# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 20:43:10 2022
#   Inital geometry file: a 147 line input string
#   Ligand name: 2-[[2,5-bis(chloranyl)phenyl]methylamino]-4-(cyclopentylamino)-~{N}-[3-(2-oxidanylidene-1,3-oxazolidin-3-yl)propyl]pyrimidine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(Cl)c(CNc2ncc(C(=O)NCCCN3CCOC3=O)c(NC4CCCC4)n2)c1
#
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
 V5W  V5W  2-[[2,5-bis(chloranyl)phenyl]methylamino]-4-(cyclopentylamino)-~{N}-[3-(2-oxidanylidene-1,3-oxazolidin-3-yl)propyl]pyrimidine-5-carboxamide  ligand  62  34  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_V5W
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
 V5W  C    C   CR6   0  -0.017   8.9344    0.4131  13.5241
 V5W  O    O   O     0  -0.472   5.1320  -11.9159  19.1623
 V5W  CL1  CL  CL    0  -0.119   9.6905   -1.5855   9.5893
 V5W  C20  C   CR6   0  -0.112   9.4265   -0.8287  11.1300
 V5W  C21  C   CR16  0  -0.198   8.6164    0.2964  11.1667
 V5W  C22  C   CR16  0  -0.238   8.3612    0.9268  12.3719
 V5W  CL   CL  CL    0  -0.123   8.6380    1.1897  15.0436
 V5W  C2   C   CR6   0   0.174  10.0042   -1.3547  12.2811
 V5W  C1   C   CR16  0  -0.255   9.7442   -0.7076  13.4847
 V5W  C3   C   CH2   0  -0.334  10.9125   -2.5640  12.2538
 V5W  N    N   NH1   0  -0.657  10.8904   -3.3332  13.4655
 V5W  C4   C   CR6   0   0.608   9.8451   -4.1081  13.8108
 V5W  N5   N   N     0  -0.486   9.9625   -4.8032  14.9529
 V5W  C19  C   CR16  0  -0.051   8.9347   -5.5829  15.2328
 V5W  C11  C   CR6   0  -0.278   7.7937   -5.7196  14.4540
 V5W  C5   C   CR6   0   0.571   7.7564   -4.8773  13.2988
 V5W  N2   N   NH1   0  -0.677   6.7081   -4.8416  12.4752
 V5W  C6   C   CH1   0  -0.063   6.5911   -3.9519  11.3445
 V5W  C10  C   CH2   0  -0.454   5.5600   -4.4396  10.3301
 V5W  C9   C   CH2   0  -0.446   5.2857   -3.2068   9.4577
 V5W  C8   C   CH2   0  -0.456   5.6919   -1.9796  10.3130
 V5W  C7   C   CH2   0  -0.439   6.0981   -2.5425  11.6768
 V5W  N1   N   N     0  -0.519   8.7980   -4.0998  13.0014
 V5W  C12  C   C     0   0.569   6.6790   -6.6185  14.8090
 V5W  O2   O   O     0  -0.516   5.5564   -6.4914  14.3132
 V5W  N3   N   NH1   0  -0.654   6.9364   -7.5852  15.7093
 V5W  C13  C   CH2   0  -0.281   5.9363   -8.5215  16.1711
 V5W  C14  C   CH2   0  -0.450   5.7504   -9.7168  15.2425
 V5W  C15  C   CH2   0  -0.306   4.7576  -10.7289  15.7995
 V5W  N4   N   NR5   0  -0.494   5.1911  -11.3018  17.0510
 V5W  C18  C   CH2   0  -0.305   6.2325  -12.2974  17.1331
 V5W  C17  C   CH2   0  -0.198   6.3539  -12.4501  18.6476
 V5W  C16  C   CR5   0   0.697   4.5220  -11.1815  18.2154
 V5W  O1   O   O     0  -0.491   3.5267  -10.5360  18.4468
 V5W  H1   H   HCR6  0   0.288   8.1753    0.6794  10.2565
 V5W  H2   H   HCR6  0   0.286   7.7271    1.8019  12.4050
 V5W  H3   H   HCR6  0   0.279  10.1769   -1.0938  14.3985
 V5W  H4   H   HCH2  0   0.258  10.6547   -3.2014  11.4081
 V5W  H5   H   HCH2  0   0.290  11.9400   -2.2333  12.0927
 V5W  H6   H   HNH1  0   0.401  11.6839   -3.3160  14.0833
 V5W  H7   H   HCR6  0   0.257   9.0211   -6.1294  16.1673
 V5W  H8   H   HNH1  0   0.407   5.8921   -5.3566  12.7813
 V5W  H9   H   HCH1  0   0.237   7.5668   -3.8783  10.8580
 V5W  H10  H   HCH2  0   0.226   4.6511   -4.7432  10.8590
 V5W  H11  H   HCH2  0   0.242   5.9067   -5.3013   9.7585
 V5W  H12  H   HCH2  0   0.230   5.8789   -3.2450   8.5434
 V5W  H13  H   HCH2  0   0.232   4.2410   -3.1643   9.1503
 V5W  H14  H   HCH2  0   0.225   6.5377   -1.4643   9.8544
 V5W  H15  H   HCH2  0   0.232   4.8890   -1.2474  10.3981
 V5W  H16  H   HCH2  0   0.220   5.2303   -2.6183  12.3389
 V5W  H17  H   HCH2  0   0.238   6.8507   -1.9381  12.1848
 V5W  H18  H   HNH1  0   0.402   7.8880   -7.7793  15.9711
 V5W  H19  H   HCH2  0   0.243   4.9879   -7.9994  16.3036
 V5W  H20  H   HCH2  0   0.251   6.2515   -8.8614  17.1582
 V5W  H21  H   HCH2  0   0.246   5.3839   -9.3784  14.2714
 V5W  H22  H   HCH2  0   0.235   6.7165  -10.1962  15.0618
 V5W  H23  H   HCH2  0   0.258   3.7890  -10.2554  15.9616
 V5W  H24  H   HCH2  0   0.257   4.6026  -11.5327  15.0745
 V5W  H25  H   HCH2  0   0.254   5.9302  -13.2240  16.6350
 V5W  H26  H   HCH2  0   0.266   7.1652  -11.9572  16.6830
 V5W  H27  H   HCH2  0   0.257   6.4539  -13.4848  18.9681
 V5W  H28  H   HCH2  0   0.250   7.1888  -11.8721  19.0472

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
 V5W  CL1  C20  single    1.737  0.020  1.737
 V5W  C9   C10  single    1.535  0.020  1.535
 V5W  C9   C8   single    1.550  0.020  1.550
 V5W  C10  C6   single    1.526  0.020  1.526
 V5W  C21  C20  aromatic  1.387  0.020  1.387
 V5W  C21  C22  aromatic  1.384  0.020  1.384
 V5W  C20  C2   aromatic  1.391  0.020  1.391
 V5W  C6   N2   single    1.443  0.020  1.443
 V5W  C6   C7   single    1.530  0.020  1.530
 V5W  C8   C7   single    1.530  0.020  1.530
 V5W  N2   C5   single    1.334  0.020  1.334
 V5W  C22  C    aromatic  1.386  0.020  1.386
 V5W  C2   C3   single    1.513  0.020  1.513
 V5W  C2   C1   aromatic  1.391  0.020  1.391
 V5W  C3   N    single    1.435  0.020  1.435
 V5W  N1   C5   aromatic  1.333  0.020  1.333
 V5W  N1   C4   aromatic  1.323  0.020  1.323
 V5W  C5   C11  aromatic  1.430  0.020  1.430
 V5W  O2   C12  double    1.234  0.020  1.234
 V5W  N    C4   single    1.346  0.020  1.346
 V5W  C    C1   aromatic  1.383  0.020  1.383
 V5W  C    CL   single    1.732  0.020  1.732
 V5W  C4   N5   aromatic  1.342  0.020  1.342
 V5W  C11  C12  single    1.475  0.020  1.475
 V5W  C11  C19  aromatic  1.388  0.020  1.388
 V5W  C12  N3   single    1.346  0.020  1.346
 V5W  N5   C19  aromatic  1.320  0.020  1.320
 V5W  C14  C13  single    1.525  0.020  1.525
 V5W  C14  C15  single    1.523  0.020  1.523
 V5W  N3   C13  single    1.446  0.020  1.446
 V5W  C15  N4   single    1.443  0.020  1.443
 V5W  N4   C16  single    1.348  0.020  1.348
 V5W  N4   C18  single    1.443  0.020  1.443
 V5W  O1   C16  double    1.209  0.020  1.209
 V5W  C16  O    single    1.345  0.020  1.345
 V5W  C18  C17  single    1.527  0.020  1.527
 V5W  O    C17  single    1.429  0.020  1.429
 V5W  C21  H1   single    0.930  0.020  1.080
 V5W  C22  H2   single    0.930  0.020  1.080
 V5W  C1   H3   single    0.930  0.020  1.080
 V5W  C3   H4   single    0.970  0.020  1.090
 V5W  C3   H5   single    0.970  0.020  1.090
 V5W  N    H6   single    0.860  0.020  1.020
 V5W  C19  H7   single    0.930  0.020  1.080
 V5W  N2   H8   single    0.860  0.020  1.020
 V5W  C6   H9   single    0.970  0.020  1.090
 V5W  C10  H10  single    0.970  0.020  1.090
 V5W  C10  H11  single    0.970  0.020  1.090
 V5W  C9   H12  single    0.970  0.020  1.090
 V5W  C9   H13  single    0.970  0.020  1.090
 V5W  C8   H14  single    0.970  0.020  1.090
 V5W  C8   H15  single    0.970  0.020  1.090
 V5W  C7   H16  single    0.970  0.020  1.090
 V5W  C7   H17  single    0.970  0.020  1.090
 V5W  N3   H18  single    0.860  0.020  1.020
 V5W  C13  H19  single    0.970  0.020  1.090
 V5W  C13  H20  single    0.970  0.020  1.090
 V5W  C14  H21  single    0.970  0.020  1.090
 V5W  C14  H22  single    0.970  0.020  1.090
 V5W  C15  H23  single    0.970  0.020  1.090
 V5W  C15  H24  single    0.970  0.020  1.090
 V5W  C18  H25  single    0.970  0.020  1.090
 V5W  C18  H26  single    0.970  0.020  1.090
 V5W  C17  H27  single    0.970  0.020  1.090
 V5W  C17  H28  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
 V5W  C1   C    CL   119.24  3.000
 V5W  CL   C    C22  119.51  3.000
 V5W  C1   C    C22  121.26  3.000
 V5W  C16  O    C17  109.77  3.000
 V5W  C2   C20  C21  121.83  3.000
 V5W  C2   C20  CL1  120.40  3.000
 V5W  C21  C20  CL1  117.76  3.000
 V5W  H1   C21  C22  119.76  3.000
 V5W  H1   C21  C20  120.22  3.000
 V5W  C22  C21  C20  120.02  3.000
 V5W  H2   C22  C21  120.23  3.000
 V5W  H2   C22  C    121.15  3.000
 V5W  C21  C22  C    118.62  3.000
 V5W  C3   C2   C1   119.98  3.000
 V5W  C1   C2   C20  117.54  3.000
 V5W  C3   C2   C20  122.46  3.000
 V5W  H3   C1   C2   119.33  3.000
 V5W  H3   C1   C    119.94  3.000
 V5W  C2   C1   C    120.73  3.000
 V5W  H5   C3   H4   106.59  3.000
 V5W  H5   C3   N    107.55  3.000
 V5W  H4   C3   N    109.75  3.000
 V5W  H5   C3   C2   109.01  3.000
 V5W  H4   C3   C2   109.84  3.000
 V5W  N    C3   C2   113.82  3.000
 V5W  H6   N    C4   117.70  3.000
 V5W  H6   N    C3   119.82  3.000
 V5W  C4   N    C3   122.48  3.000
 V5W  N1   C4   N5   126.36  3.000
 V5W  N5   C4   N    116.64  3.000
 V5W  N1   C4   N    116.99  3.000
 V5W  C19  N5   C4   114.72  3.000
 V5W  H7   C19  C11  119.90  3.000
 V5W  H7   C19  N5   114.69  3.000
 V5W  C11  C19  N5   125.39  3.000
 V5W  C12  C11  C5   122.24  3.000
 V5W  C12  C11  C19  123.10  3.000
 V5W  C5   C11  C19  114.62  3.000
 V5W  N1   C5   N2   117.43  3.000
 V5W  N1   C5   C11  120.21  3.000
 V5W  N2   C5   C11  122.35  3.000
 V5W  H8   N2   C6   119.01  3.000
 V5W  H8   N2   C5   115.67  3.000
 V5W  C6   N2   C5   124.33  3.000
 V5W  H9   C6   C7   108.81  3.000
 V5W  H9   C6   C10  109.19  3.000
 V5W  C7   C6   C10  102.77  3.000
 V5W  H9   C6   N2   108.53  3.000
 V5W  C7   C6   N2   115.08  3.000
 V5W  C10  C6   N2   112.24  3.000
 V5W  H11  C10  H10  107.34  3.000
 V5W  H11  C10  C9   113.18  3.000
 V5W  H10  C10  C9   110.43  3.000
 V5W  H11  C10  C6   112.71  3.000
 V5W  H10  C10  C6   109.17  3.000
 V5W  C9   C10  C6   103.99  3.000
 V5W  H13  C9   H12  106.63  3.000
 V5W  H13  C9   C8   112.08  3.000
 V5W  H12  C9   C8   110.35  3.000
 V5W  H13  C9   C10  111.28  3.000
 V5W  H12  C9   C10  110.56  3.000
 V5W  C8   C9   C10  105.99  3.000
 V5W  H15  C8   H14  106.65  3.000
 V5W  H15  C8   C7   111.90  3.000
 V5W  H14  C8   C7   110.03  3.000
 V5W  H15  C8   C9   112.45  3.000
 V5W  H14  C8   C9   110.19  3.000
 V5W  C7   C8   C9   105.67  3.000
 V5W  H17  C7   H16  107.69  3.000
 V5W  H17  C7   C8   113.22  3.000
 V5W  H16  C7   C8   110.75  3.000
 V5W  H17  C7   C6   112.91  3.000
 V5W  H16  C7   C6   108.86  3.000
 V5W  C8   C7   C6   103.35  3.000
 V5W  C5   N1   C4   118.55  3.000
 V5W  N3   C12  O2   121.13  3.000
 V5W  N3   C12  C11  117.00  3.000
 V5W  O2   C12  C11  121.87  3.000
 V5W  H18  N3   C13  116.51  3.000
 V5W  H18  N3   C12  119.58  3.000
 V5W  C13  N3   C12  123.13  3.000
 V5W  H20  C13  H19  106.89  3.000
 V5W  H20  C13  C14  110.01  3.000
 V5W  H19  C13  C14  110.07  3.000
 V5W  H20  C13  N3   106.92  3.000
 V5W  H19  C13  N3   109.29  3.000
 V5W  C14  C13  N3   113.42  3.000
 V5W  H22  C14  H21  106.59  3.000
 V5W  H22  C14  C15  110.18  3.000
 V5W  H21  C14  C15  108.20  3.000
 V5W  H22  C14  C13  109.67  3.000
 V5W  H21  C14  C13  109.85  3.000
 V5W  C15  C14  C13  112.18  3.000
 V5W  H24  C15  H23  106.97  3.000
 V5W  H24  C15  N4   109.01  3.000
 V5W  H23  C15  N4   108.08  3.000
 V5W  H24  C15  C14  109.77  3.000
 V5W  H23  C15  C14  110.17  3.000
 V5W  N4   C15  C14  112.65  3.000
 V5W  C16  N4   C18  111.75  3.000
 V5W  C18  N4   C15  122.68  3.000
 V5W  C16  N4   C15  124.36  3.000
 V5W  H26  C18  H25  108.22  3.000
 V5W  H26  C18  C17  111.89  3.000
 V5W  H25  C18  C17  112.87  3.000
 V5W  H26  C18  N4   112.25  3.000
 V5W  H25  C18  N4   111.03  3.000
 V5W  C17  C18  N4   100.53  3.000
 V5W  H28  C17  H27  109.00  3.000
 V5W  H28  C17  C18  111.78  3.000
 V5W  H27  C17  C18  113.24  3.000
 V5W  H28  C17  O    108.92  3.000
 V5W  H27  C17  O    109.15  3.000
 V5W  C18  C17  O    104.59  3.000
 V5W  O1   C16  N4   128.44  3.000
 V5W  O1   C16  O    122.03  3.000
 V5W  N4   C16  O    109.53  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
 V5W  CONST_01  C20  C21  C22  C       0.00   0.0  0
 V5W  CONST_02  C20  C2   C1   C       0.00   0.0  0
 V5W  CONST_03  C1   C2   C20  C21     0.00   0.0  0
 V5W  CONST_04  C1   C    C22  C21     0.00   0.0  0
 V5W  CONST_05  C2   C20  C21  C22     0.00   0.0  0
 V5W  CONST_06  C2   C1   C    C22     0.00   0.0  0
 V5W  CONST_07  C11  C5   N1   C4      0.00   0.0  0
 V5W  CONST_08  C11  C19  N5   C4      0.00   0.0  0
 V5W  CONST_09  C5   N1   C4   N5      0.00   0.0  0
 V5W  CONST_10  C5   C11  C19  N5      0.00   0.0  0
 V5W  CONST_11  N1   C5   C11  C19     0.00   0.0  0
 V5W  CONST_12  N1   C4   N5   C19     0.00   0.0  0
 V5W  CONST_13  C3   C2   C1   C     180.00   0.0  0
 V5W  CONST_14  C22  C21  C20  CL1   180.00   0.0  0
 V5W  CONST_15  C1   C2   C20  CL1   180.00   0.0  0
 V5W  CONST_16  C3   C2   C20  C21   180.00   0.0  0
 V5W  CONST_17  CL   C    C22  C21   180.00   0.0  0
 V5W  CONST_18  C2   C1   C    CL    180.00   0.0  0
 V5W  CONST_19  C5   N1   C4   N     180.00   0.0  0
 V5W  CONST_20  C19  N5   C4   N     180.00   0.0  0
 V5W  CONST_21  N2   C5   N1   C4    180.00   0.0  0
 V5W  CONST_22  C12  C11  C19  N5    180.00   0.0  0
 V5W  CONST_23  N2   C5   C11  C19   180.00   0.0  0
 V5W  CONST_24  C12  C11  C5   N1    180.00   0.0  0
 V5W  CONST_25  C6   N2   C5   C11   180.00   0.0  0
 V5W  CONST_26  N1   C5   N2   C6      0.00   0.0  0
 V5W  CONST_27  H1   C21  C22  C     180.00   0.0  0
 V5W  CONST_28  H2   C22  C21  C20   180.00   0.0  0
 V5W  CONST_29  H3   C1   C2   C20   180.00   0.0  0
 V5W  CONST_30  H7   C19  N5   C4    180.00   0.0  0
 V5W  CONST_31  N1   C4   N    C3      0.00   0.0  0
 V5W  CONST_32  N5   C4   N    C3    180.00   0.0  0
 V5W  CONST_33  H6   N    C4   N5      0.00   0.0  0
 V5W  CONST_34  H8   N2   C5   C11     0.00   0.0  0
 V5W  CONST_35  C13  N3   C12  C11   180.00   0.0  0
 V5W  CONST_36  H18  N3   C12  C11     0.00   0.0  0
 V5W  CONST_37  C13  N3   C12  O2      0.00   0.0  0
 V5W  Var_01    C18  N4   C16  O       7.39  30.0  1
 V5W  Var_02    N4   C18  C17  O      18.89  30.0  1
 V5W  Var_03    C8   C9   C10  C6    -22.25  30.0  1
 V5W  Var_04    C9   C8   C7   C6     27.99  30.0  1
 V5W  Var_05    C7   C8   C9   C10    -3.60  30.0  1
 V5W  Var_06    C16  N4   C18  C17   -16.43  30.0  1
 V5W  Var_07    N    C3   C2   C20  -151.43  30.0  2
 V5W  Var_08    C4   N    C3   C2     72.85  30.0  3
 V5W  Var_09    O2   C12  C11  C19   161.54  30.0  2
 V5W  Var_10    N4   C15  C14  C13   -62.17  30.0  3
 V5W  Var_11    C14  C13  N3   C12    83.66  30.0  3
 V5W  Var_12    C15  C14  C13  N3    176.29  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
 V5W  chir_01  C6  C10  N2  C7  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
 V5W  plan-1  O    0.020
 V5W  plan-1  N4   0.020
 V5W  plan-1  C16  0.020
 V5W  plan-1  O1   0.020
 V5W  plan-2  C    0.020
 V5W  plan-2  CL1  0.020
 V5W  plan-2  C20  0.020
 V5W  plan-2  C21  0.020
 V5W  plan-2  C22  0.020
 V5W  plan-2  CL   0.020
 V5W  plan-2  C2   0.020
 V5W  plan-2  C1   0.020
 V5W  plan-2  C3   0.020
 V5W  plan-2  H1   0.020
 V5W  plan-2  H2   0.020
 V5W  plan-2  H3   0.020
 V5W  plan-3  N    0.020
 V5W  plan-3  C4   0.020
 V5W  plan-3  N5   0.020
 V5W  plan-3  C19  0.020
 V5W  plan-3  C11  0.020
 V5W  plan-3  C5   0.020
 V5W  plan-3  N2   0.020
 V5W  plan-3  N1   0.020
 V5W  plan-3  C12  0.020
 V5W  plan-3  H7   0.020
 V5W  plan-4  C3   0.020
 V5W  plan-4  N    0.020
 V5W  plan-4  C4   0.020
 V5W  plan-4  H6   0.020
 V5W  plan-5  C5   0.020
 V5W  plan-5  N2   0.020
 V5W  plan-5  C6   0.020
 V5W  plan-5  H8   0.020
 V5W  plan-6  C11  0.020
 V5W  plan-6  C12  0.020
 V5W  plan-6  O2   0.020
 V5W  plan-6  N3   0.020
 V5W  plan-6  C13  0.020
 V5W  plan-6  H18  0.020
 V5W  plan-7  C15  0.020
 V5W  plan-7  N4   0.020
 V5W  plan-7  C18  0.020
 V5W  plan-7  C16  0.020

