# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 22:30:25 2021
#   Inital geometry file: a 100 line input string
#   Ligand name: N-(2-methylpropanoyl)adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C(=O)Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO)[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
 NKV  NKV  N-(2-methylpropanoyl)adenosine  ligand  43  24  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NKV
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
 NKV  C13  C  CH1   0  -0.028  44.7352  41.9903  117.7900
 NKV  C20  C  C     0   0.570  50.9490  49.0996  116.3930
 NKV  C22  C  CH1   0  -0.412  51.1177  50.3177  117.2841
 NKV  C24  C  CH3   0  -0.647  52.4350  51.0259  117.0092
 NKV  C02  C  CR6   0   0.516  49.5760  47.0245  116.3456
 NKV  C04  C  CR16  0   0.046  49.6487  45.3169  114.8261
 NKV  C06  C  CR56  0   0.512  48.1112  45.1668  116.3878
 NKV  C07  C  CR56  0  -0.015  48.5041  46.3693  116.9599
 NKV  C09  C  CR15  0   0.129  46.8822  45.6847  118.1173
 NKV  C11  C  CH1   0   0.211  46.2752  43.5496  116.9176
 NKV  C12  C  CH1   0  -0.055  46.0424  42.6944  118.1619
 NKV  C14  C  CH1   0  -0.023  43.9930  43.1046  117.0629
 NKV  C16  C  CH2   0  -0.168  43.1332  43.9724  117.9690
 NKV  C23  C  CH3   0  -0.649  49.9261  51.2628  117.0854
 NKV  N01  N  NH1   0  -0.725  50.0212  48.2049  116.8839
 NKV  N03  N  N     0  -0.440  50.1317  46.4765  115.2764
 NKV  N05  N  N     0  -0.433  48.6541  44.6008  115.3201
 NKV  N08  N  N     0  -0.450  47.7189  46.6750  118.0396
 NKV  N10  N  NR5   0  -0.545  47.0697  44.7283  117.1550
 NKV  O15  O  O2    0  -0.493  45.0042  43.9242  116.4658
 NKV  O17  O  OH1   0  -0.667  42.0563  43.1857  118.4148
 NKV  O18  O  OH1   0  -0.669  44.9716  40.9437  116.8827
 NKV  O19  O  OH1   0  -0.653  47.1358  41.8530  118.3696
 NKV  O21  O  O     0  -0.422  51.5413  48.9423  115.3518
 NKV  H1   H  HCH1  0   0.255  44.1881  41.6453  118.6754
 NKV  H2   H  HCH1  0   0.268  51.1110  49.9781  118.3252
 NKV  H3   H  HCH3  0   0.236  52.5569  51.8544  117.7067
 NKV  H4   H  HCH3  0   0.237  53.2888  50.3598  117.1327
 NKV  H5   H  HCH3  0   0.228  52.4659  51.4342  115.9990
 NKV  H6   H  HCR6  0   0.263  50.1395  44.9159  113.9472
 NKV  H7   H  HCR5  0   0.303  46.1009  45.6013  118.8576
 NKV  H8   H  HCH1  0   0.264  46.8143  42.9709  116.1603
 NKV  H9   H  HCH1  0   0.250  45.8583  43.3357  119.0327
 NKV  H10  H  HCH1  0   0.260  43.3640  42.6905  116.2686
 NKV  H11  H  HCH2  0   0.196  43.7327  44.3538  118.8070
 NKV  H12  H  HCH2  0   0.223  42.7962  44.8451  117.3957
 NKV  H13  H  HCH3  0   0.238  48.9725  50.7878  117.3179
 NKV  H14  H  HCH3  0   0.247  50.0287  52.1282  117.7398
 NKV  H15  H  HCH3  0   0.234  49.8821  51.6234  116.0568
 NKV  H16  H  HNH1  0   0.426  49.5733  48.4584  117.7536
 NKV  H17  H  HOH1  0   0.462  41.5252  43.7133  119.0178
 NKV  H18  H  HOH1  0   0.450  45.6759  40.3923  117.2425
 NKV  H19  H  HOH1  0   0.471  47.1170  41.5364  119.2784

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
 NKV  C04  N03  aromatic  1.334  0.020  1.334
 NKV  C04  N05  aromatic  1.321  0.020  1.321
 NKV  N03  C02  aromatic  1.324  0.020  1.324
 NKV  N05  C06  aromatic  1.325  0.020  1.325
 NKV  O21  C20  double    1.208  0.020  1.208
 NKV  C24  C22  single    1.521  0.020  1.521
 NKV  C02  N01  single    1.372  0.020  1.372
 NKV  C02  C07  aromatic  1.398  0.020  1.398
 NKV  O15  C14  single    1.432  0.020  1.432
 NKV  O15  C11  single    1.400  0.020  1.400
 NKV  C06  C07  aromatic  1.388  0.020  1.388
 NKV  C06  N10  aromatic  1.366  0.020  1.366
 NKV  C20  N01  single    1.379  0.020  1.379
 NKV  C20  C22  single    1.519  0.020  1.519
 NKV  C14  C16  single    1.521  0.020  1.521
 NKV  C14  C13  single    1.524  0.020  1.524
 NKV  C11  N10  single    1.441  0.020  1.441
 NKV  C11  C12  single    1.528  0.020  1.528
 NKV  C07  N08  aromatic  1.370  0.020  1.370
 NKV  C22  C23  single    1.534  0.020  1.534
 NKV  C16  O17  single    1.406  0.020  1.406
 NKV  N10  C09  aromatic  1.370  0.020  1.370
 NKV  O18  C13  single    1.405  0.020  1.405
 NKV  C13  C12  single    1.531  0.020  1.531
 NKV  C12  O19  single    1.395  0.020  1.395
 NKV  N08  C09  aromatic  1.299  0.020  1.299
 NKV  C13  H1   single    0.970  0.020  1.090
 NKV  C22  H2   single    0.970  0.020  1.090
 NKV  C24  H3   single    0.970  0.020  1.090
 NKV  C24  H4   single    0.970  0.020  1.090
 NKV  C24  H5   single    0.970  0.020  1.090
 NKV  C04  H6   single    0.930  0.020  1.080
 NKV  C09  H7   single    0.930  0.020  1.080
 NKV  C11  H8   single    0.970  0.020  1.090
 NKV  C12  H9   single    0.970  0.020  1.090
 NKV  C14  H10  single    0.970  0.020  1.090
 NKV  C16  H11  single    0.970  0.020  1.090
 NKV  C16  H12  single    0.970  0.020  1.090
 NKV  C23  H13  single    0.970  0.020  1.090
 NKV  C23  H14  single    0.970  0.020  1.090
 NKV  C23  H15  single    0.970  0.020  1.090
 NKV  N01  H16  single    0.860  0.020  1.020
 NKV  O17  H17  single    0.850  0.020  0.980
 NKV  O18  H18  single    0.850  0.020  0.980
 NKV  O19  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
 NKV  H1   C13  O18  111.78  3.000
 NKV  H1   C13  C14  111.86  3.000
 NKV  O18  C13  C14  108.57  3.000
 NKV  H1   C13  C12  112.01  3.000
 NKV  O18  C13  C12  110.84  3.000
 NKV  C14  C13  C12  101.28  3.000
 NKV  O21  C20  N01  123.51  3.000
 NKV  N01  C20  C22  112.72  3.000
 NKV  O21  C20  C22  123.75  3.000
 NKV  H2   C22  C23  108.03  3.000
 NKV  H2   C22  C24  108.75  3.000
 NKV  C23  C22  C24  111.26  3.000
 NKV  H2   C22  C20  107.96  3.000
 NKV  C23  C22  C20  109.39  3.000
 NKV  C24  C22  C20  111.33  3.000
 NKV  H5   C24  H4   108.16  3.000
 NKV  H5   C24  H3   107.78  3.000
 NKV  H4   C24  H3   107.73  3.000
 NKV  H5   C24  C22  111.50  3.000
 NKV  H4   C24  C22  111.93  3.000
 NKV  H3   C24  C22  109.59  3.000
 NKV  N03  C02  N01  122.48  3.000
 NKV  N01  C02  C07  118.66  3.000
 NKV  N03  C02  C07  118.86  3.000
 NKV  H6   C04  N05  116.34  3.000
 NKV  H6   C04  N03  115.55  3.000
 NKV  N05  C04  N03  128.11  3.000
 NKV  N10  C06  N05  128.90  3.000
 NKV  N10  C06  C07  105.21  3.000
 NKV  N05  C06  C07  125.88  3.000
 NKV  N08  C07  C06  110.85  3.000
 NKV  N08  C07  C02  132.94  3.000
 NKV  C06  C07  C02  116.21  3.000
 NKV  H7   C09  N10  121.80  3.000
 NKV  H7   C09  N08  124.49  3.000
 NKV  N10  C09  N08  113.71  3.000
 NKV  H8   C11  O15  111.42  3.000
 NKV  H8   C11  N10  105.95  3.000
 NKV  O15  C11  N10  109.57  3.000
 NKV  H8   C11  C12  110.02  3.000
 NKV  N10  C11  C12  114.06  3.000
 NKV  O15  C11  C12  105.92  3.000
 NKV  H9   C12  O19  111.46  3.000
 NKV  H9   C12  C11  110.17  3.000
 NKV  O19  C12  C11  109.85  3.000
 NKV  H9   C12  C13  108.57  3.000
 NKV  O19  C12  C13  115.34  3.000
 NKV  C11  C12  C13  100.94  3.000
 NKV  H10  C14  O15  108.65  3.000
 NKV  H10  C14  C16  108.86  3.000
 NKV  O15  C14  C16  108.72  3.000
 NKV  H10  C14  C13  110.46  3.000
 NKV  C16  C14  C13  114.10  3.000
 NKV  O15  C14  C13  105.88  3.000
 NKV  H12  C16  H11  106.86  3.000
 NKV  H12  C16  O17  112.05  3.000
 NKV  H11  C16  O17  111.73  3.000
 NKV  H12  C16  C14  108.43  3.000
 NKV  H11  C16  C14  110.12  3.000
 NKV  O17  C16  C14  107.61  3.000
 NKV  H15  C23  H14  107.91  3.000
 NKV  H15  C23  H13  108.05  3.000
 NKV  H14  C23  H13  107.47  3.000
 NKV  H15  C23  C22  110.92  3.000
 NKV  H14  C23  C22  109.78  3.000
 NKV  H13  C23  C22  112.54  3.000
 NKV  H16  N01  C02  114.19  3.000
 NKV  H16  N01  C20  116.21  3.000
 NKV  C02  N01  C20  129.56  3.000
 NKV  C04  N03  C02  118.71  3.000
 NKV  C06  N05  C04  112.22  3.000
 NKV  C09  N08  C07  104.26  3.000
 NKV  C11  N10  C09  127.69  3.000
 NKV  C09  N10  C06  105.96  3.000
 NKV  C11  N10  C06  126.18  3.000
 NKV  C14  O15  C11  110.70  3.000
 NKV  H17  O17  C16  108.36  3.000
 NKV  H18  O18  C13  107.93  3.000
 NKV  H19  O19  C12  108.88  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
 NKV  CONST_01  N05  C04  N03  C02     0.00   0.0  0
 NKV  CONST_02  N05  C06  C07  C02     0.00   0.0  0
 NKV  CONST_03  N10  C06  C07  C02   180.00   0.0  0
 NKV  CONST_04  C09  N08  C07  C02   180.00   0.0  0
 NKV  CONST_05  C07  C02  N03  C04     0.00   0.0  0
 NKV  CONST_06  C07  C06  N05  C04     0.00   0.0  0
 NKV  CONST_07  N10  C06  N05  C04   180.00   0.0  0
 NKV  CONST_08  N03  C04  N05  C06     0.00   0.0  0
 NKV  CONST_09  N03  C02  C07  C06     0.00   0.0  0
 NKV  CONST_10  C09  N08  C07  C06     0.00   0.0  0
 NKV  CONST_11  N08  C09  N10  C06     0.00   0.0  0
 NKV  CONST_12  C09  N10  C06  C07     0.00   0.0  0
 NKV  CONST_13  N10  C09  N08  C07     0.00   0.0  0
 NKV  CONST_14  N05  C06  N10  C09   180.00   0.0  0
 NKV  CONST_15  N08  C07  C02  N03   180.00   0.0  0
 NKV  CONST_16  N08  C07  C06  N05   180.00   0.0  0
 NKV  CONST_17  N10  C06  C07  N08     0.00   0.0  0
 NKV  CONST_18  C11  N10  C06  C07   180.00   0.0  0
 NKV  CONST_19  N05  C06  N10  C11     0.00   0.0  0
 NKV  CONST_20  N08  C09  N10  C11   180.00   0.0  0
 NKV  CONST_21  N01  C02  N03  C04   180.00   0.0  0
 NKV  CONST_22  N01  C02  C07  C06   180.00   0.0  0
 NKV  CONST_23  N08  C07  C02  N01     0.00   0.0  0
 NKV  CONST_24  H6   C04  N03  C02   180.00   0.0  0
 NKV  CONST_25  H7   C09  N10  C06   180.00   0.0  0
 NKV  CONST_26  N03  C02  N01  C20     0.00   0.0  0
 NKV  CONST_27  C07  C02  N01  C20   180.00   0.0  0
 NKV  CONST_28  H16  N01  C02  C07     0.00   0.0  0
 NKV  CONST_29  C02  N01  C20  C22   180.00   0.0  0
 NKV  CONST_30  O21  C20  N01  C02     0.00   0.0  0
 NKV  Var_01    O21  C20  C22  C24   -21.23  30.0  3
 NKV  Var_02    H3   C24  C22  C20  -176.29  30.0  3
 NKV  Var_03    H13  C23  C22  C20    59.00  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
 NKV  chir_01  C13  C14  O18  C12  negativ
 NKV  chir_02  C11  O15  N10  C12  negativ
 NKV  chir_03  C12  O19  C11  C13  negativ
 NKV  chir_04  C14  O15  C13  C16  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
 NKV  plan-1  C02  0.020
 NKV  plan-1  C04  0.020
 NKV  plan-1  C06  0.020
 NKV  plan-1  C07  0.020
 NKV  plan-1  C09  0.020
 NKV  plan-1  C11  0.020
 NKV  plan-1  N01  0.020
 NKV  plan-1  N03  0.020
 NKV  plan-1  N05  0.020
 NKV  plan-1  N08  0.020
 NKV  plan-1  N10  0.020
 NKV  plan-1  H6   0.020
 NKV  plan-1  H7   0.020
 NKV  plan-2  C20  0.020
 NKV  plan-2  C22  0.020
 NKV  plan-2  C02  0.020
 NKV  plan-2  N01  0.020
 NKV  plan-2  O21  0.020
 NKV  plan-2  H16  0.020

