# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 10:17:48 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: 4-nitrophenyl alpha-L-arabinofuranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1O[C@@H](Oc2ccc(cc2)[N+]([O-])=O)[C@H](O)[C@H]1O
#
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
 KHP  KHP  '4-nitrophenyl alpha-L-arabinofuranoside'  L-saccharide  32  19  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KHP
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
 KHP  O5'   O  OH1    0  -0.669  -2.8034   3.3320   0.6180
 KHP  C5B   C  CH2    0  -0.157  -3.5170   2.3242  -0.0553
 KHP  C4B   C  CR15   0  -0.006  -2.9889   0.9787   0.3713
 KHP  O4'   O  O      0  -0.498  -1.6519   0.8102  -0.0983
 KHP  C1B   C  CR15   0   0.253  -1.3981  -0.5310  -0.3846
 KHP  C2B   C  CR15   0  -0.053  -2.6970  -1.2991  -0.1233
 KHP  O2B   O  OH1    0  -0.658  -2.9482  -2.3405  -1.0197
 KHP  C3B   C  CR15   0   0.002  -3.7413  -0.1971  -0.2366
 KHP  O3B   O  OH1    0  -0.659  -4.9302  -0.4314   0.4593
 KHP  O1'   O  O2     0  -0.480  -0.3940  -1.0446   0.4653
 KHP  C1'   C  CR6    0   0.418   0.8920  -0.7308   0.2484
 KHP  C2'   C  CR16   0  -0.345   1.8253  -1.4275   1.0220
 KHP  C3'   C  CR16   0  -0.252   3.1732  -1.1903   0.8725
 KHP  C4'   C  CR6    0   0.229   3.5994  -0.2504  -0.0606
 KHP  N1'   N  N      1   0.328   5.0130  -0.0019  -0.2275
 KHP  O3'   O  O     -1  -0.388   5.7882  -0.6265   0.4613
 KHP  O2'   O  O      0  -0.388   5.3582   0.8177  -1.0488
 KHP  C5'   C  CR16   0  -0.253   2.6847   0.4525  -0.8306
 KHP  C6'   C  CR16   0  -0.363   1.3308   0.2200  -0.6751
 KHP  H5B   H  HOH1   0   0.458  -3.1673   4.1828   0.3574
 KHP  H5'1  H  HCH2   0   0.210  -4.5881   2.3522   0.1820
 KHP  H5'2  H  HCH2   0   0.201  -3.4261   2.4116  -1.1463
 KHP  H4'   H  HCR5   0   0.237  -3.0194   0.9017   1.4677
 KHP  H1'   H  HCR5   0   0.244  -1.0741  -0.6329  -1.4275
 KHP  H2B   H  HCR5   0   0.243  -2.6897  -1.6516   0.9181
 KHP  H1    H  HOH1   0   0.463  -2.4383  -3.1120  -0.7548
 KHP  H3B   H  HCR5   0   0.229  -3.9288   0.0051  -1.3029
 KHP  H2    H  HOH1   0   0.461  -5.4551  -1.0693  -0.0337
 KHP  H2'   H  HCR6   0   0.286   1.4811  -2.1609   1.7392
 KHP  H3'   H  HCR6   0   0.300   3.8786  -1.7404   1.4778
 KHP  H5'   H  HCR6   0   0.302   3.0104   1.1892  -1.5506
 KHP  H6'   H  HCR6   0   0.303   0.6421   0.7991  -1.2730

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
 KHP  O5'  C5B   single    1.407  0.020  1.407
 KHP  O5'  H5B   single    0.850  0.020  0.980
 KHP  C5B  C4B   single    1.507  0.020  1.507
 KHP  C5B  H5'1  single    0.970  0.020  1.090
 KHP  C5B  H5'2  single    0.970  0.020  1.090
 KHP  C4B  O4'   single    1.427  0.020  1.427
 KHP  C4B  C3B   single    1.523  0.020  1.523
 KHP  C4B  H4'   single    0.970  0.020  1.090
 KHP  O4'  C1B   single    1.395  0.020  1.395
 KHP  C1B  C2B   single    1.531  0.020  1.531
 KHP  C1B  O1'   single    1.412  0.020  1.412
 KHP  C1B  H1'   single    0.970  0.020  1.090
 KHP  C2B  O2B   single    1.397  0.020  1.397
 KHP  C2B  C3B   single    1.522  0.020  1.522
 KHP  C2B  H2B   single    0.970  0.020  1.090
 KHP  O2B  H1    single    0.850  0.020  0.980
 KHP  C3B  O3B   single    1.397  0.020  1.397
 KHP  C3B  H3B   single    0.970  0.020  1.090
 KHP  O3B  H2    single    0.850  0.020  0.980
 KHP  O1'  C1'   single    1.341  0.020  1.341
 KHP  C1'  C2'   aromatic  1.398  0.020  1.398
 KHP  C1'  C6'   aromatic  1.396  0.020  1.396
 KHP  C2'  C3'   aromatic  1.377  0.020  1.377
 KHP  C2'  H2'   single    0.930  0.020  1.080
 KHP  C3'  C4'   aromatic  1.391  0.020  1.391
 KHP  C3'  H3'   single    0.930  0.020  1.080
 KHP  C4'  N1'   single    1.445  0.020  1.445
 KHP  C4'  C5'   aromatic  1.387  0.020  1.387
 KHP  N1'  O3'   single    1.211  0.020  1.211
 KHP  N1'  O2'   double    1.211  0.020  1.211
 KHP  C5'  C6'   aromatic  1.383  0.020  1.383
 KHP  C5'  H5'   single    0.930  0.020  1.080
 KHP  C6'  H6'   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
 KHP  H5B   O5'  C5B   108.20  3.000
 KHP  H5'2  C5B  H5'1  107.07  3.000
 KHP  H5'2  C5B  C4B   108.86  3.000
 KHP  H5'1  C5B  C4B   107.67  3.000
 KHP  H5'2  C5B  O5'   112.12  3.000
 KHP  H5'1  C5B  O5'   111.93  3.000
 KHP  C4B   C5B  O5'   109.05  3.000
 KHP  H4'   C4B  C3B   109.29  3.000
 KHP  H4'   C4B  O4'   110.24  3.000
 KHP  C3B   C4B  O4'   103.91  3.000
 KHP  H4'   C4B  C5B   109.57  3.000
 KHP  C3B   C4B  C5B   113.78  3.000
 KHP  O4'   C4B  C5B   109.91  3.000
 KHP  C1B   O4'  C4B   110.58  3.000
 KHP  H1'   C1B  O1'   109.17  3.000
 KHP  H1'   C1B  C2B   111.48  3.000
 KHP  O1'   C1B  C2B   108.54  3.000
 KHP  H1'   C1B  O4'   109.77  3.000
 KHP  O1'   C1B  O4'   110.83  3.000
 KHP  C2B   C1B  O4'   107.03  3.000
 KHP  H2B   C2B  C3B   107.89  3.000
 KHP  H2B   C2B  O2B   111.71  3.000
 KHP  C3B   C2B  O2B   111.63  3.000
 KHP  H2B   C2B  C1B   108.47  3.000
 KHP  C3B   C2B  C1B   101.89  3.000
 KHP  O2B   C2B  C1B   114.64  3.000
 KHP  H1    O2B  C2B   109.02  3.000
 KHP  H3B   C3B  O3B   111.59  3.000
 KHP  H3B   C3B  C2B   108.77  3.000
 KHP  O3B   C3B  C2B   115.16  3.000
 KHP  H3B   C3B  C4B   109.20  3.000
 KHP  O3B   C3B  C4B   110.56  3.000
 KHP  C2B   C3B  C4B   100.97  3.000
 KHP  H2    O3B  C3B   108.68  3.000
 KHP  C1'   O1'  C1B   119.95  3.000
 KHP  C6'   C1'  C2'   119.71  3.000
 KHP  C6'   C1'  O1'   124.58  3.000
 KHP  C2'   C1'  O1'   115.72  3.000
 KHP  H2'   C2'  C3'   120.01  3.000
 KHP  H2'   C2'  C1'   119.48  3.000
 KHP  C3'   C2'  C1'   120.50  3.000
 KHP  H3'   C3'  C4'   121.32  3.000
 KHP  H3'   C3'  C2'   119.39  3.000
 KHP  C4'   C3'  C2'   119.28  3.000
 KHP  C5'   C4'  N1'   119.60  3.000
 KHP  C5'   C4'  C3'   120.84  3.000
 KHP  N1'   C4'  C3'   119.56  3.000
 KHP  O2'   N1'  O3'   123.56  3.000
 KHP  O2'   N1'  C4'   118.28  3.000
 KHP  O3'   N1'  C4'   118.16  3.000
 KHP  H5'   C5'  C6'   119.00  3.000
 KHP  H5'   C5'  C4'   121.11  3.000
 KHP  C6'   C5'  C4'   119.88  3.000
 KHP  H6'   C6'  C5'   118.16  3.000
 KHP  H6'   C6'  C1'   122.06  3.000
 KHP  C5'   C6'  C1'   119.78  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
 KHP  CONST_01  C4'  C3'  C2'  C1'     0.00   0.0  0
 KHP  CONST_02  C4'  C5'  C6'  C1'     0.00   0.0  0
 KHP  CONST_03  C5'  C6'  C1'  C2'     0.00   0.0  0
 KHP  CONST_04  C5'  C4'  C3'  C2'     0.00   0.0  0
 KHP  CONST_05  C6'  C1'  C2'  C3'     0.00   0.0  0
 KHP  CONST_06  C6'  C5'  C4'  C3'     0.00   0.0  0
 KHP  CONST_07  C3'  C2'  C1'  O1'   180.00   0.0  0
 KHP  CONST_08  C5'  C6'  C1'  O1'   180.00   0.0  0
 KHP  CONST_09  N1'  C4'  C3'  C2'   180.00   0.0  0
 KHP  CONST_10  C6'  C5'  C4'  N1'   180.00   0.0  0
 KHP  CONST_11  H3'  C3'  C2'  C1'   180.00   0.0  0
 KHP  CONST_12  H5'  C5'  C6'  C1'   180.00   0.0  0
 KHP  CONST_13  H6'  C6'  C1'  C2'   180.00   0.0  0
 KHP  CONST_14  H2'  C2'  C3'  C4'   180.00   0.0  0
 KHP  CONST_15  O3'  N1'  C4'  C3'     0.00   0.0  0
 KHP  CONST_16  O2'  N1'  C4'  C3'   180.00   0.0  0
 KHP  CONST_17  C5'  C4'  N1'  O3'   180.00   0.0  0
 KHP  CONST_18  C5'  C4'  N1'  O2'     0.00   0.0  0
 KHP  Var_01    C2'  C1'  O1'  C1B  -171.56  30.0  2

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
 KHP  chir_01  C4B  C5B  O4'  C3B  positiv
 KHP  chir_02  C1B  O4'  O1'  C2B  negativ
 KHP  chir_03  C2B  O2B  C1B  C3B  negativ
 KHP  chir_04  C3B  O3B  C4B  C2B  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
 KHP  plan-1  O1'  0.020
 KHP  plan-1  C1'  0.020
 KHP  plan-1  C2'  0.020
 KHP  plan-1  C3'  0.020
 KHP  plan-1  C4'  0.020
 KHP  plan-1  N1'  0.020
 KHP  plan-1  C5'  0.020
 KHP  plan-1  C6'  0.020
 KHP  plan-1  H2'  0.020
 KHP  plan-1  H3'  0.020
 KHP  plan-1  H5'  0.020
 KHP  plan-1  H6'  0.020
 KHP  plan-2  C4'  0.020
 KHP  plan-2  N1'  0.020
 KHP  plan-2  O3'  0.020
 KHP  plan-2  O2'  0.020

