# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 15:07:46 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 2-amino-4,5-anhydro-1,2,6-trideoxy-1,6-diphenyl-D-galactitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccccc1)[C@@H](O)[C@H]2O[C@@H]2Cc3ccccc3
#
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
 070  070  2-amino-4,5-anhydro-1,2,6-trideoxy-1,6-diphenyl-D-galactitol  ligand  42  21  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_070
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
 070  C27  C  CR16  0  -0.310  -5.2192   0.5329   0.7215
 070  C28  C  CR16  0  -0.240  -6.1389  -0.3468   1.2778
 070  C29  C  CR16  0  -0.272  -6.1836  -1.6679   0.8527
 070  C30  C  CR16  0  -0.241  -5.3034  -2.1010  -0.1311
 070  C31  C  CR16  0  -0.299  -4.3839  -1.2193  -0.6826
 070  C26  C  CR6   0   0.136  -4.3320   0.1093  -0.2650
 070  C25  C  CH2   0  -0.575  -3.3040   1.0482  -0.8353
 070  C24  C  CH1   0   0.011  -2.0004   0.9486  -0.0872
 070  O5   O  O2    0  -0.483  -1.2297  -0.2237  -0.3110
 070  C23  C  CH1   0  -0.046  -0.7092   1.0186  -0.7603
 070  C22  C  CH1   0  -0.016   0.5304   1.5183  -0.0541
 070  O4   O  OH1   0  -0.662   0.7355   2.8795  -0.3594
 070  C14  C  CH1   0  -0.108   1.7546   0.6371  -0.3593
 070  C15  C  CH2   0  -0.522   2.9576   1.0777   0.4826
 070  C16  C  CR6   0   0.164   4.0695   0.0686   0.4643
 070  C17  C  CR16  0  -0.313   4.0428  -1.0205   1.3335
 070  C18  C  CR16  0  -0.241   5.0500  -1.9763   1.3147
 070  C19  C  CR16  0  -0.276   6.1075  -1.8556   0.4222
 070  C20  C  CR16  0  -0.244   6.1469  -0.7738  -0.4480
 070  C21  C  CR16  0  -0.311   5.1342   0.1765  -0.4268
 070  N2   N  NH2   0  -0.790   2.1403   0.5679  -1.7556
 070  H1   H  HCR6  0   0.248  -5.1941   1.5639   1.0553
 070  H2   H  HCR6  0   0.254  -6.8232   0.0020   2.0409
 070  H3   H  HCR6  0   0.254  -6.9022  -2.3539   1.2820
 070  H4   H  HCR6  0   0.254  -5.3344  -3.1283  -0.4711
 070  H5   H  HCR6  0   0.246  -3.7052  -1.5663  -1.4528
 070  H6   H  HCH2  0   0.264  -3.1364   0.8308  -1.8933
 070  H7   H  HCH2  0   0.262  -3.6548   2.0811  -0.7715
 070  H8   H  HCH1  0   0.259  -2.0474   1.2583   0.9573
 070  H9   H  HCH1  0   0.253  -0.7156   1.1454  -1.8452
 070  H10  H  HCH1  0   0.244   0.3524   1.4751   1.0264
 070  H11  H  HOH1  0   0.440   0.9066   2.9658  -1.3038
 070  H12  H  HCH1  0   0.244   1.4839  -0.3777  -0.0458
 070  H13  H  HCH2  0   0.244   3.3206   2.0445   0.1226
 070  H14  H  HCH2  0   0.248   2.6248   1.2355   1.5118
 070  H15  H  HCR6  0   0.243   3.2252  -1.1209   2.0388
 070  H16  H  HCR6  0   0.251   5.0113  -2.8132   2.0004
 070  H17  H  HCR6  0   0.251   6.8968  -2.5960   0.4080
 070  H18  H  HCR6  0   0.250   6.9680  -0.6692  -1.1460
 070  H19  H  HCR6  0   0.240   5.1745   1.0170  -1.1091
 070  H20  H  HNH2  0   0.356   1.3880   0.2315  -2.3421
 070  H21  H  HNH2  0   0.337   2.4280   1.4699  -2.1128

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
 070  C29  C30  aromatic  1.389  0.020  1.389
 070  C29  C28  aromatic  1.389  0.020  1.389
 070  C30  C31  aromatic  1.388  0.020  1.388
 070  C28  C27  aromatic  1.389  0.020  1.389
 070  C31  C26  aromatic  1.394  0.020  1.394
 070  C27  C26  aromatic  1.393  0.020  1.393
 070  C26  C25  single    1.504  0.020  1.504
 070  O5   C24  single    1.421  0.020  1.421
 070  O5   C23  single    1.420  0.020  1.420
 070  C25  C24  single    1.506  0.020  1.506
 070  C24  C23  single    1.458  0.020  1.458
 070  C23  C22  single    1.512  0.020  1.512
 070  C18  C17  aromatic  1.389  0.020  1.389
 070  C18  C19  aromatic  1.389  0.020  1.389
 070  C17  C16  aromatic  1.394  0.020  1.394
 070  C22  C14  single    1.539  0.020  1.539
 070  C22  O4   single    1.410  0.020  1.410
 070  C14  N2   single    1.450  0.020  1.450
 070  C14  C15  single    1.533  0.020  1.533
 070  C19  C20  aromatic  1.389  0.020  1.389
 070  C16  C15  single    1.502  0.020  1.502
 070  C16  C21  aromatic  1.393  0.020  1.393
 070  C20  C21  aromatic  1.389  0.020  1.389
 070  C27  H1   single    0.930  0.020  1.080
 070  C28  H2   single    0.930  0.020  1.080
 070  C29  H3   single    0.930  0.020  1.080
 070  C30  H4   single    0.930  0.020  1.080
 070  C31  H5   single    0.930  0.020  1.080
 070  C25  H6   single    0.970  0.020  1.090
 070  C25  H7   single    0.970  0.020  1.090
 070  C24  H8   single    0.970  0.020  1.090
 070  C23  H9   single    0.970  0.020  1.090
 070  C22  H10  single    0.970  0.020  1.090
 070  O4   H11  single    0.850  0.020  0.980
 070  C14  H12  single    0.970  0.020  1.090
 070  C15  H13  single    0.970  0.020  1.090
 070  C15  H14  single    0.970  0.020  1.090
 070  C17  H15  single    0.930  0.020  1.080
 070  C18  H16  single    0.930  0.020  1.080
 070  C19  H17  single    0.930  0.020  1.080
 070  C20  H18  single    0.930  0.020  1.080
 070  C21  H19  single    0.930  0.020  1.080
 070  N2   H20  single    0.890  0.020  1.040
 070  N2   H21  single    0.890  0.020  1.040

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
 070  H1   C27  C26  119.52  3.000
 070  H1   C27  C28  119.62  3.000
 070  C26  C27  C28  120.86  3.000
 070  H2   C28  C29  120.13  3.000
 070  H2   C28  C27  119.79  3.000
 070  C29  C28  C27  120.08  3.000
 070  H3   C29  C30  120.26  3.000
 070  H3   C29  C28  120.20  3.000
 070  C30  C29  C28  119.54  3.000
 070  H4   C30  C31  119.80  3.000
 070  H4   C30  C29  120.01  3.000
 070  C31  C30  C29  120.19  3.000
 070  H5   C31  C26  119.66  3.000
 070  H5   C31  C30  119.59  3.000
 070  C26  C31  C30  120.74  3.000
 070  C25  C26  C31  120.45  3.000
 070  C25  C26  C27  120.93  3.000
 070  C31  C26  C27  118.58  3.000
 070  H7   C25  H6   107.09  3.000
 070  H7   C25  C24  108.14  3.000
 070  H6   C25  C24  109.56  3.000
 070  H7   C25  C26  110.39  3.000
 070  H6   C25  C26  110.34  3.000
 070  C24  C25  C26  111.21  3.000
 070  H8   C24  C23  117.83  3.000
 070  H8   C24  O5   114.12  3.000
 070  C23  C24  O5    59.09  3.000
 070  H8   C24  C25  114.81  3.000
 070  C23  C24  C25  122.28  3.000
 070  O5   C24  C25  116.47  3.000
 070  C23  O5   C24   61.76  3.000
 070  H9   C23  C22  115.49  3.000
 070  H9   C23  O5   114.44  3.000
 070  C22  C23  O5   116.24  3.000
 070  H9   C23  C24  117.32  3.000
 070  C22  C23  C24  121.77  3.000
 070  O5   C23  C24   59.15  3.000
 070  H10  C22  C14  107.59  3.000
 070  H10  C22  O4   105.97  3.000
 070  C14  C22  O4   113.21  3.000
 070  H10  C22  C23  108.32  3.000
 070  O4   C22  C23  109.71  3.000
 070  C14  C22  C23  111.74  3.000
 070  H11  O4   C22  108.93  3.000
 070  H12  C14  N2   107.27  3.000
 070  H12  C14  C15  107.62  3.000
 070  N2   C14  C15  109.50  3.000
 070  H12  C14  C22  106.07  3.000
 070  C15  C14  C22  110.54  3.000
 070  N2   C14  C22  115.46  3.000
 070  H14  C15  H13  106.46  3.000
 070  H14  C15  C16  109.51  3.000
 070  H13  C15  C16  110.14  3.000
 070  H14  C15  C14  108.64  3.000
 070  H13  C15  C14  109.50  3.000
 070  C16  C15  C14  112.41  3.000
 070  C21  C16  C17  118.31  3.000
 070  C21  C16  C15  121.45  3.000
 070  C17  C16  C15  120.22  3.000
 070  H15  C17  C18  119.47  3.000
 070  H15  C17  C16  119.50  3.000
 070  C18  C17  C16  121.03  3.000
 070  H16  C18  C19  120.09  3.000
 070  H16  C18  C17  119.84  3.000
 070  C19  C18  C17  120.07  3.000
 070  H17  C19  C20  120.25  3.000
 070  H17  C19  C18  120.28  3.000
 070  C20  C19  C18  119.46  3.000
 070  H18  C20  C21  119.78  3.000
 070  H18  C20  C19  120.05  3.000
 070  C21  C20  C19  120.17  3.000
 070  H19  C21  C20  119.61  3.000
 070  H19  C21  C16  119.45  3.000
 070  C20  C21  C16  120.94  3.000
 070  H21  N2   H20  107.65  3.000
 070  H21  N2   C14  111.90  3.000
 070  H20  N2   C14  112.11  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
 070  CONST_01  C30  C29  C28  C27    0.00   0.0  0
 070  CONST_02  C30  C31  C26  C27    0.00   0.0  0
 070  CONST_03  C31  C30  C29  C28    0.00   0.0  0
 070  CONST_04  C31  C26  C27  C28    0.00   0.0  0
 070  CONST_05  C26  C31  C30  C29    0.00   0.0  0
 070  CONST_06  C26  C27  C28  C29    0.00   0.0  0
 070  CONST_07  C19  C18  C17  C16    0.00   0.0  0
 070  CONST_08  C19  C20  C21  C16    0.00   0.0  0
 070  CONST_09  C20  C19  C18  C17    0.00   0.0  0
 070  CONST_10  C20  C21  C16  C17    0.00   0.0  0
 070  CONST_11  C21  C16  C17  C18    0.00   0.0  0
 070  CONST_12  C21  C20  C19  C18    0.00   0.0  0
 070  CONST_13  C25  C26  C27  C28  180.00   0.0  0
 070  CONST_14  C25  C26  C31  C30  180.00   0.0  0
 070  CONST_15  C18  C17  C16  C15  180.00   0.0  0
 070  CONST_16  C20  C21  C16  C15  180.00   0.0  0
 070  CONST_17  H3   C29  C28  C27  180.00   0.0  0
 070  CONST_18  H5   C31  C26  C27  180.00   0.0  0
 070  CONST_19  H4   C30  C29  C28  180.00   0.0  0
 070  CONST_20  H1   C27  C28  C29  180.00   0.0  0
 070  CONST_21  H2   C28  C29  C30  180.00   0.0  0
 070  CONST_22  H16  C18  C17  C16  180.00   0.0  0
 070  CONST_23  H18  C20  C21  C16  180.00   0.0  0
 070  CONST_24  H17  C19  C18  C17  180.00   0.0  0
 070  CONST_25  H19  C21  C16  C17  180.00   0.0  0
 070  CONST_26  H15  C17  C18  C19  180.00   0.0  0
 070  Var_01    C24  C25  C26  C27   92.41  30.0  2
 070  Var_02    O5   C24  C25  C26   72.87  30.0  3
 070  Var_03    C22  C23  O5   C24  112.91  30.0  1
 070  Var_04    C17  C16  C15  C14  -83.60  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
 070  chir_03  C22  C23  C14  O4   negativ
 070  chir_04  C14  N2   C15  C22  negativ
 070  chir_05  C24  O5   C25  C23  both
 070  chir_06  C23  O5   C22  C24  both

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
 070  plan-1  C27  0.020
 070  plan-1  C28  0.020
 070  plan-1  C29  0.020
 070  plan-1  C30  0.020
 070  plan-1  C31  0.020
 070  plan-1  C26  0.020
 070  plan-1  C25  0.020
 070  plan-1  H1   0.020
 070  plan-1  H2   0.020
 070  plan-1  H3   0.020
 070  plan-1  H4   0.020
 070  plan-1  H5   0.020
 070  plan-2  C15  0.020
 070  plan-2  C16  0.020
 070  plan-2  C17  0.020
 070  plan-2  C18  0.020
 070  plan-2  C19  0.020
 070  plan-2  C20  0.020
 070  plan-2  C21  0.020
 070  plan-2  H15  0.020
 070  plan-2  H16  0.020
 070  plan-2  H17  0.020
 070  plan-2  H18  0.020
 070  plan-2  H19  0.020

