# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 14:41:58 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: (5~{S})-7-azanyl-5-(4-chlorophenyl)-2,4-bis(oxidanylidene)-1,5-dihydropyrano[2,3-d]pyrimidine-6-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=C(C#N)[C@H](c2ccc(Cl)cc2)C3=C(NC(=O)NC3=O)O1
#
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
 F2K  F2K  (5~{S})-7-azanyl-5-(4-chlorophenyl)-2,4-bis(oxidanylidene)-1,5-dihydropyrano[2,3-d]pyrimidine-6-carbonitrile  ligand  31  22  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_F2K
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
 F2K  C1   C   CR6   0   0.216  -1.0510   0.1920  -0.4896
 F2K  C    C   CR16  0  -0.328  -2.0268  -0.0375  -1.4493
 F2K  O    O   O     0  -0.441   0.8003  -1.9344  -1.9424
 F2K  N    N   NR16  0  -0.734   3.3124  -0.6753   0.8817
 F2K  C10  C   CR6   0   0.584   1.5343  -1.5099  -1.0712
 F2K  C11  C   CR6   0   0.610   1.5012   2.3067   0.6799
 F2K  C12  C   CR6   0  -0.168   0.5736   2.0818  -0.2902
 F2K  C13  C   CSP   0   0.036  -0.2301   3.1556  -0.7106
 F2K  C2   C   CR16  0  -0.298  -1.3549  -0.0492   0.8464
 F2K  C3   C   CR16  0  -0.196  -2.6055  -0.5119   1.2212
 F2K  C4   C   CR6   0  -0.057  -3.5641  -0.7316   0.2422
 F2K  C5   C   CR16  0  -0.198  -3.2880  -0.4969  -1.0941
 F2K  C6   C   CR16  0  -0.376   0.3133   0.7193  -0.8907
 F2K  C7   C   CR66  0  -0.244   1.4148  -0.2031  -0.4708
 F2K  C8   C   CR66  0   0.670   2.3162   0.1445   0.4640
 F2K  C9   C   CR6   0   0.684   3.4877  -1.9420   0.3783
 F2K  N1   N   NR16  0  -0.728   2.5748  -2.2861  -0.5815
 F2K  N2   N   NS    0  -0.274  -0.8952   4.0324  -1.0678
 F2K  O1   O   O     0  -0.462   4.3734  -2.6762   0.7548
 F2K  O2   O   O     0  -0.448   2.3423   1.3271   1.0922
 F2K  CL   CL  CL    0  -0.131  -5.1338  -1.3071   0.7033
 F2K  H2   H   HCR6  0   0.263  -1.8062   0.1430  -2.4942
 F2K  H7   H   HNR6  0   0.446   3.9661  -0.3563   1.5855
 F2K  H3   H   HCR6  0   0.257  -0.6124   0.1230   1.6171
 F2K  H4   H   HCR6  0   0.280  -2.8310  -0.6957   2.2628
 F2K  H5   H   HCR6  0   0.280  -4.0401  -0.6705  -1.8517
 F2K  H6   H   HCR6  0   0.301   0.3293   0.8070  -1.9816
 F2K  H8   H   HNR6  0   0.433   2.6792  -3.2119  -0.9776
 F2K  H1   H   HNH2  0   0.427   1.2003   4.2659   1.1182
 F2K  H    H   HNH2  0   0.424   2.5825   3.5733   1.8434
 F2K  N3   N   NH2   0  -0.829   1.7057   3.4316   1.3675

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
 F2K  O    C10  double    1.216  0.020  1.216
 F2K  N1   C10  single    1.387  0.020  1.387
 F2K  N1   C9   single    1.369  0.020  1.369
 F2K  C10  C7   single    1.443  0.020  1.443
 F2K  O1   C9   double    1.210  0.020  1.210
 F2K  C9   N    single    1.374  0.020  1.374
 F2K  C7   C6   single    1.497  0.020  1.497
 F2K  C7   C8   double    1.344  0.020  1.344
 F2K  C2   C3   aromatic  1.385  0.020  1.385
 F2K  C2   C1   aromatic  1.391  0.020  1.391
 F2K  C3   C4   aromatic  1.388  0.020  1.388
 F2K  C6   C1   single    1.517  0.020  1.517
 F2K  C6   C12  single    1.512  0.020  1.512
 F2K  C1   C    aromatic  1.388  0.020  1.388
 F2K  N    C8   single    1.356  0.020  1.356
 F2K  C4   C5   aromatic  1.385  0.020  1.385
 F2K  C4   CL   single    1.734  0.020  1.734
 F2K  C    C5   aromatic  1.388  0.020  1.388
 F2K  C8   O2   single    1.339  0.020  1.339
 F2K  C12  C13  single    1.406  0.020  1.406
 F2K  C12  C11  double    1.361  0.020  1.361
 F2K  O2   C11  single    1.355  0.020  1.355
 F2K  C13  N2   triple    1.157  0.020  1.157
 F2K  C11  N3   single    1.334  0.020  1.334
 F2K  C    H2   single    0.930  0.020  1.080
 F2K  N    H7   single    0.860  0.020  1.020
 F2K  C2   H3   single    0.930  0.020  1.080
 F2K  C3   H4   single    0.930  0.020  1.080
 F2K  C5   H5   single    0.930  0.020  1.080
 F2K  C6   H6   single    0.970  0.020  1.090
 F2K  N1   H8   single    0.860  0.020  1.020
 F2K  N3   H1   single    0.890  0.020  1.040
 F2K  N3   H    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
 F2K  C6   C1   C2   120.71  3.000
 F2K  C6   C1   C    120.47  3.000
 F2K  C2   C1   C    118.81  3.000
 F2K  H2   C    C5   119.14  3.000
 F2K  H2   C    C1   119.76  3.000
 F2K  C5   C    C1   121.10  3.000
 F2K  H7   N    C9   117.57  3.000
 F2K  H7   N    C8   119.88  3.000
 F2K  C9   N    C8   122.55  3.000
 F2K  N1   C10  C7   114.95  3.000
 F2K  C7   C10  O    124.36  3.000
 F2K  N1   C10  O    120.69  3.000
 F2K  O2   C11  N3   110.94  3.000
 F2K  N3   C11  C12  127.67  3.000
 F2K  O2   C11  C12  121.36  3.000
 F2K  C6   C12  C13  118.12  3.000
 F2K  C13  C12  C11  118.47  3.000
 F2K  C6   C12  C11  123.33  3.000
 F2K  N2   C13  C12  180.00  3.000
 F2K  H3   C2   C3   118.63  3.000
 F2K  H3   C2   C1   120.38  3.000
 F2K  C3   C2   C1   121.00  3.000
 F2K  H4   C3   C4   120.57  3.000
 F2K  H4   C3   C2   120.37  3.000
 F2K  C4   C3   C2   119.06  3.000
 F2K  CL   C4   C5   119.56  3.000
 F2K  CL   C4   C3   119.35  3.000
 F2K  C5   C4   C3   121.09  3.000
 F2K  H5   C5   C4   120.68  3.000
 F2K  H5   C5   C    120.37  3.000
 F2K  C4   C5   C    118.96  3.000
 F2K  H6   C6   C7   108.56  3.000
 F2K  H6   C6   C12  108.74  3.000
 F2K  C7   C6   C12  108.50  3.000
 F2K  H6   C6   C1   107.73  3.000
 F2K  C12  C6   C1   111.30  3.000
 F2K  C7   C6   C1   111.93  3.000
 F2K  C8   C7   C6   121.95  3.000
 F2K  C8   C7   C10  117.90  3.000
 F2K  C6   C7   C10  120.15  3.000
 F2K  O2   C8   C7   124.58  3.000
 F2K  O2   C8   N    112.02  3.000
 F2K  C7   C8   N    123.40  3.000
 F2K  O1   C9   N1   123.62  3.000
 F2K  O1   C9   N    122.58  3.000
 F2K  N1   C9   N    113.80  3.000
 F2K  H8   N1   C9   115.82  3.000
 F2K  H8   N1   C10  116.80  3.000
 F2K  C9   N1   C10  127.38  3.000
 F2K  C8   O2   C11  118.90  3.000
 F2K  H    N3   H1   115.92  3.000
 F2K  H    N3   C11  119.69  3.000
 F2K  H1   N3   C11  119.61  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
 F2K  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 F2K  CONST_02  C4   C5   C    C1     0.00   0.0  0
 F2K  CONST_03  C3   C2   C1   C      0.00   0.0  0
 F2K  CONST_04  C3   C4   C5   C      0.00   0.0  0
 F2K  CONST_05  C5   C4   C3   C2     0.00   0.0  0
 F2K  CONST_06  C5   C    C1   C2     0.00   0.0  0
 F2K  CONST_07  C6   C1   C2   C3   180.00   0.0  0
 F2K  CONST_08  C6   C1   C    C5   180.00   0.0  0
 F2K  CONST_09  C10  N1   C9   N      0.00   0.0  0
 F2K  CONST_10  C9   N1   C10  C7     0.00   0.0  0
 F2K  CONST_11  N1   C9   N    C8     0.00   0.0  0
 F2K  CONST_12  CL   C4   C5   C    180.00   0.0  0
 F2K  CONST_13  CL   C4   C3   C2   180.00   0.0  0
 F2K  CONST_14  C9   N1   C10  O    180.00   0.0  0
 F2K  CONST_15  O1   C9   N1   C10  180.00   0.0  0
 F2K  CONST_16  O1   C9   N    C8   180.00   0.0  0
 F2K  CONST_17  H4   C3   C2   C1   180.00   0.0  0
 F2K  CONST_18  H5   C5   C    C1   180.00   0.0  0
 F2K  CONST_19  H3   C2   C1   C    180.00   0.0  0
 F2K  CONST_20  H2   C    C1   C2   180.00   0.0  0
 F2K  CONST_21  H8   N1   C9   N    180.00   0.0  0
 F2K  CONST_22  H7   N    C9   N1   180.00   0.0  0
 F2K  Var_01    C7   C8   O2   C11   -7.20  30.0  1
 F2K  Var_02    O2   C11  C12  C6     5.85  30.0  1
 F2K  Var_03    H1   N3   C11  C12   -6.48  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
 F2K  chir_01  C6  C7  C1  C12  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
 F2K  plan-1  C1   0.020
 F2K  plan-1  C    0.020
 F2K  plan-1  C2   0.020
 F2K  plan-1  C3   0.020
 F2K  plan-1  C4   0.020
 F2K  plan-1  C5   0.020
 F2K  plan-1  C6   0.020
 F2K  plan-1  CL   0.020
 F2K  plan-1  H2   0.020
 F2K  plan-1  H3   0.020
 F2K  plan-1  H4   0.020
 F2K  plan-1  H5   0.020
 F2K  plan-2  O    0.020
 F2K  plan-2  N    0.020
 F2K  plan-2  C10  0.020
 F2K  plan-2  C6   0.020
 F2K  plan-2  C7   0.020
 F2K  plan-2  C8   0.020
 F2K  plan-2  C9   0.020
 F2K  plan-2  N1   0.020
 F2K  plan-2  O1   0.020
 F2K  plan-2  O2   0.020
 F2K  plan-2  H7   0.020
 F2K  plan-2  H8   0.020

