# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 12:36:56 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 5'-deoxy-5'-[(3-hydrazinopropyl)(methyl)amino]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(CCCNN)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
#
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
 MHZ  MHZ  5'-deoxy-5'-[(3-hydrazinopropyl)(methyl)amino]adenosine  ligand  49  25  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MHZ
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
 MHZ  N     N  NH2   0  -0.680   3.9180   0.8516  -5.9588
 MHZ  NA    N  NH1   0  -0.506   3.0592  -0.0980  -5.2849
 MHZ  CB    C  CH2   0  -0.251   1.8471   0.5838  -4.8659
 MHZ  CC    C  CH2   0  -0.475   0.9682  -0.3532  -4.0530
 MHZ  CG    C  CH2   0  -0.265  -0.3039   0.3432  -3.5908
 MHZ  ND    N  NT    0  -0.417  -1.1248  -0.4759  -2.7121
 MHZ  CE    C  CH3   0  -0.540  -1.7474  -1.5781  -3.4175
 MHZ  C5'   C  CH2   0  -0.289  -2.0898   0.3392  -2.0046
 MHZ  C4'   C  CH1   0  -0.064  -2.8687  -0.4070  -0.9242
 MHZ  O4'   O  O2    0  -0.486  -2.0244  -1.1945  -0.0819
 MHZ  C1'   C  CH1   0   0.224  -1.7122  -0.5110   1.0896
 MHZ  N9    N  NR5   0  -0.543  -0.2671  -0.3917   1.1918
 MHZ  C4    C  CR56  0   0.483   0.4518  -0.2135   2.3368
 MHZ  N3    N  N     0  -0.447   0.0142  -0.1713   3.5947
 MHZ  C2    C  CR16  0   0.035   1.0042   0.0092   4.4500
 MHZ  N1    N  N     0  -0.475   2.3041   0.1504   4.1976
 MHZ  C6    C  CR6   0   0.452   2.7283   0.1031   2.9304
 MHZ  N6    N  NH2   0  -0.819   4.0293   0.2464   2.6702
 MHZ  C5    C  CR56  0  -0.010   1.7695  -0.0932   1.9198
 MHZ  N7    N  N     0  -0.457   1.8624  -0.2014   0.5577
 MHZ  C8    C  CR15  0   0.085   0.6339  -0.3769   0.1610
 MHZ  C2'   C  CH1   0  -0.060  -2.4264   0.8495   1.0182
 MHZ  O2'   O  OH1   0  -0.651  -2.8634   1.2314   2.2890
 MHZ  C3'   C  CH1   0   0.005  -3.5585   0.5614   0.0223
 MHZ  O3'   O  OH1   0  -0.669  -4.6239  -0.0973   0.6529
 MHZ  HN1   H  HNH2  0   0.354   4.7858   0.3524  -6.1222
 MHZ  HN2   H  HNH2  0   0.349   3.5250   0.9440  -6.8906
 MHZ  HNA1  H  HNH1  0   0.346   3.5632  -0.3411  -4.4389
 MHZ  HB1   H  HCH2  0   0.217   1.3061   0.9015  -5.7638
 MHZ  HB2   H  HCH2  0   0.192   2.0617   1.4974  -4.2917
 MHZ  HCC1  H  HCH2  0   0.223   1.5171  -0.7060  -3.1733
 MHZ  HCC2  H  HCH2  0   0.232   0.7393  -1.2345  -4.6561
 MHZ  HG1   H  HCH2  0   0.203  -0.8753   0.6911  -4.4686
 MHZ  HG2   H  HCH2  0   0.230  -0.0180   1.2429  -3.0382
 MHZ  HE1   H  HCH3  0   0.244  -2.2705  -2.2377  -2.7267
 MHZ  HE2   H  HCH3  0   0.197  -2.4683  -1.2455  -4.1801
 MHZ  HE3   H  HCH3  0   0.246  -0.9934  -2.1847  -3.9159
 MHZ  H5'1  H  HCH2  0   0.237  -1.5469   1.1765  -1.5554
 MHZ  H5'2  H  HCH2  0   0.227  -2.8376   0.7909  -2.6797
 MHZ  H4'   H  HCH1  0   0.269  -3.5904  -1.0871  -1.3830
 MHZ  H1'   H  HCH1  0   0.265  -2.0474  -1.0683   1.9703
 MHZ  H2    H  HCR6  0   0.249   0.7283   0.0499   5.4985
 MHZ  HN61  H  HNH2  0   0.402   4.6860   0.3756   3.4200
 MHZ  HN62  H  HNH2  0   0.410   4.3806   0.1967   1.7303
 MHZ  H8    H  HCR5  0   0.309   0.3165  -0.5296  -0.8637
 MHZ  H2'   H  HCH1  0   0.255  -1.7504   1.5966   0.5885
 MHZ  HO2'  H  HOH1  0   0.468  -2.9676   2.1876   2.3067
 MHZ  H3'   H  HCH1  0   0.246  -3.8882   1.4730  -0.4936
 MHZ  HO3'  H  HOH1  0   0.448  -4.7919   0.3473   1.4924

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
 MHZ  N    NA    single    1.447  0.020  1.447
 MHZ  N    HN1   single    0.890  0.020  1.040
 MHZ  N    HN2   single    0.890  0.020  1.040
 MHZ  NA   CB    single    1.452  0.020  1.452
 MHZ  NA   HNA1  single    0.890  0.020  1.040
 MHZ  CB   CC    single    1.520  0.020  1.520
 MHZ  CB   HB1   single    0.970  0.020  1.090
 MHZ  CB   HB2   single    0.970  0.020  1.090
 MHZ  CC   CG    single    1.522  0.020  1.522
 MHZ  CC   HCC1  single    0.970  0.020  1.090
 MHZ  CC   HCC2  single    0.970  0.020  1.090
 MHZ  CG   ND    single    1.455  0.020  1.455
 MHZ  CG   HG1   single    0.970  0.020  1.090
 MHZ  CG   HG2   single    0.970  0.020  1.090
 MHZ  ND   CE    single    1.449  0.020  1.449
 MHZ  ND   C5'   single    1.448  0.020  1.448
 MHZ  CE   HE1   single    0.970  0.020  1.090
 MHZ  CE   HE2   single    0.970  0.020  1.090
 MHZ  CE   HE3   single    0.970  0.020  1.090
 MHZ  C5'  C4'   single    1.527  0.020  1.527
 MHZ  C5'  H5'1  single    0.970  0.020  1.090
 MHZ  C5'  H5'2  single    0.970  0.020  1.090
 MHZ  C4'  O4'   single    1.429  0.020  1.429
 MHZ  C4'  C3'   single    1.520  0.020  1.520
 MHZ  C4'  H4'   single    0.970  0.020  1.090
 MHZ  O4'  C1'   single    1.392  0.020  1.392
 MHZ  C1'  N9    single    1.454  0.020  1.454
 MHZ  C1'  C2'   single    1.538  0.020  1.538
 MHZ  C1'  H1'   single    0.970  0.020  1.090
 MHZ  N9   C4    aromatic  1.364  0.020  1.364
 MHZ  N9   C8    aromatic  1.369  0.020  1.369
 MHZ  C4   N3    aromatic  1.332  0.020  1.332
 MHZ  C4   C5    aromatic  1.387  0.020  1.387
 MHZ  N3   C2    aromatic  1.321  0.020  1.321
 MHZ  C2   N1    aromatic  1.332  0.020  1.332
 MHZ  C2   H2    single    0.930  0.020  1.080
 MHZ  N1   C6    aromatic  1.337  0.020  1.337
 MHZ  C6   N6    single    1.334  0.020  1.334
 MHZ  C6   C5    aromatic  1.407  0.020  1.407
 MHZ  N6   HN61  single    0.860  0.020  1.020
 MHZ  N6   HN62  single    0.860  0.020  1.020
 MHZ  C5   N7    aromatic  1.370  0.020  1.370
 MHZ  N7   C8    aromatic  1.303  0.020  1.303
 MHZ  C8   H8    single    0.930  0.020  1.080
 MHZ  C2'  O2'   single    1.397  0.020  1.397
 MHZ  C2'  C3'   single    1.535  0.020  1.535
 MHZ  C2'  H2'   single    0.970  0.020  1.090
 MHZ  O2'  HO2'  single    0.850  0.020  0.980
 MHZ  C3'  O3'   single    1.402  0.020  1.402
 MHZ  C3'  H3'   single    0.970  0.020  1.090
 MHZ  O3'  HO3'  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
 MHZ  HN2   N    HN1   103.18  3.000
 MHZ  HN2   N    NA    104.91  3.000
 MHZ  HN1   N    NA    105.06  3.000
 MHZ  HNA1  NA   CB    106.65  3.000
 MHZ  HNA1  NA   N     104.52  3.000
 MHZ  CB    NA   N     108.76  3.000
 MHZ  HB2   CB   HB1   106.46  3.000
 MHZ  HB2   CB   CC    110.21  3.000
 MHZ  HB1   CB   CC    109.36  3.000
 MHZ  HB2   CB   NA    112.19  3.000
 MHZ  HB1   CB   NA    108.17  3.000
 MHZ  CC    CB   NA    110.33  3.000
 MHZ  HCC2  CC   HCC1  106.78  3.000
 MHZ  HCC2  CC   CG    111.21  3.000
 MHZ  HCC1  CC   CG    108.80  3.000
 MHZ  HCC2  CC   CB    108.86  3.000
 MHZ  HCC1  CC   CB    109.77  3.000
 MHZ  CG    CC   CB    111.32  3.000
 MHZ  HG2   CG   HG1   106.13  3.000
 MHZ  HG2   CG   ND    107.79  3.000
 MHZ  HG1   CG   ND    111.45  3.000
 MHZ  HG2   CG   CC    108.14  3.000
 MHZ  HG1   CG   CC    109.60  3.000
 MHZ  ND    CG   CC    113.41  3.000
 MHZ  C5'   ND   CE    112.32  3.000
 MHZ  C5'   ND   CG    110.74  3.000
 MHZ  CE    ND   CG    112.12  3.000
 MHZ  HE3   CE   HE2   107.74  3.000
 MHZ  HE3   CE   HE1   106.60  3.000
 MHZ  HE2   CE   HE1   107.93  3.000
 MHZ  HE3   CE   ND    110.43  3.000
 MHZ  HE2   CE   ND    112.88  3.000
 MHZ  HE1   CE   ND    111.00  3.000
 MHZ  H5'2  C5'  H5'1  105.90  3.000
 MHZ  H5'2  C5'  C4'   106.68  3.000
 MHZ  H5'1  C5'  C4'   109.67  3.000
 MHZ  H5'2  C5'  ND    112.52  3.000
 MHZ  H5'1  C5'  ND    107.50  3.000
 MHZ  C4'   C5'  ND    114.25  3.000
 MHZ  H4'   C4'  C3'   111.00  3.000
 MHZ  H4'   C4'  O4'   107.14  3.000
 MHZ  C3'   C4'  O4'   104.61  3.000
 MHZ  H4'   C4'  C5'   110.12  3.000
 MHZ  C3'   C4'  C5'   111.15  3.000
 MHZ  O4'   C4'  C5'   112.64  3.000
 MHZ  C1'   O4'  C4'   110.97  3.000
 MHZ  H1'   C1'  C2'   110.21  3.000
 MHZ  H1'   C1'  N9    106.83  3.000
 MHZ  C2'   C1'  N9    113.09  3.000
 MHZ  H1'   C1'  O4'   111.00  3.000
 MHZ  C2'   C1'  O4'   106.93  3.000
 MHZ  N9    C1'  O4'   108.81  3.000
 MHZ  C8    N9   C4    106.49  3.000
 MHZ  C8    N9   C1'   127.02  3.000
 MHZ  C4    N9   C1'   126.43  3.000
 MHZ  C5    C4   N3    126.36  3.000
 MHZ  C5    C4   N9    105.05  3.000
 MHZ  N3    C4   N9    128.58  3.000
 MHZ  C2    N3   C4    111.69  3.000
 MHZ  H2    C2   N1    115.31  3.000
 MHZ  H2    C2   N3    116.13  3.000
 MHZ  N1    C2   N3    128.56  3.000
 MHZ  C6    N1   C2    119.05  3.000
 MHZ  C5    C6   N6    122.64  3.000
 MHZ  C5    C6   N1    118.00  3.000
 MHZ  N6    C6   N1    119.36  3.000
 MHZ  HN62  N6   HN61  118.41  3.000
 MHZ  HN62  N6   C6    121.20  3.000
 MHZ  HN61  N6   C6    120.35  3.000
 MHZ  N7    C5   C6    132.78  3.000
 MHZ  N7    C5   C4    110.88  3.000
 MHZ  C6    C5   C4    116.33  3.000
 MHZ  C8    N7   C5    104.45  3.000
 MHZ  H8    C8   N7    125.68  3.000
 MHZ  H8    C8   N9    121.17  3.000
 MHZ  N7    C8   N9    113.13  3.000
 MHZ  H2'   C2'  C3'   109.18  3.000
 MHZ  H2'   C2'  O2'   111.31  3.000
 MHZ  C3'   C2'  O2'   114.25  3.000
 MHZ  H2'   C2'  C1'   109.57  3.000
 MHZ  C3'   C2'  C1'   101.91  3.000
 MHZ  O2'   C2'  C1'   110.17  3.000
 MHZ  HO2'  O2'  C2'   108.81  3.000
 MHZ  H3'   C3'  O3'   111.90  3.000
 MHZ  H3'   C3'  C2'   111.74  3.000
 MHZ  O3'   C3'  C2'   110.90  3.000
 MHZ  H3'   C3'  C4'   111.88  3.000
 MHZ  O3'   C3'  C4'   109.00  3.000
 MHZ  C2'   C3'  C4'   100.89  3.000
 MHZ  HO3'  O3'  C3'   107.89  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
 MHZ  CONST_01  C2    N3   C4  N9    180.00   0.0  0
 MHZ  CONST_02  C6    C5   C4  N9    180.00   0.0  0
 MHZ  CONST_03  N7    C5   C4  N9      0.00   0.0  0
 MHZ  CONST_04  C5    N7   C8  N9      0.00   0.0  0
 MHZ  CONST_05  N7    C8   N9  C4      0.00   0.0  0
 MHZ  CONST_06  N1    C2   N3  C4      0.00   0.0  0
 MHZ  CONST_07  N1    C6   C5  C4      0.00   0.0  0
 MHZ  CONST_08  C8    N7   C5  C4      0.00   0.0  0
 MHZ  CONST_09  C8    N9   C4  N3    180.00   0.0  0
 MHZ  CONST_10  C6    C5   C4  N3      0.00   0.0  0
 MHZ  CONST_11  N7    C5   C4  N3    180.00   0.0  0
 MHZ  CONST_12  C6    N1   C2  N3      0.00   0.0  0
 MHZ  CONST_13  C5    C4   N3  C2      0.00   0.0  0
 MHZ  CONST_14  C5    C6   N1  C2      0.00   0.0  0
 MHZ  CONST_15  N7    C5   C6  N1    180.00   0.0  0
 MHZ  CONST_16  C8    N7   C5  C6    180.00   0.0  0
 MHZ  CONST_17  C8    N9   C4  C5      0.00   0.0  0
 MHZ  CONST_18  N3    C4   N9  C1'     0.00   0.0  0
 MHZ  CONST_19  C5    C4   N9  C1'   180.00   0.0  0
 MHZ  CONST_20  N7    C8   N9  C1'   180.00   0.0  0
 MHZ  CONST_21  N6    C6   C5  C4    180.00   0.0  0
 MHZ  CONST_22  N6    C6   N1  C2    180.00   0.0  0
 MHZ  CONST_23  N7    C5   C6  N6      0.00   0.0  0
 MHZ  CONST_24  H8    C8   N9  C1'     0.00   0.0  0
 MHZ  CONST_25  H2    C2   N3  C4    180.00   0.0  0
 MHZ  CONST_26  HN61  N6   C6  N1      0.00   0.0  0
 MHZ  CONST_27  HN62  N6   C6  N1    180.00   0.0  0
 MHZ  Var_01    C4'   C5'  ND  CG   -172.28  30.0  3
 MHZ  Var_02    CC    CB   NA  N    -175.35  30.0  3
 MHZ  Var_03    CG    CC   CB  NA    179.47  30.0  3
 MHZ  Var_04    ND    CG   CC  CB   -175.00  30.0  3
 MHZ  Var_05    CE    ND   CG  CC    -70.31  30.0  3
 MHZ  Var_06    HN1   N    NA  CB    173.16  30.0  2
 MHZ  Var_07    HE1   CE   ND  CG    174.03  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
 MHZ  chir_01  C4'  C5'  O4'  C3'  negativ
 MHZ  chir_02  C1'  O4'  N9   C2'  negativ
 MHZ  chir_03  C2'  O2'  C1'  C3'  negativ
 MHZ  chir_04  C3'  O3'  C4'  C2'  positiv

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
 MHZ  plan-1  C1'   0.020
 MHZ  plan-1  N9    0.020
 MHZ  plan-1  C4    0.020
 MHZ  plan-1  N3    0.020
 MHZ  plan-1  C2    0.020
 MHZ  plan-1  N1    0.020
 MHZ  plan-1  C6    0.020
 MHZ  plan-1  N6    0.020
 MHZ  plan-1  C5    0.020
 MHZ  plan-1  N7    0.020
 MHZ  plan-1  C8    0.020
 MHZ  plan-1  H2    0.020
 MHZ  plan-1  H8    0.020
 MHZ  plan-2  C6    0.020
 MHZ  plan-2  N6    0.020
 MHZ  plan-2  HN61  0.020
 MHZ  plan-2  HN62  0.020

