# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:07:52 2022
#   Inital geometry file: a 67 line input string
#   Ligand name: (3aR,4R,5R,6R,6aS)-6-(hydroxymethyl)-2-(methylideneamino)-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: OC[C@@H]1[C@@H](O)[C@H](O)[C@H]2N=C(O[C@@H]12)N=C
#
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
 ALI  ALI  (3aR,4R,5R,6R,6aS)-6-(hydroxymethyl)-2-(methylideneamino)-4,5,6,6a-tetrahydro-3aH-cyclopenta[d][1,3]oxazole-4,5-diol  ligand  26  14  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ALI
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
 ALI  C1    C  C     0   0.010  -0.3966   0.9938   0.0229
 ALI  C2    C  C     0  -0.186   1.0895   0.8029  -0.3613
 ALI  C3    C  CR15  0   0.043   1.6047  -0.2996   0.5636
 ALI  C4    C  CR15  0   0.040   0.6518  -0.2351   1.7636
 ALI  C5    C  CR15  0  -0.339  -0.7147  -0.0350   1.1097
 ALI  C6    C  CH2   0  -0.132  -1.8358   0.4427   2.0122
 ALI  C7    C  CR5   0   0.602  -0.1605   0.4158  -2.1040
 ALI  C8    C  C2    0  -0.247  -0.1850  -0.8182  -4.0075
 ALI  N2    N  N     0  -0.432   1.0597   0.4276  -1.7635
 ALI  N7    N  N     0  -0.376  -0.6749   0.1512  -3.3591
 ALI  O3    O  OH1   0  -0.672   2.9601  -0.1058   0.8748
 ALI  O4    O  OH1   0  -0.659   0.6786  -1.3814   2.5700
 ALI  O6    O  OH1   0  -0.664  -2.1686  -0.5516   2.9492
 ALI  O7    O  O     0  -0.467  -1.0952   0.7575  -1.2046
 ALI  H1    H  H     0   0.268  -0.6296   2.0088   0.3526
 ALI  H2    H  H     0   0.265   1.6812   1.7115  -0.2191
 ALI  H3    H  HCR5  0   0.214   1.4486  -1.2696   0.0694
 ALI  HA    H  HCR5  0   0.205   0.8971   0.6666   2.3493
 ALI  H5    H  HCR5  0   0.260  -1.0115  -0.9762   0.6297
 ALI  H6C1  H  HCH2  0   0.207  -2.6990   0.7011   1.3834
 ALI  H6C2  H  HCH2  0   0.190  -1.5162   1.3738   2.5029
 ALI  H8C1  H  H     0   0.264  -0.5459  -1.0094  -5.0120
 ALI  H8C2  H  H     0   0.249   0.5808  -1.4849  -3.6122
 ALI  HB    H  HOH1  0   0.456   3.3366  -0.9415   1.1647
 ALI  H4    H  HOH1  0   0.449   1.5072  -1.3911   3.0588
 ALI  H6    H  HOH1  0   0.453  -2.9378  -0.2462   3.4385

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
 ALI  C1  C2    single  1.547  0.020  1.547
 ALI  C1  C5    single  1.530  0.020  1.530
 ALI  C1  O7    single  1.432  0.020  1.432
 ALI  C1  H1    single  0.970  0.020  1.090
 ALI  C2  C3    single  1.529  0.020  1.529
 ALI  C2  N2    single  1.452  0.020  1.452
 ALI  C2  H2    single  0.970  0.020  1.090
 ALI  C3  C4    single  1.534  0.020  1.534
 ALI  C3  O3    single  1.404  0.020  1.404
 ALI  C3  H3    single  0.970  0.020  1.090
 ALI  C4  C5    single  1.528  0.020  1.528
 ALI  C4  O4    single  1.402  0.020  1.402
 ALI  C4  HA    single  0.970  0.020  1.090
 ALI  C5  C6    single  1.516  0.020  1.516
 ALI  C5  H5    single  0.970  0.020  1.090
 ALI  C6  O6    single  1.406  0.020  1.406
 ALI  C6  H6C1  single  0.970  0.020  1.090
 ALI  C6  H6C2  single  0.970  0.020  1.090
 ALI  C7  N2    double  1.267  0.020  1.267
 ALI  C7  N7    single  1.382  0.020  1.382
 ALI  C7  O7    single  1.341  0.020  1.341
 ALI  C8  N7    double  1.265  0.020  1.265
 ALI  C8  H8C1  single  0.930  0.020  1.080
 ALI  C8  H8C2  single  0.930  0.020  1.080
 ALI  O3  HB    single  0.850  0.020  0.980
 ALI  O4  H4    single  0.850  0.020  0.980
 ALI  O6  H6    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
 ALI  H1    C1  O7    107.94  3.000
 ALI  H1    C1  C5    111.47  3.000
 ALI  O7    C1  C5    113.36  3.000
 ALI  H1    C1  C2    113.24  3.000
 ALI  O7    C1  C2    103.62  3.000
 ALI  C5    C1  C2    107.05  3.000
 ALI  H2    C2  N2    110.58  3.000
 ALI  H2    C2  C3    109.77  3.000
 ALI  N2    C2  C3    113.88  3.000
 ALI  H2    C2  C1    112.65  3.000
 ALI  N2    C2  C1    104.60  3.000
 ALI  C3    C2  C1    105.22  3.000
 ALI  H3    C3  O3    111.00  3.000
 ALI  H3    C3  C4    107.49  3.000
 ALI  O3    C3  C4    114.87  3.000
 ALI  H3    C3  C2    108.44  3.000
 ALI  O3    C3  C2    111.09  3.000
 ALI  C4    C3  C2    103.51  3.000
 ALI  HA    C4  O4    111.02  3.000
 ALI  HA    C4  C5    108.61  3.000
 ALI  O4    C4  C5    111.73  3.000
 ALI  HA    C4  C3    108.17  3.000
 ALI  O4    C4  C3    113.82  3.000
 ALI  C5    C4  C3    103.08  3.000
 ALI  H5    C5  C6    109.30  3.000
 ALI  H5    C5  C4    108.47  3.000
 ALI  C6    C5  C4    116.60  3.000
 ALI  H5    C5  C1    108.80  3.000
 ALI  C6    C5  C1    111.38  3.000
 ALI  C4    C5  C1    101.89  3.000
 ALI  H6C2  C6  H6C1  106.53  3.000
 ALI  H6C2  C6  O6    111.72  3.000
 ALI  H6C1  C6  O6    111.21  3.000
 ALI  H6C2  C6  C5    108.50  3.000
 ALI  H6C1  C6  C5    108.32  3.000
 ALI  O6    C6  C5    110.41  3.000
 ALI  O7    C7  N7    113.48  3.000
 ALI  O7    C7  N2    119.25  3.000
 ALI  N7    C7  N2    127.18  3.000
 ALI  H8C2  C8  H8C1  117.52  3.000
 ALI  H8C2  C8  N7    123.72  3.000
 ALI  H8C1  C8  N7    118.75  3.000
 ALI  C7    N2  C2    106.36  3.000
 ALI  C8    N7  C7    117.91  3.000
 ALI  HB    O3  C3    108.96  3.000
 ALI  H4    O4  C4    108.48  3.000
 ALI  H6    O6  C6    107.69  3.000
 ALI  C7    O7  C1    106.07  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
 ALI  CONST_01  O7    C7  N2  C2     0.00   0.0  0
 ALI  CONST_02  N7    C7  N2  C2   180.00   0.0  0
 ALI  Var_01    N2    C7  O7  C1    -3.28  30.0  1
 ALI  Var_02    H8C1  C8  N7  C7  -177.17   0.0  2

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
 ALI  chir_01  C1  C2  C5  O7  positiv
 ALI  chir_02  C2  N2  C1  C3  negativ
 ALI  chir_03  C3  O3  C4  C2  negativ
 ALI  chir_04  C4  O4  C3  C5  negativ
 ALI  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
 ALI  plan-1  C2    0.020
 ALI  plan-1  C7    0.020
 ALI  plan-1  C8    0.020
 ALI  plan-1  N2    0.020
 ALI  plan-1  N7    0.020
 ALI  plan-1  O7    0.020
 ALI  plan-1  H8C1  0.020
 ALI  plan-1  H8C2  0.020

