# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jun 26 20:44:34 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: methyl 5-(acetylamino)-3,5,9-trideoxy-9-[(phenylcarbonyl)amino]-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@]1(C[C@H](O)[C@@H](NC(C)=O)[C@@H](O1)[C@H](O)[C@H](O)CNC(=O)c2ccccc2)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
 BND  BND  'methyl 5-(acetylamino)-3,5,9-trideoxy-9-[(phenylcarbonyl)amino]-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid'  D-saccharide  55  30  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_BND
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
 BND  CY1   C  CH3    0  -0.419   3.7838   1.5624  -1.3602
 BND  CX1   C  C      0   0.344   2.7519  -0.8025  -2.5515
 BND  O1A   O  O      0  -0.573   2.5656  -1.4500  -1.5100
 BND  O1B   O  OC    -1  -0.596   3.4731  -1.1100  -3.5190
 BND  CX2   C  CT     0   0.437   2.0445   0.5894  -2.6823
 BND  OX2   O  O2     0  -0.508   2.9672   1.6191  -2.5123
 BND  CX3   C  CH2    0  -0.528   1.4169   0.7914  -4.0551
 BND  CX4   C  CH1    0   0.067   0.2249  -0.1336  -4.2473
 BND  OX4   O  OH1    0  -0.666  -0.4344   0.0923  -5.4710
 BND  CX5   C  CH1    0  -0.114  -0.7855   0.0934  -3.1283
 BND  NX5   N  NH1    0  -0.626  -1.8668  -0.8582  -3.2010
 BND  C10   C  C      0   0.507  -3.1308  -0.5658  -3.5673
 BND  O10   O  O      0  -0.497  -3.5146   0.5678  -3.8132
 BND  C11   C  CH3    0  -0.788  -4.0453  -1.7665  -3.6328
 BND  CX6   C  CH1    0   0.026  -0.0955  -0.0232  -1.7605
 BND  OX6   O  O2     0  -0.521   1.0565   0.7821  -1.6930
 BND  CX7   C  CH1    0  -0.001  -0.9942   0.4663  -0.6235
 BND  OX7   O  OH1    0  -0.667  -1.1770   1.8593  -0.6885
 BND  CX8   C  CH1    0  -0.032  -0.4511   0.0197   0.7438
 BND  OX8   O  OH1    0  -0.660  -0.4923  -1.3874   0.8603
 BND  CX9   C  CH2    0  -0.266  -1.2041   0.6877   1.8892
 BND  NX6   N  NH1    0  -0.651  -0.7101   0.1861   3.1509
 BND  C12   C  C      0   0.528  -0.8637   0.8415   4.3116
 BND  O12   O  O      0  -0.493  -1.4359   1.9207   4.3992
 BND  C1G   C  CR6    0  -0.034  -0.2860   0.1722   5.5184
 BND  CD1   C  CR16   0  -0.271  -0.8641   0.4322   6.7589
 BND  CE1   C  CR16   0  -0.243  -0.3576  -0.1589   7.9059
 BND  CD2   C  CR16   0  -0.290   0.8248  -0.6667   5.4466
 BND  CE2   C  CR16   0  -0.242   1.3400  -1.2462   6.5974
 BND  C1Z   C  CR16   0  -0.251   0.7465  -0.9987   7.8277
 BND  HY11  H  HCH3   0   0.232   4.3571   2.4882  -1.3411
 BND  HY12  H  HCH3   0   0.216   3.2058   1.4971  -0.4359
 BND  HY13  H  HCH3   0   0.209   4.4907   0.7282  -1.3878
 BND  HX31  H  HCH2   0   0.233   1.0805   1.8301  -4.1441
 BND  HX32  H  HCH2   0   0.247   2.1614   0.6149  -4.8329
 BND  HX4   H  HCH1   0   0.200   0.5721  -1.1776  -4.1907
 BND  HA    H  HOH1   0   0.450   0.1778  -0.1162  -6.1840
 BND  HX5   H  HCH1   0   0.256  -1.2087   1.0943  -3.2385
 BND  HB    H  HNH1   0   0.396  -1.6309  -1.8294  -3.0626
 BND  H111  H  HCH3   0   0.259  -5.0501  -1.4630  -3.9142
 BND  H112  H  HCH3   0   0.263  -3.6808  -2.4906  -4.3627
 BND  H113  H  HCH3   0   0.263  -4.0902  -2.2744  -2.6684
 BND  HX6   H  HCH1   0   0.232   0.1548  -1.0762  -1.5838
 BND  HX7   H  HCH1   0   0.239  -1.9885   0.0211  -0.7491
 BND  HC    H  HOH1   0   0.444  -0.3081   2.2597  -0.8146
 BND  HX8   H  HCH1   0   0.249   0.6075   0.2862   0.8219
 BND  HD    H  HOH1   0   0.447  -1.4085  -1.6782   0.7814
 BND  HX91  H  HCH2   0   0.254  -1.0583   1.7654   1.8517
 BND  HX92  H  HCH2   0   0.232  -2.2820   0.5043   1.7908
 BND  HE    H  HNH1   0   0.399  -0.4029  -0.7739   3.1668
 BND  HD1   H  HCR6   0   0.260  -1.7200   1.0909   6.8255
 BND  HE1   H  HCR6   0   0.262  -0.8234   0.0368   8.8628
 BND  HD2   H  HCR6   0   0.258   1.3166  -0.8540   4.5002
 BND  HE2   H  HCR6   0   0.264   2.2095  -1.8868   6.5324
 BND  H1Z   H  HCR6   0   0.264   1.1456  -1.4554   8.7240

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
 BND  CY1  OX2   single    1.413  0.020  1.413
 BND  CY1  HY11  single    0.970  0.020  1.090
 BND  CY1  HY12  single    0.970  0.020  1.090
 BND  CY1  HY13  single    0.970  0.020  1.090
 BND  CX1  O1A   deloc     1.240  0.020  1.240
 BND  CX1  O1B   deloc     1.245  0.020  1.245
 BND  CX1  CX2   single    1.567  0.020  1.567
 BND  CX2  OX2   single    1.393  0.020  1.393
 BND  CX2  CX3   single    1.523  0.020  1.523
 BND  CX2  OX6   single    1.411  0.020  1.411
 BND  CX3  CX4   single    1.521  0.020  1.521
 BND  CX3  HX31  single    0.970  0.020  1.090
 BND  CX3  HX32  single    0.970  0.020  1.090
 BND  CX4  OX4   single    1.408  0.020  1.408
 BND  CX4  CX5   single    1.525  0.020  1.525
 BND  CX4  HX4   single    0.970  0.020  1.090
 BND  OX4  HA    single    0.850  0.020  0.980
 BND  CX5  NX5   single    1.442  0.020  1.442
 BND  CX5  CX6   single    1.536  0.020  1.536
 BND  CX5  HX5   single    0.970  0.020  1.090
 BND  NX5  C10   single    1.348  0.020  1.348
 BND  NX5  HB    single    0.860  0.020  1.020
 BND  C10  O10   double    1.222  0.020  1.222
 BND  C10  C11   single    1.511  0.020  1.511
 BND  C11  H111  single    0.970  0.020  1.090
 BND  C11  H112  single    0.970  0.020  1.090
 BND  C11  H113  single    0.970  0.020  1.090
 BND  CX6  OX6   single    1.407  0.020  1.407
 BND  CX6  CX7   single    1.530  0.020  1.530
 BND  CX6  HX6   single    0.970  0.020  1.090
 BND  CX7  OX7   single    1.406  0.020  1.406
 BND  CX7  CX8   single    1.538  0.020  1.538
 BND  CX7  HX7   single    0.970  0.020  1.090
 BND  OX7  HC    single    0.850  0.020  0.980
 BND  CX8  OX8   single    1.412  0.020  1.412
 BND  CX8  CX9   single    1.525  0.020  1.525
 BND  CX8  HX8   single    0.970  0.020  1.090
 BND  OX8  HD    single    0.850  0.020  0.980
 BND  CX9  NX6   single    1.445  0.020  1.445
 BND  CX9  HX91  single    0.970  0.020  1.090
 BND  CX9  HX92  single    0.970  0.020  1.090
 BND  NX6  C12   single    1.342  0.020  1.342
 BND  NX6  HE    single    0.860  0.020  1.020
 BND  C12  O12   double    1.225  0.020  1.225
 BND  C12  C1G   single    1.496  0.020  1.496
 BND  C1G  CD1   aromatic  1.393  0.020  1.393
 BND  C1G  CD2   aromatic  1.394  0.020  1.394
 BND  CD1  CE1   aromatic  1.386  0.020  1.386
 BND  CD1  HD1   single    0.930  0.020  1.080
 BND  CE1  C1Z   aromatic  1.389  0.020  1.389
 BND  CE1  HE1   single    0.930  0.020  1.080
 BND  CD2  CE2   aromatic  1.388  0.020  1.388
 BND  CD2  HD2   single    0.930  0.020  1.080
 BND  CE2  C1Z   aromatic  1.388  0.020  1.388
 BND  CE2  HE2   single    0.930  0.020  1.080
 BND  C1Z  H1Z   single    0.930  0.020  1.080

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
 BND  HY13  CY1  HY12  108.53  3.000
 BND  HY13  CY1  HY11  107.97  3.000
 BND  HY12  CY1  HY11  108.34  3.000
 BND  HY13  CY1  OX2   112.54  3.000
 BND  HY12  CY1  OX2   112.74  3.000
 BND  HY11  CY1  OX2   106.52  3.000
 BND  CX2   CX1  O1B   114.58  3.000
 BND  CX2   CX1  O1A   117.77  3.000
 BND  O1B   CX1  O1A   127.62  3.000
 BND  OX6   CX2  CX3   108.98  3.000
 BND  OX6   CX2  OX2   106.10  3.000
 BND  CX3   CX2  OX2   106.55  3.000
 BND  OX6   CX2  CX1   112.26  3.000
 BND  CX3   CX2  CX1   112.28  3.000
 BND  OX2   CX2  CX1   110.33  3.000
 BND  CX2   OX2  CY1   116.91  3.000
 BND  HX32  CX3  HX31  107.76  3.000
 BND  HX32  CX3  CX4   110.26  3.000
 BND  HX31  CX3  CX4   109.01  3.000
 BND  HX32  CX3  CX2   109.88  3.000
 BND  HX31  CX3  CX2   109.00  3.000
 BND  CX4   CX3  CX2   110.86  3.000
 BND  HX4   CX4  CX5   108.19  3.000
 BND  HX4   CX4  OX4   110.14  3.000
 BND  CX5   CX4  OX4   107.67  3.000
 BND  HX4   CX4  CX3   108.83  3.000
 BND  CX5   CX4  CX3   109.64  3.000
 BND  OX4   CX4  CX3   112.28  3.000
 BND  HA    OX4  CX4   108.13  3.000
 BND  HX5   CX5  CX6   109.47  3.000
 BND  HX5   CX5  NX5   108.00  3.000
 BND  CX6   CX5  NX5   109.36  3.000
 BND  HX5   CX5  CX4   108.61  3.000
 BND  CX6   CX5  CX4   110.15  3.000
 BND  NX5   CX5  CX4   111.20  3.000
 BND  HB    NX5  C10   117.73  3.000
 BND  HB    NX5  CX5   116.93  3.000
 BND  C10   NX5  CX5   125.00  3.000
 BND  C11   C10  O10   122.58  3.000
 BND  C11   C10  NX5   114.01  3.000
 BND  O10   C10  NX5   123.40  3.000
 BND  H113  C11  H112  107.23  3.000
 BND  H113  C11  H111  108.72  3.000
 BND  H112  C11  H111  108.73  3.000
 BND  H113  C11  C10   110.89  3.000
 BND  H112  C11  C10   110.75  3.000
 BND  H111  C11  C10   110.43  3.000
 BND  HX6   CX6  CX7   108.76  3.000
 BND  HX6   CX6  OX6   110.79  3.000
 BND  CX7   CX6  OX6   105.20  3.000
 BND  HX6   CX6  CX5   108.59  3.000
 BND  CX7   CX6  CX5   111.93  3.000
 BND  OX6   CX6  CX5   111.53  3.000
 BND  CX6   OX6  CX2   117.47  3.000
 BND  HX7   CX7  CX8   107.71  3.000
 BND  HX7   CX7  OX7   106.20  3.000
 BND  CX8   CX7  OX7   112.01  3.000
 BND  HX7   CX7  CX6   108.52  3.000
 BND  CX8   CX7  CX6   111.13  3.000
 BND  OX7   CX7  CX6   111.04  3.000
 BND  HC    OX7  CX7   107.45  3.000
 BND  HX8   CX8  CX9   108.51  3.000
 BND  HX8   CX8  OX8   105.36  3.000
 BND  CX9   CX8  OX8   111.11  3.000
 BND  HX8   CX8  CX7   109.53  3.000
 BND  CX9   CX8  CX7   111.48  3.000
 BND  OX8   CX8  CX7   110.64  3.000
 BND  HD    OX8  CX8   108.74  3.000
 BND  HX92  CX9  HX91  107.10  3.000
 BND  HX92  CX9  NX6   110.85  3.000
 BND  HX91  CX9  NX6   109.15  3.000
 BND  HX92  CX9  CX8   110.14  3.000
 BND  HX91  CX9  CX8   109.99  3.000
 BND  NX6   CX9  CX8   109.57  3.000
 BND  HE    NX6  C12   119.11  3.000
 BND  HE    NX6  CX9   116.65  3.000
 BND  C12   NX6  CX9   123.14  3.000
 BND  C1G   C12  O12   121.13  3.000
 BND  C1G   C12  NX6   115.79  3.000
 BND  O12   C12  NX6   123.08  3.000
 BND  CD2   C1G  CD1   119.27  3.000
 BND  CD2   C1G  C12   122.38  3.000
 BND  CD1   C1G  C12   118.33  3.000
 BND  HD1   CD1  CE1   119.85  3.000
 BND  HD1   CD1  C1G   119.78  3.000
 BND  CE1   CD1  C1G   120.37  3.000
 BND  HE1   CE1  C1Z   120.07  3.000
 BND  HE1   CE1  CD1   119.83  3.000
 BND  C1Z   CE1  CD1   120.10  3.000
 BND  HD2   CD2  CE2   118.94  3.000
 BND  HD2   CD2  C1G   120.74  3.000
 BND  CE2   CD2  C1G   120.30  3.000
 BND  HE2   CE2  C1Z   120.16  3.000
 BND  HE2   CE2  CD2   119.72  3.000
 BND  C1Z   CE2  CD2   120.12  3.000
 BND  H1Z   C1Z  CE2   120.07  3.000
 BND  H1Z   C1Z  CE1   120.10  3.000
 BND  CE2   C1Z  CE1   119.83  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
 BND  CONST_01  C1Z   CE1  CD1  C1G     0.00   0.0  0
 BND  CONST_02  C1Z   CE2  CD2  C1G     0.00   0.0  0
 BND  CONST_03  CE2   CD2  C1G  CD1     0.00   0.0  0
 BND  CONST_04  CE2   C1Z  CE1  CD1     0.00   0.0  0
 BND  CONST_05  CD2   C1G  CD1  CE1     0.00   0.0  0
 BND  CONST_06  CD2   CE2  C1Z  CE1     0.00   0.0  0
 BND  CONST_07  CE1   CD1  C1G  C12   180.00   0.0  0
 BND  CONST_08  CE2   CD2  C1G  C12   180.00   0.0  0
 BND  CONST_09  HE1   CE1  CD1  C1G   180.00   0.0  0
 BND  CONST_10  HE2   CE2  CD2  C1G   180.00   0.0  0
 BND  CONST_11  HD2   CD2  C1G  CD1   180.00   0.0  0
 BND  CONST_12  H1Z   C1Z  CE1  CD1   180.00   0.0  0
 BND  CONST_13  HD1   CD1  C1G  CD2   180.00   0.0  0
 BND  CONST_14  O10   C10  NX5  CX5     0.00   0.0  0
 BND  CONST_15  C11   C10  NX5  CX5   180.00   0.0  0
 BND  CONST_16  C1G   C12  NX6  CX9   180.00   0.0  0
 BND  CONST_17  HE    NX6  C12  C1G     0.00   0.0  0
 BND  CONST_18  O12   C12  NX6  CX9     0.00   0.0  0
 BND  CONST_19  HB    NX5  C10  O10   180.00   0.0  0
 BND  Var_01    CD1   C1G  C12  NX6  -152.42  30.0  2
 BND  Var_02    HY11  CY1  OX2  CX2  -174.14  30.0  3
 BND  Var_03    C12   NX6  CX9  CX8   159.12  30.0  3
 BND  Var_04    H111  C11  C10  NX5   178.93  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
 BND  chir_01  CX2  OX2  CX3  OX6  positiv
 BND  chir_02  CX4  OX4  CX5  CX3  positiv
 BND  chir_03  CX5  NX5  CX6  CX4  negativ
 BND  chir_04  CX6  OX6  CX7  CX5  negativ
 BND  chir_05  CX7  OX7  CX6  CX8  negativ
 BND  chir_06  CX8  OX8  CX7  CX9  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
 BND  plan-1  C12  0.020
 BND  plan-1  C1G  0.020
 BND  plan-1  CD1  0.020
 BND  plan-1  CE1  0.020
 BND  plan-1  CD2  0.020
 BND  plan-1  CE2  0.020
 BND  plan-1  C1Z  0.020
 BND  plan-1  HD1  0.020
 BND  plan-1  HE1  0.020
 BND  plan-1  HD2  0.020
 BND  plan-1  HE2  0.020
 BND  plan-1  H1Z  0.020
 BND  plan-2  CX9  0.020
 BND  plan-2  NX6  0.020
 BND  plan-2  C12  0.020
 BND  plan-2  O12  0.020
 BND  plan-2  C1G  0.020
 BND  plan-2  HE   0.020
 BND  plan-3  CX5  0.020
 BND  plan-3  NX5  0.020
 BND  plan-3  C10  0.020
 BND  plan-3  O10  0.020
 BND  plan-3  C11  0.020
 BND  plan-3  HB   0.020
 BND  plan-4  CX1  0.020
 BND  plan-4  O1A  0.020
 BND  plan-4  O1B  0.020
 BND  plan-4  CX2  0.020

