# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 15:01:22 2021
#   Inital geometry file: a 119 line input string
#   Ligand name: 3-chloro-N-(3-{(2S)-1-[(4-fluorophenyl)amino]-1-oxopropan-2-yl}bicyclo[1.1.1]pentan-1-yl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](C(=O)Nc1ccc(F)cc1)C23CC(C2)(C3)NC(=O)c4cccc(Cl)c4
#
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
 U41  U41  3-chloro-N-(3-{(2S)-1-[(4-fluorophenyl)amino]-1-oxopropan-2-yl}bicyclo[1.1.1]pentan-1-yl)benzamide  ligand  47  27  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U41
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
 U41  C2    C   C     0   0.525  65.1193  50.0182  13.2812
 U41  C4    C   CT    0   0.282  62.9394  50.6126  14.1662
 U41  C5    C   CH2   0  -0.453  63.0136  50.8856  15.6828
 U41  C6    C   CT    0   0.112  61.7571  51.6208  15.1668
 U41  C7    C   CH2   0  -0.455  62.6039  52.1037  13.9680
 U41  C8    C   CH2   0  -0.474  61.4386  50.3525  14.3407
 U41  C11   C   C     0   0.549  60.1214  51.5298  16.9785
 U41  N13   N   NH1   0  -0.736  58.9319  51.0163  16.5730
 U41  C15   C   CR16  0  -0.307  56.7411  50.2549  17.1913
 U41  C16   C   CR16  0  -0.404  55.8909  49.3700  17.8352
 U41  C17   C   CR6   0   0.514  56.4414  48.3508  18.5865
 U41  C19   C   CR16  0  -0.407  57.8080  48.1875  18.6967
 U41  C21   C   CR6   0  -0.048  65.8859  49.0772  12.4038
 U41  C23   C   CR16  0  -0.247  67.9860  48.0171  11.8916
 U41  C24   C   CR16  0  -0.211  67.4090  47.3624  10.8126
 U41  C27   C   CR16  0  -0.258  65.3006  48.4318  11.3179
 U41  O1    O   O     0  -0.471  65.6837  50.9235  13.8758
 U41  N3    N   NH1   0  -0.739  63.7968  49.7969  13.3795
 U41  C9    C   CH1   0  -0.466  60.7806  52.4489  15.9656
 U41  C10   C   CH3   0  -0.661  61.4620  53.6297  16.6433
 U41  O12   O   O     0  -0.464  60.6471  51.2461  18.0389
 U41  C14   C   CR6   0   0.348  58.1242  50.1152  17.2840
 U41  C20   C   CR16  0  -0.274  58.6527  49.0690  18.0383
 U41  C22   C   CR16  0  -0.262  67.2363  48.8774  12.6773
 U41  C25   C   CR6   0  -0.022  66.0696  47.5851  10.5362
 U41  CL26  CL  CL    0  -0.119  65.3379  46.7959   9.1785
 U41  H1    H   HCH2  0   0.235  62.8461  50.0306  16.3405
 U41  H2    H   HCH2  0   0.239  63.8421  51.5030  16.0291
 U41  H3    H   HCH2  0   0.241  63.4005  52.8178  14.1781
 U41  H4    H   HCH2  0   0.236  62.0564  52.3649  13.0601
 U41  H5    H   HCH2  0   0.242  60.8061  50.4893  13.4609
 U41  H6    H   HCH2  0   0.240  61.1593  49.4572  14.9000
 U41  H7    H   HNH1  0   0.411  58.5277  51.4065  15.7356
 U41  H8    H   HCR6  0   0.280  56.3196  51.0665  16.6113
 U41  H9    H   HCR6  0   0.283  54.8176  49.4832  17.7580
 U41  H10   H   HCR6  0   0.283  58.2182  47.3730  19.2792
 U41  H11   H   HCR6  0   0.276  69.0312  47.8525  12.1157
 U41  H12   H   HCR6  0   0.288  67.9948  46.6941  10.1966
 U41  H13   H   HCR6  0   0.282  64.2635  48.5960  11.0558
 U41  H14   H   HNH1  0   0.411  63.3874  48.9892  12.9393
 U41  H15   H   HCH1  0   0.261  60.0256  52.8326  15.2705
 U41  H16   H   HCH3  0   0.242  60.7399  54.2480  17.1769
 U41  H17   H   HCH3  0   0.232  62.2181  53.3027  17.3556
 U41  H18   H   HCH3  0   0.239  61.9508  54.2588  15.8998
 U41  H19   H   HCR6  0   0.277  59.7190  48.9191  18.1095
 U41  H20   H   HCR6  0   0.267  67.6986  49.3871  13.5113
 U41  F18   F   F     0  -0.317  55.6262  47.4932  19.2235

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
 U41  CL26  C25  single    1.732  0.020  1.732
 U41  C25   C24  aromatic  1.386  0.020  1.386
 U41  C25   C27  aromatic  1.385  0.020  1.385
 U41  C24   C23  aromatic  1.388  0.020  1.388
 U41  C27   C21  aromatic  1.392  0.020  1.392
 U41  C23   C22  aromatic  1.385  0.020  1.385
 U41  C21   C22  aromatic  1.392  0.020  1.392
 U41  C21   C2   single    1.498  0.020  1.498
 U41  N3    C2   single    1.344  0.020  1.344
 U41  N3    C4   single    1.421  0.020  1.421
 U41  C2    O1   double    1.221  0.020  1.221
 U41  C7    C4   single    1.541  0.020  1.541
 U41  C7    C6   single    1.545  0.020  1.545
 U41  C4    C8   single    1.533  0.020  1.533
 U41  C4    C5   single    1.543  0.020  1.543
 U41  C8    C6   single    1.547  0.020  1.547
 U41  C6    C5   single    1.545  0.020  1.545
 U41  C6    C9   single    1.509  0.020  1.509
 U41  C9    C10  single    1.522  0.020  1.522
 U41  C9    C11  single    1.518  0.020  1.518
 U41  N13   C11  single    1.358  0.020  1.358
 U41  N13   C14  single    1.404  0.020  1.404
 U41  C11   O12  double    1.217  0.020  1.217
 U41  C15   C14  aromatic  1.393  0.020  1.393
 U41  C15   C16  aromatic  1.386  0.020  1.386
 U41  C14   C20  aromatic  1.394  0.020  1.394
 U41  C16   C17  aromatic  1.381  0.020  1.381
 U41  C20   C19  aromatic  1.387  0.020  1.387
 U41  C17   C19  aromatic  1.381  0.020  1.381
 U41  C17   F18  single    1.344  0.020  1.344
 U41  C5    H1   single    0.970  0.020  1.090
 U41  C5    H2   single    0.970  0.020  1.090
 U41  C7    H3   single    0.970  0.020  1.090
 U41  C7    H4   single    0.970  0.020  1.090
 U41  C8    H5   single    0.970  0.020  1.090
 U41  C8    H6   single    0.970  0.020  1.090
 U41  N13   H7   single    0.860  0.020  1.020
 U41  C15   H8   single    0.930  0.020  1.080
 U41  C16   H9   single    0.930  0.020  1.080
 U41  C19   H10  single    0.930  0.020  1.080
 U41  C23   H11  single    0.930  0.020  1.080
 U41  C24   H12  single    0.930  0.020  1.080
 U41  C27   H13  single    0.930  0.020  1.080
 U41  N3    H14  single    0.860  0.020  1.020
 U41  C9    H15  single    0.970  0.020  1.090
 U41  C10   H16  single    0.970  0.020  1.090
 U41  C10   H17  single    0.970  0.020  1.090
 U41  C10   H18  single    0.970  0.020  1.090
 U41  C20   H19  single    0.930  0.020  1.080
 U41  C22   H20  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
 U41  N3    C2   O1   122.75  3.000
 U41  O1    C2   C21  120.96  3.000
 U41  N3    C2   C21  116.29  3.000
 U41  N3    C4   C8   123.80  3.000
 U41  C8    C4   C7    88.03  3.000
 U41  N3    C4   C7   127.99  3.000
 U41  C8    C4   C5    88.01  3.000
 U41  C7    C4   C5    88.04  3.000
 U41  N3    C4   C5   128.08  3.000
 U41  H2    C5   H1   111.65  3.000
 U41  H2    C5   C6   117.06  3.000
 U41  H1    C5   C6   116.69  3.000
 U41  H2    C5   C4   116.69  3.000
 U41  H1    C5   C4   116.51  3.000
 U41  C6    C5   C4    73.54  3.000
 U41  C9    C6   C8   126.83  3.000
 U41  C9    C6   C7   126.43  3.000
 U41  C8    C6   C7    87.41  3.000
 U41  C9    C6   C5   127.64  3.000
 U41  C8    C6   C5    87.46  3.000
 U41  C7    C6   C5    87.83  3.000
 U41  H4    C7   H3   111.71  3.000
 U41  H4    C7   C6   116.43  3.000
 U41  H3    C7   C6   117.11  3.000
 U41  H4    C7   C4   116.58  3.000
 U41  H3    C7   C4   116.73  3.000
 U41  C6    C7   C4    73.57  3.000
 U41  H6    C8   H5   111.54  3.000
 U41  H6    C8   C6   116.84  3.000
 U41  H5    C8   C6   116.54  3.000
 U41  H6    C8   C4   116.60  3.000
 U41  H5    C8   C4   117.00  3.000
 U41  C6    C8   C4    73.75  3.000
 U41  O12   C11  C9   122.33  3.000
 U41  O12   C11  N13  123.41  3.000
 U41  C9    C11  N13  114.21  3.000
 U41  H7    N13  C14  116.01  3.000
 U41  H7    N13  C11  116.93  3.000
 U41  C14   N13  C11  126.56  3.000
 U41  H8    C15  C14  119.81  3.000
 U41  H8    C15  C16  119.26  3.000
 U41  C14   C15  C16  120.93  3.000
 U41  H9    C16  C17  120.77  3.000
 U41  H9    C16  C15  120.57  3.000
 U41  C17   C16  C15  118.66  3.000
 U41  F18   C17  C19  119.15  3.000
 U41  F18   C17  C16  119.15  3.000
 U41  C19   C17  C16  121.70  3.000
 U41  H10   C19  C20  120.20  3.000
 U41  H10   C19  C17  120.48  3.000
 U41  C20   C19  C17  119.32  3.000
 U41  C22   C21  C27  119.64  3.000
 U41  C22   C21  C2   118.14  3.000
 U41  C27   C21  C2   122.21  3.000
 U41  H11   C23  C22  119.99  3.000
 U41  H11   C23  C24  119.42  3.000
 U41  C22   C23  C24  120.59  3.000
 U41  H12   C24  C25  120.62  3.000
 U41  H12   C24  C23  120.61  3.000
 U41  C25   C24  C23  118.77  3.000
 U41  H13   C27  C25  119.20  3.000
 U41  H13   C27  C21  121.43  3.000
 U41  C25   C27  C21  119.35  3.000
 U41  H14   N3   C4   117.20  3.000
 U41  H14   N3   C2   120.00  3.000
 U41  C4    N3   C2   122.65  3.000
 U41  H15   C9   C10  108.62  3.000
 U41  H15   C9   C11  109.64  3.000
 U41  C10   C9   C11  111.53  3.000
 U41  H15   C9   C6   107.59  3.000
 U41  C11   C9   C6   107.57  3.000
 U41  C10   C9   C6   111.81  3.000
 U41  H18   C10  H17  107.95  3.000
 U41  H18   C10  H16  107.68  3.000
 U41  H17   C10  H16  108.06  3.000
 U41  H18   C10  C9   110.17  3.000
 U41  H17   C10  C9   111.65  3.000
 U41  H16   C10  C9   111.18  3.000
 U41  C20   C14  C15  119.19  3.000
 U41  C20   C14  N13  122.54  3.000
 U41  C15   C14  N13  118.24  3.000
 U41  H19   C20  C14  120.97  3.000
 U41  H19   C20  C19  118.82  3.000
 U41  C14   C20  C19  120.20  3.000
 U41  H20   C22  C23  119.92  3.000
 U41  H20   C22  C21  119.91  3.000
 U41  C23   C22  C21  120.17  3.000
 U41  CL26  C25  C27  119.09  3.000
 U41  C27   C25  C24  121.48  3.000
 U41  CL26  C25  C24  119.43  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
 U41  CONST_01  C19   C20  C14  C15    0.00   0.0  0
 U41  CONST_02  C19   C17  C16  C15    0.00   0.0  0
 U41  CONST_03  C20   C14  C15  C16    0.00   0.0  0
 U41  CONST_04  C20   C19  C17  C16    0.00   0.0  0
 U41  CONST_05  C14   C15  C16  C17    0.00   0.0  0
 U41  CONST_06  C14   C20  C19  C17    0.00   0.0  0
 U41  CONST_07  C24   C25  C27  C21    0.00   0.0  0
 U41  CONST_08  C24   C23  C22  C21    0.00   0.0  0
 U41  CONST_09  C27   C25  C24  C23    0.00   0.0  0
 U41  CONST_10  C27   C21  C22  C23    0.00   0.0  0
 U41  CONST_11  C25   C24  C23  C22    0.00   0.0  0
 U41  CONST_12  C25   C27  C21  C22    0.00   0.0  0
 U41  CONST_13  C25   C27  C21  C2   180.00   0.0  0
 U41  CONST_14  C23   C22  C21  C2   180.00   0.0  0
 U41  CONST_15  C16   C15  C14  N13  180.00   0.0  0
 U41  CONST_16  C19   C20  C14  N13  180.00   0.0  0
 U41  CONST_17  F18   C17  C16  C15  180.00   0.0  0
 U41  CONST_18  CL26  C25  C27  C21  180.00   0.0  0
 U41  CONST_19  CL26  C25  C24  C23  180.00   0.0  0
 U41  CONST_20  C20   C19  C17  F18  180.00   0.0  0
 U41  CONST_21  H19   C20  C14  C15  180.00   0.0  0
 U41  CONST_22  H10   C19  C17  C16  180.00   0.0  0
 U41  CONST_23  H8    C15  C16  C17  180.00   0.0  0
 U41  CONST_24  H9    C16  C17  C19  180.00   0.0  0
 U41  CONST_25  H11   C23  C22  C21  180.00   0.0  0
 U41  CONST_26  H13   C27  C25  C24  180.00   0.0  0
 U41  CONST_27  H20   C22  C23  C24  180.00   0.0  0
 U41  CONST_28  H12   C24  C25  C27  180.00   0.0  0
 U41  CONST_29  C21   C2   N3   C4   180.00   0.0  0
 U41  CONST_33  O1    C2   N3   C4     0.00   0.0  0
 U41  CONST_34  C14   N13  C11  C9   180.00   0.0  0
 U41  CONST_35  C14   N13  C11  O12    0.00   0.0  0
 U41  CONST_36  H14   N3   C2   C21    0.00   0.0  0
 U41  Var_01    N3    C2   C21  C27   28.15  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
 U41  chir_01  C4  C7  C8   C5   positiv
 U41  chir_02  C6  C8  C5   C9   positiv
 U41  chir_03  C9  C6  C10  C11  positiv

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
 U41  plan-1  N13   0.020
 U41  plan-1  C15   0.020
 U41  plan-1  C16   0.020
 U41  plan-1  C17   0.020
 U41  plan-1  C19   0.020
 U41  plan-1  C14   0.020
 U41  plan-1  C20   0.020
 U41  plan-1  H8    0.020
 U41  plan-1  H9    0.020
 U41  plan-1  H10   0.020
 U41  plan-1  H19   0.020
 U41  plan-1  F18   0.020
 U41  plan-2  C2    0.020
 U41  plan-2  C21   0.020
 U41  plan-2  C23   0.020
 U41  plan-2  C24   0.020
 U41  plan-2  C27   0.020
 U41  plan-2  C22   0.020
 U41  plan-2  C25   0.020
 U41  plan-2  CL26  0.020
 U41  plan-2  H11   0.020
 U41  plan-2  H12   0.020
 U41  plan-2  H13   0.020
 U41  plan-2  H20   0.020
 U41  plan-3  C2    0.020
 U41  plan-3  C4    0.020
 U41  plan-3  C21   0.020
 U41  plan-3  O1    0.020
 U41  plan-3  N3    0.020
 U41  plan-3  H14   0.020
 U41  plan-4  C11   0.020
 U41  plan-4  N13   0.020
 U41  plan-4  C9    0.020
 U41  plan-4  O12   0.020
 U41  plan-4  C14   0.020
 U41  plan-4  H7    0.020

