# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 15:48:40 2022
#   Inital geometry file: a 121 line input string
#   Ligand name: 1-[2-(3-ammoniopropoxy)-5-methoxybenzyl]-4-carbamimidoylpiperazin-1-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(OCCC[NH3+])c(C[NH+]2CCN(CC2)C(N)=N)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
 P12  P12  1-[2-(3-ammoniopropoxy)-5-methoxybenzyl]-4-carbamimidoylpiperazin-1-ium  ligand  52  23  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P12
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
 P12  C5    C  CR16  0  -0.371  -5.3845   -5.5380  -0.2391
 P12  C4    C  CR6   0   0.383  -5.1072   -5.9372  -1.5394
 P12  C3    C  CR16  0  -0.367  -3.7766   -5.9880  -1.9589
 P12  C2    C  CR6   0   0.008  -2.7464   -5.6495  -1.1015
 P12  C1    C  CR6   0   0.365  -3.0341   -5.2580   0.2137
 P12  C6    C  CR16  0  -0.352  -4.3519   -5.2025   0.6334
 P12  OA    O  O2    0  -0.504  -1.9599   -4.9698   0.9889
 P12  CB    C  CH2   0  -0.197  -2.1782   -4.4402   2.2886
 P12  CG    C  CH2   0  -0.490  -0.8379   -4.1214   2.9140
 P12  CD    C  CH2   0  -0.291   0.0030   -5.3611   3.1507
 P12  NE    N  NT3   1  -0.776   1.2331   -5.0257   3.9117
 P12  CG1   C  CH2   0  -0.321  -0.9556   -8.1021  -1.2512
 P12  CD1   C  CH2   0  -0.308  -0.1291   -9.1349  -0.5165
 P12  NE1   N  NT    0  -0.472   1.2752   -8.9344  -0.7893
 P12  CD2   C  CH2   0  -0.328   1.7234   -7.6160  -0.3942
 P12  CG2   C  CH2   0  -0.332   0.9381   -6.5521  -1.1292
 P12  NB    N  NT1   1  -0.546  -0.5232   -6.7227  -0.8821
 P12  CA    C  CH2   0  -0.393  -1.3268   -5.6617  -1.5731
 P12  NH1   N  N     0  -0.696   1.6361  -11.1625  -0.3226
 P12  NH2   N  NH2   0  -0.837   3.4363   -9.7617  -0.9508
 P12  OA1   O  O2    0  -0.474  -6.0345   -6.2877  -2.4519
 P12  CB1   C  CH3   0  -0.439  -7.3946   -6.2617  -2.0681
 P12  H5    H  HCR6  0   0.290  -6.3995   -5.4774   0.1284
 P12  H3    H  HCR6  0   0.276  -3.5524   -6.2896  -2.9753
 P12  H6    H  HCR6  0   0.293  -4.6122   -4.8976   1.6373
 P12  HB1   H  HCH2  0   0.260  -2.7750   -3.5258   2.2271
 P12  HB2   H  HCH2  0   0.243  -2.7253   -5.1601   2.9064
 P12  HG1   H  HCH2  0   0.274  -0.2967   -3.4001   2.2977
 P12  HG2   H  HCH2  0   0.277  -1.0454   -3.6368   3.8710
 P12  HD1   H  HCH2  0   0.256   0.3390   -5.8211   2.2245
 P12  HD2   H  HCH2  0   0.306  -0.5346   -6.1079   3.7311
 P12  HE1   H  HNT3  0   0.482   1.7889   -5.8574   4.1102
 P12  HE2   H  HNT3  0   0.474   1.0194   -4.5934   4.8105
 P12  HE3   H  HNT3  0   0.474   1.8362   -4.3794   3.4026
 P12  HG11  H  HCH2  0   0.303  -0.8364   -8.1918  -2.3306
 P12  HG12  H  HCH2  0   0.316  -2.0089   -8.2037  -0.9985
 P12  HD11  H  HCH2  0   0.246  -0.3449   -9.0949   0.5601
 P12  HD12  H  HCH2  0   0.297  -0.4362  -10.1172  -0.8651
 P12  HD21  H  HCH2  0   0.302   2.7735   -7.4617  -0.6253
 P12  HD22  H  HCH2  0   0.242   1.6228   -7.4738   0.6930
 P12  HG21  H  HCH2  0   0.315   1.2204   -5.5580  -0.7869
 P12  HG22  H  HCH2  0   0.314   1.0910   -6.6167  -2.2056
 P12  HB    H  HNT1  0   0.448  -0.6850   -6.6018   0.1214
 P12  HA1   H  HCH2  0   0.325  -1.2547   -5.8547  -2.6424
 P12  HA2   H  HCH2  0   0.323  -0.8308   -4.7132  -1.3676
 P12  HH11  H  H     0   0.328   2.3344  -11.8929  -0.4002
 P12  HH21  H  HNH2  0   0.392   4.0243  -10.5767  -1.0233
 P12  HH22  H  HNH2  0   0.392   3.6203   -9.1062  -1.6952
 P12  HB11  H  HCH3  0   0.229  -7.5985   -6.9439  -1.2384
 P12  HB12  H  HCH3  0   0.262  -7.9664   -6.5850  -2.9344
 P12  HB3   H  HCH3  0   0.229  -7.7219   -5.2571  -1.7872
 P12  CZ    C  C     0   0.568   2.1160  -10.0327  -0.6766

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
 P12  C5   C4    aromatic  1.388  0.020  1.388
 P12  C5   C6    aromatic  1.393  0.020  1.393
 P12  C5   H5    single    0.930  0.020  1.080
 P12  C4   C3    aromatic  1.396  0.020  1.396
 P12  C4   OA1   single    1.347  0.020  1.347
 P12  C3   C2    aromatic  1.382  0.020  1.382
 P12  C3   H3    single    0.930  0.020  1.080
 P12  C2   C1    aromatic  1.402  0.020  1.402
 P12  C2   CA    single    1.496  0.020  1.496
 P12  C1   C6    aromatic  1.384  0.020  1.384
 P12  C1   OA    single    1.356  0.020  1.356
 P12  C6   H6    single    0.930  0.020  1.080
 P12  OA   CB    single    1.420  0.020  1.420
 P12  CB   CG    single    1.513  0.020  1.513
 P12  CB   HB1   single    0.970  0.020  1.090
 P12  CB   HB2   single    0.970  0.020  1.090
 P12  CG   CD    single    1.517  0.020  1.517
 P12  CG   HG1   single    0.970  0.020  1.090
 P12  CG   HG2   single    0.970  0.020  1.090
 P12  CD   NE    single    1.485  0.020  1.485
 P12  CD   HD1   single    0.970  0.020  1.090
 P12  CD   HD2   single    0.970  0.020  1.090
 P12  NE   HE1   single    0.890  0.020  1.040
 P12  NE   HE2   single    0.890  0.020  1.040
 P12  NE   HE3   single    0.890  0.020  1.040
 P12  CG1  CD1   single    1.513  0.020  1.513
 P12  CG1  NB    single    1.492  0.020  1.492
 P12  CG1  HG11  single    0.970  0.020  1.090
 P12  CG1  HG12  single    0.970  0.020  1.090
 P12  CD1  NE1   single    1.444  0.020  1.444
 P12  CD1  HD11  single    0.970  0.020  1.090
 P12  CD1  HD12  single    0.970  0.020  1.090
 P12  NE1  CD2   single    1.447  0.020  1.447
 P12  NE1  CZ    single    1.388  0.020  1.388
 P12  CD2  CG2   single    1.513  0.020  1.513
 P12  CD2  HD21  single    0.970  0.020  1.090
 P12  CD2  HD22  single    0.970  0.020  1.090
 P12  CG2  NB    single    1.492  0.020  1.492
 P12  CG2  HG21  single    0.970  0.020  1.090
 P12  CG2  HG22  single    0.970  0.020  1.090
 P12  NB   CA    single    1.500  0.020  1.500
 P12  NB   HB    single    0.890  0.020  1.040
 P12  CA   HA1   single    0.970  0.020  1.090
 P12  CA   HA2   single    0.970  0.020  1.090
 P12  CZ   NH1   double    1.277  0.020  1.277
 P12  CZ   NH2   single    1.375  0.020  1.375
 P12  NH1  HH11  single    0.890  0.020  1.040
 P12  NH2  HH21  single    0.890  0.020  1.040
 P12  NH2  HH22  single    0.890  0.020  1.040
 P12  OA1  CB1   single    1.413  0.020  1.413
 P12  CB1  HB11  single    0.970  0.020  1.090
 P12  CB1  HB12  single    0.970  0.020  1.090
 P12  CB1  HB3   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
 P12  H5    C5   C6    118.01  3.000
 P12  H5    C5   C4    121.47  3.000
 P12  C6    C5   C4    120.53  3.000
 P12  OA1   C4   C3    116.29  3.000
 P12  OA1   C4   C5    124.87  3.000
 P12  C3    C4   C5    118.84  3.000
 P12  H3    C3   C2    119.72  3.000
 P12  H3    C3   C4    119.28  3.000
 P12  C2    C3   C4    120.99  3.000
 P12  CA    C2   C1    119.52  3.000
 P12  CA    C2   C3    120.64  3.000
 P12  C1    C2   C3    119.82  3.000
 P12  OA    C1   C6    124.93  3.000
 P12  OA    C1   C2    115.66  3.000
 P12  C6    C1   C2    119.41  3.000
 P12  H6    C6   C1    121.48  3.000
 P12  H6    C6   C5    118.11  3.000
 P12  C1    C6   C5    120.41  3.000
 P12  CB    OA   C1    118.73  3.000
 P12  HB2   CB   HB1   107.98  3.000
 P12  HB2   CB   CG    110.36  3.000
 P12  HB1   CB   CG    109.30  3.000
 P12  HB2   CB   OA    110.36  3.000
 P12  HB1   CB   OA    110.13  3.000
 P12  CG    CB   OA    108.70  3.000
 P12  HG2   CG   HG1   107.18  3.000
 P12  HG2   CG   CD    109.34  3.000
 P12  HG1   CG   CD    110.68  3.000
 P12  HG2   CG   CB    106.69  3.000
 P12  HG1   CG   CB    110.17  3.000
 P12  CD    CG   CB    112.55  3.000
 P12  HD2   CD   HD1   108.46  3.000
 P12  HD2   CD   NE    106.92  3.000
 P12  HD1   CD   NE    106.03  3.000
 P12  HD2   CD   CG    111.74  3.000
 P12  HD1   CD   CG    112.59  3.000
 P12  NE    CD   CG    110.78  3.000
 P12  HE3   NE   HE2   107.16  3.000
 P12  HE3   NE   HE1   106.95  3.000
 P12  HE2   NE   HE1   106.76  3.000
 P12  HE3   NE   CD    112.16  3.000
 P12  HE2   NE   CD    111.95  3.000
 P12  HE1   NE   CD    111.54  3.000
 P12  HG12  CG1  HG11  109.16  3.000
 P12  HG12  CG1  NB    108.03  3.000
 P12  HG11  CG1  NB    106.82  3.000
 P12  HG12  CG1  CD1   110.63  3.000
 P12  HG11  CG1  CD1   111.41  3.000
 P12  NB    CG1  CD1   110.65  3.000
 P12  HD12  CD1  HD11  106.97  3.000
 P12  HD12  CD1  NE1   109.85  3.000
 P12  HD11  CD1  NE1   111.77  3.000
 P12  HD12  CD1  CG1   107.87  3.000
 P12  HD11  CD1  CG1   110.10  3.000
 P12  NE1   CD1  CG1   110.16  3.000
 P12  CZ    NE1  CD2   120.73  3.000
 P12  CZ    NE1  CD1   117.64  3.000
 P12  CD2   NE1  CD1   112.08  3.000
 P12  HD22  CD2  HD21  106.26  3.000
 P12  HD22  CD2  CG2   109.97  3.000
 P12  HD21  CD2  CG2   107.37  3.000
 P12  HD22  CD2  NE1   111.03  3.000
 P12  HD21  CD2  NE1   111.76  3.000
 P12  CG2   CD2  NE1   110.32  3.000
 P12  HG22  CG2  HG21  109.18  3.000
 P12  HG22  CG2  NB    107.12  3.000
 P12  HG21  CG2  NB    107.84  3.000
 P12  HG22  CG2  CD2   111.44  3.000
 P12  HG21  CG2  CD2   110.78  3.000
 P12  NB    CG2  CD2   110.34  3.000
 P12  HB    NB   CA    106.47  3.000
 P12  HB    NB   CG2   107.68  3.000
 P12  CA    NB   CG2   111.57  3.000
 P12  HB    NB   CG1   107.81  3.000
 P12  CA    NB   CG1   112.64  3.000
 P12  CG2   NB   CG1   110.40  3.000
 P12  HA2   CA   HA1   108.02  3.000
 P12  HA2   CA   NB    106.56  3.000
 P12  HA1   CA   NB    106.95  3.000
 P12  HA2   CA   C2    111.43  3.000
 P12  HA1   CA   C2    111.95  3.000
 P12  NB    CA   C2    111.65  3.000
 P12  HH11  NH1  CZ    110.94  3.000
 P12  HH22  NH2  HH21  111.47  3.000
 P12  HH22  NH2  CZ    116.75  3.000
 P12  HH21  NH2  CZ    114.52  3.000
 P12  CB1   OA1  C4    118.26  3.000
 P12  HB3   CB1  HB12  108.69  3.000
 P12  HB3   CB1  HB11  108.81  3.000
 P12  HB12  CB1  HB11  108.73  3.000
 P12  HB3   CB1  OA1   112.01  3.000
 P12  HB12  CB1  OA1   106.51  3.000
 P12  HB11  CB1  OA1   111.97  3.000
 P12  NH2   CZ   NH1   126.17  3.000
 P12  NH2   CZ   NE1   114.17  3.000
 P12  NH1   CZ   NE1   119.65  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
 P12  CONST_01  C2    C3   C4   C5      0.00   0.0  0
 P12  CONST_02  C2    C1   C6   C5      0.00   0.0  0
 P12  CONST_03  C1    C6   C5   C4      0.00   0.0  0
 P12  CONST_04  C1    C2   C3   C4      0.00   0.0  0
 P12  CONST_05  C6    C5   C4   C3      0.00   0.0  0
 P12  CONST_06  C6    C1   C2   C3      0.00   0.0  0
 P12  CONST_07  OA    C1   C6   C5    180.00   0.0  0
 P12  CONST_08  CA    C2   C3   C4    180.00   0.0  0
 P12  CONST_09  OA    C1   C2   C3    180.00   0.0  0
 P12  CONST_10  OA1   C4   C3   C2    180.00   0.0  0
 P12  CONST_11  OA1   C4   C5   C6    180.00   0.0  0
 P12  CONST_12  CA    C2   C1   C6    180.00   0.0  0
 P12  CONST_13  H3    C3   C4   C5    180.00   0.0  0
 P12  CONST_14  H6    C6   C5   C4    180.00   0.0  0
 P12  CONST_15  H5    C5   C4   C3    180.00   0.0  0
 P12  CONST_16  NH1   CZ   NE1  CD1     0.00   0.0  0
 P12  CONST_17  NH2   CZ   NE1  CD1   180.00   0.0  0
 P12  CONST_20  HH11  NH1  CZ   NE1   180.00   0.0  0
 P12  CONST_21  HH21  NH2  CZ   NE1   180.00   0.0  0
 P12  Var_01    CD2   NE1  CD1  CG1    58.88  30.0  1
 P12  Var_02    CG2   CD2  NE1  CD1   -59.14  30.0  1
 P12  Var_03    NB    CG1  CD1  NE1   -56.50  30.0  1
 P12  Var_04    NB    CG2  CD2  NE1    56.69  30.0  1
 P12  Var_05    NB    CA   C2   C3   -113.88  30.0  2
 P12  Var_06    CG    CB   OA   C1   -176.40  30.0  3
 P12  Var_07    HB11  CB1  OA1  C4    -60.64  30.0  3
 P12  Var_08    CD    CG   CB   OA    -64.97  30.0  3
 P12  Var_09    NE    CD   CG   CB   -173.13  30.0  3
 P12  Var_10    HE1   NE   CD   CG    177.70  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
 P12  chir_01  NB  CG1  CG2  CA  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
 P12  plan-1  C5    0.020
 P12  plan-1  C4    0.020
 P12  plan-1  C3    0.020
 P12  plan-1  C2    0.020
 P12  plan-1  C1    0.020
 P12  plan-1  C6    0.020
 P12  plan-1  OA    0.020
 P12  plan-1  CA    0.020
 P12  plan-1  OA1   0.020
 P12  plan-1  H5    0.020
 P12  plan-1  H3    0.020
 P12  plan-1  H6    0.020
 P12  plan-2  CD1   0.020
 P12  plan-2  NE1   0.020
 P12  plan-2  CD2   0.020
 P12  plan-2  NH1   0.020
 P12  plan-2  NH2   0.020
 P12  plan-2  HH11  0.020
 P12  plan-2  HH21  0.020
 P12  plan-2  HH22  0.020
 P12  plan-2  CZ    0.020

