# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 20:31:11 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 2,4-diamino-1,2,4,5-tetradeoxy-1,5-diphenyl-L-arabinitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccccc1)[C@@H](O)[C@@H](N)Cc2ccccc2
#
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
 COR  COR  2,4-diamino-1,2,4,5-tetradeoxy-1,5-diphenyl-L-arabinitol  ligand  42  20  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_COR
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
 COR  C1    C  CH2   0  -0.544   0.6170  -0.9998  -2.5182
 COR  C2    C  CH1   0  -0.091   0.3585  -0.1554  -1.2615
 COR  N2    N  NH2   0  -0.816   0.9858   1.1609  -1.3031
 COR  C3    C  CH1   0   0.073   0.8356  -0.8893   0.0029
 COR  O3    O  OH1   0  -0.674   2.2422  -0.8477   0.0877
 COR  C4    C  CH1   0  -0.131   0.1614  -0.3281   1.2650
 COR  N4    N  NH2   0  -0.786  -1.2662  -0.5913   1.1772
 COR  C5    C  CH2   0  -0.514   0.8118  -0.8741   2.5512
 COR  C1A   C  CR6   0   0.159   0.0771  -0.3545  -3.7617
 COR  C2A   C  CR16  0  -0.331   0.8911   0.4160  -4.5892
 COR  C3A   C  CR16  0  -0.239   0.3753   1.0481  -5.7138
 COR  C4A   C  CR16  0  -0.276  -0.9702   0.9193  -6.0301
 COR  C5A   C  CR16  0  -0.239  -1.7933   0.1514  -5.2152
 COR  C6A   C  CR16  0  -0.311  -1.2719  -0.4777  -4.0935
 COR  C1B   C  CR6   0   0.134   0.1902  -0.2815   3.7832
 COR  C2B   C  CR16  0  -0.323  -0.8377  -0.9326   4.4627
 COR  C3B   C  CR16  0  -0.241  -1.4375  -0.3565   5.5761
 COR  C4B   C  CR16  0  -0.274  -1.0203   0.8883   6.0271
 COR  C5B   C  CR16  0  -0.241   0.0028   1.5498   5.3582
 COR  C6B   C  CR16  0  -0.306   0.5991   0.9685   4.2480
 COR  H11   H  HCH2  0   0.242   1.6934  -1.1683  -2.6209
 COR  H12   H  HCH2  0   0.244   0.1583  -1.9831  -2.3818
 COR  H2    H  HCH1  0   0.245  -0.7191  -0.0131  -1.1590
 COR  HN21  H  HNH2  0   0.346   1.8090   1.1571  -1.8930
 COR  HN22  H  HNH2  0   0.359   0.3601   1.8430  -1.7066
 COR  H3    H  HCH1  0   0.217   0.5686  -1.9504  -0.0791
 COR  HO3   H  HOH1  0   0.437   2.4879   0.0864   0.0742
 COR  H4    H  HCH1  0   0.228   0.2929   0.7611   1.2550
 COR  HN41  H  HNH2  0   0.336  -1.4393  -1.5808   1.3181
 COR  HN42  H  HNH2  0   0.352  -1.7545  -0.1156   1.9254
 COR  H51   H  HCH2  0   0.234   0.7052  -1.9640   2.5673
 COR  H52   H  HCH2  0   0.242   1.8815  -0.6602   2.5434
 COR  H2A   H  HCR6  0   0.243   1.9461   0.5145  -4.3599
 COR  H3A   H  HCR6  0   0.252   1.0265   1.6407  -6.3437
 COR  H4A   H  HCR6  0   0.252  -1.3740   1.4082  -6.9072
 COR  H5A   H  HCR6  0   0.252  -2.8428   0.0391  -5.4563
 COR  H6A   H  HCR6  0   0.245  -1.9216  -1.0805  -3.4685
 COR  H2B   H  HCR6  0   0.246  -1.1657  -1.9090   4.1248
 COR  H3B   H  HCR6  0   0.252  -2.2301  -0.8836   6.0920
 COR  H4B   H  HCR6  0   0.252  -1.4855   1.3389   6.8944
 COR  H5B   H  HCR6  0   0.252   0.3381   2.5198   5.7030
 COR  H6B   H  HCR6  0   0.244   1.3976   1.4930   3.7347

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
 COR  C1   C2    single    1.536  0.020  1.536
 COR  C1   C1A   single    1.501  0.020  1.501
 COR  C1   H11   single    0.970  0.020  1.090
 COR  C1   H12   single    0.970  0.020  1.090
 COR  C2   N2    single    1.459  0.020  1.459
 COR  C2   C3    single    1.538  0.020  1.538
 COR  C2   H2    single    0.970  0.020  1.090
 COR  N2   HN21  single    0.890  0.020  1.040
 COR  N2   HN22  single    0.890  0.020  1.040
 COR  C3   O3    single    1.410  0.020  1.410
 COR  C3   C4    single    1.537  0.020  1.537
 COR  C3   H3    single    0.970  0.020  1.090
 COR  O3   HO3   single    0.850  0.020  0.980
 COR  C4   N4    single    1.454  0.020  1.454
 COR  C4   C5    single    1.541  0.020  1.541
 COR  C4   H4    single    0.970  0.020  1.090
 COR  N4   HN41  single    0.890  0.020  1.040
 COR  N4   HN42  single    0.890  0.020  1.040
 COR  C5   C1B   single    1.502  0.020  1.502
 COR  C5   H51   single    0.970  0.020  1.090
 COR  C5   H52   single    0.970  0.020  1.090
 COR  C1A  C2A   aromatic  1.393  0.020  1.393
 COR  C1A  C6A   aromatic  1.395  0.020  1.395
 COR  C2A  C3A   aromatic  1.389  0.020  1.389
 COR  C2A  H2A   single    0.930  0.020  1.080
 COR  C3A  C4A   aromatic  1.388  0.020  1.388
 COR  C3A  H3A   single    0.930  0.020  1.080
 COR  C4A  C5A   aromatic  1.390  0.020  1.390
 COR  C4A  H4A   single    0.930  0.020  1.080
 COR  C5A  C6A   aromatic  1.388  0.020  1.388
 COR  C5A  H5A   single    0.930  0.020  1.080
 COR  C6A  H6A   single    0.930  0.020  1.080
 COR  C1B  C2B   aromatic  1.394  0.020  1.394
 COR  C1B  C6B   aromatic  1.395  0.020  1.395
 COR  C2B  C3B   aromatic  1.390  0.020  1.390
 COR  C2B  H2B   single    0.930  0.020  1.080
 COR  C3B  C4B   aromatic  1.388  0.020  1.388
 COR  C3B  H3B   single    0.930  0.020  1.080
 COR  C4B  C5B   aromatic  1.390  0.020  1.390
 COR  C4B  H4B   single    0.930  0.020  1.080
 COR  C5B  C6B   aromatic  1.388  0.020  1.388
 COR  C5B  H5B   single    0.930  0.020  1.080
 COR  C6B  H6B   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
 COR  H12   C1   H11   106.61  3.000
 COR  H12   C1   C1A   109.81  3.000
 COR  H11   C1   C1A   110.01  3.000
 COR  H12   C1   C2    108.76  3.000
 COR  H11   C1   C2    109.08  3.000
 COR  C1A   C1   C2    112.38  3.000
 COR  H2    C2   C3    106.93  3.000
 COR  H2    C2   N2    108.03  3.000
 COR  C3    C2   N2    108.71  3.000
 COR  H2    C2   C1    108.33  3.000
 COR  C3    C2   C1    110.99  3.000
 COR  N2    C2   C1    113.60  3.000
 COR  HN22  N2   HN21  105.87  3.000
 COR  HN22  N2   C2    110.76  3.000
 COR  HN21  N2   C2    111.28  3.000
 COR  H3    C3   C4    107.93  3.000
 COR  H3    C3   O3    106.01  3.000
 COR  C4    C3   O3    112.18  3.000
 COR  H3    C3   C2    108.94  3.000
 COR  C4    C3   C2    111.40  3.000
 COR  O3    C3   C2    110.17  3.000
 COR  HO3   O3   C3    106.34  3.000
 COR  H4    C4   C5    107.98  3.000
 COR  H4    C4   N4    107.27  3.000
 COR  C5    C4   N4    113.61  3.000
 COR  H4    C4   C3    107.60  3.000
 COR  C5    C4   C3    111.76  3.000
 COR  N4    C4   C3    108.36  3.000
 COR  HN42  N4   HN41  105.87  3.000
 COR  HN42  N4   C4    110.11  3.000
 COR  HN41  N4   C4    109.62  3.000
 COR  H52   C5   H51   106.89  3.000
 COR  H52   C5   C1B   109.53  3.000
 COR  H51   C5   C1B   109.90  3.000
 COR  H52   C5   C4    109.78  3.000
 COR  H51   C5   C4    108.89  3.000
 COR  C1B   C5   C4    111.72  3.000
 COR  C6A   C1A  C2A   118.21  3.000
 COR  C6A   C1A  C1    120.46  3.000
 COR  C2A   C1A  C1    121.30  3.000
 COR  H2A   C2A  C3A   119.42  3.000
 COR  H2A   C2A  C1A   119.55  3.000
 COR  C3A   C2A  C1A   121.03  3.000
 COR  H3A   C3A  C4A   120.09  3.000
 COR  H3A   C3A  C2A   119.77  3.000
 COR  C4A   C3A  C2A   120.14  3.000
 COR  H4A   C4A  C5A   120.25  3.000
 COR  H4A   C4A  C3A   120.29  3.000
 COR  C5A   C4A  C3A   119.46  3.000
 COR  H5A   C5A  C6A   119.82  3.000
 COR  H5A   C5A  C4A   120.06  3.000
 COR  C6A   C5A  C4A   120.12  3.000
 COR  H6A   C6A  C5A   119.52  3.000
 COR  H6A   C6A  C1A   119.44  3.000
 COR  C5A   C6A  C1A   121.04  3.000
 COR  C6B   C1B  C2B   118.19  3.000
 COR  C6B   C1B  C5    120.37  3.000
 COR  C2B   C1B  C5    121.39  3.000
 COR  H2B   C2B  C3B   119.51  3.000
 COR  H2B   C2B  C1B   119.47  3.000
 COR  C3B   C2B  C1B   121.02  3.000
 COR  H3B   C3B  C4B   120.12  3.000
 COR  H3B   C3B  C2B   119.73  3.000
 COR  C4B   C3B  C2B   120.15  3.000
 COR  H4B   C4B  C5B   120.26  3.000
 COR  H4B   C4B  C3B   120.29  3.000
 COR  C5B   C4B  C3B   119.45  3.000
 COR  H5B   C5B  C6B   119.80  3.000
 COR  H5B   C5B  C4B   120.07  3.000
 COR  C6B   C5B  C4B   120.13  3.000
 COR  H6B   C6B  C5B   119.50  3.000
 COR  H6B   C6B  C1B   119.44  3.000
 COR  C5B   C6B  C1B   121.06  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
 COR  CONST_01  C4A  C3A  C2A  C1A    0.00   0.0  0
 COR  CONST_02  C4A  C5A  C6A  C1A    0.00   0.0  0
 COR  CONST_03  C5A  C6A  C1A  C2A    0.00   0.0  0
 COR  CONST_04  C5A  C4A  C3A  C2A    0.00   0.0  0
 COR  CONST_05  C6A  C1A  C2A  C3A    0.00   0.0  0
 COR  CONST_06  C6A  C5A  C4A  C3A    0.00   0.0  0
 COR  CONST_07  C4B  C3B  C2B  C1B    0.00   0.0  0
 COR  CONST_08  C4B  C5B  C6B  C1B    0.00   0.0  0
 COR  CONST_09  C5B  C6B  C1B  C2B    0.00   0.0  0
 COR  CONST_10  C5B  C4B  C3B  C2B    0.00   0.0  0
 COR  CONST_11  C6B  C1B  C2B  C3B    0.00   0.0  0
 COR  CONST_12  C6B  C5B  C4B  C3B    0.00   0.0  0
 COR  CONST_13  C3A  C2A  C1A  C1   180.00   0.0  0
 COR  CONST_14  C5A  C6A  C1A  C1   180.00   0.0  0
 COR  CONST_15  C3B  C2B  C1B  C5   180.00   0.0  0
 COR  CONST_16  C5B  C6B  C1B  C5   180.00   0.0  0
 COR  CONST_17  H3A  C3A  C2A  C1A  180.00   0.0  0
 COR  CONST_18  H5A  C5A  C6A  C1A  180.00   0.0  0
 COR  CONST_19  H6A  C6A  C1A  C2A  180.00   0.0  0
 COR  CONST_20  H4A  C4A  C3A  C2A  180.00   0.0  0
 COR  CONST_21  H2A  C2A  C3A  C4A  180.00   0.0  0
 COR  CONST_22  H3B  C3B  C2B  C1B  180.00   0.0  0
 COR  CONST_23  H5B  C5B  C6B  C1B  180.00   0.0  0
 COR  CONST_24  H6B  C6B  C1B  C2B  180.00   0.0  0
 COR  CONST_25  H4B  C4B  C3B  C2B  180.00   0.0  0
 COR  CONST_26  H2B  C2B  C3B  C4B  180.00   0.0  0
 COR  Var_01    C2A  C1A  C1   C2    95.99  30.0  2
 COR  Var_02    C2B  C1B  C5   C4    94.94  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
 COR  chir_01  C2  C1  N2  C3  positiv
 COR  chir_02  C4  N4  C3  C5  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
 COR  plan-1  C1   0.020
 COR  plan-1  C1A  0.020
 COR  plan-1  C2A  0.020
 COR  plan-1  C3A  0.020
 COR  plan-1  C4A  0.020
 COR  plan-1  C5A  0.020
 COR  plan-1  C6A  0.020
 COR  plan-1  H2A  0.020
 COR  plan-1  H3A  0.020
 COR  plan-1  H4A  0.020
 COR  plan-1  H5A  0.020
 COR  plan-1  H6A  0.020
 COR  plan-2  C5   0.020
 COR  plan-2  C1B  0.020
 COR  plan-2  C2B  0.020
 COR  plan-2  C3B  0.020
 COR  plan-2  C4B  0.020
 COR  plan-2  C5B  0.020
 COR  plan-2  C6B  0.020
 COR  plan-2  H2B  0.020
 COR  plan-2  H3B  0.020
 COR  plan-2  H4B  0.020
 COR  plan-2  H5B  0.020
 COR  plan-2  H6B  0.020

