# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 18:58:33 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: 5'-{[(3S)-3-amino-3-carboxypropyl][(4-fluorophenyl)methyl]amino}-5'-deoxyadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCN(C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)Cc4ccc(F)cc4)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
 KB1  KB1  5'-{[(3S)-3-amino-3-carboxypropyl][(4-fluorophenyl)methyl]amino}-5'-deoxyadenosine  ligand  59  34  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_KB1
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
 KB1  N6   N  NH2    0  -0.825  -4.6136  -2.0267  -3.2884
 KB1  C6   C  CR6    0   0.449  -4.3954  -0.9747  -2.4971
 KB1  N1   N  N      0  -0.477  -5.0423   0.1717  -2.7373
 KB1  C2   C  CR16   0   0.028  -4.8304   1.2139  -1.9384
 KB1  N3   N  N      0  -0.459  -4.0334   1.2940  -0.8869
 KB1  C4   C  CR56   0   0.484  -3.3965   0.1476  -0.6625
 KB1  C5   C  CR56   0  -0.014  -3.5136  -1.0167  -1.4019
 KB1  N7   N  N      0  -0.452  -2.7054  -2.0001  -0.8916
 KB1  C8   C  CR15   0   0.109  -2.1188  -1.4470   0.1270
 KB1  N9   N  NR5    0  -0.552  -2.4985  -0.1432   0.3275
 KB1  CBF  C  CH1    0   0.213  -2.0256   0.7905   1.3112
 KB1  OAU  O  O2     0  -0.477  -0.6867   1.1125   1.0601
 KB1  CBE  C  CH1    0   0.009  -0.0372   1.4733   2.2855
 KB1  CAQ  C  CH2    0  -0.344   1.1913   0.6019   2.5063
 KB1  NBG  N  NT     0  -0.413   2.0753   0.6132   1.3629
 KB1  CAO  C  CH2    0  -0.274   2.6467  -0.6785   1.0297
 KB1  CB   C  CH2    0  -0.453   1.5945  -1.6349   0.4922
 KB1  CA   C  CH1    0  -0.233   2.0994  -3.0562   0.2755
 KB1  N    N  NH2    0  -0.782   3.1863  -3.0577  -0.6921
 KB1  C    C  C      0   0.401   0.9144  -4.0085  -0.0378
 KB1  OXT  O  OC     0  -0.615  -0.0231  -4.0066   0.7911
 KB1  O    O  O     -1  -0.611   0.9925  -4.7149  -1.0608
 KB1  CAP  C  CH2    0  -0.314   3.0442   1.6832   1.4012
 KB1  CAY  C  CR6    0   0.084   3.5258   2.0603   0.0229
 KB1  CAK  C  CR16   0  -0.286   4.8601   2.3653  -0.2183
 KB1  CAI  C  CR16   0  -0.383   5.2957   2.7490  -1.4815
 KB1  CAW  C  CR6    0   0.511   4.3704   2.8180  -2.5027
 KB1  FAG  F  F      0  -0.319   4.7787   3.1837  -3.7315
 KB1  CAJ  C  CR16   0  -0.385   3.0357   2.5161  -2.3037
 KB1  CAL  C  CR16   0  -0.258   2.6229   2.1361  -1.0360
 KB1  CBC  C  CH1    0  -0.033  -1.0781   1.2969   3.3917
 KB1  OAE  O  OH1    0  -0.657  -1.7227   2.5238   3.6238
 KB1  CBD  C  CH1    0  -0.040  -2.0375   0.2883   2.7485
 KB1  OAF  O  OH1    0  -0.640  -3.3371   0.2982   3.2568
 KB1  H1   H  HNH2   0   0.399  -5.1921  -1.9325  -4.1052
 KB1  H2   H  HNH2   0   0.431  -4.0915  -2.8773  -3.1720
 KB1  H3   H  HCR6   0   0.271  -5.3859   2.1120  -2.1865
 KB1  H4   H  HCR5   0   0.303  -1.3991  -1.9512   0.7552
 KB1  H5   H  HCH1   0   0.274  -2.6800   1.6661   1.2257
 KB1  H6   H  HCH1   0   0.269   0.2655   2.5248   2.2235
 KB1  H7   H  HCH2   0   0.252   1.6884   0.9462   3.4258
 KB1  H8   H  HCH2   0   0.257   0.8736  -0.4222   2.7128
 KB1  H10  H  HCH2   0   0.240   3.4146  -0.5268   0.2700
 KB1  H11  H  HCH2   0   0.211   3.1580  -1.1360   1.8953
 KB1  H12  H  HCH2   0   0.223   0.7589  -1.6843   1.1883
 KB1  H13  H  HCH2   0   0.235   1.1882  -1.2316  -0.4420
 KB1  H14  H  HCH1   0   0.237   2.5172  -3.3987   1.2328
 KB1  H15  H  HNH2   0   0.326   3.4442  -4.0181  -0.8850
 KB1  H16  H  HNH2   0   0.307   2.8266  -2.7135  -1.5759
 KB1  H19  H  HCH2   0   0.239   2.5676   2.5604   1.8503
 KB1  H20  H  HCH2   0   0.201   3.9081   1.4517   2.0462
 KB1  H21  H  HCR6   0   0.233   5.5814   2.3006   0.5875
 KB1  H22  H  HCR6   0   0.253   6.3369   2.9796  -1.6660
 KB1  H23  H  HCR6   0   0.252   2.3317   2.5735  -3.1236
 KB1  H24  H  HCR6   0   0.265   1.5851   1.8810  -0.8617
 KB1  H25  H  HCH1   0   0.227  -0.6271   0.9020   4.3118
 KB1  H26  H  HOH1   0   0.429  -2.5492   2.3426   4.0862
 KB1  H27  H  HCH1   0   0.231  -1.5889  -0.7127   2.7974
 KB1  H28  H  HOH1   0   0.444  -3.3680  -0.2531   4.0451

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
 KB1  O    C    deloc     1.246  0.020  1.246
 KB1  OXT  C    deloc     1.251  0.020  1.251
 KB1  C    CA   single    1.552  0.020  1.552
 KB1  CA   N    single    1.455  0.020  1.455
 KB1  CA   CB   single    1.524  0.020  1.524
 KB1  CB   CAO  single    1.520  0.020  1.520
 KB1  CAO  NBG  single    1.451  0.020  1.451
 KB1  OAE  CBC  single    1.405  0.020  1.405
 KB1  NBG  CAQ  single    1.445  0.020  1.445
 KB1  NBG  CAP  single    1.444  0.020  1.444
 KB1  CBE  CBC  single    1.529  0.020  1.529
 KB1  CBE  OAU  single    1.433  0.020  1.433
 KB1  CBE  CAQ  single    1.522  0.020  1.522
 KB1  CBC  CBD  single    1.533  0.020  1.533
 KB1  N3   C2   aromatic  1.322  0.020  1.322
 KB1  N3   C4   aromatic  1.331  0.020  1.331
 KB1  C2   N1   aromatic  1.330  0.020  1.330
 KB1  OAF  CBD  single    1.396  0.020  1.396
 KB1  CBF  OAU  single    1.400  0.020  1.400
 KB1  CBF  CBD  single    1.522  0.020  1.522
 KB1  CBF  N9   single    1.436  0.020  1.436
 KB1  CAP  CAY  single    1.508  0.020  1.508
 KB1  C4   N9   aromatic  1.368  0.020  1.368
 KB1  C4   C5   aromatic  1.384  0.020  1.384
 KB1  N1   C6   aromatic  1.338  0.020  1.338
 KB1  N9   C8   aromatic  1.373  0.020  1.373
 KB1  CAK  CAY  aromatic  1.390  0.020  1.390
 KB1  CAK  CAI  aromatic  1.390  0.020  1.390
 KB1  CAY  CAL  aromatic  1.394  0.020  1.394
 KB1  C5   C6   aromatic  1.407  0.020  1.407
 KB1  C5   N7   aromatic  1.371  0.020  1.371
 KB1  C6   N6   single    1.334  0.020  1.334
 KB1  CAI  CAW  aromatic  1.380  0.020  1.380
 KB1  C8   N7   aromatic  1.299  0.020  1.299
 KB1  CAL  CAJ  aromatic  1.386  0.020  1.386
 KB1  CAW  CAJ  aromatic  1.383  0.020  1.383
 KB1  CAW  FAG  single    1.345  0.020  1.345
 KB1  N6   H1   single    0.860  0.020  1.020
 KB1  N6   H2   single    0.860  0.020  1.020
 KB1  C2   H3   single    0.930  0.020  1.080
 KB1  C8   H4   single    0.930  0.020  1.080
 KB1  CBF  H5   single    0.970  0.020  1.090
 KB1  CBE  H6   single    0.970  0.020  1.090
 KB1  CAQ  H7   single    0.970  0.020  1.090
 KB1  CAQ  H8   single    0.970  0.020  1.090
 KB1  CAO  H10  single    0.970  0.020  1.090
 KB1  CAO  H11  single    0.970  0.020  1.090
 KB1  CB   H12  single    0.970  0.020  1.090
 KB1  CB   H13  single    0.970  0.020  1.090
 KB1  CA   H14  single    0.970  0.020  1.090
 KB1  N    H15  single    0.890  0.020  1.040
 KB1  N    H16  single    0.890  0.020  1.040
 KB1  CAP  H19  single    0.970  0.020  1.090
 KB1  CAP  H20  single    0.970  0.020  1.090
 KB1  CAK  H21  single    0.930  0.020  1.080
 KB1  CAI  H22  single    0.930  0.020  1.080
 KB1  CAJ  H23  single    0.930  0.020  1.080
 KB1  CAL  H24  single    0.930  0.020  1.080
 KB1  CBC  H25  single    0.970  0.020  1.090
 KB1  OAE  H26  single    0.850  0.020  0.980
 KB1  CBD  H27  single    0.970  0.020  1.090
 KB1  OAF  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
 KB1  H2   N6   H1   118.20  3.000
 KB1  H2   N6   C6   120.91  3.000
 KB1  H1   N6   C6   120.13  3.000
 KB1  C5   C6   N1   117.93  3.000
 KB1  C5   C6   N6   122.73  3.000
 KB1  N1   C6   N6   119.34  3.000
 KB1  C2   N1   C6   119.11  3.000
 KB1  H3   C2   N3   116.13  3.000
 KB1  H3   C2   N1   115.45  3.000
 KB1  N3   C2   N1   128.41  3.000
 KB1  C4   N3   C2   111.75  3.000
 KB1  N9   C4   C5   105.27  3.000
 KB1  C5   C4   N3   126.46  3.000
 KB1  N9   C4   N3   128.27  3.000
 KB1  N7   C5   C4   110.77  3.000
 KB1  N7   C5   C6   132.89  3.000
 KB1  C4   C5   C6   116.35  3.000
 KB1  C8   N7   C5   104.63  3.000
 KB1  H4   C8   N9   122.87  3.000
 KB1  H4   C8   N7   123.92  3.000
 KB1  N9   C8   N7   113.20  3.000
 KB1  CBF  N9   C8   128.78  3.000
 KB1  C8   N9   C4   106.13  3.000
 KB1  CBF  N9   C4   125.01  3.000
 KB1  H5   CBF  CBD  109.41  3.000
 KB1  H5   CBF  OAU  111.91  3.000
 KB1  CBD  CBF  OAU  104.64  3.000
 KB1  H5   CBF  N9   105.62  3.000
 KB1  CBD  CBF  N9   115.44  3.000
 KB1  OAU  CBF  N9   109.97  3.000
 KB1  CBE  OAU  CBF  109.75  3.000
 KB1  H6   CBE  CBC  109.85  3.000
 KB1  H6   CBE  CAQ  109.54  3.000
 KB1  CBC  CBE  CAQ  112.24  3.000
 KB1  H6   CBE  OAU  108.57  3.000
 KB1  CAQ  CBE  OAU  110.22  3.000
 KB1  CBC  CBE  OAU  106.32  3.000
 KB1  H8   CAQ  H7   105.48  3.000
 KB1  H8   CAQ  NBG  109.56  3.000
 KB1  H7   CAQ  NBG  112.48  3.000
 KB1  H8   CAQ  CBE  109.23  3.000
 KB1  H7   CAQ  CBE  107.86  3.000
 KB1  NBG  CAQ  CBE  111.99  3.000
 KB1  CAP  NBG  CAO  113.67  3.000
 KB1  CAP  NBG  CAQ  113.28  3.000
 KB1  CAO  NBG  CAQ  114.56  3.000
 KB1  H11  CAO  H10  106.11  3.000
 KB1  H11  CAO  CB   109.69  3.000
 KB1  H10  CAO  CB   109.18  3.000
 KB1  H11  CAO  NBG  111.78  3.000
 KB1  H10  CAO  NBG  108.26  3.000
 KB1  CB   CAO  NBG  111.63  3.000
 KB1  H13  CB   H12  106.10  3.000
 KB1  H13  CB   CA   110.18  3.000
 KB1  H12  CB   CA   107.63  3.000
 KB1  H13  CB   CAO  109.06  3.000
 KB1  H12  CB   CAO  109.50  3.000
 KB1  CA   CB   CAO  114.06  3.000
 KB1  H14  CA   C    105.95  3.000
 KB1  H14  CA   N    107.15  3.000
 KB1  C    CA   N    115.81  3.000
 KB1  H14  CA   CB   107.02  3.000
 KB1  N    CA   CB   110.06  3.000
 KB1  C    CA   CB   110.36  3.000
 KB1  H16  N    H15  104.25  3.000
 KB1  H16  N    CA   108.31  3.000
 KB1  H15  N    CA   108.52  3.000
 KB1  O    C    OXT  126.28  3.000
 KB1  OXT  C    CA   115.93  3.000
 KB1  O    C    CA   117.77  3.000
 KB1  H20  CAP  H19  105.63  3.000
 KB1  H20  CAP  CAY  109.69  3.000
 KB1  H19  CAP  CAY  108.28  3.000
 KB1  H20  CAP  NBG  112.68  3.000
 KB1  H19  CAP  NBG  108.21  3.000
 KB1  CAY  CAP  NBG  112.05  3.000
 KB1  CAL  CAY  CAK  118.57  3.000
 KB1  CAL  CAY  CAP  120.08  3.000
 KB1  CAK  CAY  CAP  121.34  3.000
 KB1  H21  CAK  CAI  118.93  3.000
 KB1  H21  CAK  CAY  119.80  3.000
 KB1  CAI  CAK  CAY  121.27  3.000
 KB1  H22  CAI  CAW  120.56  3.000
 KB1  H22  CAI  CAK  121.00  3.000
 KB1  CAW  CAI  CAK  118.44  3.000
 KB1  CAJ  CAW  FAG  118.93  3.000
 KB1  FAG  CAW  CAI  119.08  3.000
 KB1  CAJ  CAW  CAI  121.99  3.000
 KB1  H23  CAJ  CAL  120.90  3.000
 KB1  H23  CAJ  CAW  120.48  3.000
 KB1  CAL  CAJ  CAW  118.61  3.000
 KB1  H24  CAL  CAJ  119.81  3.000
 KB1  H24  CAL  CAY  119.07  3.000
 KB1  CAJ  CAL  CAY  121.12  3.000
 KB1  H25  CBC  CBD  111.83  3.000
 KB1  H25  CBC  OAE  111.34  3.000
 KB1  CBD  CBC  OAE  110.89  3.000
 KB1  H25  CBC  CBE  111.59  3.000
 KB1  CBD  CBC  CBE  101.44  3.000
 KB1  OAE  CBC  CBE  109.33  3.000
 KB1  H26  OAE  CBC  107.95  3.000
 KB1  H27  CBD  OAF  111.76  3.000
 KB1  H27  CBD  CBC  108.99  3.000
 KB1  OAF  CBD  CBC  115.16  3.000
 KB1  H27  CBD  CBF  109.85  3.000
 KB1  OAF  CBD  CBF  110.42  3.000
 KB1  CBC  CBD  CBF  100.03  3.000
 KB1  H28  OAF  CBD  108.91  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
 KB1  CONST_01  N3   C2   N1   C6      0.00   0.0  0
 KB1  CONST_02  N3   C4   C5   C6      0.00   0.0  0
 KB1  CONST_03  N9   C4   C5   C6    180.00   0.0  0
 KB1  CONST_04  C8   N7   C5   C6    180.00   0.0  0
 KB1  CONST_05  C4   N3   C2   N1      0.00   0.0  0
 KB1  CONST_06  C4   C5   C6   N1      0.00   0.0  0
 KB1  CONST_07  N7   C5   C6   N1    180.00   0.0  0
 KB1  CONST_08  N9   C4   N3   C2    180.00   0.0  0
 KB1  CONST_09  C5   C4   N3   C2      0.00   0.0  0
 KB1  CONST_10  C5   C6   N1   C2      0.00   0.0  0
 KB1  CONST_11  C8   N9   C4   N3    180.00   0.0  0
 KB1  CONST_12  N7   C5   C4   N3    180.00   0.0  0
 KB1  CONST_13  N7   C8   N9   C4      0.00   0.0  0
 KB1  CONST_14  C8   N7   C5   C4      0.00   0.0  0
 KB1  CONST_15  C8   N9   C4   C5      0.00   0.0  0
 KB1  CONST_16  N9   C8   N7   C5      0.00   0.0  0
 KB1  CONST_17  N9   C4   C5   N7      0.00   0.0  0
 KB1  CONST_18  CAW  CAI  CAK  CAY     0.00   0.0  0
 KB1  CONST_19  CAW  CAJ  CAL  CAY     0.00   0.0  0
 KB1  CONST_20  CAJ  CAL  CAY  CAK     0.00   0.0  0
 KB1  CONST_21  CAJ  CAW  CAI  CAK     0.00   0.0  0
 KB1  CONST_22  CAL  CAY  CAK  CAI     0.00   0.0  0
 KB1  CONST_23  CAL  CAJ  CAW  CAI     0.00   0.0  0
 KB1  CONST_24  CBF  N9   C4   N3      0.00   0.0  0
 KB1  CONST_25  CBF  N9   C4   C5    180.00   0.0  0
 KB1  CONST_26  CBF  N9   C8   N7    180.00   0.0  0
 KB1  CONST_27  C2   N1   C6   N6    180.00   0.0  0
 KB1  CONST_28  C4   C5   C6   N6    180.00   0.0  0
 KB1  CONST_29  N7   C5   C6   N6      0.00   0.0  0
 KB1  CONST_30  CAI  CAK  CAY  CAP   180.00   0.0  0
 KB1  CONST_31  CAJ  CAL  CAY  CAP   180.00   0.0  0
 KB1  CONST_32  FAG  CAW  CAI  CAK   180.00   0.0  0
 KB1  CONST_33  CAL  CAJ  CAW  FAG   180.00   0.0  0
 KB1  CONST_34  H3   C2   N1   C6    180.00   0.0  0
 KB1  CONST_35  H4   C8   N9   C4    180.00   0.0  0
 KB1  CONST_36  H22  CAI  CAK  CAY   180.00   0.0  0
 KB1  CONST_37  H23  CAJ  CAL  CAY   180.00   0.0  0
 KB1  CONST_38  H24  CAL  CAY  CAK   180.00   0.0  0
 KB1  CONST_39  H21  CAK  CAI  CAW   180.00   0.0  0
 KB1  CONST_40  H1   N6   C6   N1      0.00   0.0  0
 KB1  CONST_41  H2   N6   C6   N1    180.00   0.0  0
 KB1  Var_01    CAK  CAY  CAP  NBG  -140.05  30.0  2
 KB1  Var_02    CAO  NBG  CAQ  CBE  -139.19  30.0  1
 KB1  Var_03    CAY  CAP  NBG  CAQ  -155.06  30.0  3
 KB1  Var_04    CB   CAO  NBG  CAQ    69.09  30.0  2
 KB1  Var_05    CA   CB   CAO  NBG  -173.31  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
 KB1  chir_01  CBF  OAU  CBD  N9   positiv
 KB1  chir_02  CBE  OAU  CBC  CAQ  negativ
 KB1  chir_03  CA   N    C    CB   positiv
 KB1  chir_04  CBC  OAE  CBE  CBD  positiv
 KB1  chir_05  CBD  OAF  CBC  CBF  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
 KB1  plan-1  CAP  0.020
 KB1  plan-1  CAY  0.020
 KB1  plan-1  CAK  0.020
 KB1  plan-1  CAI  0.020
 KB1  plan-1  CAW  0.020
 KB1  plan-1  FAG  0.020
 KB1  plan-1  CAJ  0.020
 KB1  plan-1  CAL  0.020
 KB1  plan-1  H21  0.020
 KB1  plan-1  H22  0.020
 KB1  plan-1  H23  0.020
 KB1  plan-1  H24  0.020
 KB1  plan-2  N6   0.020
 KB1  plan-2  C6   0.020
 KB1  plan-2  N1   0.020
 KB1  plan-2  C2   0.020
 KB1  plan-2  N3   0.020
 KB1  plan-2  C4   0.020
 KB1  plan-2  C5   0.020
 KB1  plan-2  N7   0.020
 KB1  plan-2  C8   0.020
 KB1  plan-2  N9   0.020
 KB1  plan-2  CBF  0.020
 KB1  plan-2  H3   0.020
 KB1  plan-2  H4   0.020
 KB1  plan-3  N6   0.020
 KB1  plan-3  C6   0.020
 KB1  plan-3  H1   0.020
 KB1  plan-3  H2   0.020
 KB1  plan-4  CA   0.020
 KB1  plan-4  C    0.020
 KB1  plan-4  OXT  0.020
 KB1  plan-4  O    0.020

