# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 11:51:03 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 4,5-dideoxy-5-(3',5'-dichlorobiphenyl-4-yl)-4-[(methoxyacetyl)amino]-L-arabinonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCC(=O)N[C@@H](Cc1ccc(cc1)c2cc(Cl)cc(Cl)c2)[C@H](O)[C@@H](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
 U94  U94  '4,5-dideoxy-5-(3',5'-dichlorobiphenyl-4-yl)-4-[(methoxyacetyl)amino]-L-arabinonic acid'  ligand  49  29  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U94
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
 U94  O1    O   OC    -1  -0.694  -7.3270   0.7626  -1.0901
 U94  C2    C   C      0   0.388  -6.8542   1.2879  -0.0714
 U94  C3    C   CH1    0  -0.106  -5.4080   0.9096   0.3232
 U94  O4    O   O      0  -0.607  -7.4118   2.1033   0.6968
 U94  C5    C   CH1    0   0.043  -4.4712   1.2112  -0.8412
 U94  C6    C   CH1    0  -0.059  -3.0079   0.8698  -0.5146
 U94  C7    C   CH2    0  -0.615  -2.0377   1.3727  -1.5952
 U94  O8    O   OH1    0  -0.632  -5.0408   1.6089   1.4825
 U94  O9    O   OH1    0  -0.717  -4.6147   2.5782  -1.1578
 U94  N10   N   NH1    0  -0.569  -2.8724  -0.5613  -0.3629
 U94  C11   C   C      0   0.467  -2.2548  -1.1735   0.6643
 U94  O12   O   O      0  -0.481  -1.8617  -0.6123   1.6694
 U94  C13   C   CH2    0  -0.240  -2.0755  -2.6669   0.4403
 U94  O14   O   O2     0  -0.548  -1.6021  -3.2542   1.6097
 U94  C15   C   CH3    0  -0.380  -1.3745  -4.6331   1.4566
 U94  C16   C   CR6    0   0.165  -0.6163   1.0229  -1.2647
 U94  C17   C   CR16   0  -0.276   0.0796   1.7468  -0.2991
 U94  C18   C   CR16   0  -0.397   1.3838   1.4272   0.0336
 U94  C19   C   CR6    0   0.245   2.0400   0.3665  -0.5929
 U94  C20   C   CR16   0  -0.335   1.3440  -0.3644  -1.5539
 U94  C21   C   CR16   0  -0.259   0.0356  -0.0403  -1.8808
 U94  C22   C   CR6    0   0.141   3.4395   0.0420  -0.2551
 U94  C23   C   CR16   0  -0.304   3.8911   0.1463   1.0603
 U94  C24   C   CR6    0  -0.008   5.2107  -0.1477   1.3567
 U94  C25   C   CR16   0  -0.177   6.1097  -0.5515   0.3825
 U94  C26   C   CR6    0  -0.032   5.6415  -0.6528  -0.9176
 U94  C27   C   CR16   0  -0.312   4.3297  -0.3627  -1.2492
 U94  CL28  CL  CL     0  -0.032   6.7378  -1.1408  -2.1641
 U94  CL29  CL  CL     0  -0.117   5.7572  -0.0210   2.9937
 U94  H3    H   HCH1   0   0.265  -5.3725  -0.1733   0.5084
 U94  H5    H   HCH1   0   0.215  -4.7962   0.5771  -1.6801
 U94  H6    H   HCH1   0   0.278  -2.7392   1.3287   0.4374
 U94  H7    H   HCH2   0   0.252  -2.3159   0.9405  -2.5616
 U94  H7A   H   HCH2   0   0.247  -2.1305   2.4560  -1.6891
 U94  HO8   H   HOH1   0   0.419  -5.8239   2.1693   1.6382
 U94  HO9   H   HOH1   0   0.450  -4.3298   2.7191  -2.0650
 U94  HN10  H   HNH1   0   0.383  -3.1371  -1.1267  -1.1563
 U94  H13   H   HCH2   0   0.253  -3.0303  -3.1086   0.1187
 U94  H13A  H   HCH2   0   0.203  -1.3739  -2.8056  -0.3973
 U94  H15   H   HCH3   0   0.235  -2.2880  -5.1747   1.1836
 U94  H15A  H   HCH3   0   0.175  -0.6185  -4.8424   0.6905
 U94  H15B  H   HCH3   0   0.278  -1.0164  -5.0203   2.4094
 U94  H17   H   HCR6   0   0.263  -0.4027   2.5830   0.1936
 U94  H18   H   HCR6   0   0.258   1.9043   2.0289   0.7685
 U94  H20   H   HCR6   0   0.229   1.8173  -1.2071  -2.0429
 U94  H21   H   HCR6   0   0.244  -0.4837  -0.6280  -2.6288
 U94  H23   H   HCR6   0   0.281   3.2127   0.4366   1.8513
 U94  H25   H   HCR6   0   0.265   7.1373  -0.7794   0.6277
 U94  H27   H   HCR6   0   0.256   4.0062  -0.4290  -2.2793

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
 U94  C2    O1    deloc     1.240  0.020  1.240
 U94  C3    C2    single    1.546  0.020  1.546
 U94  C2    O4    deloc     1.251  0.020  1.251
 U94  O8    C3    single    1.403  0.020  1.403
 U94  C3    C5    single    1.525  0.020  1.525
 U94  C3    H3    single    0.970  0.020  1.090
 U94  O9    C5    single    1.411  0.020  1.411
 U94  C5    C6    single    1.538  0.020  1.538
 U94  C5    H5    single    0.970  0.020  1.090
 U94  C7    C6    single    1.537  0.020  1.537
 U94  C6    N10   single    1.446  0.020  1.446
 U94  C6    H6    single    0.970  0.020  1.090
 U94  C7    C16   single    1.501  0.020  1.501
 U94  C7    H7    single    0.970  0.020  1.090
 U94  C7    H7A   single    0.970  0.020  1.090
 U94  O8    HO8   single    0.850  0.020  0.980
 U94  O9    HO9   single    0.850  0.020  0.980
 U94  N10   C11   single    1.346  0.020  1.346
 U94  N10   HN10  single    0.860  0.020  1.020
 U94  O12   C11   double    1.216  0.020  1.216
 U94  C11   C13   single    1.521  0.020  1.521
 U94  C13   O14   single    1.392  0.020  1.392
 U94  C13   H13   single    0.970  0.020  1.090
 U94  C13   H13A  single    0.970  0.020  1.090
 U94  C15   O14   single    1.406  0.020  1.406
 U94  C15   H15   single    0.970  0.020  1.090
 U94  C15   H15A  single    0.970  0.020  1.090
 U94  C15   H15B  single    0.970  0.020  1.090
 U94  C17   C16   aromatic  1.393  0.020  1.393
 U94  C16   C21   aromatic  1.391  0.020  1.391
 U94  C18   C17   aromatic  1.383  0.020  1.383
 U94  C17   H17   single    0.930  0.020  1.080
 U94  C18   C19   aromatic  1.396  0.020  1.396
 U94  C18   H18   single    0.930  0.020  1.080
 U94  C22   C19   single    1.476  0.020  1.476
 U94  C19   C20   aromatic  1.394  0.020  1.394
 U94  C20   C21   aromatic  1.387  0.020  1.387
 U94  C20   H20   single    0.930  0.020  1.080
 U94  C21   H21   single    0.930  0.020  1.080
 U94  C23   C22   aromatic  1.395  0.020  1.395
 U94  C22   C27   aromatic  1.394  0.020  1.394
 U94  C24   C23   aromatic  1.384  0.020  1.384
 U94  C23   H23   single    0.930  0.020  1.080
 U94  CL29  C24   single    1.730  0.020  1.730
 U94  C24   C25   aromatic  1.386  0.020  1.386
 U94  C25   C26   aromatic  1.386  0.020  1.386
 U94  C25   H25   single    0.930  0.020  1.080
 U94  C26   C27   aromatic  1.384  0.020  1.384
 U94  C26   CL28  single    1.730  0.020  1.730
 U94  C27   H27   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
 U94  O4    C2   C3    114.81  3.000
 U94  O4    C2   O1    127.62  3.000
 U94  C3    C2   O1    117.57  3.000
 U94  H3    C3   O8    110.09  3.000
 U94  H3    C3   C5    107.68  3.000
 U94  O8    C3   C5    111.82  3.000
 U94  H3    C3   C2    108.31  3.000
 U94  C5    C3   C2    109.35  3.000
 U94  O8    C3   C2    109.50  3.000
 U94  H5    C5   O9    110.93  3.000
 U94  H5    C5   C6    108.36  3.000
 U94  O9    C5   C6    111.08  3.000
 U94  H5    C5   C3    106.67  3.000
 U94  C6    C5   C3    112.25  3.000
 U94  O9    C5   C3    107.50  3.000
 U94  H6    C6   N10   107.57  3.000
 U94  H6    C6   C7    108.70  3.000
 U94  N10   C6   C7    109.79  3.000
 U94  H6    C6   C5    109.06  3.000
 U94  N10   C6   C5    109.35  3.000
 U94  C7    C6   C5    112.26  3.000
 U94  H7A   C7   H7    107.12  3.000
 U94  H7A   C7   C16   109.32  3.000
 U94  H7    C7   C16   110.07  3.000
 U94  H7A   C7   C6    109.37  3.000
 U94  H7    C7   C6    109.34  3.000
 U94  C16   C7   C6    111.52  3.000
 U94  HO8   O8   C3    102.01  3.000
 U94  HO9   O9   C5    108.89  3.000
 U94  HN10  N10  C11   117.73  3.000
 U94  HN10  N10  C6    116.58  3.000
 U94  C11   N10  C6    124.99  3.000
 U94  C13   C11  O12   122.46  3.000
 U94  C13   C11  N10   112.85  3.000
 U94  O12   C11  N10   124.68  3.000
 U94  H13A  C13  H13   106.26  3.000
 U94  H13A  C13  O14   111.67  3.000
 U94  H13   C13  O14   111.80  3.000
 U94  H13A  C13  C11   108.11  3.000
 U94  H13   C13  C11   109.58  3.000
 U94  O14   C13  C11   109.31  3.000
 U94  C15   O14  C13   112.18  3.000
 U94  H15B  C15  H15A  108.47  3.000
 U94  H15B  C15  H15   108.43  3.000
 U94  H15A  C15  H15   107.84  3.000
 U94  H15B  C15  O14   107.86  3.000
 U94  H15A  C15  O14   112.02  3.000
 U94  H15   C15  O14   112.12  3.000
 U94  C21   C16  C17   118.04  3.000
 U94  C21   C16  C7    121.63  3.000
 U94  C17   C16  C7    120.31  3.000
 U94  H17   C17  C18   119.24  3.000
 U94  H17   C17  C16   119.59  3.000
 U94  C18   C17  C16   121.17  3.000
 U94  H18   C18  C19   120.05  3.000
 U94  H18   C18  C17   119.20  3.000
 U94  C19   C18  C17   120.72  3.000
 U94  C22   C19  C20   121.07  3.000
 U94  C20   C19  C18   118.25  3.000
 U94  C22   C19  C18   120.68  3.000
 U94  H20   C20  C21   119.18  3.000
 U94  H20   C20  C19   120.08  3.000
 U94  C21   C20  C19   120.73  3.000
 U94  H21   C21  C20   119.20  3.000
 U94  H21   C21  C16   119.72  3.000
 U94  C20   C21  C16   121.08  3.000
 U94  C27   C22  C23   119.17  3.000
 U94  C27   C22  C19   120.40  3.000
 U94  C23   C22  C19   120.43  3.000
 U94  H23   C23  C24   119.89  3.000
 U94  H23   C23  C22   120.44  3.000
 U94  C24   C23  C22   119.66  3.000
 U94  CL29  C24  C25   118.78  3.000
 U94  C25   C24  C23   122.00  3.000
 U94  CL29  C24  C23   119.21  3.000
 U94  H25   C25  C26   121.25  3.000
 U94  H25   C25  C24   121.25  3.000
 U94  C26   C25  C24   117.50  3.000
 U94  CL28  C26  C27   119.15  3.000
 U94  CL28  C26  C25   118.85  3.000
 U94  C27   C26  C25   121.99  3.000
 U94  H27   C27  C26   119.92  3.000
 U94  H27   C27  C22   120.38  3.000
 U94  C26   C27  C22   119.68  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
 U94  CONST_01  C19   C18  C17  C16     0.00   0.0  0
 U94  CONST_02  C19   C20  C21  C16     0.00   0.0  0
 U94  CONST_03  C20   C21  C16  C17     0.00   0.0  0
 U94  CONST_04  C22   C19  C18  C17   180.00   0.0  0
 U94  CONST_05  C20   C19  C18  C17     0.00   0.0  0
 U94  CONST_06  C21   C16  C17  C18     0.00   0.0  0
 U94  CONST_09  C21   C20  C19  C18     0.00   0.0  0
 U94  CONST_10  C24   C23  C22  C19   180.00   0.0  0
 U94  CONST_11  C26   C27  C22  C19   180.00   0.0  0
 U94  CONST_14  C22   C19  C20  C21   180.00   0.0  0
 U94  CONST_15  C25   C24  C23  C22     0.00   0.0  0
 U94  CONST_16  C25   C26  C27  C22     0.00   0.0  0
 U94  CONST_17  C26   C27  C22  C23     0.00   0.0  0
 U94  CONST_18  C26   C25  C24  C23     0.00   0.0  0
 U94  CONST_19  C27   C22  C23  C24     0.00   0.0  0
 U94  CONST_20  C27   C26  C25  C24     0.00   0.0  0
 U94  CONST_21  C18   C17  C16  C7    180.00   0.0  0
 U94  CONST_22  C20   C21  C16  C7    180.00   0.0  0
 U94  CONST_23  CL29  C24  C23  C22   180.00   0.0  0
 U94  CONST_24  CL28  C26  C27  C22   180.00   0.0  0
 U94  CONST_25  CL28  C26  C25  C24   180.00   0.0  0
 U94  CONST_26  CL29  C24  C25  C26   180.00   0.0  0
 U94  CONST_27  H18   C18  C17  C16   180.00   0.0  0
 U94  CONST_28  H20   C20  C21  C16   180.00   0.0  0
 U94  CONST_29  H21   C21  C16  C17   180.00   0.0  0
 U94  CONST_30  H17   C17  C18  C19   180.00   0.0  0
 U94  CONST_31  H23   C23  C22  C19     0.00   0.0  0
 U94  CONST_32  H27   C27  C22  C19     0.00   0.0  0
 U94  CONST_33  H25   C25  C24  C23   180.00   0.0  0
 U94  CONST_34  O12   C11  N10  C6      0.00   0.0  0
 U94  CONST_35  C13   C11  N10  C6    180.00   0.0  0
 U94  CONST_36  HN10  N10  C11  O12   180.00   0.0  0
 U94  Var_01    C17   C16  C7   C6    -76.53  30.0  2
 U94  Var_02    O14   C13  C11  N10  -171.91  30.0  3
 U94  Var_03    H15   C15  O14  C13   -60.20  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
 U94  chir_01  C3  C2   O8  C5  positiv
 U94  chir_02  C5  O9   C3  C6  positiv
 U94  chir_03  C6  N10  C7  C5  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
 U94  plan-1  C7    0.020
 U94  plan-1  C16   0.020
 U94  plan-1  C17   0.020
 U94  plan-1  C18   0.020
 U94  plan-1  C19   0.020
 U94  plan-1  C20   0.020
 U94  plan-1  C21   0.020
 U94  plan-1  C22   0.020
 U94  plan-1  H17   0.020
 U94  plan-1  H18   0.020
 U94  plan-1  H20   0.020
 U94  plan-1  H21   0.020
 U94  plan-2  C19   0.020
 U94  plan-2  C22   0.020
 U94  plan-2  C23   0.020
 U94  plan-2  C24   0.020
 U94  plan-2  C25   0.020
 U94  plan-2  C26   0.020
 U94  plan-2  C27   0.020
 U94  plan-2  CL28  0.020
 U94  plan-2  CL29  0.020
 U94  plan-2  H23   0.020
 U94  plan-2  H25   0.020
 U94  plan-2  H27   0.020
 U94  plan-3  C6    0.020
 U94  plan-3  N10   0.020
 U94  plan-3  C11   0.020
 U94  plan-3  O12   0.020
 U94  plan-3  C13   0.020
 U94  plan-3  HN10  0.020
 U94  plan-4  O1    0.020
 U94  plan-4  C2    0.020
 U94  plan-4  C3    0.020
 U94  plan-4  O4    0.020

