# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 03:37:14 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: (3Z,5S,6R,7S,8S,8aR)-3-(octylimino)hexahydro[1,3]oxazolo[3,4-a]pyridine-5,6,7,8-tetrol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCN=C1OC[C@@H]2[C@H](O)[C@H](O)[C@@H](O)[C@H](O)N12
#
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
 AM3  AM3  (3Z,5S,6R,7S,8S,8aR)-3-(octylimino)hexahydro[1,3]oxazolo[3,4-a]pyridine-5,6,7,8-tetrol  ligand  50  22  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AM3
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
 AM3  O4    O  OH1   0  -0.664  -3.4152   0.1361   2.4797
 AM3  C4    C  CH1   0   0.013  -4.0024   0.8237   1.4083
 AM3  C5    C  CR15  0  -0.159  -2.9214   1.2977   0.4601
 AM3  C6    C  CH2   0  -0.163  -1.7181   2.0251   1.0410
 AM3  O6    O  O     0  -0.483  -0.6528   1.6657   0.1471
 AM3  C3    C  CH1   0   0.007  -4.9472  -0.0646   0.5949
 AM3  O3    O  OH1   0  -0.673  -5.9494  -0.5246   1.4662
 AM3  C2    C  CH1   0  -0.000  -4.1992  -1.2309  -0.0522
 AM3  O2    O  OH1   0  -0.673  -5.1405  -1.9613  -0.8016
 AM3  C1    C  CH1   0   0.200  -3.0438  -0.7564  -0.9352
 AM3  O1    O  OH1   0  -0.685  -2.2969  -1.8648  -1.3113
 AM3  N1    N  NR5   0  -0.562  -2.2493   0.1700  -0.1506
 AM3  C7    C  CR5   0   0.779  -1.0001   0.5639  -0.5384
 AM3  N2    N  N     0  -0.561  -0.2963  -0.0292  -1.4099
 AM3  C8    C  CH2   0  -0.303   1.0531   0.4215  -1.6791
 AM3  C9    C  CH2   0  -0.430   2.0719  -0.1700  -0.7090
 AM3  C10   C  CH2   0  -0.418   3.5022   0.2361  -1.0422
 AM3  C11   C  CH2   0  -0.410   4.5206  -0.3129  -0.0510
 AM3  C12   C  CH2   0  -0.411   5.9544   0.0924  -0.3706
 AM3  C13   C  CH2   0  -0.406   6.9659  -0.4392   0.6370
 AM3  C14   C  CH2   0  -0.418   8.4018  -0.0348   0.3252
 AM3  C15   C  CH3   0  -0.662   9.4016  -0.5745   1.3386
 AM3  H4    H  HOH1  0   0.456  -4.1209  -0.1977   3.0437
 AM3  HA    H  HCH1  0   0.246  -4.5657   1.7020   1.7542
 AM3  H5    H  HCR5  0   0.273  -3.4057   1.9276  -0.3019
 AM3  H3    H  HCH1  0   0.215  -5.3787   0.5590  -0.2042
 AM3  H61C  H  HCH2  0   0.258  -1.8273   3.1069   1.0371
 AM3  H62C  H  HCH2  0   0.252  -1.4728   1.6858   2.0481
 AM3  HB    H  HOH1  0   0.454  -6.4917  -1.1667   0.9950
 AM3  H2    H  HCH1  0   0.224  -3.7616  -1.8459   0.7452
 AM3  HC    H  HOH1  0   0.460  -4.7975  -2.8472  -0.9523
 AM3  H81C  H  HCH2  0   0.221   1.3088   0.1053  -2.6935
 AM3  H82C  H  HCH2  0   0.208   1.1406   1.5144  -1.6689
 AM3  H91C  H  HCH2  0   0.215   1.8308   0.1517   0.3089
 AM3  H92C  H  HCH2  0   0.215   1.9843  -1.2608  -0.7190
 AM3  H101  H  HCH2  0   0.210   3.7544  -0.1071  -2.0514
 AM3  H102  H  HCH2  0   0.209   3.5748   1.3292  -1.0661
 AM3  H111  H  HCH2  0   0.207   4.2639   0.0316   0.9567
 AM3  H112  H  HCH2  0   0.207   4.4490  -1.4058  -0.0245
 AM3  H121  H  HCH2  0   0.206   6.2184  -0.2635  -1.3726
 AM3  H122  H  HCH2  0   0.206   6.0224   1.1854  -0.4100
 AM3  H131  H  HCH2  0   0.205   6.7001  -0.0835   1.6387
 AM3  H132  H  HCH2  0   0.205   6.8982  -1.5323   0.6772
 AM3  H141  H  HCH2  0   0.210   8.6681  -0.3886  -0.6755
 AM3  H142  H  HCH2  0   0.209   8.4705   1.0570   0.2881
 AM3  H151  H  HCH3  0   0.215   9.1763  -0.2157   2.3447
 AM3  H152  H  HCH3  0   0.215   9.3820  -1.6656   1.3679
 AM3  H153  H  HCH3  0   0.226  10.4209  -0.2687   1.1001
 AM3  H154  H  HOH1  0   0.453  -1.4537  -1.5179  -1.6701
 AM3  H155  H  HCH1  0   0.200  -3.4483  -0.2252  -1.8168

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
 AM3  O1   H154  single  0.850  0.020  0.980
 AM3  C1   H155  single  0.970  0.020  1.090
 AM3  O4   C4    single  1.402  0.020  1.402
 AM3  C4   C5    single  1.514  0.020  1.514
 AM3  C5   C6    single  1.521  0.020  1.521
 AM3  C6   O6    single  1.436  0.020  1.436
 AM3  C4   C3    single  1.531  0.020  1.531
 AM3  C3   O3    single  1.405  0.020  1.405
 AM3  C3   C2    single  1.529  0.020  1.529
 AM3  C2   O2    single  1.408  0.020  1.408
 AM3  C2   C1    single  1.530  0.020  1.530
 AM3  C1   O1    single  1.388  0.020  1.388
 AM3  C5   N1    single  1.448  0.020  1.448
 AM3  C1   N1    single  1.451  0.020  1.451
 AM3  O6   C7    single  1.343  0.020  1.343
 AM3  N1   C7    single  1.366  0.020  1.366
 AM3  C7   N2    double  1.268  0.020  1.268
 AM3  N2   C8    single  1.448  0.020  1.448
 AM3  C8   C9    single  1.526  0.020  1.526
 AM3  C9   C10   single  1.524  0.020  1.524
 AM3  C10  C11   single  1.524  0.020  1.524
 AM3  C11  C12   single  1.524  0.020  1.524
 AM3  C12  C13   single  1.523  0.020  1.523
 AM3  C13  C14   single  1.524  0.020  1.524
 AM3  C14  C15   single  1.522  0.020  1.522
 AM3  O4   H4    single  0.850  0.020  0.980
 AM3  C4   HA    single  0.970  0.020  1.090
 AM3  C5   H5    single  0.970  0.020  1.090
 AM3  C3   H3    single  0.970  0.020  1.090
 AM3  C6   H61C  single  0.970  0.020  1.090
 AM3  C6   H62C  single  0.970  0.020  1.090
 AM3  O3   HB    single  0.850  0.020  0.980
 AM3  C2   H2    single  0.970  0.020  1.090
 AM3  O2   HC    single  0.850  0.020  0.980
 AM3  C8   H81C  single  0.970  0.020  1.090
 AM3  C8   H82C  single  0.970  0.020  1.090
 AM3  C9   H91C  single  0.970  0.020  1.090
 AM3  C9   H92C  single  0.970  0.020  1.090
 AM3  C10  H101  single  0.970  0.020  1.090
 AM3  C10  H102  single  0.970  0.020  1.090
 AM3  C11  H111  single  0.970  0.020  1.090
 AM3  C11  H112  single  0.970  0.020  1.090
 AM3  C12  H121  single  0.970  0.020  1.090
 AM3  C12  H122  single  0.970  0.020  1.090
 AM3  C13  H131  single  0.970  0.020  1.090
 AM3  C13  H132  single  0.970  0.020  1.090
 AM3  C14  H141  single  0.970  0.020  1.090
 AM3  C14  H142  single  0.970  0.020  1.090
 AM3  C15  H151  single  0.970  0.020  1.090
 AM3  C15  H152  single  0.970  0.020  1.090
 AM3  C15  H153  single  0.970  0.020  1.090

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
 AM3  H4    O4   C4    108.10  3.000
 AM3  HA    C4   C3    108.34  3.000
 AM3  HA    C4   C5    108.23  3.000
 AM3  C3    C4   C5    106.83  3.000
 AM3  HA    C4   O4    111.47  3.000
 AM3  C3    C4   O4    112.33  3.000
 AM3  C5    C4   O4    109.46  3.000
 AM3  H5    C5   N1    110.97  3.000
 AM3  H5    C5   C6    109.80  3.000
 AM3  N1    C5   C6     99.57  3.000
 AM3  H5    C5   C4    107.37  3.000
 AM3  N1    C5   C4    110.59  3.000
 AM3  C6    C5   C4    118.38  3.000
 AM3  H62C  C6   H61C  109.60  3.000
 AM3  H62C  C6   O6    109.27  3.000
 AM3  H61C  C6   O6    108.74  3.000
 AM3  H62C  C6   C5    112.44  3.000
 AM3  H61C  C6   C5    113.26  3.000
 AM3  O6    C6   C5    103.26  3.000
 AM3  C7    O6   C6    109.34  3.000
 AM3  H3    C3   C2    108.44  3.000
 AM3  H3    C3   O3    110.83  3.000
 AM3  C2    C3   O3    111.20  3.000
 AM3  H3    C3   C4    107.38  3.000
 AM3  C2    C3   C4    111.44  3.000
 AM3  O3    C3   C4    107.50  3.000
 AM3  HB    O3   C3    108.44  3.000
 AM3  H2    C2   C1    106.98  3.000
 AM3  H2    C2   O2    111.25  3.000
 AM3  C1    C2   O2    111.02  3.000
 AM3  H2    C2   C3    108.35  3.000
 AM3  C1    C2   C3    112.16  3.000
 AM3  O2    C2   C3    107.10  3.000
 AM3  HC    O2   C2    108.83  3.000
 AM3  H155  C1   N1    108.95  3.000
 AM3  N1    C1   O1    111.20  3.000
 AM3  H155  C1   O1    111.36  3.000
 AM3  N1    C1   C2    107.43  3.000
 AM3  O1    C1   C2    108.36  3.000
 AM3  H155  C1   C2    109.44  3.000
 AM3  H154  O1   C1    106.23  3.000
 AM3  C7    N1   C1    122.10  3.000
 AM3  C7    N1   C5    108.64  3.000
 AM3  C1    N1   C5    118.11  3.000
 AM3  N2    C7   N1    124.62  3.000
 AM3  N2    C7   O6    126.23  3.000
 AM3  N1    C7   O6    109.15  3.000
 AM3  C8    N2   C7    119.98  3.000
 AM3  H82C  C8   H81C  106.16  3.000
 AM3  H82C  C8   C9    109.09  3.000
 AM3  H81C  C8   C9    108.77  3.000
 AM3  H82C  C8   N2    112.51  3.000
 AM3  H81C  C8   N2    107.50  3.000
 AM3  C9    C8   N2    112.54  3.000
 AM3  H92C  C9   H91C  106.49  3.000
 AM3  H92C  C9   C10   109.80  3.000
 AM3  H91C  C9   C10   109.38  3.000
 AM3  H92C  C9   C8    109.09  3.000
 AM3  H91C  C9   C8    109.28  3.000
 AM3  C10   C9   C8    112.61  3.000
 AM3  H102  C10  H101  106.09  3.000
 AM3  H102  C10  C11   109.22  3.000
 AM3  H101  C10  C11   109.43  3.000
 AM3  H102  C10  C9    109.44  3.000
 AM3  H101  C10  C9    109.52  3.000
 AM3  C11   C10  C9    112.91  3.000
 AM3  H112  C11  H111  106.03  3.000
 AM3  H112  C11  C12   109.38  3.000
 AM3  H111  C11  C12   109.26  3.000
 AM3  H112  C11  C10   109.35  3.000
 AM3  H111  C11  C10   109.18  3.000
 AM3  C12   C11  C10   113.37  3.000
 AM3  H122  C12  H121  106.04  3.000
 AM3  H122  C12  C13   109.31  3.000
 AM3  H121  C12  C13   109.36  3.000
 AM3  H122  C12  C11   109.34  3.000
 AM3  H121  C12  C11   109.40  3.000
 AM3  C13   C12  C11   113.15  3.000
 AM3  H132  C13  H131  105.98  3.000
 AM3  H132  C13  C14   109.29  3.000
 AM3  H131  C13  C14   109.24  3.000
 AM3  H132  C13  C12   109.34  3.000
 AM3  H131  C13  C12   109.29  3.000
 AM3  C14   C13  C12   113.43  3.000
 AM3  H142  C14  H141  106.04  3.000
 AM3  H142  C14  C15   109.57  3.000
 AM3  H141  C14  C15   109.53  3.000
 AM3  H142  C14  C13   109.31  3.000
 AM3  H141  C14  C13   109.30  3.000
 AM3  C15   C14  C13   112.86  3.000
 AM3  H153  C15  H152  107.63  3.000
 AM3  H153  C15  H151  107.59  3.000
 AM3  H152  C15  H151  107.46  3.000
 AM3  H153  C15  C14   111.64  3.000
 AM3  H152  C15  C14   111.13  3.000
 AM3  H151  C15  C14   111.19  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
 AM3  CONST_05  C8    N2   C7   O6      0.00   0.0  0
 AM3  CONST_06  C8    N2   C7   N1    180.00   0.0  0
 AM3  Var_01    N1    C7   O6   C6      0.22  30.0  1
 AM3  Var_02    H61C  C6   O6   C7   -139.74  30.0  1
 AM3  Var_03    C9    C8   N2   C7     84.50  30.0  3
 AM3  Var_04    C10   C9   C8   N2    176.54  30.0  3
 AM3  Var_05    C11   C10  C9   C8    178.09  30.0  3
 AM3  Var_06    C12   C11  C10  C9   -179.73  30.0  3
 AM3  Var_07    C13   C12  C11  C10   179.01  30.0  3
 AM3  Var_08    C14   C13  C12  C11  -179.86  30.0  3
 AM3  Var_09    C15   C14  C13  C12  -179.91  30.0  3
 AM3  Var_10    H151  C15  C14  C13   -59.49  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
 AM3  chir_01  C4  O4  C5  C3  negativ
 AM3  chir_02  C5  N1  C6  C4  positiv
 AM3  chir_03  C3  O3  C4  C2  negativ
 AM3  chir_04  C2  O2  C3  C1  positiv
 AM3  chir_05  C1  O1  N1  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
 AM3  plan-1  C5  0.020
 AM3  plan-1  O6  0.020
 AM3  plan-1  C1  0.020
 AM3  plan-1  N1  0.020
 AM3  plan-1  C7  0.020
 AM3  plan-1  N2  0.020
 AM3  plan-1  C8  0.020

