# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 13:03:14 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  64  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_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  -0.609  -1.3451   4.6447  -2.6268
 K15  C    C  C      0   0.385  -1.0955   4.0025  -1.5875
 K15  CA   C  CH1    0  -0.216  -2.2507   3.1950  -0.9410
 K15  N    N  NH2    0  -0.787  -3.5374   3.2694  -1.6171
 K15  CB   C  CH2    0  -0.457  -1.8429   1.7373  -0.7606
 K15  CG   C  CH2    0  -0.263  -2.7927   0.9404   0.1203
 K15  ND   N  NT     0  -0.423  -2.2377  -0.3543   0.4798
 K15  CE   C  CH2    0  -0.268  -3.2472  -1.3251   0.8682
 K15  C11  C  CH2    0  -0.430  -4.0062  -1.9247  -0.3062
 K15  C12  C  CH2    0  -0.417  -5.0529  -2.9323   0.1542
 K15  C13  C  CH2    0  -0.406  -5.7974  -3.6008  -0.9932
 K15  C14  C  CH2    0  -0.419  -6.8422  -4.6050  -0.5213
 K15  C15  C  CH3    0  -0.662  -7.5745  -5.2854  -1.6690
 K15  C5'  C  CH2    0  -0.315  -1.1785  -0.2574   1.4694
 K15  C4'  C  CH1    0   0.053  -0.0427  -1.2150   1.1820
 K15  O4'  O  O2     0  -0.493   0.6321  -0.8387  -0.0204
 K15  C1'  C  CH1    0   0.189   2.0035  -1.0693   0.0794
 K15  C2'  C  CH1    0  -0.051   2.2550  -1.7370   1.4332
 K15  O2'  O  OH1    0  -0.666   2.1844  -3.1243   1.2451
 K15  C3'  C  CH1    0  -0.036   1.0547  -1.2291   2.2393
 K15  O3'  O  OH1    0  -0.659   0.6954  -2.0644   3.3040
 K15  N9   N  NR5    0  -0.539   2.7172   0.1990  -0.0355
 K15  C8   C  CR15   0   0.096   2.2376   1.4811  -0.0039
 K15  N7   N  N      0  -0.449   3.1679   2.3802  -0.1509
 K15  C5   C  CR56   0  -0.003   4.3229   1.6595  -0.2937
 K15  C6   C  CR6    0   0.453   5.6663   2.0263  -0.4966
 K15  N6   N  NH2    0  -0.817   6.0623   3.2973  -0.5779
 K15  C4   C  CR56   0   0.483   4.0630   0.3003  -0.2308
 K15  N3   N  N      0  -0.460   4.9524  -0.6855  -0.3447
 K15  C2   C  CR16   0   0.037   6.1739  -0.2185  -0.5353
 K15  N1   N  N      0  -0.474   6.5723   1.0488  -0.6145
 K15  OXT  O  OC    -1  -0.608   0.0042   3.9505  -0.9955
 K15  H1   H  HCH1   0   0.210  -2.3925   3.6153   0.0646
 K15  H2   H  HNH2   0   0.332  -3.7930   4.2439  -1.7217
 K15  H3   H  HNH2   0   0.322  -3.4143   2.9420  -2.5691
 K15  H5   H  HCH2   0   0.207  -1.7630   1.2461  -1.7374
 K15  H6   H  HCH2   0   0.242  -0.8412   1.7197  -0.3367
 K15  H7   H  HCH2   0   0.184  -3.0576   1.5306   1.0156
 K15  H8   H  HCH2   0   0.228  -3.7279   0.7845  -0.4181
 K15  H10  H  HCH2   0   0.224  -2.7488  -2.1455   1.3928
 K15  H11  H  HCH2   0   0.191  -3.9593  -0.8934   1.5928
 K15  H12  H  HCH2   0   0.216  -4.4966  -1.1411  -0.8916
 K15  H13  H  HCH2   0   0.213  -3.2902  -2.4106  -0.9761
 K15  H14  H  HCH2   0   0.208  -4.5692  -3.7015   0.7666
 K15  H15  H  HCH2   0   0.210  -5.7733  -2.4329   0.8113
 K15  H16  H  HCH2   0   0.207  -6.2825  -2.8363  -1.6100
 K15  H17  H  HCH2   0   0.207  -5.0784  -4.1065  -1.6474
 K15  H18  H  HCH2   0   0.210  -6.3572  -5.3613   0.1038
 K15  H19  H  HCH2   0   0.210  -7.5645  -4.0968   0.1251
 K15  H20  H  HCH3   0   0.216  -6.8796  -5.8272  -2.3133
 K15  H21  H  HCH3   0   0.225  -8.3140  -5.9997  -1.3050
 K15  H22  H  HCH3   0   0.216  -8.0973  -4.5567  -2.2913
 K15  H23  H  HCH2   0   0.236  -0.7789   0.7593   1.5035
 K15  H24  H  HCH2   0   0.231  -1.5479  -0.4609   2.4859
 K15  H25  H  HCH1   0   0.232  -0.4447  -2.2306   1.0657
 K15  H26  H  HCH1   0   0.275   2.3533  -1.7043  -0.7402
 K15  H27  H  HCH1   0   0.258   3.2165  -1.4360   1.8661
 K15  H28  H  HOH1   0   0.451   1.8551  -3.5150   2.0641
 K15  H29  H  HCH1   0   0.241   1.2560  -0.2047   2.5813
 K15  H30  H  HOH1   0   0.468   1.2515  -1.8584   4.0625
 K15  H31  H  HCR5   0   0.301   1.1896   1.7054   0.1109
 K15  H32  H  HNH2   0   0.411   5.4082   4.0532  -0.4780
 K15  H33  H  HNH2   0   0.403   7.0324   3.5196  -0.7194
 K15  H34  H  HCR6   0   0.251   6.9580  -0.9604  -0.6420

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  1.385  0.020  1.385
 K15  C5   N7   aromatic  1.369  0.020  1.369
 K15  N3   C4   aromatic  1.333  0.020  1.333
 K15  C4   N9   aromatic  1.364  0.020  1.364
 K15  N7   C8   aromatic  1.302  0.020  1.302
 K15  N    CA   single    1.455  0.020  1.455
 K15  O    C    deloc     1.247  0.020  1.247
 K15  N9   C8   aromatic  1.369  0.020  1.369
 K15  N9   C1'  single    1.460  0.020  1.460
 K15  C1'  O4'  single    1.394  0.020  1.394
 K15  C1'  C2'  single    1.530  0.020  1.530
 K15  CA   C    single    1.551  0.020  1.551
 K15  CA   CB   single    1.524  0.020  1.524
 K15  C    OXT  deloc     1.250  0.020  1.250
 K15  O4'  C4'  single    1.429  0.020  1.429
 K15  CB   CG   single    1.521  0.020  1.521
 K15  CG   ND   single    1.454  0.020  1.454
 K15  C2'  O2'  single    1.402  0.020  1.402
 K15  C2'  C3'  single    1.532  0.020  1.532
 K15  C4'  C5'  single    1.513  0.020  1.513
 K15  C4'  C3'  single    1.524  0.020  1.524
 K15  C5'  ND   single    1.453  0.020  1.453
 K15  ND   CE   single    1.453  0.020  1.453
 K15  C3'  O3'  single    1.400  0.020  1.400
 K15  CE   C11  single    1.521  0.020  1.521
 K15  C11  C12  single    1.524  0.020  1.524
 K15  C12  C13  single    1.522  0.020  1.522
 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

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   115.86  3.000
 K15  OXT  C    O    126.32  3.000
 K15  CA   C    O    117.81  3.000
 K15  H1   CA   CB   106.98  3.000
 K15  H1   CA   N    106.94  3.000
 K15  CB   CA   N    109.90  3.000
 K15  H1   CA   C    106.17  3.000
 K15  CB   CA   C    110.37  3.000
 K15  N    CA   C    115.99  3.000
 K15  H3   N    H2   104.14  3.000
 K15  H3   N    CA   108.20  3.000
 K15  H2   N    CA   108.68  3.000
 K15  H6   CB   H5   105.83  3.000
 K15  H6   CB   CG   109.92  3.000
 K15  H5   CB   CG   109.07  3.000
 K15  H6   CB   CA   107.94  3.000
 K15  H5   CB   CA   110.04  3.000
 K15  CG   CB   CA   113.74  3.000
 K15  H8   CG   H7   105.71  3.000
 K15  H8   CG   ND   108.79  3.000
 K15  H7   CG   ND   111.53  3.000
 K15  H8   CG   CB   108.94  3.000
 K15  H7   CG   CB   109.83  3.000
 K15  ND   CG   CB   111.81  3.000
 K15  C5'  ND   CE   111.65  3.000
 K15  CE   ND   CG   113.32  3.000
 K15  C5'  ND   CG   112.79  3.000
 K15  H11  CE   H10  105.81  3.000
 K15  H11  CE   C11  109.81  3.000
 K15  H10  CE   C11  107.57  3.000
 K15  H11  CE   ND   111.24  3.000
 K15  H10  CE   ND   108.22  3.000
 K15  C11  CE   ND   113.79  3.000
 K15  H13  C11  H12  106.48  3.000
 K15  H13  C11  C12  109.92  3.000
 K15  H12  C11  C12  109.10  3.000
 K15  H13  C11  CE   108.73  3.000
 K15  H12  C11  CE   110.75  3.000
 K15  C12  C11  CE   111.71  3.000
 K15  H15  C12  H14  105.97  3.000
 K15  H15  C12  C13  109.31  3.000
 K15  H14  C12  C13  109.20  3.000
 K15  H15  C12  C11  109.35  3.000
 K15  H14  C12  C11  109.25  3.000
 K15  C13  C12  C11  113.48  3.000
 K15  H17  C13  H16  106.05  3.000
 K15  H17  C13  C14  109.31  3.000
 K15  H16  C13  C14  109.30  3.000
 K15  H17  C13  C12  109.37  3.000
 K15  H16  C13  C12  109.54  3.000
 K15  C14  C13  C12  113.03  3.000
 K15  H19  C14  H18  106.02  3.000
 K15  H19  C14  C15  109.60  3.000
 K15  H18  C14  C15  109.57  3.000
 K15  H19  C14  C13  109.23  3.000
 K15  H18  C14  C13  109.17  3.000
 K15  C15  C14  C13  113.01  3.000
 K15  H22  C15  H21  107.62  3.000
 K15  H22  C15  H20  107.45  3.000
 K15  H21  C15  H20  107.67  3.000
 K15  H22  C15  C14  111.22  3.000
 K15  H21  C15  C14  111.55  3.000
 K15  H20  C15  C14  111.14  3.000
 K15  H24  C5'  H23  105.43  3.000
 K15  H24  C5'  C4'  108.08  3.000
 K15  H23  C5'  C4'  108.67  3.000
 K15  H24  C5'  ND   111.84  3.000
 K15  H23  C5'  ND   110.48  3.000
 K15  C4'  C5'  ND   112.06  3.000
 K15  H25  C4'  C3'  109.17  3.000
 K15  H25  C4'  O4'  109.09  3.000
 K15  C3'  C4'  O4'  104.24  3.000
 K15  H25  C4'  C5'  109.30  3.000
 K15  C3'  C4'  C5'  114.50  3.000
 K15  O4'  C4'  C5'  110.34  3.000
 K15  C1'  O4'  C4'  111.14  3.000
 K15  H26  C1'  N9   106.79  3.000
 K15  H26  C1'  C2'  110.91  3.000
 K15  N9   C1'  C2'  111.61  3.000
 K15  H26  C1'  O4'  110.90  3.000
 K15  C2'  C1'  O4'  107.29  3.000
 K15  N9   C1'  O4'  109.37  3.000
 K15  H27  C2'  C3'  112.84  3.000
 K15  H27  C2'  O2'  111.64  3.000
 K15  C3'  C2'  O2'  111.04  3.000
 K15  H27  C2'  C1'  111.94  3.000
 K15  C3'  C2'  C1'  101.07  3.000
 K15  O2'  C2'  C1'  107.75  3.000
 K15  H28  O2'  C2'  107.69  3.000
 K15  H29  C3'  O3'  111.50  3.000
 K15  H29  C3'  C2'  109.22  3.000
 K15  O3'  C3'  C2'  113.78  3.000
 K15  H29  C3'  C4'  109.83  3.000
 K15  O3'  C3'  C4'  110.38  3.000
 K15  C2'  C3'  C4'  101.67  3.000
 K15  H30  O3'  C3'  108.86  3.000
 K15  C4   N9   C8   106.22  3.000
 K15  C8   N9   C1'  129.82  3.000
 K15  C4   N9   C1'  123.94  3.000
 K15  H31  C8   N7   124.26  3.000
 K15  H31  C8   N9   122.54  3.000
 K15  N7   C8   N9   113.18  3.000
 K15  C5   N7   C8   104.54  3.000
 K15  C4   C5   C6   116.19  3.000
 K15  C4   C5   N7   110.71  3.000
 K15  C6   C5   N7   133.09  3.000
 K15  N1   C6   N6   119.33  3.000
 K15  N1   C6   C5   117.94  3.000
 K15  N6   C6   C5   122.73  3.000
 K15  H33  N6   H32  118.42  3.000
 K15  H33  N6   C6   120.39  3.000
 K15  H32  N6   C6   121.17  3.000
 K15  N3   C4   C5   126.64  3.000
 K15  N3   C4   N9   128.02  3.000
 K15  C5   C4   N9   105.34  3.000
 K15  C2   N3   C4   111.58  3.000
 K15  H34  C2   N1   115.41  3.000
 K15  H34  C2   N3   116.14  3.000
 K15  N1   C2   N3   128.45  3.000
 K15  C2   N1   C6   119.20  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  Var_01    C4'  C5'  ND   CG   -140.33  30.0  1
 K15  Var_02    ND   CG   CB   CA   -168.72  30.0  3
 K15  Var_03    C5'  ND   CG   CB     73.75  30.0  3
 K15  Var_04    C11  CE   ND   CG     76.93  30.0  3
 K15  Var_05    C12  C11  CE   ND   -179.88  30.0  3
 K15  Var_06    C13  C12  C11  CE   -177.59  30.0  3
 K15  Var_07    C14  C13  C12  C11  -179.94  30.0  3
 K15  Var_08    C15  C14  C13  C12  -179.31  30.0  1
 K15  Var_09    H20  C15  C14  C13    59.71  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

