# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 16:38:05 2021
#   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  29  14  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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   0.271  23.8510   0.5286  59.9713
 R9J  C5   C  CR16  0  -0.305  23.9211  -0.6226  59.1856
 R9J  C6   C  CR16  0  -0.294  23.2202  -1.7684  59.5307
 R9J  C7   C  CT    0  -0.067  25.7585   2.0786  60.2606
 R9J  C8   C  CH3   0  -0.651  26.8323   0.9833  60.1483
 R9J  C9   C  CH3   0  -0.652  25.5144   2.4059  61.7338
 R9J  C10  C  C     0   0.565  26.2754   3.3197  59.5338
 R9J  O1   O  O     0  -0.435  25.8146   3.7582  58.5100
 R9J  O    O  OH1   0  -0.590  27.3278   3.8522  60.1372
 R9J  N    N  NH1   0  -0.669  24.5100   1.7145  59.5826
 R9J  C3   C  CR16  0  -0.273  23.0472   0.4908  61.1105
 R9J  C2   C  CR16  0  -0.303  22.3704  -0.6677  61.4636
 R9J  C1   C  CR6   0   0.086  22.4413  -1.8197  60.6841
 R9J  C    C  CH3   0  -0.722  21.7168  -3.0746  61.0772
 R9J  H1   H  HCR6  0   0.251  24.5313  -0.6212  58.2893
 R9J  H2   H  HCR6  0   0.245  23.2893  -2.6411  58.8915
 R9J  H3   H  HCH3  0   0.245  27.7579   1.2726  60.6446
 R9J  H4   H  HCH3  0   0.246  26.4731   0.0704  60.6243
 R9J  H5   H  HCH3  0   0.240  27.0607   0.7515  59.1066
 R9J  H6   H  HCH3  0   0.251  26.4290   2.7467  62.2146
 R9J  H7   H  HCH3  0   0.243  24.7505   3.1746  61.8539
 R9J  H8   H  HCH3  0   0.246  25.1900   1.5140  62.2675
 R9J  H9   H  HOH1  0   0.485  27.6521   4.6111  59.6289
 R9J  H10  H  HNH1  0   0.360  24.6784   1.6883  58.5848
 R9J  H11  H  HCR6  0   0.254  22.9274   1.3817  61.7126
 R9J  H12  H  HCR6  0   0.244  21.7539  -0.6630  62.3553
 R9J  H13  H  HCH3  0   0.245  22.3824  -3.7685  61.5951
 R9J  H14  H  HCH3  0   0.241  20.8859  -2.8623  61.7492
 R9J  H15  H  HCH3  0   0.242  21.3199  -3.5995  60.2081

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  double    1.205  0.020  1.205
 R9J  C5   C6   aromatic  1.387  0.020  1.387
 R9J  C5   C4   aromatic  1.396  0.020  1.396
 R9J  N    C4   single    1.411  0.020  1.411
 R9J  N    C7   single    1.467  0.020  1.467
 R9J  C6   C1   aromatic  1.393  0.020  1.393
 R9J  C10  O    single    1.325  0.020  1.325
 R9J  C10  C7   single    1.528  0.020  1.528
 R9J  C8   C7   single    1.538  0.020  1.538
 R9J  C4   C3   aromatic  1.395  0.020  1.395
 R9J  C7   C9   single    1.529  0.020  1.529
 R9J  C1   C    single    1.501  0.020  1.501
 R9J  C1   C2   aromatic  1.393  0.020  1.393
 R9J  C3   C2   aromatic  1.387  0.020  1.387
 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  O    H9   single    0.850  0.020  0.980
 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    121.12  3.000
 R9J  C3   C4   C5   117.80  3.000
 R9J  N    C4   C5   120.98  3.000
 R9J  H1   C5   C6   119.42  3.000
 R9J  H1   C5   C4   119.51  3.000
 R9J  C6   C5   C4   121.07  3.000
 R9J  H2   C6   C1   119.62  3.000
 R9J  H2   C6   C5   119.09  3.000
 R9J  C1   C6   C5   121.28  3.000
 R9J  N    C7   C10  105.64  3.000
 R9J  C10  C7   C9   109.78  3.000
 R9J  N    C7   C9   111.26  3.000
 R9J  C9   C7   C8   109.53  3.000
 R9J  C10  C7   C8   107.91  3.000
 R9J  N    C7   C8   112.57  3.000
 R9J  H5   C8   H4   107.93  3.000
 R9J  H5   C8   H3   108.27  3.000
 R9J  H4   C8   H3   107.66  3.000
 R9J  H5   C8   C7   111.53  3.000
 R9J  H4   C8   C7   109.53  3.000
 R9J  H3   C8   C7   111.77  3.000
 R9J  H8   C9   H7   108.34  3.000
 R9J  H8   C9   H6   106.88  3.000
 R9J  H7   C9   H6   108.63  3.000
 R9J  H8   C9   C7   110.15  3.000
 R9J  H7   C9   C7   111.65  3.000
 R9J  H6   C9   C7   111.02  3.000
 R9J  O    C10  O1   122.98  3.000
 R9J  O    C10  C7   112.24  3.000
 R9J  O1   C10  C7   124.76  3.000
 R9J  H9   O    C10  109.97  3.000
 R9J  H10  N    C7   108.69  3.000
 R9J  H10  N    C4   109.11  3.000
 R9J  C7   N    C4   118.60  3.000
 R9J  H11  C3   C2   119.47  3.000
 R9J  H11  C3   C4   119.74  3.000
 R9J  C2   C3   C4   120.77  3.000
 R9J  H12  C2   C1   119.53  3.000
 R9J  H12  C2   C3   118.89  3.000
 R9J  C1   C2   C3   121.56  3.000
 R9J  C    C1   C2   121.35  3.000
 R9J  C2   C1   C6   117.48  3.000
 R9J  C    C1   C6   121.17  3.000
 R9J  H15  C    H14  107.93  3.000
 R9J  H15  C    H13  107.10  3.000
 R9J  H14  C    H13  107.23  3.000
 R9J  H15  C    C1   111.68  3.000
 R9J  H14  C    C1   111.51  3.000
 R9J  H13  C    C1   111.16  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_18  H9   O    C10  C7  180.00   0.0  0
 R9J  Var_01    H13  C    C1   C6   81.96  30.0  2
 R9J  Var_02    C10  C7   N    C4  174.99  30.0  3
 R9J  Var_03    O1   C10  C7   C8  111.67  30.0  2
 R9J  Var_04    H6   C9   C7   C8   59.12  30.0  3
 R9J  Var_05    H3   C8   C7   C9  -56.41  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
 R9J  plan-3  H9   0.020

