# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 03:45:12 2022
#   Inital geometry file: a 103 line input string
#   Ligand name: 2-[[(2~{R},3~{R},4~{R})-2-(hydroxymethyl)-3-oxidanyl-3,4-dihydro-2~{H}-pyran-4-yl]oxymethyl]quinoline-7-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1OC=C[C@@H](OCc2ccc3ccc(cc3n2)C(O)=O)[C@H]1O
#
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
 5KM  5KM  "2-[[(2~{R},3~{R},4~{R})-2-(hydroxymethyl)-3-oxidanyl-3,4-dihydro-2~{H}-pyran-4-yl]oxymethyl]quinoline-7-carboxylic acid"  ligand  40  24  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5KM
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
 5KM  C1   C  CH1    0   0.002  14.3141  -6.4589   9.8546
 5KM  C2   C  CH1    0  -0.072  13.2988  -5.7926   8.9238
 5KM  C3   C  CH1    0   0.086  11.9979  -5.6192   9.7038
 5KM  C5   C  CR6    0   0.196   8.8896  -4.3334   8.2911
 5KM  C6   C  CR66   0   0.225   7.1246  -2.9788   7.7299
 5KM  C7   C  CR66   0   0.076   7.1892  -3.3635   6.3699
 5KM  O4   O  OC    -1  -0.581   4.2347  -0.1744   8.8960
 5KM  O3   O  O      0  -0.583   3.4064  -0.1017   6.8250
 5KM  C10  C  CR6    0  -0.103   5.2527  -1.5154   7.2393
 5KM  C12  C  CR16   0  -0.354   6.1462  -2.0471   8.1359
 5KM  N    N  N      0  -0.460   7.9802  -3.4724   8.6599
 5KM  C9   C  CR16   0  -0.288   5.3230  -1.9159   5.8842
 5KM  C8   C  CR16   0  -0.306   6.2645  -2.8122   5.4574
 5KM  C13  C  CR16   0  -0.184   8.1882  -4.2913   6.0020
 5KM  C14  C  CR16   0  -0.316   9.0388  -4.7738   6.9524
 5KM  O2   O  O2     0  -0.490  11.1119  -4.8454   8.9296
 5KM  O1   O  OH1    0  -0.660  13.7374  -4.5296   8.4911
 5KM  C15  C  C1     0  -0.415  12.3071  -5.0017  11.0391
 5KM  C16  C  C1     0   0.057  13.5328  -5.0398  11.5537
 5KM  O5   O  O2     0  -0.461  14.5942  -5.6437  10.9882
 5KM  C    C  CH2    0  -0.170  15.6263  -6.7609   9.1662
 5KM  O    O  OH1    0  -0.663  16.4365  -7.5099  10.0385
 5KM  H1   H  HCH1   0   0.237  13.8762  -7.4054  10.2039
 5KM  H2   H  HCH1   0   0.245  13.1170  -6.4690   8.0786
 5KM  H3   H  HCH1   0   0.229  11.5642  -6.6211   9.8471
 5KM  H7   H  HCR6   0   0.243   6.1127  -1.7576   9.1784
 5KM  H8   H  HCR6   0   0.245   4.6178  -1.4997   5.1779
 5KM  H9   H  HCR6   0   0.252   6.3129  -3.1088   4.4160
 5KM  H10  H  HCR6   0   0.266   8.2686  -4.6113   4.9699
 5KM  H11  H  HCR6   0   0.262   9.8097  -5.4882   6.6982
 5KM  H12  H  HOH1   0   0.457  14.3196  -4.6445   7.7351
 5KM  H13  H  H      0   0.259  11.5277  -4.5133  11.6090
 5KM  H14  H  H      0   0.266  13.7844  -4.5791  12.5019
 5KM  H15  H  HCH2   0   0.204  16.1105  -5.8220   8.8696
 5KM  H16  H  HCH2   0   0.206  15.3975  -7.3132   8.2451
 5KM  H17  H  HOH1   0   0.455  17.2952  -7.6276   9.6228
 5KM  C4   C  CH2    0  -0.219   9.7778  -4.8915   9.3678
 5KM  C11  C  C      0   0.403   4.2003  -0.5039   7.6962
 5KM  H4   H  HCH2   0   0.232   9.6183  -4.3170  10.2873
 5KM  H5   H  HCH2   0   0.223   9.4746  -5.9287   9.5776

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
 5KM  C8   C9   aromatic  1.368  0.020  1.368
 5KM  C8   C7   aromatic  1.411  0.020  1.411
 5KM  C9   C10  aromatic  1.415  0.020  1.415
 5KM  C13  C7   aromatic  1.412  0.020  1.412
 5KM  C13  C14  aromatic  1.364  0.020  1.364
 5KM  C7   C6   aromatic  1.415  0.020  1.415
 5KM  C10  C11  single    1.530  0.020  1.530
 5KM  C10  C12  aromatic  1.373  0.020  1.373
 5KM  O3   C11  deloc     1.245  0.020  1.245
 5KM  C14  C5   aromatic  1.417  0.020  1.417
 5KM  C11  O4   deloc     1.245  0.020  1.245
 5KM  C6   C12  aromatic  1.411  0.020  1.411
 5KM  C6   N    aromatic  1.357  0.020  1.357
 5KM  C5   N    aromatic  1.306  0.020  1.306
 5KM  C5   C4   single    1.503  0.020  1.503
 5KM  O2   C4   single    1.405  0.020  1.405
 5KM  O2   C3   single    1.408  0.020  1.408
 5KM  O1   C2   single    1.405  0.020  1.405
 5KM  C2   C3   single    1.527  0.020  1.527
 5KM  C2   C1   single    1.530  0.020  1.530
 5KM  C    O    single    1.407  0.020  1.407
 5KM  C    C1   single    1.512  0.020  1.512
 5KM  C3   C15  single    1.503  0.020  1.503
 5KM  C1   O5   single    1.424  0.020  1.424
 5KM  O5   C16  single    1.346  0.020  1.346
 5KM  C15  C16  double    1.330  0.020  1.330
 5KM  C1   H1   single    0.970  0.020  1.090
 5KM  C2   H2   single    0.970  0.020  1.090
 5KM  C3   H3   single    0.970  0.020  1.090
 5KM  C4   H4   single    0.970  0.020  1.090
 5KM  C4   H5   single    0.970  0.020  1.090
 5KM  C12  H7   single    0.930  0.020  1.080
 5KM  C9   H8   single    0.930  0.020  1.080
 5KM  C8   H9   single    0.930  0.020  1.080
 5KM  C13  H10  single    0.930  0.020  1.080
 5KM  C14  H11  single    0.930  0.020  1.080
 5KM  O1   H12  single    0.850  0.020  0.980
 5KM  C15  H13  single    0.930  0.020  1.080
 5KM  C16  H14  single    0.930  0.020  1.080
 5KM  C    H15  single    0.970  0.020  1.090
 5KM  C    H16  single    0.970  0.020  1.090
 5KM  O    H17  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
 5KM  H1   C1   C    108.55  3.000
 5KM  H1   C1   O5   108.54  3.000
 5KM  C    C1   O5   107.82  3.000
 5KM  H1   C1   C2   107.69  3.000
 5KM  O5   C1   C2   111.44  3.000
 5KM  C    C1   C2   112.69  3.000
 5KM  H2   C2   O1   111.62  3.000
 5KM  H2   C2   C3   108.80  3.000
 5KM  O1   C2   C3   108.74  3.000
 5KM  H2   C2   C1   108.05  3.000
 5KM  C3   C2   C1   107.70  3.000
 5KM  O1   C2   C1   111.81  3.000
 5KM  H3   C3   C15  109.82  3.000
 5KM  H3   C3   O2   108.88  3.000
 5KM  C15  C3   O2   113.08  3.000
 5KM  H3   C3   C2   107.39  3.000
 5KM  C15  C3   C2   108.98  3.000
 5KM  O2   C3   C2   108.52  3.000
 5KM  C14  C5   N    123.04  3.000
 5KM  N    C5   C4   117.01  3.000
 5KM  C14  C5   C4   119.93  3.000
 5KM  N    C6   C12  118.71  3.000
 5KM  N    C6   C7   122.09  3.000
 5KM  C12  C6   C7   119.21  3.000
 5KM  C13  C7   C8   123.49  3.000
 5KM  C13  C7   C6   117.48  3.000
 5KM  C8   C7   C6   119.04  3.000
 5KM  C9   C10  C12  118.92  3.000
 5KM  C12  C10  C11  120.59  3.000
 5KM  C9   C10  C11  120.50  3.000
 5KM  H7   C12  C10  120.35  3.000
 5KM  H7   C12  C6   118.38  3.000
 5KM  C10  C12  C6   121.27  3.000
 5KM  C6   N    C5   119.05  3.000
 5KM  H8   C9   C8   119.81  3.000
 5KM  H8   C9   C10  118.96  3.000
 5KM  C8   C9   C10  121.23  3.000
 5KM  H9   C8   C9   120.64  3.000
 5KM  H9   C8   C7   119.02  3.000
 5KM  C9   C8   C7   120.34  3.000
 5KM  H10  C13  C14  120.87  3.000
 5KM  H10  C13  C7   119.65  3.000
 5KM  C14  C13  C7   119.48  3.000
 5KM  H11  C14  C13  120.97  3.000
 5KM  H11  C14  C5   120.17  3.000
 5KM  C13  C14  C5   118.86  3.000
 5KM  C4   O2   C3   114.07  3.000
 5KM  H12  O1   C2   108.90  3.000
 5KM  H13  C15  C16  118.23  3.000
 5KM  H13  C15  C3   120.34  3.000
 5KM  C16  C15  C3   121.43  3.000
 5KM  H14  C16  O5   112.04  3.000
 5KM  H14  C16  C15  122.71  3.000
 5KM  O5   C16  C15  125.25  3.000
 5KM  C16  O5   C1   115.87  3.000
 5KM  H16  C    H15  107.20  3.000
 5KM  H16  C    O    111.86  3.000
 5KM  H15  C    O    111.66  3.000
 5KM  H16  C    C1   107.55  3.000
 5KM  H15  C    C1   109.58  3.000
 5KM  O    C    C1   108.89  3.000
 5KM  H17  O    C    108.15  3.000
 5KM  H5   C4   H4   107.10  3.000
 5KM  H5   C4   O2   110.60  3.000
 5KM  H4   C4   O2   112.50  3.000
 5KM  H5   C4   C5   108.87  3.000
 5KM  H4   C4   C5   108.68  3.000
 5KM  O2   C4   C5   109.00  3.000
 5KM  C10  C11  O3   116.31  3.000
 5KM  O3   C11  O4   127.33  3.000
 5KM  C10  C11  O4   116.35  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
 5KM  CONST_01  C7   C13  C14  C5      0.00   0.0  0
 5KM  CONST_02  C7   C6   N    C5      0.00   0.0  0
 5KM  CONST_03  C12  C6   N    C5    180.00   0.0  0
 5KM  CONST_04  C9   C8   C7   C6      0.00   0.0  0
 5KM  CONST_05  C14  C13  C7   C6      0.00   0.0  0
 5KM  CONST_06  C9   C10  C12  C6      0.00   0.0  0
 5KM  CONST_07  C14  C5   N    C6      0.00   0.0  0
 5KM  CONST_08  C10  C9   C8   C7      0.00   0.0  0
 5KM  CONST_09  C10  C12  C6   C7      0.00   0.0  0
 5KM  CONST_10  N    C6   C12  C10   180.00   0.0  0
 5KM  CONST_11  C8   C9   C10  C12     0.00   0.0  0
 5KM  CONST_12  C8   C7   C6   C12     0.00   0.0  0
 5KM  CONST_13  C13  C7   C6   C12   180.00   0.0  0
 5KM  CONST_14  C8   C7   C6   N     180.00   0.0  0
 5KM  CONST_15  C13  C7   C6   N       0.00   0.0  0
 5KM  CONST_16  C13  C14  C5   N       0.00   0.0  0
 5KM  CONST_17  C13  C7   C8   C9    180.00   0.0  0
 5KM  CONST_18  C14  C13  C7   C8    180.00   0.0  0
 5KM  CONST_19  C13  C14  C5   C4    180.00   0.0  0
 5KM  CONST_20  C6   N    C5   C4    180.00   0.0  0
 5KM  CONST_21  C11  C10  C12  C6    180.00   0.0  0
 5KM  CONST_22  C8   C9   C10  C11   180.00   0.0  0
 5KM  CONST_23  H10  C13  C14  C5    180.00   0.0  0
 5KM  CONST_24  H9   C8   C7   C6    180.00   0.0  0
 5KM  CONST_25  H10  C13  C7   C6    180.00   0.0  0
 5KM  CONST_26  H8   C9   C8   C7    180.00   0.0  0
 5KM  CONST_27  H11  C14  C13  C7    180.00   0.0  0
 5KM  CONST_28  H7   C12  C6   C7    180.00   0.0  0
 5KM  CONST_29  H9   C8   C9   C10   180.00   0.0  0
 5KM  CONST_30  H8   C9   C10  C12   180.00   0.0  0
 5KM  CONST_31  H7   C12  C6   N       0.00   0.0  0
 5KM  CONST_32  H11  C14  C5   N     180.00   0.0  0
 5KM  CONST_33  H7   C12  C10  C9    180.00   0.0  0
 5KM  CONST_34  H10  C13  C7   C8      0.00   0.0  0
 5KM  CONST_35  H9   C8   C7   C13     0.00   0.0  0
 5KM  Var_01    C15  C16  O5   C1     -9.52  30.0  1
 5KM  Var_02    O5   C16  C15  C3     -2.04  30.0  1
 5KM  Var_03    H14  C16  O5   C1    170.12  30.0  1
 5KM  Var_04    H14  C16  C15  C3    178.35  30.0  1
 5KM  Var_05    H13  C15  C16  O5    177.84  30.0  1
 5KM  Var_06    C5   C4   O2   C3   -165.75  30.0  3
 5KM  Var_07    C9   C10  C11  O4   -177.80  30.0  3
 5KM  Var_08    C12  C10  C11  O4      2.04  30.0  3
 5KM  Var_09    C9   C10  C11  O3      2.12  30.0  3
 5KM  Var_10    C12  C10  C11  O3   -178.04  30.0  3
 5KM  Var_11    O2   C4   C5   N    -133.52  30.0  2
 5KM  Var_12    O2   C4   C5   C14    48.13  30.0  2
 5KM  Var_13    H4   C4   C5   N     -10.58  30.0  2
 5KM  Var_14    H5   C4   C5   N     105.75  30.0  2
 5KM  Var_15    H4   C4   C5   C14   171.07  30.0  2
 5KM  Var_16    H5   C4   C5   C14   -72.60  30.0  2
 5KM  Var_17    H4   C4   O2   C3     73.63  30.0  3
 5KM  Var_18    H5   C4   O2   C3    -46.09  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
 5KM  chir_01  C1  C2  C    O5  negativ
 5KM  chir_02  C2  O1  C1   C3  negativ
 5KM  chir_03  C3  O2  C15  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
 5KM  plan-1  C5   0.020
 5KM  plan-1  C6   0.020
 5KM  plan-1  C7   0.020
 5KM  plan-1  C10  0.020
 5KM  plan-1  C12  0.020
 5KM  plan-1  N    0.020
 5KM  plan-1  C9   0.020
 5KM  plan-1  C8   0.020
 5KM  plan-1  C13  0.020
 5KM  plan-1  C14  0.020
 5KM  plan-1  H7   0.020
 5KM  plan-1  H8   0.020
 5KM  plan-1  H9   0.020
 5KM  plan-1  H10  0.020
 5KM  plan-1  H11  0.020
 5KM  plan-1  C4   0.020
 5KM  plan-1  C11  0.020
 5KM  plan-2  O4   0.020
 5KM  plan-2  O3   0.020
 5KM  plan-2  C10  0.020
 5KM  plan-2  C11  0.020

