# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:12:58 2022
#   Inital geometry file: a 61 line input string
#   Ligand name: O-[(2E)-3-aminoprop-2-enoyl]-L-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N/C=C/C(=O)OC[C@H](N)C(O)=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
 1X6  1X6  O-[(2E)-3-aminoprop-2-enoyl]-L-serine  L-peptide  21  12  .  2012-08-28  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_1X6
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
 1X6  N     N  NH2    0  -0.814  11.2393  19.4654  58.8087
 1X6  CA    C  CH1    0  -0.248   9.9194  19.4506  58.2024
 1X6  C     C  C      0   0.412   9.9496  18.8246  56.7813
 1X6  O     O  O      0  -0.602   8.9517  19.0469  56.0692
 1X6  CB    C  CH2    0  -0.153   9.3565  20.8620  58.1397
 1X6  OG    O  O2     0  -0.490   9.2642  21.3943  59.4640
 1X6  C7    C  C      0   0.561  10.0082  22.4473  59.8282
 1X6  O8    O  O      0  -0.494  10.7155  23.0662  59.0548
 1X6  C6    C  C1     0  -0.528   9.8352  22.7363  61.2347
 1X6  C5    C  C1     0   0.078  10.4958  23.7807  61.7978
 1X6  N4    N  NH2    0  -0.775  10.4428  24.1600  63.0750
 1X6  OXT   O  OC    -1  -0.593  10.9440  18.1330  56.4914
 1X6  HN1   H  HNH2   0   0.333  11.1696  19.3576  59.8110
 1X6  HN2   H  HNH2   0   0.336  11.7473  18.6641  58.4573
 1X6  HA    H  HCH1   0   0.207   9.2066  18.8363  58.7788
 1X6  HB1C  H  HCH2   0   0.217   9.9854  21.4950  57.5129
 1X6  HB2C  H  HCH2   0   0.218   8.3483  20.8576  57.7285
 1X6  H6    H  H      0   0.249   9.1799  22.1085  61.8261
 1X6  H5    H  H      0   0.276  11.1453  24.3903  61.1797
 1X6  H41N  H  HNH2   0   0.408  10.9562  24.9601  63.3962
 1X6  H42N  H  HNH2   0   0.403   9.8643  23.6831  63.7459

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
 1X6  N   CA    single  1.458  0.019  1.458
 1X6  CA  C     single  1.525  0.021  1.525
 1X6  CA  CB    single  1.530  0.020  1.530
 1X6  C   O     deloc   1.231  0.020  1.231
 1X6  CB  OG    single  1.430  0.020  1.430
 1X6  OG  C7    single  1.340  0.020  1.340
 1X6  C7  O8    double  1.217  0.020  1.217
 1X6  C7  C6    single  1.446  0.020  1.446
 1X6  C6  C5    double  1.358  0.020  1.358
 1X6  C5  N4    single  1.333  0.020  1.333
 1X6  C   OXT   deloc   1.245  0.020  1.245
 1X6  N   HN1   single  0.890  0.020  1.040
 1X6  N   HN2   single  0.890  0.020  1.040
 1X6  CA  HA    single  0.970  0.020  0.970
 1X6  CB  HB1C  single  0.970  0.020  1.090
 1X6  CB  HB2C  single  0.970  0.020  1.090
 1X6  C6  H6    single  0.930  0.020  1.080
 1X6  C5  H5    single  0.930  0.020  1.080
 1X6  N4  H41N  single  0.860  0.020  1.020
 1X6  N4  H42N  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
 1X6  HN2   N   HN1   107.13  3.000
 1X6  HN2   N   CA    107.65  3.000
 1X6  HN1   N   CA    110.50  3.000
 1X6  HA    CA  CB    109.00  3.000
 1X6  HA    CA  C     109.00  3.000
 1X6  CB    CA  C     110.10  1.900
 1X6  HA    CA  N     110.00  3.000
 1X6  CB    CA  N     110.50  1.700
 1X6  C     CA  N     111.00  2.800
 1X6  OXT   C   O     127.27  3.000
 1X6  OXT   C   CA    116.89  3.000
 1X6  O     C   CA    120.80  1.700
 1X6  HB2C  CB  HB1C  108.62  3.000
 1X6  HB2C  CB  OG    106.94  3.000
 1X6  HB1C  CB  OG    110.70  3.000
 1X6  HB2C  CB  CA    110.76  3.000
 1X6  HB1C  CB  CA    110.43  3.000
 1X6  OG    CB  CA    109.34  3.000
 1X6  C7    OG  CB    120.55  3.000
 1X6  C6    C7  O8    125.87  3.000
 1X6  C6    C7  OG    110.79  3.000
 1X6  O8    C7  OG    123.34  3.000
 1X6  H6    C6  C5    120.90  3.000
 1X6  H6    C6  C7    119.18  3.000
 1X6  C5    C6  C7    119.92  3.000
 1X6  H5    C5  N4    114.20  3.000
 1X6  H5    C5  C6    119.17  3.000
 1X6  N4    C5  C6    126.63  3.000
 1X6  H42N  N4  H41N  117.30  3.000
 1X6  H42N  N4  C5    121.78  3.000
 1X6  H41N  N4  C5    120.87  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
 1X6  Var_01  N4    C5  C6  C7  -179.49   0.0  2
 1X6  Var_02  O8    C7  OG  CB     5.57  30.0  3
 1X6  Var_03  C5    C6  C7  OG  -179.30  30.0  2
 1X6  Var_04  H41N  N4  C5  C6  -178.83  30.0  2

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
 1X6  chir_01  CA  N  C  CB  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
 1X6  plan-1  CA   0.020
 1X6  plan-1  C    0.020
 1X6  plan-1  O    0.020
 1X6  plan-1  OXT  0.020
 1X6  plan-2  OG   0.020
 1X6  plan-2  C7   0.020
 1X6  plan-2  O8   0.020
 1X6  plan-2  C6   0.020
 1X6  plan-3  C7   0.020
 1X6  plan-3  C6   0.020
 1X6  plan-3  C5   0.020
 1X6  plan-3  N4   0.020
 1X6  plan-3  H6   0.020
 1X6  plan-3  H5   0.020

