# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 19:03:22 2020
#   Inital geometry file: a 123 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]butanamide (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC(=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
 NP6  NP6  'N-[(2Z,3R,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[(phenylcarbamoyl)oxy]imino}tetrahydro-2H-pyran-3-yl]butanamide (non-preferred name)'  ligand  50  27  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NP6
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
 NP6  C2    C  CH3   0  -0.664   0.2484   6.5796  -0.2376
 NP6  C1    C  CH2   0  -0.422   0.5752   5.3154   0.5444
 NP6  C3    C  CH2   0  -0.579   1.4291   4.3562  -0.2734
 NP6  C4    C  C     0   0.571   1.8130   3.0996   0.4754
 NP6  O1    O  O     0  -0.492   1.9723   3.0759   1.6860
 NP6  N1    N  NH1   0  -0.636   1.9992   2.0174  -0.3082
 NP6  C5    C  CH1   0  -0.198   2.3805   0.7321   0.1890
 NP6  C6    C  CH1   0   0.049   3.5812   0.1655  -0.5627
 NP6  O2    O  OH1   0  -0.658   4.6525   1.0381  -0.3517
 NP6  C7    C  CH1   0  -0.023   3.8787  -1.2375  -0.0487
 NP6  O3    O  OH1   0  -0.665   4.9678  -1.7357  -0.7856
 NP6  C8    C  CH1   0  -0.024   2.6515  -2.1255  -0.2484
 NP6  C9    C  CH2   0  -0.157   2.8200  -3.4911   0.3757
 NP6  O4    O  OH1   0  -0.665   1.6962  -4.2757   0.0677
 NP6  O5    O  O2    0  -0.456   1.4838  -1.5406   0.3505
 NP6  C10   C  C     0   0.500   1.2299  -0.2504   0.1737
 NP6  N2    N  N     0  -0.171   0.0509   0.2158   0.1023
 NP6  O6    O  O2    0  -0.406  -0.8845  -0.7979   0.1703
 NP6  C11   C  C     0   0.749  -2.1457  -0.3662  -0.0587
 NP6  O7    O  O     0  -0.464  -2.4445   0.7586  -0.3618
 NP6  N3    N  NH1   0  -0.775  -2.9765  -1.4227   0.1094
 NP6  C12   C  CR6   0   0.371  -4.3670  -1.4568  -0.0304
 NP6  C13   C  CR16  0  -0.316  -5.1357  -0.4103  -0.5406
 NP6  C14   C  CR16  0  -0.245  -6.5132  -0.5584  -0.6430
 NP6  C15   C  CR16  0  -0.273  -7.1453  -1.7291  -0.2524
 NP6  C16   C  CR16  0  -0.245  -6.3760  -2.7707   0.2501
 NP6  C17   C  CR16  0  -0.342  -5.0029  -2.6378   0.3613
 NP6  H21C  H  HCH3  0   0.220  -0.3060   6.3505  -1.1494
 NP6  H22C  H  HCH3  0   0.232  -0.3578   7.2649   0.3550
 NP6  H23C  H  HCH3  0   0.220   1.1574   7.1085  -0.5308
 NP6  H11C  H  HCH2  0   0.227   1.0970   5.5768   1.4664
 NP6  H12C  H  HCH2  0   0.226  -0.3513   4.8186   0.8432
 NP6  H31C  H  HCH2  0   0.251   0.9171   4.0986  -1.2044
 NP6  H32C  H  HCH2  0   0.271   2.3590   4.8537  -0.5714
 NP6  H1    H  HNH1  0   0.403   1.7879   2.0937  -1.2908
 NP6  H5    H  HCH1  0   0.308   2.6731   0.8525   1.2380
 NP6  H6    H  HCH1  0   0.231   3.3302   0.0920  -1.6341
 NP6  H2    H  HOH1  0   0.456   5.4112   0.7030  -0.8417
 NP6  H7    H  HCH1  0   0.245   4.1144  -1.1767   1.0231
 NP6  H3    H  HOH1  0   0.467   5.5020  -2.3040  -0.2236
 NP6  H8    H  HCH1  0   0.257   2.4656  -2.2348  -1.3243
 NP6  H91C  H  HCH2  0   0.211   3.7416  -3.9308  -0.0222
 NP6  H92C  H  HCH2  0   0.209   2.9593  -3.3730   1.4592
 NP6  H4    H  HOH1  0   0.460   1.8473  -5.1598   0.4139
 NP6  HA    H  HNH1  0   0.419  -2.5493  -2.2867   0.4103
 NP6  H13   H  HCR6  0   0.278  -4.6807   0.5122  -0.8612
 NP6  H17   H  HCR6  0   0.271  -4.4164  -3.4581   0.7586
 NP6  H14   H  HCR6  0   0.259  -7.0946   0.2639  -1.0399
 NP6  H15   H  HCR6  0   0.255  -8.2188  -1.8303  -0.3385
 NP6  H16   H  HCR6  0   0.261  -6.8438  -3.6951   0.5626

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
 NP6  C2   C1    single    1.522  0.020  1.522
 NP6  C1   C3    single    1.522  0.020  1.522
 NP6  C3   C4    single    1.512  0.020  1.512
 NP6  C4   O1    double    1.221  0.020  1.221
 NP6  C4   N1    single    1.349  0.020  1.349
 NP6  N1   C5    single    1.430  0.020  1.430
 NP6  C5   C6    single    1.526  0.020  1.526
 NP6  C5   C10   single    1.513  0.020  1.513
 NP6  C6   O2    single    1.398  0.020  1.398
 NP6  C6   C7    single    1.524  0.020  1.524
 NP6  C7   O3    single    1.406  0.020  1.406
 NP6  C7   C8    single    1.528  0.020  1.528
 NP6  C8   C9    single    1.511  0.020  1.511
 NP6  C8   O5    single    1.437  0.020  1.437
 NP6  C9   O4    single    1.405  0.020  1.405
 NP6  O5   C10   single    1.327  0.020  1.327
 NP6  C10  N2    double    1.270  0.020  1.270
 NP6  N2   O6    single    1.381  0.020  1.381
 NP6  O6   C11   single    1.353  0.020  1.353
 NP6  C11  O7    double    1.203  0.020  1.203
 NP6  C11  N3    single    1.355  0.020  1.355
 NP6  N3   C12   single    1.398  0.020  1.398
 NP6  C12  C13   aromatic  1.395  0.020  1.395
 NP6  C12  C17   aromatic  1.397  0.020  1.397
 NP6  C13  C14   aromatic  1.389  0.020  1.389
 NP6  C14  C15   aromatic  1.387  0.020  1.387
 NP6  C15  C16   aromatic  1.389  0.020  1.389
 NP6  C16  C17   aromatic  1.384  0.020  1.384
 NP6  C2   H21C  single    0.970  0.020  1.090
 NP6  C2   H22C  single    0.970  0.020  1.090
 NP6  C2   H23C  single    0.970  0.020  1.090
 NP6  C1   H11C  single    0.970  0.020  1.090
 NP6  C1   H12C  single    0.970  0.020  1.090
 NP6  C3   H31C  single    0.970  0.020  1.090
 NP6  C3   H32C  single    0.970  0.020  1.090
 NP6  N1   H1    single    0.860  0.020  1.020
 NP6  C5   H5    single    0.970  0.020  1.090
 NP6  C6   H6    single    0.970  0.020  1.090
 NP6  O2   H2    single    0.850  0.020  0.980
 NP6  C7   H7    single    0.970  0.020  1.090
 NP6  O3   H3    single    0.850  0.020  0.980
 NP6  C8   H8    single    0.970  0.020  1.090
 NP6  C9   H91C  single    0.970  0.020  1.090
 NP6  C9   H92C  single    0.970  0.020  1.090
 NP6  O4   H4    single    0.850  0.020  0.980
 NP6  N3   HA    single    0.860  0.020  1.020
 NP6  C13  H13   single    0.930  0.020  1.080
 NP6  C17  H17   single    0.930  0.020  1.080
 NP6  C14  H14   single    0.930  0.020  1.080
 NP6  C15  H15   single    0.930  0.020  1.080
 NP6  C16  H16   single    0.930  0.020  1.080

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
 NP6  H23C  C2   H22C  107.73  3.000
 NP6  H23C  C2   H21C  107.48  3.000
 NP6  H22C  C2   H21C  107.67  3.000
 NP6  H23C  C2   C1    111.20  3.000
 NP6  H22C  C2   C1    111.24  3.000
 NP6  H21C  C2   C1    111.34  3.000
 NP6  H12C  C1   H11C  106.45  3.000
 NP6  H12C  C1   C3    109.63  3.000
 NP6  H11C  C1   C3    109.67  3.000
 NP6  H12C  C1   C2    109.64  3.000
 NP6  H11C  C1   C2    109.74  3.000
 NP6  C3    C1   C2    111.58  3.000
 NP6  H32C  C3   H31C  105.83  3.000
 NP6  H32C  C3   C4    107.24  3.000
 NP6  H31C  C3   C4    110.17  3.000
 NP6  H32C  C3   C1    109.63  3.000
 NP6  H31C  C3   C1    110.07  3.000
 NP6  C4    C3   C1    113.57  3.000
 NP6  N1    C4   O1    122.83  3.000
 NP6  N1    C4   C3    114.45  3.000
 NP6  O1    C4   C3    122.69  3.000
 NP6  H1    N1   C5    117.57  3.000
 NP6  H1    N1   C4    118.47  3.000
 NP6  C5    N1   C4    123.77  3.000
 NP6  H5    C5   C10   106.51  3.000
 NP6  H5    C5   C6    107.60  3.000
 NP6  C10   C5   C6    110.63  3.000
 NP6  H5    C5   N1    107.78  3.000
 NP6  C10   C5   N1    112.17  3.000
 NP6  C6    C5   N1    111.86  3.000
 NP6  H6    C6   C7    108.11  3.000
 NP6  H6    C6   O2    111.27  3.000
 NP6  C7    C6   O2    111.98  3.000
 NP6  H6    C6   C5    108.92  3.000
 NP6  C7    C6   C5    109.23  3.000
 NP6  O2    C6   C5    107.28  3.000
 NP6  H2    O2   C6    108.04  3.000
 NP6  H7    C7   C8    109.38  3.000
 NP6  H7    C7   O3    111.38  3.000
 NP6  C8    C7   O3    110.34  3.000
 NP6  H7    C7   C6    108.66  3.000
 NP6  C8    C7   C6    109.53  3.000
 NP6  O3    C7   C6    107.50  3.000
 NP6  H3    O3   C7    109.48  3.000
 NP6  H8    C8   O5    108.15  3.000
 NP6  H8    C8   C9    109.51  3.000
 NP6  O5    C8   C9    106.64  3.000
 NP6  H8    C8   C7    108.79  3.000
 NP6  O5    C8   C7    111.20  3.000
 NP6  C9    C8   C7    112.45  3.000
 NP6  H92C  C9   H91C  107.13  3.000
 NP6  H92C  C9   O4    112.19  3.000
 NP6  H91C  C9   O4    111.66  3.000
 NP6  H92C  C9   C8    108.92  3.000
 NP6  H91C  C9   C8    107.84  3.000
 NP6  O4    C9   C8    108.97  3.000
 NP6  H4    O4   C9    107.99  3.000
 NP6  C10   O5   C8    119.73  3.000
 NP6  N2    C10  O5    122.84  3.000
 NP6  N2    C10  C5    117.92  3.000
 NP6  O5    C10  C5    118.98  3.000
 NP6  O6    N2   C10   110.89  3.000
 NP6  C11   O6   N2    112.89  3.000
 NP6  N3    C11  O7    127.47  3.000
 NP6  N3    C11  O6    107.58  3.000
 NP6  O7    C11  O6    124.95  3.000
 NP6  HA    N3   C12   115.45  3.000
 NP6  HA    N3   C11   116.41  3.000
 NP6  C12   N3   C11   128.08  3.000
 NP6  C17   C12  C13   119.06  3.000
 NP6  C17   C12  N3    116.44  3.000
 NP6  C13   C12  N3    124.49  3.000
 NP6  H13   C13  C14   119.21  3.000
 NP6  H13   C13  C12   121.23  3.000
 NP6  C14   C13  C12   119.56  3.000
 NP6  H14   C14  C15   119.99  3.000
 NP6  H14   C14  C13   118.59  3.000
 NP6  C15   C14  C13   121.42  3.000
 NP6  H15   C15  C16   120.55  3.000
 NP6  H15   C15  C14   120.60  3.000
 NP6  C16   C15  C14   118.85  3.000
 NP6  H16   C16  C17   119.19  3.000
 NP6  H16   C16  C15   120.37  3.000
 NP6  C17   C16  C15   120.44  3.000
 NP6  H17   C17  C16   119.58  3.000
 NP6  H17   C17  C12   119.75  3.000
 NP6  C16   C17  C12   120.67  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
 NP6  CONST_01  C15   C14  C13  C12    0.00   0.0  0
 NP6  CONST_02  C15   C16  C17  C12    0.00   0.0  0
 NP6  CONST_03  C16   C17  C12  C13    0.00   0.0  0
 NP6  CONST_04  C16   C15  C14  C13    0.00   0.0  0
 NP6  CONST_05  C17   C12  C13  C14    0.00   0.0  0
 NP6  CONST_06  C17   C16  C15  C14    0.00   0.0  0
 NP6  CONST_07  C14   C13  C12  N3   180.00   0.0  0
 NP6  CONST_08  C16   C17  C12  N3   180.00   0.0  0
 NP6  CONST_09  H14   C14  C13  C12  180.00   0.0  0
 NP6  CONST_10  H16   C16  C17  C12  180.00   0.0  0
 NP6  CONST_11  H17   C17  C12  C13  180.00   0.0  0
 NP6  CONST_12  H15   C15  C14  C13  180.00   0.0  0
 NP6  CONST_13  H13   C13  C14  C15  180.00   0.0  0
 NP6  CONST_14  C13   C12  N3   C11    0.00   0.0  0
 NP6  CONST_15  C17   C12  N3   C11  180.00   0.0  0
 NP6  CONST_16  HA    N3   C12  C13  180.00   0.0  0
 NP6  CONST_17  C5    N1   C4   C3   180.00   0.0  0
 NP6  CONST_18  C5    N1   C4   O1     0.00   0.0  0
 NP6  CONST_19  C12   N3   C11  O6   180.00   0.0  0
 NP6  CONST_20  C12   N3   C11  O7     0.00   0.0  0
 NP6  CONST_21  H1    N1   C4   C3     0.00   0.0  0
 NP6  Var_01    N2    C10  O5   C8   146.97  30.0  1
 NP6  Var_02    C4    C3   C1   C2   178.40  30.0  3
 NP6  Var_03    O1    C4   C3   C1   -30.74  30.0  3
 NP6  Var_04    O7    C11  O6   N2     3.78  30.0  3
 NP6  Var_05    H21C  C2   C1   C3    60.24  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
 NP6  chir_01  C5  N1  C6  C10  positiv
 NP6  chir_02  C6  O2  C5  C7   positiv
 NP6  chir_03  C7  O3  C8  C6   positiv
 NP6  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
 NP6  plan-1  N3   0.020
 NP6  plan-1  C12  0.020
 NP6  plan-1  C13  0.020
 NP6  plan-1  C14  0.020
 NP6  plan-1  C15  0.020
 NP6  plan-1  C16  0.020
 NP6  plan-1  C17  0.020
 NP6  plan-1  H13  0.020
 NP6  plan-1  H17  0.020
 NP6  plan-1  H14  0.020
 NP6  plan-1  H15  0.020
 NP6  plan-1  H16  0.020
 NP6  plan-2  C11  0.020
 NP6  plan-2  N3   0.020
 NP6  plan-2  C12  0.020
 NP6  plan-2  HA   0.020
 NP6  plan-3  C3   0.020
 NP6  plan-3  C4   0.020
 NP6  plan-3  O1   0.020
 NP6  plan-3  N1   0.020
 NP6  plan-3  C5   0.020
 NP6  plan-3  H1   0.020
 NP6  plan-4  O6   0.020
 NP6  plan-4  C11  0.020
 NP6  plan-4  O7   0.020
 NP6  plan-4  N3   0.020

