# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 05:07:05 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: ~{N}-[(1~{R},2~{S})-1-(2-bromanyl-4-cyano-phenoxy)-1-(2-cyclopropylpyrimidin-5-yl)propan-2-yl]-2,2-bis(fluoranyl)propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NC(=O)C(C)(F)F)[C@H](Oc1ccc(cc1Br)C#N)c2cnc(nc2)C3CC3
#
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
 B9T  B9T  ~{N}-[(1~{R},2~{S})-1-(2-bromanyl-4-cyano-phenoxy)-1-(2-cyclopropylpyrimidin-5-yl)propan-2-yl]-2,2-bis(fluoranyl)propanamide  ligand  48  29  .  2022-09-16  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_B9T
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
 B9T  C1   C   CH3   0  -0.681   0.3019   3.0980  -0.7025
 B9T  C2   C   CH1   0  -0.115  -0.5652   1.8501  -0.7434
 B9T  C7   C   CR16  0  -0.021  -1.0105  -1.3905  -0.8709
 B9T  C9   C   CR6   0   0.430  -2.7547  -2.4487   0.1225
 B9T  C11  C   CR16  0  -0.055  -1.8712  -0.6496   1.1784
 B9T  C12  C   CH1   0  -0.365  -3.7625  -3.5216   0.0728
 B9T  C13  C   CH2   0  -0.471  -5.1624  -3.2402   0.5613
 B9T  C14  C   CH2   0  -0.466  -4.2742  -4.1274   1.3540
 B9T  C16  C   CR6   0   0.488   2.3735   0.4565   0.3179
 B9T  C19  C   CR6   0  -0.018   4.8578   0.6709   1.5701
 B9T  C20  C   CR16  0  -0.205   4.6812  -0.2479   0.5355
 B9T  C21  C   CR6   0  -0.235   3.4502  -0.3509  -0.0780
 B9T  N25  N   NH1   0  -0.640  -1.9141   2.1714  -0.3256
 B9T  C4   C   CH1   0  -0.047  -0.0264   0.7169   0.1553
 B9T  C6   C   CR6   0  -0.017  -0.9499  -0.4642   0.1605
 B9T  N8   N   N     0  -0.426  -1.8920  -2.3778  -0.8895
 B9T  N10  N   N     0  -0.426  -2.7689  -1.6207   1.1632
 B9T  O15  O   O2    0  -0.473   1.2333   0.2990  -0.3560
 B9T  C17  C   CR16  0  -0.358   2.5715   1.3768   1.3465
 B9T  C18  C   CR16  0  -0.219   3.7991   1.4811   1.9706
 B9T  BR2  BR  BR    0   0.003   3.2050  -1.5924  -1.4651
 B9T  C23  C   CSP   0   0.058   6.1256   0.7771   2.2107
 B9T  N24  N   NS    0  -0.251   7.1506   0.8632   2.7306
 B9T  C26  C   C     0   0.441  -3.0075   1.7330  -0.9593
 B9T  O27  O   O     0  -0.462  -3.0132   1.0207  -1.9453
 B9T  C28  C   CT    0   0.683  -4.3560   2.1707  -0.3649
 B9T  C29  C   CH3   0  -0.768  -5.2744   1.0167  -0.0815
 B9T  F30  F   F     0  -0.340  -4.1596   2.9069   0.7690
 B9T  F31  F   F     0  -0.343  -4.9225   3.0239  -1.2664
 B9T  H1   H   HCH3  0   0.238   0.3532   3.5158   0.3050
 B9T  H2   H   HCH3  0   0.254   1.3168   2.8886  -1.0359
 B9T  H3   H   HCH3  0   0.265  -0.1105   3.8599  -1.3626
 B9T  H4   H   HCH1  0   0.278  -0.6139   1.4764  -1.7677
 B9T  H5   H   HCR6  0   0.273  -0.3237  -1.3431  -1.7091
 B9T  H6   H   HCR6  0   0.278  -1.8891   0.0161   2.0363
 B9T  H7   H   HCH1  0   0.275  -3.6653  -4.1806  -0.7803
 B9T  H8   H   HCH2  0   0.257  -5.3597  -2.2451   0.9388
 B9T  H9   H   HCH2  0   0.264  -5.9739  -3.6840   0.0002
 B9T  H10  H   HCH2  0   0.264  -4.4664  -5.1922   1.3472
 B9T  H11  H   HCH2  0   0.257  -3.8613  -3.7429   2.2773
 B9T  H12  H   HCR6  0   0.304   5.5045  -0.8770   0.2258
 B9T  H13  H   HNH1  0   0.416  -2.0193   2.7817   0.4706
 B9T  H14  H   HCH1  0   0.281   0.0629   1.0872   1.1817
 B9T  H15  H   HCR6  0   0.300   1.7755   2.0335   1.6669
 B9T  H16  H   HCR6  0   0.295   3.9314   2.2012   2.7657
 B9T  H17  H   HCH3  0   0.256  -4.8115   0.3235   0.6202
 B9T  H18  H   HCH3  0   0.276  -6.2086   1.3755   0.3497
 B9T  H19  H   HCH3  0   0.267  -5.4952   0.4753  -0.9988

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
 B9T  N24  C23  triple    1.152  0.020  1.152
 B9T  C23  C19  single    1.424  0.020  1.424
 B9T  C19  C20  aromatic  1.395  0.020  1.395
 B9T  C19  C18  aromatic  1.392  0.020  1.392
 B9T  C20  C21  aromatic  1.379  0.020  1.379
 B9T  C18  C17  aromatic  1.381  0.020  1.381
 B9T  C21  BR2  single    1.878  0.020  1.878
 B9T  C21  C16  aromatic  1.403  0.020  1.403
 B9T  C17  C16  aromatic  1.394  0.020  1.394
 B9T  C16  O15  single    1.334  0.020  1.334
 B9T  O15  C4   single    1.422  0.020  1.422
 B9T  C4   C6   single    1.499  0.020  1.499
 B9T  C4   C2   single    1.543  0.020  1.543
 B9T  C1   C2   single    1.520  0.020  1.520
 B9T  C6   C11  aromatic  1.385  0.020  1.385
 B9T  C6   C7   aromatic  1.388  0.020  1.388
 B9T  C11  N10  aromatic  1.323  0.020  1.323
 B9T  C2   N25  single    1.448  0.020  1.448
 B9T  C7   N8   aromatic  1.324  0.020  1.324
 B9T  N10  C9   aromatic  1.330  0.020  1.330
 B9T  N8   C9   aromatic  1.332  0.020  1.332
 B9T  C9   C12  single    1.473  0.020  1.473
 B9T  N25  C26  single    1.338  0.020  1.338
 B9T  C13  C12  single    1.509  0.020  1.509
 B9T  C13  C14  single    1.485  0.020  1.485
 B9T  C12  C14  single    1.507  0.020  1.507
 B9T  O27  C26  double    1.216  0.020  1.216
 B9T  C26  C28  single    1.537  0.020  1.537
 B9T  F30  C28  single    1.366  0.020  1.366
 B9T  C28  C29  single    1.502  0.020  1.502
 B9T  C28  F31  single    1.364  0.020  1.364
 B9T  C1   H1   single    0.970  0.020  1.090
 B9T  C1   H2   single    0.970  0.020  1.090
 B9T  C1   H3   single    0.970  0.020  1.090
 B9T  C2   H4   single    0.970  0.020  1.090
 B9T  C7   H5   single    0.930  0.020  1.080
 B9T  C11  H6   single    0.930  0.020  1.080
 B9T  C12  H7   single    0.970  0.020  1.090
 B9T  C13  H8   single    0.970  0.020  1.090
 B9T  C13  H9   single    0.970  0.020  1.090
 B9T  C14  H10  single    0.970  0.020  1.090
 B9T  C14  H11  single    0.970  0.020  1.090
 B9T  C20  H12  single    0.930  0.020  1.080
 B9T  N25  H13  single    0.860  0.020  1.020
 B9T  C4   H14  single    0.970  0.020  1.090
 B9T  C17  H15  single    0.930  0.020  1.080
 B9T  C18  H16  single    0.930  0.020  1.080
 B9T  C29  H17  single    0.970  0.020  1.090
 B9T  C29  H18  single    0.970  0.020  1.090
 B9T  C29  H19  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
 B9T  H3   C1   H2   107.57  3.000
 B9T  H3   C1   H1   108.02  3.000
 B9T  H2   C1   H1   108.21  3.000
 B9T  H3   C1   C2   109.99  3.000
 B9T  H2   C1   C2   111.45  3.000
 B9T  H1   C1   C2   111.46  3.000
 B9T  H4   C2   C4   108.10  3.000
 B9T  H4   C2   N25  107.77  3.000
 B9T  C4   C2   N25  108.67  3.000
 B9T  H4   C2   C1   109.38  3.000
 B9T  N25  C2   C1   109.96  3.000
 B9T  C4   C2   C1   112.82  3.000
 B9T  H5   C7   N8   116.32  3.000
 B9T  H5   C7   C6   121.17  3.000
 B9T  N8   C7   C6   122.51  3.000
 B9T  N10  C9   N8   124.64  3.000
 B9T  N8   C9   C12  117.16  3.000
 B9T  N10  C9   C12  118.20  3.000
 B9T  H6   C11  N10  116.61  3.000
 B9T  H6   C11  C6   120.62  3.000
 B9T  N10  C11  C6   122.77  3.000
 B9T  H7   C12  C14  117.13  3.000
 B9T  H7   C12  C13  116.87  3.000
 B9T  C14  C12  C13   58.98  3.000
 B9T  H7   C12  C9   114.12  3.000
 B9T  C14  C12  C9   119.77  3.000
 B9T  C13  C12  C9   119.20  3.000
 B9T  H9   C13  H8   114.92  3.000
 B9T  H9   C13  C14  118.72  3.000
 B9T  H8   C13  C14  118.18  3.000
 B9T  H9   C13  C12  116.84  3.000
 B9T  H8   C13  C12  116.96  3.000
 B9T  C14  C13  C12   60.43  3.000
 B9T  H11  C14  H10  115.01  3.000
 B9T  H11  C14  C13  118.13  3.000
 B9T  H10  C14  C13  118.59  3.000
 B9T  H11  C14  C12  116.94  3.000
 B9T  H10  C14  C12  116.78  3.000
 B9T  C13  C14  C12   60.59  3.000
 B9T  C17  C16  O15  124.89  3.000
 B9T  O15  C16  C21  116.46  3.000
 B9T  C17  C16  C21  118.63  3.000
 B9T  C23  C19  C18  120.28  3.000
 B9T  C18  C19  C20  120.03  3.000
 B9T  C23  C19  C20  119.69  3.000
 B9T  H12  C20  C21  120.57  3.000
 B9T  H12  C20  C19  119.95  3.000
 B9T  C21  C20  C19  119.48  3.000
 B9T  BR2  C21  C20  119.64  3.000
 B9T  BR2  C21  C16  119.26  3.000
 B9T  C20  C21  C16  121.10  3.000
 B9T  H13  N25  C26  119.14  3.000
 B9T  H13  N25  C2   117.33  3.000
 B9T  C26  N25  C2   123.50  3.000
 B9T  H14  C4   O15  111.36  3.000
 B9T  H14  C4   C6   108.27  3.000
 B9T  O15  C4   C6   108.38  3.000
 B9T  H14  C4   C2   109.03  3.000
 B9T  C6   C4   C2   111.43  3.000
 B9T  O15  C4   C2   108.39  3.000
 B9T  C4   C6   C11  121.17  3.000
 B9T  C11  C6   C7   115.32  3.000
 B9T  C4   C6   C7   123.38  3.000
 B9T  C9   N8   C7   117.42  3.000
 B9T  C11  N10  C9   117.31  3.000
 B9T  C4   O15  C16  122.74  3.000
 B9T  H15  C17  C18  118.35  3.000
 B9T  H15  C17  C16  121.02  3.000
 B9T  C18  C17  C16  120.63  3.000
 B9T  H16  C18  C17  119.44  3.000
 B9T  H16  C18  C19  120.42  3.000
 B9T  C17  C18  C19  120.14  3.000
 B9T  N24  C23  C19  180.00  3.000
 B9T  C28  C26  O27  118.43  3.000
 B9T  C28  C26  N25  116.14  3.000
 B9T  O27  C26  N25  125.43  3.000
 B9T  F31  C28  F30  105.73  3.000
 B9T  F31  C28  C29  110.57  3.000
 B9T  F30  C28  C29  110.21  3.000
 B9T  F31  C28  C26  106.66  3.000
 B9T  C29  C28  C26  112.99  3.000
 B9T  F30  C28  C26  110.38  3.000
 B9T  H19  C29  H18  108.89  3.000
 B9T  H19  C29  H17  108.22  3.000
 B9T  H18  C29  H17  108.59  3.000
 B9T  H19  C29  C28  110.33  3.000
 B9T  H18  C29  C28  110.23  3.000
 B9T  H17  C29  C28  110.52  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
 B9T  CONST_01  N10  C11  C6   C7      0.00   0.0  0
 B9T  CONST_02  N10  C9   N8   C7      0.00   0.0  0
 B9T  CONST_03  C6   C11  N10  C9      0.00   0.0  0
 B9T  CONST_04  C6   C7   N8   C9      0.00   0.0  0
 B9T  CONST_05  N8   C7   C6   C11     0.00   0.0  0
 B9T  CONST_06  N8   C9   N10  C11     0.00   0.0  0
 B9T  CONST_07  C19  C20  C21  C16     0.00   0.0  0
 B9T  CONST_08  C19  C18  C17  C16     0.00   0.0  0
 B9T  CONST_09  C17  C18  C19  C20     0.00   0.0  0
 B9T  CONST_10  C17  C16  C21  C20     0.00   0.0  0
 B9T  CONST_11  C18  C19  C20  C21     0.00   0.0  0
 B9T  CONST_12  C18  C17  C16  C21     0.00   0.0  0
 B9T  CONST_13  C12  C9   N8   C7    180.00   0.0  0
 B9T  CONST_14  C12  C9   N10  C11   180.00   0.0  0
 B9T  CONST_15  BR2  C21  C20  C19   180.00   0.0  0
 B9T  CONST_16  O15  C16  C21  C20   180.00   0.0  0
 B9T  CONST_17  C23  C19  C20  C21   180.00   0.0  0
 B9T  CONST_18  N10  C11  C6   C4    180.00   0.0  0
 B9T  CONST_19  N8   C7   C6   C4    180.00   0.0  0
 B9T  CONST_20  C18  C17  C16  O15   180.00   0.0  0
 B9T  CONST_21  C23  C19  C18  C17   180.00   0.0  0
 B9T  CONST_22  BR2  C21  C16  C17   180.00   0.0  0
 B9T  CONST_23  H6   C11  C6   C7    180.00   0.0  0
 B9T  CONST_24  H5   C7   N8   C9    180.00   0.0  0
 B9T  CONST_25  H12  C20  C21  C16   180.00   0.0  0
 B9T  CONST_26  H16  C18  C17  C16   180.00   0.0  0
 B9T  CONST_27  H15  C17  C18  C19   180.00   0.0  0
 B9T  CONST_28  O27  C26  N25  C2      0.00   0.0  0
 B9T  CONST_29  C28  C26  N25  C2    180.00   0.0  0
 B9T  CONST_30  H13  N25  C26  O27   180.00   0.0  0
 B9T  Var_01    C14  C13  C12  C9   -109.13  30.0  1
 B9T  Var_02    N10  C9   C12  C13    37.55  30.0  2
 B9T  Var_03    C17  C16  O15  C4    -21.32  30.0  3
 B9T  Var_04    F30  C28  C26  N25    -2.47  30.0  3
 B9T  Var_05    H17  C29  C28  C26    59.18  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
 B9T  chir_01  C2   C4   C1   N25  positiv
 B9T  chir_03  C4   O15  C2   C6   negativ
 B9T  chir_04  C12  C9   C13  C14  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
 B9T  plan-1  C16  0.020
 B9T  plan-1  C19  0.020
 B9T  plan-1  C20  0.020
 B9T  plan-1  C21  0.020
 B9T  plan-1  O15  0.020
 B9T  plan-1  C17  0.020
 B9T  plan-1  C18  0.020
 B9T  plan-1  BR2  0.020
 B9T  plan-1  C23  0.020
 B9T  plan-1  N24  0.020
 B9T  plan-1  H12  0.020
 B9T  plan-1  H15  0.020
 B9T  plan-1  H16  0.020
 B9T  plan-2  C7   0.020
 B9T  plan-2  C9   0.020
 B9T  plan-2  C11  0.020
 B9T  plan-2  C12  0.020
 B9T  plan-2  C4   0.020
 B9T  plan-2  C6   0.020
 B9T  plan-2  N8   0.020
 B9T  plan-2  N10  0.020
 B9T  plan-2  H5   0.020
 B9T  plan-2  H6   0.020
 B9T  plan-3  C2   0.020
 B9T  plan-3  N25  0.020
 B9T  plan-3  C26  0.020
 B9T  plan-3  O27  0.020
 B9T  plan-3  C28  0.020
 B9T  plan-3  H13  0.020

