# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 09:39:18 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 2-[1,1-bis(fluoranyl)ethyl]-~{N}-[(2~{S})-7-bromanyl-1,2,3,4-tetrahydronaphthalen-2-yl]-5-methyl-[1,2,4]triazolo[1,5-a]pyrimidin-7-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N[C@H]2CCc3ccc(Br)cc3C2)n4nc(nc4n1)C(C)(F)F
#
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
 5Y5  5Y5  2-[1,1-bis(fluoranyl)ethyl]-~{N}-[(2~{S})-7-bromanyl-1,2,3,4-tetrahydronaphthalen-2-yl]-5-methyl-[1,2,4]triazolo[1,5-a]pyrimidin-7-amine  ligand  44  26  .  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_5Y5
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
 5Y5  C2    C   CH1   0  -0.083   0.2465  -0.9005   1.0489
 5Y5  C3    C   CH2   0  -0.497   1.1645  -0.4110  -0.0684
 5Y5  C4    C   CR6   0   0.081   2.6102  -0.7516   0.1838
 5Y5  C5    C   CR6   0   0.078   2.9766  -1.7691   1.0652
 5Y5  C6    C   CH2   0  -0.508   1.9499  -2.5265   1.8661
 5Y5  C7    C   CR6   0   0.734  -1.8080   0.4184   0.8113
 5Y5  C8    C   CR16  0  -0.479  -1.3524   1.6141   1.3514
 5Y5  C17   C   CR6   0  -0.114   4.9305  -0.3606  -0.3229
 5Y5  C16   C   CR16  0  -0.234   5.3149  -1.3737   0.5445
 5Y5  C15   C   CR16  0  -0.290   4.3293  -2.0634   1.2288
 5Y5  C14   C   CH3   0  -0.761  -7.3496  -0.0601  -1.1869
 5Y5  C12   C   CR5   0   0.258  -4.9375  -0.0018  -0.4182
 5Y5  C11   C   CR56  0   0.587  -3.8809   1.5793   0.4495
 5Y5  C1    C   CH2   0  -0.463   0.5301  -2.3648   1.3437
 5Y5  BR1   BR  BR    0  -0.055   6.2510   0.6071  -1.2693
 5Y5  C18   C   CR16  0  -0.272   3.5965  -0.0463  -0.5051
 5Y5  N1    N   NH1   0  -0.679  -1.1501  -0.7296   0.6978
 5Y5  C9    C   CR6   0   0.255  -2.2015   2.7264   1.4026
 5Y5  N2    N   N     0  -0.438  -3.0954   0.4578   0.3704
 5Y5  N5    N   N     0  -0.492  -3.4526   2.7235   0.9626
 5Y5  N3    N   N     0  -0.311  -3.7697  -0.5586  -0.1845
 5Y5  N4    N   N     0  -0.515  -5.0693   1.2803  -0.0601
 5Y5  F1    F   F     0  -0.349  -6.2112  -1.9428  -0.3501
 5Y5  F2    F   F     0  -0.350  -5.6086  -1.1902  -2.2970
 5Y5  H2    H   HCH1  0   0.267   0.4375  -0.3229   1.9585
 5Y5  H32   H   HCH2  0   0.263   0.8438  -0.8765  -1.0064
 5Y5  H31   H   HCH2  0   0.266   1.0587   0.6674  -0.2090
 5Y5  H61   H   HCH2  0   0.263   2.2117  -3.5860   1.8925
 5Y5  H62   H   HCH2  0   0.258   1.9949  -2.1825   2.9043
 5Y5  H8    H   HCR6  0   0.293  -0.3437   1.6908   1.7269
 5Y5  H103  H   HCH3  0   0.266  -1.2741   4.6247   1.1385
 5Y5  H101  H   HCH3  0   0.257  -2.4775   4.5873   2.4219
 5Y5  H102  H   HCH3  0   0.253  -0.8811   3.8559   2.6707
 5Y5  H16   H   HCR6  0   0.276   6.3563  -1.6268   0.6898
 5Y5  H15   H   HCR6  0   0.260   4.6212  -2.8559   1.9080
 5Y5  H142  H   HCH3  0   0.260  -7.7150   0.2395  -0.2068
 5Y5  H143  H   HCH3  0   0.260  -7.2329   0.8356  -1.7937
 5Y5  H141  H   HCH3  0   0.269  -8.0905  -0.7073  -1.6553
 5Y5  H11   H   HCH2  0   0.263  -0.1777  -2.7473   2.0810
 5Y5  H12   H   HCH2  0   0.245   0.3964  -2.9496   0.4281
 5Y5  H18   H   HCR6  0   0.270   3.3039   0.7489  -1.1799
 5Y5  HN1   H   HNH1  0   0.419  -1.6133  -1.4846   0.2113
 5Y5  C10   C   CH3   0  -0.729  -1.6802   4.0170   1.9499
 5Y5  C13   C   CT    0   0.717  -6.0430  -0.7881  -1.0628

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
 5Y5  C10  C9    single    1.496  0.020  1.496
 5Y5  N5   C9    aromatic  1.326  0.020  1.326
 5Y5  N5   C11   aromatic  1.325  0.020  1.325
 5Y5  C9   C8    aromatic  1.400  0.020  1.400
 5Y5  C11  N4    aromatic  1.327  0.020  1.327
 5Y5  C11  N2    aromatic  1.372  0.020  1.372
 5Y5  N4   C12   aromatic  1.338  0.020  1.338
 5Y5  C8   C7    aromatic  1.389  0.020  1.389
 5Y5  F2   C13   single    1.369  0.020  1.369
 5Y5  N2   C7    aromatic  1.361  0.020  1.361
 5Y5  N2   N3    aromatic  1.340  0.020  1.340
 5Y5  C7   N1    single    1.328  0.020  1.328
 5Y5  C12  C13   single    1.502  0.020  1.502
 5Y5  C12  N3    aromatic  1.315  0.020  1.315
 5Y5  C13  C14   single    1.501  0.020  1.501
 5Y5  C13  F1    single    1.367  0.020  1.367
 5Y5  N1   C2    single    1.450  0.020  1.450
 5Y5  C2   C1    single    1.520  0.020  1.520
 5Y5  C2   C3    single    1.527  0.020  1.527
 5Y5  C1   C6    single    1.521  0.020  1.521
 5Y5  C3   C4    single    1.507  0.020  1.507
 5Y5  C6   C5    single    1.506  0.020  1.506
 5Y5  C4   C5    aromatic  1.395  0.020  1.395
 5Y5  C4   C18   aromatic  1.395  0.020  1.395
 5Y5  C5   C15   aromatic  1.394  0.020  1.394
 5Y5  C18  C17   aromatic  1.383  0.020  1.383
 5Y5  C15  C16   aromatic  1.384  0.020  1.384
 5Y5  C17  C16   aromatic  1.388  0.020  1.388
 5Y5  C17  BR1   single    1.891  0.020  1.891
 5Y5  C2   H2    single    0.970  0.020  1.090
 5Y5  C3   H32   single    0.970  0.020  1.090
 5Y5  C3   H31   single    0.970  0.020  1.090
 5Y5  C6   H61   single    0.970  0.020  1.090
 5Y5  C6   H62   single    0.970  0.020  1.090
 5Y5  C8   H8    single    0.930  0.020  1.080
 5Y5  C10  H103  single    0.970  0.020  1.090
 5Y5  C10  H101  single    0.970  0.020  1.090
 5Y5  C10  H102  single    0.970  0.020  1.090
 5Y5  C16  H16   single    0.930  0.020  1.080
 5Y5  C15  H15   single    0.930  0.020  1.080
 5Y5  C14  H142  single    0.970  0.020  1.090
 5Y5  C14  H143  single    0.970  0.020  1.090
 5Y5  C14  H141  single    0.970  0.020  1.090
 5Y5  C1   H11   single    0.970  0.020  1.090
 5Y5  C1   H12   single    0.970  0.020  1.090
 5Y5  C18  H18   single    0.930  0.020  1.080
 5Y5  N1   HN1   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
 5Y5  H2    C2   N1    107.88  3.000
 5Y5  H2    C2   C1    108.34  3.000
 5Y5  N1    C2   C1    109.88  3.000
 5Y5  H2    C2   C3    109.52  3.000
 5Y5  C1    C2   C3    109.79  3.000
 5Y5  N1    C2   C3    111.35  3.000
 5Y5  H31   C3   H32   106.32  3.000
 5Y5  H31   C3   C4    109.73  3.000
 5Y5  H32   C3   C4    109.16  3.000
 5Y5  H31   C3   C2    110.63  3.000
 5Y5  H32   C3   C2    108.33  3.000
 5Y5  C4    C3   C2    112.46  3.000
 5Y5  C18   C4   C5    119.68  3.000
 5Y5  C18   C4   C3    118.79  3.000
 5Y5  C5    C4   C3    121.51  3.000
 5Y5  C15   C5   C6    119.53  3.000
 5Y5  C15   C5   C4    118.88  3.000
 5Y5  C6    C5   C4    121.57  3.000
 5Y5  H62   C6   H61   105.79  3.000
 5Y5  H62   C6   C1    109.31  3.000
 5Y5  H61   C6   C1    109.59  3.000
 5Y5  H62   C6   C5    108.56  3.000
 5Y5  H61   C6   C5    109.71  3.000
 5Y5  C1    C6   C5    113.58  3.000
 5Y5  N2    C7   N1    117.76  3.000
 5Y5  N1    C7   C8    127.95  3.000
 5Y5  N2    C7   C8    114.28  3.000
 5Y5  H8    C8   C9    119.84  3.000
 5Y5  H8    C8   C7    120.21  3.000
 5Y5  C9    C8   C7    119.95  3.000
 5Y5  C18   C17  BR1   119.44  3.000
 5Y5  BR1   C17  C16   119.53  3.000
 5Y5  C18   C17  C16   121.03  3.000
 5Y5  H16   C16  C15   120.17  3.000
 5Y5  H16   C16  C17   121.44  3.000
 5Y5  C15   C16  C17   118.39  3.000
 5Y5  H15   C15  C16   118.85  3.000
 5Y5  H15   C15  C5    119.29  3.000
 5Y5  C16   C15  C5    121.86  3.000
 5Y5  H141  C14  H143  108.79  3.000
 5Y5  H141  C14  H142  108.81  3.000
 5Y5  H143  C14  H142  108.16  3.000
 5Y5  H141  C14  C13   109.84  3.000
 5Y5  H143  C14  C13   110.61  3.000
 5Y5  H142  C14  C13   110.58  3.000
 5Y5  N4    C12  N3    116.48  3.000
 5Y5  N3    C12  C13   120.55  3.000
 5Y5  N4    C12  C13   122.96  3.000
 5Y5  N4    C11  N5    129.25  3.000
 5Y5  N4    C11  N2    107.84  3.000
 5Y5  N5    C11  N2    122.91  3.000
 5Y5  H12   C1   H11   107.38  3.000
 5Y5  H12   C1   C6    110.14  3.000
 5Y5  H11   C1   C6    109.63  3.000
 5Y5  H12   C1   C2    109.24  3.000
 5Y5  H11   C1   C2    110.34  3.000
 5Y5  C6    C1   C2    110.06  3.000
 5Y5  H18   C18  C17   120.64  3.000
 5Y5  H18   C18  C4    119.21  3.000
 5Y5  C17   C18  C4    120.15  3.000
 5Y5  HN1   N1   C7    117.38  3.000
 5Y5  HN1   N1   C2    118.03  3.000
 5Y5  C7    N1   C2    123.94  3.000
 5Y5  N5    C9   C10   116.88  3.000
 5Y5  N5    C9   C8    123.93  3.000
 5Y5  C10   C9   C8    119.18  3.000
 5Y5  N3    N2   C11   110.85  3.000
 5Y5  N3    N2   C7    126.02  3.000
 5Y5  C11   N2   C7    123.13  3.000
 5Y5  C9    N5   C11   115.80  3.000
 5Y5  N2    N3   C12   101.50  3.000
 5Y5  C11   N4   C12   103.33  3.000
 5Y5  H102  C10  H101  109.17  3.000
 5Y5  H102  C10  H103  107.55  3.000
 5Y5  H101  C10  H103  107.65  3.000
 5Y5  H102  C10  C9    111.75  3.000
 5Y5  H101  C10  C9    110.83  3.000
 5Y5  H103  C10  C9    109.75  3.000
 5Y5  F2    C13  F1    105.13  3.000
 5Y5  F1    C13  C12   108.00  3.000
 5Y5  F2    C13  C12   107.89  3.000
 5Y5  F1    C13  C14   110.22  3.000
 5Y5  C12   C13  C14   114.98  3.000
 5Y5  F2    C13  C14   110.13  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
 5Y5  CONST_01  C16   C15  C5   C4     0.00   0.0  0
 5Y5  CONST_02  C16   C17  C18  C4     0.00   0.0  0
 5Y5  CONST_03  C17   C18  C4   C5     0.00   0.0  0
 5Y5  CONST_04  C17   C16  C15  C5     0.00   0.0  0
 5Y5  CONST_05  N5    C9   C8   C7     0.00   0.0  0
 5Y5  CONST_06  N5    C11  N2   C7     0.00   0.0  0
 5Y5  CONST_07  N4    C11  N2   C7   180.00   0.0  0
 5Y5  CONST_08  C12   N3   N2   C7   180.00   0.0  0
 5Y5  CONST_09  C11   N5   C9   C8     0.00   0.0  0
 5Y5  CONST_10  C11   N2   C7   C8     0.00   0.0  0
 5Y5  CONST_11  N3    N2   C7   C8   180.00   0.0  0
 5Y5  CONST_12  C18   C4   C5   C15    0.00   0.0  0
 5Y5  CONST_13  C18   C17  C16  C15    0.00   0.0  0
 5Y5  CONST_14  N5    C11  N4   C12  180.00   0.0  0
 5Y5  CONST_15  N2    C11  N4   C12    0.00   0.0  0
 5Y5  CONST_16  C11   N2   N3   C12    0.00   0.0  0
 5Y5  CONST_17  N3    C12  N4   C11    0.00   0.0  0
 5Y5  CONST_18  N4    C11  N5   C9   180.00   0.0  0
 5Y5  CONST_19  N2    C11  N5   C9     0.00   0.0  0
 5Y5  CONST_20  N2    C7   C8   C9     0.00   0.0  0
 5Y5  CONST_21  N4    C12  N3   N2     0.00   0.0  0
 5Y5  CONST_22  N3    N2   C11  N5   180.00   0.0  0
 5Y5  CONST_23  N4    C11  N2   N3     0.00   0.0  0
 5Y5  CONST_24  BR1   C17  C18  C4   180.00   0.0  0
 5Y5  CONST_25  C10   C9   C8   C7   180.00   0.0  0
 5Y5  CONST_26  C11   N5   C9   C10  180.00   0.0  0
 5Y5  CONST_27  BR1   C17  C16  C15  180.00   0.0  0
 5Y5  CONST_28  C11   N4   C12  C13  180.00   0.0  0
 5Y5  CONST_29  N2    N3   C12  C13  180.00   0.0  0
 5Y5  CONST_30  N1    C7   N2   C11  180.00   0.0  0
 5Y5  CONST_31  C9    C8   C7   N1   180.00   0.0  0
 5Y5  CONST_32  N3    N2   C7   N1     0.00   0.0  0
 5Y5  CONST_33  C8    C7   N1   C2     0.00   0.0  0
 5Y5  CONST_34  N2    C7   N1   C2   180.00   0.0  0
 5Y5  CONST_35  H18   C18  C4   C3     0.00   0.0  0
 5Y5  CONST_36  H15   C15  C5   C4   180.00   0.0  0
 5Y5  CONST_37  H16   C16  C15  C5   180.00   0.0  0
 5Y5  CONST_38  H8    C8   C7   N2   180.00   0.0  0
 5Y5  CONST_39  HN1   N1   C7   C8   180.00   0.0  0
 5Y5  Var_01    C5    C6   C1   C2   -46.05  30.0  1
 5Y5  Var_02    C5    C4   C3   C2    20.51  30.0  1
 5Y5  Var_03    C1    C6   C5   C4    16.43  30.0  1
 5Y5  Var_04    N4    C12  C13  C14   -4.32  30.0  2
 5Y5  Var_05    H103  C10  C9   C8    91.72  30.0  2
 5Y5  Var_06    H142  C14  C13  C12  -59.40  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
 5Y5  chir_01  C2  N1  C1  C3  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
 5Y5  plan-1  C7   0.020
 5Y5  plan-1  C8   0.020
 5Y5  plan-1  C12  0.020
 5Y5  plan-1  C11  0.020
 5Y5  plan-1  N1   0.020
 5Y5  plan-1  C9   0.020
 5Y5  plan-1  N2   0.020
 5Y5  plan-1  N5   0.020
 5Y5  plan-1  N3   0.020
 5Y5  plan-1  N4   0.020
 5Y5  plan-1  H8   0.020
 5Y5  plan-1  C10  0.020
 5Y5  plan-1  C13  0.020
 5Y5  plan-2  C3   0.020
 5Y5  plan-2  C4   0.020
 5Y5  plan-2  C5   0.020
 5Y5  plan-2  C6   0.020
 5Y5  plan-2  C17  0.020
 5Y5  plan-2  C16  0.020
 5Y5  plan-2  C15  0.020
 5Y5  plan-2  BR1  0.020
 5Y5  plan-2  C18  0.020
 5Y5  plan-2  H16  0.020
 5Y5  plan-2  H15  0.020
 5Y5  plan-2  H18  0.020
 5Y5  plan-3  C2   0.020
 5Y5  plan-3  C7   0.020
 5Y5  plan-3  N1   0.020
 5Y5  plan-3  HN1  0.020

