# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 15:17:11 2022
#   Inital geometry file: a 101 line input string
#   Ligand name: (5R,7R,8S,9S,10R)-7-(hydroxymethyl)-3-(4-methoxyphenyl)-1,6-dioxa-2-azaspiro[4.5]dec-2-ene-8,9,10-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)C2=NO[C@@]3(C2)O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O
#
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
 M07  M07  (5R,7R,8S,9S,10R)-7-(hydroxymethyl)-3-(4-methoxyphenyl)-1,6-dioxa-2-azaspiro[4.5]dec-2-ene-8,9,10-triol  ligand  42  23  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M07
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
 M07  C15   C  CH3   0  -0.440   7.2838  -0.9225   0.7069
 M07  O8    O  O2    0  -0.465   6.4130  -0.8658  -0.4077
 M07  C12   C  CR6   0   0.385   5.1204  -0.5721  -0.2033
 M07  C11   C  CR16  0  -0.365   4.5547  -0.3392   1.0523
 M07  C10   C  CR16  0  -0.268   3.2079  -0.0386   1.1565
 M07  C13   C  CR16  0  -0.326   4.3122  -0.5011  -1.3393
 M07  C14   C  CR16  0  -0.302   2.9697  -0.2010  -1.2199
 M07  C9    C  CR6   0   0.036   2.3906   0.0371   0.0288
 M07  C8    C  CR5   0   0.212   0.9711   0.3574   0.1290
 M07  C7    C  CH2   0  -0.610   0.0405   0.4848  -1.0326
 M07  N1    N  N     0  -0.132   0.3994   0.5765   1.2466
 M07  O7    O  O     0  -0.424  -0.9292   0.8698   1.0417
 M07  C1    C  CR5   0   0.499  -1.2946   0.5964  -0.3100
 M07  O5    O  O2    0  -0.498  -1.9340  -0.6346  -0.3971
 M07  C5    C  CH1   0  -0.028  -3.1748  -0.7582   0.2871
 M07  C6    C  CH2   0  -0.160  -3.6712  -2.1668   0.0470
 M07  O6    O  OH1   0  -0.668  -2.7656  -3.0775   0.6197
 M07  C4    C  CH1   0  -0.006  -4.1604   0.2902  -0.2363
 M07  O4    O  OH1   0  -0.671  -5.3637   0.2842   0.4988
 M07  C3    C  CH1   0   0.002  -3.5490   1.6782  -0.0975
 M07  O3    O  OH1   0  -0.672  -4.3590   2.6675  -0.6828
 M07  C2    C  CH1   0   0.002  -2.2004   1.7227  -0.8042
 M07  O2    O  OH1   0  -0.664  -1.5287   2.9353  -0.6037
 M07  H151  H  HCH3  0   0.232   6.9977  -1.7101   1.4086
 M07  H152  H  HCH3  0   0.263   8.2721  -1.1453   0.3138
 M07  H153  H  HCH3  0   0.232   7.3234   0.0304   1.2402
 M07  H11   H  HCR6  0   0.285   5.1479  -0.3884   1.9551
 M07  H10   H  HCR6  0   0.262   2.7907   0.1397   2.1389
 M07  H13   H  HCR6  0   0.269   4.7445  -0.6833  -2.3149
 M07  H14   H  HCR6  0   0.264   2.3684  -0.1521  -2.1189
 M07  H71   H  HCH2  0   0.304   0.2776   1.3708  -1.6259
 M07  H72   H  HCH2  0   0.296   0.0644  -0.3773  -1.6995
 M07  H5    H  HCH1  0   0.233  -3.0353  -0.6078   1.3666
 M07  H61   H  HCH2  0   0.203  -4.6692  -2.2598   0.4914
 M07  H62   H  HCH2  0   0.200  -3.7842  -2.3244  -1.0348
 M07  HO6   H  HOH1  0   0.457  -3.1127  -3.9642   0.4888
 M07  H4    H  HCH1  0   0.228  -4.3479   0.0961  -1.3026
 M07  HO4   H  HOH1  0   0.462  -5.9874  -0.3137   0.0782
 M07  H3    H  HCH1  0   0.220  -3.3977   1.8815   0.9741
 M07  HO3   H  HOH1  0   0.454  -5.1982   2.6838  -0.2112
 M07  H2    H  HCH1  0   0.239  -2.3736   1.5362  -1.8752
 M07  HO2   H  HOH1  0   0.459  -1.9853   3.6191  -1.1032

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
 M07  O3   C3    single    1.406  0.020  1.406
 M07  O4   C4    single    1.410  0.020  1.410
 M07  C3   C4    single    1.523  0.020  1.523
 M07  C3   C2    single    1.523  0.020  1.523
 M07  C4   C5    single    1.531  0.020  1.531
 M07  O2   C2    single    1.401  0.020  1.401
 M07  C2   C1    single    1.527  0.020  1.527
 M07  O6   C6    single    1.406  0.020  1.406
 M07  C5   C6    single    1.513  0.020  1.513
 M07  C5   O5    single    1.422  0.020  1.422
 M07  C1   O5    single    1.390  0.020  1.390
 M07  C1   O7    single    1.427  0.020  1.427
 M07  C1   C7    single    1.522  0.020  1.522
 M07  O7   N1    single    1.376  0.020  1.376
 M07  C7   C8    single    1.494  0.020  1.494
 M07  N1   C8    double    1.274  0.020  1.274
 M07  C8   C9    single    1.459  0.020  1.459
 M07  C10  C9    aromatic  1.395  0.020  1.395
 M07  C10  C11   aromatic  1.384  0.020  1.384
 M07  C9   C14   aromatic  1.397  0.020  1.397
 M07  C11  C12   aromatic  1.397  0.020  1.397
 M07  C14  C13   aromatic  1.381  0.020  1.381
 M07  C12  C13   aromatic  1.396  0.020  1.396
 M07  C12  O8    single    1.341  0.020  1.341
 M07  O8   C15   single    1.416  0.020  1.416
 M07  C15  H151  single    0.970  0.020  1.090
 M07  C15  H152  single    0.970  0.020  1.090
 M07  C15  H153  single    0.970  0.020  1.090
 M07  C11  H11   single    0.930  0.020  1.080
 M07  C10  H10   single    0.930  0.020  1.080
 M07  C13  H13   single    0.930  0.020  1.080
 M07  C14  H14   single    0.930  0.020  1.080
 M07  C7   H71   single    0.970  0.020  1.090
 M07  C7   H72   single    0.970  0.020  1.090
 M07  C5   H5    single    0.970  0.020  1.090
 M07  C6   H61   single    0.970  0.020  1.090
 M07  C6   H62   single    0.970  0.020  1.090
 M07  O6   HO6   single    0.850  0.020  0.980
 M07  C4   H4    single    0.970  0.020  1.090
 M07  O4   HO4   single    0.850  0.020  0.980
 M07  C3   H3    single    0.970  0.020  1.090
 M07  O3   HO3   single    0.850  0.020  0.980
 M07  C2   H2    single    0.970  0.020  1.090
 M07  O2   HO2   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
 M07  H153  C15  H152  108.81  3.000
 M07  H153  C15  H151  108.94  3.000
 M07  H152  C15  H151  108.82  3.000
 M07  H153  C15  O8    111.82  3.000
 M07  H152  C15  O8    106.43  3.000
 M07  H151  C15  O8    111.93  3.000
 M07  C12   O8   C15   118.79  3.000
 M07  C13   C12  C11   119.25  3.000
 M07  C13   C12  O8    116.43  3.000
 M07  C11   C12  O8    124.33  3.000
 M07  H11   C11  C10   118.74  3.000
 M07  H11   C11  C12   121.38  3.000
 M07  C10   C11  C12   119.88  3.000
 M07  H10   C10  C9    119.94  3.000
 M07  H10   C10  C11   118.65  3.000
 M07  C9    C10  C11   121.41  3.000
 M07  H13   C13  C14   120.18  3.000
 M07  H13   C13  C12   119.58  3.000
 M07  C14   C13  C12   120.24  3.000
 M07  H14   C14  C9    120.29  3.000
 M07  H14   C14  C13   118.56  3.000
 M07  C9    C14  C13   121.16  3.000
 M07  C8    C9   C14   120.15  3.000
 M07  C14   C9   C10   118.07  3.000
 M07  C8    C9   C10   121.77  3.000
 M07  N1    C8   C7    112.82  3.000
 M07  N1    C8   C9    122.32  3.000
 M07  C7    C8   C9    124.86  3.000
 M07  H72   C7   H71   107.72  3.000
 M07  H72   C7   C1    111.57  3.000
 M07  H71   C7   C1    112.87  3.000
 M07  H72   C7   C8    113.24  3.000
 M07  H71   C7   C8    110.87  3.000
 M07  C1    C7   C8    100.57  3.000
 M07  O7    N1   C8    109.83  3.000
 M07  C1    O7   N1    110.34  3.000
 M07  C2    C1   O5    111.09  3.000
 M07  O5    C1   O7    110.30  3.000
 M07  C2    C1   O7    108.49  3.000
 M07  O7    C1   C7    103.84  3.000
 M07  O5    C1   C7    107.99  3.000
 M07  C2    C1   C7    114.87  3.000
 M07  C5    O5   C1    116.62  3.000
 M07  H5    C5   C4    108.89  3.000
 M07  H5    C5   C6    108.96  3.000
 M07  C4    C5   C6    111.85  3.000
 M07  H5    C5   O5    110.48  3.000
 M07  C6    C5   O5    106.91  3.000
 M07  C4    C5   O5    109.73  3.000
 M07  H62   C6   H61   107.05  3.000
 M07  H62   C6   O6    111.97  3.000
 M07  H61   C6   O6    111.48  3.000
 M07  H62   C6   C5    108.88  3.000
 M07  H61   C6   C5    108.26  3.000
 M07  O6    C6   C5    109.10  3.000
 M07  HO6   O6   C6    108.02  3.000
 M07  H4    C4   C3    108.52  3.000
 M07  H4    C4   O4    111.05  3.000
 M07  C3    C4   O4    107.40  3.000
 M07  H4    C4   C5    108.68  3.000
 M07  C3    C4   C5    109.54  3.000
 M07  O4    C4   C5    111.60  3.000
 M07  HO4   O4   C4    109.17  3.000
 M07  H3    C3   C2    108.93  3.000
 M07  H3    C3   O3    110.75  3.000
 M07  C2    C3   O3    107.24  3.000
 M07  H3    C3   C4    108.18  3.000
 M07  C2    C3   C4    109.86  3.000
 M07  O3    C3   C4    111.84  3.000
 M07  HO3   O3   C3    108.07  3.000
 M07  H2    C2   O2    111.18  3.000
 M07  H2    C2   C3    107.88  3.000
 M07  O2    C2   C3    112.55  3.000
 M07  H2    C2   C1    106.45  3.000
 M07  O2    C2   C1    107.92  3.000
 M07  C3    C2   C1    110.70  3.000
 M07  HO2   O2   C2    108.27  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
 M07  CONST_01  C9    C10  C11  C12    0.00   0.0  0
 M07  CONST_02  C9    C14  C13  C12    0.00   0.0  0
 M07  CONST_03  C14   C9   C10  C11    0.00   0.0  0
 M07  CONST_04  C14   C13  C12  C11    0.00   0.0  0
 M07  CONST_05  C13   C14  C9   C10    0.00   0.0  0
 M07  CONST_06  C13   C12  C11  C10    0.00   0.0  0
 M07  CONST_07  C8    C9   C10  C11  180.00   0.0  0
 M07  CONST_08  C8    C9   C14  C13  180.00   0.0  0
 M07  CONST_09  C10   C11  C12  O8   180.00   0.0  0
 M07  CONST_10  C14   C13  C12  O8   180.00   0.0  0
 M07  CONST_11  H10   C10  C11  C12  180.00   0.0  0
 M07  CONST_12  H14   C14  C13  C12  180.00   0.0  0
 M07  CONST_13  H13   C13  C12  C11  180.00   0.0  0
 M07  CONST_14  H11   C11  C12  C13  180.00   0.0  0
 M07  Var_01    C7    C8   C9   C10  178.64  30.0  3
 M07  Var_02    C1    C7   C8   C9   171.31  30.0  1
 M07  Var_03    C11   C12  O8   C15   -1.31  30.0  2
 M07  Var_04    H151  C15  O8   C12   62.76  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
 M07  chir_01  C1  O5  O7  C7  negativ
 M07  chir_02  C5  O5  C6  C4  positiv
 M07  chir_03  C4  O4  C5  C3  positiv
 M07  chir_04  C3  O3  C4  C2  negativ
 M07  chir_05  C2  O2  C3  C1  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
 M07  plan-1  O8   0.020
 M07  plan-1  C12  0.020
 M07  plan-1  C11  0.020
 M07  plan-1  C10  0.020
 M07  plan-1  C13  0.020
 M07  plan-1  C14  0.020
 M07  plan-1  C9   0.020
 M07  plan-1  C8   0.020
 M07  plan-1  H11  0.020
 M07  plan-1  H10  0.020
 M07  plan-1  H13  0.020
 M07  plan-1  H14  0.020

