# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 07:46:26 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 6-chloro-2-{[(1S)-1-furo[2,3-c]pyridin-5-ylethyl]sulfanyl}pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](Sc1nc(N)cc(Cl)n1)c2cc3ccoc3cn2
#
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
 PNU  PNU  6-chloro-2-{[(1S)-1-furo[2,3-c]pyridin-5-ylethyl]sulfanyl}pyrimidin-4-amine  ligand  31  20  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PNU
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
 PNU  C1    C   CR6   0   0.242   0.6704  -0.0731   2.1035
 PNU  N2    N   N     0  -0.473   1.7029  -0.3504   2.8781
 PNU  C3    C   CR6   0   0.521   1.4678  -0.4558   4.1905
 PNU  C4    C   CR16  0  -0.376   0.1659  -0.2680   4.7074
 PNU  C5    C   CR6   0   0.206  -0.7947   0.0151   3.7774
 PNU  N6    N   N     0  -0.424  -0.5841   0.1174   2.4751
 PNU  C7    C   CR56  0   0.267  -0.2283  -0.8639  -4.3486
 PNU  C8    C   CR16  0  -0.137  -0.9155  -1.5659  -3.3765
 PNU  N9    N   N     0  -0.417  -0.9696  -1.0919  -2.1436
 PNU  C10   C   CR6   0   0.260  -0.3665   0.0661  -1.8391
 PNU  C11   C   CR16  0  -0.398   0.3446   0.8216  -2.7588
 PNU  C12   C   CR56  0   0.156   0.4155   0.3382  -4.0630
 PNU  C13   C   CR15  0  -0.384   1.0059   0.7571  -5.3008
 PNU  O14   O   O     0  -0.422  -0.0682  -1.1879  -5.6481
 PNU  C15   C   CR15  0   0.039   0.6774  -0.1970  -6.1969
 PNU  C16   C   CH1   0  -0.459  -0.4896   0.5016  -0.3994
 PNU  S17   S   S2    0   0.067   1.0877   0.0171   0.4011
 PNU  N18   N   NH2   0  -0.822   2.4967  -0.7423   4.9867
 PNU  CL19  CL  CL    0  -0.096  -2.4247   0.2676   4.2971
 PNU  C21   C   CH3   0  -0.641  -0.7852   1.9799  -0.2134
 PNU  HC4   H   HCR6  0   0.300  -0.0455  -0.3419   5.7639
 PNU  H11C  H   HCR6  0   0.274   0.8226   1.7508  -2.4786
 PNU  H13C  H   HCR5  0   0.275   1.5885   1.6427  -5.4939
 PNU  H15C  H   HCR5  0   0.299   0.9002  -0.3019  -7.2468
 PNU  H16C  H   HCH1  0   0.308  -1.2710  -0.0996   0.0647
 PNU  H181  H   HNH2  0   0.406   3.4205  -0.8470   4.6033
 PNU  H182  H   HNH2  0   0.415   2.3857  -0.8103   5.9831
 PNU  H211  H   HCH3  0   0.234   0.0148   2.6106  -0.5992
 PNU  H212  H   HCH3  0   0.244  -1.7077   2.2426  -0.7339
 PNU  H213  H   HCH3  0   0.254  -0.9168   2.2094   0.8419
 PNU  HC8   H   HCR6  0   0.279  -1.4203  -2.5023  -3.5867

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
 PNU  C1   N2    aromatic  1.320  0.020  1.320
 PNU  C1   N6    aromatic  1.322  0.020  1.322
 PNU  C1   S17   single    1.755  0.020  1.755
 PNU  N2   C3    aromatic  1.337  0.020  1.337
 PNU  C3   C4    aromatic  1.413  0.020  1.413
 PNU  C3   N18   single    1.332  0.020  1.332
 PNU  C4   C5    aromatic  1.367  0.020  1.367
 PNU  C4   HC4   single    0.930  0.020  1.080
 PNU  C5   N6    aromatic  1.323  0.020  1.323
 PNU  C5   CL19  single    1.729  0.020  1.729
 PNU  C7   C8    aromatic  1.382  0.020  1.382
 PNU  C7   C12   aromatic  1.393  0.020  1.393
 PNU  C7   O14   aromatic  1.349  0.020  1.349
 PNU  C8   N9    aromatic  1.322  0.020  1.322
 PNU  C8   HC8   single    0.930  0.020  1.080
 PNU  N9   C10   aromatic  1.341  0.020  1.341
 PNU  C10  C11   aromatic  1.387  0.020  1.387
 PNU  C10  C16   single    1.509  0.020  1.509
 PNU  C11  C12   aromatic  1.393  0.020  1.393
 PNU  C11  H11C  single    0.930  0.020  1.080
 PNU  C12  C13   aromatic  1.434  0.020  1.434
 PNU  C13  C15   aromatic  1.349  0.020  1.349
 PNU  C13  H13C  single    0.930  0.020  1.080
 PNU  O14  C15   aromatic  1.356  0.020  1.356
 PNU  C15  H15C  single    0.930  0.020  1.080
 PNU  C16  S17   single    1.834  0.020  1.834
 PNU  C16  C21   single    1.519  0.020  1.519
 PNU  C16  H16C  single    0.970  0.020  1.090
 PNU  N18  H181  single    0.860  0.020  1.020
 PNU  N18  H182  single    0.860  0.020  1.020
 PNU  C21  H211  single    0.970  0.020  1.090
 PNU  C21  H212  single    0.970  0.020  1.090
 PNU  C21  H213  single    0.970  0.020  1.090

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
 PNU  S17   C1   N6    119.39  3.000
 PNU  S17   C1   N2    113.20  3.000
 PNU  N6    C1   N2    127.40  3.000
 PNU  C3    N2   C1    117.05  3.000
 PNU  N18   C3   C4    121.42  3.000
 PNU  N18   C3   N2    117.88  3.000
 PNU  C4    C3   N2    120.69  3.000
 PNU  HC4   C4   C5    122.84  3.000
 PNU  HC4   C4   C3    121.94  3.000
 PNU  C5    C4   C3    115.22  3.000
 PNU  CL19  C5   N6    115.76  3.000
 PNU  CL19  C5   C4    119.22  3.000
 PNU  N6    C5   C4    125.02  3.000
 PNU  C5    N6   C1    114.62  3.000
 PNU  O14   C7   C12   110.48  3.000
 PNU  O14   C7   C8    127.93  3.000
 PNU  C12   C7   C8    121.59  3.000
 PNU  HC8   C8   N9    118.12  3.000
 PNU  HC8   C8   C7    122.26  3.000
 PNU  N9    C8   C7    119.62  3.000
 PNU  C10   N9   C8    120.21  3.000
 PNU  C16   C10  C11   121.16  3.000
 PNU  C16   C10  N9    115.42  3.000
 PNU  C11   C10  N9    123.41  3.000
 PNU  H11C  C11  C12   121.21  3.000
 PNU  H11C  C11  C10   121.52  3.000
 PNU  C12   C11  C10   117.27  3.000
 PNU  C13   C12  C11   136.71  3.000
 PNU  C13   C12  C7    105.39  3.000
 PNU  C11   C12  C7    117.89  3.000
 PNU  H13C  C13  C15   126.42  3.000
 PNU  H13C  C13  C12   128.13  3.000
 PNU  C15   C13  C12   105.45  3.000
 PNU  C15   O14  C7    106.24  3.000
 PNU  H15C  C15  O14   115.88  3.000
 PNU  H15C  C15  C13   131.68  3.000
 PNU  O14   C15  C13   112.44  3.000
 PNU  H16C  C16  C21   110.20  3.000
 PNU  H16C  C16  S17   106.56  3.000
 PNU  C21   C16  S17   111.78  3.000
 PNU  H16C  C16  C10   107.79  3.000
 PNU  C21   C16  C10   114.43  3.000
 PNU  S17   C16  C10   105.66  3.000
 PNU  C16   S17  C1    103.44  3.000
 PNU  H182  N18  H181  118.19  3.000
 PNU  H182  N18  C3    121.46  3.000
 PNU  H181  N18  C3    120.26  3.000
 PNU  H213  C21  H212  108.03  3.000
 PNU  H213  C21  H211  108.07  3.000
 PNU  H212  C21  H211  108.21  3.000
 PNU  H213  C21  C16   110.34  3.000
 PNU  H212  C21  C16   109.90  3.000
 PNU  H211  C21  C16   112.16  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
 PNU  CONST_01  C4    C3   N2   C1     0.00  0.0  0
 PNU  CONST_02  C4    C5   N6   C1     0.00  0.0  0
 PNU  CONST_03  C5    N6   C1   N2     0.00  0.0  0
 PNU  CONST_04  C5    C4   C3   N2     0.00  0.0  0
 PNU  CONST_05  N6    C1   N2   C3     0.00  0.0  0
 PNU  CONST_06  N6    C5   C4   C3     0.00  0.0  0
 PNU  CONST_07  C10   N9   C8   C7     0.00  0.0  0
 PNU  CONST_08  C10   C11  C12  C7     0.00  0.0  0
 PNU  CONST_09  C15   C13  C12  C7     0.00  0.0  0
 PNU  CONST_10  C13   C15  O14  C7     0.00  0.0  0
 PNU  CONST_11  C11   C12  C7   C8     0.00  0.0  0
 PNU  CONST_12  C13   C12  C7   C8   180.00  0.0  0
 PNU  CONST_13  C15   O14  C7   C8   180.00  0.0  0
 PNU  CONST_14  C11   C10  N9   C8     0.00  0.0  0
 PNU  CONST_15  C12   C7   C8   N9     0.00  0.0  0
 PNU  CONST_16  O14   C7   C8   N9   180.00  0.0  0
 PNU  CONST_17  C12   C11  C10  N9     0.00  0.0  0
 PNU  CONST_18  C13   C12  C11  C10  180.00  0.0  0
 PNU  CONST_19  O14   C7   C12  C11  180.00  0.0  0
 PNU  CONST_20  C15   C13  C12  C11  180.00  0.0  0
 PNU  CONST_21  C15   O14  C7   C12    0.00  0.0  0
 PNU  CONST_22  O14   C15  C13  C12    0.00  0.0  0
 PNU  CONST_23  O14   C7   C12  C13    0.00  0.0  0
 PNU  CONST_24  N18   C3   N2   C1   180.00  0.0  0
 PNU  CONST_25  CL19  C5   N6   C1   180.00  0.0  0
 PNU  CONST_26  S17   C1   N2   C3   180.00  0.0  0
 PNU  CONST_27  CL19  C5   C4   C3   180.00  0.0  0
 PNU  CONST_28  N18   C3   C4   C5   180.00  0.0  0
 PNU  CONST_29  S17   C1   N6   C5   180.00  0.0  0
 PNU  CONST_30  C16   C10  N9   C8   180.00  0.0  0
 PNU  CONST_31  C16   C10  C11  C12  180.00  0.0  0
 PNU  CONST_32  HC4   C4   C3   N2   180.00  0.0  0
 PNU  CONST_33  H11C  C11  C12  C7   180.00  0.0  0
 PNU  CONST_34  H13C  C13  C12  C7   180.00  0.0  0
 PNU  CONST_35  H15C  C15  O14  C7   180.00  0.0  0
 PNU  CONST_36  HC8   C8   N9   C10  180.00  0.0  0
 PNU  CONST_37  H181  N18  C3   N2     0.00  0.0  0
 PNU  CONST_38  H182  N18  C3   N2   180.00  0.0  0

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
 PNU  chir_01  C16  C10  S17  C21  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
 PNU  plan-1  C1    0.020
 PNU  plan-1  N2    0.020
 PNU  plan-1  C3    0.020
 PNU  plan-1  C4    0.020
 PNU  plan-1  C5    0.020
 PNU  plan-1  N6    0.020
 PNU  plan-1  S17   0.020
 PNU  plan-1  N18   0.020
 PNU  plan-1  CL19  0.020
 PNU  plan-1  HC4   0.020
 PNU  plan-2  C7    0.020
 PNU  plan-2  C8    0.020
 PNU  plan-2  N9    0.020
 PNU  plan-2  C10   0.020
 PNU  plan-2  C11   0.020
 PNU  plan-2  C12   0.020
 PNU  plan-2  C13   0.020
 PNU  plan-2  O14   0.020
 PNU  plan-2  C15   0.020
 PNU  plan-2  C16   0.020
 PNU  plan-2  H11C  0.020
 PNU  plan-2  H13C  0.020
 PNU  plan-2  H15C  0.020
 PNU  plan-2  HC8   0.020
 PNU  plan-3  C3    0.020
 PNU  plan-3  N18   0.020
 PNU  plan-3  H181  0.020
 PNU  plan-3  H182  0.020

