# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 13:01:26 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: N-[(2Z,3R,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[(phenylcarbamoyl)oxy]imino}tetrahydro-2H-pyran-3-yl]-2-ethylbutanamide (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(CC)C(=O)N[C@@H]/1[C@@H](O)[C@H](O)[C@@H](CO)OC/1=N/OC(=O)Nc2ccccc2
#
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
 8M7  8M7  'N-[(2Z,3R,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[(phenylcarbamoyl)oxy]imino}tetrahydro-2H-pyran-3-yl]-2-ethylbutanamide (non-preferred name)'  ligand  56  29  .  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_8M7
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
 8M7  C1    C  CH2   0  -0.430  -3.3390   3.9238   0.9722
 8M7  C2    C  CH3   0  -0.673  -4.6140   3.9582   0.1408
 8M7  C3    C  CH1   0  -0.394  -2.0392   3.7820   0.1567
 8M7  C4    C  C     0   0.592  -2.0673   2.4695  -0.6082
 8M7  C5    C  CH1   0  -0.201  -1.9843   0.0380  -0.3072
 8M7  C6    C  CH1   0   0.052  -3.1293  -0.6781   0.4046
 8M7  C7    C  CH1   0  -0.020  -3.1768  -2.1296  -0.0518
 8M7  C8    C  CH1   0  -0.025  -1.8419  -2.8013   0.2679
 8M7  C9    C  CH2   0  -0.158  -1.7552  -4.2099  -0.2708
 8M7  C10   C  C     0   0.502  -0.6999  -0.7508  -0.1980
 8M7  C11   C  C     0   0.750   2.6468  -0.3173   0.0887
 8M7  C12   C  CR6   0   0.371   5.0151  -1.0315   0.1276
 8M7  O1    O  O     0  -0.490  -2.3040   2.3969  -1.8041
 8M7  O2    O  OH1   0  -0.651  -4.3033   0.0135   0.0931
 8M7  O3    O  OH1   0  -0.666  -4.2230  -2.7619   0.6431
 8M7  N1    N  NH1   0  -0.630  -1.8351   1.3818   0.1559
 8M7  N2    N  N     0  -0.175   0.3901  -0.1033  -0.1206
 8M7  N3    N  NH1   0  -0.775   3.6384  -1.2351  -0.0048
 8M7  O4    O  OH1   0  -0.665  -0.5458  -4.7860   0.1528
 8M7  O5    O  O2    0  -0.456  -0.7443  -2.0722  -0.3064
 8M7  O6    O  O2    0  -0.406   1.4731  -0.9605  -0.1075
 8M7  O7    O  O     0  -0.466   2.7585   0.8593   0.3112
 8M7  C13   C  CR16  0  -0.316   5.5981   0.1549   0.5740
 8M7  C14   C  CR16  0  -0.245   6.9808   0.2430   0.6742
 8M7  C15   C  CR16  0  -0.273   7.7993  -0.8263   0.3434
 8M7  C16   C  CR16  0  -0.245   7.2148  -2.0080  -0.0939
 8M7  C17   C  CR16  0  -0.342   5.8388  -2.1110  -0.2015
 8M7  C18   C  CH2   0  -0.417  -1.7632   4.9602  -0.7760
 8M7  C19   C  CH3   0  -0.674  -1.6677   6.2939  -0.0469
 8M7  H12   H  HCH2  0   0.239  -3.2667   4.8305   1.5767
 8M7  H11   H  HCH2  0   0.233  -3.4032   3.1017   1.6898
 8M7  H22   H  HCH3  0   0.228  -4.7687   3.0216  -0.3956
 8M7  H21   H  HCH3  0   0.232  -5.4816   4.1105   0.7835
 8M7  H23   H  HCH3  0   0.222  -4.6041   4.7663  -0.5913
 8M7  H31   H  HCH1  0   0.258  -1.2172   3.7271   0.8816
 8M7  H51   H  HCH1  0   0.307  -2.2313   0.0811  -1.3737
 8M7  H61   H  HCH1  0   0.230  -2.9344  -0.6651   1.4896
 8M7  H71   H  HCH1  0   0.243  -3.3456  -2.1530  -1.1380
 8M7  H81   H  HCH1  0   0.257  -1.7074  -2.8184   1.3570
 8M7  H92   H  HCH2  0   0.214  -2.6213  -4.7657   0.1057
 8M7  H91   H  HCH2  0   0.208  -1.8392  -4.1807  -1.3658
 8M7  H25   H  HOH1  0   0.456  -5.0204  -0.3642   0.6127
 8M7  H33   H  HOH1  0   0.467  -4.6212  -3.4315   0.0800
 8M7  H13   H  HNH1  0   0.401  -1.6234   1.5147   1.1328
 8M7  H32   H  HNH1  0   0.419   3.3599  -2.1739  -0.2507
 8M7  H41   H  HOH1  0   0.460  -0.5436  -5.7078  -0.1200
 8M7  H131  H  HCR6  0   0.278   4.9957   1.0064   0.8452
 8M7  H141  H  HCR6  0   0.259   7.4174   1.1701   1.0226
 8M7  H151  H  HCR6  0   0.256   8.8746  -0.7422   0.4258
 8M7  H161  H  HCR6  0   0.260   7.8306  -2.8579  -0.3579
 8M7  H171  H  HCR6  0   0.271   5.3967  -3.0371  -0.5501
 8M7  H182  H  HCH2  0   0.231  -0.8220   4.7762  -1.3003
 8M7  H181  H  HCH2  0   0.224  -2.5308   5.0217  -1.5498
 8M7  H192  H  HCH3  0   0.219  -0.9510   6.2490   0.7755
 8M7  H193  H  HCH3  0   0.233  -1.3403   7.0799  -0.7280
 8M7  H191  H  HCH3  0   0.223  -2.6274   6.6048   0.3673

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
 8M7  C15  C16   aromatic  1.389  0.020  1.389
 8M7  C15  C14   aromatic  1.387  0.020  1.387
 8M7  C16  C17   aromatic  1.384  0.020  1.384
 8M7  C14  C13   aromatic  1.389  0.020  1.389
 8M7  C17  C12   aromatic  1.397  0.020  1.397
 8M7  C13  C12   aromatic  1.395  0.020  1.395
 8M7  C12  N3    single    1.398  0.020  1.398
 8M7  N3   C11   single    1.354  0.020  1.354
 8M7  O7   C11   double    1.203  0.020  1.203
 8M7  C11  O6    single    1.353  0.020  1.353
 8M7  O6   N2    single    1.381  0.020  1.381
 8M7  C1   C2    single    1.523  0.020  1.523
 8M7  C1   C3    single    1.541  0.020  1.541
 8M7  N2   C10   double    1.270  0.020  1.270
 8M7  O1   C4    double    1.221  0.020  1.221
 8M7  C10  O5    single    1.327  0.020  1.327
 8M7  C10  C5    single    1.511  0.020  1.511
 8M7  C3   C18   single    1.528  0.020  1.528
 8M7  C3   C4    single    1.519  0.020  1.519
 8M7  C18  C19   single    1.523  0.020  1.523
 8M7  C4   N1    single    1.349  0.020  1.349
 8M7  O5   C8    single    1.437  0.020  1.437
 8M7  N1   C5    single    1.429  0.020  1.429
 8M7  C5   C6    single    1.527  0.020  1.527
 8M7  O4   C9    single    1.405  0.020  1.405
 8M7  C9   C8    single    1.511  0.020  1.511
 8M7  C8   C7    single    1.528  0.020  1.528
 8M7  C6   C7    single    1.522  0.020  1.522
 8M7  C6   O2    single    1.398  0.020  1.398
 8M7  C7   O3    single    1.406  0.020  1.406
 8M7  C1   H12   single    0.970  0.020  1.090
 8M7  C1   H11   single    0.970  0.020  1.090
 8M7  C2   H22   single    0.970  0.020  1.090
 8M7  C2   H21   single    0.970  0.020  1.090
 8M7  C2   H23   single    0.970  0.020  1.090
 8M7  C3   H31   single    0.970  0.020  1.090
 8M7  C5   H51   single    0.970  0.020  1.090
 8M7  C6   H61   single    0.970  0.020  1.090
 8M7  C7   H71   single    0.970  0.020  1.090
 8M7  C8   H81   single    0.970  0.020  1.090
 8M7  C9   H92   single    0.970  0.020  1.090
 8M7  C9   H91   single    0.970  0.020  1.090
 8M7  O2   H25   single    0.850  0.020  0.980
 8M7  O3   H33   single    0.850  0.020  0.980
 8M7  N1   H13   single    0.860  0.020  1.020
 8M7  N3   H32   single    0.860  0.020  1.020
 8M7  O4   H41   single    0.850  0.020  0.980
 8M7  C13  H131  single    0.930  0.020  1.080
 8M7  C14  H141  single    0.930  0.020  1.080
 8M7  C15  H151  single    0.930  0.020  1.080
 8M7  C16  H161  single    0.930  0.020  1.080
 8M7  C17  H171  single    0.930  0.020  1.080
 8M7  C18  H182  single    0.970  0.020  1.090
 8M7  C18  H181  single    0.970  0.020  1.090
 8M7  C19  H192  single    0.970  0.020  1.090
 8M7  C19  H193  single    0.970  0.020  1.090
 8M7  C19  H191  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
 8M7  H11   C1   H12   105.36  3.000
 8M7  H11   C1   C3    109.13  3.000
 8M7  H12   C1   C3    108.27  3.000
 8M7  H11   C1   C2    109.05  3.000
 8M7  H12   C1   C2    109.81  3.000
 8M7  C3    C1   C2    114.80  3.000
 8M7  H23   C2   H21   107.43  3.000
 8M7  H23   C2   H22   107.91  3.000
 8M7  H21   C2   H22   107.29  3.000
 8M7  H23   C2   C1    112.07  3.000
 8M7  H21   C2   C1    110.34  3.000
 8M7  H22   C2   C1    111.59  3.000
 8M7  H31   C3   C18   107.85  3.000
 8M7  H31   C3   C4    107.65  3.000
 8M7  C18   C3   C4    111.23  3.000
 8M7  H31   C3   C1    106.67  3.000
 8M7  C4    C3   C1    109.29  3.000
 8M7  C18   C3   C1    113.86  3.000
 8M7  N1    C4   O1    122.68  3.000
 8M7  N1    C4   C3    114.08  3.000
 8M7  O1    C4   C3    123.23  3.000
 8M7  H51   C5   N1    107.58  3.000
 8M7  H51   C5   C10   106.41  3.000
 8M7  N1    C5   C10   112.25  3.000
 8M7  H51   C5   C6    107.66  3.000
 8M7  N1    C5   C6    111.61  3.000
 8M7  C10   C5   C6    111.03  3.000
 8M7  H61   C6   O2    111.22  3.000
 8M7  H61   C6   C7    108.17  3.000
 8M7  O2    C6   C7    112.26  3.000
 8M7  H61   C6   C5    108.71  3.000
 8M7  O2    C6   C5    107.10  3.000
 8M7  C7    C6   C5    109.32  3.000
 8M7  H71   C7   O3    111.37  3.000
 8M7  H71   C7   C8    109.36  3.000
 8M7  O3    C7   C8    110.42  3.000
 8M7  H71   C7   C6    108.74  3.000
 8M7  O3    C7   C6    107.68  3.000
 8M7  C8    C7   C6    109.21  3.000
 8M7  H81   C8   O5    108.11  3.000
 8M7  H81   C8   C9    109.41  3.000
 8M7  O5    C8   C9    106.66  3.000
 8M7  H81   C8   C7    108.75  3.000
 8M7  C9    C8   C7    112.67  3.000
 8M7  O5    C8   C7    111.13  3.000
 8M7  H91   C9   H92   107.19  3.000
 8M7  H91   C9   O4    112.16  3.000
 8M7  H92   C9   O4    111.64  3.000
 8M7  H91   C9   C8    109.04  3.000
 8M7  H92   C9   C8    107.76  3.000
 8M7  O4    C9   C8    108.92  3.000
 8M7  O5    C10  N2    122.79  3.000
 8M7  O5    C10  C5    119.05  3.000
 8M7  N2    C10  C5    117.88  3.000
 8M7  O7    C11  O6    124.93  3.000
 8M7  O6    C11  N3    107.64  3.000
 8M7  O7    C11  N3    127.42  3.000
 8M7  C17   C12  C13   119.08  3.000
 8M7  C13   C12  N3    124.45  3.000
 8M7  C17   C12  N3    116.47  3.000
 8M7  H25   O2   C6    108.14  3.000
 8M7  H33   O3   C7    109.38  3.000
 8M7  H13   N1   C5    117.37  3.000
 8M7  H13   N1   C4    118.59  3.000
 8M7  C5    N1   C4    123.81  3.000
 8M7  O6    N2   C10   110.92  3.000
 8M7  H32   N3   C12   115.48  3.000
 8M7  H32   N3   C11   116.42  3.000
 8M7  C12   N3   C11   128.01  3.000
 8M7  H41   O4   C9    108.03  3.000
 8M7  C10   O5   C8    119.88  3.000
 8M7  N2    O6   C11   112.75  3.000
 8M7  H131  C13  C14   119.22  3.000
 8M7  H131  C13  C12   121.25  3.000
 8M7  C14   C13  C12   119.53  3.000
 8M7  H141  C14  C15   119.95  3.000
 8M7  H141  C14  C13   118.62  3.000
 8M7  C15   C14  C13   121.43  3.000
 8M7  H151  C15  C16   120.56  3.000
 8M7  H151  C15  C14   120.57  3.000
 8M7  C16   C15  C14   118.87  3.000
 8M7  H161  C16  C17   119.23  3.000
 8M7  H161  C16  C15   120.36  3.000
 8M7  C17   C16  C15   120.41  3.000
 8M7  H171  C17  C16   119.62  3.000
 8M7  H171  C17  C12   119.70  3.000
 8M7  C16   C17  C12   120.68  3.000
 8M7  H181  C18  H182  105.95  3.000
 8M7  H181  C18  C19   109.51  3.000
 8M7  H182  C18  C19   108.85  3.000
 8M7  H181  C18  C3    110.44  3.000
 8M7  H182  C18  C3    108.58  3.000
 8M7  C19   C18  C3    113.23  3.000
 8M7  H191  C19  H193  107.22  3.000
 8M7  H191  C19  H192  107.66  3.000
 8M7  H193  C19  H192  107.64  3.000
 8M7  H191  C19  C18   112.10  3.000
 8M7  H193  C19  C18   110.55  3.000
 8M7  H192  C19  C18   111.45  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
 8M7  CONST_01  C15   C16  C17  C12     0.00   0.0  0
 8M7  CONST_02  C15   C14  C13  C12     0.00   0.0  0
 8M7  CONST_03  C16   C15  C14  C13     0.00   0.0  0
 8M7  CONST_04  C16   C17  C12  C13     0.00   0.0  0
 8M7  CONST_05  C17   C16  C15  C14     0.00   0.0  0
 8M7  CONST_06  C17   C12  C13  C14     0.00   0.0  0
 8M7  CONST_07  C16   C17  C12  N3    180.00   0.0  0
 8M7  CONST_08  C14   C13  C12  N3    180.00   0.0  0
 8M7  CONST_09  H161  C16  C17  C12   180.00   0.0  0
 8M7  CONST_10  H141  C14  C13  C12   180.00   0.0  0
 8M7  CONST_11  H151  C15  C14  C13   180.00   0.0  0
 8M7  CONST_12  H171  C17  C12  C13   180.00   0.0  0
 8M7  CONST_13  H131  C13  C14  C15   180.00   0.0  0
 8M7  CONST_14  C17   C12  N3   C11   180.00   0.0  0
 8M7  CONST_15  C13   C12  N3   C11     0.00   0.0  0
 8M7  CONST_16  H32   N3   C12  C13   180.00   0.0  0
 8M7  CONST_17  C5    N1   C4   C3    180.00   0.0  0
 8M7  CONST_18  O1    C4   N1   C5      0.00   0.0  0
 8M7  CONST_19  O7    C11  N3   C12     0.00   0.0  0
 8M7  CONST_20  O6    C11  N3   C12   180.00   0.0  0
 8M7  CONST_21  H13   N1   C4   C3      0.00   0.0  0
 8M7  Var_01    N2    C10  O5   C8    148.23  30.0  1
 8M7  Var_02    C19   C18  C3   C1     58.38  30.0  3
 8M7  Var_03    O1    C4   C3   C1    103.11  30.0  3
 8M7  Var_04    C18   C3   C1   C2     63.60  30.0  3
 8M7  Var_05    N3    C11  O6   N2   -176.04  30.0  2
 8M7  Var_06    H22   C2   C1   C3     63.69  30.0  3
 8M7  Var_07    H192  C19  C18  C3     52.79  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
 8M7  chir_01  C5  C10  N1  C6  positiv
 8M7  chir_02  C6  O2   C5  C7  positiv
 8M7  chir_03  C7  O3   C8  C6  positiv
 8M7  chir_04  C8  O5   C7  C9  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
 8M7  plan-1  C12   0.020
 8M7  plan-1  N3    0.020
 8M7  plan-1  C13   0.020
 8M7  plan-1  C14   0.020
 8M7  plan-1  C15   0.020
 8M7  plan-1  C16   0.020
 8M7  plan-1  C17   0.020
 8M7  plan-1  H131  0.020
 8M7  plan-1  H141  0.020
 8M7  plan-1  H151  0.020
 8M7  plan-1  H161  0.020
 8M7  plan-1  H171  0.020
 8M7  plan-2  C11   0.020
 8M7  plan-2  C12   0.020
 8M7  plan-2  N3    0.020
 8M7  plan-2  H32   0.020
 8M7  plan-3  C3    0.020
 8M7  plan-3  C4    0.020
 8M7  plan-3  C5    0.020
 8M7  plan-3  O1    0.020
 8M7  plan-3  N1    0.020
 8M7  plan-3  H13   0.020
 8M7  plan-4  C11   0.020
 8M7  plan-4  N3    0.020
 8M7  plan-4  O6    0.020
 8M7  plan-4  O7    0.020

