# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 05:28:54 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: 5'-{[(3S)-3-amino-3-carboxypropyl](hexyl)amino}-5'-deoxyadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCN(CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
#
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
 K15  K15  5'-{[(3S)-3-amino-3-carboxypropyl](hexyl)amino}-5'-deoxyadenosine  ligand  65  32  .  2021-08-12  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_K15
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
 K15  O    O  O     0  -0.440  -0.4521   3.8920  -2.7718
 K15  C    C  C     0   0.520  -0.7025   3.6762  -1.6125
 K15  CA   C  CH1   0  -0.206  -1.9638   2.9880  -1.1064
 K15  N    N  NH2   0  -0.778  -3.0383   2.9401  -2.0671
 K15  CB   C  CH2   0  -0.446  -1.5823   1.5774  -0.6475
 K15  CG   C  CH2   0  -0.270  -2.6968   0.8756   0.1161
 K15  ND   N  NT    0  -0.422  -2.2562  -0.4120   0.6201
 K15  CE   C  CH2   0  -0.266  -3.3397  -1.3288   0.9271
 K15  C11  C  CH2   0  -0.434  -4.0206  -1.9219  -0.2981
 K15  C12  C  CH2   0  -0.415  -5.0961  -2.9269   0.0971
 K15  C13  C  CH2   0  -0.407  -5.7927  -3.5747  -1.0917
 K15  C14  C  CH2   0  -0.418  -6.8560  -4.5851  -0.6777
 K15  C15  C  CH3   0  -0.663  -7.5467  -5.2419  -1.8643
 K15  C5'  C  CH2   0  -0.323  -1.3041  -0.3100   1.7128
 K15  C4'  C  CH1   0   0.051  -0.1228  -1.2394   1.5235
 K15  O4'  O  O2    0  -0.483   0.5882  -0.8860   0.3399
 K15  C1'  C  CH1   0   0.165   1.9689  -1.0138   0.5113
 K15  C2'  C  CH1   0  -0.039   2.1980  -1.5900   1.9109
 K15  O2'  O  OH1   0  -0.665   2.2519  -2.9856   1.7886
 K15  C3'  C  CH1   0  -0.040   0.9186  -1.1560   2.6366
 K15  O3'  O  OH1   0  -0.657   0.5624  -1.9928   3.7007
 K15  N9   N  NR5   0  -0.534   2.5951   0.2837   0.3134
 K15  C8   C  CR15  0   0.118   2.1348   1.5174   0.6850
 K15  N7   N  N     0  -0.448   2.9180   2.4923   0.3282
 K15  C5   C  CR56  0  -0.005   3.9587   1.8740  -0.3134
 K15  C6   C  CR6   0   0.457   5.1227   2.3585  -0.9374
 K15  N6   N  NH2   0  -0.816   5.4270   3.6566  -0.9858
 K15  C4   C  CR56  0   0.489   3.7770   0.5004  -0.3346
 K15  N3   N  N     0  -0.458   4.5938  -0.3982  -0.8806
 K15  C2   C  CR16  0   0.044   5.6497   0.1739  -1.4325
 K15  N1   N  N     0  -0.474   5.9540   1.4680  -1.4900
 K15  OXT  O  OH1   0  -0.591   0.1176   3.9886  -0.6143
 K15  H1   H  HCH1  0   0.266  -2.3098   3.5494  -0.2314
 K15  H2   H  HNH2  0   0.354  -3.3177   3.8744  -2.3370
 K15  H3   H  HNH2  0   0.344  -2.7303   2.4769  -2.9134
 K15  H5   H  HCH2  0   0.234  -1.2963   0.9719  -1.5127
 K15  H6   H  HCH2  0   0.239  -0.6967   1.6432  -0.0176
 K15  H7   H  HCH2  0   0.194  -3.0626   1.5316   0.9250
 K15  H8   H  HCH2  0   0.239  -3.5394   0.7240  -0.5580
 K15  H10  H  HCH2  0   0.226  -2.9203  -2.1588   1.5038
 K15  H11  H  HCH2  0   0.192  -4.0960  -0.8590   1.5796
 K15  H12  H  HCH2  0   0.216  -4.4724  -1.1362  -0.9110
 K15  H13  H  HCH2  0   0.214  -3.2652  -2.4087  -0.9222
 K15  H14  H  HCH2  0   0.209  -4.6462  -3.7078   0.7204
 K15  H15  H  HCH2  0   0.210  -5.8419  -2.4305   0.7275
 K15  H16  H  HCH2  0   0.207  -6.2521  -2.7996  -1.7148
 K15  H17  H  HCH2  0   0.207  -5.0486  -4.0712  -1.7243
 K15  H18  H  HCH2  0   0.210  -6.3954  -5.3542  -0.0499
 K15  H19  H  HCH2  0   0.210  -7.6004  -4.0875  -0.0484
 K15  H20  H  HCH3  0   0.216  -6.8296  -5.7715  -2.4942
 K15  H21  H  HCH3  0   0.226  -8.2986  -5.9629  -1.5414
 K15  H22  H  HCH3  0   0.216  -8.0476  -4.5009  -2.4902
 K15  H23  H  HCH2  0   0.235  -0.9378   0.7159   1.8081
 K15  H24  H  HCH2  0   0.240  -1.7649  -0.5412   2.6833
 K15  H25  H  HCH1  0   0.235  -0.4851  -2.2730   1.4368
 K15  H26  H  HCH1  0   0.275   2.4032  -1.6712  -0.2472
 K15  H27  H  HCH1  0   0.257   3.1082  -1.1874   2.3719
 K15  H28  H  HOH1  0   0.451   1.8932  -3.3655   2.6005
 K15  H29  H  HCH1  0   0.238   1.0241  -0.1138   2.9693
 K15  H30  H  HOH1  0   0.469   1.0536  -1.7271   4.4850
 K15  H31  H  HCR5  0   0.282   1.2063   1.6442   1.2186
 K15  H32  H  HNH2  0   0.410   4.7803   4.3507  -0.6548
 K15  H33  H  HNH2  0   0.403   6.2341   3.9670  -1.4986
 K15  H34  H  HCR6  0   0.252   6.3652  -0.4937  -1.9006
 K15  H35  H  HOH1  0   0.476   0.9573   4.3370  -0.9488

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
 K15  N6   C6   single    1.334  0.020  1.334
 K15  N1   C6   aromatic  1.338  0.020  1.338
 K15  N1   C2   aromatic  1.331  0.020  1.331
 K15  C6   C5   aromatic  1.407  0.020  1.407
 K15  C2   N3   aromatic  1.322  0.020  1.322
 K15  C5   C4   aromatic  1.386  0.020  1.386
 K15  C5   N7   aromatic  1.370  0.020  1.370
 K15  N3   C4   aromatic  1.331  0.020  1.331
 K15  C4   N9   aromatic  1.365  0.020  1.365
 K15  N7   C8   aromatic  1.300  0.020  1.300
 K15  N    CA   single    1.442  0.020  1.442
 K15  O    C    double    1.206  0.020  1.206
 K15  N9   C8   aromatic  1.368  0.020  1.368
 K15  N9   C1'  single    1.454  0.020  1.454
 K15  C1'  O4'  single    1.397  0.020  1.397
 K15  C1'  C2'  single    1.531  0.020  1.531
 K15  CA   C    single    1.523  0.020  1.523
 K15  CA   CB   single    1.532  0.020  1.532
 K15  C    OXT  single    1.329  0.020  1.329
 K15  O4'  C4'  single    1.425  0.020  1.425
 K15  CB   CG   single    1.522  0.020  1.522
 K15  CG   ND   single    1.451  0.020  1.451
 K15  C2'  O2'  single    1.402  0.020  1.402
 K15  C2'  C3'  single    1.534  0.020  1.534
 K15  C4'  C5'  single    1.515  0.020  1.515
 K15  C4'  C3'  single    1.527  0.020  1.527
 K15  C5'  ND   single    1.453  0.020  1.453
 K15  ND   CE   single    1.452  0.020  1.452
 K15  C3'  O3'  single    1.400  0.020  1.400
 K15  CE   C11  single    1.522  0.020  1.522
 K15  C11  C12  single    1.524  0.020  1.524
 K15  C12  C13  single    1.523  0.020  1.523
 K15  C14  C13  single    1.524  0.020  1.524
 K15  C14  C15  single    1.522  0.020  1.522
 K15  CA   H1   single    0.970  0.020  1.090
 K15  N    H2   single    0.890  0.020  1.040
 K15  N    H3   single    0.890  0.020  1.040
 K15  CB   H5   single    0.970  0.020  1.090
 K15  CB   H6   single    0.970  0.020  1.090
 K15  CG   H7   single    0.970  0.020  1.090
 K15  CG   H8   single    0.970  0.020  1.090
 K15  CE   H10  single    0.970  0.020  1.090
 K15  CE   H11  single    0.970  0.020  1.090
 K15  C11  H12  single    0.970  0.020  1.090
 K15  C11  H13  single    0.970  0.020  1.090
 K15  C12  H14  single    0.970  0.020  1.090
 K15  C12  H15  single    0.970  0.020  1.090
 K15  C13  H16  single    0.970  0.020  1.090
 K15  C13  H17  single    0.970  0.020  1.090
 K15  C14  H18  single    0.970  0.020  1.090
 K15  C14  H19  single    0.970  0.020  1.090
 K15  C15  H20  single    0.970  0.020  1.090
 K15  C15  H21  single    0.970  0.020  1.090
 K15  C15  H22  single    0.970  0.020  1.090
 K15  C5'  H23  single    0.970  0.020  1.090
 K15  C5'  H24  single    0.970  0.020  1.090
 K15  C4'  H25  single    0.970  0.020  1.090
 K15  C1'  H26  single    0.970  0.020  1.090
 K15  C2'  H27  single    0.970  0.020  1.090
 K15  O2'  H28  single    0.850  0.020  0.980
 K15  C3'  H29  single    0.970  0.020  1.090
 K15  O3'  H30  single    0.850  0.020  0.980
 K15  C8   H31  single    0.930  0.020  1.080
 K15  N6   H32  single    0.860  0.020  1.020
 K15  N6   H33  single    0.860  0.020  1.020
 K15  C2   H34  single    0.930  0.020  1.080
 K15  OXT  H35  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
 K15  OXT  C    CA   111.56  3.000
 K15  OXT  C    O    123.50  3.000
 K15  CA   C    O    124.92  3.000
 K15  H1   CA   CB   108.14  3.000
 K15  H1   CA   N    108.28  3.000
 K15  CB   CA   N    110.77  3.000
 K15  H1   CA   C    107.18  3.000
 K15  CB   CA   C    108.02  3.000
 K15  N    CA   C    114.24  3.000
 K15  H3   N    H2   106.46  3.000
 K15  H3   N    CA   110.19  3.000
 K15  H2   N    CA   110.65  3.000
 K15  H6   CB   H5   106.16  3.000
 K15  H6   CB   CG   109.46  3.000
 K15  H5   CB   CG   109.44  3.000
 K15  H6   CB   CA   108.68  3.000
 K15  H5   CB   CA   109.74  3.000
 K15  CG   CB   CA   113.11  3.000
 K15  H8   CG   H7   106.25  3.000
 K15  H8   CG   ND   109.04  3.000
 K15  H7   CG   ND   111.92  3.000
 K15  H8   CG   CB   108.66  3.000
 K15  H7   CG   CB   109.64  3.000
 K15  ND   CG   CB   111.16  3.000
 K15  C5'  ND   CE   111.98  3.000
 K15  CE   ND   CG   114.02  3.000
 K15  C5'  ND   CG   113.45  3.000
 K15  H11  CE   H10  105.90  3.000
 K15  H11  CE   C11  109.58  3.000
 K15  H10  CE   C11  107.46  3.000
 K15  H11  CE   ND   111.56  3.000
 K15  H10  CE   ND   107.72  3.000
 K15  C11  CE   ND   114.18  3.000
 K15  H13  C11  H12  106.56  3.000
 K15  H13  C11  C12  109.98  3.000
 K15  H12  C11  C12  109.12  3.000
 K15  H13  C11  CE   108.88  3.000
 K15  H12  C11  CE   110.84  3.000
 K15  C12  C11  CE   111.34  3.000
 K15  H15  C12  H14  105.97  3.000
 K15  H15  C12  C13  109.31  3.000
 K15  H14  C12  C13  109.19  3.000
 K15  H15  C12  C11  109.32  3.000
 K15  H14  C12  C11  109.13  3.000
 K15  C13  C12  C11  113.64  3.000
 K15  H17  C13  H16  106.08  3.000
 K15  H17  C13  C14  109.28  3.000
 K15  H16  C13  C14  109.33  3.000
 K15  H17  C13  C12  109.45  3.000
 K15  H16  C13  C12  109.57  3.000
 K15  C14  C13  C12  112.91  3.000
 K15  H19  C14  H18  106.01  3.000
 K15  H19  C14  C15  109.62  3.000
 K15  H18  C14  C15  109.57  3.000
 K15  H19  C14  C13  109.22  3.000
 K15  H18  C14  C13  109.15  3.000
 K15  C15  C14  C13  113.02  3.000
 K15  H22  C15  H21  107.59  3.000
 K15  H22  C15  H20  107.45  3.000
 K15  H21  C15  H20  107.64  3.000
 K15  H22  C15  C14  111.24  3.000
 K15  H21  C15  C14  111.56  3.000
 K15  H20  C15  C14  111.17  3.000
 K15  H24  C5'  H23  105.12  3.000
 K15  H24  C5'  C4'  107.96  3.000
 K15  H23  C5'  C4'  108.98  3.000
 K15  H24  C5'  ND   112.00  3.000
 K15  H23  C5'  ND   110.54  3.000
 K15  C4'  C5'  ND   111.95  3.000
 K15  H25  C4'  C3'  109.51  3.000
 K15  H25  C4'  O4'  109.41  3.000
 K15  C3'  C4'  O4'  104.58  3.000
 K15  H25  C4'  C5'  109.26  3.000
 K15  C3'  C4'  C5'  114.03  3.000
 K15  O4'  C4'  C5'  109.92  3.000
 K15  C1'  O4'  C4'  111.62  3.000
 K15  H26  C1'  N9   105.72  3.000
 K15  H26  C1'  C2'  110.39  3.000
 K15  N9   C1'  C2'  113.32  3.000
 K15  H26  C1'  O4'  111.24  3.000
 K15  C2'  C1'  O4'  107.13  3.000
 K15  N9   C1'  O4'  109.10  3.000
 K15  H27  C2'  C3'  112.92  3.000
 K15  H27  C2'  O2'  111.72  3.000
 K15  C3'  C2'  O2'  110.80  3.000
 K15  H27  C2'  C1'  111.73  3.000
 K15  C3'  C2'  C1'  101.61  3.000
 K15  O2'  C2'  C1'  107.50  3.000
 K15  H28  O2'  C2'  107.70  3.000
 K15  H29  C3'  O3'  111.17  3.000
 K15  H29  C3'  C2'  109.36  3.000
 K15  O3'  C3'  C2'  113.75  3.000
 K15  H29  C3'  C4'  109.76  3.000
 K15  O3'  C3'  C4'  110.37  3.000
 K15  C2'  C3'  C4'  102.04  3.000
 K15  H30  O3'  C3'  108.93  3.000
 K15  C4   N9   C8   106.08  3.000
 K15  C8   N9   C1'  128.51  3.000
 K15  C4   N9   C1'  125.38  3.000
 K15  H31  C8   N7   124.48  3.000
 K15  H31  C8   N9   122.01  3.000
 K15  N7   C8   N9   113.50  3.000
 K15  C5   N7   C8   104.34  3.000
 K15  C4   C5   C6   116.30  3.000
 K15  C4   C5   N7   110.79  3.000
 K15  C6   C5   N7   132.91  3.000
 K15  N1   C6   N6   119.40  3.000
 K15  N1   C6   C5   117.92  3.000
 K15  N6   C6   C5   122.68  3.000
 K15  H33  N6   H32  118.12  3.000
 K15  H33  N6   C6   120.14  3.000
 K15  H32  N6   C6   120.89  3.000
 K15  N3   C4   C5   126.50  3.000
 K15  N3   C4   N9   128.21  3.000
 K15  C5   C4   N9   105.28  3.000
 K15  C2   N3   C4   111.67  3.000
 K15  H34  C2   N1   115.41  3.000
 K15  H34  C2   N3   116.15  3.000
 K15  N1   C2   N3   128.44  3.000
 K15  C2   N1   C6   119.17  3.000
 K15  H35  OXT  C    111.11  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
 K15  CONST_01  C6   C5   C4   N9    180.00   0.0  0
 K15  CONST_02  N7   C5   C4   N9      0.00   0.0  0
 K15  CONST_03  C2   N3   C4   N9    180.00   0.0  0
 K15  CONST_04  C5   N7   C8   N9      0.00   0.0  0
 K15  CONST_05  C6   C5   N7   C8    180.00   0.0  0
 K15  CONST_06  C4   C5   N7   C8      0.00   0.0  0
 K15  CONST_07  C5   C4   N9   C8      0.00   0.0  0
 K15  CONST_08  N3   C4   N9   C8    180.00   0.0  0
 K15  CONST_09  N1   C6   C5   N7    180.00   0.0  0
 K15  CONST_10  N3   C4   C5   N7    180.00   0.0  0
 K15  CONST_11  C4   N9   C8   N7      0.00   0.0  0
 K15  CONST_12  C2   N1   C6   C5      0.00   0.0  0
 K15  CONST_13  C2   N3   C4   C5      0.00   0.0  0
 K15  CONST_14  N3   C2   N1   C6      0.00   0.0  0
 K15  CONST_15  N3   C4   C5   C6      0.00   0.0  0
 K15  CONST_16  N1   C6   C5   C4      0.00   0.0  0
 K15  CONST_17  N1   C2   N3   C4      0.00   0.0  0
 K15  CONST_18  C5   C4   N9   C1'   180.00   0.0  0
 K15  CONST_19  N3   C4   N9   C1'     0.00   0.0  0
 K15  CONST_20  N7   C8   N9   C1'   180.00   0.0  0
 K15  CONST_21  N6   C6   C5   N7      0.00   0.0  0
 K15  CONST_22  C2   N1   C6   N6    180.00   0.0  0
 K15  CONST_23  C4   C5   C6   N6    180.00   0.0  0
 K15  CONST_24  H31  C8   N9   C1'     0.00   0.0  0
 K15  CONST_25  H34  C2   N1   C6    180.00   0.0  0
 K15  CONST_26  H32  N6   C6   C5      0.00   0.0  0
 K15  CONST_27  H33  N6   C6   C5    180.00   0.0  0
 K15  CONST_28  H35  OXT  C    O       0.00   0.0  0
 K15  Var_01    C4'  C5'  ND   CG   -133.79  30.0  2
 K15  Var_02    ND   CG   CB   CA   -175.52  30.0  3
 K15  Var_03    C5'  ND   CG   CB     71.00  30.0  3
 K15  Var_04    C11  CE   ND   CG     73.51  30.0  3
 K15  Var_05    C12  C11  CE   ND    177.04  30.0  3
 K15  Var_06    C13  C12  C11  CE   -178.82  30.0  3
 K15  Var_07    C14  C13  C12  C11   179.50  30.0  3
 K15  Var_08    C15  C14  C13  C12  -179.57  30.0  1
 K15  Var_09    H20  C15  C14  C13    59.58  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
 K15  chir_01  CA   N    C    CB   positiv
 K15  chir_02  C4'  O4'  C5'  C3'  positiv
 K15  chir_03  C1'  O4'  N9   C2'  negativ
 K15  chir_04  C2'  O2'  C1'  C3'  negativ
 K15  chir_05  C3'  O3'  C4'  C2'  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
 K15  plan-1  C1'  0.020
 K15  plan-1  N9   0.020
 K15  plan-1  C8   0.020
 K15  plan-1  N7   0.020
 K15  plan-1  C5   0.020
 K15  plan-1  C6   0.020
 K15  plan-1  N6   0.020
 K15  plan-1  C4   0.020
 K15  plan-1  N3   0.020
 K15  plan-1  C2   0.020
 K15  plan-1  N1   0.020
 K15  plan-1  H31  0.020
 K15  plan-1  H34  0.020
 K15  plan-2  C6   0.020
 K15  plan-2  N6   0.020
 K15  plan-2  H32  0.020
 K15  plan-2  H33  0.020
 K15  plan-3  O    0.020
 K15  plan-3  C    0.020
 K15  plan-3  CA   0.020
 K15  plan-3  OXT  0.020
 K15  plan-3  H35  0.020

