# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 07:27:51 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: 1,5-anhydro-2,3,4-trideoxy-3-{[(4S)-3,3-dimethyl-1-(8-methylquinolin-2-yl)piperidine-4-carbonyl]amino}-D-erythro-hexitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc2ccc(nc12)N3CC[C@H](C(=O)N[C@H]4CCO[C@H](CO)C4)C(C)(C)C3
#
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
 6PW  6PW  1,5-anhydro-2,3,4-trideoxy-3-{[(4S)-3,3-dimethyl-1-(8-methylquinolin-2-yl)piperidine-4-carbonyl]amino}-D-erythro-hexitol  ligand  63  30  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6PW
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
 6PW  O1   O  O2    0  -0.489   6.6737   0.4715  -0.0563
 6PW  C7   C  CR16  0  -0.315  -6.9884  -1.5324   0.5190
 6PW  O2   O  OH1   0  -0.671   7.5195   0.3284   2.6122
 6PW  C6   C  CR16  0  -0.263  -7.6372  -0.9315  -0.5773
 6PW  C1   C  CR66  0   0.172  -5.0216  -0.2011   0.1321
 6PW  N1   N  NT    0  -0.493  -1.8301   1.3315   0.2461
 6PW  C5   C  CR16  0  -0.338  -6.9879   0.0233  -1.3138
 6PW  C4   C  CR16  0  -0.395  -3.6678   1.6910  -1.3145
 6PW  C3   C  CR16  0  -0.182  -4.9336   1.3700  -1.6862
 6PW  C2   C  CR66  0   0.056  -5.6748   0.3991  -0.9698
 6PW  C17  C  C     0   0.594   1.9853  -0.1908  -1.0106
 6PW  N2   N  NH1   0  -0.639   3.1558  -0.2854  -0.3553
 6PW  C18  C  CH1   0  -0.113   4.3164  -0.9828  -0.8818
 6PW  C22  C  CH2   0  -0.448   5.1276  -0.1019  -1.8350
 6PW  C21  C  CH2   0  -0.190   5.8436   0.9971  -1.0714
 6PW  C20  C  CH1   0   0.013   5.9571  -0.2679   0.9090
 6PW  C23  C  CH2   0  -0.154   6.9329  -0.7669   1.9519
 6PW  C19  C  CH2   0  -0.480   5.2165  -1.4375   0.2654
 6PW  C14  C  CH1   0  -0.372   0.8888   0.5512  -0.2684
 6PW  C11  C  CT    0  -0.085  -0.0673  -0.3994   0.5060
 6PW  C13  C  CH3   0  -0.648  -0.7525  -1.4180  -0.4048
 6PW  C12  C  CH3   0  -0.657   0.6883  -1.1414   1.6082
 6PW  C10  C  CH2   0  -0.293  -1.1277   0.4858   1.1886
 6PW  C15  C  CH2   0  -0.419   0.1267   1.4808  -1.2137
 6PW  C16  C  CH2   0  -0.339  -0.9374   2.2433  -0.4378
 6PW  C    C  CR6   0   0.527  -3.0903   1.0324  -0.1790
 6PW  C8   C  CR6   0   0.050  -5.7078  -1.1930   0.8881
 6PW  C9   C  CH3   0  -0.711  -5.0293  -1.8358   2.0580
 6PW  N    N  N     0  -0.503  -3.7667   0.1283   0.4965
 6PW  H2   H  HOH1  0   0.456   8.1031  -0.0154   3.2941
 6PW  H3   H  HCR6  0   0.250  -8.6460  -1.2297  -0.8304
 6PW  H4   H  HCR6  0   0.251  -7.4712   0.4960  -2.1609
 6PW  H5   H  HCR6  0   0.272  -3.1191   2.4200  -1.8902
 6PW  H6   H  HCR6  0   0.265  -5.3805   1.8543  -2.5465
 6PW  H7   H  HNH1  0   0.395   3.2302   0.1617   0.5442
 6PW  H8   H  HCH1  0   0.264   3.9577  -1.8624  -1.4185
 6PW  H9   H  HCH2  0   0.236   5.8598  -0.7276  -2.3530
 6PW  H10  H  HCH2  0   0.246   4.4815   0.3348  -2.5985
 6PW  H11  H  HCH2  0   0.199   5.1116   1.6966  -0.6424
 6PW  H12  H  HCH2  0   0.242   6.4864   1.5738  -1.7379
 6PW  H13  H  HCH1  0   0.203   5.2310   0.3928   1.4152
 6PW  H14  H  HCH2  0   0.197   7.6848  -1.4006   1.4611
 6PW  H15  H  HCH2  0   0.203   6.3786  -1.4109   2.6465
 6PW  H16  H  HCH2  0   0.253   4.6317  -1.9719   1.0182
 6PW  H17  H  HCH2  0   0.249   5.9465  -2.1450  -0.1376
 6PW  H18  H  HCH1  0   0.248   1.3629   1.1873   0.4912
 6PW  H19  H  HCH3  0   0.228  -1.4549  -2.0218   0.1725
 6PW  H20  H  HCH3  0   0.229  -1.3163  -0.9499  -1.2119
 6PW  H21  H  HCH3  0   0.234  -0.0312  -2.0950  -0.8618
 6PW  H22  H  HCH3  0   0.228   1.2320  -0.4510   2.2569
 6PW  H23  H  HCH3  0   0.235  -0.0061  -1.7061   2.2335
 6PW  H24  H  HCH3  0   0.236   1.4076  -1.8509   1.1977
 6PW  H25  H  HCH2  0   0.238  -0.6334   1.1300   1.9257
 6PW  H26  H  HCH2  0   0.275  -1.8434  -0.1367   1.7203
 6PW  H27  H  HCH2  0   0.248   0.8172   2.1942  -1.6705
 6PW  H28  H  HCH2  0   0.238  -0.3349   0.9180  -2.0274
 6PW  H29  H  HCH2  0   0.268  -1.4807   2.9240  -1.0867
 6PW  H30  H  HCH2  0   0.246  -0.4538   2.8711   0.3189
 6PW  H31  H  HCH3  0   0.240  -4.0801  -2.2890   1.7690
 6PW  H32  H  HCH3  0   0.237  -4.7996  -1.1050   2.8356
 6PW  H33  H  HCH3  0   0.235  -5.6595  -2.6083   2.4971
 6PW  H1   H  HCR6  0   0.245  -7.5185  -2.2864   1.0892
 6PW  O    O  O     0  -0.500   1.8149  -0.6714  -2.1237

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
 6PW  C6   C5   aromatic  1.370  0.020  1.370
 6PW  C6   C7   aromatic  1.408  0.020  1.408
 6PW  C5   C2   aromatic  1.408  0.020  1.408
 6PW  C7   C8   aromatic  1.375  0.020  1.375
 6PW  C8   C1   aromatic  1.423  0.020  1.423
 6PW  C8   C9   single    1.497  0.020  1.497
 6PW  C2   C1   aromatic  1.415  0.020  1.415
 6PW  C2   C3   aromatic  1.416  0.020  1.416
 6PW  C1   N    aromatic  1.348  0.020  1.348
 6PW  C3   C4   aromatic  1.358  0.020  1.358
 6PW  N    C    aromatic  1.316  0.020  1.316
 6PW  C4   C    aromatic  1.434  0.020  1.434
 6PW  C    N1   single    1.363  0.020  1.363
 6PW  N1   C10  single    1.448  0.020  1.448
 6PW  N1   C16  single    1.448  0.020  1.448
 6PW  C10  C11  single    1.541  0.020  1.541
 6PW  C16  C15  single    1.522  0.020  1.522
 6PW  C13  C11  single    1.529  0.020  1.529
 6PW  C11  C12  single    1.528  0.020  1.528
 6PW  C11  C14  single    1.555  0.020  1.555
 6PW  C15  C14  single    1.529  0.020  1.529
 6PW  C14  C17  single    1.518  0.020  1.518
 6PW  C17  O    double    1.224  0.020  1.224
 6PW  C17  N2   single    1.345  0.020  1.345
 6PW  N2   C18  single    1.453  0.020  1.453
 6PW  C18  C19  single    1.527  0.020  1.527
 6PW  C18  C22  single    1.531  0.020  1.531
 6PW  C19  C20  single    1.527  0.020  1.527
 6PW  C20  C23  single    1.513  0.020  1.513
 6PW  C20  O1   single    1.411  0.020  1.411
 6PW  C23  O2   single    1.407  0.020  1.407
 6PW  C22  C21  single    1.518  0.020  1.518
 6PW  C21  O1   single    1.413  0.020  1.413
 6PW  C7   H1   single    0.930  0.020  1.080
 6PW  O2   H2   single    0.850  0.020  0.980
 6PW  C6   H3   single    0.930  0.020  1.080
 6PW  C5   H4   single    0.930  0.020  1.080
 6PW  C4   H5   single    0.930  0.020  1.080
 6PW  C3   H6   single    0.930  0.020  1.080
 6PW  N2   H7   single    0.860  0.020  1.020
 6PW  C18  H8   single    0.970  0.020  1.090
 6PW  C22  H9   single    0.970  0.020  1.090
 6PW  C22  H10  single    0.970  0.020  1.090
 6PW  C21  H11  single    0.970  0.020  1.090
 6PW  C21  H12  single    0.970  0.020  1.090
 6PW  C20  H13  single    0.970  0.020  1.090
 6PW  C23  H14  single    0.970  0.020  1.090
 6PW  C23  H15  single    0.970  0.020  1.090
 6PW  C19  H16  single    0.970  0.020  1.090
 6PW  C19  H17  single    0.970  0.020  1.090
 6PW  C14  H18  single    0.970  0.020  1.090
 6PW  C13  H19  single    0.970  0.020  1.090
 6PW  C13  H20  single    0.970  0.020  1.090
 6PW  C13  H21  single    0.970  0.020  1.090
 6PW  C12  H22  single    0.970  0.020  1.090
 6PW  C12  H23  single    0.970  0.020  1.090
 6PW  C12  H24  single    0.970  0.020  1.090
 6PW  C10  H25  single    0.970  0.020  1.090
 6PW  C10  H26  single    0.970  0.020  1.090
 6PW  C15  H27  single    0.970  0.020  1.090
 6PW  C15  H28  single    0.970  0.020  1.090
 6PW  C16  H29  single    0.970  0.020  1.090
 6PW  C16  H30  single    0.970  0.020  1.090
 6PW  C9   H31  single    0.970  0.020  1.090
 6PW  C9   H32  single    0.970  0.020  1.090
 6PW  C9   H33  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
 6PW  C20  O1   C21  112.83  3.000
 6PW  H1   C7   C8   119.07  3.000
 6PW  H1   C7   C6   118.75  3.000
 6PW  C8   C7   C6   122.18  3.000
 6PW  H2   O2   C23  107.92  3.000
 6PW  H3   C6   C5   120.55  3.000
 6PW  H3   C6   C7   119.60  3.000
 6PW  C5   C6   C7   119.84  3.000
 6PW  N    C1   C8   118.39  3.000
 6PW  N    C1   C2   122.47  3.000
 6PW  C8   C1   C2   119.13  3.000
 6PW  C    N1   C16  124.12  3.000
 6PW  C16  N1   C10  112.10  3.000
 6PW  C    N1   C10  121.55  3.000
 6PW  H4   C5   C2   119.36  3.000
 6PW  H4   C5   C6   120.86  3.000
 6PW  C2   C5   C6   119.78  3.000
 6PW  H5   C4   C    121.87  3.000
 6PW  H5   C4   C3   119.20  3.000
 6PW  C    C4   C3   118.92  3.000
 6PW  H6   C3   C2   119.48  3.000
 6PW  H6   C3   C4   119.75  3.000
 6PW  C2   C3   C4   120.77  3.000
 6PW  C3   C2   C5   123.19  3.000
 6PW  C3   C2   C1   116.32  3.000
 6PW  C5   C2   C1   120.50  3.000
 6PW  C14  C17  N2   115.15  3.000
 6PW  N2   C17  O    122.44  3.000
 6PW  C14  C17  O    122.41  3.000
 6PW  H7   N2   C18  118.53  3.000
 6PW  H7   N2   C17  117.92  3.000
 6PW  C18  N2   C17  123.54  3.000
 6PW  H8   C18  C19  108.86  3.000
 6PW  H8   C18  C22  109.39  3.000
 6PW  C19  C18  C22  109.07  3.000
 6PW  H8   C18  N2   107.61  3.000
 6PW  C22  C18  N2   111.89  3.000
 6PW  C19  C18  N2   109.97  3.000
 6PW  H10  C22  H9   107.09  3.000
 6PW  H10  C22  C21  109.96  3.000
 6PW  H9   C22  C21  109.68  3.000
 6PW  H10  C22  C18  110.62  3.000
 6PW  H9   C22  C18  108.70  3.000
 6PW  C21  C22  C18  110.70  3.000
 6PW  H12  C21  H11  107.12  3.000
 6PW  H12  C21  C22  110.70  3.000
 6PW  H11  C21  C22  110.05  3.000
 6PW  H12  C21  O1   106.83  3.000
 6PW  H11  C21  O1   110.33  3.000
 6PW  C22  C21  O1   111.67  3.000
 6PW  H13  C20  C19  109.43  3.000
 6PW  H13  C20  C23  107.78  3.000
 6PW  C19  C20  C23  110.54  3.000
 6PW  H13  C20  O1   109.50  3.000
 6PW  C23  C20  O1   108.47  3.000
 6PW  C19  C20  O1   111.06  3.000
 6PW  H15  C23  H14  106.85  3.000
 6PW  H15  C23  C20  107.70  3.000
 6PW  H14  C23  C20  108.88  3.000
 6PW  H15  C23  O2   111.73  3.000
 6PW  H14  C23  O2   111.91  3.000
 6PW  C20  C23  O2   109.61  3.000
 6PW  H17  C19  H16  107.14  3.000
 6PW  H17  C19  C20  109.10  3.000
 6PW  H16  C19  C20  110.11  3.000
 6PW  H17  C19  C18  108.01  3.000
 6PW  H16  C19  C18  110.34  3.000
 6PW  C20  C19  C18  111.99  3.000
 6PW  H18  C14  C15  106.89  3.000
 6PW  H18  C14  C11  105.96  3.000
 6PW  C15  C14  C11  111.91  3.000
 6PW  H18  C14  C17  108.03  3.000
 6PW  C15  C14  C17  110.79  3.000
 6PW  C11  C14  C17  112.89  3.000
 6PW  C10  C11  C12  107.44  3.000
 6PW  C12  C11  C13  109.13  3.000
 6PW  C10  C11  C13  109.78  3.000
 6PW  C12  C11  C14  110.61  3.000
 6PW  C13  C11  C14  112.72  3.000
 6PW  C10  C11  C14  107.02  3.000
 6PW  H21  C13  H20  107.38  3.000
 6PW  H21  C13  H19  107.71  3.000
 6PW  H20  C13  H19  107.24  3.000
 6PW  H21  C13  C11  111.54  3.000
 6PW  H20  C13  C11  112.75  3.000
 6PW  H19  C13  C11  109.99  3.000
 6PW  H24  C12  H23  107.37  3.000
 6PW  H24  C12  H22  107.85  3.000
 6PW  H23  C12  H22  107.66  3.000
 6PW  H24  C12  C11  111.74  3.000
 6PW  H23  C12  C11  110.47  3.000
 6PW  H22  C12  C11  111.56  3.000
 6PW  H26  C10  H25  107.72  3.000
 6PW  H26  C10  C11  109.92  3.000
 6PW  H25  C10  C11  108.97  3.000
 6PW  H26  C10  N1   109.47  3.000
 6PW  H25  C10  N1   108.24  3.000
 6PW  C11  C10  N1   112.39  3.000
 6PW  H28  C15  H27  106.98  3.000
 6PW  H28  C15  C16  110.04  3.000
 6PW  H27  C15  C16  109.14  3.000
 6PW  H28  C15  C14  110.98  3.000
 6PW  H27  C15  C14  109.90  3.000
 6PW  C16  C15  C14  109.75  3.000
 6PW  H30  C16  H29  105.92  3.000
 6PW  H30  C16  C15  109.30  3.000
 6PW  H29  C16  C15  111.05  3.000
 6PW  H30  C16  N1   107.86  3.000
 6PW  H29  C16  N1   111.63  3.000
 6PW  C15  C16  N1   110.88  3.000
 6PW  N    C    C4   121.00  3.000
 6PW  C4   C    N1   121.22  3.000
 6PW  N    C    N1   117.77  3.000
 6PW  C9   C8   C1   119.71  3.000
 6PW  C9   C8   C7   121.71  3.000
 6PW  C1   C8   C7   118.57  3.000
 6PW  H33  C9   H32  108.02  3.000
 6PW  H33  C9   H31  108.40  3.000
 6PW  H32  C9   H31  106.49  3.000
 6PW  H33  C9   C8   110.92  3.000
 6PW  H32  C9   C8   111.37  3.000
 6PW  H31  C9   C8   111.45  3.000
 6PW  C    N    C1   120.52  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
 6PW  CONST_01  C2   C5   C6   C7      0.00   0.0  0
 6PW  CONST_02  C2   C1   C8   C7      0.00   0.0  0
 6PW  CONST_03  N    C1   C8   C7    180.00   0.0  0
 6PW  CONST_04  C1   C2   C5   C6      0.00   0.0  0
 6PW  CONST_05  C3   C2   C5   C6    180.00   0.0  0
 6PW  CONST_06  C1   C8   C7   C6      0.00   0.0  0
 6PW  CONST_07  C4   C3   C2   C1      0.00   0.0  0
 6PW  CONST_08  C4   C    N    C1      0.00   0.0  0
 6PW  CONST_09  C8   C7   C6   C5      0.00   0.0  0
 6PW  CONST_10  C8   C1   C2   C5      0.00   0.0  0
 6PW  CONST_11  N    C1   C2   C5    180.00   0.0  0
 6PW  CONST_12  C4   C3   C2   C5    180.00   0.0  0
 6PW  CONST_13  C8   C1   C2   C3    180.00   0.0  0
 6PW  CONST_14  N    C1   C2   C3      0.00   0.0  0
 6PW  CONST_15  N    C    C4   C3      0.00   0.0  0
 6PW  CONST_16  C    N    C1   C2      0.00   0.0  0
 6PW  CONST_17  C    C4   C3   C2      0.00   0.0  0
 6PW  CONST_18  C8   C1   N    C     180.00   0.0  0
 6PW  CONST_19  N1   C    N    C1    180.00   0.0  0
 6PW  CONST_20  C3   C4   C    N1    180.00   0.0  0
 6PW  CONST_21  C9   C8   C7   C6    180.00   0.0  0
 6PW  CONST_22  C9   C8   C1   C2    180.00   0.0  0
 6PW  CONST_23  N    C1   C8   C9      0.00   0.0  0
 6PW  CONST_24  H4   C5   C6   C7    180.00   0.0  0
 6PW  CONST_25  H1   C7   C8   C1    180.00   0.0  0
 6PW  CONST_26  H6   C3   C2   C1    180.00   0.0  0
 6PW  CONST_27  H5   C4   C    N1      0.00   0.0  0
 6PW  CONST_28  H3   C6   C5   C2    180.00   0.0  0
 6PW  CONST_29  C14  C17  N2   C18   180.00   0.0  0
 6PW  CONST_30  C18  N2   C17  O       0.00   0.0  0
 6PW  CONST_31  H7   N2   C17  C14     0.00   0.0  0
 6PW  Var_01    C18  C22  C21  O1     56.42  30.0  1
 6PW  Var_02    C14  C11  C10  N1     55.99  30.0  1
 6PW  Var_03    C14  C15  C16  N1    -56.29  30.0  1
 6PW  Var_04    C10  N1   C    C4   -166.18  30.0  2
 6PW  Var_05    C    N1   C10  C11   102.66  30.0  1
 6PW  Var_06    C15  C16  N1   C10    59.91  30.0  1
 6PW  Var_07    H31  C9   C8   C7    124.14  30.0  2
 6PW  Var_08    H19  C13  C11  C14  -176.69  30.0  3
 6PW  Var_09    H22  C12  C11  C14    52.82  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
 6PW  chir_01  C18  N2   C19  C22  positiv
 6PW  chir_02  C20  O1   C19  C23  negativ
 6PW  chir_03  C14  C11  C15  C17  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
 6PW  plan-1  C17  0.020
 6PW  plan-1  N2   0.020
 6PW  plan-1  C18  0.020
 6PW  plan-1  C14  0.020
 6PW  plan-1  H7   0.020
 6PW  plan-1  O    0.020
 6PW  plan-2  C7   0.020
 6PW  plan-2  C6   0.020
 6PW  plan-2  C1   0.020
 6PW  plan-2  N1   0.020
 6PW  plan-2  C5   0.020
 6PW  plan-2  C4   0.020
 6PW  plan-2  C3   0.020
 6PW  plan-2  C2   0.020
 6PW  plan-2  C    0.020
 6PW  plan-2  C8   0.020
 6PW  plan-2  C9   0.020
 6PW  plan-2  N    0.020
 6PW  plan-2  H3   0.020
 6PW  plan-2  H4   0.020
 6PW  plan-2  H5   0.020
 6PW  plan-2  H6   0.020
 6PW  plan-2  H1   0.020

