# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 22:00:36 2022
#   Inital geometry file: a 74 line input string
#   Ligand name: 2-methyl-N-(4-methylphenyl)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(NC(C)(C)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
 R9J  R9J  2-methyl-N-(4-methylphenyl)-L-alanine  ligand  28  14  .  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_R9J
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
 R9J  C4   C  CR6    0   0.369  24.0050   0.3410  59.9728
 R9J  C5   C  CR16   0  -0.354  23.3856  -0.4087  58.9519
 R9J  C6   C  CR16   0  -0.279  22.5907  -1.5018  59.2348
 R9J  C7   C  CT     0  -0.035  25.7793   2.1195  60.3731
 R9J  C8   C  CH3    0  -0.660  26.8098   1.1448  60.9620
 R9J  C9   C  CH3    0  -0.645  25.1890   3.0072  61.4723
 R9J  C10  C  C      0   0.442  26.5429   3.0277  59.3455
 R9J  O1   O  O      0  -0.590  26.2733   2.8691  58.1365
 R9J  O    O  OC    -1  -0.589  27.3744   3.8154  59.8258
 R9J  N    N  NH1    0  -0.713  24.7385   1.4398  59.6213
 R9J  C3   C  CR16   0  -0.336  23.7755  -0.0871  61.2885
 R9J  C2   C  CR16   0  -0.294  22.9776  -1.1946  61.5520
 R9J  C1   C  CR6    0   0.060  22.3635  -1.9284  60.5449
 R9J  C    C  CH3    0  -0.722  21.4960  -3.1193  60.8388
 R9J  H1   H  HCR6   0   0.241  23.5396  -0.1171  57.9185
 R9J  H2   H  HCR6   0   0.233  22.1389  -2.0428  58.4100
 R9J  H3   H  HCH3   0   0.225  27.6095   1.6929  61.4589
 R9J  H4   H  HCH3   0   0.225  26.3676   0.4720  61.6965
 R9J  H5   H  HCH3   0   0.221  27.2565   0.5307  60.1773
 R9J  H6   H  HCH3   0   0.221  25.9758   3.5623  61.9795
 R9J  H7   H  HCH3   0   0.218  24.4824   3.7250  61.0524
 R9J  H8   H  HCH3   0   0.219  24.6601   2.4280  62.2298
 R9J  H10  H  HNH1   0   0.364  24.8961   1.5653  58.6293
 R9J  H11  H  HCR6   0   0.245  24.2093   0.4406  62.1251
 R9J  H12  H  HCR6   0   0.233  22.8317  -1.4868  62.5864
 R9J  H13  H  HCH3   0   0.233  21.8522  -4.0163  60.3283
 R9J  H14  H  HCH3   0   0.236  21.4721  -3.3385  61.9062
 R9J  H15  H  HCH3   0   0.233  20.4651  -2.9601  60.5153

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
 R9J  O1   C10  deloc     1.249  0.020  1.249
 R9J  C5   C6   aromatic  1.381  0.020  1.381
 R9J  C5   C4   aromatic  1.410  0.020  1.410
 R9J  N    C4   single    1.367  0.020  1.367
 R9J  N    C7   single    1.453  0.020  1.453
 R9J  C6   C1   aromatic  1.396  0.020  1.396
 R9J  C10  O    deloc     1.242  0.020  1.242
 R9J  C10  C7   single    1.570  0.020  1.570
 R9J  C8   C7   single    1.536  0.020  1.536
 R9J  C4   C3   aromatic  1.402  0.020  1.402
 R9J  C7   C9   single    1.531  0.020  1.531
 R9J  C1   C    single    1.502  0.020  1.502
 R9J  C1   C2   aromatic  1.389  0.020  1.389
 R9J  C3   C2   aromatic  1.390  0.020  1.390
 R9J  C5   H1   single    0.930  0.020  1.080
 R9J  C6   H2   single    0.930  0.020  1.080
 R9J  C8   H3   single    0.970  0.020  1.090
 R9J  C8   H4   single    0.970  0.020  1.090
 R9J  C8   H5   single    0.970  0.020  1.090
 R9J  C9   H6   single    0.970  0.020  1.090
 R9J  C9   H7   single    0.970  0.020  1.090
 R9J  C9   H8   single    0.970  0.020  1.090
 R9J  N    H10  single    0.890  0.020  1.040
 R9J  C3   H11  single    0.930  0.020  1.080
 R9J  C2   H12  single    0.930  0.020  1.080
 R9J  C    H13  single    0.970  0.020  1.090
 R9J  C    H14  single    0.970  0.020  1.090
 R9J  C    H15  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
 R9J  C3   C4   N    125.05  3.000
 R9J  C3   C4   C5   116.43  3.000
 R9J  N    C4   C5   118.49  3.000
 R9J  H1   C5   C6   119.32  3.000
 R9J  H1   C5   C4   118.98  3.000
 R9J  C6   C5   C4   121.70  3.000
 R9J  H2   C6   C1   119.55  3.000
 R9J  H2   C6   C5   118.60  3.000
 R9J  C1   C6   C5   121.85  3.000
 R9J  N    C7   C10  106.29  3.000
 R9J  C10  C7   C9   108.79  3.000
 R9J  N    C7   C9   111.50  3.000
 R9J  C9   C7   C8   110.57  3.000
 R9J  C10  C7   C8   106.96  3.000
 R9J  N    C7   C8   112.47  3.000
 R9J  H5   C8   H4   107.64  3.000
 R9J  H5   C8   H3   108.09  3.000
 R9J  H4   C8   H3   107.52  3.000
 R9J  H5   C8   C7   110.85  3.000
 R9J  H4   C8   C7   112.21  3.000
 R9J  H3   C8   C7   110.37  3.000
 R9J  H8   C9   H7   107.61  3.000
 R9J  H8   C9   H6   107.33  3.000
 R9J  H7   C9   H6   108.17  3.000
 R9J  H8   C9   C7   112.20  3.000
 R9J  H7   C9   C7   110.77  3.000
 R9J  H6   C9   C7   110.58  3.000
 R9J  O    C10  O1   126.83  3.000
 R9J  O    C10  C7   116.07  3.000
 R9J  O1   C10  C7   117.08  3.000
 R9J  H10  N    C7   109.74  3.000
 R9J  H10  N    C4   115.79  3.000
 R9J  C7   N    C4   128.86  3.000
 R9J  H11  C3   C2   118.22  3.000
 R9J  H11  C3   C4   120.78  3.000
 R9J  C2   C3   C4   120.99  3.000
 R9J  H12  C2   C1   119.31  3.000
 R9J  H12  C2   C3   118.20  3.000
 R9J  C1   C2   C3   122.48  3.000
 R9J  C    C1   C2   122.15  3.000
 R9J  C2   C1   C6   116.55  3.000
 R9J  C    C1   C6   121.31  3.000
 R9J  H15  C    H14  107.38  3.000
 R9J  H15  C    H13  106.82  3.000
 R9J  H14  C    H13  107.45  3.000
 R9J  H15  C    C1   111.81  3.000
 R9J  H14  C    C1   111.32  3.000
 R9J  H13  C    C1   111.80  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
 R9J  CONST_01  C1   C6   C5  C4    0.00   0.0  0
 R9J  CONST_02  C1   C2   C3  C4    0.00   0.0  0
 R9J  CONST_03  C2   C1   C6  C5    0.00   0.0  0
 R9J  CONST_04  C2   C3   C4  C5    0.00   0.0  0
 R9J  CONST_05  C3   C4   C5  C6    0.00   0.0  0
 R9J  CONST_06  C3   C2   C1  C6    0.00   0.0  0
 R9J  CONST_07  C    C1   C6  C5  180.00   0.0  0
 R9J  CONST_08  N    C4   C5  C6  180.00   0.0  0
 R9J  CONST_09  C2   C3   C4  N   180.00   0.0  0
 R9J  CONST_10  C    C1   C2  C3  180.00   0.0  0
 R9J  CONST_11  H2   C6   C5  C4  180.00   0.0  0
 R9J  CONST_12  H12  C2   C3  C4  180.00   0.0  0
 R9J  CONST_13  H11  C3   C4  C5  180.00   0.0  0
 R9J  CONST_14  H1   C5   C4  C3  180.00   0.0  0
 R9J  CONST_17  H10  N    C4  C5    0.00   0.0  0
 R9J  Var_01    H13  C    C1  C6   56.86  30.0  2
 R9J  Var_02    C10  C7   N   C4  163.98  30.0  3
 R9J  Var_03    O1   C10  C7  C8  110.81  30.0  2
 R9J  Var_04    H6   C9   C7  C8   58.07  30.0  3
 R9J  Var_05    H3   C8   C7  C9  -58.51  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
 R9J  plan-1  C4   0.020
 R9J  plan-1  C5   0.020
 R9J  plan-1  C6   0.020
 R9J  plan-1  N    0.020
 R9J  plan-1  C3   0.020
 R9J  plan-1  C2   0.020
 R9J  plan-1  C1   0.020
 R9J  plan-1  C    0.020
 R9J  plan-1  H1   0.020
 R9J  plan-1  H2   0.020
 R9J  plan-1  H11  0.020
 R9J  plan-1  H12  0.020
 R9J  plan-2  C4   0.020
 R9J  plan-2  C7   0.020
 R9J  plan-2  N    0.020
 R9J  plan-2  H10  0.020
 R9J  plan-3  C7   0.020
 R9J  plan-3  C10  0.020
 R9J  plan-3  O1   0.020
 R9J  plan-3  O    0.020

