# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 11:46:51 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 5'-O-[(R)-(carboxyoxy)(hydroxy)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)OC(O)=O)[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
 KG4  KG4  5'-O-[(R)-(carboxyoxy)(hydroxy)phosphoryl]adenosine  ligand  38  26  .  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_KG4
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
 KG4  O1A  O  OP    -1  -0.808  -3.5259   0.9859   1.7853
 KG4  PA   P  P      0   1.334  -3.7770   0.0581   0.6363
 KG4  O2A  O  O      0  -0.801  -4.5309  -1.2190   0.8396
 KG4  O3A  O  O2     0  -0.647  -4.2894   0.8643  -0.7012
 KG4  CB   C  C      0   0.562  -5.5525   1.4700  -0.7088
 KG4  O2B  O  O      0  -0.620  -6.2385   1.3322   0.3094
 KG4  O1B  O  OC    -1  -0.614  -5.7963   2.0666  -1.7595
 KG4  O5'  O  O2     0  -0.624  -2.3228  -0.3022  -0.0745
 KG4  C5'  C  CH2    0  -0.148  -1.3565  -0.9180   0.7408
 KG4  C4'  C  CR15   0   0.004  -0.3809  -1.6750  -0.1267
 KG4  C3'  C  CR15   0  -0.045   0.7366  -2.3456   0.6671
 KG4  O3'  O  OH1    0  -0.656   0.3343  -3.6204   1.0836
 KG4  C2'  C  CR15   0  -0.041   1.8840  -2.3611  -0.3481
 KG4  O2'  O  OH1    0  -0.665   1.7102  -3.3839  -1.2896
 KG4  C1'  C  CR15   0   0.177   1.6535  -1.0340  -1.0663
 KG4  O4'  O  O      0  -0.495   0.2830  -0.7913  -1.0342
 KG4  N9   N  NR5    0  -0.539   2.3493   0.0644  -0.3969
 KG4  C4   C  CR56   0   0.487   3.7018   0.2380  -0.3612
 KG4  C5   C  CR56   0  -0.003   3.8992   1.4295   0.3189
 KG4  N7   N  N      0  -0.451   2.7021   1.9842   0.6843
 KG4  C8   C  CR15   0   0.102   1.8088   1.1495   0.2371
 KG4  N3   N  N      0  -0.459   4.6477  -0.5507  -0.8700
 KG4  C2   C  CR16   0   0.039   5.8569  -0.0652  -0.6499
 KG4  N1   N  N      0  -0.474   6.1970   1.0543  -0.0159
 KG4  C6   C  CR6    0   0.456   5.2357   1.8365   0.4875
 KG4  N6   N  NH2    0  -0.817   5.5717   2.9564   1.1295
 KG4  H3   H  HCH2   0   0.204  -0.8241  -0.1786   1.3529
 KG4  H4   H  HCH2   0   0.220  -1.8013  -1.6433   1.4342
 KG4  H5   H  HCR5   0   0.246  -0.9254  -2.4298  -0.7068
 KG4  H6   H  HCR5   0   0.246   1.0233  -1.7175   1.5213
 KG4  H7   H  HOH1   0   0.469   0.9032  -3.9052   1.8061
 KG4  H8   H  HCR5   0   0.262   2.8688  -2.4098   0.1303
 KG4  H9   H  HOH1   0   0.452   1.3703  -4.1581  -0.8237
 KG4  H10  H  HCR5   0   0.285   2.0098  -1.0671  -2.0994
 KG4  H11  H  HCR5   0   0.296   0.7437   1.2851   0.3298
 KG4  H12  H  HCR6   0   0.251   6.6846  -0.6523  -1.0336
 KG4  H13  H  HNH2   0   0.411   4.8683   3.5918   1.4628
 KG4  H14  H  HNH2   0   0.403   6.5337   3.2439   1.1778

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
 KG4  N6   C6   single    1.334  0.020  1.334
 KG4  N7   C8   aromatic  1.302  0.020  1.302
 KG4  N7   C5   aromatic  1.369  0.020  1.369
 KG4  C8   N9   aromatic  1.368  0.020  1.368
 KG4  C6   C5   aromatic  1.407  0.020  1.407
 KG4  C6   N1   aromatic  1.338  0.020  1.338
 KG4  C5   C4   aromatic  1.386  0.020  1.386
 KG4  O2A  PA   deloc     1.497  0.020  1.497
 KG4  N1   C2   aromatic  1.331  0.020  1.331
 KG4  N9   C4   aromatic  1.364  0.020  1.364
 KG4  N9   C1'  single    1.462  0.020  1.462
 KG4  C4   N3   aromatic  1.333  0.020  1.333
 KG4  O1A  PA   deloc     1.498  0.020  1.498
 KG4  C2'  O2'  single    1.401  0.020  1.401
 KG4  C2'  C1'  single    1.526  0.020  1.526
 KG4  C2'  C3'  single    1.532  0.020  1.532
 KG4  PA   O5'  single    1.658  0.020  1.658
 KG4  PA   O3A  single    1.644  0.020  1.644
 KG4  C2   N3   aromatic  1.321  0.020  1.321
 KG4  C1'  O4'  single    1.392  0.020  1.392
 KG4  C5'  O5'  single    1.406  0.020  1.406
 KG4  C5'  C4'  single    1.509  0.020  1.509
 KG4  O4'  C4'  single    1.430  0.020  1.430
 KG4  C3'  C4'  single    1.526  0.020  1.526
 KG4  C3'  O3'  single    1.400  0.020  1.400
 KG4  O3A  CB   deloc     1.401  0.020  1.401
 KG4  O2B  CB   deloc     1.235  0.020  1.235
 KG4  CB   O1B  deloc     1.233  0.020  1.233
 KG4  C5'  H3   single    0.970  0.020  1.090
 KG4  C5'  H4   single    0.970  0.020  1.090
 KG4  C4'  H5   single    0.970  0.020  1.090
 KG4  C3'  H6   single    0.970  0.020  1.090
 KG4  O3'  H7   single    0.850  0.020  0.980
 KG4  C2'  H8   single    0.970  0.020  1.090
 KG4  O2'  H9   single    0.850  0.020  0.980
 KG4  C1'  H10  single    0.970  0.020  1.090
 KG4  C8   H11  single    0.930  0.020  1.080
 KG4  C2   H12  single    0.930  0.020  1.080
 KG4  N6   H13  single    0.860  0.020  1.020
 KG4  N6   H14  single    0.860  0.020  1.020

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
 KG4  O5'  PA   O3A   91.79  3.000
 KG4  O3A  PA   O2A  111.84  3.000
 KG4  O5'  PA   O2A  108.33  3.000
 KG4  O3A  PA   O1A  111.88  3.000
 KG4  O5'  PA   O1A  108.44  3.000
 KG4  O2A  PA   O1A  120.57  3.000
 KG4  CB   O3A  PA   119.84  3.000
 KG4  O1B  CB   O2B  130.29  3.000
 KG4  O1B  CB   O3A  113.10  3.000
 KG4  O2B  CB   O3A  116.61  3.000
 KG4  C5'  O5'  PA   116.70  3.000
 KG4  H4   C5'  H3   106.82  3.000
 KG4  H4   C5'  C4'  107.08  3.000
 KG4  H3   C5'  C4'  110.18  3.000
 KG4  H4   C5'  O5'  112.15  3.000
 KG4  H3   C5'  O5'  111.20  3.000
 KG4  C4'  C5'  O5'  109.31  3.000
 KG4  H5   C4'  O4'  108.67  3.000
 KG4  H5   C4'  C3'  109.65  3.000
 KG4  O4'  C4'  C3'  105.17  3.000
 KG4  H5   C4'  C5'  109.17  3.000
 KG4  C3'  C4'  C5'  113.26  3.000
 KG4  O4'  C4'  C5'  110.79  3.000
 KG4  H6   C3'  C2'  109.01  3.000
 KG4  H6   C3'  O3'  111.36  3.000
 KG4  C2'  C3'  O3'  113.77  3.000
 KG4  H6   C3'  C4'  110.15  3.000
 KG4  O3'  C3'  C4'  110.15  3.000
 KG4  C2'  C3'  C4'  102.02  3.000
 KG4  H7   O3'  C3'  108.84  3.000
 KG4  H8   C2'  C1'  112.31  3.000
 KG4  H8   C2'  O2'  111.86  3.000
 KG4  C1'  C2'  O2'  107.45  3.000
 KG4  H8   C2'  C3'  112.59  3.000
 KG4  C1'  C2'  C3'  100.95  3.000
 KG4  O2'  C2'  C3'  111.09  3.000
 KG4  H9   O2'  C2'  107.75  3.000
 KG4  H10  C1'  N9   107.47  3.000
 KG4  H10  C1'  O4'  110.36  3.000
 KG4  N9   C1'  O4'  109.08  3.000
 KG4  H10  C1'  C2'  111.66  3.000
 KG4  O4'  C1'  C2'  106.82  3.000
 KG4  N9   C1'  C2'  111.46  3.000
 KG4  C1'  O4'  C4'  111.34  3.000
 KG4  C8   N9   C4   106.18  3.000
 KG4  C4   N9   C1'  125.40  3.000
 KG4  C8   N9   C1'  128.31  3.000
 KG4  N3   C4   C5   126.52  3.000
 KG4  N3   C4   N9   128.21  3.000
 KG4  C5   C4   N9   105.27  3.000
 KG4  C6   C5   N7   132.95  3.000
 KG4  C6   C5   C4   116.27  3.000
 KG4  N7   C5   C4   110.78  3.000
 KG4  C8   N7   C5   104.39  3.000
 KG4  H11  C8   N7   124.60  3.000
 KG4  H11  C8   N9   122.02  3.000
 KG4  N7   C8   N9   113.37  3.000
 KG4  C2   N3   C4   111.62  3.000
 KG4  H12  C2   N1   115.39  3.000
 KG4  H12  C2   N3   116.13  3.000
 KG4  N1   C2   N3   128.48  3.000
 KG4  C6   N1   C2   119.18  3.000
 KG4  N6   C6   N1   119.41  3.000
 KG4  N1   C6   C5   117.93  3.000
 KG4  N6   C6   C5   122.66  3.000
 KG4  H14  N6   H13  118.24  3.000
 KG4  H14  N6   C6   120.28  3.000
 KG4  H13  N6   C6   120.95  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
 KG4  CONST_01  C5   N7   C8   N9      0.00   0.0  0
 KG4  CONST_02  N7   C5   C4   N9      0.00   0.0  0
 KG4  CONST_03  C6   C5   C4   N9    180.00   0.0  0
 KG4  CONST_04  C2   N3   C4   N9    180.00   0.0  0
 KG4  CONST_05  C8   N7   C5   C4      0.00   0.0  0
 KG4  CONST_06  N1   C6   C5   C4      0.00   0.0  0
 KG4  CONST_07  N7   C8   N9   C4      0.00   0.0  0
 KG4  CONST_08  N1   C2   N3   C4      0.00   0.0  0
 KG4  CONST_09  C2   N1   C6   C5      0.00   0.0  0
 KG4  CONST_10  C8   N9   C4   C5      0.00   0.0  0
 KG4  CONST_11  C2   N3   C4   C5      0.00   0.0  0
 KG4  CONST_12  N1   C6   C5   N7    180.00   0.0  0
 KG4  CONST_13  N3   C4   C5   N7    180.00   0.0  0
 KG4  CONST_14  C6   C5   N7   C8    180.00   0.0  0
 KG4  CONST_15  N3   C4   N9   C8    180.00   0.0  0
 KG4  CONST_16  C6   C5   C4   N3      0.00   0.0  0
 KG4  CONST_17  C6   N1   C2   N3      0.00   0.0  0
 KG4  CONST_18  N7   C8   N9   C1'   180.00   0.0  0
 KG4  CONST_19  C5   C4   N9   C1'   180.00   0.0  0
 KG4  CONST_20  N3   C4   N9   C1'     0.00   0.0  0
 KG4  CONST_21  N6   C6   C5   C4    180.00   0.0  0
 KG4  CONST_22  N6   C6   C5   N7      0.00   0.0  0
 KG4  CONST_23  N6   C6   N1   C2    180.00   0.0  0
 KG4  CONST_24  H11  C8   N9   C1'     0.00   0.0  0
 KG4  CONST_25  H12  C2   N3   C4    180.00   0.0  0
 KG4  CONST_26  H13  N6   C6   C5      0.00   0.0  0
 KG4  CONST_27  H14  N6   C6   C5    180.00   0.0  0
 KG4  CONST_28  O2B  CB   O3A  PA      0.00   0.0  0
 KG4  CONST_29  O1B  CB   O3A  PA    180.00   0.0  0
 KG4  Var_01    C4'  C5'  O5'  PA    156.60  30.0  2
 KG4  Var_02    O5'  PA   O3A  CB   -178.98  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
 KG4  chir_02  C4'  C5'  O4'  C3'  negativ
 KG4  chir_03  C3'  O3'  C4'  C2'  positiv
 KG4  chir_04  C2'  O2'  C3'  C1'  positiv
 KG4  chir_05  C1'  O4'  N9   C2'  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
 KG4  plan-1  C1'  0.020
 KG4  plan-1  N9   0.020
 KG4  plan-1  C4   0.020
 KG4  plan-1  C5   0.020
 KG4  plan-1  N7   0.020
 KG4  plan-1  C8   0.020
 KG4  plan-1  N3   0.020
 KG4  plan-1  C2   0.020
 KG4  plan-1  N1   0.020
 KG4  plan-1  C6   0.020
 KG4  plan-1  N6   0.020
 KG4  plan-1  H11  0.020
 KG4  plan-1  H12  0.020
 KG4  plan-2  C6   0.020
 KG4  plan-2  N6   0.020
 KG4  plan-2  H13  0.020
 KG4  plan-2  H14  0.020
 KG4  plan-3  PA   0.020
 KG4  plan-3  O3A  0.020
 KG4  plan-3  CB   0.020
 KG4  plan-3  O2B  0.020
 KG4  plan-3  O1B  0.020

