# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 11:02:58 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[3-(6-azanyl-9~{H}-purin-8-yl)prop-2-ynoxymethyl]oxolane-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](COCC#Cc4[nH]c5ncnc(N)c5n4)[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
 K3B  K3B  (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[3-(6-azanyl-9~{H}-purin-8-yl)prop-2-ynoxymethyl]oxolane-3,4-diol  ligand  50  32  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_K3B
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
 K3B  C2   C  CR16  0   0.046   5.6989  -2.1086   1.6247
 K3B  C4   C  CR56  0   0.492   4.2377  -0.9299   0.4882
 K3B  C5   C  CR56  0  -0.012   3.8952  -2.0108  -0.3086
 K3B  C6   C  CR6   0   0.460   4.5729  -3.2163  -0.0485
 K3B  N9   N  NR5   0  -0.539   3.4574   0.1003   0.0472
 K3B  C1'  C  CH1   0   0.213   3.4415   1.4451   0.5663
 K3B  C2'  C  CH1   0  -0.053   3.9633   2.4950  -0.4163
 K3B  C3'  C  CH1   0  -0.025   3.2059   3.7421   0.0500
 K3B  C4'  C  CH1   0  -0.052   1.8534   3.1409   0.4093
 K3B  C5'  C  CH2   0  -0.149   0.9112   3.1241  -0.7782
 K3B  C8   C  CR15  0   0.114   2.6927  -0.4069  -0.9690
 K3B  CAP  C  CH2   0  -0.315  -1.1910   2.3872  -1.4591
 K3B  CAQ  C  CSP   0   0.067  -2.3263   1.5746  -1.0487
 K3B  CAR  C  CSP   0   0.113  -3.2728   0.9050  -0.7290
 K3B  CAS  C  CR5   0   0.237  -4.3826   0.1133  -0.3492
 K3B  CAU  C  CR56  0   0.473  -5.9882  -0.6634   0.9212
 K3B  CAW  C  CR16  0   0.042  -7.7085  -1.8570   1.5813
 K3B  CAY  C  CR6   0   0.446  -6.9523  -2.2628  -0.5531
 K3B  CAZ  C  CR56  0  -0.012  -5.9687  -1.2794  -0.3249
 K3B  N1   N  N     0  -0.475   5.4780  -3.2255   0.9370
 K3B  N3   N  N     0  -0.456   5.1343  -0.9234   1.4712
 K3B  N6   N  NH2   0  -0.817   4.3451  -4.3364  -0.7350
 K3B  N7   N  N     0  -0.449   2.9241  -1.6618  -1.2121
 K3B  NAT  N  NR15  0  -0.675  -4.9658   0.2276   0.8835
 K3B  NAV  N  N     0  -0.451  -6.8397  -0.9179   1.9130
 K3B  NAX  N  N     0  -0.470  -7.8127  -2.5261   0.4352
 K3B  NBA  N  N     0  -0.436  -4.9623  -0.7866  -1.1024
 K3B  NBB  N  NH2   0  -0.813  -7.0441  -2.9350  -1.6998
 K3B  O2'  O  OH1   0  -0.652   5.3530   2.5807  -0.3226
 K3B  O3'  O  OH1   0  -0.667   3.7854   4.2779   1.2091
 K3B  O4'  O  O2    0  -0.487   2.1246   1.8117   0.8613
 K3B  O5'  O  O2    0  -0.480  -0.2442   2.4080  -0.4225
 K3B  H1   H  HCR6  0   0.252   6.4407  -2.1853   2.4122
 K3B  H2   H  HCH1  0   0.264   4.0677   1.4293   1.4652
 K3B  H3   H  HCH1  0   0.253   3.6441   2.2431  -1.4356
 K3B  H4   H  HCH1  0   0.255   3.1214   4.4909  -0.7486
 K3B  H5   H  HCH1  0   0.269   1.3846   3.6920   1.2297
 K3B  H6   H  HCH2  0   0.235   0.6711   4.1621  -1.0451
 K3B  H7   H  HCH2  0   0.209   1.3909   2.6724  -1.6600
 K3B  H8   H  HCR5  0   0.291   1.9659   0.1977  -1.4902
 K3B  H9   H  HCH2  0   0.255  -0.7712   1.9650  -2.3824
 K3B  H10  H  HCH2  0   0.257  -1.5401   3.3989  -1.7067
 K3B  H11  H  HCR6  0   0.254  -8.4368  -2.1209   2.3409
 K3B  H12  H  HNH2  0   0.411   3.6995  -4.3540  -1.5046
 K3B  H13  H  HNH2  0   0.404   4.8727  -5.1687  -0.5355
 K3B  H14  H  HNR5  0   0.432  -4.6807   0.8543   1.6219
 K3B  H16  H  HNH2  0   0.405  -7.7970  -3.5854  -1.8457
 K3B  H17  H  HNH2  0   0.413  -6.4529  -2.7113  -2.4812
 K3B  H18  H  HOH1  0   0.471   5.6979   2.9744  -1.1303
 K3B  H19  H  HOH1  0   0.450   4.7381   4.3297   1.0676

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
 K3B  N6   C6   single    1.333  0.020  1.333
 K3B  N7   C8   aromatic  1.299  0.020  1.299
 K3B  N7   C5   aromatic  1.372  0.020  1.372
 K3B  C6   C5   aromatic  1.407  0.020  1.407
 K3B  C6   N1   aromatic  1.338  0.020  1.338
 K3B  O2'  C2'  single    1.395  0.020  1.395
 K3B  C8   N9   aromatic  1.369  0.020  1.369
 K3B  C5   C4   aromatic  1.386  0.020  1.386
 K3B  C2'  C3'  single    1.532  0.020  1.532
 K3B  C2'  C1'  single    1.530  0.020  1.530
 K3B  N1   C2   aromatic  1.330  0.020  1.330
 K3B  N9   C4   aromatic  1.365  0.020  1.365
 K3B  N9   C1'  single    1.442  0.020  1.442
 K3B  C4   N3   aromatic  1.331  0.020  1.331
 K3B  C3'  O3'  single    1.402  0.020  1.402
 K3B  C3'  C4'  single    1.523  0.020  1.523
 K3B  C2   N3   aromatic  1.322  0.020  1.322
 K3B  C1'  O4'  single    1.398  0.020  1.398
 K3B  O4'  C4'  single    1.430  0.020  1.430
 K3B  C4'  C5'  single    1.516  0.020  1.516
 K3B  C5'  O5'  single    1.405  0.020  1.405
 K3B  NBB  CAY  single    1.332  0.020  1.332
 K3B  O5'  CAP  single    1.404  0.020  1.404
 K3B  CAY  NAX  aromatic  1.337  0.020  1.337
 K3B  CAY  CAZ  aromatic  1.409  0.020  1.409
 K3B  NBA  CAZ  aromatic  1.364  0.020  1.364
 K3B  NBA  CAS  aromatic  1.309  0.020  1.309
 K3B  NAX  CAW  aromatic  1.331  0.020  1.331
 K3B  CAZ  CAU  aromatic  1.390  0.020  1.390
 K3B  CAS  CAR  single    1.415  0.020  1.415
 K3B  CAS  NAT  aromatic  1.368  0.020  1.368
 K3B  CAP  CAQ  single    1.455  0.020  1.455
 K3B  CAR  CAQ  triple    1.203  0.020  1.203
 K3B  CAW  NAV  aromatic  1.322  0.020  1.322
 K3B  CAU  NAT  aromatic  1.357  0.020  1.357
 K3B  CAU  NAV  aromatic  1.332  0.020  1.332
 K3B  C2   H1   single    0.930  0.020  1.080
 K3B  C1'  H2   single    0.970  0.020  1.090
 K3B  C2'  H3   single    0.970  0.020  1.090
 K3B  C3'  H4   single    0.970  0.020  1.090
 K3B  C4'  H5   single    0.970  0.020  1.090
 K3B  C5'  H6   single    0.970  0.020  1.090
 K3B  C5'  H7   single    0.970  0.020  1.090
 K3B  C8   H8   single    0.930  0.020  1.080
 K3B  CAP  H9   single    0.970  0.020  1.090
 K3B  CAP  H10  single    0.970  0.020  1.090
 K3B  CAW  H11  single    0.930  0.020  1.080
 K3B  N6   H12  single    0.860  0.020  1.020
 K3B  N6   H13  single    0.860  0.020  1.020
 K3B  NAT  H14  single    0.860  0.020  1.020
 K3B  NBB  H16  single    0.860  0.020  1.020
 K3B  NBB  H17  single    0.860  0.020  1.020
 K3B  O2'  H18  single    0.850  0.020  0.980
 K3B  O3'  H19  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
 K3B  H1   C2   N3   116.10  3.000
 K3B  H1   C2   N1   115.45  3.000
 K3B  N3   C2   N1   128.46  3.000
 K3B  N3   C4   N9   128.32  3.000
 K3B  N3   C4   C5   126.52  3.000
 K3B  N9   C4   C5   105.16  3.000
 K3B  N7   C5   C6   132.90  3.000
 K3B  C6   C5   C4   116.29  3.000
 K3B  N7   C5   C4   110.81  3.000
 K3B  N6   C6   N1   119.27  3.000
 K3B  N1   C6   C5   117.89  3.000
 K3B  N6   C6   C5   122.84  3.000
 K3B  C8   N9   C1'  127.34  3.000
 K3B  C1'  N9   C4   126.43  3.000
 K3B  C8   N9   C4   106.22  3.000
 K3B  H2   C1'  O4'  111.65  3.000
 K3B  H2   C1'  C2'  110.00  3.000
 K3B  O4'  C1'  C2'  106.07  3.000
 K3B  H2   C1'  N9   106.00  3.000
 K3B  O4'  C1'  N9   109.32  3.000
 K3B  C2'  C1'  N9   113.90  3.000
 K3B  H3   C2'  O2'  111.48  3.000
 K3B  H3   C2'  C3'  109.01  3.000
 K3B  O2'  C2'  C3'  114.96  3.000
 K3B  H3   C2'  C1'  109.87  3.000
 K3B  C3'  C2'  C1'  101.22  3.000
 K3B  O2'  C2'  C1'  109.80  3.000
 K3B  H4   C3'  O3'  111.86  3.000
 K3B  H4   C3'  C4'  111.86  3.000
 K3B  O3'  C3'  C4'  108.84  3.000
 K3B  H4   C3'  C2'  111.83  3.000
 K3B  C4'  C3'  C2'  100.93  3.000
 K3B  O3'  C3'  C2'  111.00  3.000
 K3B  H5   C4'  O4'  108.21  3.000
 K3B  H5   C4'  C5'  109.07  3.000
 K3B  O4'  C4'  C5'  110.81  3.000
 K3B  H5   C4'  C3'  111.01  3.000
 K3B  C5'  C4'  C3'  111.81  3.000
 K3B  O4'  C4'  C3'  105.85  3.000
 K3B  H7   C5'  H6   106.76  3.000
 K3B  H7   C5'  O5'  110.61  3.000
 K3B  H6   C5'  O5'  111.31  3.000
 K3B  H7   C5'  C4'  111.17  3.000
 K3B  H6   C5'  C4'  108.41  3.000
 K3B  O5'  C5'  C4'  108.57  3.000
 K3B  H8   C8   N7   124.79  3.000
 K3B  H8   C8   N9   121.80  3.000
 K3B  N7   C8   N9   113.41  3.000
 K3B  H10  CAP  H9   106.61  3.000
 K3B  H10  CAP  O5'  111.54  3.000
 K3B  H9   CAP  O5'  111.62  3.000
 K3B  H10  CAP  CAQ  109.27  3.000
 K3B  H9   CAP  CAQ  108.69  3.000
 K3B  O5'  CAP  CAQ  109.04  3.000
 K3B  CAR  CAQ  CAP  180.00  3.000
 K3B  CAS  CAR  CAQ  180.00  3.000
 K3B  NBA  CAS  NAT  112.77  3.000
 K3B  NAT  CAS  CAR  121.95  3.000
 K3B  NBA  CAS  CAR  125.28  3.000
 K3B  NAV  CAU  NAT  128.91  3.000
 K3B  NAV  CAU  CAZ  126.29  3.000
 K3B  NAT  CAU  CAZ  104.80  3.000
 K3B  H11  CAW  NAX  115.34  3.000
 K3B  H11  CAW  NAV  116.01  3.000
 K3B  NAX  CAW  NAV  128.66  3.000
 K3B  NBB  CAY  NAX  119.52  3.000
 K3B  NAX  CAY  CAZ  117.84  3.000
 K3B  NBB  CAY  CAZ  122.64  3.000
 K3B  NBA  CAZ  CAY  132.44  3.000
 K3B  NBA  CAZ  CAU  111.18  3.000
 K3B  CAY  CAZ  CAU  116.39  3.000
 K3B  C6   N1   C2   119.17  3.000
 K3B  C4   N3   C2   111.68  3.000
 K3B  H13  N6   H12  118.34  3.000
 K3B  H13  N6   C6   120.24  3.000
 K3B  H12  N6   C6   121.26  3.000
 K3B  C8   N7   C5   104.39  3.000
 K3B  H14  NAT  CAU  126.88  3.000
 K3B  H14  NAT  CAS  126.18  3.000
 K3B  CAU  NAT  CAS  106.94  3.000
 K3B  CAW  NAV  CAU  111.67  3.000
 K3B  CAY  NAX  CAW  119.16  3.000
 K3B  CAZ  NBA  CAS  104.31  3.000
 K3B  H17  NBB  H16  118.14  3.000
 K3B  H17  NBB  CAY  121.09  3.000
 K3B  H16  NBB  CAY  120.18  3.000
 K3B  H18  O2'  C2'  109.01  3.000
 K3B  H19  O3'  C3'  107.91  3.000
 K3B  C4'  O4'  C1'  110.83  3.000
 K3B  CAP  O5'  C5'  112.04  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
 K3B  CONST_01  C5   C6   N1   C2      0.00   0.0  0
 K3B  CONST_02  C5   C4   N3   C2      0.00   0.0  0
 K3B  CONST_03  N9   C4   N3   C2    180.00   0.0  0
 K3B  CONST_04  C8   N7   C5   C4      0.00   0.0  0
 K3B  CONST_05  N1   C6   C5   C4      0.00   0.0  0
 K3B  CONST_06  N7   C8   N9   C4      0.00   0.0  0
 K3B  CONST_07  N1   C2   N3   C4      0.00   0.0  0
 K3B  CONST_08  N9   C8   N7   C5      0.00   0.0  0
 K3B  CONST_09  C8   N9   C4   C5      0.00   0.0  0
 K3B  CONST_10  C8   N7   C5   C6    180.00   0.0  0
 K3B  CONST_11  N9   C4   C5   C6    180.00   0.0  0
 K3B  CONST_12  N3   C4   C5   C6      0.00   0.0  0
 K3B  CONST_13  N3   C2   N1   C6      0.00   0.0  0
 K3B  CONST_14  N7   C5   C4   N9      0.00   0.0  0
 K3B  CONST_15  N3   C4   N9   C8    180.00   0.0  0
 K3B  CONST_16  CAY  CAZ  NBA  CAS   180.00   0.0  0
 K3B  CONST_17  CAU  CAZ  NBA  CAS     0.00   0.0  0
 K3B  CONST_18  CAZ  CAU  NAT  CAS     0.00   0.0  0
 K3B  CONST_19  NAV  CAU  NAT  CAS   180.00   0.0  0
 K3B  CONST_20  NAX  CAY  CAZ  CAU     0.00   0.0  0
 K3B  CONST_21  NBA  CAS  NAT  CAU     0.00   0.0  0
 K3B  CONST_22  NAX  CAW  NAV  CAU     0.00   0.0  0
 K3B  CONST_23  CAZ  CAY  NAX  CAW     0.00   0.0  0
 K3B  CONST_24  CAZ  CAU  NAV  CAW     0.00   0.0  0
 K3B  CONST_25  NAT  CAU  NAV  CAW   180.00   0.0  0
 K3B  CONST_26  NAV  CAW  NAX  CAY     0.00   0.0  0
 K3B  CONST_27  NAT  CAU  CAZ  CAY   180.00   0.0  0
 K3B  CONST_28  NAV  CAU  CAZ  CAY     0.00   0.0  0
 K3B  CONST_29  NAT  CAS  NBA  CAZ     0.00   0.0  0
 K3B  CONST_30  N7   C5   C6   N1    180.00   0.0  0
 K3B  CONST_31  N7   C5   C4   N3    180.00   0.0  0
 K3B  CONST_32  NBA  CAZ  CAU  NAT     0.00   0.0  0
 K3B  CONST_33  NBA  CAZ  CAU  NAV   180.00   0.0  0
 K3B  CONST_34  NBA  CAZ  CAY  NAX   180.00   0.0  0
 K3B  CONST_35  C1'  N9   C4   C5    180.00   0.0  0
 K3B  CONST_36  N7   C8   N9   C1'   180.00   0.0  0
 K3B  CONST_37  N3   C4   N9   C1'     0.00   0.0  0
 K3B  CONST_38  N6   C6   N1   C2    180.00   0.0  0
 K3B  CONST_39  N6   C6   C5   C4    180.00   0.0  0
 K3B  CONST_40  CAZ  NBA  CAS  CAR   180.00   0.0  0
 K3B  CONST_41  CAU  NAT  CAS  CAR   180.00   0.0  0
 K3B  CONST_42  NBB  CAY  CAZ  CAU   180.00   0.0  0
 K3B  CONST_43  NBB  CAY  NAX  CAW   180.00   0.0  0
 K3B  CONST_44  N7   C5   C6   N6      0.00   0.0  0
 K3B  CONST_45  NBB  CAY  CAZ  NBA     0.00   0.0  0
 K3B  CONST_46  H8   C8   N9   C4    180.00   0.0  0
 K3B  CONST_47  H1   C2   N3   C4    180.00   0.0  0
 K3B  CONST_48  H11  CAW  NAV  CAU   180.00   0.0  0
 K3B  CONST_49  H14  NAT  CAU  CAZ   180.00   0.0  0
 K3B  CONST_50  H12  N6   C6   C5      0.00   0.0  0
 K3B  CONST_51  H13  N6   C6   C5    180.00   0.0  0
 K3B  CONST_52  H16  NBB  CAY  CAZ   180.00   0.0  0
 K3B  CONST_53  H17  NBB  CAY  CAZ     0.00   0.0  0
 K3B  Var_01    CAQ  CAP  O5'  C5'   177.09  30.0  3
 K3B  Var_02    O5'  CAP  CAQ  CAR  -173.78  30.0  1
 K3B  Var_03    H6   C5'  O5'  CAP    58.66  30.0  2

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
 K3B  chir_01  C1'  C2'  N9   O4'  positiv
 K3B  chir_02  C2'  O2'  C1'  C3'  negativ
 K3B  chir_03  C3'  O3'  C2'  C4'  negativ
 K3B  chir_04  C4'  O4'  C3'  C5'  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
 K3B  plan-1  C2   0.020
 K3B  plan-1  C4   0.020
 K3B  plan-1  C5   0.020
 K3B  plan-1  C6   0.020
 K3B  plan-1  N9   0.020
 K3B  plan-1  C1'  0.020
 K3B  plan-1  C8   0.020
 K3B  plan-1  N1   0.020
 K3B  plan-1  N3   0.020
 K3B  plan-1  N6   0.020
 K3B  plan-1  N7   0.020
 K3B  plan-1  H1   0.020
 K3B  plan-1  H8   0.020
 K3B  plan-2  CAQ  0.020
 K3B  plan-2  CAR  0.020
 K3B  plan-2  CAS  0.020
 K3B  plan-2  CAU  0.020
 K3B  plan-2  CAW  0.020
 K3B  plan-2  CAY  0.020
 K3B  plan-2  CAZ  0.020
 K3B  plan-2  NAT  0.020
 K3B  plan-2  NAV  0.020
 K3B  plan-2  NAX  0.020
 K3B  plan-2  NBA  0.020
 K3B  plan-2  NBB  0.020
 K3B  plan-2  H11  0.020
 K3B  plan-2  H14  0.020
 K3B  plan-3  C6   0.020
 K3B  plan-3  N6   0.020
 K3B  plan-3  H12  0.020
 K3B  plan-3  H13  0.020
 K3B  plan-4  CAY  0.020
 K3B  plan-4  NBB  0.020
 K3B  plan-4  H16  0.020
 K3B  plan-4  H17  0.020

