# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 05:45:13 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 3-amino-1-{2-[(3-chlorophenyl)carbonyl]hydrazino}-3,4-dideoxy-5-S-(1-methylethyl)-5-thio-D-threo-pentose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)SCC[C@@H](N)[C@H](O)C(=O)NNC(=O)c1cccc(Cl)c1
#
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
 AO5  AO5  3-amino-1-{2-[(3-chlorophenyl)carbonyl]hydrazino}-3,4-dideoxy-5-S-(1-methylethyl)-5-thio-D-threo-pentose  ligand  45  23  .  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_AO5
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
 AO5  C1    C   CH1   0  -0.355  -6.9774   1.4418   0.7323
 AO5  C2    C   CH3   0  -0.637  -6.5258   2.8235   0.2879
 AO5  C3    C   CH3   0  -0.649  -8.4851   1.2756   0.6100
 AO5  S4    S   S2    0  -0.036  -6.1996   0.1173  -0.2564
 AO5  C5    C   CH2   0  -0.557  -4.4557   0.2757   0.2222
 AO5  C6    C   CH2   0  -0.428  -3.6616  -0.8861  -0.3562
 AO5  C7    C   CH1   0  -0.111  -2.1702  -0.7837  -0.0175
 AO5  N8    N   NH2   0  -0.792  -1.8629  -0.7649   1.4012
 AO5  C9    C   CH1   0  -0.076  -1.3944  -1.9376  -0.6774
 AO5  O10   O   OH1   0  -0.661  -1.7391  -3.1817  -0.1415
 AO5  C11   C   C     0   0.524   0.1033  -1.7008  -0.5196
 AO5  O12   O   O     0  -0.452   0.7880  -2.3392   0.2521
 AO5  N13   N   NH1   0  -0.492   0.5974  -0.7257  -1.3205
 AO5  N14   N   NH1   0  -0.504   1.8758  -0.2938  -1.1801
 AO5  C15   C   C     0   0.526   2.1947   0.6361  -0.2459
 AO5  O16   O   O     0  -0.442   1.3613   1.2011   0.4324
 AO5  C17   C   CR6   0  -0.042   3.6534   0.9291  -0.1280
 AO5  C18   C   CR16  0  -0.259   4.0417   2.2194   0.2208
 AO5  C19   C   CR16  0  -0.247   5.3863   2.5249   0.3521
 AO5  C20   C   CR16  0  -0.207   6.3538   1.5486   0.1596
 AO5  C21   C   CR6   0  -0.023   5.9534   0.2628  -0.1673
 AO5  C22   C   CR16  0  -0.245   4.6144  -0.0602  -0.3167
 AO5  CL23  CL  CL    0  -0.116   7.1478  -0.9710  -0.3864
 AO5  H1    H   HCH1  0   0.262  -6.6827   1.2776   1.7725
 AO5  H21   H   HCH3  0   0.238  -5.4485   2.9534   0.3890
 AO5  H22A  H   HCH3  0   0.224  -6.7933   3.0009  -0.7546
 AO5  H23   H   HCH3  0   0.232  -7.0067   3.5912   0.8979
 AO5  H31   H   HCH3  0   0.229  -8.8141   1.4074  -0.4226
 AO5  H32   H   HCH3  0   0.240  -8.8130   0.2933   0.9500
 AO5  H33   H   HCH3  0   0.241  -8.9908   2.0275   1.2174
 AO5  H51   H   HCH2  0   0.258  -4.0547   1.2242  -0.1416
 AO5  H52   H   HCH2  0   0.253  -4.3932   0.2809   1.3124
 AO5  H61   H   HCH2  0   0.237  -4.0611  -1.8309   0.0231
 AO5  H62   H   HCH2  0   0.235  -3.7816  -0.9037  -1.4436
 AO5  H7    H   HCH1  0   0.242  -1.7941   0.1522  -0.4438
 AO5  HN81  H   HNH2  0   0.358  -2.0691   0.1416   1.7972
 AO5  HN82  H   HNH2  0   0.344  -2.4430  -1.4306   1.8976
 AO5  H9    H   HCH1  0   0.269  -1.6392  -1.9601  -1.7456
 AO5  H10   H   HOH1  0   0.445  -1.2125  -3.3138   0.6568
 AO5  H13   H   HNH1  0   0.420  -0.0120  -0.1781  -1.9107
 AO5  H14   H   HNH1  0   0.426   2.5644  -0.6875  -1.8027
 AO5  H18   H   HCR6  0   0.272   3.2945   2.9852   0.3779
 AO5  H19   H   HCR6  0   0.278   5.6901   3.5301   0.6104
 AO5  H20   H   HCR6  0   0.289   7.4031   1.7861   0.2689
 AO5  H22   H   HCR6  0   0.288   4.3331  -1.0792  -0.5480

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
 AO5  C1   C2    single    1.520  0.020  1.520
 AO5  C1   C3    single    1.522  0.020  1.522
 AO5  C1   S4    single    1.827  0.020  1.827
 AO5  C1   H1    single    0.970  0.020  1.090
 AO5  C2   H21   single    0.970  0.020  1.090
 AO5  C2   H22A  single    0.970  0.020  1.090
 AO5  C2   H23   single    0.970  0.020  1.090
 AO5  C3   H31   single    0.970  0.020  1.090
 AO5  C3   H32   single    0.970  0.020  1.090
 AO5  C3   H33   single    0.970  0.020  1.090
 AO5  S4   C5    single    1.815  0.020  1.815
 AO5  C5   C6    single    1.521  0.020  1.521
 AO5  C5   H51   single    0.970  0.020  1.090
 AO5  C5   H52   single    0.970  0.020  1.090
 AO5  C6   C7    single    1.533  0.020  1.533
 AO5  C6   H61   single    0.970  0.020  1.090
 AO5  C6   H62   single    0.970  0.020  1.090
 AO5  C7   N8    single    1.452  0.020  1.452
 AO5  C7   C9    single    1.539  0.020  1.539
 AO5  C7   H7    single    0.970  0.020  1.090
 AO5  N8   HN81  single    0.890  0.020  1.040
 AO5  N8   HN82  single    0.890  0.020  1.040
 AO5  C9   O10   single    1.398  0.020  1.398
 AO5  C9   C11   single    1.525  0.020  1.525
 AO5  C9   H9    single    0.970  0.020  1.090
 AO5  O10  H10   single    0.850  0.020  0.980
 AO5  C11  O12   double    1.213  0.020  1.213
 AO5  C11  N13   single    1.355  0.020  1.355
 AO5  N13  N14   single    1.357  0.020  1.357
 AO5  N13  H13   single    0.860  0.020  1.020
 AO5  N14  C15   single    1.356  0.020  1.356
 AO5  N14  H14   single    0.860  0.020  1.020
 AO5  C15  O16   double    1.214  0.020  1.214
 AO5  C15  C17   single    1.493  0.020  1.493
 AO5  C17  C18   aromatic  1.392  0.020  1.392
 AO5  C17  C22   aromatic  1.392  0.020  1.392
 AO5  C18  C19   aromatic  1.385  0.020  1.385
 AO5  C18  H18   single    0.930  0.020  1.080
 AO5  C19  C20   aromatic  1.388  0.020  1.388
 AO5  C19  H19   single    0.930  0.020  1.080
 AO5  C20  C21   aromatic  1.386  0.020  1.386
 AO5  C20  H20   single    0.930  0.020  1.080
 AO5  C21  C22   aromatic  1.386  0.020  1.386
 AO5  C21  CL23  single    1.731  0.020  1.731
 AO5  C22  H22   single    0.930  0.020  1.080

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
 AO5  H1    C1   S4    106.93  3.000
 AO5  H1    C1   C3    109.09  3.000
 AO5  S4    C1   C3    107.41  3.000
 AO5  H1    C1   C2    109.55  3.000
 AO5  S4    C1   C2    111.98  3.000
 AO5  C3    C1   C2    111.72  3.000
 AO5  H23   C2   H22A  108.15  3.000
 AO5  H23   C2   H21   107.43  3.000
 AO5  H22A  C2   H21   108.16  3.000
 AO5  H23   C2   C1    110.18  3.000
 AO5  H22A  C2   C1    110.76  3.000
 AO5  H21   C2   C1    112.02  3.000
 AO5  H33   C3   H32   107.94  3.000
 AO5  H33   C3   H31   107.69  3.000
 AO5  H32   C3   H31   108.25  3.000
 AO5  H33   C3   C1    109.83  3.000
 AO5  H32   C3   C1    111.80  3.000
 AO5  H31   C3   C1    111.19  3.000
 AO5  C5    S4   C1    101.72  3.000
 AO5  H52   C5   H51   107.90  3.000
 AO5  H52   C5   C6    110.69  3.000
 AO5  H51   C5   C6    110.18  3.000
 AO5  H52   C5   S4    108.58  3.000
 AO5  H51   C5   S4    109.92  3.000
 AO5  C6    C5   S4    109.54  3.000
 AO5  H62   C6   H61   106.91  3.000
 AO5  H62   C6   C7    109.10  3.000
 AO5  H61   C6   C7    109.67  3.000
 AO5  H62   C6   C5    109.44  3.000
 AO5  H61   C6   C5    109.71  3.000
 AO5  C7    C6   C5    111.89  3.000
 AO5  H7    C7   C9    107.51  3.000
 AO5  H7    C7   N8    107.26  3.000
 AO5  C9    C7   N8    108.78  3.000
 AO5  H7    C7   C6    107.78  3.000
 AO5  C9    C7   C6    110.22  3.000
 AO5  N8    C7   C6    115.01  3.000
 AO5  HN82  N8   HN81  106.29  3.000
 AO5  HN82  N8   C7    110.44  3.000
 AO5  HN81  N8   C7    110.58  3.000
 AO5  H9    C9   C11   108.87  3.000
 AO5  H9    C9   O10   107.48  3.000
 AO5  C11   C9   O10   109.93  3.000
 AO5  H9    C9   C7    108.70  3.000
 AO5  C11   C9   C7    109.53  3.000
 AO5  O10   C9   C7    112.25  3.000
 AO5  H10   O10  C9    107.72  3.000
 AO5  N13   C11  O12   123.28  3.000
 AO5  N13   C11  C9    114.13  3.000
 AO5  O12   C11  C9    122.58  3.000
 AO5  H13   N13  N14   117.17  3.000
 AO5  H13   N13  C11   121.04  3.000
 AO5  N14   N13  C11   120.76  3.000
 AO5  H14   N14  C15   122.17  3.000
 AO5  H14   N14  N13   117.09  3.000
 AO5  C15   N14  N13   120.74  3.000
 AO5  C17   C15  O16   122.37  3.000
 AO5  C17   C15  N14   114.76  3.000
 AO5  O16   C15  N14   122.86  3.000
 AO5  C22   C17  C18   120.02  3.000
 AO5  C22   C17  C15   121.63  3.000
 AO5  C18   C17  C15   118.32  3.000
 AO5  H18   C18  C19   120.05  3.000
 AO5  H18   C18  C17   120.01  3.000
 AO5  C19   C18  C17   119.93  3.000
 AO5  H19   C19  C20   119.41  3.000
 AO5  H19   C19  C18   120.03  3.000
 AO5  C20   C19  C18   120.56  3.000
 AO5  H20   C20  C21   120.53  3.000
 AO5  H20   C20  C19   120.52  3.000
 AO5  C21   C20  C19   118.94  3.000
 AO5  CL23  C21  C22   119.14  3.000
 AO5  CL23  C21  C20   119.45  3.000
 AO5  C22   C21  C20   121.41  3.000
 AO5  H22   C22  C21   119.60  3.000
 AO5  H22   C22  C17   121.25  3.000
 AO5  C21   C22  C17   119.13  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
 AO5  CONST_01  C20   C19  C18  C17    0.00   0.0  0
 AO5  CONST_02  C20   C21  C22  C17    0.00   0.0  0
 AO5  CONST_03  C21   C22  C17  C18    0.00   0.0  0
 AO5  CONST_04  C21   C20  C19  C18    0.00   0.0  0
 AO5  CONST_05  C22   C17  C18  C19    0.00   0.0  0
 AO5  CONST_06  C22   C21  C20  C19    0.00   0.0  0
 AO5  CONST_07  C19   C18  C17  C15  180.00   0.0  0
 AO5  CONST_08  C21   C22  C17  C15  180.00   0.0  0
 AO5  CONST_09  CL23  C21  C22  C17  180.00   0.0  0
 AO5  CONST_10  CL23  C21  C20  C19  180.00   0.0  0
 AO5  CONST_11  H19   C19  C18  C17  180.00   0.0  0
 AO5  CONST_12  H22   C22  C17  C18  180.00   0.0  0
 AO5  CONST_13  H20   C20  C19  C18  180.00   0.0  0
 AO5  CONST_14  H18   C18  C19  C20  180.00   0.0  0
 AO5  CONST_15  C17   C15  N14  N13  180.00   0.0  0
 AO5  CONST_16  H14   N14  C15  C17    0.00   0.0  0
 AO5  CONST_17  N14   N13  C11  C9   180.00   0.0  0
 AO5  CONST_18  N14   N13  C11  O12    0.00   0.0  0
 AO5  CONST_19  O16   C15  N14  N13    0.00   0.0  0
 AO5  CONST_20  H13   N13  C11  C9     0.00   0.0  0
 AO5  Var_01    C18   C17  C15  N14  147.63  30.0  2
 AO5  Var_02    C6    C5   S4   C1   171.98  30.0  3
 AO5  Var_03    C7    C6   C5   S4   178.36  30.0  3
 AO5  Var_04    C15   N14  N13  C11  -83.04  30.0  2
 AO5  Var_05    H31   C3   C1   C2    60.20  30.0  3
 AO5  Var_06    H21   C2   C1   C3   179.06  30.0  3
 AO5  Var_07    H1    C1   S4   C5   -53.62  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
 AO5  chir_01  C7  C6   N8  C9   negativ
 AO5  chir_02  C9  O10  C7  C11  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
 AO5  plan-1  C15   0.020
 AO5  plan-1  C17   0.020
 AO5  plan-1  C18   0.020
 AO5  plan-1  C19   0.020
 AO5  plan-1  C20   0.020
 AO5  plan-1  C21   0.020
 AO5  plan-1  C22   0.020
 AO5  plan-1  CL23  0.020
 AO5  plan-1  H18   0.020
 AO5  plan-1  H19   0.020
 AO5  plan-1  H20   0.020
 AO5  plan-1  H22   0.020
 AO5  plan-2  C9    0.020
 AO5  plan-2  C11   0.020
 AO5  plan-2  O12   0.020
 AO5  plan-2  N13   0.020
 AO5  plan-2  N14   0.020
 AO5  plan-2  H13   0.020
 AO5  plan-3  N13   0.020
 AO5  plan-3  N14   0.020
 AO5  plan-3  C15   0.020
 AO5  plan-3  O16   0.020
 AO5  plan-3  C17   0.020
 AO5  plan-3  H14   0.020

