# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 12:02:51 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: 2-[(2~{R},3~{S},4~{R},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)-1-[3-[3-(trifluoromethyl)phenyl]propyl]pyrrolidin-2-yl]-~{N}-methyl-ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)C[C@@H]1[C@H](O)[C@H](O)[C@@H](CO)N1CCCc2cccc(c2)C(F)(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
 XHA  XHA  2-[(2~{R},3~{S},4~{R},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)-1-[3-[3-(trifluoromethyl)phenyl]propyl]pyrrolidin-2-yl]-~{N}-methyl-ethanamide  ligand  52  27  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_XHA
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
 XHA  C4   C  CH1   0  -0.043  -3.2056   1.0740  -0.3158
 XHA  C14  C  CR16  0  -0.222   3.5365  -2.7375   1.3429
 XHA  C5   C  CH1   0  -0.017  -4.5311   1.1270   0.4358
 XHA  C6   C  CH1   0  -0.012  -5.0676  -0.2834   0.2156
 XHA  C11  C  CH2   0  -0.522   0.7870  -1.4695  -0.9484
 XHA  C7   C  CH1   0  -0.030  -3.8202  -1.1534   0.3689
 XHA  C8   C  CH2   0  -0.213  -3.9662  -2.5090  -0.2962
 XHA  C10  C  CH2   0  -0.416  -0.3789  -1.0102  -0.0710
 XHA  C12  C  CR6   0   0.163   2.0674  -1.5569  -0.1717
 XHA  C13  C  CR16  0  -0.302   2.3805  -2.6883   0.5808
 XHA  N1   N  NH1   0  -0.624   0.1172   2.6024  -0.2517
 XHA  N2   N  NT    0  -0.474  -2.7568  -0.2935  -0.1215
 XHA  C3   C  CH2   0  -0.570  -2.2169   2.1354   0.1728
 XHA  C1   C  CH3   0  -0.524   1.2763   2.9805  -1.0235
 XHA  C2   C  C     0   0.547  -1.0974   2.4454  -0.7996
 XHA  O1   O  O     0  -0.504  -1.2919   2.5872  -2.0012
 XHA  O2   O  OH1   0  -0.675  -4.3108   1.3673   1.8056
 XHA  O3   O  OH1   0  -0.669  -6.0572  -0.6685   1.1374
 XHA  O4   O  OH1   0  -0.668  -4.2689  -2.3628  -1.6646
 XHA  C15  C  CR16  0  -0.308   4.4068  -1.6553   1.3738
 XHA  C16  C  CR6   0  -0.167   4.1054  -0.5259   0.6264
 XHA  C17  C  CT    0   1.050   4.9964   0.6753   0.6294
 XHA  F1   F  F     0  -0.315   5.3677   1.0250  -0.6111
 XHA  F2   F  F     0  -0.317   4.3763   1.7476   1.1510
 XHA  F3   F  F     0  -0.302   6.1149   0.4929   1.3353
 XHA  C18  C  CR16  0  -0.341   2.9452  -0.4812  -0.1400
 XHA  H1   H  HCH1  0   0.217  -3.4204   1.2821  -1.3758
 XHA  H3   H  HCH1  0   0.224  -5.1904   1.8926   0.0041
 XHA  H4   H  HCH1  0   0.229  -5.4321  -0.3563  -0.8157
 XHA  H5   H  HCH2  0   0.246   0.5505  -2.4399  -1.3933
 XHA  H6   H  HCH2  0   0.239   0.9069  -0.7675  -1.7785
 XHA  H7   H  HCH1  0   0.206  -3.6859  -1.3803   1.4394
 XHA  H8   H  HCH2  0   0.213  -3.0507  -3.0971  -0.1475
 XHA  H9   H  HCH2  0   0.220  -4.7625  -3.0415   0.2404
 XHA  H12  H  HCH2  0   0.226  -0.5655  -1.7526   0.7111
 XHA  H13  H  HCH2  0   0.219  -0.1043  -0.0822   0.4365
 XHA  H14  H  HCR6  0   0.258   1.7099  -3.5394   0.5683
 XHA  H15  H  HNH1  0   0.403   0.2191   2.5079   0.7443
 XHA  H17  H  HCH2  0   0.276  -2.7549   3.0803   0.3069
 XHA  H18  H  HCH2  0   0.251  -1.8285   1.8509   1.1515
 XHA  H19  H  HCH3  0   0.238   1.4578   2.2804  -1.8390
 XHA  H20  H  HCH3  0   0.246   1.1765   3.9793  -1.4510
 XHA  H21  H  HCH3  0   0.242   2.1437   2.9768  -0.3691
 XHA  H22  H  HOH1  0   0.444  -5.0547   0.9857   2.2869
 XHA  H23  H  HOH1  0   0.460  -6.9039  -0.3192   0.8425
 XHA  H24  H  HOH1  0   0.457  -4.3539  -3.2404  -2.0474
 XHA  H25  H  HCR6  0   0.269   5.3039  -1.7091   1.9747
 XHA  H26  H  HCR6  0   0.257   2.7127   0.3956  -0.7335
 XHA  C9   C  CH2   0  -0.293  -1.6479  -0.7908  -0.8906
 XHA  H2   H  HCR6  0   0.265   3.7670  -3.6234   1.9196
 XHA  H10  H  HCH2  0   0.228  -1.4328  -0.0861  -1.7000
 XHA  H11  H  HCH2  0   0.237  -1.9026  -1.7244  -1.3986

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
 XHA  F1   C17  single    1.341  0.020  1.341
 XHA  F2   C17  single    1.344  0.020  1.344
 XHA  C17  F3   single    1.335  0.020  1.335
 XHA  C17  C16  single    1.496  0.020  1.496
 XHA  C15  C16  aromatic  1.387  0.020  1.387
 XHA  C15  C14  aromatic  1.389  0.020  1.389
 XHA  C16  C18  aromatic  1.391  0.020  1.391
 XHA  C14  C13  aromatic  1.385  0.020  1.385
 XHA  C18  C12  aromatic  1.389  0.020  1.389
 XHA  C13  C12  aromatic  1.394  0.020  1.394
 XHA  C12  C11  single    1.500  0.020  1.500
 XHA  C11  C10  single    1.530  0.020  1.530
 XHA  C10  C9   single    1.526  0.020  1.526
 XHA  C4   C5   single    1.525  0.020  1.525
 XHA  C4   C3   single    1.531  0.020  1.531
 XHA  C4   N2   single    1.452  0.020  1.452
 XHA  C5   C6   single    1.525  0.020  1.525
 XHA  C5   O2   single    1.408  0.020  1.408
 XHA  C9   N2   single    1.438  0.020  1.438
 XHA  C3   C2   single    1.515  0.020  1.515
 XHA  C6   O3   single    1.406  0.020  1.406
 XHA  C6   C7   single    1.529  0.020  1.529
 XHA  O4   C8   single    1.409  0.020  1.409
 XHA  N2   C7   single    1.453  0.020  1.453
 XHA  C7   C8   single    1.517  0.020  1.517
 XHA  C2   N1   single    1.342  0.020  1.342
 XHA  C2   O1   double    1.226  0.020  1.226
 XHA  N1   C1   single    1.443  0.020  1.443
 XHA  C4   H1   single    0.970  0.020  1.090
 XHA  C14  H2   single    0.930  0.020  1.080
 XHA  C5   H3   single    0.970  0.020  1.090
 XHA  C6   H4   single    0.970  0.020  1.090
 XHA  C11  H5   single    0.970  0.020  1.090
 XHA  C11  H6   single    0.970  0.020  1.090
 XHA  C7   H7   single    0.970  0.020  1.090
 XHA  C8   H8   single    0.970  0.020  1.090
 XHA  C8   H9   single    0.970  0.020  1.090
 XHA  C9   H10  single    0.970  0.020  1.090
 XHA  C9   H11  single    0.970  0.020  1.090
 XHA  C10  H12  single    0.970  0.020  1.090
 XHA  C10  H13  single    0.970  0.020  1.090
 XHA  C13  H14  single    0.930  0.020  1.080
 XHA  N1   H15  single    0.860  0.020  1.020
 XHA  C3   H17  single    0.970  0.020  1.090
 XHA  C3   H18  single    0.970  0.020  1.090
 XHA  C1   H19  single    0.970  0.020  1.090
 XHA  C1   H20  single    0.970  0.020  1.090
 XHA  C1   H21  single    0.970  0.020  1.090
 XHA  O2   H22  single    0.850  0.020  0.980
 XHA  O3   H23  single    0.850  0.020  0.980
 XHA  O4   H24  single    0.850  0.020  0.980
 XHA  C15  H25  single    0.930  0.020  1.080
 XHA  C18  H26  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
 XHA  H1   C4   C3   107.59  3.000
 XHA  H1   C4   N2   111.53  3.000
 XHA  C3   C4   N2   114.24  3.000
 XHA  H1   C4   C5   107.36  3.000
 XHA  N2   C4   C5   103.62  3.000
 XHA  C3   C4   C5   112.34  3.000
 XHA  H2   C14  C15  119.51  3.000
 XHA  H2   C14  C13  120.00  3.000
 XHA  C15  C14  C13  120.48  3.000
 XHA  H3   C5   O2   110.93  3.000
 XHA  H3   C5   C6   112.12  3.000
 XHA  O2   C5   C6   110.69  3.000
 XHA  H3   C5   C4   110.63  3.000
 XHA  O2   C5   C4   110.46  3.000
 XHA  C6   C5   C4   101.69  3.000
 XHA  H4   C6   O3   111.38  3.000
 XHA  H4   C6   C7   109.14  3.000
 XHA  O3   C6   C7   110.65  3.000
 XHA  H4   C6   C5   108.32  3.000
 XHA  C7   C6   C5   102.99  3.000
 XHA  O3   C6   C5   113.97  3.000
 XHA  H6   C11  H5   106.53  3.000
 XHA  H6   C11  C12  109.68  3.000
 XHA  H5   C11  C12  110.09  3.000
 XHA  H6   C11  C10  109.04  3.000
 XHA  H5   C11  C10  109.57  3.000
 XHA  C12  C11  C10  111.78  3.000
 XHA  H7   C7   N2   111.13  3.000
 XHA  H7   C7   C8   104.69  3.000
 XHA  N2   C7   C8   116.83  3.000
 XHA  H7   C7   C6   108.30  3.000
 XHA  C8   C7   C6   112.71  3.000
 XHA  N2   C7   C6   103.10  3.000
 XHA  H9   C8   H8   106.18  3.000
 XHA  H9   C8   O4   111.66  3.000
 XHA  H8   C8   O4   111.48  3.000
 XHA  H9   C8   C7   106.79  3.000
 XHA  H8   C8   C7   109.81  3.000
 XHA  O4   C8   C7   110.72  3.000
 XHA  H13  C10  H12  106.67  3.000
 XHA  H13  C10  C9   109.65  3.000
 XHA  H12  C10  C9   109.85  3.000
 XHA  H13  C10  C11  109.26  3.000
 XHA  H12  C10  C11  109.64  3.000
 XHA  C9   C10  C11  111.64  3.000
 XHA  C18  C12  C13  118.31  3.000
 XHA  C13  C12  C11  121.22  3.000
 XHA  C18  C12  C11  120.41  3.000
 XHA  H14  C13  C12  119.48  3.000
 XHA  H14  C13  C14  119.65  3.000
 XHA  C12  C13  C14  120.86  3.000
 XHA  H15  N1   C2   119.03  3.000
 XHA  H15  N1   C1   118.22  3.000
 XHA  C2   N1   C1   122.65  3.000
 XHA  C9   N2   C7   122.70  3.000
 XHA  C7   N2   C4   112.10  3.000
 XHA  C9   N2   C4   119.49  3.000
 XHA  H18  C3   H17  106.86  3.000
 XHA  H18  C3   C2   111.48  3.000
 XHA  H17  C3   C2   105.36  3.000
 XHA  H18  C3   C4   109.61  3.000
 XHA  H17  C3   C4   108.66  3.000
 XHA  C2   C3   C4   114.48  3.000
 XHA  H21  C1   H20  108.19  3.000
 XHA  H21  C1   H19  108.40  3.000
 XHA  H20  C1   H19  108.06  3.000
 XHA  H21  C1   N1   108.56  3.000
 XHA  H20  C1   N1   112.08  3.000
 XHA  H19  C1   N1   111.44  3.000
 XHA  O1   C2   C3   122.39  3.000
 XHA  O1   C2   N1   122.05  3.000
 XHA  C3   C2   N1   115.52  3.000
 XHA  H22  O2   C5   107.29  3.000
 XHA  H23  O3   C6   108.60  3.000
 XHA  H24  O4   C8   108.12  3.000
 XHA  H25  C15  C16  121.35  3.000
 XHA  H25  C15  C14  119.57  3.000
 XHA  C16  C15  C14  119.08  3.000
 XHA  C18  C16  C17  118.17  3.000
 XHA  C18  C16  C15  120.27  3.000
 XHA  C17  C16  C15  121.55  3.000
 XHA  F3   C17  F2   106.87  3.000
 XHA  F3   C17  F1   107.02  3.000
 XHA  F2   C17  F1   106.18  3.000
 XHA  F3   C17  C16  112.98  3.000
 XHA  F2   C17  C16  111.51  3.000
 XHA  F1   C17  C16  111.87  3.000
 XHA  H26  C18  C16  120.42  3.000
 XHA  H26  C18  C12  118.59  3.000
 XHA  C16  C18  C12  120.98  3.000
 XHA  H11  C9   H10  104.60  3.000
 XHA  H11  C9   N2   111.36  3.000
 XHA  H10  C9   N2   108.93  3.000
 XHA  H11  C9   C10  108.69  3.000
 XHA  H10  C9   C10  109.04  3.000
 XHA  N2   C9   C10  113.80  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
 XHA  CONST_01  C18  C16  C15  C14     0.00   0.0  0
 XHA  CONST_02  C18  C12  C13  C14     0.00   0.0  0
 XHA  CONST_03  C15  C16  C18  C12     0.00   0.0  0
 XHA  CONST_04  C15  C14  C13  C12     0.00   0.0  0
 XHA  CONST_05  C16  C15  C14  C13     0.00   0.0  0
 XHA  CONST_06  C16  C18  C12  C13     0.00   0.0  0
 XHA  CONST_07  C17  C16  C15  C14   180.00   0.0  0
 XHA  CONST_08  C11  C12  C13  C14   180.00   0.0  0
 XHA  CONST_09  C16  C18  C12  C11   180.00   0.0  0
 XHA  CONST_10  C17  C16  C18  C12   180.00   0.0  0
 XHA  CONST_11  H2   C14  C13  C12   180.00   0.0  0
 XHA  CONST_12  H25  C15  C14  C13   180.00   0.0  0
 XHA  CONST_13  H26  C18  C12  C13   180.00   0.0  0
 XHA  CONST_14  H14  C13  C14  C15   180.00   0.0  0
 XHA  CONST_15  C1   N1   C2   C3    180.00   0.0  0
 XHA  CONST_16  O1   C2   N1   C1      0.00   0.0  0
 XHA  CONST_17  H15  N1   C2   C3      0.00   0.0  0
 XHA  Var_01    C10  C9   N2   C4    109.47  30.0  1
 XHA  Var_02    C18  C12  C11  C10   -93.45  30.0  3
 XHA  Var_03    F1   C17  C16  C15   125.16  30.0  2
 XHA  Var_04    N1   C2   C3   C4   -138.78  30.0  3
 XHA  Var_05    N2   C9   C10  C11  -177.06  30.0  3
 XHA  Var_06    C12  C11  C10  C9    174.43  30.0  1
 XHA  Var_07    H19  C1   N1   C2    -56.96  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
 XHA  chir_01  C4  C5  C3  N2  negativ
 XHA  chir_02  C5  O2  C6  C4  positiv
 XHA  chir_03  C6  O3  C5  C7  negativ
 XHA  chir_04  C7  N2  C6  C8  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
 XHA  plan-1  C14  0.020
 XHA  plan-1  C11  0.020
 XHA  plan-1  C12  0.020
 XHA  plan-1  C13  0.020
 XHA  plan-1  C15  0.020
 XHA  plan-1  C16  0.020
 XHA  plan-1  C17  0.020
 XHA  plan-1  C18  0.020
 XHA  plan-1  H14  0.020
 XHA  plan-1  H25  0.020
 XHA  plan-1  H26  0.020
 XHA  plan-1  H2   0.020
 XHA  plan-2  N1   0.020
 XHA  plan-2  C3   0.020
 XHA  plan-2  C1   0.020
 XHA  plan-2  C2   0.020
 XHA  plan-2  O1   0.020
 XHA  plan-2  H15  0.020

