# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 07:28:41 2020
#   Inital geometry file: a 151 line input string
#   Ligand name: N-[4-(4-bromophenyl)-1-{[2-(trifluoromethyl)phenyl]methyl}piperidine-4-carbonyl]-3-cyclopropyl-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H](CC1CC1)NC(=O)C2(CCN(CC2)Cc3ccccc3C(F)(F)F)c4ccc(Br)cc4
#
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
 BQA  BQA  N-[4-(4-bromophenyl)-1-{[2-(trifluoromethyl)phenyl]methyl}piperidine-4-carbonyl]-3-cyclopropyl-L-alanine  ligand  62  35  .  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_BQA
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
 BQA  N1   N   NT     0  -0.393  -2.5896  -0.2837   0.0762
 BQA  C2   C   CH2    0  -0.455   3.1442  -3.9572   0.4905
 BQA  C4   C   CH2    0  -0.498   5.4254  -2.7534   0.8866
 BQA  C7   C   CT     0  -0.319   0.3411  -0.1872  -0.2630
 BQA  C6   C   C      0   0.416   0.7628  -4.8173   0.2098
 BQA  C9   C   C1     0  -0.335   2.1022   1.2109   0.9634
 BQA  C10  C   C1     0  -0.204   3.2766   1.9537   0.9822
 BQA  C11  C   C      0  -0.132   3.9929   2.1166  -0.1902
 BQA  F2   F   F      0  -0.304  -3.8935   1.7180   1.7318
 BQA  F    F   F      0  -0.319  -5.5376   0.4767   2.3500
 BQA  F1   F   F      0  -0.305  -5.8482   2.5615   1.9585
 BQA  C22  C   CR6    0  -0.266  -5.5140   1.1555   0.0911
 BQA  C21  C   CR16   0  -0.282  -6.4357   1.9567  -0.5749
 BQA  C20  C   CR16   0  -0.254  -6.8114   1.6731  -1.8803
 BQA  C19  C   CR16   0  -0.234  -6.2667   0.5769  -2.5254
 BQA  C18  C   CR16   0  -0.301  -5.3464  -0.2204  -1.8604
 BQA  C17  C   CR6    0   0.157  -4.9460   0.0461  -0.5557
 BQA  C16  C   CH2    0  -0.384  -3.9161  -0.8674   0.0679
 BQA  C15  C   CH2    0  -0.290  -1.7065  -0.9891   0.9846
 BQA  C14  C   CH2    0  -0.474  -0.3735  -0.2696   1.0925
 BQA  C24  C   CH2    0  -0.287  -2.0124  -0.2036  -1.2504
 BQA  C25  C   CH2    0  -0.398  -0.6529   0.4809  -1.2272
 BQA  C8   C   C      0   0.209   1.6279   0.6290  -0.2074
 BQA  C13  C   C1     0  -0.282   2.3756   0.8128  -1.3721
 BQA  C12  C   C1     0  -0.216   3.5492   1.5478  -1.3756
 BQA  BR   BR  BR     0  -0.056   5.5952   3.1184  -0.1771
 BQA  C    C   C      0   0.606   0.7471  -1.5814  -0.7935
 BQA  O    O   O      0  -0.506   0.6105  -1.8811  -1.9746
 BQA  N    N   NH1    0  -0.593   1.3201  -2.3906   0.0987
 BQA  C1   C   CH1    0  -0.221   1.7891  -3.7243  -0.1835
 BQA  C3   C   CH1    0  -0.213   4.1898  -2.9598   0.0628
 BQA  C5   C   CH2    0  -0.469   4.3801  -1.6799   0.8126
 BQA  H2   H   HCH2   0   0.218   3.0285  -3.9246   1.5808
 BQA  H3   H   HCH2   0   0.237   3.4703  -4.9696   0.2469
 BQA  H4   H   HCH2   0   0.235   5.5171  -3.3114   1.8113
 BQA  H5   H   HCH2   0   0.242   6.3652  -2.5936   0.3733
 BQA  H6   H   H      0   0.264   1.5678   1.0985   1.8963
 BQA  H7   H   H      0   0.277   3.6166   2.3901   1.9118
 BQA  H8   H   HCR6   0   0.270  -6.8808   2.8103  -0.0846
 BQA  H9   H   HCR6   0   0.267  -7.5300   2.3073  -2.3815
 BQA  H10  H   HCR6   0   0.266  -6.5533   0.3397  -3.5414
 BQA  H11  H   HCR6   0   0.262  -4.9200  -1.0776  -2.3678
 BQA  H12  H   HCH2   0   0.224  -3.9382  -1.8257  -0.4777
 BQA  H13  H   HCH2   0   0.252  -4.1893  -1.1085   1.0955
 BQA  H14  H   HCH2   0   0.236  -2.1713  -1.0154   1.9731
 BQA  H15  H   HCH2   0   0.217  -1.5432  -2.0387   0.6855
 BQA  H16  H   HCH2   0   0.241   0.2315  -0.7456   1.8679
 BQA  H17  H   HCH2   0   0.249  -0.5649   0.7466   1.4473
 BQA  H18  H   HCH2   0   0.194  -1.9245  -1.2022  -1.7100
 BQA  H19  H   HCH2   0   0.242  -2.6741   0.3792  -1.8948
 BQA  H20  H   HCH2   0   0.234  -0.7880   1.5156  -0.9008
 BQA  H21  H   HCH2   0   0.242  -0.2566   0.5189  -2.2417
 BQA  H22  H   H      0   0.261   2.0475   0.3698  -2.3038
 BQA  H23  H   H      0   0.276   4.1038   1.6680  -2.2968
 BQA  H24  H   HNH1   0   0.382   1.3533  -2.0994   1.0608
 BQA  H25  H   HCH1   0   0.242   1.9377  -3.7929  -1.2640
 BQA  H27  H   HCH1   0   0.238   4.3301  -2.8947  -1.0127
 BQA  H28  H   HCH2   0   0.228   3.7657  -1.5124   1.6891
 BQA  H29  H   HCH2   0   0.247   4.5903  -0.7786   0.2513
 BQA  O2   O   O      0  -0.582  -0.3108  -4.4554   0.7194
 BQA  O1   O   OC    -1  -0.617   1.1231  -5.9871  -0.0334
 BQA  C23  C   CT     0   1.055  -5.1903   1.4788   1.5232

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
 BQA  BR   C11  single    1.890  0.020  1.890
 BQA  C4   C5   single    1.500  0.020  1.500
 BQA  C4   C3   single    1.499  0.020  1.499
 BQA  C11  C12  aromatic  1.388  0.020  1.388
 BQA  C11  C10  aromatic  1.383  0.020  1.383
 BQA  C12  C13  aromatic  1.385  0.020  1.385
 BQA  C5   C3   single    1.496  0.020  1.496
 BQA  C3   C2   single    1.507  0.020  1.507
 BQA  C10  C9   aromatic  1.390  0.020  1.390
 BQA  C13  C8   aromatic  1.396  0.020  1.396
 BQA  C2   C1   single    1.531  0.020  1.531
 BQA  C9   C8   aromatic  1.391  0.020  1.391
 BQA  C8   C7   single    1.525  0.020  1.525
 BQA  C1   N    single    1.442  0.020  1.442
 BQA  C1   C6   single    1.550  0.020  1.550
 BQA  O    C    double    1.226  0.020  1.226
 BQA  C    N    single    1.334  0.020  1.334
 BQA  C    C7   single    1.546  0.020  1.546
 BQA  C7   C25  single    1.538  0.020  1.538
 BQA  C7   C14  single    1.535  0.020  1.535
 BQA  O2   C6   deloc     1.242  0.020  1.242
 BQA  C6   O1   deloc     1.248  0.020  1.248
 BQA  C25  C24  single    1.522  0.020  1.522
 BQA  C14  C15  single    1.519  0.020  1.519
 BQA  C24  N1   single    1.449  0.020  1.449
 BQA  C15  N1   single    1.450  0.020  1.450
 BQA  N1   C16  single    1.449  0.020  1.449
 BQA  C16  C17  single    1.511  0.020  1.511
 BQA  F    C23  single    1.345  0.020  1.345
 BQA  C17  C18  aromatic  1.391  0.020  1.391
 BQA  C17  C22  aromatic  1.404  0.020  1.404
 BQA  C18  C19  aromatic  1.387  0.020  1.387
 BQA  C23  C22  single    1.503  0.020  1.503
 BQA  C23  F1   single    1.340  0.020  1.340
 BQA  C23  F2   single    1.335  0.020  1.335
 BQA  C22  C21  aromatic  1.391  0.020  1.391
 BQA  C19  C20  aromatic  1.384  0.020  1.384
 BQA  C21  C20  aromatic  1.388  0.020  1.388
 BQA  C2   H2   single    0.970  0.020  1.090
 BQA  C2   H3   single    0.970  0.020  1.090
 BQA  C4   H4   single    0.970  0.020  1.090
 BQA  C4   H5   single    0.970  0.020  1.090
 BQA  C9   H6   single    0.930  0.020  1.080
 BQA  C10  H7   single    0.930  0.020  1.080
 BQA  C21  H8   single    0.930  0.020  1.080
 BQA  C20  H9   single    0.930  0.020  1.080
 BQA  C19  H10  single    0.930  0.020  1.080
 BQA  C18  H11  single    0.930  0.020  1.080
 BQA  C16  H12  single    0.970  0.020  1.090
 BQA  C16  H13  single    0.970  0.020  1.090
 BQA  C15  H14  single    0.970  0.020  1.090
 BQA  C15  H15  single    0.970  0.020  1.090
 BQA  C14  H16  single    0.970  0.020  1.090
 BQA  C14  H17  single    0.970  0.020  1.090
 BQA  C24  H18  single    0.970  0.020  1.090
 BQA  C24  H19  single    0.970  0.020  1.090
 BQA  C25  H20  single    0.970  0.020  1.090
 BQA  C25  H21  single    0.970  0.020  1.090
 BQA  C13  H22  single    0.930  0.020  1.080
 BQA  C12  H23  single    0.930  0.020  1.080
 BQA  N    H24  single    0.860  0.020  1.020
 BQA  C1   H25  single    0.970  0.020  1.090
 BQA  C3   H27  single    0.970  0.020  1.090
 BQA  C5   H28  single    0.970  0.020  1.090
 BQA  C5   H29  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
 BQA  C24  N1   C15  110.97  3.000
 BQA  C15  N1   C16  111.41  3.000
 BQA  C24  N1   C16  112.44  3.000
 BQA  H3   C2   H2   106.32  3.000
 BQA  H3   C2   C3   110.08  3.000
 BQA  H2   C2   C3   109.60  3.000
 BQA  H3   C2   C1   107.90  3.000
 BQA  H2   C2   C1   109.85  3.000
 BQA  C3   C2   C1   112.86  3.000
 BQA  H5   C4   H4   114.02  3.000
 BQA  H5   C4   C5   118.41  3.000
 BQA  H4   C4   C5   118.00  3.000
 BQA  H5   C4   C3   118.37  3.000
 BQA  H4   C4   C3   117.88  3.000
 BQA  C5   C4   C3    59.81  3.000
 BQA  C    C7   C8   105.88  3.000
 BQA  C    C7   C25  110.27  3.000
 BQA  C8   C7   C25  109.62  3.000
 BQA  C25  C7   C14  106.04  3.000
 BQA  C    C7   C14  112.15  3.000
 BQA  C8   C7   C14  112.93  3.000
 BQA  O1   C6   O2   127.05  3.000
 BQA  O1   C6   C1   114.86  3.000
 BQA  O2   C6   C1   118.09  3.000
 BQA  H6   C9   C8   120.96  3.000
 BQA  H6   C9   C10  117.49  3.000
 BQA  C8   C9   C10  121.55  3.000
 BQA  H7   C10  C11  121.20  3.000
 BQA  H7   C10  C9   119.53  3.000
 BQA  C11  C10  C9   119.28  3.000
 BQA  BR   C11  C12  119.62  3.000
 BQA  C12  C11  C10  120.67  3.000
 BQA  BR   C11  C10  119.71  3.000
 BQA  C17  C22  C21  120.17  3.000
 BQA  C21  C22  C23  118.35  3.000
 BQA  C17  C22  C23  121.44  3.000
 BQA  H8   C21  C20  118.48  3.000
 BQA  H8   C21  C22  120.72  3.000
 BQA  C20  C21  C22  120.80  3.000
 BQA  H9   C20  C19  120.67  3.000
 BQA  H9   C20  C21  119.73  3.000
 BQA  C19  C20  C21  119.60  3.000
 BQA  H10  C19  C18  119.99  3.000
 BQA  H10  C19  C20  120.48  3.000
 BQA  C18  C19  C20  119.53  3.000
 BQA  H11  C18  C17  118.53  3.000
 BQA  H11  C18  C19  119.42  3.000
 BQA  C17  C18  C19  122.05  3.000
 BQA  C16  C17  C18  117.87  3.000
 BQA  C18  C17  C22  117.85  3.000
 BQA  C16  C17  C22  124.27  3.000
 BQA  H13  C16  H12  105.61  3.000
 BQA  H13  C16  C17  110.60  3.000
 BQA  H12  C16  C17  107.90  3.000
 BQA  H13  C16  N1   108.24  3.000
 BQA  H12  C16  N1   111.78  3.000
 BQA  C17  C16  N1   112.50  3.000
 BQA  H15  C15  H14  106.58  3.000
 BQA  H15  C15  C14  109.88  3.000
 BQA  H14  C15  C14  108.69  3.000
 BQA  H15  C15  N1   112.52  3.000
 BQA  H14  C15  N1   108.62  3.000
 BQA  C14  C15  N1   110.40  3.000
 BQA  H17  C14  H16  105.76  3.000
 BQA  H17  C14  C15  108.05  3.000
 BQA  H16  C14  C15  109.27  3.000
 BQA  H17  C14  C7   108.56  3.000
 BQA  H16  C14  C7   113.10  3.000
 BQA  C15  C14  C7   111.80  3.000
 BQA  H19  C24  H18  106.60  3.000
 BQA  H19  C24  C25  108.07  3.000
 BQA  H18  C24  C25  110.02  3.000
 BQA  H19  C24  N1   109.17  3.000
 BQA  H18  C24  N1   111.30  3.000
 BQA  C25  C24  N1   111.51  3.000
 BQA  H21  C25  H20  106.85  3.000
 BQA  H21  C25  C24  109.04  3.000
 BQA  H20  C25  C24  108.65  3.000
 BQA  H21  C25  C7   111.34  3.000
 BQA  H20  C25  C7   107.69  3.000
 BQA  C24  C25  C7   113.05  3.000
 BQA  C13  C8   C9   117.68  3.000
 BQA  C9   C8   C7   122.85  3.000
 BQA  C13  C8   C7   119.47  3.000
 BQA  H22  C13  C12  118.16  3.000
 BQA  H22  C13  C8   120.12  3.000
 BQA  C12  C13  C8   121.72  3.000
 BQA  H23  C12  C13  119.70  3.000
 BQA  H23  C12  C11  121.19  3.000
 BQA  C13  C12  C11  119.11  3.000
 BQA  N    C    O    122.95  3.000
 BQA  N    C    C7   115.49  3.000
 BQA  O    C    C7   121.45  3.000
 BQA  H24  N    C1   116.38  3.000
 BQA  H24  N    C    118.58  3.000
 BQA  C1   N    C    124.75  3.000
 BQA  H25  C1   N    107.21  3.000
 BQA  H25  C1   C6   107.25  3.000
 BQA  N    C1   C6   112.79  3.000
 BQA  H25  C1   C2   107.78  3.000
 BQA  C6   C1   C2   111.53  3.000
 BQA  N    C1   C2   110.03  3.000
 BQA  H27  C3   C5   115.38  3.000
 BQA  H27  C3   C4   115.41  3.000
 BQA  C5   C3   C4    60.12  3.000
 BQA  H27  C3   C2   114.21  3.000
 BQA  C5   C3   C2   120.83  3.000
 BQA  C4   C3   C2   120.47  3.000
 BQA  H29  C5   H28  113.64  3.000
 BQA  H29  C5   C3   118.51  3.000
 BQA  H28  C5   C3   117.76  3.000
 BQA  H29  C5   C4   119.08  3.000
 BQA  H28  C5   C4   117.76  3.000
 BQA  C3   C5   C4    60.07  3.000
 BQA  C22  C23  F1   112.19  3.000
 BQA  F1   C23  F    106.00  3.000
 BQA  C22  C23  F    111.70  3.000
 BQA  F1   C23  F2   106.35  3.000
 BQA  C22  C23  F2   113.36  3.000
 BQA  F    C23  F2   106.75  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
 BQA  CONST_01  C12  C11  C10  C9      0.00   0.0  0
 BQA  CONST_02  C12  C13  C8   C9      0.00   0.0  0
 BQA  CONST_03  C13  C12  C11  C10     0.00   0.0  0
 BQA  CONST_04  C13  C8   C9   C10     0.00   0.0  0
 BQA  CONST_05  C8   C13  C12  C11     0.00   0.0  0
 BQA  CONST_06  C8   C9   C10  C11     0.00   0.0  0
 BQA  CONST_07  C19  C18  C17  C22     0.00   0.0  0
 BQA  CONST_08  C19  C20  C21  C22     0.00   0.0  0
 BQA  CONST_09  C18  C17  C22  C21     0.00   0.0  0
 BQA  CONST_10  C18  C19  C20  C21     0.00   0.0  0
 BQA  CONST_11  C17  C18  C19  C20     0.00   0.0  0
 BQA  CONST_12  C17  C22  C21  C20     0.00   0.0  0
 BQA  CONST_13  C12  C13  C8   C7    180.00   0.0  0
 BQA  CONST_14  C10  C9   C8   C7    180.00   0.0  0
 BQA  CONST_15  BR   C11  C10  C9    180.00   0.0  0
 BQA  CONST_16  C18  C17  C22  C23   180.00   0.0  0
 BQA  CONST_17  C20  C21  C22  C23   180.00   0.0  0
 BQA  CONST_18  C16  C17  C22  C21   180.00   0.0  0
 BQA  CONST_19  C16  C17  C18  C19   180.00   0.0  0
 BQA  CONST_20  BR   C11  C12  C13   180.00   0.0  0
 BQA  CONST_21  H22  C13  C8   C7      0.00   0.0  0
 BQA  CONST_22  H6   C9   C8   C7      0.00   0.0  0
 BQA  CONST_23  H23  C12  C11  C10   180.00   0.0  0
 BQA  CONST_24  H11  C18  C17  C22   180.00   0.0  0
 BQA  CONST_25  H9   C20  C21  C22   180.00   0.0  0
 BQA  CONST_26  H10  C19  C20  C21   180.00   0.0  0
 BQA  CONST_27  H8   C21  C20  C19   180.00   0.0  0
 BQA  CONST_28  H7   C10  C9   C8    180.00   0.0  0
 BQA  CONST_29  C1   N    C    C7    180.00   0.0  0
 BQA  CONST_30  H24  N    C    C7      0.00   0.0  0
 BQA  CONST_31  C1   N    C    O       0.00   0.0  0
 BQA  Var_01    C7   C25  C24  N1     55.55  30.0  1
 BQA  Var_02    C7   C14  C15  N1    -60.74  30.0  1
 BQA  Var_03    C25  C24  N1   C15   -57.57  30.0  1
 BQA  Var_04    C24  N1   C15  C14    60.15  30.0  1
 BQA  Var_05    C18  C17  C16  N1    101.81  30.0  2
 BQA  Var_06    C5   C4   C3   C2   -110.35  30.0  1
 BQA  Var_07    C1   C2   C3   C4    161.51  30.0  3
 BQA  Var_08    C17  C22  C23  F2     60.45  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
 BQA  chir_01  C7  C8  C25  C14  positiv
 BQA  chir_02  C1  N   C2   C6   negativ
 BQA  chir_03  C3  C4  C5   C2   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
 BQA  plan-1  C7   0.020
 BQA  plan-1  C9   0.020
 BQA  plan-1  C10  0.020
 BQA  plan-1  C11  0.020
 BQA  plan-1  C8   0.020
 BQA  plan-1  C13  0.020
 BQA  plan-1  C12  0.020
 BQA  plan-1  BR   0.020
 BQA  plan-1  H6   0.020
 BQA  plan-1  H7   0.020
 BQA  plan-1  H22  0.020
 BQA  plan-1  H23  0.020
 BQA  plan-2  C22  0.020
 BQA  plan-2  C21  0.020
 BQA  plan-2  C20  0.020
 BQA  plan-2  C19  0.020
 BQA  plan-2  C18  0.020
 BQA  plan-2  C17  0.020
 BQA  plan-2  C16  0.020
 BQA  plan-2  H8   0.020
 BQA  plan-2  H9   0.020
 BQA  plan-2  H10  0.020
 BQA  plan-2  H11  0.020
 BQA  plan-2  C23  0.020
 BQA  plan-3  C6   0.020
 BQA  plan-3  C1   0.020
 BQA  plan-3  O2   0.020
 BQA  plan-3  O1   0.020
 BQA  plan-4  C7   0.020
 BQA  plan-4  C    0.020
 BQA  plan-4  O    0.020
 BQA  plan-4  N    0.020
 BQA  plan-4  C1   0.020
 BQA  plan-4  H24  0.020

