# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:28:02 2022
#   Inital geometry file: a 79 line input string
#   Ligand name: 8-aminoadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc2c(N)ncnc2n1[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
 3BH  3BH  '8-aminoadenosine         '  ligand  34  20  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3BH
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
 3BH  O15   O  OH1   0  -0.653  -0.9942   2.1350  -1.4758
 3BH  C8    C  CR15  0  -0.008  -1.6254   1.0169  -0.9405
 3BH  C14   C  CR15  0  -0.050  -3.0488   1.2190  -0.4153
 3BH  O19   O  OH1   0  -0.667  -3.0984   2.4636   0.2294
 3BH  C13   C  CR15  0  -0.030  -3.1619   0.0410   0.5559
 3BH  C18   C  CH2   0  -0.192  -3.7459  -1.1847  -0.1250
 3BH  O20   O  OH1   0  -0.667  -3.5083  -2.3096   0.6875
 3BH  O7    O  O     0  -0.501  -1.8341  -0.2104   1.0310
 3BH  C3    C  CR15  0   0.210  -0.9111   0.5818   0.3367
 3BH  N1    N  NR5   0  -0.590   0.3093  -0.1528   0.1251
 3BH  C2    C  CR56  0   0.489   1.5679   0.3614   0.3210
 3BH  N6    N  N     0  -0.457   1.9000   1.5344   0.8437
 3BH  C12   C  CR16  0   0.033   3.2130   1.7009   0.8920
 3BH  N16   N  N     0  -0.470   4.1591   0.8608   0.4901
 3BH  C11   C  CR6   0   0.424   3.8020  -0.3177  -0.0364
 3BH  N17   N  NH2   0  -0.822   4.7586  -1.1547  -0.4733
 3BH  C5    C  CR56  0   0.021   2.4367  -0.6132  -0.1360
 3BH  N9    N  N     0  -0.508   1.7504  -1.7143  -0.5861
 3BH  C4    C  CR5   0   0.611   0.4915  -1.4089  -0.4195
 3BH  N10   N  NH2   0  -0.861  -0.5556  -2.1956  -0.7837
 3BH  HO15  H  HOH1  0   0.463  -1.3269   2.2806  -2.3668
 3BH  H8    H  HCR5  0   0.244  -1.6363   0.1777  -1.6482
 3BH  H14   H  HCR5  0   0.253  -3.7980   1.1470  -1.2148
 3BH  HO19  H  HOH1  0   0.457  -3.9578   2.5512   0.6538
 3BH  H13   H  HCR5  0   0.259  -3.7822   0.2991   1.4205
 3BH  H18   H  HCH2  0   0.238  -4.8177  -1.0005  -0.2698
 3BH  H18A  H  HCH2  0   0.207  -3.3106  -1.3184  -1.1246
 3BH  HO20  H  HOH1  0   0.464  -3.9251  -3.0718   0.2743
 3BH  H3    H  HCR5  0   0.259  -0.6215   1.4656   0.9170
 3BH  H12   H  HCR6  0   0.247   3.5619   2.6381   1.3119
 3BH  HN17  H  HNH2  0   0.396   5.7153  -0.9723  -0.2223
 3BH  HN1A  H  HNH2  0   0.402   4.5208  -2.1060  -0.6950
 3BH  HN10  H  HNH2  0   0.405  -1.3358  -2.2447  -0.1424
 3BH  HN1B  H  HNH2  0   0.394  -0.2647  -3.1108  -1.0927

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
 3BH  O15  C8    single    1.391  0.020  1.391
 3BH  C8   C14   single    1.531  0.020  1.531
 3BH  C8   C3    single    1.527  0.020  1.527
 3BH  C14  O19   single    1.403  0.020  1.403
 3BH  C14  C13   single    1.531  0.020  1.531
 3BH  C13  C18   single    1.519  0.020  1.519
 3BH  C13  O7    single    1.433  0.020  1.433
 3BH  C18  O20   single    1.408  0.020  1.408
 3BH  O7   C3    single    1.401  0.020  1.401
 3BH  C3   N1    single    1.440  0.020  1.440
 3BH  N1   C2    aromatic  1.374  0.020  1.374
 3BH  N1   C4    aromatic  1.381  0.020  1.381
 3BH  C2   N6    aromatic  1.326  0.020  1.326
 3BH  C2   C5    aromatic  1.383  0.020  1.383
 3BH  N6   C12   aromatic  1.324  0.020  1.324
 3BH  C12  N16   aromatic  1.328  0.020  1.328
 3BH  N16  C11   aromatic  1.339  0.020  1.339
 3BH  C11  N17   single    1.344  0.020  1.344
 3BH  C11  C5    aromatic  1.400  0.020  1.400
 3BH  C5   N9    aromatic  1.373  0.020  1.373
 3BH  N9   C4    aromatic  1.306  0.020  1.306
 3BH  C4   N10   single    1.359  0.020  1.359
 3BH  O15  HO15  single    0.850  0.020  0.980
 3BH  C8   H8    single    0.970  0.020  1.090
 3BH  C14  H14   single    0.970  0.020  1.090
 3BH  O19  HO19  single    0.850  0.020  0.980
 3BH  C13  H13   single    0.970  0.020  1.090
 3BH  C18  H18   single    0.970  0.020  1.090
 3BH  C18  H18A  single    0.970  0.020  1.090
 3BH  O20  HO20  single    0.850  0.020  0.980
 3BH  C3   H3    single    0.970  0.020  1.090
 3BH  C12  H12   single    0.930  0.020  1.080
 3BH  N17  HN17  single    0.890  0.020  1.040
 3BH  N17  HN1A  single    0.890  0.020  1.040
 3BH  N10  HN10  single    0.890  0.020  1.040
 3BH  N10  HN1B  single    0.890  0.020  1.040

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
 3BH  HO15  O15  C8    108.73  3.000
 3BH  H8    C8   C3    109.03  3.000
 3BH  H8    C8   C14   108.24  3.000
 3BH  C3    C8   C14   100.70  3.000
 3BH  H8    C8   O15   111.77  3.000
 3BH  C3    C8   O15   109.80  3.000
 3BH  C14   C8   O15   116.61  3.000
 3BH  H14   C14  C13   111.16  3.000
 3BH  H14   C14  O19   111.63  3.000
 3BH  C13   C14  O19   112.87  3.000
 3BH  H14   C14  C8    112.09  3.000
 3BH  C13   C14  C8    100.65  3.000
 3BH  O19   C14  C8    107.93  3.000
 3BH  HO19  O19  C14   108.36  3.000
 3BH  H13   C13  O7    107.73  3.000
 3BH  H13   C13  C18   109.04  3.000
 3BH  O7    C13  C18   111.31  3.000
 3BH  H13   C13  C14   111.19  3.000
 3BH  O7    C13  C14   106.08  3.000
 3BH  C18   C13  C14   111.41  3.000
 3BH  H18A  C18  H18   106.71  3.000
 3BH  H18A  C18  O20   111.16  3.000
 3BH  H18   C18  O20   112.04  3.000
 3BH  H18A  C18  C13   110.72  3.000
 3BH  H18   C18  C13   107.42  3.000
 3BH  O20   C18  C13   108.74  3.000
 3BH  HO20  O20  C18   108.19  3.000
 3BH  C3    O7   C13   110.31  3.000
 3BH  H3    C3   N1    105.38  3.000
 3BH  H3    C3   O7    111.58  3.000
 3BH  N1    C3   O7    110.05  3.000
 3BH  H3    C3   C8    109.67  3.000
 3BH  N1    C3   C8    114.77  3.000
 3BH  O7    C3   C8    105.52  3.000
 3BH  C4    N1   C2    106.01  3.000
 3BH  C4    N1   C3    129.32  3.000
 3BH  C2    N1   C3    124.37  3.000
 3BH  C5    C2   N6    126.58  3.000
 3BH  C5    C2   N1    105.35  3.000
 3BH  N6    C2   N1    128.07  3.000
 3BH  C12   N6   C2    111.95  3.000
 3BH  H12   C12  N16   115.77  3.000
 3BH  H12   C12  N6    116.21  3.000
 3BH  N16   C12  N6    128.02  3.000
 3BH  C11   N16  C12   119.06  3.000
 3BH  C5    C11  N17   122.64  3.000
 3BH  C5    C11  N16   118.27  3.000
 3BH  N17   C11  N16   119.07  3.000
 3BH  HN1A  N17  HN17  116.85  3.000
 3BH  HN1A  N17  C11   119.51  3.000
 3BH  HN17  N17  C11   118.88  3.000
 3BH  N9    C5   C11   132.82  3.000
 3BH  N9    C5   C2    111.05  3.000
 3BH  C11   C5   C2    116.12  3.000
 3BH  C4    N9   C5    104.62  3.000
 3BH  N10   C4   N9    124.96  3.000
 3BH  N10   C4   N1    122.03  3.000
 3BH  N9    C4   N1    112.96  3.000
 3BH  HN1B  N10  HN10  111.89  3.000
 3BH  HN1B  N10  C4    112.64  3.000
 3BH  HN10  N10  C4    116.90  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
 3BH  CONST_01  C12   N6   C2   N1   180.00  0.0  0
 3BH  CONST_02  C11   C5   C2   N1   180.00  0.0  0
 3BH  CONST_03  N9    C5   C2   N1     0.00  0.0  0
 3BH  CONST_04  C5    N9   C4   N1     0.00  0.0  0
 3BH  CONST_05  N9    C4   N1   C2     0.00  0.0  0
 3BH  CONST_06  N16   C12  N6   C2     0.00  0.0  0
 3BH  CONST_07  N16   C11  C5   C2     0.00  0.0  0
 3BH  CONST_08  C4    N9   C5   C2     0.00  0.0  0
 3BH  CONST_09  C4    N1   C2   N6   180.00  0.0  0
 3BH  CONST_10  C11   C5   C2   N6     0.00  0.0  0
 3BH  CONST_11  N9    C5   C2   N6   180.00  0.0  0
 3BH  CONST_12  C11   N16  C12  N6     0.00  0.0  0
 3BH  CONST_13  C5    C2   N6   C12    0.00  0.0  0
 3BH  CONST_14  C5    C11  N16  C12    0.00  0.0  0
 3BH  CONST_15  N9    C5   C11  N16  180.00  0.0  0
 3BH  CONST_16  C4    N9   C5   C11  180.00  0.0  0
 3BH  CONST_17  C4    N1   C2   C5     0.00  0.0  0
 3BH  CONST_18  N6    C2   N1   C3     0.00  0.0  0
 3BH  CONST_19  C5    C2   N1   C3   180.00  0.0  0
 3BH  CONST_20  N9    C4   N1   C3   180.00  0.0  0
 3BH  CONST_21  N10   C4   N1   C3     0.00  0.0  0
 3BH  CONST_22  N10   C4   N1   C2   180.00  0.0  0
 3BH  CONST_23  N17   C11  C5   C2   180.00  0.0  0
 3BH  CONST_24  N17   C11  N16  C12  180.00  0.0  0
 3BH  CONST_25  N9    C5   C11  N17    0.00  0.0  0
 3BH  CONST_26  N10   C4   N9   C5   180.00  0.0  0
 3BH  CONST_27  H12   C12  N6   C2   180.00  0.0  0
 3BH  CONST_29  HN1B  N10  C4   N1   180.00  0.0  0
 3BH  CONST_30  HN17  N17  C11  N16    0.00  0.0  0
 3BH  CONST_31  HN1A  N17  C11  N16  180.00  0.0  0

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
 3BH  chir_01  C8   O15  C14  C3   positiv
 3BH  chir_02  C14  O19  C8   C13  negativ
 3BH  chir_03  C13  O7   C14  C18  negativ
 3BH  chir_04  C3   O7   N1   C8   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
 3BH  plan-1  C3    0.020
 3BH  plan-1  N1    0.020
 3BH  plan-1  C2    0.020
 3BH  plan-1  N6    0.020
 3BH  plan-1  C12   0.020
 3BH  plan-1  N16   0.020
 3BH  plan-1  C11   0.020
 3BH  plan-1  N17   0.020
 3BH  plan-1  C5    0.020
 3BH  plan-1  N9    0.020
 3BH  plan-1  C4    0.020
 3BH  plan-1  N10   0.020
 3BH  plan-1  H12   0.020
 3BH  plan-2  C11   0.020
 3BH  plan-2  N17   0.020
 3BH  plan-2  HN17  0.020
 3BH  plan-2  HN1A  0.020
 3BH  plan-3  C4    0.020
 3BH  plan-3  N10   0.020
 3BH  plan-3  HN10  0.020
 3BH  plan-3  HN1B  0.020

