# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 03:24:32 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: N~2~-(phosphonoacetyl)-L-asparagine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)C[C@H](NC(=O)C[P](O)(O)=O)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
 1IP  1IP  N~2~-(phosphonoacetyl)-L-asparagine  L-peptide  27  16  .  2022-03-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1IP
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
 1IP  OAG   O  O     0  -0.711   6.1066   3.6925  -3.5218
 1IP  PAP   P  P     0   1.375   6.2490   2.8820  -2.2891
 1IP  OAH   O  OH1   0  -0.746   6.3753   1.2973  -2.5149
 1IP  OAE   O  OH1   0  -0.744   7.5077   3.2936  -1.3748
 1IP  CAJ   C  CH2   0  -0.884   4.9269   2.9455  -1.0612
 1IP  CAM   C  C     0   0.579   3.6399   2.3433  -1.5758
 1IP  OAC   O  O     0  -0.475   3.3444   2.3490  -2.7585
 1IP  N     N  NH1   0  -0.632   2.8502   1.8096  -0.6271
 1IP  CA    C  CH1   0  -0.197   1.5303   1.3299  -0.9287
 1IP  C     C  C     0   0.556   0.5717   2.4938  -1.1440
 1IP  O1    O  O     0  -0.424   0.8362   3.6440  -0.9169
 1IP  O     O  OH1   0  -0.590  -0.5937   2.0726  -1.6103
 1IP  CB    C  CH2   0  -0.609   1.0425   0.4158   0.1918
 1IP  CG    C  C     0   0.537   1.9017  -0.8343   0.2791
 1IP  OD1   O  O     0  -0.486   2.2365  -1.4463  -0.7236
 1IP  ND2   N  NH2   0  -0.799   2.2262  -1.2131   1.5200
 1IP  HOAH  H  HOH1  0   0.494   6.8071   1.0485  -3.3433
 1IP  HOAE  H  HOH1  0   0.493   8.2035   3.7562  -1.8601
 1IP  HAJ1  H  HCH2  0   0.336   4.7483   3.9986  -0.8230
 1IP  HAJ2  H  HCH2  0   0.316   5.2590   2.4674  -0.1377
 1IP  HN    H  HNH1  0   0.412   3.0964   1.9479   0.3411
 1IP  HA    H  HCH1  0   0.305   1.5641   0.7508  -1.8547
 1IP  HO    H  HOH1  0   0.488  -1.2017   2.8184  -1.7276
 1IP  HB1   H  HCH2  0   0.311   0.0209   0.0908  -0.0162
 1IP  HB2   H  HCH2  0   0.281   1.0121   0.9564   1.1408
 1IP  HD21  H  HNH2  0   0.404   2.7526  -2.0579   1.6757
 1IP  HD22  H  HNH2  0   0.411   1.9519  -0.6830   2.3285

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
 1IP  OAG  PAP   double  1.482  0.020  1.482
 1IP  PAP  OAH   single  1.606  0.020  1.606
 1IP  PAP  CAJ   single  1.805  0.020  1.805
 1IP  PAP  OAE   single  1.609  0.020  1.609
 1IP  OAH  HOAH  single  0.850  0.020  0.980
 1IP  OAE  HOAE  single  0.850  0.020  0.980
 1IP  CAJ  CAM   single  1.511  0.020  1.511
 1IP  CAJ  HAJ1  single  0.970  0.020  1.090
 1IP  CAJ  HAJ2  single  0.970  0.020  1.090
 1IP  CAM  N     single  1.345  0.020  1.345
 1IP  CAM  OAC   double  1.219  0.020  1.219
 1IP  N    CA    single  1.458  0.019  1.458
 1IP  N    HN    single  0.860  0.020  1.020
 1IP  CA   CB    single  1.521  0.033  1.521
 1IP  CA   C     single  1.525  0.021  1.525
 1IP  CA   HA    single  0.970  0.020  0.970
 1IP  C    O1    double  1.202  0.020  1.202
 1IP  C    O     single  1.231  0.020  1.231
 1IP  O    HO    single  0.850  0.020  0.980
 1IP  CB   CG    single  1.519  0.020  1.519
 1IP  CB   HB1   single  0.970  0.020  1.090
 1IP  CB   HB2   single  0.970  0.020  1.090
 1IP  CG   OD1   double  1.222  0.020  1.222
 1IP  CG   ND2   single  1.337  0.020  1.337
 1IP  ND2  HD21  single  0.860  0.020  1.020
 1IP  ND2  HD22  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
 1IP  CAJ   PAP  OAE   100.22  3.000
 1IP  OAE   PAP  OAH   105.71  3.000
 1IP  CAJ   PAP  OAH   100.83  3.000
 1IP  OAE   PAP  OAG   114.07  3.000
 1IP  CAJ   PAP  OAG   118.43  3.000
 1IP  OAH   PAP  OAG   115.48  3.000
 1IP  HOAH  OAH  PAP   114.18  3.000
 1IP  HOAE  OAE  PAP   113.60  3.000
 1IP  HAJ2  CAJ  HAJ1  106.67  3.000
 1IP  HAJ2  CAJ  CAM   111.88  3.000
 1IP  HAJ1  CAJ  CAM   108.58  3.000
 1IP  HAJ2  CAJ  PAP   109.70  3.000
 1IP  HAJ1  CAJ  PAP   107.54  3.000
 1IP  CAM   CAJ  PAP   112.21  3.000
 1IP  N     CAM  OAC   122.95  3.000
 1IP  OAC   CAM  CAJ   122.34  3.000
 1IP  N     CAM  CAJ   114.71  3.000
 1IP  HN    N    CA    118.14  3.000
 1IP  HN    N    CAM   118.65  3.000
 1IP  CA    N    CAM   121.61  3.000
 1IP  HA    CA   CB    109.00  3.000
 1IP  HA    CA   C     110.00  3.000
 1IP  CB    CA   C     110.50  1.500
 1IP  HA    CA   N     110.00  3.000
 1IP  C     CA   N     111.00  2.800
 1IP  CB    CA   N     110.40  1.500
 1IP  O     C    O1    124.38  3.000
 1IP  O     C    CA    120.80  1.700
 1IP  O1    C    CA    124.48  3.000
 1IP  HO    O    C     110.48  3.000
 1IP  HB2   CB   HB1   106.66  3.000
 1IP  HB2   CB   CG    111.89  3.000
 1IP  HB1   CB   CG    107.16  3.000
 1IP  HB2   CB   CA    110.51  3.000
 1IP  HB1   CB   CA    109.72  3.000
 1IP  CG    CB   CA    110.75  3.000
 1IP  ND2   CG   OD1   123.59  3.000
 1IP  ND2   CG   CB    115.06  3.000
 1IP  OD1   CG   CB    121.34  3.000
 1IP  HD22  ND2  HD21  117.43  3.000
 1IP  HD22  ND2  CG    122.06  3.000
 1IP  HD21  ND2  CG    120.51  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
 1IP  CONST_01  CA    N    CAM  CAJ  180.00   0.0  0
 1IP  CONST_02  CA    N    CAM  OAC    0.00   0.0  0
 1IP  CONST_03  HN    N    CAM  CAJ    0.00   0.0  0
 1IP  CONST_04  HD21  ND2  CG   CB   180.00   0.0  0
 1IP  CONST_05  HD22  ND2  CG   CB     0.00   0.0  0
 1IP  CONST_06  HO    O    C    CA   180.00   0.0  0
 1IP  Var_01    CAM   CAJ  PAP  OAG   66.31  30.0  3
 1IP  Var_02    N     CAM  CAJ  PAP  151.31  30.0  3
 1IP  Var_03    OD1   CG   CB   CA   -44.01  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
 1IP  chir_01  CA  N  CB  C  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
 1IP  plan-1  CAJ   0.020
 1IP  plan-1  CAM   0.020
 1IP  plan-1  OAC   0.020
 1IP  plan-1  N     0.020
 1IP  plan-1  CA    0.020
 1IP  plan-1  HN    0.020
 1IP  plan-2  CB    0.020
 1IP  plan-2  CG    0.020
 1IP  plan-2  OD1   0.020
 1IP  plan-2  ND2   0.020
 1IP  plan-2  HD21  0.020
 1IP  plan-2  HD22  0.020
 1IP  plan-3  CA    0.020
 1IP  plan-3  C     0.020
 1IP  plan-3  O1    0.020
 1IP  plan-3  O     0.020
 1IP  plan-3  HO    0.020

