# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 00:23:53 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: (1~{R},2~{R})-2-[(4~{R})-2-azanyl-5,5-bis(fluoranyl)-4-methyl-6~{H}-1,3-oxazin-4-yl]-~{N}-(3-chloranylquinolin-8-yl)cyclopropane-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@]1(N=C(N)OCC1(F)F)[C@@H]2C[C@H]2C(=O)Nc3cccc4cc(Cl)cnc34
#
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
 5T7  5T7  (1~{R},2~{R})-2-[(4~{R})-2-azanyl-5,5-bis(fluoranyl)-4-methyl-6~{H}-1,3-oxazin-4-yl]-~{N}-(3-chloranylquinolin-8-yl)cyclopropane-1-carboxamide  ligand  44  27  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_5T7
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
 5T7  C5   C   C     0   0.623   4.5260   0.6451  -1.9338
 5T7  C7   C   CH1   0  -0.464   1.1852  -0.6470   0.9083
 5T7  C8   C   CH2   0  -0.459   2.1603  -1.0369   1.9911
 5T7  C10  C   C     0   0.615   0.1631   0.3854   1.2205
 5T7  N12  N   NH1   0  -0.757  -1.0323   0.1672   0.6115
 5T7  C13  C   CH3   0  -0.685   3.1986  -2.1045  -0.7515
 5T7  C17  C   CR6   0   0.344  -2.1997   0.9121   0.6831
 5T7  C20  C   CR16  0  -0.331  -4.6892   2.2579   0.6755
 5T7  C21  C   CR66  0   0.155  -3.2931   0.4022  -0.0849
 5T7  C22  C   CR66  0   0.081  -4.5332   1.0786  -0.0836
 5T7  C24  C   CR6   0  -0.123  -5.3372  -0.6158  -1.5622
 5T7  C1   C   CT    0  -0.075   3.5699  -0.7124  -0.2342
 5T7  C2   C   CT    0   0.741   4.9970  -0.7257   0.3196
 5T7  C3   C   CH2   0  -0.277   6.0245  -0.7643  -0.7900
 5T7  O4   O   O2    0  -0.466   5.8082   0.3144  -1.6797
 5T7  N6   N   N     0  -0.476   3.4867   0.2295  -1.3335
 5T7  C9   C   CH1   0  -0.192   2.6251  -0.2116   0.8505
 5T7  O11  O   O     0  -0.471   0.3862   1.3321   1.9562
 5T7  F14  F   F     0  -0.346   5.2190   0.3981   1.0647
 5T7  F15  F   F     0  -0.331   5.2069  -1.7776   1.1556
 5T7  N16  N   NH2   0  -0.826   4.4556   1.5037  -2.9855
 5T7  C18  C   CR16  0  -0.335  -2.3838   2.0657   1.4124
 5T7  C19  C   CR16  0  -0.243  -3.6285   2.7258   1.3990
 5T7  C23  C   CR16  0  -0.130  -5.5761   0.5274  -0.8581
 5T7  C25  C   CR16  0  -0.030  -4.0656  -1.2237  -1.5035
 5T7  N26  N   N     0  -0.446  -3.0932  -0.7287  -0.7930
 5T7  CL2  CL  CL    0  -0.106  -6.5632  -1.3454  -2.5299
 5T7  H1   H   HCH1  0   0.285   0.8740  -1.4406   0.2399
 5T7  H2   H   HCH2  0   0.268   2.0624  -0.5526   2.9542
 5T7  H3   H   HCH2  0   0.267   2.4247  -2.0844   2.0426
 5T7  H4   H   HNH1  0   0.418  -1.1135  -0.6501   0.0197
 5T7  H5   H   HCH3  0   0.244   3.0836  -2.8463   0.0383
 5T7  H6   H   HCH3  0   0.253   2.2607  -2.0441  -1.3014
 5T7  H7   H   HCH3  0   0.253   3.9451  -2.4800  -1.4516
 5T7  H8   H   HCR6  0   0.265  -5.6405   2.7739   0.6779
 5T7  H9   H   HCH2  0   0.287   7.0317  -0.6536  -0.3872
 5T7  H10  H   HCH2  0   0.264   5.9742  -1.7154  -1.3254
 5T7  H11  H   HCH1  0   0.273   2.7647   0.8382   1.0803
 5T7  H12  H   HNH2  0   0.393   3.5923   2.0152  -3.0642
 5T7  H13  H   HNH2  0   0.395   5.2768   2.0473  -3.1978
 5T7  H14  H   HCR6  0   0.287  -1.5840   2.4783   2.0036
 5T7  H15  H   HCR6  0   0.268  -3.7333   3.6292   1.9851
 5T7  H16  H   HCR6  0   0.296  -6.5435   1.0126  -0.8814
 5T7  H17  H   HCR6  0   0.291  -3.8731  -2.1341  -2.0600

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
 5T7  CL2  C24  single    1.724  0.020  1.724
 5T7  C24  C25  aromatic  1.411  0.020  1.411
 5T7  C24  C23  aromatic  1.364  0.020  1.364
 5T7  C25  N26  aromatic  1.302  0.020  1.302
 5T7  C23  C22  aromatic  1.411  0.020  1.411
 5T7  N26  C21  aromatic  1.349  0.020  1.349
 5T7  C22  C21  aromatic  1.413  0.020  1.413
 5T7  C22  C20  aromatic  1.411  0.020  1.411
 5T7  C21  C17  aromatic  1.430  0.020  1.430
 5T7  C20  C19  aromatic  1.367  0.020  1.367
 5T7  C17  N12  single    1.387  0.020  1.387
 5T7  C17  C18  aromatic  1.377  0.020  1.377
 5T7  C19  C18  aromatic  1.409  0.020  1.409
 5T7  N12  C10  single    1.359  0.020  1.359
 5T7  N16  C5   single    1.359  0.020  1.359
 5T7  C10  C7   single    1.486  0.020  1.486
 5T7  C10  O11  double    1.220  0.020  1.220
 5T7  C7   C8   single    1.508  0.020  1.508
 5T7  C7   C9   single    1.505  0.020  1.505
 5T7  C8   C9   single    1.483  0.020  1.483
 5T7  C5   N6   double    1.270  0.020  1.270
 5T7  C5   O4   single    1.348  0.020  1.348
 5T7  N6   C1   single    1.450  0.020  1.450
 5T7  O4   C3   single    1.415  0.020  1.415
 5T7  C9   C1   single    1.523  0.020  1.523
 5T7  C1   C13  single    1.531  0.020  1.531
 5T7  C1   C2   single    1.531  0.020  1.531
 5T7  C3   C2   single    1.513  0.020  1.513
 5T7  C2   F15  single    1.360  0.020  1.360
 5T7  C2   F14  single    1.367  0.020  1.367
 5T7  C7   H1   single    0.970  0.020  1.090
 5T7  C8   H2   single    0.970  0.020  1.090
 5T7  C8   H3   single    0.970  0.020  1.090
 5T7  N12  H4   single    0.860  0.020  1.020
 5T7  C13  H5   single    0.970  0.020  1.090
 5T7  C13  H6   single    0.970  0.020  1.090
 5T7  C13  H7   single    0.970  0.020  1.090
 5T7  C20  H8   single    0.930  0.020  1.080
 5T7  C3   H9   single    0.970  0.020  1.090
 5T7  C3   H10  single    0.970  0.020  1.090
 5T7  C9   H11  single    0.970  0.020  1.090
 5T7  N16  H12  single    0.890  0.020  1.040
 5T7  N16  H13  single    0.890  0.020  1.040
 5T7  C18  H14  single    0.930  0.020  1.080
 5T7  C19  H15  single    0.930  0.020  1.080
 5T7  C23  H16  single    0.930  0.020  1.080
 5T7  C25  H17  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
 5T7  N16  C5   N6   122.00  3.000
 5T7  N6   C5   O4   127.50  3.000
 5T7  N16  C5   O4   110.48  3.000
 5T7  H1   C7   C9   117.58  3.000
 5T7  H1   C7   C10  116.17  3.000
 5T7  C9   C7   C10  117.72  3.000
 5T7  H1   C7   C8   116.06  3.000
 5T7  C9   C7   C8    58.94  3.000
 5T7  C10  C7   C8   118.26  3.000
 5T7  H3   C8   H2   114.40  3.000
 5T7  H3   C8   C9   119.93  3.000
 5T7  H2   C8   C9   117.64  3.000
 5T7  H3   C8   C7   116.27  3.000
 5T7  H2   C8   C7   117.69  3.000
 5T7  C9   C8   C7    60.43  3.000
 5T7  O11  C10  N12  123.76  3.000
 5T7  O11  C10  C7   122.70  3.000
 5T7  N12  C10  C7   113.54  3.000
 5T7  H4   N12  C17  113.35  3.000
 5T7  H4   N12  C10  117.52  3.000
 5T7  C17  N12  C10  129.13  3.000
 5T7  H7   C13  H6   106.54  3.000
 5T7  H7   C13  H5   107.66  3.000
 5T7  H6   C13  H5   108.23  3.000
 5T7  H7   C13  C1   111.36  3.000
 5T7  H6   C13  C1   109.21  3.000
 5T7  H5   C13  C1   113.56  3.000
 5T7  C18  C17  C21  118.74  3.000
 5T7  C18  C17  N12  126.15  3.000
 5T7  C21  C17  N12  115.11  3.000
 5T7  H8   C20  C19  121.19  3.000
 5T7  H8   C20  C22  119.80  3.000
 5T7  C19  C20  C22  119.02  3.000
 5T7  N26  C21  C22  122.14  3.000
 5T7  C22  C21  C17  119.99  3.000
 5T7  N26  C21  C17  117.87  3.000
 5T7  C23  C22  C21  117.47  3.000
 5T7  C21  C22  C20  119.85  3.000
 5T7  C23  C22  C20  122.68  3.000
 5T7  CL2  C24  C25  118.82  3.000
 5T7  C25  C24  C23  119.85  3.000
 5T7  CL2  C24  C23  121.33  3.000
 5T7  C9   C1   N6   106.90  3.000
 5T7  C9   C1   C2   108.88  3.000
 5T7  N6   C1   C2   109.47  3.000
 5T7  C2   C1   C13  109.90  3.000
 5T7  C9   C1   C13  112.90  3.000
 5T7  N6   C1   C13  108.70  3.000
 5T7  F15  C2   F14  106.01  3.000
 5T7  F14  C2   C3   108.09  3.000
 5T7  F15  C2   C3   109.05  3.000
 5T7  F14  C2   C1   109.97  3.000
 5T7  F15  C2   C1   111.90  3.000
 5T7  C3   C2   C1   111.60  3.000
 5T7  H10  C3   H9   108.18  3.000
 5T7  H10  C3   O4   110.39  3.000
 5T7  H9   C3   O4   107.22  3.000
 5T7  H10  C3   C2   110.51  3.000
 5T7  H9   C3   C2   110.73  3.000
 5T7  O4   C3   C2   109.75  3.000
 5T7  C3   O4   C5   116.80  3.000
 5T7  C1   N6   C5   121.60  3.000
 5T7  H11  C9   C1   112.92  3.000
 5T7  H11  C9   C8   114.61  3.000
 5T7  C1   C9   C8   124.01  3.000
 5T7  H11  C9   C7   113.28  3.000
 5T7  C1   C9   C7   121.71  3.000
 5T7  C8   C9   C7    60.63  3.000
 5T7  H13  N16  H12  114.11  3.000
 5T7  H13  N16  C5   117.50  3.000
 5T7  H12  N16  C5   115.20  3.000
 5T7  H14  C18  C19  118.80  3.000
 5T7  H14  C18  C17  120.83  3.000
 5T7  C19  C18  C17  120.37  3.000
 5T7  H15  C19  C18  118.14  3.000
 5T7  H15  C19  C20  119.84  3.000
 5T7  C18  C19  C20  122.03  3.000
 5T7  H16  C23  C24  121.41  3.000
 5T7  H16  C23  C22  119.82  3.000
 5T7  C24  C23  C22  118.77  3.000
 5T7  H17  C25  N26  117.82  3.000
 5T7  H17  C25  C24  120.04  3.000
 5T7  N26  C25  C24  122.14  3.000
 5T7  C25  N26  C21  119.63  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
 5T7  CONST_01  C25  N26  C21  C17   180.00   0.0  0
 5T7  CONST_02  C23  C22  C21  C17   180.00   0.0  0
 5T7  CONST_03  C20  C22  C21  C17     0.00   0.0  0
 5T7  CONST_04  C20  C19  C18  C17     0.00   0.0  0
 5T7  CONST_05  C24  C23  C22  C20   180.00   0.0  0
 5T7  CONST_06  N26  C21  C22  C20   180.00   0.0  0
 5T7  CONST_07  C24  C25  N26  C21     0.00   0.0  0
 5T7  CONST_08  C24  C23  C22  C21     0.00   0.0  0
 5T7  CONST_09  C19  C20  C22  C21     0.00   0.0  0
 5T7  CONST_10  C19  C18  C17  C21     0.00   0.0  0
 5T7  CONST_11  C25  C24  C23  C22     0.00   0.0  0
 5T7  CONST_12  C25  N26  C21  C22     0.00   0.0  0
 5T7  CONST_13  C18  C17  C21  C22     0.00   0.0  0
 5T7  CONST_14  C18  C19  C20  C22     0.00   0.0  0
 5T7  CONST_15  N26  C21  C17  C18   180.00   0.0  0
 5T7  CONST_16  C23  C22  C20  C19   180.00   0.0  0
 5T7  CONST_17  N26  C25  C24  C23     0.00   0.0  0
 5T7  CONST_18  N26  C21  C22  C23     0.00   0.0  0
 5T7  CONST_19  O4   C5   N6   C1      0.00   0.0  0
 5T7  CONST_20  N26  C21  C17  N12     0.00   0.0  0
 5T7  CONST_21  C22  C21  C17  N12   180.00   0.0  0
 5T7  CONST_22  C19  C18  C17  N12   180.00   0.0  0
 5T7  CONST_23  CL2  C24  C23  C22   180.00   0.0  0
 5T7  CONST_24  CL2  C24  C25  N26   180.00   0.0  0
 5T7  CONST_25  N16  C5   N6   C1    180.00   0.0  0
 5T7  CONST_26  H15  C19  C18  C17   180.00   0.0  0
 5T7  CONST_27  H16  C23  C22  C20     0.00   0.0  0
 5T7  CONST_28  H14  C18  C19  C20   180.00   0.0  0
 5T7  CONST_29  H17  C25  N26  C21   180.00   0.0  0
 5T7  CONST_30  H8   C20  C22  C21   180.00   0.0  0
 5T7  CONST_31  C17  N12  C10  C7    180.00   0.0  0
 5T7  CONST_32  C21  C17  N12  C10   180.00   0.0  0
 5T7  CONST_33  C18  C17  N12  C10     0.00   0.0  0
 5T7  CONST_34  H4   N12  C17  C21     0.00   0.0  0
 5T7  CONST_37  O11  C10  N12  C17     0.00   0.0  0
 5T7  Var_01    C2   C3   O4   C5    -37.52  30.0  1
 5T7  Var_02    C1   C9   C8   C7   -110.36  30.0  1
 5T7  Var_03    O4   C3   C2   C1     55.07  30.0  1
 5T7  Var_04    N6   C5   O4   C3     10.59  30.0  1
 5T7  Var_05    N12  C10  C7   C8   -144.76  30.0  1

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
 5T7  chir_02  C1  C9   N6  C2  negativ
 5T7  chir_03  C7  C10  C8  C9  both
 5T7  chir_04  C9  C7   C8  C1  both

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
 5T7  plan-1  C7   0.020
 5T7  plan-1  C10  0.020
 5T7  plan-1  N12  0.020
 5T7  plan-1  C17  0.020
 5T7  plan-1  O11  0.020
 5T7  plan-1  H4   0.020
 5T7  plan-2  N12  0.020
 5T7  plan-2  C17  0.020
 5T7  plan-2  C20  0.020
 5T7  plan-2  C21  0.020
 5T7  plan-2  C22  0.020
 5T7  plan-2  C24  0.020
 5T7  plan-2  C18  0.020
 5T7  plan-2  C19  0.020
 5T7  plan-2  C23  0.020
 5T7  plan-2  C25  0.020
 5T7  plan-2  N26  0.020
 5T7  plan-2  CL2  0.020
 5T7  plan-2  H8   0.020
 5T7  plan-2  H14  0.020
 5T7  plan-2  H15  0.020
 5T7  plan-2  H16  0.020
 5T7  plan-2  H17  0.020
 5T7  plan-3  C5   0.020
 5T7  plan-3  C1   0.020
 5T7  plan-3  O4   0.020
 5T7  plan-3  N6   0.020
 5T7  plan-3  N16  0.020
 5T7  plan-3  H12  0.020
 5T7  plan-3  H13  0.020

