# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 14:21:34 2022
#   Inital geometry file: a 103 line input string
#   Ligand name: 2-(2-methyl-5-nitro-1H-imidazol-1-yl)ethyl [(1R)-2,2,2-trichloro-1-(pyrimidin-2-ylamino)ethyl]carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(n1CCOC(=O)N[C@@H](Nc2ncccn2)C(Cl)(Cl)Cl)[N+]([O-])=O
#
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
 WR7  WR7  '2-(2-methyl-5-nitro-1H-imidazol-1-yl)ethyl [(1R)-2,2,2-trichloro-1-(pyrimidin-2-ylamino)ethyl]carbamate'  ligand  41  27  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WR7
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
 WR7  C1    C   CR16   0  -0.014   4.4768   4.1185   0.6276
 WR7  N1    N   N      0  -0.456   3.9850   2.9669   1.0542
 WR7  O1    O   O2     0  -0.478  -1.3737  -0.4188   0.2948
 WR7  CL1   CL  CL     0  -0.003   3.1900  -1.9581   1.1828
 WR7  C2    C   CR6    0   0.622   3.3294   2.2347   0.1525
 WR7  N2    N   N      0  -0.459   3.1311   2.5570  -1.1219
 WR7  O2    O   O      0  -0.492  -0.3476   0.2623  -1.5876
 WR7  CL2   CL  CL     0   0.020   4.4950  -0.7891  -1.1064
 WR7  C3    C   CR16   0   0.002   3.6334   3.7150  -1.5232
 WR7  N3    N   NH1    0  -0.662   2.8248   1.0549   0.6059
 WR7  O3    O   O      0  -0.396  -4.7343   1.7981   0.7040
 WR7  C4    C   CR16   0  -0.384   4.3323   4.5599  -0.6786
 WR7  N4    N   NH1    0  -0.657   0.8158  -0.1727   0.3229
 WR7  O4    O   O     -1  -0.397  -6.7617   2.1025   0.0818
 WR7  C5    C   CH1    0   0.089   2.1103   0.1287  -0.2009
 WR7  N5    N   NR5    0  -0.492  -4.9749  -0.9432   0.1078
 WR7  C6    C   CT     0  -0.191   2.9317  -1.1751  -0.3875
 WR7  N6    N   N      0  -0.445  -6.7460  -1.8703  -0.8430
 WR7  C7    C   C      0   0.773  -0.3073  -0.0794  -0.4290
 WR7  C8    C   CH2    0  -0.156  -2.6359  -0.4020  -0.3623
 WR7  C9    C   CH2    0  -0.374  -3.6416  -0.8605   0.6809
 WR7  C10   C   CR15   0  -0.130  -7.0073  -0.5653  -0.6618
 WR7  C11   C   CR5    0   0.483  -5.5265  -2.0757  -0.3772
 WR7  C12   C   CR5    0   0.409  -5.9245   0.0391  -0.0772
 WR7  C13   C   CH3    0  -0.766  -4.8397  -3.3899  -0.3761
 WR7  H10   H   HCR5   0   0.299  -7.9400  -0.1114  -0.9566
 WR7  H1    H   HCR6   0   0.277   5.0098   4.7152   1.3596
 WR7  H3    H   HCR6   0   0.276   3.4701   3.9762  -2.5627
 WR7  H13   H   HCH3   0   0.277  -4.5944  -3.7171   0.6352
 WR7  HN3   H   HNH1   0   0.404   2.9902   0.8424   1.5783
 WR7  H13A  H   HCH3   0   0.285  -5.4974  -4.1303  -0.8232
 WR7  H13B  H   HCH3   0   0.272  -3.9135  -3.3656  -0.9524
 WR7  H4    H   HCR6   0   0.277   4.7391   5.5012  -1.0145
 WR7  HN4   H   HNH1   0   0.413   0.7339  -0.4716   1.2841
 WR7  H5    H   HCH1   0   0.330   1.9931   0.5637  -1.1937
 WR7  H8    H   HCH2   0   0.253  -2.8735   0.5998  -0.7222
 WR7  H8A   H   HCH2   0   0.248  -2.6346  -1.0835  -1.2162
 WR7  H9    H   HCH2   0   0.302  -3.6519  -0.1986   1.5418
 WR7  H9A   H   HCH2   0   0.297  -3.3799  -1.8546   1.0390
 WR7  CL3   CL  CL     0   0.017   2.0593  -2.2847  -1.4473
 WR7  N7    N   N      1   0.328  -5.7920   1.3965   0.2618

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
 WR7  C1   N1    aromatic  1.323  0.020  1.323
 WR7  C1   C4    aromatic  1.386  0.020  1.386
 WR7  C1   H1    single    0.930  0.020  1.080
 WR7  N1   C2    aromatic  1.334  0.020  1.334
 WR7  O1   C7    single    1.333  0.020  1.333
 WR7  O1   C8    single    1.423  0.020  1.423
 WR7  CL1  C6    single    1.774  0.020  1.774
 WR7  C2   N2    aromatic  1.329  0.020  1.329
 WR7  C2   N3    single    1.361  0.020  1.361
 WR7  N2   C3    aromatic  1.324  0.020  1.324
 WR7  O2   C7    double    1.209  0.020  1.209
 WR7  CL2  C6    single    1.763  0.020  1.763
 WR7  C3   C4    aromatic  1.384  0.020  1.384
 WR7  C3   H3    single    0.930  0.020  1.080
 WR7  N3   C5    single    1.421  0.020  1.421
 WR7  N3   HN3   single    0.860  0.020  1.020
 WR7  O3   N7    double    1.215  0.020  1.215
 WR7  CL3  C6    single    1.765  0.020  1.765
 WR7  C4   H4    single    0.930  0.020  1.080
 WR7  N4   C5    single    1.429  0.020  1.429
 WR7  N4   C7    single    1.355  0.020  1.355
 WR7  N4   HN4   single    0.860  0.020  1.020
 WR7  O4   N7    single    1.213  0.020  1.213
 WR7  C5   C6    single    1.552  0.020  1.552
 WR7  C5   H5    single    0.970  0.020  1.090
 WR7  N5   C9    single    1.454  0.020  1.454
 WR7  N5   C11   aromatic  1.350  0.020  1.350
 WR7  N5   C12   aromatic  1.379  0.020  1.379
 WR7  N6   C10   aromatic  1.343  0.020  1.343
 WR7  N6   C11   aromatic  1.321  0.020  1.321
 WR7  N7   C12   single    1.405  0.020  1.405
 WR7  C8   C9    single    1.520  0.020  1.520
 WR7  C8   H8    single    0.970  0.020  1.090
 WR7  C8   H8A   single    0.970  0.020  1.090
 WR7  C9   H9    single    0.970  0.020  1.090
 WR7  C9   H9A   single    0.970  0.020  1.090
 WR7  C10  C12   aromatic  1.371  0.020  1.371
 WR7  C10  H10   single    0.930  0.020  1.080
 WR7  C11  C13   single    1.483  0.020  1.483
 WR7  C13  H13   single    0.970  0.020  1.090
 WR7  C13  H13A  single    0.970  0.020  1.090
 WR7  C13  H13B  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
 WR7  H1    C1   C4    120.80  3.000
 WR7  H1    C1   N1    116.36  3.000
 WR7  C4    C1   N1    122.84  3.000
 WR7  C2    N1   C1    116.27  3.000
 WR7  C8    O1   C7    117.12  3.000
 WR7  N3    C2   N2    118.31  3.000
 WR7  N3    C2   N1    115.66  3.000
 WR7  N2    C2   N1    126.03  3.000
 WR7  C3    N2   C2    116.48  3.000
 WR7  H3    C3   C4    120.93  3.000
 WR7  H3    C3   N2    116.36  3.000
 WR7  C4    C3   N2    122.70  3.000
 WR7  HN3   N3   C5    119.49  3.000
 WR7  HN3   N3   C2    116.29  3.000
 WR7  C5    N3   C2    124.22  3.000
 WR7  H4    C4   C3    122.20  3.000
 WR7  H4    C4   C1    122.12  3.000
 WR7  C3    C4   C1    115.67  3.000
 WR7  HN4   N4   C7    118.78  3.000
 WR7  HN4   N4   C5    119.00  3.000
 WR7  C7    N4   C5    122.22  3.000
 WR7  H5    C5   C6    106.42  3.000
 WR7  H5    C5   N4    108.70  3.000
 WR7  C6    C5   N4    110.26  3.000
 WR7  H5    C5   N3    108.12  3.000
 WR7  C6    C5   N3    110.47  3.000
 WR7  N4    C5   N3    112.64  3.000
 WR7  C12   N5   C11   105.55  3.000
 WR7  C12   N5   C9    130.10  3.000
 WR7  C11   N5   C9    124.35  3.000
 WR7  C5    C6   CL3   109.79  3.000
 WR7  C5    C6   CL2   109.53  3.000
 WR7  CL3   C6   CL2   109.33  3.000
 WR7  C5    C6   CL1   109.96  3.000
 WR7  CL3   C6   CL1   109.03  3.000
 WR7  CL2   C6   CL1   109.18  3.000
 WR7  C11   N6   C10   106.44  3.000
 WR7  N4    C7   O2    125.39  3.000
 WR7  N4    C7   O1    110.14  3.000
 WR7  O2    C7   O1    124.47  3.000
 WR7  H8A   C8   H8    108.38  3.000
 WR7  H8A   C8   C9    110.43  3.000
 WR7  H8    C8   C9    111.07  3.000
 WR7  H8A   C8   O1    110.64  3.000
 WR7  H8    C8   O1    110.88  3.000
 WR7  C9    C8   O1    105.45  3.000
 WR7  H9A   C9   H9    107.34  3.000
 WR7  H9A   C9   C8    110.01  3.000
 WR7  H9    C9   C8    111.51  3.000
 WR7  H9A   C9   N5    107.35  3.000
 WR7  H9    C9   N5    109.78  3.000
 WR7  C8    C9   N5    110.70  3.000
 WR7  H10   C10  C12   127.88  3.000
 WR7  H10   C10  N6    122.71  3.000
 WR7  C12   C10  N6    109.41  3.000
 WR7  C13   C11  N6    124.43  3.000
 WR7  C13   C11  N5    123.65  3.000
 WR7  N6    C11  N5    111.92  3.000
 WR7  C10   C12  N7    127.10  3.000
 WR7  C10   C12  N5    106.68  3.000
 WR7  N7    C12  N5    126.22  3.000
 WR7  H13B  C13  H13A  108.16  3.000
 WR7  H13B  C13  H13   107.79  3.000
 WR7  H13A  C13  H13   108.25  3.000
 WR7  H13B  C13  C11   111.90  3.000
 WR7  H13A  C13  C11   108.86  3.000
 WR7  H13   C13  C11   111.75  3.000
 WR7  C12   N7   O4    116.81  3.000
 WR7  C12   N7   O3    119.29  3.000
 WR7  O4    N7   O3    123.91  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
 WR7  CONST_01  N2   C2   N1   C1      0.00   0.0  0
 WR7  CONST_02  N2   C3   C4   C1      0.00   0.0  0
 WR7  CONST_03  C3   C4   C1   N1      0.00   0.0  0
 WR7  CONST_04  C3   N2   C2   N1      0.00   0.0  0
 WR7  CONST_05  C4   C1   N1   C2      0.00   0.0  0
 WR7  CONST_06  C4   C3   N2   C2      0.00   0.0  0
 WR7  CONST_07  C10  N6   C11  N5      0.00   0.0  0
 WR7  CONST_08  N6   C10  C12  N5      0.00   0.0  0
 WR7  CONST_09  C12  N5   C11  N6      0.00   0.0  0
 WR7  CONST_10  C11  N5   C12  C10     0.00   0.0  0
 WR7  CONST_11  C12  C10  N6   C11     0.00   0.0  0
 WR7  CONST_12  N3   C2   N1   C1    180.00   0.0  0
 WR7  CONST_13  N3   C2   N2   C3    180.00   0.0  0
 WR7  CONST_14  N7   C12  C10  N6    180.00   0.0  0
 WR7  CONST_15  C9   N5   C11  N6    180.00   0.0  0
 WR7  CONST_16  C11  N5   C12  N7    180.00   0.0  0
 WR7  CONST_17  C10  C12  N5   C9    180.00   0.0  0
 WR7  CONST_18  C13  C11  N6   C10   180.00   0.0  0
 WR7  CONST_19  C13  C11  N5   C12   180.00   0.0  0
 WR7  CONST_20  H3   C3   C4   C1    180.00   0.0  0
 WR7  CONST_21  H4   C4   C1   N1    180.00   0.0  0
 WR7  CONST_22  H1   C1   N1   C2    180.00   0.0  0
 WR7  CONST_23  H10  C10  C12  N5    180.00   0.0  0
 WR7  CONST_24  C5   N3   C2   N1    180.00   0.0  0
 WR7  CONST_25  C5   N3   C2   N2      0.00   0.0  0
 WR7  CONST_26  N5   C12  N7   O3      0.00   0.0  0
 WR7  CONST_27  C10  C12  N7   O3    180.00   0.0  0
 WR7  CONST_28  N5   C12  N7   O4    180.00   0.0  0
 WR7  CONST_29  C10  C12  N7   O4      0.00   0.0  0
 WR7  CONST_30  HN3  N3   C2   N1      0.00   0.0  0
 WR7  Var_01    C11  N5   C9   C8     95.76  30.0  2
 WR7  Var_02    H13  C13  C11  N5     60.68  30.0  2
 WR7  Var_03    N5   C9   C8   O1   -177.44  30.0  3
 WR7  Var_04    C5   N4   C7   O1    179.77  30.0  1
 WR7  Var_05    C9   C8   O1   C7    178.55  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
 WR7  chir_01  C5  N3  N4  C6  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
 WR7  plan-1  N5   0.020
 WR7  plan-1  N6   0.020
 WR7  plan-1  C9   0.020
 WR7  plan-1  C10  0.020
 WR7  plan-1  C11  0.020
 WR7  plan-1  C12  0.020
 WR7  plan-1  C13  0.020
 WR7  plan-1  H10  0.020
 WR7  plan-1  N7   0.020
 WR7  plan-2  C1   0.020
 WR7  plan-2  N1   0.020
 WR7  plan-2  C2   0.020
 WR7  plan-2  N2   0.020
 WR7  plan-2  C3   0.020
 WR7  plan-2  N3   0.020
 WR7  plan-2  C4   0.020
 WR7  plan-2  H1   0.020
 WR7  plan-2  H3   0.020
 WR7  plan-2  H4   0.020
 WR7  plan-3  C2   0.020
 WR7  plan-3  N3   0.020
 WR7  plan-3  C5   0.020
 WR7  plan-3  HN3  0.020
 WR7  plan-4  O3   0.020
 WR7  plan-4  O4   0.020
 WR7  plan-4  C12  0.020
 WR7  plan-4  N7   0.020
 WR7  plan-5  O1   0.020
 WR7  plan-5  O2   0.020
 WR7  plan-5  N4   0.020
 WR7  plan-5  C7   0.020

