# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 18:01:44 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 1-(4-methoxybenzyl)-3-(5-nitro-1,3-thiazol-2-yl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(CNC(=O)Nc2sc(cn2)[N+]([O-])=O)cc1
#
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
 TMU  TMU  1-(4-methoxybenzyl)-3-(5-nitro-1,3-thiazol-2-yl)urea  ligand  33  21  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_TMU
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
 TMU  C1    C  CR5    0   0.346  -2.4544  -0.1669   0.0141
 TMU  S2    S  S2     0   0.272  -3.4040   1.2554   0.3421
 TMU  N3    N  N      0  -0.395  -3.1340  -1.2380  -0.2980
 TMU  N4    N  NH1    0  -0.746  -1.1083  -0.0681   0.0953
 TMU  C5    C  CR5    0  -0.065  -4.8004   0.2927   0.0238
 TMU  C6    C  CR15   0   0.030  -4.4561  -0.9861  -0.2926
 TMU  C7    C  C      0   0.759  -0.1895  -1.1207  -0.0413
 TMU  N8    N  N      1   0.360  -6.0877   0.8495   0.1043
 TMU  N9    N  NH1    0  -0.675   1.0851  -0.7033   0.0185
 TMU  O10   O  O      0  -0.481  -0.5231  -2.2767  -0.1911
 TMU  O11   O  O     -1  -0.398  -7.0389   0.1348  -0.1244
 TMU  O12   O  O      0  -0.400  -6.1611   2.0254   0.4019
 TMU  C13   C  CH2    0  -0.312   2.1890  -1.6459  -0.0762
 TMU  C14   C  CR6    0   0.017   3.4956  -0.9101  -0.0019
 TMU  C15   C  CR16   0  -0.266   4.0813  -0.6095   1.2277
 TMU  C16   C  CR16   0  -0.270   4.1391  -0.4804  -1.1539
 TMU  C17   C  CR16   0  -0.330   5.2699   0.0911   1.3017
 TMU  C18   C  CR16   0  -0.371   5.3353   0.2251  -1.1011
 TMU  C19   C  CR6    0   0.375   5.9085   0.5175   0.1342
 TMU  O20   O  O2     0  -0.469   7.0608   1.1925   0.2974
 TMU  C21   C  CH3    0  -0.437   7.7375   1.6610  -0.8525
 TMU  HN4   H  HNH1   0   0.436  -0.7352   0.8458   0.3086
 TMU  H6    H  HCR5   0   0.317  -5.1565  -1.7739  -0.5317
 TMU  HN9   H  HNH1   0   0.411   1.3074   0.2740   0.1210
 TMU  H131  H  HCH2   0   0.258   2.1237  -2.1993  -1.0158
 TMU  H132  H  HCH2   0   0.257   2.1199  -2.3769   0.7328
 TMU  H15   H  HCR6   0   0.256   3.6040  -0.9321   2.1455
 TMU  H16   H  HCR6   0   0.258   3.7079  -0.7002  -2.1232
 TMU  H17   H  HCR6   0   0.264   5.7155   0.3110   2.2639
 TMU  H18   H  HCR6   0   0.280   5.8002   0.5312  -2.0282
 TMU  H211  H  HCH3   0   0.260   8.6241   2.1817  -0.4994
 TMU  H212  H  HCH3   0   0.229   8.0477   0.8413  -1.5057
 TMU  H213  H  HCH3   0   0.229   7.1256   2.3594  -1.4289

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
 TMU  C1   S2    aromatic  1.741  0.020  1.741
 TMU  C1   N3    aromatic  1.306  0.020  1.306
 TMU  C1   N4    single    1.352  0.020  1.352
 TMU  S2   C5    aromatic  1.726  0.020  1.726
 TMU  N3   C6    aromatic  1.346  0.020  1.346
 TMU  N4   C7    single    1.404  0.020  1.404
 TMU  N4   HN4   single    0.860  0.020  1.020
 TMU  C5   C6    aromatic  1.362  0.020  1.362
 TMU  C5   N8    single    1.405  0.020  1.405
 TMU  C6   H6    single    0.930  0.020  1.080
 TMU  C7   N9    single    1.342  0.020  1.342
 TMU  C7   O10   double    1.213  0.020  1.213
 TMU  N8   O11   single    1.212  0.020  1.212
 TMU  N8   O12   double    1.215  0.020  1.215
 TMU  N9   C13   single    1.455  0.020  1.455
 TMU  N9   HN9   single    0.860  0.020  1.020
 TMU  C13  C14   single    1.501  0.020  1.501
 TMU  C13  H131  single    0.970  0.020  1.090
 TMU  C13  H132  single    0.970  0.020  1.090
 TMU  C14  C15   aromatic  1.395  0.020  1.395
 TMU  C14  C16   aromatic  1.388  0.020  1.388
 TMU  C15  C17   aromatic  1.382  0.020  1.382
 TMU  C15  H15   single    0.930  0.020  1.080
 TMU  C16  C18   aromatic  1.390  0.020  1.390
 TMU  C16  H16   single    0.930  0.020  1.080
 TMU  C17  C19   aromatic  1.397  0.020  1.397
 TMU  C17  H17   single    0.930  0.020  1.080
 TMU  C18  C19   aromatic  1.393  0.020  1.393
 TMU  C18  H18   single    0.930  0.020  1.080
 TMU  C19  O20   single    1.345  0.020  1.345
 TMU  O20  C21   single    1.414  0.020  1.414
 TMU  C21  H211  single    0.970  0.020  1.090
 TMU  C21  H212  single    0.970  0.020  1.090
 TMU  C21  H213  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
 TMU  N4    C1   N3    126.31  3.000
 TMU  N4    C1   S2    118.16  3.000
 TMU  N3    C1   S2    115.53  3.000
 TMU  C5    S2   C1     87.19  3.000
 TMU  C6    N3   C1    110.90  3.000
 TMU  HN4   N4   C7    117.22  3.000
 TMU  HN4   N4   C1    116.52  3.000
 TMU  C7    N4   C1    126.22  3.000
 TMU  N8    C5   C6    128.11  3.000
 TMU  N8    C5   S2    120.65  3.000
 TMU  C6    C5   S2    111.24  3.000
 TMU  H6    C6   C5    124.90  3.000
 TMU  H6    C6   N3    119.95  3.000
 TMU  C5    C6   N3    115.15  3.000
 TMU  O10   C7   N9    124.27  3.000
 TMU  O10   C7   N4    123.15  3.000
 TMU  N9    C7   N4    112.58  3.000
 TMU  O12   N8   O11   124.73  3.000
 TMU  O12   N8   C5    116.93  3.000
 TMU  O11   N8   C5    118.34  3.000
 TMU  HN9   N9   C13   117.89  3.000
 TMU  HN9   N9   C7    121.04  3.000
 TMU  C13   N9   C7    121.07  3.000
 TMU  H132  C13  H131  107.11  3.000
 TMU  H132  C13  C14   110.26  3.000
 TMU  H131  C13  C14   110.05  3.000
 TMU  H132  C13  N9    109.71  3.000
 TMU  H131  C13  N9    109.81  3.000
 TMU  C14   C13  N9    109.86  3.000
 TMU  C16   C14  C15   118.06  3.000
 TMU  C16   C14  C13   120.94  3.000
 TMU  C15   C14  C13   120.98  3.000
 TMU  H15   C15  C17   118.98  3.000
 TMU  H15   C15  C14   119.84  3.000
 TMU  C17   C15  C14   121.18  3.000
 TMU  H16   C16  C18   118.65  3.000
 TMU  H16   C16  C14   119.69  3.000
 TMU  C18   C16  C14   121.65  3.000
 TMU  H17   C17  C19   119.49  3.000
 TMU  H17   C17  C15   120.30  3.000
 TMU  C19   C17  C15   120.21  3.000
 TMU  H18   C18  C19   121.61  3.000
 TMU  H18   C18  C16   118.76  3.000
 TMU  C19   C18  C16   119.63  3.000
 TMU  O20   C19  C18   124.43  3.000
 TMU  O20   C19  C17   116.31  3.000
 TMU  C18   C19  C17   119.27  3.000
 TMU  C21   O20  C19   118.52  3.000
 TMU  H213  C21  H212  108.84  3.000
 TMU  H213  C21  H211  108.77  3.000
 TMU  H212  C21  H211  108.77  3.000
 TMU  H213  C21  O20   111.88  3.000
 TMU  H212  C21  O20   111.92  3.000
 TMU  H211  C21  O20   106.55  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
 TMU  CONST_01  C6    C5   S2   C1     0.00   0.0  0
 TMU  CONST_02  C5    C6   N3   C1     0.00   0.0  0
 TMU  CONST_03  C6    N3   C1   S2     0.00   0.0  0
 TMU  CONST_04  N3    C6   C5   S2     0.00   0.0  0
 TMU  CONST_05  C5    S2   C1   N3     0.00   0.0  0
 TMU  CONST_06  C19   C17  C15  C14    0.00   0.0  0
 TMU  CONST_07  C19   C18  C16  C14    0.00   0.0  0
 TMU  CONST_08  C18   C16  C14  C15    0.00   0.0  0
 TMU  CONST_09  C18   C19  C17  C15    0.00   0.0  0
 TMU  CONST_10  C17   C15  C14  C16    0.00   0.0  0
 TMU  CONST_11  C17   C19  C18  C16    0.00   0.0  0
 TMU  CONST_12  N8    C5   S2   C1   180.00   0.0  0
 TMU  CONST_13  N8    C5   C6   N3   180.00   0.0  0
 TMU  CONST_14  C5    S2   C1   N4   180.00   0.0  0
 TMU  CONST_15  C6    N3   C1   N4   180.00   0.0  0
 TMU  CONST_16  C17   C15  C14  C13  180.00   0.0  0
 TMU  CONST_17  C18   C16  C14  C13  180.00   0.0  0
 TMU  CONST_18  O20   C19  C17  C15  180.00   0.0  0
 TMU  CONST_19  O20   C19  C18  C16  180.00   0.0  0
 TMU  CONST_20  H6    C6   N3   C1   180.00   0.0  0
 TMU  CONST_21  H17   C17  C15  C14  180.00   0.0  0
 TMU  CONST_22  H18   C18  C16  C14  180.00   0.0  0
 TMU  CONST_23  H16   C16  C14  C15  180.00   0.0  0
 TMU  CONST_24  H15   C15  C14  C16  180.00   0.0  0
 TMU  CONST_25  C7    N4   C1   S2   180.00   0.0  0
 TMU  CONST_26  O11   N8   C5   S2   180.00   0.0  0
 TMU  CONST_27  O12   N8   C5   S2     0.00   0.0  0
 TMU  CONST_28  C7    N4   C1   N3     0.00   0.0  0
 TMU  CONST_29  O11   N8   C5   C6     0.00   0.0  0
 TMU  CONST_30  O12   N8   C5   C6   180.00   0.0  0
 TMU  CONST_31  HN4   N4   C1   S2     0.00   0.0  0
 TMU  CONST_32  O10   C7   N4   C1     0.00   0.0  0
 TMU  CONST_33  N9    C7   N4   C1   180.00   0.0  0
 TMU  CONST_34  C13   N9   C7   O10    0.00   0.0  0
 TMU  CONST_35  C13   N9   C7   N4   180.00   0.0  0
 TMU  CONST_36  HN9   N9   C7   O10  180.00   0.0  0
 TMU  Var_01    C15   C14  C13  N9    86.21  30.0  2
 TMU  Var_02    C14   C13  N9   C7   179.13  30.0  3
 TMU  Var_03    H211  C21  O20  C19  179.31  30.0  3

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
 TMU  plan-1  C1   0.020
 TMU  plan-1  S2   0.020
 TMU  plan-1  N3   0.020
 TMU  plan-1  N4   0.020
 TMU  plan-1  C5   0.020
 TMU  plan-1  C6   0.020
 TMU  plan-1  N8   0.020
 TMU  plan-1  H6   0.020
 TMU  plan-2  C13  0.020
 TMU  plan-2  C14  0.020
 TMU  plan-2  C15  0.020
 TMU  plan-2  C16  0.020
 TMU  plan-2  C17  0.020
 TMU  plan-2  C18  0.020
 TMU  plan-2  C19  0.020
 TMU  plan-2  O20  0.020
 TMU  plan-2  H15  0.020
 TMU  plan-2  H16  0.020
 TMU  plan-2  H17  0.020
 TMU  plan-2  H18  0.020
 TMU  plan-3  C1   0.020
 TMU  plan-3  N4   0.020
 TMU  plan-3  C7   0.020
 TMU  plan-3  N9   0.020
 TMU  plan-3  O10  0.020
 TMU  plan-3  C13  0.020
 TMU  plan-3  HN4  0.020
 TMU  plan-3  HN9  0.020
 TMU  plan-4  C5   0.020
 TMU  plan-4  N8   0.020
 TMU  plan-4  O11  0.020
 TMU  plan-4  O12  0.020

