# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 12:13:20 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: N-[(4R)-6,8-dichloro-3,4-dihydro-2H-chromen-4-yl]-N'-(5-fluoro-1H-imidazo[4,5-b]pyridin-2-yl)propane-1,3-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc2[nH]c(NCCCN[C@@H]3CCOc4c(Cl)cc(Cl)cc34)nc2n1
#
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
 4RD  4RD  N-[(4R)-6,8-dichloro-3,4-dihydro-2H-chromen-4-yl]-N'-(5-fluoro-1H-imidazo[4,5-b]pyridin-2-yl)propane-1,3-diamine  ligand  45  27  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_4RD
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
 4RD  C1   C   CR16  0  -0.484   -8.7328   0.9142   0.6814
 4RD  C2   C   CR16  0  -0.202   -7.4499   1.4396   0.8329
 4RD  C3   C   CR56  0   0.265   -6.4156   0.6654   0.3623
 4RD  C4   C   CR5   0   0.700   -4.5647  -0.3259  -0.2838
 4RD  C5   C   CH2   0  -0.275   -2.2280   0.3427   0.0441
 4RD  C6   C   CH2   0  -0.488   -0.8552  -0.1220  -0.4100
 4RD  C7   C   CH2   0  -0.256    0.2446   0.7587   0.1607
 4RD  C8   C   CH1   0  -0.080    2.6632   0.9780   0.3432
 4RD  C9   C   CH2   0  -0.514    2.8572   2.4152  -0.1421
 4RD  C10  C   CH2   0  -0.188    4.1361   2.9784   0.4297
 4RD  C11  C   CR6   0   0.473    5.1634   0.8923  -0.0044
 4RD  C15  C   CR16  0  -0.251    3.9461  -1.1807   0.0825
 4RD  C16  C   CR6   0  -0.040    3.9519   0.2081   0.1338
 4RD  C14  C   CR6   0  -0.058    5.1235  -1.8809  -0.1016
 4RD  C13  C   CR16  0  -0.187    6.3325  -1.2217  -0.2501
 4RD  C12  C   CR6   0  -0.187    6.3366   0.1595  -0.2001
 4RD  CL   CL  CL    0  -0.101    7.8273   1.0119  -0.3870
 4RD  O    O   O2    0  -0.463    5.2781   2.2260   0.0229
 4RD  N2   N   NH1   0  -0.600    1.5481   0.2689  -0.2453
 4RD  N1   N   NH1   0  -0.683   -3.2588  -0.5111  -0.5090
 4RD  N    N   NR15  0  -0.739   -5.0474   0.7974   0.3151
 4RD  N3   N   N     0  -0.527   -5.5131  -1.1800  -0.6279
 4RD  C17  C   CR56  0   0.287   -6.6692  -0.5855  -0.2362
 4RD  N4   N   N     0  -0.466   -7.8932  -1.0825  -0.3768
 4RD  C    C   CR6   0   0.529   -8.8575  -0.3284   0.0790
 4RD  F    F   F     0  -0.312  -10.0922  -0.8373  -0.0630
 4RD  H1   H   HCR6  0   0.281   -9.6040   1.4552   1.0211
 4RD  H2   H   HCR6  0   0.285   -7.2935   2.4034   1.2983
 4RD  H3   H   HCH2  0   0.239   -2.2706   0.3461   1.1397
 4RD  H4   H   HCH2  0   0.243   -2.3905   1.3719  -0.2888
 4RD  H5   H   HCH2  0   0.241   -0.6897  -1.1546  -0.0906
 4RD  H6   H   HCH2  0   0.241   -0.8108  -0.1094  -1.5031
 4RD  H7   H   HCH2  0   0.203    0.0594   1.8025  -0.1319
 4RD  H8   H   HCH2  0   0.227    0.2004   0.7327   1.2538
 4RD  H9   H   HCH1  0   0.261    2.4753   1.0130   1.4237
 4RD  H10  H   HCH2  0   0.247    2.8869   2.4420  -1.2359
 4RD  H11  H   HCH2  0   0.263    2.0263   3.0459   0.1775
 4RD  H12  H   HCH2  0   0.257    4.3170   3.9958   0.0879
 4RD  H13  H   HCH2  0   0.234    4.0916   2.9936   1.5239
 4RD  H14  H   HCR6  0   0.277    3.0033  -1.7014   0.1788
 4RD  H15  H   HCR6  0   0.298    7.2544  -1.7656  -0.4015
 4RD  H16  H   HNH1  0   0.345    1.6262   0.2910  -1.2566
 4RD  H18  H   HNH1  0   0.405   -2.9984  -1.4354  -0.8142
 4RD  H19  H   HNR5  0   0.431   -4.5113   1.5730   0.6702
 4RD  CL1  CL  CL    0  -0.131    5.0926  -3.6142  -0.1563

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
 4RD  C9   C10  single    1.510  0.020  1.510
 4RD  C9   C8   single    1.529  0.020  1.529
 4RD  CL   C12  single    1.727  0.020  1.727
 4RD  CL1  C14  single    1.734  0.020  1.734
 4RD  C13  C12  aromatic  1.382  0.020  1.382
 4RD  C13  C14  aromatic  1.385  0.020  1.385
 4RD  C12  C11  aromatic  1.397  0.020  1.397
 4RD  O    C11  single    1.339  0.020  1.339
 4RD  O    C10  single    1.427  0.020  1.427
 4RD  C14  C15  aromatic  1.382  0.020  1.382
 4RD  C11  C16  aromatic  1.398  0.020  1.398
 4RD  C15  C16  aromatic  1.390  0.020  1.390
 4RD  C16  C8   single    1.516  0.020  1.516
 4RD  C8   N2   single    1.447  0.020  1.447
 4RD  N2   C7   single    1.450  0.020  1.450
 4RD  C7   C6   single    1.520  0.020  1.520
 4RD  C6   C5   single    1.519  0.020  1.519
 4RD  C5   N1   single    1.448  0.020  1.448
 4RD  N1   C4   single    1.338  0.020  1.338
 4RD  C4   N3   aromatic  1.322  0.020  1.322
 4RD  C4   N    aromatic  1.361  0.020  1.361
 4RD  N3   C17  aromatic  1.358  0.020  1.358
 4RD  N    C3   aromatic  1.375  0.020  1.375
 4RD  C17  C3   aromatic  1.410  0.020  1.410
 4RD  C17  N4   aromatic  1.329  0.020  1.329
 4RD  C3   C2   aromatic  1.375  0.020  1.375
 4RD  N4   C    aromatic  1.306  0.020  1.306
 4RD  C2   C1   aromatic  1.395  0.020  1.395
 4RD  C    C1   aromatic  1.387  0.020  1.387
 4RD  C    F    single    1.343  0.020  1.343
 4RD  C1   H1   single    0.930  0.020  1.080
 4RD  C2   H2   single    0.930  0.020  1.080
 4RD  C5   H3   single    0.970  0.020  1.090
 4RD  C5   H4   single    0.970  0.020  1.090
 4RD  C6   H5   single    0.970  0.020  1.090
 4RD  C6   H6   single    0.970  0.020  1.090
 4RD  C7   H7   single    0.970  0.020  1.090
 4RD  C7   H8   single    0.970  0.020  1.090
 4RD  C8   H9   single    0.970  0.020  1.090
 4RD  C9   H10  single    0.970  0.020  1.090
 4RD  C9   H11  single    0.970  0.020  1.090
 4RD  C10  H12  single    0.970  0.020  1.090
 4RD  C10  H13  single    0.970  0.020  1.090
 4RD  C15  H14  single    0.930  0.020  1.080
 4RD  C13  H15  single    0.930  0.020  1.080
 4RD  N2   H16  single    0.890  0.020  1.040
 4RD  N1   H18  single    0.890  0.020  1.040
 4RD  N    H19  single    0.860  0.020  1.020

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
 4RD  H1   C1   C    120.85  3.000
 4RD  H1   C1   C2   121.27  3.000
 4RD  C    C1   C2   117.88  3.000
 4RD  H2   C2   C3   122.69  3.000
 4RD  H2   C2   C1   121.03  3.000
 4RD  C3   C2   C1   116.28  3.000
 4RD  C17  C3   N    104.45  3.000
 4RD  C17  C3   C2   120.64  3.000
 4RD  N    C3   C2   134.91  3.000
 4RD  N3   C4   N    113.16  3.000
 4RD  N    C4   N1   122.29  3.000
 4RD  N3   C4   N1   124.54  3.000
 4RD  H4   C5   H3   107.19  3.000
 4RD  H4   C5   N1   109.44  3.000
 4RD  H3   C5   N1   110.84  3.000
 4RD  H4   C5   C6   109.34  3.000
 4RD  H3   C5   C6   109.56  3.000
 4RD  N1   C5   C6   110.41  3.000
 4RD  H6   C6   H5   107.25  3.000
 4RD  H6   C6   C7   109.82  3.000
 4RD  H5   C6   C7   109.14  3.000
 4RD  H6   C6   C5   109.38  3.000
 4RD  H5   C6   C5   109.78  3.000
 4RD  C7   C6   C5   111.37  3.000
 4RD  H8   C7   H7   106.36  3.000
 4RD  H8   C7   N2   107.93  3.000
 4RD  H7   C7   N2   113.41  3.000
 4RD  H8   C7   C6   109.39  3.000
 4RD  H7   C7   C6   109.16  3.000
 4RD  N2   C7   C6   110.45  3.000
 4RD  H9   C8   N2   106.51  3.000
 4RD  H9   C8   C16  107.33  3.000
 4RD  N2   C8   C16  110.50  3.000
 4RD  H9   C8   C9   107.71  3.000
 4RD  N2   C8   C9   115.42  3.000
 4RD  C16  C8   C9   109.01  3.000
 4RD  H11  C9   H10  107.41  3.000
 4RD  H11  C9   C10  108.57  3.000
 4RD  H10  C9   C10  110.26  3.000
 4RD  H11  C9   C8   110.72  3.000
 4RD  H10  C9   C8   110.10  3.000
 4RD  C10  C9   C8   109.74  3.000
 4RD  H13  C10  H12  107.91  3.000
 4RD  H13  C10  O    108.95  3.000
 4RD  H12  C10  O    105.68  3.000
 4RD  H13  C10  C9   110.44  3.000
 4RD  H12  C10  C9   111.74  3.000
 4RD  O    C10  C9   111.92  3.000
 4RD  O    C11  C12  116.96  3.000
 4RD  O    C11  C16  124.04  3.000
 4RD  C12  C11  C16  119.00  3.000
 4RD  H14  C15  C14  120.71  3.000
 4RD  H14  C15  C16  118.79  3.000
 4RD  C14  C15  C16  120.50  3.000
 4RD  C15  C16  C11  119.28  3.000
 4RD  C15  C16  C8   120.60  3.000
 4RD  C11  C16  C8   120.12  3.000
 4RD  C13  C14  CL1  119.19  3.000
 4RD  C13  C14  C15  121.12  3.000
 4RD  CL1  C14  C15  119.69  3.000
 4RD  H15  C13  C12  120.35  3.000
 4RD  H15  C13  C14  121.34  3.000
 4RD  C12  C13  C14  118.31  3.000
 4RD  CL   C12  C13  119.46  3.000
 4RD  C13  C12  C11  121.79  3.000
 4RD  CL   C12  C11  118.75  3.000
 4RD  C11  O    C10  117.54  3.000
 4RD  H16  N2   C8   109.60  3.000
 4RD  H16  N2   C7   109.93  3.000
 4RD  C8   N2   C7   114.42  3.000
 4RD  H18  N1   C5   118.20  3.000
 4RD  H18  N1   C4   115.48  3.000
 4RD  C5   N1   C4   123.28  3.000
 4RD  H19  N    C4   126.98  3.000
 4RD  H19  N    C3   126.24  3.000
 4RD  C4   N    C3   106.77  3.000
 4RD  C17  N3   C4   104.65  3.000
 4RD  N4   C17  N3   126.17  3.000
 4RD  N4   C17  C3   122.86  3.000
 4RD  N3   C17  C3   110.97  3.000
 4RD  C    N4   C17  115.29  3.000
 4RD  F    C    N4   115.03  3.000
 4RD  F    C    C1   117.92  3.000
 4RD  N4   C    C1   127.05  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
 4RD  CONST_01  N    C3   C2   C1    180.00   0.0  0
 4RD  CONST_02  C17  C3   C2   C1      0.00   0.0  0
 4RD  CONST_03  C17  N4   C    C1      0.00   0.0  0
 4RD  CONST_04  C4   N    C3   C2    180.00   0.0  0
 4RD  CONST_05  N3   C17  C3   C2    180.00   0.0  0
 4RD  CONST_06  N4   C17  C3   C2      0.00   0.0  0
 4RD  CONST_07  N4   C    C1   C2      0.00   0.0  0
 4RD  CONST_08  N3   C4   N    C3      0.00   0.0  0
 4RD  CONST_09  C4   N3   C17  C3      0.00   0.0  0
 4RD  CONST_10  C    N4   C17  C3      0.00   0.0  0
 4RD  CONST_11  C    C1   C2   C3      0.00   0.0  0
 4RD  CONST_12  N4   C17  N3   C4    180.00   0.0  0
 4RD  CONST_13  C17  C3   N    C4      0.00   0.0  0
 4RD  CONST_14  C14  C13  C12  C11     0.00   0.0  0
 4RD  CONST_15  C14  C15  C16  C11     0.00   0.0  0
 4RD  CONST_16  C12  C13  C14  C15     0.00   0.0  0
 4RD  CONST_17  C12  C11  C16  C15     0.00   0.0  0
 4RD  CONST_18  C13  C12  C11  C16     0.00   0.0  0
 4RD  CONST_19  C13  C14  C15  C16     0.00   0.0  0
 4RD  CONST_20  C17  N3   C4   N       0.00   0.0  0
 4RD  CONST_21  N3   C17  C3   N       0.00   0.0  0
 4RD  CONST_22  N4   C17  C3   N     180.00   0.0  0
 4RD  CONST_23  C    N4   C17  N3    180.00   0.0  0
 4RD  CONST_24  F    C    C1   C2    180.00   0.0  0
 4RD  CONST_25  N1   C4   N    C3    180.00   0.0  0
 4RD  CONST_26  CL   C12  C11  C16   180.00   0.0  0
 4RD  CONST_27  CL1  C14  C15  C16   180.00   0.0  0
 4RD  CONST_28  C12  C13  C14  CL1   180.00   0.0  0
 4RD  CONST_29  CL   C12  C13  C14   180.00   0.0  0
 4RD  CONST_30  O    C11  C12  CL      0.00   0.0  0
 4RD  CONST_31  C17  N3   C4   N1    180.00   0.0  0
 4RD  CONST_32  F    C    N4   C17   180.00   0.0  0
 4RD  CONST_33  H19  N    C3   C2      0.00   0.0  0
 4RD  CONST_34  H1   C1   C2   C3    180.00   0.0  0
 4RD  CONST_35  H14  C15  C16  C8      0.00   0.0  0
 4RD  CONST_36  H15  C13  C12  C11   180.00   0.0  0
 4RD  CONST_37  H2   C2   C3   N       0.00   0.0  0
 4RD  CONST_38  N3   C4   N1   C5    180.00   0.0  0
 4RD  CONST_39  N    C4   N1   C5      0.00   0.0  0
 4RD  CONST_40  H18  N1   C4   N     180.00   0.0  0
 4RD  Var_01    O    C10  C9   C8     60.53  30.0  1
 4RD  Var_02    C12  C11  O    C10  -170.32  30.0  1
 4RD  Var_03    C6   C5   N1   C4   -179.35  30.0  1
 4RD  Var_04    C8   N2   C7   C6   -175.03  30.0  1
 4RD  Var_05    N2   C7   C6   C5    177.93  30.0  1
 4RD  Var_06    N1   C5   C6   C7   -179.90  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
 4RD  chir_01  C8  C9  C16  N2  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
 4RD  plan-1  C1   0.020
 4RD  plan-1  C2   0.020
 4RD  plan-1  C3   0.020
 4RD  plan-1  C4   0.020
 4RD  plan-1  N1   0.020
 4RD  plan-1  N    0.020
 4RD  plan-1  N3   0.020
 4RD  plan-1  C17  0.020
 4RD  plan-1  N4   0.020
 4RD  plan-1  C    0.020
 4RD  plan-1  F    0.020
 4RD  plan-1  H1   0.020
 4RD  plan-1  H2   0.020
 4RD  plan-1  H19  0.020
 4RD  plan-2  C8   0.020
 4RD  plan-2  C11  0.020
 4RD  plan-2  C15  0.020
 4RD  plan-2  C16  0.020
 4RD  plan-2  C14  0.020
 4RD  plan-2  C13  0.020
 4RD  plan-2  C12  0.020
 4RD  plan-2  CL   0.020
 4RD  plan-2  O    0.020
 4RD  plan-2  H14  0.020
 4RD  plan-2  H15  0.020
 4RD  plan-2  CL1  0.020
 4RD  plan-3  C4   0.020
 4RD  plan-3  C5   0.020
 4RD  plan-3  N1   0.020
 4RD  plan-3  H18  0.020

