# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 05:28:13 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: 4-(aminomethyl)-D-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1ccc(C[C@@H](N)C(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
 1G8  1G8  4-(aminomethyl)-D-phenylalanine  D-peptide  27  14  .  2022-08-09  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_1G8
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
 1G8  C25  C  C      0   0.402   3.6391   0.2294   0.0017
 1G8  O26  O  O      0  -0.605   4.3232  -0.8027  -0.1454
 1G8  C15  C  CH1    0  -0.191   2.1635   0.0444   0.4218
 1G8  C16  C  CH2    0  -0.526   1.2903   0.2088  -0.8472
 1G8  C17  C  CR6    0   0.116  -0.1754   0.0888  -0.5522
 1G8  C22  C  CR16   0  -0.292  -0.9037   1.1886  -0.0931
 1G8  C21  C  CR16   0  -0.270  -2.2434   1.0759   0.2386
 1G8  C20  C  CR6    0   0.087  -2.9050  -0.1484   0.1364
 1G8  C23  C  CH2    0  -0.350  -4.3564  -0.2761   0.5181
 1G8  N24  N  NH2    0  -0.790  -5.1724   0.7175  -0.1636
 1G8  C19  C  CR16   0  -0.301  -2.1866  -1.2428  -0.3271
 1G8  C18  C  CR16   0  -0.310  -0.8422  -1.1275  -0.6654
 1G8  N14  N  NH2    0  -0.799   1.9762  -1.2083   1.1247
 1G8  H32  H  HCH1   0   0.208   1.9025   0.8647   1.1003
 1G8  H33  H  HCH2   0   0.236   1.5024   1.1849  -1.2899
 1G8  H34  H  HCH2   0   0.233   1.5846  -0.5510  -1.5781
 1G8  H35  H  HCR6   0   0.240  -0.4099   2.1495   0.0026
 1G8  H36  H  HCR6   0   0.241  -2.7861   1.9488   0.5804
 1G8  H37  H  HCH2   0   0.211  -4.6763  -1.3124   0.3426
 1G8  H38  H  HCH2   0   0.234  -4.4580  -0.1067   1.5941
 1G8  H39  H  HNH2   0   0.341  -5.1951   0.5099  -1.1543
 1G8  H40  H  HNH2   0   0.350  -6.1290   0.6410   0.1582
 1G8  H42  H  HCR6   0   0.244  -2.6808  -2.2026  -0.4297
 1G8  H43  H  HCR6   0   0.246  -0.3112  -1.9975  -1.0349
 1G8  H44  H  HNH2   0   0.337   0.9925  -1.4446   1.1756
 1G8  OXT  O  OC    -1  -0.618   4.0073   1.4028  -0.2034
 1G8  H2   H  HNH2   0   0.327   2.4331  -1.9447   0.6019

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
 1G8  O26  C25  deloc     1.247  0.020  1.247
 1G8  C25  C15  single    1.545  0.020  1.545
 1G8  C16  C15  single    1.549  0.020  1.549
 1G8  C16  C17  single    1.500  0.020  1.500
 1G8  C18  C19  aromatic  1.391  0.020  1.391
 1G8  C18  C17  aromatic  1.392  0.020  1.392
 1G8  C15  N14  single    1.449  0.020  1.449
 1G8  C19  C20  aromatic  1.389  0.020  1.389
 1G8  C17  C22  aromatic  1.397  0.020  1.397
 1G8  C20  C21  aromatic  1.395  0.020  1.395
 1G8  C20  C23  single    1.506  0.020  1.506
 1G8  C22  C21  aromatic  1.385  0.020  1.385
 1G8  C23  N24  single    1.455  0.020  1.455
 1G8  C15  H32  single    0.970  0.020  1.090
 1G8  C16  H33  single    0.970  0.020  1.090
 1G8  C16  H34  single    0.970  0.020  1.090
 1G8  C22  H35  single    0.930  0.020  1.080
 1G8  C21  H36  single    0.930  0.020  1.080
 1G8  C23  H37  single    0.970  0.020  1.090
 1G8  C23  H38  single    0.970  0.020  1.090
 1G8  N24  H39  single    0.890  0.020  1.040
 1G8  N24  H40  single    0.890  0.020  1.040
 1G8  C19  H42  single    0.930  0.020  1.080
 1G8  C18  H43  single    0.930  0.020  1.080
 1G8  N14  H44  single    0.890  0.020  1.040
 1G8  C25  OXT  deloc     1.247  0.020  1.247
 1G8  N14  H2   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
 1G8  OXT  C25  C15  116.06  3.000
 1G8  OXT  C25  O26  126.70  3.000
 1G8  C15  C25  O26  117.19  3.000
 1G8  H32  C15  N14  108.42  3.000
 1G8  H32  C15  C16  107.06  3.000
 1G8  N14  C15  C16  114.60  3.000
 1G8  H32  C15  C25  107.82  3.000
 1G8  N14  C15  C25  111.03  3.000
 1G8  C16  C15  C25  107.63  3.000
 1G8  H34  C16  H33  107.30  3.000
 1G8  H34  C16  C17  109.79  3.000
 1G8  H33  C16  C17  109.93  3.000
 1G8  H34  C16  C15  108.77  3.000
 1G8  H33  C16  C15  108.50  3.000
 1G8  C17  C16  C15  112.41  3.000
 1G8  C18  C17  C22  117.72  3.000
 1G8  C22  C17  C16  120.75  3.000
 1G8  C18  C17  C16  121.47  3.000
 1G8  H35  C22  C21  119.43  3.000
 1G8  H35  C22  C17  119.29  3.000
 1G8  C21  C22  C17  121.28  3.000
 1G8  H36  C21  C20  119.51  3.000
 1G8  H36  C21  C22  119.65  3.000
 1G8  C20  C21  C22  120.84  3.000
 1G8  C19  C20  C23  121.08  3.000
 1G8  C23  C20  C21  120.85  3.000
 1G8  C19  C20  C21  118.07  3.000
 1G8  H38  C23  H37  106.03  3.000
 1G8  H38  C23  N24  107.63  3.000
 1G8  H37  C23  N24  113.95  3.000
 1G8  H38  C23  C20  109.00  3.000
 1G8  H37  C23  C20  108.67  3.000
 1G8  N24  C23  C20  111.33  3.000
 1G8  H40  N24  H39  105.92  3.000
 1G8  H40  N24  C23  109.23  3.000
 1G8  H39  N24  C23  109.33  3.000
 1G8  H42  C19  C18  119.39  3.000
 1G8  H42  C19  C20  119.56  3.000
 1G8  C18  C19  C20  121.05  3.000
 1G8  H43  C18  C19  119.32  3.000
 1G8  H43  C18  C17  119.63  3.000
 1G8  C19  C18  C17  121.04  3.000
 1G8  H2   N14  H44  107.14  3.000
 1G8  H2   N14  C15  108.67  3.000
 1G8  H44  N14  C15  110.59  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
 1G8  CONST_01  C20  C19  C18  C17    0.00   0.0  0
 1G8  CONST_02  C20  C21  C22  C17    0.00   0.0  0
 1G8  CONST_03  C19  C18  C17  C22    0.00   0.0  0
 1G8  CONST_04  C19  C20  C21  C22    0.00   0.0  0
 1G8  CONST_05  C18  C19  C20  C21    0.00   0.0  0
 1G8  CONST_06  C18  C17  C22  C21    0.00   0.0  0
 1G8  CONST_07  C19  C18  C17  C16  180.00   0.0  0
 1G8  CONST_08  C21  C22  C17  C16  180.00   0.0  0
 1G8  CONST_09  C23  C20  C21  C22  180.00   0.0  0
 1G8  CONST_10  C18  C19  C20  C23  180.00   0.0  0
 1G8  CONST_11  H42  C19  C18  C17  180.00   0.0  0
 1G8  CONST_12  H36  C21  C22  C17  180.00   0.0  0
 1G8  CONST_13  H43  C18  C17  C22  180.00   0.0  0
 1G8  CONST_14  H35  C22  C21  C20  180.00   0.0  0
 1G8  Var_01    C18  C17  C16  C15  -93.27  30.0  2
 1G8  Var_02    N24  C23  C20  C21   52.63  30.0  2
 1G8  Var_03    H39  N24  C23  C20   68.00  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
 1G8  chir_01  C15  C25  C16  N14  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
 1G8  plan-1  C16  0.020
 1G8  plan-1  C17  0.020
 1G8  plan-1  C22  0.020
 1G8  plan-1  C21  0.020
 1G8  plan-1  C20  0.020
 1G8  plan-1  C23  0.020
 1G8  plan-1  C19  0.020
 1G8  plan-1  C18  0.020
 1G8  plan-1  H35  0.020
 1G8  plan-1  H36  0.020
 1G8  plan-1  H42  0.020
 1G8  plan-1  H43  0.020
 1G8  plan-2  C25  0.020
 1G8  plan-2  O26  0.020
 1G8  plan-2  C15  0.020
 1G8  plan-2  OXT  0.020

