# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 23:37:47 2021
#   Inital geometry file: a 119 line input string
#   Ligand name: a 3 line input string
#   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)C(N)=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
 NXD  NXD  'methyl 5-(acetylamino)-9-{[amino(oxo)acetyl]amino}-3,5,9-trideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid'  D-saccharide  50  27  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NXD
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
 NXD  C11   C  CH3   0  -0.809  -5.2110  13.3711  30.7133
 NXD  C10   C  C     0   0.495  -3.7147  13.4822  30.5692
 NXD  O10   O  O     0  -0.491  -3.0949  14.4504  30.9838
 NXD  N5    N  NH1   0  -0.634  -3.0732  12.4561  29.9614
 NXD  C5    C  CH1   0  -0.121  -3.6496  11.2562  29.4055
 NXD  C4    C  CH1   0   0.062  -3.1926  10.0200  30.1859
 NXD  O4    O  OH1   0  -0.658  -3.6215  10.0599  31.5219
 NXD  C3    C  CH2   0  -0.530  -3.7834   8.7746  29.5480
 NXD  C2    C  CT    0   0.463  -3.4727   8.7025  28.0547
 NXD  C1    C  C     0   0.487  -1.9895   8.3629  27.7474
 NXD  O1B   O  OH1   0  -0.572  -1.5523   7.3682  28.4913
 NXD  O1A   O  O     0  -0.424  -1.3359   8.9037  26.8915
 NXD  O2    O  O2    0  -0.492  -4.2672   7.6979  27.5304
 NXD  CB    C  CH3   0  -0.435  -4.1601   7.4241  26.1401
 NXD  O6    O  O2    0  -0.501  -3.8053   9.8961  27.4191
 NXD  C6    C  CH1   0  -0.007  -3.2459  11.0892  27.9387
 NXD  C7    C  CH1   0   0.005  -3.6939  12.2266  27.0323
 NXD  O7    O  OH1   0  -0.672  -5.0902  12.3865  27.1471
 NXD  C8    C  CH1   0   0.026  -3.3009  11.9585  25.5661
 NXD  O8    O  OH1   0  -0.683  -1.9319  11.6563  25.4416
 NXD  C9    C  CH2   0  -0.316  -3.5711  13.1967  24.7187
 NXD  NAB   N  NH1   0  -0.613  -3.2260  13.0046  23.3311
 NXD  CAC   C  C     0   0.442  -4.0414  12.4431  22.4450
 NXD  OAD   O  O     0  -0.478  -5.1789  12.0573  22.6681
 NXD  CAF   C  C     0   0.424  -3.4150  12.3193  21.0440
 NXD  OAG   O  O     0  -0.469  -2.2762  12.7014  20.8258
 NXD  NAK   N  NH2   0  -0.783  -4.2342  11.7690  20.1555
 NXD  H111  H  HCH3  0   0.263  -5.4935  12.4670  31.2532
 NXD  H113  H  HCH3  0   0.264  -5.7005  13.3347  29.7393
 NXD  H112  H  HCH3  0   0.271  -5.5862  14.2338  31.2570
 NXD  HN5   H  HNH1  0   0.392  -2.0687  12.5581  29.8916
 NXD  H5    H  HCH1  0   0.284  -4.7360  11.3193  29.4709
 NXD  H4    H  HCH1  0   0.216  -2.0924   9.9720  30.1374
 NXD  HO4   H  HOH1  0   0.453  -3.1540  10.7723  31.9701
 NXD  H32   H  HCH2  0   0.270  -4.8728   8.8081  29.6467
 NXD  H31   H  HCH2  0   0.280  -3.4357   7.8791  30.0635
 NXD  HO1B  H  HOH1  0   0.492  -0.6417   7.1350  28.2495
 NXD  HB1   H  HCH3  0   0.252  -4.9390   6.6994  25.9148
 NXD  HB2   H  HCH3  0   0.222  -3.1978   6.9771  25.8746
 NXD  HB3   H  HCH3  0   0.234  -4.3199   8.3103  25.5248
 NXD  H6    H  HCH1  0   0.242  -2.1485  11.0600  27.8964
 NXD  H7    H  HCH1  0   0.238  -3.1604  13.1245  27.3717
 NXD  HO7   H  HOH1  0   0.464  -5.3097  13.3177  27.0593
 NXD  H8    H  HCH1  0   0.228  -3.9243  11.1396  25.1855
 NXD  HO8   H  HOH1  0   0.455  -1.7903  10.7390  25.7048
 NXD  H92   H  HCH2  0   0.264  -2.9855  14.0394  25.0918
 NXD  H91   H  HCH2  0   0.257  -4.6225  13.4739  24.7906
 NXD  HAB   H  HNH1  0   0.410  -2.2986  13.2517  23.0252
 NXD  HAK1  H  HNH2  0   0.414  -3.9424  11.6291  19.2019
 NXD  HAK2  H  HNH2  0   0.415  -5.1586  11.4730  20.4212

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
 NXD  C11  C10   single  1.507  0.020  1.507
 NXD  C11  H111  single  0.970  0.020  1.090
 NXD  C11  H113  single  0.970  0.020  1.090
 NXD  C11  H112  single  0.970  0.020  1.090
 NXD  C10  O10   double  1.222  0.020  1.222
 NXD  C10  N5    single  1.354  0.020  1.354
 NXD  N5   C5    single  1.443  0.020  1.443
 NXD  N5   HN5   single  0.860  0.020  1.020
 NXD  C5   C4    single  1.532  0.020  1.532
 NXD  C5   C6    single  1.530  0.020  1.530
 NXD  C5   H5    single  0.970  0.020  1.090
 NXD  C4   O4    single  1.404  0.020  1.404
 NXD  C4   C3    single  1.519  0.020  1.519
 NXD  C4   H4    single  0.970  0.020  1.090
 NXD  O4   HO4   single  0.850  0.020  0.980
 NXD  C3   C2    single  1.527  0.020  1.527
 NXD  C3   H32   single  0.970  0.020  1.090
 NXD  C3   H31   single  0.970  0.020  1.090
 NXD  C2   C1    single  1.552  0.020  1.552
 NXD  C2   O2    single  1.384  0.020  1.384
 NXD  C2   O6    single  1.393  0.020  1.393
 NXD  C1   O1B   single  1.317  0.020  1.317
 NXD  C1   O1A   double  1.205  0.020  1.205
 NXD  O1B  HO1B  single  0.850  0.020  0.980
 NXD  O2   CB    single  1.421  0.020  1.421
 NXD  CB   HB1   single  0.970  0.020  1.090
 NXD  CB   HB2   single  0.970  0.020  1.090
 NXD  CB   HB3   single  0.970  0.020  1.090
 NXD  O6   C6    single  1.416  0.020  1.416
 NXD  C6   C7    single  1.522  0.020  1.522
 NXD  C6   H6    single  0.970  0.020  1.090
 NXD  C7   O7    single  1.410  0.020  1.410
 NXD  C7   C8    single  1.541  0.020  1.541
 NXD  C7   H7    single  0.970  0.020  1.090
 NXD  O7   HO7   single  0.850  0.020  0.980
 NXD  C8   O8    single  1.407  0.020  1.407
 NXD  C8   C9    single  1.525  0.020  1.525
 NXD  C8   H8    single  0.970  0.020  1.090
 NXD  O8   HO8   single  0.850  0.020  0.980
 NXD  C9   NAB   single  1.443  0.020  1.443
 NXD  C9   H92   single  0.970  0.020  1.090
 NXD  C9   H91   single  0.970  0.020  1.090
 NXD  NAB  CAC   single  1.329  0.020  1.329
 NXD  NAB  HAB   single  0.860  0.020  1.020
 NXD  CAC  OAD   double  1.222  0.020  1.222
 NXD  CAC  CAF   single  1.540  0.020  1.540
 NXD  CAF  OAG   double  1.221  0.020  1.221
 NXD  CAF  NAK   single  1.328  0.020  1.328
 NXD  NAK  HAK1  single  0.860  0.020  1.020
 NXD  NAK  HAK2  single  0.860  0.020  1.020

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
 NXD  H112  C11  H113  108.57  3.000
 NXD  H112  C11  H111  108.73  3.000
 NXD  H113  C11  H111  107.35  3.000
 NXD  H112  C11  C10   109.40  3.000
 NXD  H113  C11  C10   111.26  3.000
 NXD  H111  C11  C10   111.44  3.000
 NXD  N5    C10  O10   120.81  3.000
 NXD  N5    C10  C11   117.21  3.000
 NXD  O10   C10  C11   121.97  3.000
 NXD  HN5   N5   C5    116.98  3.000
 NXD  HN5   N5   C10   115.14  3.000
 NXD  C5    N5   C10   127.87  3.000
 NXD  H5    C5   C6    109.06  3.000
 NXD  H5    C5   C4    108.27  3.000
 NXD  C6    C5   C4    108.75  3.000
 NXD  H5    C5   N5    109.08  3.000
 NXD  C6    C5   N5    110.78  3.000
 NXD  C4    C5   N5    110.84  3.000
 NXD  H4    C4   C3    109.51  3.000
 NXD  H4    C4   O4    110.37  3.000
 NXD  C3    C4   O4    107.71  3.000
 NXD  H4    C4   C5    108.09  3.000
 NXD  C3    C4   C5    109.38  3.000
 NXD  O4    C4   C5    111.77  3.000
 NXD  HO4   O4   C4    108.41  3.000
 NXD  H31   C3   H32   107.45  3.000
 NXD  H31   C3   C2    111.02  3.000
 NXD  H32   C3   C2    106.99  3.000
 NXD  H31   C3   C4    110.54  3.000
 NXD  H32   C3   C4    108.92  3.000
 NXD  C2    C3   C4    111.74  3.000
 NXD  O6    C2   O2    108.19  3.000
 NXD  O6    C2   C1    108.99  3.000
 NXD  O2    C2   C1    108.34  3.000
 NXD  O6    C2   C3    110.93  3.000
 NXD  O2    C2   C3    106.74  3.000
 NXD  C1    C2   C3    113.47  3.000
 NXD  O1A   C1   O1B   124.06  3.000
 NXD  O1A   C1   C2    124.10  3.000
 NXD  O1B   C1   C2    111.76  3.000
 NXD  HO1B  O1B  C1    110.63  3.000
 NXD  CB    O2   C2    117.86  3.000
 NXD  HB3   CB   HB2   108.91  3.000
 NXD  HB3   CB   HB1   108.64  3.000
 NXD  HB2   CB   HB1   107.91  3.000
 NXD  HB3   CB   O2    112.60  3.000
 NXD  HB2   CB   O2    112.49  3.000
 NXD  HB1   CB   O2    106.09  3.000
 NXD  C6    O6   C2    117.40  3.000
 NXD  H6    C6   C7    106.92  3.000
 NXD  H6    C6   O6    110.98  3.000
 NXD  C7    C6   O6    107.14  3.000
 NXD  H6    C6   C5    107.65  3.000
 NXD  C7    C6   C5    114.31  3.000
 NXD  O6    C6   C5    109.84  3.000
 NXD  H7    C7   C8    108.20  3.000
 NXD  H7    C7   O7    111.29  3.000
 NXD  C8    C7   O7    110.47  3.000
 NXD  H7    C7   C6    106.50  3.000
 NXD  C8    C7   C6    111.19  3.000
 NXD  O7    C7   C6    109.13  3.000
 NXD  HO7   O7   C7    109.19  3.000
 NXD  H8    C8   C9    108.21  3.000
 NXD  H8    C8   O8    111.20  3.000
 NXD  C9    C8   O8    107.31  3.000
 NXD  H8    C8   C7    108.35  3.000
 NXD  C9    C8   C7    110.01  3.000
 NXD  O8    C8   C7    111.69  3.000
 NXD  HO8   O8   C8    108.83  3.000
 NXD  H91   C9   H92   107.38  3.000
 NXD  H91   C9   NAB   109.15  3.000
 NXD  H92   C9   NAB   107.65  3.000
 NXD  H91   C9   C8    109.93  3.000
 NXD  H92   C9   C8    109.99  3.000
 NXD  NAB   C9   C8    112.58  3.000
 NXD  HAB   NAB  CAC   117.79  3.000
 NXD  HAB   NAB  C9    118.65  3.000
 NXD  CAC   NAB  C9    123.44  3.000
 NXD  CAF   CAC  OAD   121.30  3.000
 NXD  CAF   CAC  NAB   113.03  3.000
 NXD  OAD   CAC  NAB   125.66  3.000
 NXD  NAK   CAF  OAG   125.84  3.000
 NXD  NAK   CAF  CAC   113.03  3.000
 NXD  OAG   CAF  CAC   121.13  3.000
 NXD  HAK2  NAK  HAK1  118.38  3.000
 NXD  HAK2  NAK  CAF   120.79  3.000
 NXD  HAK1  NAK  CAF   120.83  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
 NXD  CONST_01  C5    N5   C10  C11     0.00   0.0  0
 NXD  CONST_02  C5    N5   C10  O10   180.00   0.0  0
 NXD  CONST_03  HO1B  O1B  C1   C2    180.00   0.0  0
 NXD  CONST_04  OAD   CAC  NAB  C9      0.00   0.0  0
 NXD  CONST_05  CAF   CAC  NAB  C9    180.00   0.0  0
 NXD  CONST_06  NAK   CAF  CAC  NAB   180.00   0.0  0
 NXD  CONST_07  NAK   CAF  CAC  OAD     0.00   0.0  0
 NXD  CONST_08  HN5   N5   C10  C11   180.00   0.0  0
 NXD  CONST_09  HAK1  NAK  CAF  CAC   180.00   0.0  0
 NXD  CONST_10  HAK2  NAK  CAF  CAC     0.00   0.0  0
 NXD  CONST_11  HAB   NAB  CAC  OAD   180.00   0.0  0
 NXD  Var_01    HB1   CB   O2   C2   -173.42  30.0  3
 NXD  Var_02    CAC   NAB  C9   C8     84.39  30.0  3
 NXD  Var_03    H111  C11  C10  O10  -122.72  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
 NXD  chir_01  C5  N5  C4  C6  positiv
 NXD  chir_02  C4  O4  C5  C3  positiv
 NXD  chir_03  C2  O6  C1  C3  negativ
 NXD  chir_04  C6  O6  C5  C7  positiv
 NXD  chir_05  C7  O7  C6  C8  negativ
 NXD  chir_06  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
 NXD  plan-1  C11   0.020
 NXD  plan-1  C10   0.020
 NXD  plan-1  O10   0.020
 NXD  plan-1  N5    0.020
 NXD  plan-1  C5    0.020
 NXD  plan-1  HN5   0.020
 NXD  plan-2  C9    0.020
 NXD  plan-2  NAB   0.020
 NXD  plan-2  CAC   0.020
 NXD  plan-2  OAD   0.020
 NXD  plan-2  CAF   0.020
 NXD  plan-2  OAG   0.020
 NXD  plan-2  NAK   0.020
 NXD  plan-2  HAB   0.020
 NXD  plan-2  HAK1  0.020
 NXD  plan-2  HAK2  0.020
 NXD  plan-3  C2    0.020
 NXD  plan-3  C1    0.020
 NXD  plan-3  O1B   0.020
 NXD  plan-3  O1A   0.020
 NXD  plan-3  HO1B  0.020

