# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Nov 17 13:20:02 2022
#   Inital geometry file: a 76 line input string
#   Ligand name: 3-deoxy-4-O-methyl-alpha-D-manno-oct-2-ulopyranosonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1C[C@@](O)(O[C@H]([C@H](O)CO)[C@@H]1O)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
 K71  K71  "3-deoxy-4-O-methyl-alpha-D-manno-oct-2-ulopyranosonic acid"  ligand  33  17  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_K71
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
 K71  CAQ  C  CH3   0  -0.408  20.0374   0.0557  35.0007
 K71  OAI  O  O2    0  -0.485  19.0301   0.4447  35.9011
 K71  CAC  C  CH1   0   0.062  19.4949   1.0459  37.0809
 K71  CAB  C  CH1   0  -0.017  20.1356   2.4174  36.8585
 K71  OAJ  O  OH1   0  -0.672  19.2358   3.2228  36.1382
 K71  CAD  C  CH2   0  -0.503  18.3019   1.1556  38.0210
 K71  CAE  C  CT    0   0.405  18.7086   1.8503  39.3218
 K71  CAG  C  C     0   0.486  17.4387   2.2351  40.1028
 K71  OAM  O  OH1   0  -0.584  16.8892   1.1718  40.6662
 K71  OAL  O  O     0  -0.412  16.9874   3.3461  40.1634
 K71  OAH  O  OH1   0  -0.654  19.5006   0.9621  40.0435
 K71  OAF  O  O2    0  -0.510  19.3519   3.0560  39.0747
 K71  CAA  C  CH1   0   0.012  20.4909   2.9977  38.2309
 K71  CAK  C  CH1   0  -0.015  21.0112   4.4340  38.1680
 K71  OAN  O  OH1   0  -0.670  22.0604   4.4408  37.2259
 K71  CAO  C  CH2   0  -0.177  21.4465   4.9660  39.5252
 K71  OAP  O  OH1   0  -0.667  22.4407   4.1349  40.0732
 K71  H1   H  HCH3  0   0.236  19.5643  -0.5298  34.2131
 K71  H2   H  HCH3  0   0.209  20.5424   0.9064  34.5317
 K71  H3   H  HCH3  0   0.204  20.8002  -0.5679  35.4820
 K71  H4   H  HCH1  0   0.221  20.2638   0.4086  37.5436
 K71  H5   H  HCH1  0   0.241  21.0758   2.2830  36.3106
 K71  H6   H  HOH1  0   0.455  19.7241   3.9559  35.7521
 K71  H7   H  HCH2  0   0.262  17.5094   1.7331  37.5386
 K71  H8   H  HCH2  0   0.268  17.8993   0.1651  38.2384
 K71  H9   H  HOH1  0   0.485  16.0683   1.4220  41.1178
 K71  H10  H  HOH1  0   0.458  19.8093   1.3818  40.8564
 K71  H11  H  HCH1  0   0.231  21.2639   2.3539  38.6694
 K71  H12  H  HCH1  0   0.215  20.1833   5.0799  37.8403
 K71  H13  H  HOH1  0   0.456  22.3274   5.3529  37.0737
 K71  H14  H  HCH2  0   0.207  21.8116   5.9940  39.3833
 K71  H15  H  HCH2  0   0.204  20.5645   5.0384  40.1716
 K71  H16  H  HOH1  0   0.455  22.6661   4.4704  40.9451

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
 K71  CAQ  OAI  single  1.406  0.020  1.406
 K71  OAI  CAC  single  1.403  0.020  1.403
 K71  OAJ  CAB  single  1.406  0.020  1.406
 K71  CAB  CAC  single  1.530  0.020  1.530
 K71  CAB  CAA  single  1.532  0.020  1.532
 K71  CAC  CAD  single  1.523  0.020  1.523
 K71  OAN  CAK  single  1.410  0.020  1.410
 K71  CAD  CAE  single  1.530  0.020  1.530
 K71  CAK  CAA  single  1.529  0.020  1.529
 K71  CAK  CAO  single  1.521  0.020  1.521
 K71  CAA  OAF  single  1.419  0.020  1.419
 K71  OAF  CAE  single  1.389  0.020  1.389
 K71  CAE  OAH  single  1.392  0.020  1.392
 K71  CAE  CAG  single  1.540  0.020  1.540
 K71  CAO  OAP  single  1.407  0.020  1.407
 K71  OAL  CAG  double  1.201  0.020  1.201
 K71  CAG  OAM  single  1.323  0.020  1.323
 K71  CAQ  H1   single  0.970  0.020  1.090
 K71  CAQ  H2   single  0.970  0.020  1.090
 K71  CAQ  H3   single  0.970  0.020  1.090
 K71  CAC  H4   single  0.970  0.020  1.090
 K71  CAB  H5   single  0.970  0.020  1.090
 K71  OAJ  H6   single  0.850  0.020  0.980
 K71  CAD  H7   single  0.970  0.020  1.090
 K71  CAD  H8   single  0.970  0.020  1.090
 K71  OAM  H9   single  0.850  0.020  0.980
 K71  OAH  H10  single  0.850  0.020  0.980
 K71  CAA  H11  single  0.970  0.020  1.090
 K71  CAK  H12  single  0.970  0.020  1.090
 K71  OAN  H13  single  0.850  0.020  0.980
 K71  CAO  H14  single  0.970  0.020  1.090
 K71  CAO  H15  single  0.970  0.020  1.090
 K71  OAP  H16  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
 K71  H3   CAQ  H2   108.01  3.000
 K71  H3   CAQ  H1   108.29  3.000
 K71  H2   CAQ  H1   107.94  3.000
 K71  H3   CAQ  OAI  112.01  3.000
 K71  H2   CAQ  OAI  112.94  3.000
 K71  H1   CAQ  OAI  107.49  3.000
 K71  CAC  OAI  CAQ  114.81  3.000
 K71  H4   CAC  CAD  109.23  3.000
 K71  H4   CAC  CAB  106.72  3.000
 K71  CAD  CAC  CAB  110.69  3.000
 K71  H4   CAC  OAI  109.68  3.000
 K71  CAD  CAC  OAI  106.88  3.000
 K71  CAB  CAC  OAI  113.61  3.000
 K71  H5   CAB  CAA  107.17  3.000
 K71  H5   CAB  OAJ  111.28  3.000
 K71  CAA  CAB  OAJ  112.98  3.000
 K71  H5   CAB  CAC  108.77  3.000
 K71  CAA  CAB  CAC  107.85  3.000
 K71  OAJ  CAB  CAC  108.66  3.000
 K71  H6   OAJ  CAB  108.50  3.000
 K71  H8   CAD  H7   107.47  3.000
 K71  H8   CAD  CAE  109.93  3.000
 K71  H7   CAD  CAE  109.15  3.000
 K71  H8   CAD  CAC  110.29  3.000
 K71  H7   CAD  CAC  109.49  3.000
 K71  CAE  CAD  CAC  110.45  3.000
 K71  OAF  CAE  OAH  112.51  3.000
 K71  OAH  CAE  CAG  111.46  3.000
 K71  OAF  CAE  CAG  104.79  3.000
 K71  CAG  CAE  CAD  109.00  3.000
 K71  OAH  CAE  CAD  107.60  3.000
 K71  OAF  CAE  CAD  111.47  3.000
 K71  OAL  CAG  OAM  124.48  3.000
 K71  OAM  CAG  CAE  110.96  3.000
 K71  OAL  CAG  CAE  124.54  3.000
 K71  H9   OAM  CAG  110.03  3.000
 K71  H10  OAH  CAE  109.94  3.000
 K71  CAA  OAF  CAE  116.23  3.000
 K71  H11  CAA  CAK  109.14  3.000
 K71  H11  CAA  OAF  110.61  3.000
 K71  CAK  CAA  OAF  105.01  3.000
 K71  H11  CAA  CAB  107.40  3.000
 K71  OAF  CAA  CAB  111.23  3.000
 K71  CAK  CAA  CAB  113.45  3.000
 K71  H12  CAK  CAO  106.01  3.000
 K71  H12  CAK  OAN  110.98  3.000
 K71  CAO  CAK  OAN  112.42  3.000
 K71  H12  CAK  CAA  107.92  3.000
 K71  CAO  CAK  CAA  112.91  3.000
 K71  OAN  CAK  CAA  106.57  3.000
 K71  H13  OAN  CAK  108.46  3.000
 K71  H15  CAO  H14  106.35  3.000
 K71  H15  CAO  OAP  112.20  3.000
 K71  H14  CAO  OAP  111.58  3.000
 K71  H15  CAO  CAK  108.60  3.000
 K71  H14  CAO  CAK  107.86  3.000
 K71  OAP  CAO  CAK  110.06  3.000
 K71  H16  OAP  CAO  108.24  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
 K71  CONST_01  H9  OAM  CAG  CAE  180.00   0.0  0
 K71  CONST_02  H9  OAM  CAG  OAL    0.00   0.0  0
 K71  Var_01    H1  CAQ  OAI  CAC  171.27  30.0  3
 K71  Var_02    H2  CAQ  OAI  CAC  -69.77  30.0  3
 K71  Var_03    H3  CAQ  OAI  CAC   52.44  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
 K71  chir_01  CAC  OAI  CAB  CAD  negativ
 K71  chir_02  CAB  OAJ  CAA  CAC  negativ
 K71  chir_03  CAE  OAF  CAG  CAD  negativ
 K71  chir_04  CAA  OAF  CAK  CAB  positiv
 K71  chir_05  CAK  OAN  CAA  CAO  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
 K71  plan-1  CAE  0.020
 K71  plan-1  CAG  0.020
 K71  plan-1  OAM  0.020
 K71  plan-1  OAL  0.020
 K71  plan-1  H9   0.020

