294
 76O  H49  H  HCR5   0   0.301   1.9444  -1.4901   2.2153
 76O  H35  H  HCR5   0   0.291   2.1004  -1.7397  -1.6162
 76O  H36  H  HCR5   0   0.264  -1.0297  -2.5226  -1.1347
 76O  H51  H  HCH2   0   0.302  -2.5268  -2.0898   0.6634
 76O  H50  H  HCH2   0   0.267  -1.3848  -1.1059   1.5514
 76O  H37  H  HCH1   0   0.306  -2.3309  -0.3281  -1.2456
 76O  H52  H  HCH2   0   0.258  -3.4870   0.5620   1.4314
 76O  H53  H  HCH2   0   0.272  -3.8251   1.3150  -0.1208
 76O  H56  H  HCH2   0   0.316  -2.2199   2.5532  -0.9555
 76O  H57  H  HCH2   0   0.319  -1.2080   1.5783  -2.0270
 76O  H58  H  HCR6   0   0.258   1.3163   1.7853  -1.8766
 76O  H59  H  HCR6   0   0.263   3.2132   3.2777  -1.3855
 76O  H60  H  HCR6   0   0.265   2.8666   5.3345  -0.0638
 76O  H44  H  HCR5   0   0.248   0.2898  -2.8072   1.6006
 76O  H47  H  HNH2   0   0.413   5.5048   1.7990   2.6421
 76O  H46  H  HNH2   0   0.406   6.4908   2.6268   1.4923
 76O  H48  H  HCR6   0   0.258   5.2054   1.2378  -2.5695
 76O  H54  H  HCH2   0   0.275  -4.6459  -0.9732  -0.9532
 76O  H55  H  HCH2   0   0.262  -4.6246  -1.5096   0.7150
 76O  H38  H  HCH1   0   0.309  -6.1738   0.8806  -0.3694
 76O  H39  H  HNT3   0   0.459  -5.8545  -0.1599   2.3362
 76O  H41  H  HNT3   0   0.467  -6.0769   1.3913   1.8323
 76O  H40  H  HNT3   0   0.456  -7.3442   0.2968   1.8073
 76O  H43  H  HNT2   0   0.465  -1.2548   1.3510   0.9024
 76O  H42  H  HNT2   0   0.463  -0.2916   0.4956  -0.1107
 76O  H61  H  HCR6   0   0.265   0.6072   5.8970   0.7752
 76O  H62  H  HCR6   0   0.265  -1.2930   4.3993   0.3014
 76O  H63  H  HOH1   0   0.473  -0.2847  -4.9183   1.2700
 76O  H45  H  HCR5   0   0.267   2.2909  -3.5838   0.4744
 76O  H64  H  HOH1   0   0.454   0.7894  -4.7539  -1.1252
 76O  C24  C  CH2    0  -0.401  -1.2597   2.0510  -1.0474

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
 76O  O22  C20  deloc     1.246  0.020  1.246
 76O  N19  C18  single    1.490  0.020  1.490
 76O  C20  C18  single    1.556  0.020  1.556
 76O  C20  O21  deloc     1.235  0.020  1.235
 76O  C18  C17  single    1.517  0.020  1.517
 76O  N3   C4   aromatic  1.330  0.020  1.330
 76O  N3   C2   aromatic  1.339  0.020  1.339
 76O  N1   C2   single    1.332  0.020  1.332
 76O  C17  C16  single    1.527  0.020  1.527
 76O  C4   N5   aromatic  1.323  0.020  1.323
 76O  C2   C10  aromatic  1.408  0.020  1.408
 76O  N5   C6   aromatic  1.329  0.020  1.329
 76O  C10  C6   aromatic  1.384  0.020  1.384
 76O  C10  N9   aromatic  1.372  0.020  1.372
 76O  C6   N7   aromatic  1.369  0.020  1.369
 76O  N9   C8   aromatic  1.297  0.020  1.297
 76O  N7   C8   aromatic  1.372  0.020  1.372
 76O  N7   C11  single    1.437  0.020  1.437
 76O  C11  O12  single    1.416  0.020  1.416
 76O  C11  C33  single    1.533  0.020  1.533
 76O  O12  C13  single    1.428  0.020  1.428
 76O  C16  C15  single    1.522  0.020  1.522
 76O  O34  C33  single    1.401  0.020  1.401
 76O  C33  C31  single    1.538  0.020  1.538
 76O  C15  N23  single    1.506  0.020  1.506
 76O  C15  C14  single    1.527  0.020  1.527
 76O  C13  C31  single    1.524  0.020  1.524
 76O  C13  C14  single    1.517  0.020  1.517
 76O  C31  O32  single    1.396  0.020  1.396
 76O  N23  C24  single    1.493  0.020  1.493
 76O  C24  C25  single    1.499  0.020  1.499
 76O  C30  C25  aromatic  1.391  0.020  1.391
 76O  C30  C29  aromatic  1.388  0.020  1.388
 76O  C25  C26  aromatic  1.393  0.020  1.393
 76O  C29  C28  aromatic  1.388  0.020  1.388
 76O  C26  C27  aromatic  1.387  0.020  1.387
 76O  C28  C27  aromatic  1.389  0.020  1.389
 76O  C8   H49  single    0.930  0.020  1.080
 76O  C11  H35  single    0.970  0.020  1.090
 76O  C13  H36  single    0.970  0.020  1.090
 76O  C14  H51  single    0.970  0.020  1.090
 76O  C14  H50  single    0.970  0.020  1.090
 76O  C15  H37  single    0.970  0.020  1.090
 76O  C16  H52  single    0.970  0.020  1.090
 76O  C16  H53  single    0.970  0.020  1.090
 76O  C24  H56  single    0.970  0.020  1.090
 76O  C24  H57  single    0.970  0.020  1.090
 76O  C26  H58  single    0.930  0.020  1.080
 76O  C27  H59  single    0.930  0.020  1.080
 76O  C28  H60  single    0.930  0.020  1.080
 76O  C31  H44  single    0.970  0.020  1.090
 76O  N1   H47  single    0.860  0.020  1.020
 76O  N1   H46  single    0.860  0.020  1.020
 76O  C4   H48  single    0.930  0.020  1.080
 76O  C17  H54  single    0.970  0.020  1.090
 76O  C17  H55  single    0.970  0.020  1.090
 76O  C18  H38  single    0.970  0.020  1.090
 76O  N19  H39  single    0.890  0.020  1.040
 76O  N19  H41  single    0.890  0.020  1.040
 76O  N19  H40  single    0.890  0.020  1.040
 76O  N23  H43  single    0.890  0.020  1.040
 76O  N23  H42  single    0.890  0.020  1.040
 76O  C29  H61  single    0.930  0.020  1.080
 76O  C30  H62  single    0.930  0.020  1.080
 76O  O32  H63  single    0.850  0.020  0.980
 76O  C33  H45  single    0.970  0.020  1.090
 76O  O34  H64  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
 76O  N3   C2   N1   119.39  3.000
 76O  N1   C2   C10  122.80  3.000
 76O  N3   C2   C10  117.80  3.000
 76O  N7   C6   N5   128.05  3.000
 76O  N7   C6   C10  105.23  3.000
 76O  N5   C6   C10  126.72  3.000
 76O  H49  C8   N9   124.71  3.000
 76O  H49  C8   N7   121.91  3.000
 76O  N9   C8   N7   113.38  3.000
 76O  N9   C10  C6   110.82  3.000
 76O  N9   C10  C2   132.93  3.000
 76O  C6   C10  C2   116.25  3.000
 76O  H35  C11  C33  110.41  3.000
 76O  H35  C11  O12  110.18  3.000
 76O  C33  C11  O12  106.29  3.000
 76O  H35  C11  N7   106.24  3.000
 76O  C33  C11  N7   114.91  3.000
 76O  O12  C11  N7   108.81  3.000
 76O  H36  C13  O12  109.17  3.000
 76O  H36  C13  C31  109.82  3.000
 76O  O12  C13  C31  103.77  3.000
 76O  H36  C13  C14  109.06  3.000
 76O  C31  C13  C14  114.87  3.000
 76O  O12  C13  C14  109.94  3.000
 76O  H50  C14  H51  106.34  3.000
 76O  H50  C14  C15  109.65  3.000
 76O  H51  C14  C15  108.94  3.000
 76O  H50  C14  C13  111.14  3.000
 76O  H51  C14  C13  106.95  3.000
 76O  C15  C14  C13  113.51  3.000
 76O  H37  C15  N23  105.67  3.000
 76O  H37  C15  C16  109.33  3.000
 76O  N23  C15  C16  109.57  3.000
 76O  H37  C15  C14  110.08  3.000
 76O  N23  C15  C14  107.76  3.000
 76O  C16  C15  C14  114.08  3.000
 76O  H53  C16  H52  106.93  3.000
 76O  H53  C16  C17  108.46  3.000
 76O  H52  C16  C17  111.15  3.000
 76O  H53  C16  C15  109.15  3.000
 76O  H52  C16  C15  109.10  3.000
 76O  C17  C16  C15  111.92  3.000
 76O  C30  C25  C26  119.47  3.000
 76O  C26  C25  C24  120.27  3.000
 76O  C30  C25  C24  120.21  3.000
 76O  H58  C26  C27  119.58  3.000
 76O  H58  C26  C25  120.22  3.000
 76O  C27  C26  C25  120.20  3.000
 76O  H59  C27  C28  119.93  3.000
 76O  H59  C27  C26  119.99  3.000
 76O  C28  C27  C26  120.07  3.000
 76O  H60  C28  C29  120.07  3.000
 76O  H60  C28  C27  119.97  3.000
 76O  C29  C28  C27  119.96  3.000
 76O  H44  C31  C33  109.61  3.000
 76O  H44  C31  O32  111.42  3.000
 76O  C33  C31  O32  113.81  3.000
 76O  H44  C31  C13  109.43  3.000
 76O  O32  C31  C13  110.26  3.000
 76O  C33  C31  C13  101.87  3.000
 76O  H46  N1   H47  118.33  3.000
 76O  H46  N1   C2   120.39  3.000
 76O  H47  N1   C2   121.25  3.000
 76O  C4   N3   C2   119.25  3.000
 76O  H48  C4   N5   116.13  3.000
 76O  H48  C4   N3   115.49  3.000
 76O  N5   C4   N3   128.38  3.000
 76O  C4   N5   C6   111.60  3.000
 76O  C11  N7   C8   128.48  3.000
 76O  C11  N7   C6   125.23  3.000
 76O  C8   N7   C6   106.04  3.000
 76O  C10  N9   C8   104.52  3.000
 76O  C13  O12  C11  111.61  3.000
 76O  H55  C17  H54  106.71  3.000
 76O  H55  C17  C18  109.26  3.000
 76O  H54  C17  C18  106.68  3.000
 76O  H55  C17  C16  111.02  3.000
 76O  H54  C17  C16  109.72  3.000
 76O  C18  C17  C16  113.16  3.000
 76O  H38  C18  C20  107.64  3.000
 76O  H38  C18  N19  106.00  3.000
 76O  C20  C18  N19  107.29  3.000
 76O  H38  C18  C17  109.65  3.000
 76O  C20  C18  C17  114.03  3.000
 76O  N19  C18  C17  111.83  3.000
 76O  H40  N19  H41  109.62  3.000
 76O  H40  N19  H39  106.68  3.000
 76O  H41  N19  H39  107.81  3.000
 76O  H40  N19  C18  105.50  3.000
 76O  H41  N19  C18  114.14  3.000
 76O  H39  N19  C18  112.81  3.000
 76O  O22  C20  O21  128.91  3.000
 76O  O21  C20  C18  115.92  3.000
 76O  O22  C20  C18  115.14  3.000
 76O  H42  N23  H43  106.08  3.000
 76O  H42  N23  C24  107.94  3.000
 76O  H43  N23  C24  109.43  3.000
 76O  H42  N23  C15  106.69  3.000
 76O  H43  N23  C15  109.54  3.000
 76O  C24  N23  C15  116.61  3.000
 76O  H61  C29  C30  119.81  3.000
 76O  H61  C29  C28  120.21  3.000
 76O  C30  C29  C28  119.98  3.000
 76O  H62  C30  C29  119.87  3.000
 76O  H62  C30  C25  119.81  3.000
 76O  C29  C30  C25  120.31  3.000
 76O  H63  O32  C31  109.02  3.000
 76O  H45  C33  O34  111.62  3.000
 76O  H45  C33  C31  112.67  3.000
 76O  O34  C33  C31  110.59  3.000
 76O  H45  C33  C11  111.65  3.000
 76O  C31  C33  C11  102.56  3.000
 76O  O34  C33  C11  107.27  3.000
 76O  H64  O34  C33  107.64  3.000
 76O  H57  C24  H56  108.57  3.000
 76O  H57  C24  N23  106.67  3.000
 76O  H56  C24  N23  108.17  3.000
 76O  H57  C24  C25  112.24  3.000
 76O  H56  C24  C25  111.82  3.000
 76O  N23  C24  C25  109.16  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
 76O  CONST_01  N5   C4   N3   C2      0.00   0.0  0
 76O  CONST_02  N5   C6   C10  C2      0.00   0.0  0
 76O  CONST_03  N7   C6   C10  C2    180.00   0.0  0
 76O  CONST_04  C8   N9   C10  C2    180.00   0.0  0
 76O  CONST_05  N3   C4   N5   C6      0.00   0.0  0
 76O  CONST_06  N3   C2   C10  C6      0.00   0.0  0
 76O  CONST_07  C8   N9   C10  C6      0.00   0.0  0
 76O  CONST_08  N9   C8   N7   C6      0.00   0.0  0
 76O  CONST_09  N5   C6   N7   C8    180.00   0.0  0
 76O  CONST_10  C10  C6   N7   C8      0.00   0.0  0
 76O  CONST_11  C4   N3   C2   C10     0.00   0.0  0
 76O  CONST_12  C4   N5   C6   C10     0.00   0.0  0
 76O  CONST_13  N7   C8   N9   C10     0.00   0.0  0
 76O  CONST_14  C28  C29  C30  C25     0.00   0.0  0
 76O  CONST_15  C28  C27  C26  C25     0.00   0.0  0
 76O  CONST_16  C29  C30  C25  C26     0.00   0.0  0
 76O  CONST_17  C29  C28  C27  C26     0.00   0.0  0
 76O  CONST_18  C30  C25  C26  C27     0.00   0.0  0
 76O  CONST_19  C30  C29  C28  C27     0.00   0.0  0
 76O  CONST_20  N9   C10  C2   N3    180.00   0.0  0
 76O  CONST_21  N7   C6   N5   C4    180.00   0.0  0
 76O  CONST_22  N9   C10  C6   N5    180.00   0.0  0
 76O  CONST_23  N9   C10  C6   N7      0.00   0.0  0
 76O  CONST_24  C11  N7   C6   C10   180.00   0.0  0
 76O  CONST_25  N5   C6   N7   C11     0.00   0.0  0
 76O  CONST_26  N9   C8   N7   C11   180.00   0.0  0
 76O  CONST_27  N1   C2   C10  C6    180.00   0.0  0
 76O  CONST_28  C29  C30  C25  C24   180.00   0.0  0
 76O  CONST_29  C27  C26  C25  C24   180.00   0.0  0
 76O  CONST_30  C4   N3   C2   N1    180.00   0.0  0
 76O  CONST_31  N9   C10  C2   N1      0.00   0.0  0
 76O  CONST_32  H48  C4   N3   C2    180.00   0.0  0
 76O  CONST_33  H49  C8   N7   C6    180.00   0.0  0
 76O  CONST_34  H61  C29  C30  C25   180.00   0.0  0
 76O  CONST_35  H59  C27  C26  C25   180.00   0.0  0
 76O  CONST_36  H62  C30  C25  C26   180.00   0.0  0
 76O  CONST_37  H60  C28  C27  C26   180.00   0.0  0
 76O  CONST_38  H58  C26  C27  C28   180.00   0.0  0
 76O  CONST_39  H47  N1   C2   C10     0.00   0.0  0
 76O  CONST_40  H46  N1   C2   C10   180.00   0.0  0
 76O  Var_01    N23  C24  C25  C26    80.98  30.0  2
 76O  Var_02    C25  C24  N23  C15  -176.60  30.0  3
 76O  Var_03    C18  C17  C16  C15  -164.44  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
 76O  chir_01  C11  N7   O12  C33  positiv
 76O  chir_02  C13  O12  C31  C14  negativ
 76O  chir_03  C15  N23  C14  C16  negativ
 76O  chir_04  C31  O32  C33  C13  negativ
 76O  chir_05  C18  N19  C20  C17  positiv
 76O  chir_06  C33  C11  O34  C31  positiv

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
 76O  plan-1  C25  0.020
 76O  plan-1  C26  0.020
 76O  plan-1  C27  0.020
 76O  plan-1  C28  0.020
 76O  plan-1  C29  0.020
 76O  plan-1  C30  0.020
 76O  plan-1  H58  0.020
 76O  plan-1  H59  0.020
 76O  plan-1  H60  0.020
 76O  plan-1  H61  0.020
 76O  plan-1  H62  0.020
 76O  plan-1  C24  0.020
 76O  plan-2  C2   0.020
 76O  plan-2  C6   0.020
 76O  plan-2  C8   0.020
 76O  plan-2  C10  0.020
 76O  plan-2  C11  0.020
 76O  plan-2  N1   0.020
 76O  plan-2  N3   0.020
 76O  plan-2  C4   0.020
 76O  plan-2  N5   0.020
 76O  plan-2  N7   0.020
 76O  plan-2  N9   0.020
 76O  plan-2  H49  0.020
 76O  plan-2  H48  0.020
 76O  plan-3  C2   0.020
 76O  plan-3  N1   0.020
 76O  plan-3  H47  0.020
 76O  plan-3  H46  0.020
 76O  plan-4  C18  0.020
 76O  plan-4  C20  0.020
 76O  plan-4  O21  0.020
 76O  plan-4  O22  0.020

