# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 09:54:10 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: (6R)-5-(acetylamino)-6-[(1S,2S)-3-(acetylamino)-1,2-dihydroxypropyl]-3,5-dideoxy-beta-L-threo-hex-2-ulopyranosonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)NC[C@H](O)[C@H](O)[C@@H]1O[C@](O)(C[C@H](O)[C@H]1NC(C)=O)C(O)=O
#
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
 5KQ  5KQ  '(6R)-5-(acetylamino)-6-[(1S,2S)-3-(acetylamino)-1,2-dihydroxypropyl]-3,5-dideoxy-beta-L-threo-hex-2-ulopyranosonic acid'  L-saccharide  46  24  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5KQ
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
 5KQ  CAW  C  CH3   0  -0.784   1.9428   4.2703  -1.1653
 5KQ  CAV  C  C     0   0.522   1.9825   3.2159  -0.0870
 5KQ  OAX  O  O     0  -0.498   2.2654   3.4906   1.0691
 5KQ  NAU  N  NH1   0  -0.635   1.6821   1.9697  -0.5037
 5KQ  CAT  C  CH1   0  -0.126   1.8001   0.7874   0.3156
 5KQ  CAR  C  CH1   0   0.071   3.0308  -0.0048  -0.1338
 5KQ  OAS  O  OH1   0  -0.660   4.1656   0.7742   0.1610
 5KQ  CAQ  C  CH2   0  -0.550   3.1125  -1.3603   0.5604
 5KQ  CAL  C  CT    0   0.415   1.8096  -2.1476   0.5713
 5KQ  CAN  C  C     0   0.518   1.4456  -2.8751  -0.7421
 5KQ  OAP  O  OH1   0  -0.575   1.7889  -2.2196  -1.8310
 5KQ  OAO  O  O     0  -0.436   0.8719  -3.9340  -0.7380
 5KQ  OAM  O  OH1   0  -0.651   1.8967  -3.0924   1.5664
 5KQ  OAK  O  O2    0  -0.505   0.7266  -1.3056   0.8977
 5KQ  CAJ  C  CH1   0   0.012   0.5459  -0.0879   0.1922
 5KQ  CAH  C  CH1   0  -0.000  -0.7389   0.4991   0.8196
 5KQ  OAI  O  OH1   0  -0.647  -0.7952   1.8998   0.8662
 5KQ  CAF  C  CH1   0   0.000  -1.9981  -0.0559   0.1256
 5KQ  OAG  O  OH1   0  -0.656  -1.9054  -1.4231  -0.1952
 5KQ  CAE  C  CH2   0  -0.312  -3.2438   0.2291   0.9651
 5KQ  NAD  N  NH1   0  -0.620  -4.4594  -0.1913   0.3124
 5KQ  CAB  C  C     0   0.516  -5.1683   0.5974  -0.5127
 5KQ  OAC  O  O     0  -0.509  -4.8683   1.7630  -0.7390
 5KQ  CAA  C  CH3   0  -0.777  -6.3884  -0.0415  -1.1286
 5KQ  H1   H  HCH3  0   0.269   2.9607   4.5936  -1.3870
 5KQ  H2   H  HCH3  0   0.249   1.4847   3.9302  -2.0924
 5KQ  H3   H  HCH3  0   0.264   1.3965   5.1413  -0.8064
 5KQ  H4   H  HNH1  0   0.398   1.5512   1.8262  -1.4936
 5KQ  H5   H  HCH1  0   0.267   1.9302   1.0997   1.3543
 5KQ  H6   H  HCH1  0   0.218   2.9494  -0.1520  -1.2171
 5KQ  H7   H  HOH1  0   0.455   4.9081   0.4294  -0.3445
 5KQ  H8   H  HCH2  0   0.268   3.9142  -1.9601   0.1210
 5KQ  H9   H  HCH2  0   0.266   3.3775  -1.1852   1.6072
 5KQ  H10  H  HOH1  0   0.493   1.4992  -2.6975  -2.6250
 5KQ  H11  H  HOH1  0   0.457   1.2516  -3.7946   1.4018
 5KQ  H12  H  HCH1  0   0.235   0.3693  -0.2759  -0.8771
 5KQ  H13  H  HCH1  0   0.240  -0.7357   0.1844   1.8697
 5KQ  H14  H  HOH1  0   0.446  -0.7752   2.2464  -0.0317
 5KQ  H15  H  HCH1  0   0.238  -2.0990   0.4591  -0.8380
 5KQ  H16  H  HOH1  0   0.443  -1.7069  -1.9215   0.6048
 5KQ  H17  H  HCH2  0   0.253  -3.1692  -0.3034   1.9173
 5KQ  H18  H  HCH2  0   0.253  -3.3093   1.2912   1.1950
 5KQ  H19  H  HNH1  0   0.399  -4.7243  -1.1580   0.3993
 5KQ  H20  H  HCH3  0   0.247  -6.4736  -1.1071  -0.9246
 5KQ  H21  H  HCH3  0   0.266  -7.2833   0.4515  -0.7473
 5KQ  H22  H  HCH3  0   0.263  -6.3720   0.1065  -2.2077

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
 5KQ  OAO  CAN  double  1.204  0.020  1.204
 5KQ  OAS  CAR  single  1.408  0.020  1.408
 5KQ  CAN  OAP  single  1.316  0.020  1.316
 5KQ  CAN  CAL  single  1.545  0.020  1.545
 5KQ  CAR  CAQ  single  1.525  0.020  1.525
 5KQ  CAR  CAT  single  1.531  0.020  1.531
 5KQ  CAQ  CAL  single  1.522  0.020  1.522
 5KQ  CAL  OAM  single  1.375  0.020  1.375
 5KQ  CAL  OAK  single  1.410  0.020  1.410
 5KQ  NAU  CAT  single  1.443  0.020  1.443
 5KQ  NAU  CAV  single  1.348  0.020  1.348
 5KQ  CAT  CAJ  single  1.534  0.020  1.534
 5KQ  CAW  CAV  single  1.509  0.020  1.509
 5KQ  CAJ  OAK  single  1.419  0.020  1.419
 5KQ  CAJ  CAH  single  1.546  0.020  1.546
 5KQ  CAV  OAX  double  1.221  0.020  1.221
 5KQ  OAG  CAF  single  1.407  0.020  1.407
 5KQ  CAF  CAH  single  1.541  0.020  1.541
 5KQ  CAF  CAE  single  1.529  0.020  1.529
 5KQ  CAH  OAI  single  1.403  0.020  1.403
 5KQ  NAD  CAE  single  1.442  0.020  1.442
 5KQ  NAD  CAB  single  1.344  0.020  1.344
 5KQ  CAA  CAB  single  1.509  0.020  1.509
 5KQ  CAB  OAC  double  1.225  0.020  1.225
 5KQ  CAW  H1   single  0.970  0.020  1.090
 5KQ  CAW  H2   single  0.970  0.020  1.090
 5KQ  CAW  H3   single  0.970  0.020  1.090
 5KQ  NAU  H4   single  0.860  0.020  1.020
 5KQ  CAT  H5   single  0.970  0.020  1.090
 5KQ  CAR  H6   single  0.970  0.020  1.090
 5KQ  OAS  H7   single  0.850  0.020  0.980
 5KQ  CAQ  H8   single  0.970  0.020  1.090
 5KQ  CAQ  H9   single  0.970  0.020  1.090
 5KQ  OAP  H10  single  0.850  0.020  0.980
 5KQ  OAM  H11  single  0.850  0.020  0.980
 5KQ  CAJ  H12  single  0.970  0.020  1.090
 5KQ  CAH  H13  single  0.970  0.020  1.090
 5KQ  OAI  H14  single  0.850  0.020  0.980
 5KQ  CAF  H15  single  0.970  0.020  1.090
 5KQ  OAG  H16  single  0.850  0.020  0.980
 5KQ  CAE  H17  single  0.970  0.020  1.090
 5KQ  CAE  H18  single  0.970  0.020  1.090
 5KQ  NAD  H19  single  0.860  0.020  1.020
 5KQ  CAA  H20  single  0.970  0.020  1.090
 5KQ  CAA  H21  single  0.970  0.020  1.090
 5KQ  CAA  H22  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
 5KQ  H3   CAW  H2   108.63  3.000
 5KQ  H3   CAW  H1   107.35  3.000
 5KQ  H2   CAW  H1   108.19  3.000
 5KQ  H3   CAW  CAV  109.67  3.000
 5KQ  H2   CAW  CAV  113.66  3.000
 5KQ  H1   CAW  CAV  109.14  3.000
 5KQ  NAU  CAV  OAX  123.51  3.000
 5KQ  OAX  CAV  CAW  121.69  3.000
 5KQ  NAU  CAV  CAW  114.79  3.000
 5KQ  H4   NAU  CAT  116.81  3.000
 5KQ  H4   NAU  CAV  117.64  3.000
 5KQ  CAT  NAU  CAV  124.31  3.000
 5KQ  H5   CAT  CAJ  109.69  3.000
 5KQ  H5   CAT  CAR  109.35  3.000
 5KQ  CAJ  CAT  CAR  109.77  3.000
 5KQ  H5   CAT  NAU  108.38  3.000
 5KQ  CAJ  CAT  NAU  110.78  3.000
 5KQ  CAR  CAT  NAU  108.84  3.000
 5KQ  H6   CAR  CAQ  109.54  3.000
 5KQ  H6   CAR  OAS  109.94  3.000
 5KQ  CAQ  CAR  OAS  110.69  3.000
 5KQ  H6   CAR  CAT  107.45  3.000
 5KQ  CAQ  CAR  CAT  111.68  3.000
 5KQ  OAS  CAR  CAT  107.47  3.000
 5KQ  H7   OAS  CAR  108.29  3.000
 5KQ  H9   CAQ  H8   107.14  3.000
 5KQ  H9   CAQ  CAL  106.46  3.000
 5KQ  H8   CAQ  CAL  110.29  3.000
 5KQ  H9   CAQ  CAR  107.83  3.000
 5KQ  H8   CAQ  CAR  110.12  3.000
 5KQ  CAL  CAQ  CAR  114.65  3.000
 5KQ  OAK  CAL  OAM  106.94  3.000
 5KQ  OAK  CAL  CAN  107.28  3.000
 5KQ  OAM  CAL  CAN  107.86  3.000
 5KQ  OAK  CAL  CAQ  110.50  3.000
 5KQ  OAM  CAL  CAQ  107.84  3.000
 5KQ  CAN  CAL  CAQ  116.05  3.000
 5KQ  OAO  CAN  OAP  124.39  3.000
 5KQ  OAP  CAN  CAL  114.04  3.000
 5KQ  OAO  CAN  CAL  121.56  3.000
 5KQ  H10  OAP  CAN  110.71  3.000
 5KQ  H11  OAM  CAL  109.47  3.000
 5KQ  CAJ  OAK  CAL  119.68  3.000
 5KQ  H12  CAJ  CAH  109.03  3.000
 5KQ  H12  CAJ  OAK  110.92  3.000
 5KQ  CAH  CAJ  OAK  103.30  3.000
 5KQ  H12  CAJ  CAT  107.87  3.000
 5KQ  CAH  CAJ  CAT  115.48  3.000
 5KQ  OAK  CAJ  CAT  110.21  3.000
 5KQ  H13  CAH  CAF  109.29  3.000
 5KQ  H13  CAH  OAI  104.77  3.000
 5KQ  CAF  CAH  OAI  109.99  3.000
 5KQ  H13  CAH  CAJ  106.10  3.000
 5KQ  OAI  CAH  CAJ  115.22  3.000
 5KQ  CAF  CAH  CAJ  111.08  3.000
 5KQ  H14  OAI  CAH  109.13  3.000
 5KQ  H15  CAF  CAE  108.65  3.000
 5KQ  H15  CAF  OAG  105.18  3.000
 5KQ  CAE  CAF  OAG  111.10  3.000
 5KQ  H15  CAF  CAH  107.55  3.000
 5KQ  CAE  CAF  CAH  110.57  3.000
 5KQ  OAG  CAF  CAH  113.49  3.000
 5KQ  H16  OAG  CAF  109.08  3.000
 5KQ  H18  CAE  H17  107.18  3.000
 5KQ  H18  CAE  NAD  109.22  3.000
 5KQ  H17  CAE  NAD  108.04  3.000
 5KQ  H18  CAE  CAF  110.29  3.000
 5KQ  H17  CAE  CAF  109.37  3.000
 5KQ  NAD  CAE  CAF  112.57  3.000
 5KQ  H19  NAD  CAB  118.57  3.000
 5KQ  H19  NAD  CAE  117.57  3.000
 5KQ  CAB  NAD  CAE  123.47  3.000
 5KQ  CAA  CAB  OAC  121.72  3.000
 5KQ  OAC  CAB  NAD  122.88  3.000
 5KQ  CAA  CAB  NAD  115.39  3.000
 5KQ  H22  CAA  H21  107.30  3.000
 5KQ  H22  CAA  H20  108.66  3.000
 5KQ  H21  CAA  H20  108.23  3.000
 5KQ  H22  CAA  CAB  109.55  3.000
 5KQ  H21  CAA  CAB  109.23  3.000
 5KQ  H20  CAA  CAB  113.67  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
 5KQ  CONST_01  CAT  NAU  CAV  CAW  180.00   0.0  0
 5KQ  CONST_02  CAT  NAU  CAV  OAX    0.00   0.0  0
 5KQ  CONST_03  H10  OAP  CAN  CAL  180.00   0.0  0
 5KQ  CONST_04  CAA  CAB  NAD  CAE  180.00   0.0  0
 5KQ  CONST_05  OAC  CAB  NAD  CAE    0.00   0.0  0
 5KQ  CONST_06  H4   NAU  CAV  CAW    0.00   0.0  0
 5KQ  CONST_07  H19  NAD  CAB  OAC  180.00   0.0  0
 5KQ  Var_01    CAB  NAD  CAE  CAF  -89.29  30.0  1
 5KQ  Var_02    H1   CAW  CAV  OAX   70.93  30.0  3
 5KQ  Var_03    H20  CAA  CAB  NAD   -7.32  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
 5KQ  chir_01  CAT  CAR  NAU  CAJ  negativ
 5KQ  chir_02  CAR  OAS  CAT  CAQ  positiv
 5KQ  chir_03  CAL  OAK  CAQ  CAN  positiv
 5KQ  chir_04  CAJ  OAK  CAT  CAH  positiv
 5KQ  chir_05  CAH  OAI  CAJ  CAF  positiv
 5KQ  chir_06  CAF  OAG  CAH  CAE  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
 5KQ  plan-1  CAW  0.020
 5KQ  plan-1  CAV  0.020
 5KQ  plan-1  OAX  0.020
 5KQ  plan-1  NAU  0.020
 5KQ  plan-1  CAT  0.020
 5KQ  plan-1  H4   0.020
 5KQ  plan-2  CAE  0.020
 5KQ  plan-2  NAD  0.020
 5KQ  plan-2  CAB  0.020
 5KQ  plan-2  OAC  0.020
 5KQ  plan-2  CAA  0.020
 5KQ  plan-2  H19  0.020
 5KQ  plan-3  CAL  0.020
 5KQ  plan-3  CAN  0.020
 5KQ  plan-3  OAP  0.020
 5KQ  plan-3  OAO  0.020
 5KQ  plan-3  H10  0.020

