# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 14:23:58 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](Oc2c[nH]c3ccc(Br)c(Cl)c23)[C@@H](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
 XMM  XMM  '5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside'  D-saccharide  38  23  .  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_XMM
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
 XMM  O2   O   OH1   0  -0.666  -3.7860   0.8183  -2.0942
 XMM  C2   C   CH1   0  -0.037  -2.7542   1.0774  -1.1772
 XMM  C3   C   CH1   0   0.003  -3.3656   1.7143   0.0678
 XMM  O3   O   OH1   0  -0.672  -4.1279   2.8593  -0.2294
 XMM  C4   C   CH1   0   0.036  -4.2801   0.7236   0.7807
 XMM  O4   O   OH1   0  -0.675  -4.7358   1.2440   2.0064
 XMM  C5   C   CH1   0  -0.016  -3.5039  -0.5584   1.0828
 XMM  O5   O   O2    0  -0.484  -2.9240  -1.0834  -0.1029
 XMM  C6   C   CH2   0  -0.158  -4.3868  -1.6424   1.6633
 XMM  O6   O   OH1   0  -0.667  -3.5738  -2.7334   2.0292
 XMM  C1   C   CH1   0   0.225  -2.0664  -0.2334  -0.7863
 XMM  O1   O   O2    0  -0.501  -0.9358   0.1052  -0.0118
 XMM  C7   C   CR5   0   0.194  -0.0242  -0.8820   0.1689
 XMM  C8   C   CR56  0   0.085   1.2526  -0.9565  -0.4667
 XMM  C9   C   CR56  0   0.351   1.8840  -2.1096   0.0509
 XMM  N1   N   NR15  0  -0.683   1.0236  -2.6906   0.9271
 XMM  C11  C   CR15  0  -0.083  -0.1270  -1.9612   1.0026
 XMM  C10  C   CR6   0  -0.142   1.9343  -0.1798  -1.4098
 XMM  CL   CL  CL    0  -0.104   1.1688   1.2141  -2.0722
 XMM  C13  C   CR6   0  -0.093   3.2056  -0.5587  -1.7966
 XMM  BR   BR  BR    0  -0.026   4.1635   0.4522  -3.0634
 XMM  C14  C   CR16  0  -0.276   3.8180  -1.7049  -1.2603
 XMM  C12  C   CR16  0  -0.285   3.1660  -2.4909  -0.3374
 XMM  HO2  H   HOH1  0   0.458  -3.3962   0.6152  -2.9500
 XMM  H2   H   HCH1  0   0.236  -1.9998   1.7525  -1.6038
 XMM  H3   H   HCH1  0   0.230  -2.5441   1.9641   0.7525
 XMM  HO3  H   HOH1  0   0.458  -3.5337   3.6073  -0.3404
 XMM  H4   H   HCH1  0   0.215  -5.1257   0.4766   0.1218
 XMM  HO4  H   HOH1  0   0.453  -5.1671   2.0860   1.8262
 XMM  H5   H   HCH1  0   0.227  -2.7232  -0.3245   1.8212
 XMM  H61  H   HCH2  0   0.197  -5.1445  -1.9293   0.9207
 XMM  H62  H   HCH2  0   0.215  -4.9196  -1.2298   2.5259
 XMM  HO6  H   HOH1  0   0.458  -4.1177  -3.3679   2.5043
 XMM  H1   H   HCH1  0   0.252  -1.7516  -0.7838  -1.6815
 XMM  HN1  H   HNR5  0   0.420   1.1978  -3.5388   1.4401
 XMM  H11  H   HCR5  0   0.297  -0.9383  -2.2660   1.6437
 XMM  H14  H   HCR6  0   0.281   4.8156  -1.9739  -1.5783
 XMM  H12  H   HCR6  0   0.279   3.6418  -3.3729   0.0702

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
 XMM  O2   C2   single    1.405  0.020  1.405
 XMM  O2   HO2  single    0.850  0.020  0.980
 XMM  C2   C3   single    1.526  0.020  1.526
 XMM  C2   C1   single    1.531  0.020  1.531
 XMM  C2   H2   single    0.970  0.020  1.090
 XMM  C3   O3   single    1.407  0.020  1.407
 XMM  C3   C4   single    1.525  0.020  1.525
 XMM  C3   H3   single    0.970  0.020  1.090
 XMM  O3   HO3  single    0.850  0.020  0.980
 XMM  C4   O4   single    1.407  0.020  1.407
 XMM  C4   C5   single    1.529  0.020  1.529
 XMM  C4   H4   single    0.970  0.020  1.090
 XMM  O4   HO4  single    0.850  0.020  0.980
 XMM  C5   O5   single    1.420  0.020  1.420
 XMM  C5   C6   single    1.514  0.020  1.514
 XMM  C5   H5   single    0.970  0.020  1.090
 XMM  O5   C1   single    1.387  0.020  1.387
 XMM  C6   O6   single    1.409  0.020  1.409
 XMM  C6   H61  single    0.970  0.020  1.090
 XMM  C6   H62  single    0.970  0.020  1.090
 XMM  O6   HO6  single    0.850  0.020  0.980
 XMM  C1   O1   single    1.412  0.020  1.412
 XMM  C1   H1   single    0.970  0.020  1.090
 XMM  O1   C7   single    1.356  0.020  1.356
 XMM  C7   C8   aromatic  1.428  0.020  1.428
 XMM  C7   C11  aromatic  1.368  0.020  1.368
 XMM  C8   C9   aromatic  1.413  0.020  1.413
 XMM  C8   C10  aromatic  1.399  0.020  1.399
 XMM  C9   N1   aromatic  1.358  0.020  1.358
 XMM  C9   C12  aromatic  1.393  0.020  1.393
 XMM  N1   C11  aromatic  1.364  0.020  1.364
 XMM  N1   HN1  single    0.860  0.020  1.020
 XMM  C11  H11  single    0.930  0.020  1.080
 XMM  C10  CL   single    1.723  0.020  1.723
 XMM  C10  C13  aromatic  1.382  0.020  1.382
 XMM  C13  BR   single    1.883  0.020  1.883
 XMM  C13  C14  aromatic  1.406  0.020  1.406
 XMM  C14  C12  aromatic  1.376  0.020  1.376
 XMM  C14  H14  single    0.930  0.020  1.080
 XMM  C12  H12  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
 XMM  HO2  O2   C2   108.79  3.000
 XMM  H2   C2   C1   108.47  3.000
 XMM  H2   C2   C3   109.60  3.000
 XMM  C1   C2   C3   109.21  3.000
 XMM  H2   C2   O2   111.36  3.000
 XMM  C1   C2   O2   109.80  3.000
 XMM  C3   C2   O2   108.38  3.000
 XMM  H3   C3   C4   107.75  3.000
 XMM  H3   C3   O3   110.60  3.000
 XMM  C4   C3   O3   107.60  3.000
 XMM  H3   C3   C2   107.69  3.000
 XMM  C4   C3   C2   110.51  3.000
 XMM  O3   C3   C2   112.60  3.000
 XMM  HO3  O3   C3   108.81  3.000
 XMM  H4   C4   C5   108.68  3.000
 XMM  H4   C4   O4   110.84  3.000
 XMM  C5   C4   O4   107.60  3.000
 XMM  H4   C4   C3   109.07  3.000
 XMM  C5   C4   C3   109.43  3.000
 XMM  O4   C4   C3   111.17  3.000
 XMM  HO4  O4   C4   107.77  3.000
 XMM  H5   C5   C6   107.99  3.000
 XMM  H5   C5   O5   110.44  3.000
 XMM  C6   C5   O5   107.07  3.000
 XMM  H5   C5   C4   108.34  3.000
 XMM  C6   C5   C4   112.35  3.000
 XMM  O5   C5   C4   110.62  3.000
 XMM  C1   O5   C5   115.92  3.000
 XMM  H62  C6   H61  107.17  3.000
 XMM  H62  C6   O6   111.60  3.000
 XMM  H61  C6   O6   111.79  3.000
 XMM  H62  C6   C5   108.43  3.000
 XMM  H61  C6   C5   109.26  3.000
 XMM  O6   C6   C5   108.52  3.000
 XMM  HO6  O6   C6   108.24  3.000
 XMM  H1   C1   O1   109.77  3.000
 XMM  H1   C1   O5   105.78  3.000
 XMM  O1   C1   O5   111.82  3.000
 XMM  H1   C1   C2   110.50  3.000
 XMM  O1   C1   C2   107.13  3.000
 XMM  O5   C1   C2   111.87  3.000
 XMM  C7   O1   C1   115.91  3.000
 XMM  C11  C7   C8   107.30  3.000
 XMM  C11  C7   O1   127.25  3.000
 XMM  C8   C7   O1   125.43  3.000
 XMM  C10  C8   C9   118.83  3.000
 XMM  C10  C8   C7   134.97  3.000
 XMM  C9   C8   C7   106.20  3.000
 XMM  C12  C9   N1   130.22  3.000
 XMM  C12  C9   C8   122.18  3.000
 XMM  N1   C9   C8   107.60  3.000
 XMM  HN1  N1   C11  124.63  3.000
 XMM  HN1  N1   C9   125.42  3.000
 XMM  C11  N1   C9   109.94  3.000
 XMM  H11  C11  N1   121.09  3.000
 XMM  H11  C11  C7   129.96  3.000
 XMM  N1   C11  C7   108.95  3.000
 XMM  C13  C10  CL   121.54  3.000
 XMM  C13  C10  C8   119.00  3.000
 XMM  CL   C10  C8   119.46  3.000
 XMM  C14  C13  BR   118.22  3.000
 XMM  C14  C13  C10  121.17  3.000
 XMM  BR   C13  C10  120.61  3.000
 XMM  H14  C14  C12  119.48  3.000
 XMM  H14  C14  C13  119.52  3.000
 XMM  C12  C14  C13  121.00  3.000
 XMM  H12  C12  C14  120.66  3.000
 XMM  H12  C12  C9   121.53  3.000
 XMM  C14  C12  C9   117.81  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
 XMM  CONST_01  N1   C9   C8   C7     0.00   0.0  0
 XMM  CONST_02  C12  C9   C8   C7   180.00   0.0  0
 XMM  CONST_03  C13  C10  C8   C7   180.00   0.0  0
 XMM  CONST_04  C9   N1   C11  C7     0.00   0.0  0
 XMM  CONST_05  N1   C11  C7   C8     0.00   0.0  0
 XMM  CONST_06  C11  N1   C9   C8     0.00   0.0  0
 XMM  CONST_07  C14  C12  C9   C8     0.00   0.0  0
 XMM  CONST_08  C14  C13  C10  C8     0.00   0.0  0
 XMM  CONST_09  C11  C7   C8   C9     0.00   0.0  0
 XMM  CONST_10  C13  C10  C8   C9     0.00   0.0  0
 XMM  CONST_11  C13  C14  C12  C9     0.00   0.0  0
 XMM  CONST_12  C10  C8   C9   N1   180.00   0.0  0
 XMM  CONST_13  C14  C12  C9   N1   180.00   0.0  0
 XMM  CONST_14  C10  C8   C7   C11  180.00   0.0  0
 XMM  CONST_15  C12  C9   N1   C11  180.00   0.0  0
 XMM  CONST_16  C12  C9   C8   C10    0.00   0.0  0
 XMM  CONST_17  C12  C14  C13  C10    0.00   0.0  0
 XMM  CONST_18  C9   C8   C7   O1   180.00   0.0  0
 XMM  CONST_19  C10  C8   C7   O1     0.00   0.0  0
 XMM  CONST_20  N1   C11  C7   O1   180.00   0.0  0
 XMM  CONST_21  CL   C10  C8   C7     0.00   0.0  0
 XMM  CONST_22  BR   C13  C10  C8   180.00   0.0  0
 XMM  CONST_23  CL   C10  C8   C9   180.00   0.0  0
 XMM  CONST_24  C14  C13  C10  CL   180.00   0.0  0
 XMM  CONST_25  C12  C14  C13  BR   180.00   0.0  0
 XMM  CONST_26  HN1  N1   C11  C7   180.00   0.0  0
 XMM  CONST_27  H11  C11  C7   C8   180.00   0.0  0
 XMM  CONST_28  H12  C12  C9   C8   180.00   0.0  0
 XMM  CONST_29  H14  C14  C12  C9   180.00   0.0  0
 XMM  Var_01    C8   C7   O1   C1   106.32  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
 XMM  chir_01  C2  O2  C3  C1  negativ
 XMM  chir_02  C3  O3  C2  C4  positiv
 XMM  chir_03  C4  O4  C5  C3  positiv
 XMM  chir_04  C5  O5  C4  C6  negativ
 XMM  chir_05  C1  O5  O1  C2  positiv

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
 XMM  plan-1  O1   0.020
 XMM  plan-1  C7   0.020
 XMM  plan-1  C8   0.020
 XMM  plan-1  C9   0.020
 XMM  plan-1  N1   0.020
 XMM  plan-1  C11  0.020
 XMM  plan-1  C10  0.020
 XMM  plan-1  CL   0.020
 XMM  plan-1  C13  0.020
 XMM  plan-1  BR   0.020
 XMM  plan-1  C14  0.020
 XMM  plan-1  C12  0.020
 XMM  plan-1  HN1  0.020
 XMM  plan-1  H11  0.020
 XMM  plan-1  H14  0.020
 XMM  plan-1  H12  0.020

