# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  9 14:17:45 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: N-(3-methylbut-2-en-1-yl)adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)=CCNc1ncnc2n(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
 ZIR  ZIR  N-(3-methylbut-2-en-1-yl)adenosine  ligand  45  24  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ZIR
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
 ZIR  N1    N  N     0  -0.492   2.2361  -1.7625  -1.1596
 ZIR  C2    C  CR16  0   0.041   1.1331  -2.4020  -1.5437
 ZIR  N3    N  N     0  -0.459  -0.1226  -2.0059  -1.4432
 ZIR  C4    C  CR56  0   0.482  -0.2116  -0.7978  -0.8866
 ZIR  C5    C  CR56  0  -0.003   0.8383  -0.0106  -0.4447
 ZIR  C6    C  CR6   0   0.510   2.1308  -0.5522  -0.6013
 ZIR  N7    N  N     0  -0.453   0.3750   1.1705   0.0695
 ZIR  C8    C  CR15  0   0.099  -0.9190   1.0945  -0.0571
 ZIR  N9    N  NR5   0  -0.532  -1.3382  -0.0735  -0.6298
 ZIR  C1'   C  CH1   0   0.170  -2.6971  -0.5263  -0.8990
 ZIR  N10   N  NH1   0  -0.652   3.2299   0.1035  -0.2190
 ZIR  C11   C  CH2   0  -0.320   4.5714  -0.4468  -0.2939
 ZIR  C12   C  C1    0  -0.312   5.5785   0.6574  -0.2461
 ZIR  C13   C  C     0   0.102   6.5066   0.8599   0.6923
 ZIR  C14   C  CH3   0  -0.705   7.4668   2.0076   0.5834
 ZIR  C15   C  CH3   0  -0.721   6.7066   0.0071   1.9094
 ZIR  C2'   C  CH1   0  -0.039  -3.2151  -1.4439   0.2082
 ZIR  O2'   O  OH1   0  -0.664  -4.1512  -2.3169  -0.3604
 ZIR  C3'   C  CH1   0  -0.042  -3.8997  -0.4313   1.1331
 ZIR  O3'   O  OH1   0  -0.656  -4.9134  -0.9814   1.9250
 ZIR  C4'   C  CH1   0   0.010  -4.4872   0.5543   0.1282
 ZIR  O4'   O  O2    0  -0.495  -3.5481   0.5791  -0.9472
 ZIR  C5'   C  CH2   0  -0.157  -4.6906   1.9381   0.6928
 ZIR  O5'   O  OH1   0  -0.667  -5.2744   2.7542  -0.2914
 ZIR  H2    H  HCR6  0   0.251   1.2927  -3.3765  -1.9930
 ZIR  H8    H  HCR5  0   0.297  -1.6089   1.8694   0.2366
 ZIR  H1'   H  HCH1  0   0.282  -2.6722  -1.0424  -1.8627
 ZIR  HN10  H  HNH1  0   0.402   3.1036   0.9597   0.2971
 ZIR  H11   H  HCH2  0   0.245   4.7307  -1.1813   0.4988
 ZIR  H11A  H  HCH2  0   0.255   4.6635  -0.9873  -1.2376
 ZIR  H12   H  H     0   0.240   5.5321   1.3526  -1.0801
 ZIR  H14   H  HCH3  0   0.236   7.3845   2.6640   1.4528
 ZIR  H14A  H  HCH3  0   0.237   8.4983   1.6473   0.5641
 ZIR  H14B  H  HCH3  0   0.240   7.3006   2.6058  -0.3119
 ZIR  H15   H  HCH3  0   0.243   5.9737  -0.7893   2.0189
 ZIR  H15A  H  HCH3  0   0.242   7.6981  -0.4523   1.8921
 ZIR  H15B  H  HCH3  0   0.240   6.6688   0.6232   2.8109
 ZIR  H2'   H  HCH1  0   0.260  -2.4000  -1.9847   0.7045
 ZIR  HO2'  H  HOH1  0   0.452  -4.7972  -2.5388   0.3219
 ZIR  H3'   H  HCH1  0   0.243  -3.1390   0.0685   1.7485
 ZIR  HO3'  H  HOH1  0   0.470  -4.5174  -1.3681   2.7129
 ZIR  H4'   H  HCH1  0   0.245  -5.4488   0.1728  -0.2393
 ZIR  H5'   H  HCH2  0   0.215  -5.3330   1.8378   1.5775
 ZIR  H5'A  H  HCH2  0   0.200  -3.7299   2.3403   1.0425
 ZIR  HO5'  H  HOH1  0   0.459  -5.4306   3.6217   0.0924

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
 ZIR  C6   N1    aromatic  1.337  0.020  1.337
 ZIR  N1   C2    aromatic  1.332  0.020  1.332
 ZIR  N3   C2    aromatic  1.321  0.020  1.321
 ZIR  C2   H2    single    0.930  0.020  1.080
 ZIR  C4   N3    aromatic  1.333  0.020  1.333
 ZIR  C5   C4    aromatic  1.385  0.020  1.385
 ZIR  N9   C4    aromatic  1.364  0.020  1.364
 ZIR  N7   C5    aromatic  1.369  0.020  1.369
 ZIR  C5   C6    aromatic  1.410  0.020  1.410
 ZIR  N10  C6    single    1.336  0.020  1.336
 ZIR  N7   C8    aromatic  1.302  0.020  1.302
 ZIR  C8   N9    aromatic  1.367  0.020  1.367
 ZIR  C8   H8    single    0.930  0.020  1.080
 ZIR  N9   C1'   single    1.457  0.020  1.457
 ZIR  C2'  C1'   single    1.528  0.020  1.528
 ZIR  C1'  O4'   single    1.396  0.020  1.396
 ZIR  C1'  H1'   single    0.970  0.020  1.090
 ZIR  N10  C11   single    1.452  0.020  1.452
 ZIR  N10  HN10  single    0.860  0.020  1.020
 ZIR  C12  C11   single    1.495  0.020  1.495
 ZIR  C11  H11   single    0.970  0.020  1.090
 ZIR  C11  H11A  single    0.970  0.020  1.090
 ZIR  C12  C13   double    1.335  0.020  1.335
 ZIR  C12  H12   single    0.930  0.020  1.080
 ZIR  C14  C13   single    1.500  0.020  1.500
 ZIR  C13  C15   single    1.500  0.020  1.500
 ZIR  C14  H14   single    0.970  0.020  1.090
 ZIR  C14  H14A  single    0.970  0.020  1.090
 ZIR  C14  H14B  single    0.970  0.020  1.090
 ZIR  C15  H15   single    0.970  0.020  1.090
 ZIR  C15  H15A  single    0.970  0.020  1.090
 ZIR  C15  H15B  single    0.970  0.020  1.090
 ZIR  O2'  C2'   single    1.401  0.020  1.401
 ZIR  C2'  C3'   single    1.533  0.020  1.533
 ZIR  C2'  H2'   single    0.970  0.020  1.090
 ZIR  O2'  HO2'  single    0.850  0.020  0.980
 ZIR  C3'  C4'   single    1.525  0.020  1.525
 ZIR  C3'  O3'   single    1.399  0.020  1.399
 ZIR  C3'  H3'   single    0.970  0.020  1.090
 ZIR  O3'  HO3'  single    0.850  0.020  0.980
 ZIR  C5'  C4'   single    1.508  0.020  1.508
 ZIR  C4'  O4'   single    1.428  0.020  1.428
 ZIR  C4'  H4'   single    0.970  0.020  1.090
 ZIR  C5'  O5'   single    1.406  0.020  1.406
 ZIR  C5'  H5'   single    0.970  0.020  1.090
 ZIR  C5'  H5'A  single    0.970  0.020  1.090
 ZIR  O5'  HO5'  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
 ZIR  C6    N1   C2    119.34  3.000
 ZIR  H2    C2   N3    116.16  3.000
 ZIR  H2    C2   N1    115.41  3.000
 ZIR  N3    C2   N1    128.43  3.000
 ZIR  C4    N3   C2    111.54  3.000
 ZIR  N9    C4   C5    105.33  3.000
 ZIR  N9    C4   N3    127.96  3.000
 ZIR  C5    C4   N3    126.71  3.000
 ZIR  N7    C5   C6    133.10  3.000
 ZIR  C6    C5   C4    116.18  3.000
 ZIR  N7    C5   C4    110.72  3.000
 ZIR  N10   C6   C5    122.27  3.000
 ZIR  N10   C6   N1    119.94  3.000
 ZIR  C5    C6   N1    117.79  3.000
 ZIR  C8    N7   C5    104.44  3.000
 ZIR  H8    C8   N9    122.14  3.000
 ZIR  H8    C8   N7    124.56  3.000
 ZIR  N9    C8   N7    113.29  3.000
 ZIR  C1'   N9   C8    128.97  3.000
 ZIR  C1'   N9   C4    124.78  3.000
 ZIR  C8    N9   C4    106.22  3.000
 ZIR  H1'   C1'  O4'   110.93  3.000
 ZIR  H1'   C1'  C2'   111.27  3.000
 ZIR  O4'   C1'  C2'   107.09  3.000
 ZIR  H1'   C1'  N9    106.75  3.000
 ZIR  O4'   C1'  N9    109.20  3.000
 ZIR  C2'   C1'  N9    111.64  3.000
 ZIR  HN10  N10  C11   117.66  3.000
 ZIR  HN10  N10  C6    117.43  3.000
 ZIR  C11   N10  C6    124.02  3.000
 ZIR  H11A  C11  H11   106.39  3.000
 ZIR  H11A  C11  C12   109.66  3.000
 ZIR  H11   C11  C12   112.03  3.000
 ZIR  H11A  C11  N10   108.08  3.000
 ZIR  H11   C11  N10   110.62  3.000
 ZIR  C12   C11  N10   109.92  3.000
 ZIR  H12   C12  C13   118.16  3.000
 ZIR  H12   C12  C11   114.78  3.000
 ZIR  C13   C12  C11   127.05  3.000
 ZIR  C15   C13  C14   114.12  3.000
 ZIR  C15   C13  C12   125.23  3.000
 ZIR  C14   C13  C12   120.65  3.000
 ZIR  H14B  C14  H14A  108.09  3.000
 ZIR  H14B  C14  H14   108.22  3.000
 ZIR  H14A  C14  H14   106.45  3.000
 ZIR  H14B  C14  C13   112.46  3.000
 ZIR  H14A  C14  C13   110.68  3.000
 ZIR  H14   C14  C13   110.71  3.000
 ZIR  H15B  C15  H15A  106.35  3.000
 ZIR  H15B  C15  H15   107.85  3.000
 ZIR  H15A  C15  H15   107.77  3.000
 ZIR  H15B  C15  C13   110.14  3.000
 ZIR  H15A  C15  C13   110.32  3.000
 ZIR  H15   C15  C13   114.09  3.000
 ZIR  H2'   C2'  C3'   112.62  3.000
 ZIR  H2'   C2'  O2'   111.90  3.000
 ZIR  C3'   C2'  O2'   110.99  3.000
 ZIR  H2'   C2'  C1'   111.84  3.000
 ZIR  C3'   C2'  C1'   101.06  3.000
 ZIR  O2'   C2'  C1'   107.86  3.000
 ZIR  HO2'  O2'  C2'   107.67  3.000
 ZIR  H3'   C3'  C4'   109.98  3.000
 ZIR  H3'   C3'  O3'   111.31  3.000
 ZIR  C4'   C3'  O3'   110.36  3.000
 ZIR  H3'   C3'  C2'   109.22  3.000
 ZIR  O3'   C3'  C2'   113.92  3.000
 ZIR  C4'   C3'  C2'   101.62  3.000
 ZIR  HO3'  O3'  C3'   108.85  3.000
 ZIR  H4'   C4'  C5'   109.03  3.000
 ZIR  H4'   C4'  O4'   109.26  3.000
 ZIR  C5'   C4'  O4'   110.78  3.000
 ZIR  H4'   C4'  C3'   109.47  3.000
 ZIR  O4'   C4'  C3'   104.72  3.000
 ZIR  C5'   C4'  C3'   113.46  3.000
 ZIR  C4'   O4'  C1'   111.17  3.000
 ZIR  H5'A  C5'  H5'   106.77  3.000
 ZIR  H5'A  C5'  O5'   111.94  3.000
 ZIR  H5'   C5'  O5'   111.98  3.000
 ZIR  H5'A  C5'  C4'   109.70  3.000
 ZIR  H5'   C5'  C4'   107.26  3.000
 ZIR  O5'   C5'  C4'   109.06  3.000
 ZIR  HO5'  O5'  C5'   108.17  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
 ZIR  CONST_01  C4    C5   C6   N1     0.00   0.0  0
 ZIR  CONST_02  N7    C5   C6   N1   180.00   0.0  0
 ZIR  CONST_03  C4    N3   C2   N1     0.00   0.0  0
 ZIR  CONST_04  C5    C6   N1   C2     0.00   0.0  0
 ZIR  CONST_05  C5    C4   N3   C2     0.00   0.0  0
 ZIR  CONST_06  N9    C4   N3   C2   180.00   0.0  0
 ZIR  CONST_07  C6    N1   C2   N3     0.00   0.0  0
 ZIR  CONST_08  N7    C5   C4   N3   180.00   0.0  0
 ZIR  CONST_09  C6    C5   C4   N3     0.00   0.0  0
 ZIR  CONST_10  C8    N9   C4   N3   180.00   0.0  0
 ZIR  CONST_11  C8    N7   C5   C4     0.00   0.0  0
 ZIR  CONST_12  N7    C8   N9   C4     0.00   0.0  0
 ZIR  CONST_13  C8    N9   C4   C5     0.00   0.0  0
 ZIR  CONST_14  N9    C8   N7   C5     0.00   0.0  0
 ZIR  CONST_15  N9    C4   C5   C6   180.00   0.0  0
 ZIR  CONST_16  C8    N7   C5   C6   180.00   0.0  0
 ZIR  CONST_17  N9    C4   C5   N7     0.00   0.0  0
 ZIR  CONST_18  C1'   N9   C4   N3     0.00   0.0  0
 ZIR  CONST_19  C1'   N9   C4   C5   180.00   0.0  0
 ZIR  CONST_20  C1'   N9   C8   N7   180.00   0.0  0
 ZIR  CONST_21  N10   C6   N1   C2   180.00   0.0  0
 ZIR  CONST_22  N10   C6   C5   C4   180.00   0.0  0
 ZIR  CONST_23  N10   C6   C5   N7     0.00   0.0  0
 ZIR  CONST_24  H2    C2   N3   C4   180.00   0.0  0
 ZIR  CONST_25  H8    C8   N9   C4   180.00   0.0  0
 ZIR  CONST_26  C11   N10  C6   N1     0.00   0.0  0
 ZIR  CONST_27  C11   N10  C6   C5   180.00   0.0  0
 ZIR  CONST_28  HN10  N10  C6   N1   180.00   0.0  0
 ZIR  Var_01    C12   C11  N10  C6   160.65  30.0  3
 ZIR  Var_02    C14   C13  C12  C11  178.85   0.0  2
 ZIR  Var_03    C13   C12  C11  N10  117.21  30.0  2
 ZIR  Var_04    H14   C14  C13  C12  121.28  30.0  3
 ZIR  Var_05    H15   C15  C13  C12   -3.82  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
 ZIR  chir_01  C1'  N9   C2'  O4'  negativ
 ZIR  chir_02  C2'  O2'  C3'  C1'  positiv
 ZIR  chir_03  C3'  O3'  C4'  C2'  positiv
 ZIR  chir_04  C4'  O4'  C3'  C5'  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
 ZIR  plan-1  N1    0.020
 ZIR  plan-1  C2    0.020
 ZIR  plan-1  N3    0.020
 ZIR  plan-1  C4    0.020
 ZIR  plan-1  C5    0.020
 ZIR  plan-1  C6    0.020
 ZIR  plan-1  N7    0.020
 ZIR  plan-1  C8    0.020
 ZIR  plan-1  N9    0.020
 ZIR  plan-1  C1'   0.020
 ZIR  plan-1  N10   0.020
 ZIR  plan-1  H2    0.020
 ZIR  plan-1  H8    0.020
 ZIR  plan-2  C6    0.020
 ZIR  plan-2  N10   0.020
 ZIR  plan-2  C11   0.020
 ZIR  plan-2  HN10  0.020
 ZIR  plan-3  C11   0.020
 ZIR  plan-3  C12   0.020
 ZIR  plan-3  C13   0.020
 ZIR  plan-3  C14   0.020
 ZIR  plan-3  C15   0.020
 ZIR  plan-3  H12   0.020

