# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 02:20:50 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: D-methioninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCC[C@@H](N)C(N)=O
#
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
 QXV  QXV  'D-methioninamide         '  D-peptide  21  9  .  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_QXV
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
 QXV  N    N  NH2   0  -0.776  -1.2343   1.8225   0.2497
 QXV  CA   C  CH1   0  -0.211  -1.2431   0.3947   0.4760
 QXV  C    C  C     0   0.493  -2.5000  -0.3006  -0.0577
 QXV  O    O  O     0  -0.490  -3.0927   0.1179  -1.0425
 QXV  CB   C  CH2   0  -0.425  -0.0222  -0.2619  -0.1820
 QXV  CG   C  CH2   0  -0.539   1.2842   0.2833   0.3722
 QXV  SD   S  S2    0  -0.049   2.6829  -0.5567  -0.4246
 QXV  CE   C  CH3   0  -0.764   4.0546   0.2967   0.3826
 QXV  NXT  N  NH2   0  -0.796  -2.8696  -1.4012   0.6100
 QXV  H1   H  HNH2  0   0.341  -1.4221   2.0080  -0.7288
 QXV  H2   H  HNH2  0   0.352  -1.9892   2.2584   0.7645
 QXV  H4   H  HCH1  0   0.255  -1.1782   0.2232   1.5552
 QXV  H5   H  HCH2  0   0.248  -0.0655  -1.3422  -0.0233
 QXV  H6   H  HCH2  0   0.241  -0.0662  -0.1006  -1.2638
 QXV  H7   H  HCH2  0   0.265   1.3593   1.3558   0.1931
 QXV  H8   H  HCH2  0   0.256   1.3369   0.1178   1.4511
 QXV  H9   H  HCH3  0   0.260   4.0290   1.3656   0.1749
 QXV  H10  H  HCH3  0   0.260   4.0359   0.1390   1.4601
 QXV  H11  H  HCH3  0   0.272   4.9814  -0.1138  -0.0138
 QXV  H12  H  HNH2  0   0.407  -2.3618  -1.7279   1.4144
 QXV  H13  H  HNH2  0   0.400  -3.6338  -1.9703   0.2832

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
 QXV  N    CA   single  1.458  0.019  1.458
 QXV  CA   C    single  1.525  0.021  1.525
 QXV  CA   CB   single  1.521  0.033  1.521
 QXV  O    C    double  1.231  0.020  1.231
 QXV  C    NXT  single  1.339  0.020  1.339
 QXV  CG   CB   single  1.520  0.020  1.520
 QXV  CG   SD   single  1.816  0.020  1.816
 QXV  CE   SD   single  1.806  0.020  1.806
 QXV  N    H1   single  0.890  0.020  1.040
 QXV  N    H2   single  0.890  0.020  1.040
 QXV  CA   H4   single  0.970  0.020  1.090
 QXV  CB   H5   single  0.970  0.020  1.090
 QXV  CB   H6   single  0.970  0.020  1.090
 QXV  CG   H7   single  0.970  0.020  1.090
 QXV  CG   H8   single  0.970  0.020  1.090
 QXV  CE   H9   single  0.970  0.020  1.090
 QXV  CE   H10  single  0.970  0.020  1.090
 QXV  CE   H11  single  0.970  0.020  1.090
 QXV  NXT  H12  single  0.860  0.020  1.020
 QXV  NXT  H13  single  0.860  0.020  1.020

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
 QXV  H2   N    H1   105.90  3.000
 QXV  H2   N    CA   109.95  3.000
 QXV  H1   N    CA   109.32  3.000
 QXV  H4   CA   CB   107.97  3.000
 QXV  H4   CA   C    108.71  3.000
 QXV  CB   CA   C    110.50  1.500
 QXV  H4   CA   N    107.99  3.000
 QXV  CB   CA   N    110.40  1.500
 QXV  C    CA   N    111.00  2.800
 QXV  NXT  C    O    123.28  3.000
 QXV  NXT  C    CA   115.19  3.000
 QXV  O    C    CA   120.80  1.700
 QXV  H6   CB   H5   106.72  3.000
 QXV  H6   CB   CG   110.00  3.000
 QXV  H5   CB   CG   109.61  3.000
 QXV  H6   CB   CA   109.19  3.000
 QXV  H5   CB   CA   109.23  3.000
 QXV  CG   CB   CA   111.96  3.000
 QXV  H8   CG   H7   107.94  3.000
 QXV  H8   CG   SD   109.03  3.000
 QXV  H7   CG   SD   109.27  3.000
 QXV  H8   CG   CB   110.31  3.000
 QXV  H7   CG   CB   110.62  3.000
 QXV  SD   CG   CB   109.64  3.000
 QXV  CE   SD   CG    99.81  3.000
 QXV  H11  CE   H10  108.68  3.000
 QXV  H11  CE   H9   108.71  3.000
 QXV  H10  CE   H9   109.29  3.000
 QXV  H11  CE   SD   107.80  3.000
 QXV  H10  CE   SD   111.15  3.000
 QXV  H9   CE   SD   111.14  3.000
 QXV  H13  NXT  H12  117.32  3.000
 QXV  H13  NXT  C    120.79  3.000
 QXV  H12  NXT  C    121.75  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
 QXV  CONST_01  H12  NXT  C   CA    0.00   0.0  0
 QXV  CONST_02  H13  NXT  C   CA  180.00   0.0  0
 QXV  Var_01    SD   CG   CB  CA  178.93  30.0  1
 QXV  Var_02    H9   CE   SD  CG  -60.69  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
 QXV  chir_01  CA  N  C  CB  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
 QXV  plan-1  CA   0.020
 QXV  plan-1  C    0.020
 QXV  plan-1  O    0.020
 QXV  plan-1  NXT  0.020
 QXV  plan-1  H12  0.020
 QXV  plan-1  H13  0.020

