# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 31 03:57:46 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  50  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   OH1   0  -0.592  -7.2171   0.3848  -1.1953
 U94  C2    C   C     0   0.512  -6.8508   1.0822  -0.1300
 U94  C3    C   CH1   0  -0.084  -5.4115   0.7855   0.2691
 U94  O4    O   O     0  -0.431  -7.5690   1.8510   0.4535
 U94  C5    C   CH1   0   0.013  -4.4680   1.2390  -0.8521
 U94  C6    C   CH1   0  -0.090  -3.0010   0.9361  -0.5123
 U94  C7    C   CH2   0  -0.546  -2.0430   1.5188  -1.5655
 U94  O8    O   OH1   0  -0.648  -5.1124   1.3601   1.5032
 U94  O9    O   OH1   0  -0.673  -4.6935   2.6186  -1.0240
 U94  N10   N   NH1   0  -0.649  -2.8280  -0.4931  -0.4008
 U94  C11   C   C     0   0.508  -2.1779  -1.1031   0.6124
 U94  O12   O   O     0  -0.465  -1.8129  -0.5463   1.6287
 U94  C13   C   CH2   0  -0.252  -1.9237  -2.5781   0.3522
 U94  O14   O   O2    0  -0.475  -1.5166  -3.1883   1.5349
 U94  C15   C   CH3   0  -0.401  -1.2211  -4.5512   1.3535
 U94  C16   C   CR6   0   0.141  -0.6193   1.1546  -1.2617
 U94  C17   C   CR16  0  -0.276   0.1249   1.8979  -0.3498
 U94  C18   C   CR16  0  -0.291   1.4163   1.5301  -0.0129
 U94  C19   C   CR6   0   0.072   2.0070   0.4000  -0.5790
 U94  C20   C   CR16  0  -0.290   1.2667  -0.3412  -1.4989
 U94  C21   C   CR16  0  -0.302  -0.0255   0.0327  -1.8327
 U94  C22   C   CR6   0   0.081   3.3813   0.0032  -0.2149
 U94  C23   C   CR16  0  -0.264   3.8386   0.1635   1.0928
 U94  C24   C   CR6   0  -0.029   5.1308  -0.2110   1.4175
 U94  C25   C   CR16  0  -0.189   5.9965  -0.7507   0.4798
 U94  C26   C   CR6   0  -0.028   5.5241  -0.9037  -0.8137
 U94  C27   C   CR16  0  -0.264   4.2390  -0.5364  -1.1730
 U94  CL28  CL  CL    0  -0.112   6.5808  -1.5608  -2.0161
 U94  CL29  CL  CL    0  -0.112   5.6827  -0.0155   3.0457
 U94  HO1   H   HOH1  0   0.487  -8.1302   0.5981  -1.4409
 U94  H3    H   HCH1  0   0.294  -5.3101  -0.2974   0.3866
 U94  H5    H   HCH1  0   0.240  -4.7284   0.6818  -1.7624
 U94  H6    H   HCH1  0   0.272  -2.7596   1.3727   0.4568
 U94  H7    H   HCH2  0   0.256  -2.3215   1.1504  -2.5577
 U94  H7A   H   HCH2  0   0.262  -2.1479   2.6051  -1.5818
 U94  HO8   H   HOH1  0   0.449  -5.2389   2.3140   1.4465
 U94  HO9   H   HOH1  0   0.468  -4.3841   2.8892  -1.8935
 U94  HN10  H   HNH1  0   0.398  -3.0435  -1.0443  -1.2188
 U94  H13   H   HCH2  0   0.234  -2.8299  -3.0457  -0.0598
 U94  H13A  H   HCH2  0   0.235  -1.1526  -2.6548  -0.4310
 U94  H15   H   HCH3  0   0.209  -2.0926  -5.1196   1.0077
 U94  H15A  H   HCH3  0   0.208  -0.4115  -4.7035   0.6300
 U94  H15B  H   HCH3  0   0.238  -0.9062  -4.9552   2.3145
 U94  H17   H   HCR6  0   0.249  -0.3082   2.7826   0.1019
 U94  H18   H   HCR6  0   0.256   1.9760   2.1438   0.6820
 U94  H20   H   HCR6  0   0.257   1.6901  -1.2323  -1.9459
 U94  H21   H   HCR6  0   0.253  -0.5799  -0.5632  -2.5483
 U94  H23   H   HCR6  0   0.284   3.1846   0.5599   1.8578
 U94  H25   H   HCR6  0   0.302   7.0022  -1.0421   0.7477
 U94  H27   H   HCR6  0   0.284   3.9128  -0.6491  -2.1981

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    single    1.325  0.020  1.325
 U94  O1    HO1   single    0.850  0.020  0.980
 U94  C3    C2    single    1.523  0.020  1.523
 U94  C2    O4    double    1.203  0.020  1.203
 U94  O8    C3    single    1.394  0.020  1.394
 U94  C3    C5    single    1.534  0.020  1.534
 U94  C3    H3    single    0.970  0.020  1.090
 U94  O9    C5    single    1.408  0.020  1.408
 U94  C5    C6    single    1.536  0.020  1.536
 U94  C5    H5    single    0.970  0.020  1.090
 U94  C7    C6    single    1.538  0.020  1.538
 U94  C6    N10   single    1.444  0.020  1.444
 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    1.350  0.020  1.350
 U94  N10   HN10  single    0.860  0.020  1.020
 U94  O12   C11   double    1.215  0.020  1.215
 U94  C11   C13   single    1.519  0.020  1.519
 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  1.392  0.020  1.392
 U94  C16   C21   aromatic  1.392  0.020  1.392
 U94  C18   C17   aromatic  1.384  0.020  1.384
 U94  C17   H17   single    0.930  0.020  1.080
 U94  C18   C19   aromatic  1.395  0.020  1.395
 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  1.386  0.020  1.386
 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  1.395  0.020  1.395
 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  HO1   O1   C2    110.38  3.000
 U94  O4    C2   C3    124.17  3.000
 U94  O4    C2   O1    124.15  3.000
 U94  C3    C2   O1    111.68  3.000
 U94  H3    C3   O8    107.04  3.000
 U94  H3    C3   C5    108.31  3.000
 U94  O8    C3   C5    113.16  3.000
 U94  H3    C3   C2    107.98  3.000
 U94  C5    C3   C2    109.40  3.000
 U94  O8    C3   C2    110.76  3.000
 U94  H5    C5   O9    110.96  3.000
 U94  H5    C5   C6    108.04  3.000
 U94  O9    C5   C6    111.91  3.000
 U94  H5    C5   C3    108.05  3.000
 U94  C6    C5   C3    111.56  3.000
 U94  O9    C5   C3    106.28  3.000
 U94  H6    C6   N10   107.53  3.000
 U94  H6    C6   C7    108.60  3.000
 U94  N10   C6   C7    110.68  3.000
 U94  H6    C6   C5    109.22  3.000
 U94  N10   C6   C5    109.07  3.000
 U94  C7    C6   C5    111.63  3.000
 U94  H7A   C7   H7    107.28  3.000
 U94  H7A   C7   C16   109.62  3.000
 U94  H7    C7   C16   110.07  3.000
 U94  H7A   C7   C6    109.11  3.000
 U94  H7    C7   C6    109.55  3.000
 U94  C16   C7   C6    111.12  3.000
 U94  HO8   O8   C3    109.13  3.000
 U94  HO9   O9   C5    109.54  3.000
 U94  HN10  N10  C11   117.66  3.000
 U94  HN10  N10  C6    116.89  3.000
 U94  C11   N10  C6    124.27  3.000
 U94  C13   C11  O12   122.55  3.000
 U94  C13   C11  N10   113.01  3.000
 U94  O12   C11  N10   124.44  3.000
 U94  H13A  C13  H13   106.31  3.000
 U94  H13A  C13  O14   111.65  3.000
 U94  H13   C13  O14   111.89  3.000
 U94  H13A  C13  C11   107.85  3.000
 U94  H13   C13  C11   109.82  3.000
 U94  O14   C13  C11   109.21  3.000
 U94  C15   O14  C13   112.13  3.000
 U94  H15B  C15  H15A  108.49  3.000
 U94  H15B  C15  H15   108.41  3.000
 U94  H15A  C15  H15   107.86  3.000
 U94  H15B  C15  O14   107.85  3.000
 U94  H15A  C15  O14   112.01  3.000
 U94  H15   C15  O14   112.10  3.000
 U94  C21   C16  C17   118.10  3.000
 U94  C21   C16  C7    121.15  3.000
 U94  C17   C16  C7    120.68  3.000
 U94  H17   C17  C18   119.23  3.000
 U94  H17   C17  C16   119.69  3.000
 U94  C18   C17  C16   121.08  3.000
 U94  H18   C18  C19   120.04  3.000
 U94  H18   C18  C17   119.19  3.000
 U94  C19   C18  C17   120.76  3.000
 U94  C22   C19  C20   120.95  3.000
 U94  C20   C19  C18   118.27  3.000
 U94  C22   C19  C18   120.79  3.000
 U94  H20   C20  C21   119.14  3.000
 U94  H20   C20  C19   120.14  3.000
 U94  C21   C20  C19   120.70  3.000
 U94  H21   C21  C20   119.18  3.000
 U94  H21   C21  C16   119.73  3.000
 U94  C20   C21  C16   121.09  3.000
 U94  C27   C22  C23   119.14  3.000
 U94  C27   C22  C19   120.48  3.000
 U94  C23   C22  C19   120.38  3.000
 U94  H23   C23  C24   119.85  3.000
 U94  H23   C23  C22   120.47  3.000
 U94  C24   C23  C22   119.68  3.000
 U94  CL29  C24  C25   118.79  3.000
 U94  C25   C24  C23   122.00  3.000
 U94  CL29  C24  C23   119.21  3.000
 U94  H25   C25  C26   121.26  3.000
 U94  H25   C25  C24   121.24  3.000
 U94  C26   C25  C24   117.50  3.000
 U94  CL28  C26  C27   119.18  3.000
 U94  CL28  C26  C25   118.84  3.000
 U94  C27   C26  C25   121.98  3.000
 U94  H27   C27  C26   119.89  3.000
 U94  H27   C27  C22   120.39  3.000
 U94  C26   C27  C22   119.70  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  CONST_37  HO1   O1   C2   C3    180.00   0.0  0
 U94  Var_01    C17   C16  C7   C6    -83.05  30.0  2
 U94  Var_02    O14   C13  C11  N10  -167.47  30.0  3
 U94  Var_03    H15   C15  O14  C13   -61.09  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
 U94  plan-4  HO1   0.020

