# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 23:10:12 2021
#   Inital geometry file: a 61 line input string
#   Ligand name: 2-[(1~{S})-1-azanylpropyl]phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](N)c1ccccc1O
#
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
 SYG  SYG  2-[(1~{S})-1-azanylpropyl]phenol  ligand  24  11  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SYG
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
 SYG  C4   C  CR16  0  -0.304  14.5903  25.6849  -22.1695
 SYG  C5   C  CR16  0  -0.277  14.9500  24.5199  -22.8340
 SYG  C6   C  CR16  0  -0.258  14.0668  23.9684  -23.7522
 SYG  C7   C  CR16  0  -0.343  12.8509  24.5828  -24.0118
 SYG  C8   C  CR6   0   0.310  12.4922  25.7522  -23.3417
 SYG  O    O  OH1   0  -0.660  11.3088  26.3238  -23.6223
 SYG  C3   C  CR6   0   0.012  13.3683  26.3079  -22.3925
 SYG  C2   C  CH1   0  -0.156  12.9682  27.5275  -21.5942
 SYG  N    N  NH2   0  -0.831  12.2568  28.4661  -22.4690
 SYG  C1   C  CH2   0  -0.418  12.0571  27.1653  -20.4153
 SYG  C    C  CH3   0  -0.668  12.7219  26.2589  -19.3917
 SYG  H1   H  HCR6  0   0.247  15.2738  26.1243  -21.4515
 SYG  H2   H  HCR6  0   0.246  15.9063  24.0532  -22.6385
 SYG  H3   H  HCR6  0   0.250  14.3272  23.0597  -24.2802
 SYG  H4   H  HCR6  0   0.251  12.1694  24.1616  -24.7411
 SYG  H5   H  HOH1  0   0.467  11.3671  27.2592  -23.2697
 SYG  H6   H  HCH1  0   0.245  13.8780  27.9809  -21.1790
 SYG  H7   H  HNH2  0   0.375  11.8293  29.2060  -21.9255
 SYG  H8   H  HNH2  0   0.375  12.9020  28.9117  -23.1106
 SYG  H10  H  HCH2  0   0.231  11.7533  28.0972  -19.9269
 SYG  H11  H  HCH2  0   0.224  11.1401  26.7000  -20.7879
 SYG  H12  H  HCH3  0   0.235  12.0666  26.1004  -18.5354
 SYG  H13  H  HCH3  0   0.228  12.9606  25.2814  -19.8112
 SYG  H14  H  HCH3  0   0.220  13.6508  26.6962  -19.0212

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
 SYG  C6  C7   aromatic  1.387  0.020  1.387
 SYG  C6  C5   aromatic  1.388  0.020  1.388
 SYG  C7  C8   aromatic  1.395  0.020  1.395
 SYG  C5  C4   aromatic  1.389  0.020  1.389
 SYG  C8  O    single    1.344  0.020  1.344
 SYG  C8  C3   aromatic  1.406  0.020  1.406
 SYG  N   C2   single    1.467  0.020  1.467
 SYG  C4  C3   aromatic  1.390  0.020  1.390
 SYG  C3  C2   single    1.512  0.020  1.512
 SYG  C2  C1   single    1.533  0.020  1.533
 SYG  C1  C    single    1.520  0.020  1.520
 SYG  C4  H1   single    0.930  0.020  1.080
 SYG  C5  H2   single    0.930  0.020  1.080
 SYG  C6  H3   single    0.930  0.020  1.080
 SYG  C7  H4   single    0.930  0.020  1.080
 SYG  O   H5   single    0.850  0.020  0.980
 SYG  C2  H6   single    0.970  0.020  1.090
 SYG  N   H7   single    0.890  0.020  1.040
 SYG  N   H8   single    0.890  0.020  1.040
 SYG  C1  H10  single    0.970  0.020  1.090
 SYG  C1  H11  single    0.970  0.020  1.090
 SYG  C   H12  single    0.970  0.020  1.090
 SYG  C   H13  single    0.970  0.020  1.090
 SYG  C   H14  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
 SYG  H1   C4  C3   118.61  3.000
 SYG  H1   C4  C5   119.58  3.000
 SYG  C3   C4  C5   121.81  3.000
 SYG  H2   C5  C6   120.69  3.000
 SYG  H2   C5  C4   120.30  3.000
 SYG  C6   C5  C4   119.01  3.000
 SYG  H3   C6  C7   119.43  3.000
 SYG  H3   C6  C5   120.19  3.000
 SYG  C7   C6  C5   120.37  3.000
 SYG  H4   C7  C8   119.19  3.000
 SYG  H4   C7  C6   120.35  3.000
 SYG  C8   C7  C6   120.46  3.000
 SYG  C3   C8  O    121.43  3.000
 SYG  C3   C8  C7   119.70  3.000
 SYG  O    C8  C7   118.87  3.000
 SYG  H5   O   C8   105.81  3.000
 SYG  C2   C3  C8   120.69  3.000
 SYG  C2   C3  C4   120.64  3.000
 SYG  C8   C3  C4   118.62  3.000
 SYG  H6   C2  C1   107.41  3.000
 SYG  H6   C2  N    111.30  3.000
 SYG  C1   C2  N    108.75  3.000
 SYG  H6   C2  C3   108.27  3.000
 SYG  C1   C2  C3   111.88  3.000
 SYG  N    C2  C3   109.24  3.000
 SYG  H8   N   H7   106.69  3.000
 SYG  H8   N   C2   110.50  3.000
 SYG  H7   N   C2   110.61  3.000
 SYG  H11  C1  H10  106.34  3.000
 SYG  H11  C1  C    110.02  3.000
 SYG  H10  C1  C    109.17  3.000
 SYG  H11  C1  C2   109.68  3.000
 SYG  H10  C1  C2   107.86  3.000
 SYG  C    C1  C2   113.50  3.000
 SYG  H14  C   H13  107.67  3.000
 SYG  H14  C   H12  107.66  3.000
 SYG  H13  C   H12  107.68  3.000
 SYG  H14  C   C1   111.21  3.000
 SYG  H13  C   C1   111.79  3.000
 SYG  H12  C   C1   110.66  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
 SYG  CONST_01  C7   C6  C5  C4    0.00   0.0  0
 SYG  CONST_02  C7   C8  C3  C4    0.00   0.0  0
 SYG  CONST_03  C8   C7  C6  C5    0.00   0.0  0
 SYG  CONST_04  C8   C3  C4  C5    0.00   0.0  0
 SYG  CONST_05  C3   C8  C7  C6    0.00   0.0  0
 SYG  CONST_06  C3   C4  C5  C6    0.00   0.0  0
 SYG  CONST_07  O    C8  C3  C4  180.00   0.0  0
 SYG  CONST_08  C2   C3  C4  C5  180.00   0.0  0
 SYG  CONST_09  O    C8  C7  C6  180.00   0.0  0
 SYG  CONST_10  C2   C3  C8  C7  180.00   0.0  0
 SYG  CONST_11  H3   C6  C5  C4  180.00   0.0  0
 SYG  CONST_12  H4   C7  C6  C5  180.00   0.0  0
 SYG  CONST_13  H1   C4  C5  C6  180.00   0.0  0
 SYG  CONST_14  H2   C5  C6  C7  180.00   0.0  0
 SYG  Var_01    H12  C   C1  C2  175.16  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
 SYG  chir_01  C2  N  C3  C1  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
 SYG  plan-1  C4  0.020
 SYG  plan-1  C5  0.020
 SYG  plan-1  C6  0.020
 SYG  plan-1  C7  0.020
 SYG  plan-1  C8  0.020
 SYG  plan-1  O   0.020
 SYG  plan-1  C3  0.020
 SYG  plan-1  C2  0.020
 SYG  plan-1  H1  0.020
 SYG  plan-1  H2  0.020
 SYG  plan-1  H3  0.020
 SYG  plan-1  H4  0.020

