# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 03:11:36 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: 5-{4-[2-(4-bromophenoxy)ethyl]piperazin-1-yl}-4H-1,2,4-triazol-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1[nH]c(nn1)N2CCN(CCOc3ccc(Br)cc3)CC2
#
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
 3RM  3RM  5-{4-[2-(4-bromophenoxy)ethyl]piperazin-1-yl}-4H-1,2,4-triazol-3-amine  ligand  41  22  .  2021-08-04  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_3RM
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
 3RM  C1    C   CR16  0  -0.344   2.6798  -0.0291   1.3291
 3RM  N1    N   NT    0  -0.419  -1.7877  -1.6912   0.0259
 3RM  O1    O   O2    0  -0.461   1.0382  -1.4496   0.4916
 3RM  BR1   BR  BR    0  -0.060   6.4762   1.0810   0.1078
 3RM  C2    C   CR16  0  -0.211   3.9261   0.5645   1.2642
 3RM  N2    N   NT    0  -0.519  -4.2503  -0.3130  -0.2912
 3RM  C3    C   CR6   0  -0.138   4.7715   0.2694   0.2011
 3RM  N3    N   N     0  -0.400  -5.3836   1.6411  -1.0628
 3RM  C4    C   CR16  0  -0.211   4.3732  -0.6130  -0.7869
 3RM  N4    N   N     0  -0.385  -6.6045   2.2293  -0.7958
 3RM  C5    C   CR16  0  -0.380   3.1196  -1.2103  -0.7208
 3RM  N5    N   NR15  0  -0.703  -6.3949   0.4662   0.4704
 3RM  C6    C   CR6   0   0.397   2.2626  -0.9230   0.3394
 3RM  N6    N   NH2   0  -0.847  -8.4406   1.6977   0.6375
 3RM  C7    C   CH2   0  -0.211   0.5454  -2.3415  -0.4950
 3RM  C8    C   CH2   0  -0.299  -0.8408  -2.7822  -0.0817
 3RM  C9    C   CH2   0  -0.301  -2.1871  -1.1647  -1.2646
 3RM  C10   C   CH2   0  -0.294  -3.0970   0.0368  -1.1032
 3RM  C11   C   CH2   0  -0.316  -3.8840  -0.8980   0.9912
 3RM  C12   C   CH2   0  -0.286  -2.9649  -2.0823   0.7757
 3RM  C13   C   CR5   0   0.697  -5.2784   0.5913  -0.3051
 3RM  C14   C   CR5   0   0.573  -7.1861   1.5167   0.1193
 3RM  H1    H   HCR6  0   0.273   2.0173   0.2001   2.1544
 3RM  H2    H   HCR6  0   0.280   4.2261   1.2521   2.0438
 3RM  H4    H   HCR6  0   0.281   5.0239  -0.8526  -1.6173
 3RM  H5    H   HCR6  0   0.290   2.8386  -1.8964  -1.5078
 3RM  HN5   H   HNR5  0   0.425  -6.6244  -0.2703   1.1192
 3RM  HN6   H   HNH2  0   0.388  -8.8161   2.6115   0.4330
 3RM  HN6A  H   HNH2  0   0.392  -8.5247   1.4915   1.6221
 3RM  H7    H   HCH2  0   0.231   0.5387  -1.8560  -1.4767
 3RM  H7A   H   HCH2  0   0.243   1.1859  -3.2263  -0.5745
 3RM  H8    H   HCH2  0   0.248  -0.7730  -3.2770   0.8905
 3RM  H8A   H   HCH2  0   0.214  -1.1697  -3.5530  -0.7982
 3RM  H9    H   HCH2  0   0.248  -1.3102  -0.8392  -1.8268
 3RM  H9A   H   HCH2  0   0.202  -2.6958  -1.9321  -1.8733
 3RM  H10   H   HCH2  0   0.256  -3.4368   0.3628  -2.0851
 3RM  H10A  H   HCH2  0   0.221  -2.5363   0.8676  -0.6542
 3RM  H11   H   HCH2  0   0.230  -3.3920  -0.1580   1.6365
 3RM  H11A  H   HCH2  0   0.249  -4.7715  -1.2552   1.5132
 3RM  H12   H   HCH2  0   0.202  -3.5270  -2.8869   0.2714
 3RM  H12A  H   HCH2  0   0.249  -2.6597  -2.4619   1.7527

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
 3RM  C1   C2    aromatic  1.382  0.020  1.382
 3RM  C1   C6    aromatic  1.397  0.020  1.397
 3RM  N1   C8    single    1.449  0.020  1.449
 3RM  N1   C9    single    1.450  0.020  1.450
 3RM  N1   C12   single    1.449  0.020  1.449
 3RM  O1   C6    single    1.342  0.020  1.342
 3RM  O1   C7    single    1.418  0.020  1.418
 3RM  BR1  C3    single    1.890  0.020  1.890
 3RM  C2   C3    aromatic  1.390  0.020  1.390
 3RM  N2   C10   single    1.453  0.020  1.453
 3RM  N2   C11   single    1.456  0.020  1.456
 3RM  N2   C13   single    1.369  0.020  1.369
 3RM  C3   C4    aromatic  1.383  0.020  1.383
 3RM  N3   N4    aromatic  1.381  0.020  1.381
 3RM  N3   C13   aromatic  1.299  0.020  1.299
 3RM  C4   C5    aromatic  1.390  0.020  1.390
 3RM  N4   C14   aromatic  1.298  0.020  1.298
 3RM  C5   C6    aromatic  1.393  0.020  1.393
 3RM  N5   C13   aromatic  1.365  0.020  1.365
 3RM  N5   C14   aromatic  1.361  0.020  1.361
 3RM  N6   C14   single    1.369  0.020  1.369
 3RM  C7   C8    single    1.512  0.020  1.512
 3RM  C9   C10   single    1.516  0.020  1.516
 3RM  C11  C12   single    1.515  0.020  1.515
 3RM  C1   H1    single    0.930  0.020  1.080
 3RM  C2   H2    single    0.930  0.020  1.080
 3RM  C4   H4    single    0.930  0.020  1.080
 3RM  C5   H5    single    0.930  0.020  1.080
 3RM  N5   HN5   single    0.860  0.020  1.020
 3RM  N6   HN6   single    0.890  0.020  1.040
 3RM  N6   HN6A  single    0.890  0.020  1.040
 3RM  C7   H7    single    0.970  0.020  1.090
 3RM  C7   H7A   single    0.970  0.020  1.090
 3RM  C8   H8    single    0.970  0.020  1.090
 3RM  C8   H8A   single    0.970  0.020  1.090
 3RM  C9   H9    single    0.970  0.020  1.090
 3RM  C9   H9A   single    0.970  0.020  1.090
 3RM  C10  H10   single    0.970  0.020  1.090
 3RM  C10  H10A  single    0.970  0.020  1.090
 3RM  C11  H11   single    0.970  0.020  1.090
 3RM  C11  H11A  single    0.970  0.020  1.090
 3RM  C12  H12   single    0.970  0.020  1.090
 3RM  C12  H12A  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
 3RM  H1    C1   C6   119.51  3.000
 3RM  H1    C1   C2   119.78  3.000
 3RM  C6    C1   C2   120.71  3.000
 3RM  C12   N1   C9   109.55  3.000
 3RM  C12   N1   C8   111.48  3.000
 3RM  C9    N1   C8   112.79  3.000
 3RM  C7    O1   C6   119.02  3.000
 3RM  H2    C2   C3   121.16  3.000
 3RM  H2    C2   C1   119.29  3.000
 3RM  C3    C2   C1   119.56  3.000
 3RM  C13   N2   C11  117.58  3.000
 3RM  C13   N2   C10  115.55  3.000
 3RM  C11   N2   C10  112.90  3.000
 3RM  C4    C3   C2   120.43  3.000
 3RM  C4    C3   BR1  119.89  3.000
 3RM  C2    C3   BR1  119.68  3.000
 3RM  C13   N3   N4   107.64  3.000
 3RM  H4    C4   C5   118.93  3.000
 3RM  H4    C4   C3   121.08  3.000
 3RM  C5    C4   C3   119.99  3.000
 3RM  C14   N4   N3   107.37  3.000
 3RM  H5    C5   C6   121.66  3.000
 3RM  H5    C5   C4   118.18  3.000
 3RM  C6    C5   C4   120.15  3.000
 3RM  HN5   N5   C14  126.69  3.000
 3RM  HN5   N5   C13  128.23  3.000
 3RM  C14   N5   C13  104.96  3.000
 3RM  C5    C6   O1   124.53  3.000
 3RM  C5    C6   C1   119.16  3.000
 3RM  O1    C6   C1   116.31  3.000
 3RM  HN6A  N6   HN6  110.58  3.000
 3RM  HN6A  N6   C14  114.73  3.000
 3RM  HN6   N6   C14  112.58  3.000
 3RM  H7A   C7   H7   107.25  3.000
 3RM  H7A   C7   C8   108.69  3.000
 3RM  H7    C7   C8   111.63  3.000
 3RM  H7A   C7   O1   110.82  3.000
 3RM  H7    C7   O1   110.30  3.000
 3RM  C8    C7   O1   108.16  3.000
 3RM  H8A   C8   H8   106.26  3.000
 3RM  H8A   C8   C7   107.44  3.000
 3RM  H8    C8   C7   108.56  3.000
 3RM  H8A   C8   N1   112.32  3.000
 3RM  H8    C8   N1   108.38  3.000
 3RM  C7    C8   N1   113.58  3.000
 3RM  H9A   C9   H9   107.07  3.000
 3RM  H9A   C9   C10  109.46  3.000
 3RM  H9    C9   C10  107.50  3.000
 3RM  H9A   C9   N1   111.43  3.000
 3RM  H9    C9   N1   110.21  3.000
 3RM  C10   C9   N1   111.00  3.000
 3RM  H10A  C10  H10  107.55  3.000
 3RM  H10A  C10  C9   109.68  3.000
 3RM  H10   C10  C9   109.18  3.000
 3RM  H10A  C10  N2   111.03  3.000
 3RM  H10   C10  N2   109.16  3.000
 3RM  C9    C10  N2   110.19  3.000
 3RM  H11A  C11  H11  107.72  3.000
 3RM  H11A  C11  C12  107.82  3.000
 3RM  H11   C11  C12  109.79  3.000
 3RM  H11A  C11  N2   110.40  3.000
 3RM  H11   C11  N2   111.07  3.000
 3RM  C12   C11  N2   109.96  3.000
 3RM  H12A  C12  H12  107.33  3.000
 3RM  H12A  C12  C11  108.31  3.000
 3RM  H12   C12  C11  109.03  3.000
 3RM  H12A  C12  N1   109.25  3.000
 3RM  H12   C12  N1   111.97  3.000
 3RM  C11   C12  N1   110.82  3.000
 3RM  N5    C13  N3   109.83  3.000
 3RM  N5    C13  N2   123.21  3.000
 3RM  N3    C13  N2   126.90  3.000
 3RM  N6    C14  N5   122.48  3.000
 3RM  N6    C14  N4   127.22  3.000
 3RM  N5    C14  N4   110.20  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
 3RM  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 3RM  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 3RM  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 3RM  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 3RM  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 3RM  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 3RM  CONST_07  N5   C14  N4   N3     0.00   0.0  0
 3RM  CONST_08  C14  N5   C13  N3     0.00   0.0  0
 3RM  CONST_09  N5   C13  N3   N4     0.00   0.0  0
 3RM  CONST_10  C13  N5   C14  N4     0.00   0.0  0
 3RM  CONST_11  C14  N4   N3   C13    0.00   0.0  0
 3RM  CONST_12  N4   N3   C13  N2   180.00   0.0  0
 3RM  CONST_13  C14  N5   C13  N2   180.00   0.0  0
 3RM  CONST_14  BR1  C3   C2   C1   180.00   0.0  0
 3RM  CONST_15  C2   C1   C6   O1   180.00   0.0  0
 3RM  CONST_16  C4   C5   C6   O1   180.00   0.0  0
 3RM  CONST_17  C5   C4   C3   BR1  180.00   0.0  0
 3RM  CONST_18  N6   C14  N4   N3   180.00   0.0  0
 3RM  CONST_19  C13  N5   C14  N6   180.00   0.0  0
 3RM  CONST_20  H5   C5   C6   C1   180.00   0.0  0
 3RM  CONST_21  H4   C4   C3   C2   180.00   0.0  0
 3RM  CONST_22  HN5  N5   C13  N2     0.00   0.0  0
 3RM  CONST_23  H1   C1   C2   C3   180.00   0.0  0
 3RM  CONST_24  H2   C2   C3   C4   180.00   0.0  0
 3RM  Var_01    N2   C10  C9   N1   -56.02  30.0  1
 3RM  Var_02    N2   C11  C12  N1    56.80  30.0  1
 3RM  Var_03    C10  N2   C13  N3     7.59  30.0  2
 3RM  Var_04    C11  C12  N1   C9   -59.77  30.0  1
 3RM  Var_05    C12  C11  N2   C10  -54.26  30.0  1
 3RM  Var_06    C12  N1   C9   C10   59.34  30.0  1
 3RM  Var_07    C9   N1   C8   C7    72.68  30.0  1
 3RM  Var_08    O1   C7   C8   N1    60.95  30.0  1
 3RM  Var_09    C8   C7   O1   C6   179.97  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
 3RM  plan-1  N2    0.020
 3RM  plan-1  N3    0.020
 3RM  plan-1  N4    0.020
 3RM  plan-1  N5    0.020
 3RM  plan-1  N6    0.020
 3RM  plan-1  C13   0.020
 3RM  plan-1  C14   0.020
 3RM  plan-1  HN5   0.020
 3RM  plan-2  C1    0.020
 3RM  plan-2  O1    0.020
 3RM  plan-2  BR1   0.020
 3RM  plan-2  C2    0.020
 3RM  plan-2  C3    0.020
 3RM  plan-2  C4    0.020
 3RM  plan-2  C5    0.020
 3RM  plan-2  C6    0.020
 3RM  plan-2  H1    0.020
 3RM  plan-2  H2    0.020
 3RM  plan-2  H4    0.020
 3RM  plan-2  H5    0.020
 3RM  plan-3  N6    0.020
 3RM  plan-3  C14   0.020
 3RM  plan-3  HN6   0.020
 3RM  plan-3  HN6A  0.020

