# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 01:44:06 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: (3aR,4R,5R,6R,6aS)-2-(dimethylamino)-6-(hydroxymethyl)-4,5,6,6a-tetrahydro-3aH-cyclopenta[d][1,3]oxazole-4,5-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)C1=N[C@@H]2[C@@H](O)[C@H](O)[C@@H](CO)[C@@H]2O1
#
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
 AMI  AMI  (3aR,4R,5R,6R,6aS)-2-(dimethylamino)-6-(hydroxymethyl)-4,5,6,6a-tetrahydro-3aH-cyclopenta[d][1,3]oxazole-4,5-diol  ligand  31  15  .  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_AMI
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
 AMI  C1   C  CR15  0   0.011  -0.4576  -1.0754  -0.2310
 AMI  C2   C  CR15  0  -0.171   1.0716  -0.8209  -0.1690
 AMI  C3   C  CH1   0   0.012   1.3708   0.2158  -1.2581
 AMI  C4   C  CH1   0   0.010   0.0308   0.9354  -1.4912
 AMI  C5   C  CH1   0  -0.321  -1.0347  -0.1505  -1.3063
 AMI  C6   C  CH2   0  -0.148  -1.3472  -0.9399  -2.5703
 AMI  C7   C  CR5   0   0.741   0.1756  -0.2763   1.7531
 AMI  C8   C  CH3   0  -0.518   1.0548   0.7331   3.7298
 AMI  C9   C  CH3   0  -0.524  -1.3780   0.4805   3.4680
 AMI  N2   N  N     0  -0.512   1.3070  -0.3088   1.1631
 AMI  N7   N  NT    0  -0.499  -0.0473   0.1143   3.0268
 AMI  O3   O  OH1   0  -0.669   1.8001  -0.4762  -2.4096
 AMI  O4   O  OH1   0  -0.664  -0.1996   1.9149  -0.5018
 AMI  O6   O  OH1   0  -0.671  -1.8561  -0.0560  -3.5434
 AMI  O7   O  O     0  -0.494  -0.9038  -0.7100   1.0797
 AMI  H1   H  HCR5  0   0.256  -0.7299  -2.1209  -0.3935
 AMI  H2   H  HCR5  0   0.244   1.6615  -1.7252  -0.3506
 AMI  H3   H  HCH1  0   0.225   2.1425   0.9197  -0.9152
 AMI  H4   H  HCH1  0   0.225  -0.0047   1.3800  -2.4960
 AMI  H5   H  HCH1  0   0.263  -1.9720   0.2964  -0.9594
 AMI  H61  H  HCH2  0   0.207  -0.4539  -1.4606  -2.9293
 AMI  H62  H  HCH2  0   0.204  -2.0830  -1.7143  -2.3134
 AMI  H81  H  HCH3  0   0.241   0.8636   0.6862   4.8007
 AMI  H82  H  HCH3  0   0.250   1.9794   0.2009   3.5225
 AMI  H83  H  HCH3  0   0.226   1.1917   1.7825   3.4502
 AMI  H91  H  HCH3  0   0.243  -1.4054   0.4449   4.5560
 AMI  H92  H  HCH3  0   0.227  -1.6601   1.4909   3.1560
 AMI  H93  H  HCH3  0   0.255  -2.1247  -0.2169   3.0988
 AMI  HO3  H  HOH1  0   0.451   1.8815   0.1544  -3.1320
 AMI  HO4  H  HOH1  0   0.446   0.5548   2.5121  -0.4849
 AMI  HO6  H  HOH1  0   0.455  -1.9494  -0.5407  -4.3682

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
 AMI  C1  C2   single  1.551  0.020  1.551
 AMI  C1  C5   single  1.531  0.020  1.531
 AMI  C1  O7   single  1.432  0.020  1.432
 AMI  C1  H1   single  0.970  0.020  1.090
 AMI  C2  C3   single  1.533  0.020  1.533
 AMI  C2  N2   single  1.446  0.020  1.446
 AMI  C2  H2   single  0.970  0.020  1.090
 AMI  C3  C4   single  1.539  0.020  1.539
 AMI  C3  O3   single  1.410  0.020  1.410
 AMI  C3  H3   single  0.970  0.020  1.090
 AMI  C4  C5   single  1.533  0.020  1.533
 AMI  C4  O4   single  1.411  0.020  1.411
 AMI  C4  H4   single  0.970  0.020  1.090
 AMI  C5  C6   single  1.523  0.020  1.523
 AMI  C5  H5   single  0.970  0.020  1.090
 AMI  C6  O6   single  1.410  0.020  1.410
 AMI  C6  H61  single  0.970  0.020  1.090
 AMI  C6  H62  single  0.970  0.020  1.090
 AMI  C7  N2   double  1.276  0.020  1.276
 AMI  C7  N7   single  1.351  0.020  1.351
 AMI  C7  O7   single  1.344  0.020  1.344
 AMI  C8  N7   single  1.446  0.020  1.446
 AMI  C8  H81  single  0.970  0.020  1.090
 AMI  C8  H82  single  0.970  0.020  1.090
 AMI  C8  H83  single  0.970  0.020  1.090
 AMI  C9  N7   single  1.449  0.020  1.449
 AMI  C9  H91  single  0.970  0.020  1.090
 AMI  C9  H92  single  0.970  0.020  1.090
 AMI  C9  H93  single  0.970  0.020  1.090
 AMI  O3  HO3  single  0.850  0.020  0.980
 AMI  O4  HO4  single  0.850  0.020  0.980
 AMI  O6  HO6  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
 AMI  H1   C1  O7   107.61  3.000
 AMI  H1   C1  C5   112.31  3.000
 AMI  O7   C1  C5   111.79  3.000
 AMI  H1   C1  C2   114.12  3.000
 AMI  O7   C1  C2   103.22  3.000
 AMI  C5   C1  C2   107.48  3.000
 AMI  H2   C2  N2   110.95  3.000
 AMI  H2   C2  C3   109.61  3.000
 AMI  N2   C2  C3   112.52  3.000
 AMI  H2   C2  C1   112.89  3.000
 AMI  N2   C2  C1   104.79  3.000
 AMI  C3   C2  C1   105.95  3.000
 AMI  H3   C3  O3   110.80  3.000
 AMI  H3   C3  C4   111.05  3.000
 AMI  O3   C3  C4   111.77  3.000
 AMI  H3   C3  C2   110.39  3.000
 AMI  O3   C3  C2   107.91  3.000
 AMI  C4   C3  C2   104.71  3.000
 AMI  H4   C4  O4   110.78  3.000
 AMI  H4   C4  C5   111.99  3.000
 AMI  O4   C4  C5   107.08  3.000
 AMI  H4   C4  C3   110.84  3.000
 AMI  O4   C4  C3   111.13  3.000
 AMI  C5   C4  C3   104.82  3.000
 AMI  H5   C5  C6   107.39  3.000
 AMI  H5   C5  C4   110.13  3.000
 AMI  C6   C5  C4   114.19  3.000
 AMI  H5   C5  C1   110.29  3.000
 AMI  C6   C5  C1   110.32  3.000
 AMI  C4   C5  C1   104.52  3.000
 AMI  H62  C6  H61  106.73  3.000
 AMI  H62  C6  O6   111.20  3.000
 AMI  H61  C6  O6   111.50  3.000
 AMI  H62  C6  C5   107.98  3.000
 AMI  H61  C6  C5   110.57  3.000
 AMI  O6   C6  C5   108.79  3.000
 AMI  O7   C7  N7   115.67  3.000
 AMI  O7   C7  N2   118.17  3.000
 AMI  N7   C7  N2   126.12  3.000
 AMI  H83  C8  H82  108.32  3.000
 AMI  H83  C8  H81  108.33  3.000
 AMI  H82  C8  H81  108.41  3.000
 AMI  H83  C8  N7   112.42  3.000
 AMI  H82  C8  N7   110.24  3.000
 AMI  H81  C8  N7   109.02  3.000
 AMI  H93  C9  H92  108.58  3.000
 AMI  H93  C9  H91  107.54  3.000
 AMI  H92  C9  H91  107.97  3.000
 AMI  H93  C9  N7   111.43  3.000
 AMI  H92  C9  N7   112.54  3.000
 AMI  H91  C9  N7   108.61  3.000
 AMI  C7   N2  C2   106.89  3.000
 AMI  C9   N7  C8   116.34  3.000
 AMI  C9   N7  C7   120.78  3.000
 AMI  C8   N7  C7   117.15  3.000
 AMI  HO3  O3  C3   108.48  3.000
 AMI  HO4  O4  C4   108.36  3.000
 AMI  HO6  O6  C6   108.13  3.000
 AMI  C7   O7  C1   106.90  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
 AMI  CONST_01  O7   C7  N2  C2     0.00   0.0  0
 AMI  CONST_02  N7   C7  N2  C2   180.00   0.0  0
 AMI  CONST_03  N2   C7  N7  C8     0.00   0.0  0
 AMI  CONST_04  O7   C7  N7  C8   180.00   0.0  0
 AMI  Var_01    N2   C7  O7  C1    -2.04  30.0  1
 AMI  Var_02    H81  C8  N7  C7  -160.96  30.0  3
 AMI  Var_03    H91  C9  N7  C7   161.81  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
 AMI  chir_01  C1  C2  C5  O7  positiv
 AMI  chir_02  C2  N2  C1  C3  negativ
 AMI  chir_03  C3  O3  C2  C4  positiv
 AMI  chir_04  C4  O4  C3  C5  negativ
 AMI  chir_05  C5  C1  C4  C6  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
 AMI  plan-1  C2  0.020
 AMI  plan-1  C7  0.020
 AMI  plan-1  C8  0.020
 AMI  plan-1  C9  0.020
 AMI  plan-1  N2  0.020
 AMI  plan-1  N7  0.020
 AMI  plan-1  O7  0.020

