# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 07:24:54 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 5'-O-prop-2-yn-1-yladenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](COCC#C)[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
 AOC  AOC  5'-O-prop-2-yn-1-yladenosine  ligand  37  22  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AOC
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
 AOC  CAA   C  CSP1  0  -0.509  -4.9897  -3.4667   1.0945
 AOC  CAE   C  CSP   0   0.234  -4.6943  -2.5376   0.3933
 AOC  CAH   C  CH2   0  -0.274  -4.3483  -1.4131  -0.4666
 AOC  O5'   O  O2    0  -0.482  -3.5424  -0.5148   0.2543
 AOC  C5'   C  CH2   0  -0.142  -3.1597   0.5906  -0.5223
 AOC  C4'   C  CH1   0  -0.048  -2.2818   1.4878   0.3258
 AOC  O4'   O  O2    0  -0.487  -1.1379   0.7680   0.7942
 AOC  C3'   C  CH1   0  -0.030  -1.7377   2.6763  -0.4569
 AOC  O3'   O  OH1   0  -0.667  -1.5047   3.7328   0.4369
 AOC  C2'   C  CH1   0  -0.052  -0.4198   2.1032  -0.9859
 AOC  O2'   O  OH1   0  -0.652   0.5578   3.0480  -1.2983
 AOC  C1'   C  CH1   0   0.211   0.0335   1.2623   0.2062
 AOC  N9    N  NR5   0  -0.541   0.8961   0.1639  -0.1425
 AOC  C8    C  CR15  0   0.116   0.6150  -0.8814  -0.9823
 AOC  N7    N  N     0  -0.447   1.5728  -1.7552  -1.0573
 AOC  C5    C  CR56  0  -0.011   2.5440  -1.2704  -0.2191
 AOC  C4    C  CR56  0   0.493   2.1410  -0.0808   0.3653
 AOC  N3    N  N     0  -0.458   2.8350   0.6501   1.2334
 AOC  C2    C  CR16  0   0.046   4.0097   0.1057   1.5006
 AOC  N1    N  N     0  -0.474   4.5283  -1.0198   1.0177
 AOC  C6    C  CR6   0   0.461   3.8180  -1.7439   0.1452
 AOC  N6    N  NH2   0  -0.816   4.3332  -2.8760  -0.3355
 AOC  HAA   H  H     0   0.282  -5.2463  -4.2903   1.7207
 AOC  HAH1  H  HCH2  0   0.248  -3.8280  -1.7849  -1.3601
 AOC  HAH2  H  HCH2  0   0.250  -5.2690  -0.9299  -0.8198
 AOC  H5'   H  HCH2  0   0.205  -2.6294   0.2653  -1.4303
 AOC  H5''  H  HCH2  0   0.229  -4.0356   1.1640  -0.8555
 AOC  H4'   H  HCH1  0   0.267  -2.8552   1.8273   1.1938
 AOC  H3'   H  HCH1  0   0.256  -2.4095   2.9744  -1.2731
 AOC  HO3'  H  HOH1  0   0.451  -0.8794   4.3399   0.0242
 AOC  H2'   H  HCH1  0   0.249  -0.6373   1.4526  -1.8428
 AOC  HO2'  H  HOH1  0   0.471   0.3970   3.3801  -2.1878
 AOC  H1'   H  HCH1  0   0.263   0.6026   1.8832   0.9066
 AOC  H8    H  HCR5  0   0.290  -0.3224  -0.9497  -1.5140
 AOC  H2    H  HCR6  0   0.253   4.6349   0.6422   2.2058
 AOC  H61   H  HNH2  0   0.412   3.8420  -3.4219  -1.0216
 AOC  H62   H  HNH2  0   0.404   5.2635  -3.1572  -0.0787

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
 AOC  N6   C6    single    1.334  0.020  1.334
 AOC  N7   C5    aromatic  1.371  0.020  1.371
 AOC  N7   C8    aromatic  1.299  0.020  1.299
 AOC  C6   C5    aromatic  1.407  0.020  1.407
 AOC  C6   N1    aromatic  1.338  0.020  1.338
 AOC  C5   C4    aromatic  1.385  0.020  1.385
 AOC  C8   N9    aromatic  1.370  0.020  1.370
 AOC  N1   C2    aromatic  1.330  0.020  1.330
 AOC  O2'  C2'   single    1.395  0.020  1.395
 AOC  C2'  C3'   single    1.531  0.020  1.531
 AOC  C2'  C1'   single    1.528  0.020  1.528
 AOC  C4   N9    aromatic  1.367  0.020  1.367
 AOC  C4   N3    aromatic  1.330  0.020  1.330
 AOC  N9   C1'   single    1.439  0.020  1.439
 AOC  C2   N3    aromatic  1.322  0.020  1.322
 AOC  O3'  C3'   single    1.403  0.020  1.403
 AOC  C3'  C4'   single    1.524  0.020  1.524
 AOC  C1'  O4'   single    1.401  0.020  1.401
 AOC  O4'  C4'   single    1.430  0.020  1.430
 AOC  C4'  C5'   single    1.515  0.020  1.515
 AOC  C5'  O5'   single    1.404  0.020  1.404
 AOC  O5'  CAH   single    1.406  0.020  1.406
 AOC  CAH  CAE   single    1.457  0.020  1.457
 AOC  CAE  CAA   triple    1.201  0.020  1.201
 AOC  CAA  HAA   single    0.913  0.020  1.066
 AOC  CAH  HAH1  single    0.939  0.020  1.096
 AOC  CAH  HAH2  single    0.939  0.020  1.096
 AOC  C5'  H5'   single    0.939  0.020  1.096
 AOC  C5'  H5''  single    0.939  0.020  1.096
 AOC  C4'  H4'   single    0.939  0.020  1.096
 AOC  C3'  H3'   single    0.939  0.020  1.096
 AOC  O3'  HO3'  single    0.832  0.020  0.971
 AOC  C2'  H2'   single    0.939  0.020  1.096
 AOC  O2'  HO2'  single    0.832  0.020  0.971
 AOC  C1'  H1'   single    0.939  0.020  1.096
 AOC  C8   H8    single    0.929  0.020  1.085
 AOC  C2   H2    single    0.929  0.020  1.085
 AOC  N6   H61   single    0.868  0.020  1.013
 AOC  N6   H62   single    0.868  0.020  1.013

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
 AOC  HAA   CAA  CAE   180.00  3.000
 AOC  CAH   CAE  CAA   180.00  3.000
 AOC  HAH2  CAH  HAH1  106.52  3.000
 AOC  HAH2  CAH  O5'   111.38  3.000
 AOC  HAH1  CAH  O5'   111.21  3.000
 AOC  HAH2  CAH  CAE   109.28  3.000
 AOC  HAH1  CAH  CAE   109.34  3.000
 AOC  O5'   CAH  CAE   109.06  3.000
 AOC  C5'   O5'  CAH   112.06  3.000
 AOC  H5''  C5'  H5'   106.75  3.000
 AOC  H5''  C5'  C4'   108.83  3.000
 AOC  H5'   C5'  C4'   110.96  3.000
 AOC  H5''  C5'  O5'   111.18  3.000
 AOC  H5'   C5'  O5'   110.79  3.000
 AOC  C4'   C5'  O5'   108.33  3.000
 AOC  H4'   C4'  C3'   110.65  3.000
 AOC  H4'   C4'  O4'   108.38  3.000
 AOC  C3'   C4'  O4'   105.97  3.000
 AOC  H4'   C4'  C5'   108.91  3.000
 AOC  O4'   C4'  C5'   110.41  3.000
 AOC  C3'   C4'  C5'   112.42  3.000
 AOC  C1'   O4'  C4'   110.72  3.000
 AOC  H3'   C3'  C2'   111.79  3.000
 AOC  H3'   C3'  O3'   111.75  3.000
 AOC  C2'   C3'  O3'   111.04  3.000
 AOC  H3'   C3'  C4'   112.02  3.000
 AOC  O3'   C3'  C4'   108.62  3.000
 AOC  C2'   C3'  C4'   101.12  3.000
 AOC  HO3'  O3'  C3'   108.01  3.000
 AOC  H2'   C2'  C1'   109.98  3.000
 AOC  H2'   C2'  O2'   111.43  3.000
 AOC  C1'   C2'  O2'   109.85  3.000
 AOC  H2'   C2'  C3'   108.73  3.000
 AOC  C1'   C2'  C3'   101.06  3.000
 AOC  O2'   C2'  C3'   115.28  3.000
 AOC  HO2'  O2'  C2'   108.87  3.000
 AOC  H1'   C1'  N9    106.03  3.000
 AOC  H1'   C1'  C2'   109.95  3.000
 AOC  N9    C1'  C2'   114.13  3.000
 AOC  H1'   C1'  O4'   111.47  3.000
 AOC  N9    C1'  O4'   109.48  3.000
 AOC  C2'   C1'  O4'   105.88  3.000
 AOC  C4    N9   C8    106.14  3.000
 AOC  C4    N9   C1'   126.34  3.000
 AOC  C8    N9   C1'   127.42  3.000
 AOC  H8    C8   N7    124.70  3.000
 AOC  H8    C8   N9    121.88  3.000
 AOC  N7    C8   N9    113.42  3.000
 AOC  C5    N7   C8    104.43  3.000
 AOC  C6    C5   C4    116.30  3.000
 AOC  C4    C5   N7    110.81  3.000
 AOC  C6    C5   N7    132.88  3.000
 AOC  N3    C4   C5    126.54  3.000
 AOC  N3    C4   N9    128.27  3.000
 AOC  C5    C4   N9    105.19  3.000
 AOC  C2    N3   C4    111.66  3.000
 AOC  H2    C2   N1    115.47  3.000
 AOC  H2    C2   N3    116.10  3.000
 AOC  N1    C2   N3    128.43  3.000
 AOC  C6    N1   C2    119.20  3.000
 AOC  N6    C6   N1    119.31  3.000
 AOC  N1    C6   C5    117.86  3.000
 AOC  N6    C6   C5    122.83  3.000
 AOC  H62   N6   H61   118.35  3.000
 AOC  H62   N6   C6    120.19  3.000
 AOC  H61   N6   C6    121.23  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
 AOC  CONST_01  C5   N7   C8   N9      0.00   0.0  0
 AOC  CONST_02  N7   C5   C4   N9      0.00   0.0  0
 AOC  CONST_03  C6   C5   C4   N9    180.00   0.0  0
 AOC  CONST_04  C2   N3   C4   N9    180.00   0.0  0
 AOC  CONST_05  C6   C5   N7   C8    180.00   0.0  0
 AOC  CONST_06  C4   C5   N7   C8      0.00   0.0  0
 AOC  CONST_07  C5   C4   N9   C8      0.00   0.0  0
 AOC  CONST_08  N3   C4   N9   C8    180.00   0.0  0
 AOC  CONST_09  N1   C6   C5   N7    180.00   0.0  0
 AOC  CONST_10  N3   C4   C5   N7    180.00   0.0  0
 AOC  CONST_11  C4   N9   C8   N7      0.00   0.0  0
 AOC  CONST_12  C2   N1   C6   C5      0.00   0.0  0
 AOC  CONST_13  C2   N3   C4   C5      0.00   0.0  0
 AOC  CONST_14  N1   C6   C5   C4      0.00   0.0  0
 AOC  CONST_15  N1   C2   N3   C4      0.00   0.0  0
 AOC  CONST_16  C6   C5   C4   N3      0.00   0.0  0
 AOC  CONST_17  C6   N1   C2   N3      0.00   0.0  0
 AOC  CONST_18  N7   C8   N9   C1'   180.00   0.0  0
 AOC  CONST_19  C5   C4   N9   C1'   180.00   0.0  0
 AOC  CONST_20  N3   C4   N9   C1'     0.00   0.0  0
 AOC  CONST_21  N6   C6   C5   N7      0.00   0.0  0
 AOC  CONST_22  N6   C6   C5   C4    180.00   0.0  0
 AOC  CONST_23  N6   C6   N1   C2    180.00   0.0  0
 AOC  CONST_24  H8   C8   N9   C1'     0.00   0.0  0
 AOC  CONST_25  H2   C2   N3   C4    180.00   0.0  0
 AOC  CONST_26  H61  N6   C6   C5      0.00   0.0  0
 AOC  CONST_27  H62  N6   C6   C5    180.00   0.0  0
 AOC  Var_01    C4'  C5'  O5'  CAH  -179.15  30.0  2
 AOC  Var_02    O5'  CAH  CAE  CAA   157.23  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
 AOC  chir_01  C4'  C3'  O4'  C5'  positiv
 AOC  chir_02  C3'  O3'  C2'  C4'  negativ
 AOC  chir_03  C2'  O2'  C1'  C3'  negativ
 AOC  chir_04  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
 AOC  plan-1  C1'  0.020
 AOC  plan-1  N9   0.020
 AOC  plan-1  C8   0.020
 AOC  plan-1  N7   0.020
 AOC  plan-1  C5   0.020
 AOC  plan-1  C4   0.020
 AOC  plan-1  N3   0.020
 AOC  plan-1  C2   0.020
 AOC  plan-1  N1   0.020
 AOC  plan-1  C6   0.020
 AOC  plan-1  N6   0.020
 AOC  plan-1  H8   0.020
 AOC  plan-1  H2   0.020
 AOC  plan-2  C6   0.020
 AOC  plan-2  N6   0.020
 AOC  plan-2  H61  0.020
 AOC  plan-2  H62  0.020

