# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 16:20:22 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  24  16  .  2022-03-10  2022-03-10
;
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  -0.876   6.0353   0.8233  -1.6133
 1IP  PAP   P  P      0   1.168   5.7934   1.8962  -0.5594
 1IP  OAH   O  OP    -1  -0.937   4.9268   1.3862   0.6406
 1IP  OAE   O  OP    -1  -0.977   7.0309   2.6578  -0.0970
 1IP  CAJ   C  CH2    0  -0.880   4.7129   3.1838  -1.3946
 1IP  CAM   C  C      0   0.535   3.3521   2.6688  -1.7958
 1IP  OAC   O  O      0  -0.386   2.8994   2.7600  -2.9371
 1IP  N     N  NH1    0  -0.668   2.6912   2.1084  -0.7746
 1IP  CA    C  CH1    0  -0.172   1.3864   1.5153  -0.8501
 1IP  C     C  C      0   0.409   0.2332   2.5469  -0.6705
 1IP  O1    O  O      0  -0.521   0.5305   3.7507  -0.6654
 1IP  O     O  OC    -1  -0.685  -0.9113   2.0529  -0.6108
 1IP  CB    C  CH2    0  -0.587   1.2954   0.3834   0.1840
 1IP  CG    C  C      0   0.539   2.0334  -0.8825  -0.2167
 1IP  OD1   O  O      0  -0.461   1.4160  -1.8796  -0.5933
 1IP  ND2   N  NH2    0  -0.833   3.3676  -0.8345  -0.1555
 1IP  HAJ1  H  HCH2   0   0.176   5.2370   3.5617  -2.2752
 1IP  HAJ2  H  HCH2   0   0.254   4.5857   4.0266  -0.7083
 1IP  HN    H  HNH1   0   0.371   3.2723   1.9274   0.0484
 1IP  HA    H  HCH1   0   0.209   1.2490   1.0835  -1.8494
 1IP  HB1   H  HCH2   0   0.244   0.2461   0.1217   0.3063
 1IP  HB2   H  HCH2   0   0.294   1.6628   0.7478   1.1489
 1IP  HD21  H  HNH2   0   0.390   3.8802  -1.6772  -0.3634
 1IP  HD22  H  HNH2   0   0.396   3.9230  -0.0282   0.1740

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   deloc   1.523  0.020  1.523
 1IP  PAP  OAH   deloc   1.566  0.020  1.566
 1IP  PAP  CAJ   single  1.877  0.020  1.877
 1IP  PAP  OAE   deloc   1.525  0.020  1.525
 1IP  CAJ  CAM   single  1.509  0.020  1.509
 1IP  CAJ  HAJ1  single  0.970  0.020  1.090
 1IP  CAJ  HAJ2  single  0.970  0.020  1.090
 1IP  CAM  N     single  1.339  0.020  1.339
 1IP  CAM  OAC   double  1.231  0.020  1.231
 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    deloc   1.240  0.020  1.240
 1IP  C    O     deloc   1.231  0.020  1.231
 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  1.232  0.020  1.232
 1IP  CG   ND2   single  1.336  0.020  1.336
 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   105.04  3.000
 1IP  OAE   PAP  OAH   112.30  3.000
 1IP  CAJ   PAP  OAH   104.23  3.000
 1IP  OAE   PAP  OAG   115.64  3.000
 1IP  CAJ   PAP  OAG   105.47  3.000
 1IP  OAH   PAP  OAG   112.88  3.000
 1IP  HAJ2  CAJ  HAJ1  107.15  3.000
 1IP  HAJ2  CAJ  CAM   108.95  3.000
 1IP  HAJ1  CAJ  CAM   109.66  3.000
 1IP  HAJ2  CAJ  PAP   108.43  3.000
 1IP  HAJ1  CAJ  PAP   108.65  3.000
 1IP  CAM   CAJ  PAP   113.78  3.000
 1IP  N     CAM  OAC   123.80  3.000
 1IP  OAC   CAM  CAJ   123.55  3.000
 1IP  N     CAM  CAJ   112.65  3.000
 1IP  HN    N    CA    119.03  3.000
 1IP  HN    N    CAM   114.01  3.000
 1IP  CA    N    CAM   125.55  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    127.16  3.000
 1IP  O     C    CA    120.80  1.700
 1IP  O1    C    CA    117.77  3.000
 1IP  HB2   CB   HB1   107.72  3.000
 1IP  HB2   CB   CG    110.29  3.000
 1IP  HB1   CB   CG    107.32  3.000
 1IP  HB2   CB   CA    109.16  3.000
 1IP  HB1   CB   CA    108.06  3.000
 1IP  CG    CB   CA    114.06  3.000
 1IP  ND2   CG   OD1   122.92  3.000
 1IP  ND2   CG   CB    116.29  3.000
 1IP  OD1   CG   CB    120.78  3.000
 1IP  HD22  ND2  HD21  116.41  3.000
 1IP  HD22  ND2  CG    125.41  3.000
 1IP  HD21  ND2  CG    117.92  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  Var_01    CAM   CAJ  PAP  OAG    63.85  30.0  3
 1IP  Var_02    N     CAM  CAJ  PAP    53.91  30.0  3
 1IP  Var_03    OD1   CG   CB   CA   -105.67  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

