# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 16:48:26 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 5-[3-(3-fluorophenoxy)propoxy]quinazoline-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(N)c2c(OCCCOc3cccc(F)c3)cccc2n1
#
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
 2CY  2CY  5-[3-(3-fluorophenoxy)propoxy]quinazoline-2,4-diamine  ligand  41  24  .  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_2CY
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
 2CY  N1    N  N     0  -0.535   6.0447  -0.1727  -0.0165
 2CY  C2    C  CR6   0   0.516   5.9983   1.1431  -0.0342
 2CY  N3    N  N     0  -0.513   4.8936   1.9062  -0.0302
 2CY  C4    C  CR6   0   0.500   3.7169   1.3075  -0.0149
 2CY  C5    C  CR66  0  -0.187   3.6160  -0.1339  -0.0085
 2CY  C6    C  CR66  0   0.267   4.8581  -0.8169  -0.0062
 2CY  C7    C  CR6   0   0.420   2.4115  -0.8871  -0.0007
 2CY  C8    C  CR16  0  -0.425   2.4500  -2.2666   0.0094
 2CY  C9    C  CR16  0  -0.230   3.6889  -2.9216   0.0138
 2CY  C10   C  CR16  0  -0.354   4.8685  -2.2284   0.0066
 2CY  N11   N  NH2   0  -0.824   7.1706   1.8147  -0.0952
 2CY  N12   N  NH2   0  -0.827   2.6509   2.1100  -0.0033
 2CY  O13   O  O2    0  -0.499   1.2609  -0.1904  -0.0056
 2CY  C14   C  CH2   0  -0.175   0.0213  -0.8822  -0.0020
 2CY  C15   C  CH2   0  -0.503  -1.0842   0.1538  -0.0066
 2CY  C16   C  CH2   0  -0.176  -2.4364  -0.5317  -0.0027
 2CY  O17   O  O2    0  -0.473  -3.4306   0.4786  -0.0069
 2CY  C18   C  CR6   0   0.404  -4.7255   0.1172  -0.0052
 2CY  C19   C  CR16  0  -0.391  -5.1760  -1.2017  -0.0008
 2CY  C20   C  CR16  0  -0.225  -6.5427  -1.4553   0.0007
 2CY  C21   C  CR16  0  -0.431  -7.4738  -0.4297  -0.0017
 2CY  C22   C  CR6   0   0.534  -6.9909   0.8672  -0.0064
 2CY  C23   C  CR16  0  -0.502  -5.6470   1.1671  -0.0083
 2CY  F24   F  F     0  -0.316  -7.8688   1.8834  -0.0091
 2CY  H8    H  HCR6  0   0.284   1.5467  -2.8589   0.0146
 2CY  H9    H  HCR6  0   0.262   3.7015  -4.0039   0.0220
 2CY  H10   H  HCR6  0   0.247   5.8215  -2.7404   0.0087
 2CY  HN11  H  HNH2  0   0.388   8.0167   1.3130   0.1118
 2CY  HN1A  H  HNH2  0   0.389   7.1680   2.7983   0.1111
 2CY  HN12  H  HNH2  0   0.396   2.7998   3.1045  -0.0102
 2CY  HN1B  H  HNH2  0   0.420   1.7127   1.7564   0.0045
 2CY  H14   H  HCH2  0   0.236  -0.0509  -1.5272  -0.8836
 2CY  H14A  H  HCH2  0   0.236  -0.0509  -1.5188   0.8857
 2CY  H15   H  HCH2  0   0.254  -0.9932   0.7942   0.8743
 2CY  H15A  H  HCH2  0   0.254  -0.9941   0.7857  -0.8937
 2CY  H16   H  HCH2  0   0.232  -2.5403  -1.1753  -0.8837
 2CY  H16A  H  HCH2  0   0.232  -2.5391  -1.1669   0.8844
 2CY  H19   H  HCR6  0   0.285  -4.4900  -2.0363   0.0015
 2CY  H20   H  HCR6  0   0.271  -6.8844  -2.4820   0.0048
 2CY  H21   H  HCR6  0   0.277  -8.5368  -0.6273   0.0003
 2CY  H23   H  HCR6  0   0.284  -5.3086   2.1958  -0.0124

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
 2CY  C2   N1    aromatic  1.317  0.020  1.317
 2CY  N1   C6    aromatic  1.350  0.020  1.350
 2CY  N11  C2    single    1.352  0.020  1.352
 2CY  C2   N3    aromatic  1.343  0.020  1.343
 2CY  N3   C4    aromatic  1.320  0.020  1.320
 2CY  C4   C5    aromatic  1.445  0.020  1.445
 2CY  C4   N12   single    1.334  0.020  1.334
 2CY  C6   C5    aromatic  1.418  0.020  1.418
 2CY  C5   C7    aromatic  1.421  0.020  1.421
 2CY  C6   C10   aromatic  1.412  0.020  1.412
 2CY  C7   C8    aromatic  1.380  0.020  1.380
 2CY  C7   O13   single    1.345  0.020  1.345
 2CY  C9   C8    aromatic  1.401  0.020  1.401
 2CY  C8   H8    single    0.930  0.020  1.080
 2CY  C10  C9    aromatic  1.368  0.020  1.368
 2CY  C9   H9    single    0.930  0.020  1.080
 2CY  C10  H10   single    0.930  0.020  1.080
 2CY  N11  HN11  single    0.890  0.020  1.040
 2CY  N11  HN1A  single    0.890  0.020  1.040
 2CY  N12  HN12  single    0.860  0.020  1.020
 2CY  N12  HN1B  single    0.860  0.020  1.020
 2CY  O13  C14   single    1.420  0.020  1.420
 2CY  C14  C15   single    1.515  0.020  1.515
 2CY  C14  H14   single    0.970  0.020  1.090
 2CY  C14  H14A  single    0.970  0.020  1.090
 2CY  C15  C16   single    1.516  0.020  1.516
 2CY  C15  H15   single    0.970  0.020  1.090
 2CY  C15  H15A  single    0.970  0.020  1.090
 2CY  O17  C16   single    1.417  0.020  1.417
 2CY  C16  H16   single    0.970  0.020  1.090
 2CY  C16  H16A  single    0.970  0.020  1.090
 2CY  O17  C18   single    1.344  0.020  1.344
 2CY  C19  C18   aromatic  1.394  0.020  1.394
 2CY  C18  C23   aromatic  1.397  0.020  1.397
 2CY  C20  C19   aromatic  1.390  0.020  1.390
 2CY  C19  H19   single    0.930  0.020  1.080
 2CY  C20  C21   aromatic  1.385  0.020  1.385
 2CY  C20  H20   single    0.930  0.020  1.080
 2CY  C21  C22   aromatic  1.384  0.020  1.384
 2CY  C21  H21   single    0.930  0.020  1.080
 2CY  C22  C23   aromatic  1.377  0.020  1.377
 2CY  C22  F24   single    1.343  0.020  1.343
 2CY  C23  H23   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
 2CY  C6    N1   C2    116.48  3.000
 2CY  N11   C2   N3    115.54  3.000
 2CY  N3    C2   N1    126.65  3.000
 2CY  N11   C2   N1    117.80  3.000
 2CY  C4    N3   C2    118.40  3.000
 2CY  N12   C4   C5    122.97  3.000
 2CY  N12   C4   N3    116.06  3.000
 2CY  C5    C4   N3    120.97  3.000
 2CY  C7    C5   C6    119.17  3.000
 2CY  C7    C5   C4    126.02  3.000
 2CY  C6    C5   C4    114.80  3.000
 2CY  C10   C6   C5    119.23  3.000
 2CY  C10   C6   N1    118.08  3.000
 2CY  C5    C6   N1    122.69  3.000
 2CY  O13   C7   C8    122.80  3.000
 2CY  O13   C7   C5    116.78  3.000
 2CY  C8    C7   C5    120.42  3.000
 2CY  H8    C8   C9    118.88  3.000
 2CY  H8    C8   C7    121.66  3.000
 2CY  C9    C8   C7    119.46  3.000
 2CY  H9    C9   C10   119.77  3.000
 2CY  H9    C9   C8    118.53  3.000
 2CY  C10   C9   C8    121.69  3.000
 2CY  H10   C10  C9    121.31  3.000
 2CY  H10   C10  C6    118.67  3.000
 2CY  C9    C10  C6    120.02  3.000
 2CY  HN1A  N11  HN11  116.65  3.000
 2CY  HN1A  N11  C2    118.33  3.000
 2CY  HN11  N11  C2    118.19  3.000
 2CY  HN1B  N12  HN12  119.17  3.000
 2CY  HN1B  N12  C4    122.37  3.000
 2CY  HN12  N12  C4    118.45  3.000
 2CY  C14   O13  C7    119.64  3.000
 2CY  H14A  C14  H14   107.82  3.000
 2CY  H14A  C14  C15   110.60  3.000
 2CY  H14   C14  C15   110.63  3.000
 2CY  H14A  C14  O13   110.06  3.000
 2CY  H14   C14  O13   110.04  3.000
 2CY  C15   C14  O13   107.69  3.000
 2CY  H15A  C15  H15   107.98  3.000
 2CY  H15A  C15  C16   109.70  3.000
 2CY  H15   C15  C16   109.70  3.000
 2CY  H15A  C15  C14   109.73  3.000
 2CY  H15   C15  C14   109.72  3.000
 2CY  C16   C15  C14   109.98  3.000
 2CY  H16A  C16  H16   107.54  3.000
 2CY  H16A  C16  O17   110.47  3.000
 2CY  H16   C16  O17   110.47  3.000
 2CY  H16A  C16  C15   110.35  3.000
 2CY  H16   C16  C15   110.37  3.000
 2CY  O17   C16  C15   107.66  3.000
 2CY  C18   O17  C16   118.95  3.000
 2CY  C23   C18  C19   119.86  3.000
 2CY  C23   C18  O17   115.68  3.000
 2CY  C19   C18  O17   124.45  3.000
 2CY  H19   C19  C20   118.90  3.000
 2CY  H19   C19  C18   121.72  3.000
 2CY  C20   C19  C18   119.38  3.000
 2CY  H20   C20  C21   119.36  3.000
 2CY  H20   C20  C19   118.92  3.000
 2CY  C21   C20  C19   121.72  3.000
 2CY  H21   C21  C22   120.96  3.000
 2CY  H21   C21  C20   121.70  3.000
 2CY  C22   C21  C20   117.35  3.000
 2CY  F24   C22  C23   118.24  3.000
 2CY  F24   C22  C21   118.76  3.000
 2CY  C23   C22  C21   123.00  3.000
 2CY  H23   C23  C22   120.79  3.000
 2CY  H23   C23  C18   120.51  3.000
 2CY  C22   C23  C18   118.70  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
 2CY  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 2CY  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 2CY  CONST_03  C7    C5   C6   N1    180.00   0.0  0
 2CY  CONST_04  C9    C10  C6   N1    180.00   0.0  0
 2CY  CONST_05  C5    C6   N1   C2      0.00   0.0  0
 2CY  CONST_06  C10   C6   N1   C2    180.00   0.0  0
 2CY  CONST_07  C5    C4   N3   C2      0.00   0.0  0
 2CY  CONST_08  C6    N1   C2   N3      0.00   0.0  0
 2CY  CONST_09  C6    C5   C4   N3      0.00   0.0  0
 2CY  CONST_10  C7    C5   C4   N3    180.00   0.0  0
 2CY  CONST_11  C10   C6   C5   C4    180.00   0.0  0
 2CY  CONST_12  C8    C7   C5   C4    180.00   0.0  0
 2CY  CONST_13  C9    C10  C6   C5      0.00   0.0  0
 2CY  CONST_14  C9    C8   C7   C5      0.00   0.0  0
 2CY  CONST_15  C8    C7   C5   C6      0.00   0.0  0
 2CY  CONST_16  C8    C9   C10  C6      0.00   0.0  0
 2CY  CONST_17  C10   C6   C5   C7      0.00   0.0  0
 2CY  CONST_18  C10   C9   C8   C7      0.00   0.0  0
 2CY  CONST_19  C21   C20  C19  C18     0.00   0.0  0
 2CY  CONST_20  C21   C22  C23  C18     0.00   0.0  0
 2CY  CONST_21  C22   C23  C18  C19     0.00   0.0  0
 2CY  CONST_22  C22   C21  C20  C19     0.00   0.0  0
 2CY  CONST_23  C23   C18  C19  C20     0.00   0.0  0
 2CY  CONST_24  C23   C22  C21  C20     0.00   0.0  0
 2CY  CONST_25  N12   C4   N3   C2    180.00   0.0  0
 2CY  CONST_26  N11   C2   N3   C4    180.00   0.0  0
 2CY  CONST_27  O13   C7   C5   C4      0.00   0.0  0
 2CY  CONST_28  N11   C2   N1   C6    180.00   0.0  0
 2CY  CONST_29  N12   C4   C5   C6    180.00   0.0  0
 2CY  CONST_30  O13   C7   C5   C6    180.00   0.0  0
 2CY  CONST_31  N12   C4   C5   C7      0.00   0.0  0
 2CY  CONST_32  O13   C7   C8   C9    180.00   0.0  0
 2CY  CONST_33  C20   C19  C18  O17   180.00   0.0  0
 2CY  CONST_34  C22   C23  C18  O17   180.00   0.0  0
 2CY  CONST_35  F24   C22  C23  C18   180.00   0.0  0
 2CY  CONST_36  F24   C22  C21  C20   180.00   0.0  0
 2CY  CONST_37  H10   C10  C6   N1      0.00   0.0  0
 2CY  CONST_38  H8    C8   C7   C5    180.00   0.0  0
 2CY  CONST_39  H9    C9   C10  C6    180.00   0.0  0
 2CY  CONST_40  H20   C20  C19  C18   180.00   0.0  0
 2CY  CONST_41  H23   C23  C18  C19   180.00   0.0  0
 2CY  CONST_42  H21   C21  C20  C19   180.00   0.0  0
 2CY  CONST_43  H19   C19  C20  C21   180.00   0.0  0
 2CY  CONST_45  HN1A  N11  C2   N1    180.00   0.0  0
 2CY  CONST_46  HN12  N12  C4   N3      0.00   0.0  0
 2CY  CONST_47  HN1B  N12  C4   N3    180.00   0.0  0
 2CY  Var_01    C19   C18  O17  C16    -0.06  30.0  2
 2CY  Var_02    C15   C14  O13  C7    179.91  30.0  3
 2CY  Var_03    H16   C16  O17  C18    59.39  30.0  3
 2CY  Var_04    C16   C15  C14  O13  -179.99  30.0  3
 2CY  Var_05    O17   C16  C15  C14   179.98  30.0  3

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
 2CY  plan-1  O17   0.020
 2CY  plan-1  C18   0.020
 2CY  plan-1  C19   0.020
 2CY  plan-1  C20   0.020
 2CY  plan-1  C21   0.020
 2CY  plan-1  C22   0.020
 2CY  plan-1  C23   0.020
 2CY  plan-1  F24   0.020
 2CY  plan-1  H19   0.020
 2CY  plan-1  H20   0.020
 2CY  plan-1  H21   0.020
 2CY  plan-1  H23   0.020
 2CY  plan-2  N1    0.020
 2CY  plan-2  C2    0.020
 2CY  plan-2  N3    0.020
 2CY  plan-2  C4    0.020
 2CY  plan-2  C5    0.020
 2CY  plan-2  C6    0.020
 2CY  plan-2  C7    0.020
 2CY  plan-2  C8    0.020
 2CY  plan-2  C9    0.020
 2CY  plan-2  C10   0.020
 2CY  plan-2  N11   0.020
 2CY  plan-2  N12   0.020
 2CY  plan-2  O13   0.020
 2CY  plan-2  H8    0.020
 2CY  plan-2  H9    0.020
 2CY  plan-2  H10   0.020
 2CY  plan-3  C2    0.020
 2CY  plan-3  N11   0.020
 2CY  plan-3  HN11  0.020
 2CY  plan-3  HN1A  0.020
 2CY  plan-4  C4    0.020
 2CY  plan-4  N12   0.020
 2CY  plan-4  HN12  0.020
 2CY  plan-4  HN1B  0.020

