# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 17:01:27 2021
#   Inital geometry file: a 162 line input string
#   Ligand name: a 3 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCC(=O)OC[C@@H](O)[C@@H](OC)[C@@H]1OC(=C[C@H](NC(N)=N)[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
 LVO  LVO  '5-(acetylamino)-2,6-anhydro-4-carbamimidamido-3,4,5-trideoxy-7-O-methyl-9-O-octanoyl-D-glycero-D-galacto-non-2-enonic acid'  D-saccharide  69  33  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_LVO
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
 LVO  C2    C  C     0   0.237  31.7771  13.6833  -22.0764
 LVO  C3    C  C1    0  -0.323  32.4448  14.8019  -21.7955
 LVO  C4    C  CH1   0  -0.052  31.9593  15.7690  -20.7621
 LVO  C5    C  CH1   0  -0.143  30.9034  15.0958  -19.8688
 LVO  C6    C  CH1   0   0.047  29.9292  14.3062  -20.7477
 LVO  O6    O  O2    0  -0.481  30.6210  13.3168  -21.4962
 LVO  C1    C  C     0   0.498  32.2199  12.6705  -23.0715
 LVO  O1B   O  OH1   0  -0.589  33.3601  12.9927  -23.6616
 LVO  O1A   O  O     0  -0.432  31.5966  11.6663  -23.3033
 LVO  C7    C  CH1   0  -0.003  28.8483  13.5734  -19.9586
 LVO  C8    C  CH1   0  -0.000  27.8407  12.8772  -20.8842
 LVO  C9    C  CH2   0  -0.208  26.7503  12.1943  -20.0674
 LVO  O9    O  O2    0  -0.473  25.7748  11.6072  -20.9348
 LVO  CAN   C  C     0   0.603  25.9397  10.3452  -21.3342
 LVO  OAV   O  O     0  -0.446  26.8584   9.6500  -20.9823
 LVO  O7    O  O2    0  -0.499  29.4432  12.6109  -19.1230
 LVO  C13   C  CH3   0  -0.425  29.1875  12.7571  -17.7431
 LVO  O8    O  OH1   0  -0.670  27.2928  13.8697  -21.7210
 LVO  N4    N  NH1   0  -0.652  33.0556  16.3020  -19.9984
 LVO  C12   C  C     0   0.564  33.0628  17.5986  -19.5487
 LVO  N13   N  NH2   0  -0.841  34.0360  17.8408  -18.6058
 LVO  N12   N  N     0  -0.709  32.2790  18.4741  -20.0617
 LVO  C11   C  CH3   0  -0.784  29.9043  17.6892  -17.3307
 LVO  O10   O  O     0  -0.493  31.3086  15.7527  -17.1391
 LVO  N5    N  NH1   0  -0.620  30.2028  16.0831  -19.0891
 LVO  H3    H  H     0   0.279  33.3612  15.0375  -22.3174
 LVO  H4    H  HCH1  0   0.284  31.4977  16.6220  -21.2700
 LVO  H5    H  HCH1  0   0.279  31.4051  14.4114  -19.1814
 LVO  H6    H  HCH1  0   0.258  29.4475  15.0033  -21.4455
 LVO  H7    H  HCH1  0   0.247  28.3072  14.3315  -19.3755
 LVO  H8    H  HCH1  0   0.234  28.3697  12.1145  -21.4712
 LVO  H91   H  HCH2  0   0.247  27.1673  11.4440  -19.3969
 LVO  H92   H  HCH2  0   0.254  26.2022  12.9291  -19.4759
 LVO  C15   C  CH2   0  -0.584  24.8516   9.9277  -22.2847
 LVO  H131  H  HCH3  0   0.237  29.6292  11.8984  -17.2390
 LVO  H132  H  HCH3  0   0.225  29.6352  13.6648  -17.3303
 LVO  H133  H  HCH3  0   0.211  28.1163  12.7688  -17.5159
 LVO  HO8   H  HOH1  0   0.458  26.8126  13.4434  -22.4368
 LVO  HN41  H  HNH1  0   0.382  33.5881  15.6281  -19.4712
 LVO  HN13  H  HNH2  0   0.387  33.9450  18.7137  -18.1115
 LVO  HN14  H  HNH2  0   0.384  34.2688  17.0823  -17.9830
 LVO  HN12  H  H     0   0.320  32.4264  19.3812  -19.6366
 LVO  H111  H  HCH3  0   0.261  30.0339  17.7929  -16.2567
 LVO  H112  H  HCH3  0   0.265  30.3780  18.5392  -17.8257
 LVO  H113  H  HCH3  0   0.260  28.8411  17.7258  -17.5672
 LVO  HN5   H  HNH1  0   0.398  29.6911  16.7782  -19.6127
 LVO  C16   C  CH2   0  -0.419  24.7284   8.4210  -22.4532
 LVO  C17   C  CH2   0  -0.415  23.6469   8.0534  -23.4611
 LVO  C18   C  CH2   0  -0.412  23.4666   6.5491  -23.6186
 LVO  C19   C  CH2   0  -0.407  22.3962   6.1794  -24.6375
 LVO  C20   C  CH2   0  -0.418  22.1998   4.6760  -24.7895
 LVO  C21   C  CH3   0  -0.663  21.1280   4.3194  -25.8102
 LVO  HOB1  H  HOH1  0   0.491  33.6041  12.3079  -24.3016
 LVO  H23   H  HCH2  0   0.267  23.9022  10.3592  -21.9585
 LVO  H24   H  HCH2  0   0.278  25.0720  10.3968  -23.2510
 LVO  H25   H  HCH2  0   0.226  25.6841   8.0014  -22.7760
 LVO  H26   H  HCH2  0   0.225  24.4968   7.9619  -21.4875
 LVO  H27   H  HCH2  0   0.212  22.6948   8.5018  -23.1572
 LVO  H28   H  HCH2  0   0.213  23.8930   8.4938  -24.4337
 LVO  H29   H  HCH2  0   0.209  24.4204   6.0971  -23.9126
 LVO  H30   H  HCH2  0   0.209  23.2101   6.1118  -22.6473
 LVO  H31   H  HCH2  0   0.206  21.4451   6.6403  -24.3480
 LVO  H32   H  HCH2  0   0.207  22.6572   6.6104  -25.6105
 LVO  H33   H  HCH2  0   0.210  23.1494   4.2145  -25.0780
 LVO  H34   H  HCH2  0   0.210  21.9377   4.2461  -23.8177
 LVO  H35   H  HCH3  0   0.226  21.0038   3.2397  -25.9013
 LVO  H36   H  HCH3  0   0.216  20.1607   4.7404  -25.5292
 LVO  H37   H  HCH3  0   0.216  21.3797   4.7079  -26.7989
 LVO  C10   C  C     0   0.522  30.5451  16.4169  -17.8225

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
 LVO  C2   C3    double  1.333  0.020  1.333
 LVO  C2   O6    single  1.344  0.020  1.344
 LVO  C3   C4    single  1.496  0.020  1.496
 LVO  C3   H3    single  0.930  0.020  1.080
 LVO  C4   N4    single  1.439  0.020  1.439
 LVO  C4   C5    single  1.538  0.020  1.538
 LVO  C4   H4    single  0.970  0.020  1.090
 LVO  C5   N5    single  1.440  0.020  1.440
 LVO  C5   H5    single  0.970  0.020  1.090
 LVO  C6   C5    single  1.531  0.020  1.531
 LVO  C6   C7    single  1.526  0.020  1.526
 LVO  C6   H6    single  0.970  0.020  1.090
 LVO  O6   C6    single  1.420  0.020  1.420
 LVO  C1   C2    single  1.487  0.020  1.487
 LVO  O1B  C1    single  1.324  0.020  1.324
 LVO  O1A  C1    double  1.204  0.020  1.204
 LVO  C7   O7    single  1.407  0.020  1.407
 LVO  C7   H7    single  0.970  0.020  1.090
 LVO  C8   C7    single  1.535  0.020  1.535
 LVO  C8   C9    single  1.524  0.020  1.524
 LVO  C8   H8    single  0.970  0.020  1.090
 LVO  C9   H91   single  0.970  0.020  1.090
 LVO  C9   H92   single  0.970  0.020  1.090
 LVO  O9   C9    single  1.431  0.020  1.431
 LVO  CAN  O9    single  1.334  0.020  1.334
 LVO  CAN  OAV   double  1.205  0.020  1.205
 LVO  CAN  C15   single  1.504  0.020  1.504
 LVO  O7   C13   single  1.411  0.020  1.411
 LVO  C13  H131  single  0.970  0.020  1.090
 LVO  C13  H132  single  0.970  0.020  1.090
 LVO  C13  H133  single  0.970  0.020  1.090
 LVO  O8   C8    single  1.409  0.020  1.409
 LVO  O8   HO8   single  0.850  0.020  0.980
 LVO  N4   C12   single  1.372  0.020  1.372
 LVO  N4   HN41  single  0.890  0.020  1.040
 LVO  C12  N13   single  1.377  0.020  1.377
 LVO  N13  HN13  single  0.890  0.020  1.040
 LVO  N13  HN14  single  0.890  0.020  1.040
 LVO  N12  C12   double  1.282  0.020  1.282
 LVO  N12  HN12  single  0.890  0.020  1.040
 LVO  C10  O10   double  1.221  0.020  1.221
 LVO  C10  C11   single  1.507  0.020  1.507
 LVO  C11  H111  single  0.970  0.020  1.090
 LVO  C11  H112  single  0.970  0.020  1.090
 LVO  C11  H113  single  0.970  0.020  1.090
 LVO  N5   C10   single  1.354  0.020  1.354
 LVO  N5   HN5   single  0.890  0.020  1.040
 LVO  C15  C16   single  1.521  0.020  1.521
 LVO  C16  C17   single  1.523  0.020  1.523
 LVO  C17  C18   single  1.523  0.020  1.523
 LVO  C18  C19   single  1.523  0.020  1.523
 LVO  C19  C20   single  1.524  0.020  1.524
 LVO  C20  C21   single  1.522  0.020  1.522
 LVO  O1B  HOB1  single  0.850  0.020  0.980
 LVO  C15  H23   single  0.970  0.020  1.090
 LVO  C15  H24   single  0.970  0.020  1.090
 LVO  C16  H25   single  0.970  0.020  1.090
 LVO  C16  H26   single  0.970  0.020  1.090
 LVO  C17  H27   single  0.970  0.020  1.090
 LVO  C17  H28   single  0.970  0.020  1.090
 LVO  C18  H29   single  0.970  0.020  1.090
 LVO  C18  H30   single  0.970  0.020  1.090
 LVO  C19  H31   single  0.970  0.020  1.090
 LVO  C19  H32   single  0.970  0.020  1.090
 LVO  C20  H33   single  0.970  0.020  1.090
 LVO  C20  H34   single  0.970  0.020  1.090
 LVO  C21  H35   single  0.970  0.020  1.090
 LVO  C21  H36   single  0.970  0.020  1.090
 LVO  C21  H37   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
 LVO  C1    C2   O6    111.05  3.000
 LVO  C1    C2   C3    124.29  3.000
 LVO  O6    C2   C3    124.66  3.000
 LVO  H3    C3   C4    117.89  3.000
 LVO  H3    C3   C2    120.41  3.000
 LVO  C4    C3   C2    121.70  3.000
 LVO  H4    C4   N4    106.20  3.000
 LVO  H4    C4   C5    108.72  3.000
 LVO  N4    C4   C5    112.15  3.000
 LVO  H4    C4   C3    108.66  3.000
 LVO  C5    C4   C3    109.93  3.000
 LVO  N4    C4   C3    111.03  3.000
 LVO  H5    C5   N5    108.20  3.000
 LVO  H5    C5   C6    109.29  3.000
 LVO  N5    C5   C6    110.78  3.000
 LVO  C6    C5   C4    109.21  3.000
 LVO  H5    C5   C4    108.93  3.000
 LVO  N5    C5   C4    110.39  3.000
 LVO  H6    C6   C7    108.83  3.000
 LVO  H6    C6   O6    108.73  3.000
 LVO  C7    C6   O6    106.45  3.000
 LVO  O6    C6   C5    110.59  3.000
 LVO  H6    C6   C5    108.46  3.000
 LVO  C7    C6   C5    113.67  3.000
 LVO  C6    O6   C2    117.16  3.000
 LVO  O1A   C1   O1B   124.25  3.000
 LVO  O1A   C1   C2    122.85  3.000
 LVO  O1B   C1   C2    112.89  3.000
 LVO  HOB1  O1B  C1    109.85  3.000
 LVO  H7    C7   O7    111.42  3.000
 LVO  H7    C7   C8    108.04  3.000
 LVO  O7    C7   C8    108.99  3.000
 LVO  C8    C7   C6    111.78  3.000
 LVO  H7    C7   C6    106.98  3.000
 LVO  O7    C7   C6    109.64  3.000
 LVO  H8    C8   O8    111.04  3.000
 LVO  O8    C8   C9    110.84  3.000
 LVO  H8    C8   C9    108.66  3.000
 LVO  O8    C8   C7    107.09  3.000
 LVO  H8    C8   C7    108.72  3.000
 LVO  C9    C8   C7    110.47  3.000
 LVO  H92   C9   H91   108.81  3.000
 LVO  H92   C9   O9    105.22  3.000
 LVO  H91   C9   O9    110.58  3.000
 LVO  O9    C9   C8    110.28  3.000
 LVO  H92   C9   C8    110.38  3.000
 LVO  H91   C9   C8    111.39  3.000
 LVO  CAN   O9   C9    119.03  3.000
 LVO  C15   CAN  OAV   125.19  3.000
 LVO  C15   CAN  O9    111.25  3.000
 LVO  OAV   CAN  O9    123.56  3.000
 LVO  C13   O7   C7    115.68  3.000
 LVO  H133  C13  H132  108.27  3.000
 LVO  H133  C13  H131  108.01  3.000
 LVO  H132  C13  H131  108.29  3.000
 LVO  H133  C13  O7    112.41  3.000
 LVO  H132  C13  O7    112.40  3.000
 LVO  H131  C13  O7    107.30  3.000
 LVO  HO8   O8   C8    108.90  3.000
 LVO  HN41  N4   C12   117.24  3.000
 LVO  HN41  N4   C4    115.63  3.000
 LVO  C12   N4   C4    121.87  3.000
 LVO  N12   C12  N13   125.88  3.000
 LVO  N12   C12  N4    120.72  3.000
 LVO  N13   C12  N4    113.22  3.000
 LVO  HN14  N13  HN13  111.68  3.000
 LVO  HN14  N13  C12   116.99  3.000
 LVO  HN13  N13  C12   115.13  3.000
 LVO  HN12  N12  C12   110.78  3.000
 LVO  H113  C11  H112  107.38  3.000
 LVO  H113  C11  H111  109.12  3.000
 LVO  H112  C11  H111  108.79  3.000
 LVO  H113  C11  C10   111.86  3.000
 LVO  H112  C11  C10   108.96  3.000
 LVO  H111  C11  C10   110.63  3.000
 LVO  HN5   N5   C10   116.33  3.000
 LVO  HN5   N5   C5    115.97  3.000
 LVO  C10   N5   C5    123.55  3.000
 LVO  H24   C15  H23   105.59  3.000
 LVO  H24   C15  C16   110.02  3.000
 LVO  H23   C15  C16   110.72  3.000
 LVO  H24   C15  CAN   107.02  3.000
 LVO  H23   C15  CAN   109.29  3.000
 LVO  C16   C15  CAN   113.80  3.000
 LVO  H26   C16  H25   106.54  3.000
 LVO  H26   C16  C17   109.42  3.000
 LVO  H25   C16  C17   109.44  3.000
 LVO  H26   C16  C15   109.58  3.000
 LVO  H25   C16  C15   110.02  3.000
 LVO  C17   C16  C15   111.71  3.000
 LVO  H28   C17  H27   106.08  3.000
 LVO  H28   C17  C18   109.38  3.000
 LVO  H27   C17  C18   109.28  3.000
 LVO  H28   C17  C16   109.32  3.000
 LVO  H27   C17  C16   109.55  3.000
 LVO  C18   C17  C16   113.00  3.000
 LVO  H30   C18  H29   106.09  3.000
 LVO  H30   C18  C19   109.36  3.000
 LVO  H29   C18  C19   109.40  3.000
 LVO  H30   C18  C17   109.28  3.000
 LVO  H29   C18  C17   109.39  3.000
 LVO  C19   C18  C17   113.08  3.000
 LVO  H32   C19  H31   106.01  3.000
 LVO  H32   C19  C20   109.28  3.000
 LVO  H31   C19  C20   109.24  3.000
 LVO  H32   C19  C18   109.34  3.000
 LVO  H31   C19  C18   109.34  3.000
 LVO  C20   C19  C18   113.37  3.000
 LVO  H34   C20  H33   106.03  3.000
 LVO  H34   C20  C21   109.55  3.000
 LVO  H33   C20  C21   109.59  3.000
 LVO  H34   C20  C19   109.26  3.000
 LVO  H33   C20  C19   109.30  3.000
 LVO  C21   C20  C19   112.88  3.000
 LVO  H37   C21  H36   107.47  3.000
 LVO  H37   C21  H35   107.63  3.000
 LVO  H36   C21  H35   107.60  3.000
 LVO  H37   C21  C20   111.19  3.000
 LVO  H36   C21  C20   111.15  3.000
 LVO  H35   C21  C20   111.60  3.000
 LVO  N5    C10  O10   123.20  3.000
 LVO  N5    C10  C11   113.95  3.000
 LVO  O10   C10  C11   122.85  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
 LVO  CONST_01  O10   C10  N5   C5      0.00   0.0  0
 LVO  CONST_02  C11   C10  N5   C5    180.00   0.0  0
 LVO  CONST_03  N13   C12  N4   C4    180.00   0.0  0
 LVO  CONST_05  HOB1  O1B  C1   C2    180.00   0.0  0
 LVO  CONST_06  HN5   N5   C10  C11     0.00   0.0  0
 LVO  CONST_07  HN13  N13  C12  N4    180.00   0.0  0
 LVO  CONST_09  HN12  N12  C12  N4    180.00   0.0  0
 LVO  CONST_10  HN41  N4   C12  N13     0.00   0.0  0
 LVO  Var_01    O6    C2   C3   C4      0.90  30.0  1
 LVO  Var_02    O1B   C1   C2   C3     -0.03  30.0  2
 LVO  Var_03    OAV   CAN  O9   C9      1.62  30.0  1
 LVO  Var_04    C16   C15  CAN  O9   -162.67  30.0  3
 LVO  Var_05    C17   C16  C15  CAN  -177.99  30.0  3
 LVO  Var_06    C18   C17  C16  C15  -178.09  30.0  3
 LVO  Var_07    C19   C18  C17  C16  -179.37  30.0  3
 LVO  Var_08    C20   C19  C18  C17  -179.38  30.0  3
 LVO  Var_09    C21   C20  C19  C18  -179.99  30.0  3
 LVO  Var_10    H131  C13  O7   C7    174.84  30.0  3
 LVO  Var_11    H91   C9   O9   CAN   -33.17  30.0  3
 LVO  Var_12    H111  C11  C10  O10   -12.75  30.0  3
 LVO  Var_13    H35   C21  C20  C19  -179.92  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
 LVO  chir_01  C4  C3  N4  C5  positiv
 LVO  chir_02  C5  N5  C6  C4  negativ
 LVO  chir_03  C6  O6  C5  C7  positiv
 LVO  chir_04  C7  O7  C8  C6  positiv
 LVO  chir_05  C8  O8  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
 LVO  plan-1  C5    0.020
 LVO  plan-1  C11   0.020
 LVO  plan-1  O10   0.020
 LVO  plan-1  N5    0.020
 LVO  plan-1  HN5   0.020
 LVO  plan-1  C10   0.020
 LVO  plan-2  C4    0.020
 LVO  plan-2  N4    0.020
 LVO  plan-2  C12   0.020
 LVO  plan-2  N13   0.020
 LVO  plan-2  N12   0.020
 LVO  plan-2  HN41  0.020
 LVO  plan-2  HN13  0.020
 LVO  plan-2  HN14  0.020
 LVO  plan-2  HN12  0.020
 LVO  plan-3  C2    0.020
 LVO  plan-3  C1    0.020
 LVO  plan-3  O1B   0.020
 LVO  plan-3  O1A   0.020
 LVO  plan-3  HOB1  0.020
 LVO  plan-4  O9    0.020
 LVO  plan-4  CAN   0.020
 LVO  plan-4  OAV   0.020
 LVO  plan-4  C15   0.020

