# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Nov 17 17:58:44 2022
#   Inital geometry file: a 96 line input string
#   Ligand name: 4-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(CO[P](O)(O)=O)[C@@H](O)C(=O)NCCCC(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
 J1O  J1O  "4-[[(2R)-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]butanoic acid"  ligand  40  20  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_J1O
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
 J1O  OAH  O  OH1   0  -0.738  53.5237  -6.0618  25.1014
 J1O  PAT  P  P     0   1.438  53.5440  -7.5214  24.4529
 J1O  OAI  O  OH1   0  -0.728  53.2054  -8.4503  25.7050
 J1O  OAE  O  O     0  -0.703  54.7491  -7.8690  23.6741
 J1O  OAO  O  O2    0  -0.590  52.1624  -7.5355  23.6613
 J1O  CAM  C  CH2   0  -0.134  52.0454  -6.8513  22.4068
 J1O  CAS  C  CT    0  -0.156  50.6076  -6.3566  22.2261
 J1O  CAA  C  CH3   0  -0.680  50.2689  -5.3637  23.3391
 J1O  CAB  C  CH3   0  -0.662  49.6319  -7.5330  22.2694
 J1O  CAR  C  CH1   0  -0.040  50.5878  -5.6500  20.8389
 J1O  OAG  O  OH1   0  -0.659  50.9160  -6.5226  19.7935
 J1O  CAQ  C  C     0   0.515  49.2345  -5.0056  20.5328
 J1O  OAD  O  O     0  -0.489  48.3731  -5.6469  19.9440
 J1O  NAN  N  NH1   0  -0.624  49.0766  -3.7346  20.9196
 J1O  CAK  C  CH2   0  -0.285  47.8040  -3.0471  20.8741
 J1O  CAJ  C  CH2   0  -0.450  46.9161  -3.4023  22.0624
 J1O  CAL  C  CH2   0  -0.549  45.5833  -2.6549  21.9998
 J1O  CAP  C  C     0   0.529  44.7082  -2.9309  23.1916
 J1O  OAF  O  O     0  -0.436  44.3124  -2.0984  23.9685
 J1O  OAC  O  OH1   0  -0.591  44.4122  -4.2234  23.3051
 J1O  H1   H  HOH1  0   0.497  54.3925  -5.7345  25.3705
 J1O  H2   H  HOH1  0   0.498  53.4061  -9.3867  25.5716
 J1O  H3   H  HCH2  0   0.252  52.3191  -7.5441  21.6106
 J1O  H4   H  HCH2  0   0.237  52.7288  -5.9958  22.3660
 J1O  H5   H  HCH3  0   0.248  50.4081  -5.8208  24.3178
 J1O  H6   H  HCH3  0   0.232  50.9028  -4.4740  23.2981
 J1O  H7   H  HCH3  0   0.245  49.2297  -5.0402  23.2879
 J1O  H8   H  HCH3  0   0.239  49.6795  -8.0370  23.2345
 J1O  H9   H  HCH3  0   0.237  48.6029  -7.2012  22.1341
 J1O  H10  H  HCH3  0   0.230  49.8511  -8.2781  21.5029
 J1O  H11  H  HCH1  0   0.258  51.3553  -4.8661  20.8579
 J1O  H12  H  HOH1  0   0.445  50.0966  -6.9401  19.4972
 J1O  H13  H  HNH1  0   0.407  49.8293  -3.2872  21.4184
 J1O  H14  H  HCH2  0   0.257  48.0077  -1.9761  20.8612
 J1O  H15  H  HCH2  0   0.248  47.3005  -3.2887  19.9373
 J1O  H16  H  HCH2  0   0.247  46.7449  -4.4799  22.0729
 J1O  H17  H  HCH2  0   0.242  47.4401  -3.1496  22.9876
 J1O  H18  H  HCH2  0   0.263  45.7535  -1.5793  21.9465
 J1O  H19  H  HCH2  0   0.273  45.0440  -2.9457  21.0933
 J1O  H20  H  HOH1  0   0.478  43.8582  -4.3669  24.0872

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
 J1O  OAD  CAQ  double  1.225  0.020  1.225
 J1O  OAG  CAR  single  1.401  0.020  1.401
 J1O  CAQ  CAR  single  1.530  0.020  1.530
 J1O  CAQ  NAN  single  1.338  0.020  1.338
 J1O  CAR  CAS  single  1.557  0.020  1.557
 J1O  CAK  NAN  single  1.447  0.020  1.447
 J1O  CAK  CAJ  single  1.525  0.020  1.525
 J1O  CAL  CAJ  single  1.529  0.020  1.529
 J1O  CAL  CAP  single  1.504  0.020  1.504
 J1O  CAB  CAS  single  1.529  0.020  1.529
 J1O  CAS  CAM  single  1.531  0.020  1.531
 J1O  CAS  CAA  single  1.529  0.020  1.529
 J1O  CAM  OAO  single  1.434  0.020  1.434
 J1O  CAP  OAF  double  1.206  0.020  1.206
 J1O  CAP  OAC  single  1.331  0.020  1.331
 J1O  OAO  PAT  single  1.592  0.020  1.592
 J1O  OAE  PAT  double  1.476  0.020  1.476
 J1O  PAT  OAH  single  1.597  0.020  1.597
 J1O  PAT  OAI  single  1.595  0.020  1.595
 J1O  OAH  H1   single  0.850  0.020  0.980
 J1O  OAI  H2   single  0.850  0.020  0.980
 J1O  CAM  H3   single  0.970  0.020  1.090
 J1O  CAM  H4   single  0.970  0.020  1.090
 J1O  CAA  H5   single  0.970  0.020  1.090
 J1O  CAA  H6   single  0.970  0.020  1.090
 J1O  CAA  H7   single  0.970  0.020  1.090
 J1O  CAB  H8   single  0.970  0.020  1.090
 J1O  CAB  H9   single  0.970  0.020  1.090
 J1O  CAB  H10  single  0.970  0.020  1.090
 J1O  CAR  H11  single  0.970  0.020  1.090
 J1O  OAG  H12  single  0.850  0.020  0.980
 J1O  NAN  H13  single  0.860  0.020  1.020
 J1O  CAK  H14  single  0.970  0.020  1.090
 J1O  CAK  H15  single  0.970  0.020  1.090
 J1O  CAJ  H16  single  0.970  0.020  1.090
 J1O  CAJ  H17  single  0.970  0.020  1.090
 J1O  CAL  H18  single  0.970  0.020  1.090
 J1O  CAL  H19  single  0.970  0.020  1.090
 J1O  OAC  H20  single  0.850  0.020  0.980

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
 J1O  H1   OAH  PAT  114.27  3.000
 J1O  OAO  PAT  OAE  116.35  3.000
 J1O  OAE  PAT  OAI  116.75  3.000
 J1O  OAO  PAT  OAI  101.59  3.000
 J1O  OAI  PAT  OAH  102.17  3.000
 J1O  OAE  PAT  OAH  116.08  3.000
 J1O  OAO  PAT  OAH  101.47  3.000
 J1O  H2   OAI  PAT  114.30  3.000
 J1O  CAM  OAO  PAT  120.10  3.000
 J1O  H4   CAM  H3   108.20  3.000
 J1O  H4   CAM  CAS  109.21  3.000
 J1O  H3   CAM  CAS  110.78  3.000
 J1O  H4   CAM  OAO  110.75  3.000
 J1O  H3   CAM  OAO  108.38  3.000
 J1O  CAS  CAM  OAO  109.51  3.000
 J1O  CAR  CAS  CAB  111.49  3.000
 J1O  CAB  CAS  CAA  109.73  3.000
 J1O  CAR  CAS  CAA  110.55  3.000
 J1O  CAA  CAS  CAM  109.38  3.000
 J1O  CAB  CAS  CAM  110.32  3.000
 J1O  CAR  CAS  CAM  105.29  3.000
 J1O  H7   CAA  H6   108.04  3.000
 J1O  H7   CAA  H5   106.78  3.000
 J1O  H6   CAA  H5   107.53  3.000
 J1O  H7   CAA  CAS  111.70  3.000
 J1O  H6   CAA  CAS  111.88  3.000
 J1O  H5   CAA  CAS  110.68  3.000
 J1O  H10  CAB  H9   108.08  3.000
 J1O  H10  CAB  H8   107.31  3.000
 J1O  H9   CAB  H8   106.98  3.000
 J1O  H10  CAB  CAS  112.17  3.000
 J1O  H9   CAB  CAS  111.40  3.000
 J1O  H8   CAB  CAS  110.67  3.000
 J1O  H11  CAR  CAQ  108.74  3.000
 J1O  H11  CAR  OAG  107.10  3.000
 J1O  CAQ  CAR  OAG  108.69  3.000
 J1O  H11  CAR  CAS  107.45  3.000
 J1O  CAQ  CAR  CAS  112.38  3.000
 J1O  OAG  CAR  CAS  112.29  3.000
 J1O  H12  OAG  CAR  107.42  3.000
 J1O  NAN  CAQ  OAD  123.60  3.000
 J1O  NAN  CAQ  CAR  116.54  3.000
 J1O  OAD  CAQ  CAR  119.85  3.000
 J1O  H13  NAN  CAK  117.48  3.000
 J1O  H13  NAN  CAQ  118.47  3.000
 J1O  CAK  NAN  CAQ  123.09  3.000
 J1O  H15  CAK  H14  107.08  3.000
 J1O  H15  CAK  CAJ  110.42  3.000
 J1O  H14  CAK  CAJ  110.29  3.000
 J1O  H15  CAK  NAN  109.13  3.000
 J1O  H14  CAK  NAN  107.62  3.000
 J1O  CAJ  CAK  NAN  112.13  3.000
 J1O  H17  CAJ  H16  107.18  3.000
 J1O  H17  CAJ  CAL  109.85  3.000
 J1O  H16  CAJ  CAL  110.27  3.000
 J1O  H17  CAJ  CAK  109.06  3.000
 J1O  H16  CAJ  CAK  109.20  3.000
 J1O  CAL  CAJ  CAK  111.20  3.000
 J1O  H19  CAL  H18  107.38  3.000
 J1O  H19  CAL  CAP  108.72  3.000
 J1O  H18  CAL  CAP  108.09  3.000
 J1O  H19  CAL  CAJ  109.49  3.000
 J1O  H18  CAL  CAJ  110.37  3.000
 J1O  CAP  CAL  CAJ  112.64  3.000
 J1O  OAC  CAP  OAF  122.87  3.000
 J1O  OAC  CAP  CAL  112.03  3.000
 J1O  OAF  CAP  CAL  125.09  3.000
 J1O  H20  OAC  CAP  109.86  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
 J1O  CONST_01  CAK  NAN  CAQ  CAR   180.00   0.0  0
 J1O  CONST_02  CAK  NAN  CAQ  OAD     0.00   0.0  0
 J1O  CONST_03  H13  NAN  CAQ  CAR     0.00   0.0  0
 J1O  CONST_04  H13  NAN  CAQ  OAD   180.00   0.0  0
 J1O  CONST_05  H20  OAC  CAP  CAL   180.00   0.0  0
 J1O  CONST_06  H20  OAC  CAP  OAF     0.00   0.0  0
 J1O  Var_01    CAM  OAO  PAT  OAH    77.63  30.0  1
 J1O  Var_02    CAS  CAM  OAO  PAT  -149.55  30.0  1
 J1O  Var_03    CAM  OAO  PAT  OAI  -177.23  30.0  1
 J1O  Var_04    CAM  OAO  PAT  OAE   -49.32  30.0  1
 J1O  Var_05    CAR  CAS  CAM  OAO  -179.36  30.0  2
 J1O  Var_06    CAB  CAS  CAM  OAO   -58.95  30.0  2
 J1O  Var_07    CAA  CAS  CAM  OAO    61.83  30.0  2
 J1O  Var_08    CAJ  CAK  NAN  CAQ    80.13  30.0  2
 J1O  Var_09    CAL  CAJ  CAK  NAN   179.47  30.0  3
 J1O  Var_10    CAP  CAL  CAJ  CAK  -177.25  30.0  1
 J1O  Var_11    OAF  CAP  CAL  CAJ   119.86  30.0  3
 J1O  Var_12    OAC  CAP  CAL  CAJ   -59.92  30.0  3
 J1O  Var_13    H3   CAM  OAO  PAT    89.49  30.0  1
 J1O  Var_14    H4   CAM  OAO  PAT   -29.05  30.0  1
 J1O  Var_15    H8   CAB  CAS  CAM    61.59  30.0  3
 J1O  Var_16    H9   CAB  CAS  CAM  -179.53  30.0  3
 J1O  Var_17    H10  CAB  CAS  CAM   -58.23  30.0  3
 J1O  Var_18    H5   CAA  CAS  CAM   -57.14  30.0  3
 J1O  Var_19    H6   CAA  CAS  CAM    62.76  30.0  3
 J1O  Var_20    H7   CAA  CAS  CAM  -175.98  30.0  3
 J1O  Var_21    H8   CAB  CAS  CAA   -58.99  30.0  3
 J1O  Var_22    H9   CAB  CAS  CAA    59.90  30.0  3
 J1O  Var_23    H10  CAB  CAS  CAA  -178.80  30.0  3
 J1O  Var_24    H3   CAM  CAS  CAA  -178.68  30.0  3
 J1O  Var_25    H4   CAM  CAS  CAA   -59.60  30.0  3
 J1O  Var_26    H3   CAM  CAS  CAB    60.54  30.0  3
 J1O  Var_27    H4   CAM  CAS  CAB   179.61  30.0  3
 J1O  Var_28    H5   CAA  CAS  CAB    64.00  30.0  3
 J1O  Var_29    H6   CAA  CAS  CAB  -176.10  30.0  3
 J1O  Var_30    H7   CAA  CAS  CAB   -54.84  30.0  3
 J1O  Var_31    H8   CAB  CAS  CAR   178.20  30.0  3
 J1O  Var_32    H9   CAB  CAS  CAR   -62.91  30.0  3
 J1O  Var_33    H10  CAB  CAS  CAR    58.39  30.0  3
 J1O  Var_34    H3   CAM  CAS  CAR   -59.87  30.0  3
 J1O  Var_35    H4   CAM  CAS  CAR    59.21  30.0  3
 J1O  Var_36    H5   CAA  CAS  CAR  -172.63  30.0  3
 J1O  Var_37    H6   CAA  CAS  CAR   -52.73  30.0  3
 J1O  Var_38    H7   CAA  CAS  CAR    68.53  30.0  3
 J1O  Var_39    H14  CAK  NAN  CAQ  -158.40  30.0  2
 J1O  Var_40    H15  CAK  NAN  CAQ   -42.53  30.0  2
 J1O  Var_41    H16  CAJ  CAK  NAN   -58.63  30.0  3
 J1O  Var_42    H17  CAJ  CAK  NAN    58.19  30.0  3
 J1O  Var_43    H18  CAL  CAJ  CAK   -56.33  30.0  1
 J1O  Var_44    H19  CAL  CAJ  CAK    61.66  30.0  1
 J1O  Var_45    H13  NAN  CAK  CAJ   -88.52  30.0  3
 J1O  Var_46    H14  CAK  CAJ  CAL    59.56  30.0  1
 J1O  Var_47    H15  CAK  CAJ  CAL   -58.59  30.0  1
 J1O  Var_48    H16  CAJ  CAL  CAP    61.47  30.0  3
 J1O  Var_49    H17  CAJ  CAL  CAP   -56.43  30.0  3
 J1O  Var_50    H18  CAL  CAP  OAF    -2.35  30.0  2
 J1O  Var_51    H19  CAL  CAP  OAF  -118.61  30.0  2
 J1O  Var_52    H18  CAL  CAP  OAC   177.87  30.0  2
 J1O  Var_53    H19  CAL  CAP  OAC    61.60  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
 J1O  chir_01  CAR  OAG  CAQ  CAS  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
 J1O  plan-1  CAR  0.020
 J1O  plan-1  CAQ  0.020
 J1O  plan-1  OAD  0.020
 J1O  plan-1  NAN  0.020
 J1O  plan-1  CAK  0.020
 J1O  plan-1  H13  0.020
 J1O  plan-2  CAL  0.020
 J1O  plan-2  CAP  0.020
 J1O  plan-2  OAF  0.020
 J1O  plan-2  OAC  0.020
 J1O  plan-2  H20  0.020

