# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun  4 08:04:35 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 2,4-dinitrophenyl 2-deoxy-2-fluoro-beta-D-mannopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](Oc2ccc(cc2[N+]([O-])=O)[N+]([O-])=O)[C@@H](F)[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
 M2F  M2F  '2,4-dinitrophenyl 2-deoxy-2-fluoro-beta-D-mannopyranoside'  D-saccharide  37  24  .  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 (reasonable std)
;

data_comp_M2F
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
 M2F  O1B   O  O     -1  -0.368  -2.8095   3.0015   1.1847
 M2F  N1B   N  N      1   0.338  -2.0621   2.5597   0.3448
 M2F  O2B   O  O      0  -0.355  -1.2659   3.2123  -0.2803
 M2F  C6B   C  CR6    0   0.161  -2.1634   1.1384   0.0512
 M2F  C1A   C  CR16   0  -0.293  -3.4297   0.5940   0.0149
 M2F  C2B   C  CR6    0   0.251  -3.5654  -0.7410  -0.3134
 M2F  N1C   N  N      1   0.329  -4.8925  -1.3207  -0.3781
 M2F  O3C   O  O     -1  -0.374  -5.8349  -0.6094  -0.1216
 M2F  O2C   O  O      0  -0.372  -4.9842  -2.4853  -0.6848
 M2F  C3B   C  CR16   0  -0.236  -2.4537  -1.5306  -0.5693
 M2F  C4B   C  CR16   0  -0.359  -1.1896  -0.9844  -0.4936
 M2F  C5B   C  CR6    0   0.445  -1.0154   0.3678  -0.1921
 M2F  O1    O  O2     0  -0.463   0.1638   0.9720  -0.0791
 M2F  C1    C  CH1    0   0.234   1.3349   0.3120  -0.4694
 M2F  O5    O  O2     0  -0.492   1.6161  -0.6546   0.4867
 M2F  C2    C  CH1    0   0.128   2.4512   1.3368  -0.5375
 M2F  F2    F  F      0  -0.367   2.5542   1.9654   0.6924
 M2F  C3    C  CH1    0  -0.042   3.7502   0.6097  -0.8574
 M2F  O3    O  OH1    0  -0.666   4.8598   1.4659  -0.7982
 M2F  C4    C  CH1    0   0.036   3.9918  -0.5473   0.1130
 M2F  O4    O  OH1    0  -0.669   5.0737  -1.3369  -0.3069
 M2F  C5    C  CH1    0  -0.027   2.7509  -1.4416   0.1563
 M2F  C6    C  CH2    0  -0.154   2.8568  -2.5396   1.1900
 M2F  O6    O  OH1    0  -0.665   1.7142  -3.3544   1.0922
 M2F  H1A   H  HCR6   0   0.333  -4.2933   1.2121   0.2142
 M2F  H3B   H  HCR6   0   0.319  -2.5560  -2.5785  -0.8103
 M2F  H4B   H  HCR6   0   0.323  -0.3439  -1.6373  -0.6469
 M2F  H1    H  HCH1   0   0.246   1.2036  -0.1355  -1.4686
 M2F  H2    H  HCH1   0   0.257   2.2330   2.0954  -1.2948
 M2F  H5    H  HCH1   0   0.237   2.6097  -1.8965  -0.8374
 M2F  H3    H  HCH1   0   0.240   3.6343   0.1798  -1.8630
 M2F  HA    H  HOH1   0   0.464   4.9328   1.9436  -1.6302
 M2F  H4    H  HCH1   0   0.227   4.1649  -0.1394   1.1202
 M2F  HB    H  HOH1   0   0.457   5.8669  -0.7911  -0.2957
 M2F  H61C  H  HCH2   0   0.218   3.7767  -3.1026   1.0025
 M2F  H62C  H  HCH2   0   0.202   2.9546  -2.0845   2.1854
 M2F  H6    H  HOH1   0   0.458   1.8303  -4.0994   1.6886

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
 M2F  O1B  N1B   single    1.208  0.020  1.208
 M2F  N1B  O2B   double    1.204  0.020  1.204
 M2F  N1B  C6B   single    1.455  0.020  1.455
 M2F  C6B  C1A   aromatic  1.379  0.020  1.379
 M2F  C6B  C5B   aromatic  1.404  0.020  1.404
 M2F  C1A  C2B   aromatic  1.381  0.020  1.381
 M2F  C2B  N1C   single    1.450  0.020  1.450
 M2F  C2B  C3B   aromatic  1.387  0.020  1.387
 M2F  N1C  O3C   single    1.208  0.020  1.208
 M2F  N1C  O2C   double    1.208  0.020  1.208
 M2F  C3B  C4B   aromatic  1.379  0.020  1.379
 M2F  C4B  C5B   aromatic  1.396  0.020  1.396
 M2F  C5B  O1    single    1.330  0.020  1.330
 M2F  O1   C1    single    1.400  0.020  1.400
 M2F  C1   O5    single    1.388  0.020  1.388
 M2F  C1   C2    single    1.517  0.020  1.517
 M2F  O5   C5    single    1.420  0.020  1.420
 M2F  C2   F2    single    1.385  0.020  1.385
 M2F  C2   C3    single    1.523  0.020  1.523
 M2F  C3   O3    single    1.403  0.020  1.403
 M2F  C3   C4    single    1.529  0.020  1.529
 M2F  C4   O4    single    1.404  0.020  1.404
 M2F  C4   C5    single    1.530  0.020  1.530
 M2F  C5   C6    single    1.512  0.020  1.512
 M2F  C6   O6    single    1.407  0.020  1.407
 M2F  C1A  H1A   single    0.930  0.020  1.080
 M2F  C3B  H3B   single    0.930  0.020  1.080
 M2F  C4B  H4B   single    0.930  0.020  1.080
 M2F  C1   H1    single    0.970  0.020  1.090
 M2F  C2   H2    single    0.970  0.020  1.090
 M2F  C5   H5    single    0.970  0.020  1.090
 M2F  C3   H3    single    0.970  0.020  1.090
 M2F  O3   HA    single    0.850  0.020  0.980
 M2F  C4   H4    single    0.970  0.020  1.090
 M2F  O4   HB    single    0.850  0.020  0.980
 M2F  C6   H61C  single    0.970  0.020  1.090
 M2F  C6   H62C  single    0.970  0.020  1.090
 M2F  O6   H6    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
 M2F  C6B   N1B  O2B   118.07  3.000
 M2F  C6B   N1B  O1B   117.03  3.000
 M2F  O2B   N1B  O1B   124.88  3.000
 M2F  C5B   C6B  C1A   121.98  3.000
 M2F  C5B   C6B  N1B   120.95  3.000
 M2F  C1A   C6B  N1B   117.06  3.000
 M2F  H1A   C1A  C2B   121.21  3.000
 M2F  H1A   C1A  C6B   120.22  3.000
 M2F  C2B   C1A  C6B   118.56  3.000
 M2F  C3B   C2B  N1C   119.85  3.000
 M2F  C3B   C2B  C1A   121.00  3.000
 M2F  N1C   C2B  C1A   119.14  3.000
 M2F  O2C   N1C  O3C   124.22  3.000
 M2F  O2C   N1C  C2B   117.80  3.000
 M2F  O3C   N1C  C2B   117.98  3.000
 M2F  H3B   C3B  C4B   118.90  3.000
 M2F  H3B   C3B  C2B   121.16  3.000
 M2F  C4B   C3B  C2B   119.93  3.000
 M2F  H4B   C4B  C5B   121.24  3.000
 M2F  H4B   C4B  C3B   118.09  3.000
 M2F  C5B   C4B  C3B   120.65  3.000
 M2F  O1    C5B  C4B   124.68  3.000
 M2F  O1    C5B  C6B   117.45  3.000
 M2F  C4B   C5B  C6B   117.84  3.000
 M2F  C1    O1   C5B   120.26  3.000
 M2F  H1    C1   C2    108.73  3.000
 M2F  H1    C1   O5    111.45  3.000
 M2F  C2    C1   O5    110.63  3.000
 M2F  H1    C1   O1    110.14  3.000
 M2F  C2    C1   O1    108.04  3.000
 M2F  O5    C1   O1    107.80  3.000
 M2F  C5    O5   C1    112.80  3.000
 M2F  H2    C2   C3    110.85  3.000
 M2F  H2    C2   F2    108.35  3.000
 M2F  C3    C2   F2    109.87  3.000
 M2F  H2    C2   C1    110.66  3.000
 M2F  C3    C2   C1    108.34  3.000
 M2F  F2    C2   C1    108.75  3.000
 M2F  H3    C3   C4    107.53  3.000
 M2F  H3    C3   O3    111.13  3.000
 M2F  C4    C3   O3    108.06  3.000
 M2F  H3    C3   C2    106.79  3.000
 M2F  C4    C3   C2    111.27  3.000
 M2F  O3    C3   C2    111.99  3.000
 M2F  HA    O3   C3    109.06  3.000
 M2F  H4    C4   C5    108.56  3.000
 M2F  H4    C4   O4    111.17  3.000
 M2F  C5    C4   O4    107.75  3.000
 M2F  H4    C4   C3    108.98  3.000
 M2F  C5    C4   C3    109.39  3.000
 M2F  O4    C4   C3    110.95  3.000
 M2F  HB    O4   C4    108.22  3.000
 M2F  H5    C5   C6    109.01  3.000
 M2F  H5    C5   C4    108.64  3.000
 M2F  C6    C5   C4    112.77  3.000
 M2F  H5    C5   O5    109.64  3.000
 M2F  C6    C5   O5    107.43  3.000
 M2F  C4    C5   O5    109.32  3.000
 M2F  H62C  C6   H61C  107.06  3.000
 M2F  H62C  C6   O6    112.03  3.000
 M2F  H61C  C6   O6    111.89  3.000
 M2F  H62C  C6   C5    108.95  3.000
 M2F  H61C  C6   C5    108.38  3.000
 M2F  O6    C6   C5    108.44  3.000
 M2F  H6    O6   C6    107.92  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
 M2F  CONST_01  C3B  C2B  C1A  C6B    0.00  0.0  0
 M2F  CONST_02  C3B  C4B  C5B  C6B    0.00  0.0  0
 M2F  CONST_03  C4B  C5B  C6B  C1A    0.00  0.0  0
 M2F  CONST_04  C4B  C3B  C2B  C1A    0.00  0.0  0
 M2F  CONST_05  C5B  C6B  C1A  C2B    0.00  0.0  0
 M2F  CONST_06  C5B  C4B  C3B  C2B    0.00  0.0  0
 M2F  CONST_07  C2B  C1A  C6B  N1B  180.00  0.0  0
 M2F  CONST_08  C4B  C5B  C6B  N1B  180.00  0.0  0
 M2F  CONST_09  N1C  C2B  C1A  C6B  180.00  0.0  0
 M2F  CONST_10  O1   C5B  C6B  C1A  180.00  0.0  0
 M2F  CONST_11  C4B  C3B  C2B  N1C  180.00  0.0  0
 M2F  CONST_12  O1   C5B  C4B  C3B  180.00  0.0  0
 M2F  CONST_13  H4B  C4B  C5B  C6B  180.00  0.0  0
 M2F  CONST_14  H3B  C3B  C2B  C1A  180.00  0.0  0
 M2F  CONST_15  H1A  C1A  C2B  C3B  180.00  0.0  0
 M2F  CONST_20  O3C  N1C  C2B  C1A    0.00  0.0  0
 M2F  CONST_21  O2C  N1C  C2B  C1A  180.00  0.0  0
 M2F  CONST_22  C3B  C2B  N1C  O3C  180.00  0.0  0
 M2F  CONST_23  C3B  C2B  N1C  O2C    0.00  0.0  0

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
 M2F  chir_01  C1  O1  O5  C2  positiv
 M2F  chir_02  C2  F2  C3  C1  negativ
 M2F  chir_03  C3  O3  C2  C4  positiv
 M2F  chir_04  C4  O4  C5  C3  positiv
 M2F  chir_05  C5  O5  C4  C6  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
 M2F  plan-1  N1B  0.020
 M2F  plan-1  C6B  0.020
 M2F  plan-1  C1A  0.020
 M2F  plan-1  C2B  0.020
 M2F  plan-1  N1C  0.020
 M2F  plan-1  C3B  0.020
 M2F  plan-1  C4B  0.020
 M2F  plan-1  C5B  0.020
 M2F  plan-1  O1   0.020
 M2F  plan-1  H1A  0.020
 M2F  plan-1  H3B  0.020
 M2F  plan-1  H4B  0.020
 M2F  plan-2  O1B  0.020
 M2F  plan-2  N1B  0.020
 M2F  plan-2  O2B  0.020
 M2F  plan-2  C6B  0.020
 M2F  plan-3  C2B  0.020
 M2F  plan-3  N1C  0.020
 M2F  plan-3  O3C  0.020
 M2F  plan-3  O2C  0.020

