# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 13:13:51 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: 1-[4-(hydroxymethyl)phenyl]guanidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)Nc1ccc(CO)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
 1JZ  1JZ  1-[4-(hydroxymethyl)phenyl]guanidine  ligand  23  12  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1JZ
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
 1JZ  C10   C  C     0   0.560  -3.1024   0.3181  -0.1952
 1JZ  C12   C  CR16  0  -0.283   1.2479   1.1585   0.2732
 1JZ  C8    C  CR16  0  -0.348   0.1845  -1.3720   0.0789
 1JZ  C7    C  CR16  0  -0.275   1.5499  -1.1994   0.1982
 1JZ  O2    O  OH1   0  -0.670   4.1190   0.2265  -0.9404
 1JZ  C6    C  CR6   0   0.067   2.1117   0.0714   0.3025
 1JZ  C9    C  CR6   0   0.364  -0.6813  -0.2699   0.0519
 1JZ  C11   C  CR16  0  -0.313  -0.1275   1.0089   0.1522
 1JZ  N3    N  NH1   0  -0.750  -2.0372  -0.5424  -0.0524
 1JZ  N4    N  NH2   0  -0.844  -4.3024  -0.3583  -0.2479
 1JZ  N5    N  N     0  -0.694  -2.9445   1.5802  -0.3206
 1JZ  H12   H  HCR6  0   0.246   1.6511   2.1622   0.3516
 1JZ  H8    H  HCR6  0   0.261  -0.2216  -2.3748   0.0059
 1JZ  H7    H  HCR6  0   0.250   2.1895  -2.0744   0.2169
 1JZ  H5    H  HCH2  0   0.205   4.0350  -0.5433   0.9898
 1JZ  H5A   H  HCH2  0   0.205   3.8259   1.2031   0.8752
 1JZ  HO2   H  HOH1  0   0.453   5.0763   0.3017  -0.8779
 1JZ  H11   H  HCR6  0   0.286  -0.7703   1.8735   0.1266
 1JZ  HN3   H  HNH1  0   0.404  -2.2595  -1.5231  -0.1182
 1JZ  HN4   H  HNH2  0   0.389  -4.3790  -1.1977   0.3065
 1JZ  HN4A  H  HNH2  0   0.391  -5.1207   0.2226  -0.1582
 1JZ  HN5   H  H     0   0.329  -3.8435   2.0435  -0.3849
 1JZ  C5    C  CH2   0  -0.231   3.5973   0.2536   0.3763

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
 1JZ  N5   C10   double    1.278  0.020  1.278
 1JZ  N4   C10   single    1.379  0.020  1.379
 1JZ  C10  N3    single    1.377  0.020  1.377
 1JZ  C11  C12   aromatic  1.389  0.020  1.389
 1JZ  C6   C12   aromatic  1.389  0.020  1.389
 1JZ  C12  H12   single    0.930  0.020  1.080
 1JZ  C8   C9    aromatic  1.402  0.020  1.402
 1JZ  C8   C7    aromatic  1.381  0.020  1.381
 1JZ  C8   H8    single    0.930  0.020  1.080
 1JZ  C7   C6    aromatic  1.393  0.020  1.393
 1JZ  C7   H7    single    0.930  0.020  1.080
 1JZ  C6   C5    single    1.499  0.020  1.499
 1JZ  C5   O2    single    1.416  0.020  1.416
 1JZ  C5   H5    single    0.970  0.020  1.090
 1JZ  C5   H5A   single    0.970  0.020  1.090
 1JZ  O2   HO2   single    0.850  0.020  0.980
 1JZ  N3   C9    single    1.387  0.020  1.387
 1JZ  C9   C11   aromatic  1.397  0.020  1.397
 1JZ  C11  H11   single    0.930  0.020  1.080
 1JZ  N3   HN3   single    0.860  0.020  1.020
 1JZ  N4   HN4   single    0.890  0.020  1.040
 1JZ  N4   HN4A  single    0.890  0.020  1.040
 1JZ  N5   HN5   single    0.890  0.020  1.040

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
 1JZ  N5    C10  N4   126.04  3.000
 1JZ  N4    C10  N3   111.76  3.000
 1JZ  N5    C10  N3   122.12  3.000
 1JZ  H12   C12  C11  118.31  3.000
 1JZ  H12   C12  C6   119.45  3.000
 1JZ  C11   C12  C6   122.24  3.000
 1JZ  H8    C8   C9   119.63  3.000
 1JZ  H8    C8   C7   119.44  3.000
 1JZ  C9    C8   C7   120.93  3.000
 1JZ  H7    C7   C6   119.80  3.000
 1JZ  H7    C7   C8   118.94  3.000
 1JZ  C6    C7   C8   121.26  3.000
 1JZ  HO2   O2   C5   107.73  3.000
 1JZ  C5    C6   C7   120.95  3.000
 1JZ  C5    C6   C12  121.50  3.000
 1JZ  C7    C6   C12  117.48  3.000
 1JZ  N3    C9   C11  124.94  3.000
 1JZ  C11   C9   C8   118.25  3.000
 1JZ  N3    C9   C8   116.79  3.000
 1JZ  H11   C11  C9   119.75  3.000
 1JZ  H11   C11  C12  120.42  3.000
 1JZ  C9    C11  C12  119.83  3.000
 1JZ  HN3   N3   C9   114.32  3.000
 1JZ  HN3   N3   C10  115.52  3.000
 1JZ  C9    N3   C10  129.89  3.000
 1JZ  HN4A  N4   HN4  111.66  3.000
 1JZ  HN4A  N4   C10  114.88  3.000
 1JZ  HN4   N4   C10  116.96  3.000
 1JZ  HN5   N5   C10  110.37  3.000
 1JZ  H5A   C5   H5   106.94  3.000
 1JZ  H5A   C5   C6   109.53  3.000
 1JZ  H5    C5   C6   109.56  3.000
 1JZ  H5A   C5   O2   111.26  3.000
 1JZ  H5    C5   O2   111.05  3.000
 1JZ  C6    C5   O2   108.48  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
 1JZ  CONST_01  C8    C9   C11  C12    0.00   0.0  0
 1JZ  CONST_02  C8    C7   C6   C12    0.00   0.0  0
 1JZ  CONST_03  C11   C9   C8   C7     0.00   0.0  0
 1JZ  CONST_04  C11   C12  C6   C7     0.00   0.0  0
 1JZ  CONST_05  C9    C11  C12  C6     0.00   0.0  0
 1JZ  CONST_06  C9    C8   C7   C6     0.00   0.0  0
 1JZ  CONST_07  N3    C9   C11  C12  180.00   0.0  0
 1JZ  CONST_08  C5    C6   C7   C8   180.00   0.0  0
 1JZ  CONST_09  N3    C9   C8   C7   180.00   0.0  0
 1JZ  CONST_10  C11   C12  C6   C5   180.00   0.0  0
 1JZ  CONST_11  H7    C7   C6   C12  180.00   0.0  0
 1JZ  CONST_12  H11   C11  C9   C8   180.00   0.0  0
 1JZ  CONST_13  H12   C12  C6   C7   180.00   0.0  0
 1JZ  CONST_14  H8    C8   C7   C6   180.00   0.0  0
 1JZ  CONST_15  C8    C9   N3   C10  180.00   0.0  0
 1JZ  CONST_16  C11   C9   N3   C10    0.00   0.0  0
 1JZ  CONST_17  HN3   N3   C9   C8     0.00   0.0  0
 1JZ  CONST_18  N5    C10  N3   C9     0.00   0.0  0
 1JZ  CONST_19  N4    C10  N3   C9   180.00   0.0  0
 1JZ  CONST_20  HN5   N5   C10  N3   180.00   0.0  0
 1JZ  CONST_22  HN4A  N4   C10  N3   180.00   0.0  0
 1JZ  Var_01    O2    C5   C6   C12  -94.17  30.0  2

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
 1JZ  plan-1  C12   0.020
 1JZ  plan-1  C8    0.020
 1JZ  plan-1  C7    0.020
 1JZ  plan-1  C6    0.020
 1JZ  plan-1  C9    0.020
 1JZ  plan-1  C11   0.020
 1JZ  plan-1  N3    0.020
 1JZ  plan-1  H12   0.020
 1JZ  plan-1  H8    0.020
 1JZ  plan-1  H7    0.020
 1JZ  plan-1  H11   0.020
 1JZ  plan-1  C5    0.020
 1JZ  plan-2  C10   0.020
 1JZ  plan-2  C9    0.020
 1JZ  plan-2  N3    0.020
 1JZ  plan-2  N4    0.020
 1JZ  plan-2  N5    0.020
 1JZ  plan-2  HN3   0.020
 1JZ  plan-2  HN4   0.020
 1JZ  plan-2  HN4A  0.020
 1JZ  plan-2  HN5   0.020

