# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 03:58:03 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: (2~{R})-~{N}-[3-[2-[[(2~{S})-2-formamido-3-methyl-butanoyl]amino]ethylamino]-3-oxidanylidene-propyl]-3,3-dimethyl-2-oxidanyl-4-[oxidanyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxy-butanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](NC=O)C(=O)NCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P](O)(=O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 JQG  JQG  (2~{R})-~{N}-[3-[2-[[(2~{S})-2-formamido-3-methyl-butanoyl]amino]ethylamino]-3-oxidanylidene-propyl]-3,3-dimethyl-2-oxidanyl-4-[oxidanyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxy-butanamide  ligand  63  31  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JQG
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
 JQG  C02   C  C     0   0.562   -6.7426   0.3549   0.5578
 JQG  C04   C  CH2   0  -0.297   -4.3504   0.6994   0.1390
 JQG  C05   C  CH2   0  -0.298   -3.6060  -0.3645   0.9474
 JQG  C07   C  C     0   0.568   -1.2096  -0.0819   0.5023
 JQG  C08   C  CH2   0  -0.628    0.0857   0.4636   1.0680
 JQG  C09   C  CH2   0  -0.243    1.2266   0.3865   0.0688
 JQG  C11   C  C     0   0.516    3.4343   1.4466  -0.0607
 JQG  C12   C  CH1   0  -0.032    4.6517   1.9435   0.7217
 JQG  C14   C  CT    0  -0.168    5.7377   0.8486   0.9282
 JQG  C15   C  CH3   0  -0.672    5.1461  -0.3392   1.6906
 JQG  C16   C  CH2   0  -0.154    6.2595   0.3931  -0.4322
 JQG  C22   C  CH3   0  -0.646    6.8686   1.4689   1.7543
 JQG  C25   C  CH1   0  -0.213   -8.0442  -0.1508  -0.0613
 JQG  C26   C  CH1   0  -0.226   -8.5586   0.8315  -1.1374
 JQG  C27   C  CH3   0  -0.656   -9.8070   0.2833  -1.8179
 JQG  C28   C  CH3   0  -0.669   -8.8135   2.2294  -0.5835
 JQG  N03   N  NH1   0  -0.630   -5.6730   0.2631  -0.2447
 JQG  N06   N  NH1   0  -0.636   -2.2753   0.0600   1.3094
 JQG  N10   N  NH1   0  -0.636    2.4273   0.9474   0.6564
 JQG  N29   N  NH1   0  -0.584   -8.9999  -0.3839   0.9904
 JQG  O01   O  O     0  -0.487   -6.7037   0.8388   1.6794
 JQG  O13   O  OH1   0  -0.661    5.1556   3.0797   0.0754
 JQG  O17   O  OC2   0  -0.570    7.3169  -0.5614  -0.2142
 JQG  O19   O  OP    0  -0.612    7.4104  -1.7060  -2.5788
 JQG  O21   O  OP    0  -0.418    8.9605   0.0266  -2.1257
 JQG  O23   O  O     0  -0.499    3.4199   1.5436  -1.2835
 JQG  O24   O  O     0  -0.496   -1.2737  -0.6166  -0.5951
 JQG  O31   O  O     0  -0.492   -9.7535  -2.4338   0.3374
 JQG  P18   P  P     0   1.445    8.1567  -1.1280  -1.4214
 JQG  H041  H  HCH2  0   0.249   -4.4230   1.6228   0.7140
 JQG  H042  H  HCH2  0   0.261   -3.7980   0.9268  -0.7720
 JQG  H052  H  HCH2  0   0.259   -4.1518  -0.5819   1.8650
 JQG  H051  H  HCH2  0   0.248   -3.5502  -1.2912   0.3761
 JQG  H081  H  HCH2  0   0.281   -0.0689   1.4999   1.3811
 JQG  H082  H  HCH2  0   0.284    0.3355  -0.0965   1.9748
 JQG  H092  H  HCH2  0   0.250    1.4016  -0.6483  -0.2342
 JQG  H091  H  HCH2  0   0.254    0.9813   0.9514  -0.8293
 JQG  H121  H  HCH1  0   0.260    4.3314   2.2474   1.7250
 JQG  H153  H  HCH3  0   0.236    4.4213  -0.8983   1.0967
 JQG  H152  H  HCH3  0   0.252    5.9297  -1.0352   1.9882
 JQG  H151  H  HCH3  0   0.237    4.6496  -0.0062   2.6051
 JQG  H162  H  HCH2  0   0.259    5.4738  -0.0874  -1.0175
 JQG  H161  H  HCH2  0   0.249    6.6514   1.2404  -1.0000
 JQG  H223  H  HCH3  0   0.233    6.4907   1.8085   2.7206
 JQG  H222  H  HCH3  0   0.241    7.6562   0.7423   1.9502
 JQG  H221  H  HCH3  0   0.238    7.3184   2.3231   1.2491
 JQG  H251  H  HCH1  0   0.288   -7.8487  -1.1091  -0.5497
 JQG  H261  H  HCH1  0   0.235   -7.7702   0.9022  -1.8940
 JQG  H273  H  HCH3  0   0.223  -10.6535   0.2475  -1.1303
 JQG  H272  H  HCH3  0   0.235  -10.0925   0.9233  -2.6538
 JQG  H271  H  HCH3  0   0.231   -9.6480  -0.7227  -2.2078
 JQG  H283  H  HCH3  0   0.236   -7.9135   2.6905  -0.1751
 JQG  H282  H  HCH3  0   0.238   -9.1809   2.8825  -1.3759
 JQG  H281  H  HCH3  0   0.221   -9.5724   2.2160   0.2012
 JQG  H301  H  H     0   0.206  -10.3588  -1.4661   2.0210
 JQG  H031  H  HNH1  0   0.408   -5.7684  -0.2144  -1.1268
 JQG  H061  H  HNH1  0   0.405   -2.1601   0.5513   2.1813
 JQG  H101  H  HNH1  0   0.407    2.5358   0.8870   1.6573
 JQG  H291  H  HNH1  0   0.403   -9.0443   0.2869   1.7415
 JQG  H131  H  HOH1  0   0.447    4.9662   2.9876  -0.8678
 JQG  O1    O  OP    0  -0.708    9.1102  -2.0759  -0.5927
 JQG  H1    H  H     0   0.514    9.7212  -2.6044  -1.1258
 JQG  C30   C  C1    0   0.256   -9.7395  -1.4936   1.1125

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
 JQG  C27  C26   single  1.524  0.020  1.524
 JQG  C28  C26   single  1.525  0.020  1.525
 JQG  C26  C25   single  1.545  0.020  1.545
 JQG  C25  N29   single  1.440  0.020  1.440
 JQG  C25  C02   single  1.528  0.020  1.528
 JQG  N29  C30   single  1.339  0.020  1.339
 JQG  C30  O31   double  1.219  0.020  1.219
 JQG  C02  O01   double  1.222  0.020  1.222
 JQG  C02  N03   single  1.340  0.020  1.340
 JQG  N03  C04   single  1.445  0.020  1.445
 JQG  C04  C05   single  1.530  0.020  1.530
 JQG  C05  N06   single  1.443  0.020  1.443
 JQG  N06  C07   single  1.344  0.020  1.344
 JQG  O24  C07   double  1.222  0.020  1.222
 JQG  C07  C08   single  1.515  0.020  1.515
 JQG  C08  C09   single  1.519  0.020  1.519
 JQG  C09  N10   single  1.450  0.020  1.450
 JQG  C15  C14   single  1.530  0.020  1.530
 JQG  O23  C11   double  1.227  0.020  1.227
 JQG  C22  C14   single  1.532  0.020  1.532
 JQG  N10  C11   single  1.333  0.020  1.333
 JQG  C11  C12   single  1.530  0.020  1.530
 JQG  C14  C12   single  1.556  0.020  1.556
 JQG  C14  C16   single  1.527  0.020  1.527
 JQG  C12  O13   single  1.401  0.020  1.401
 JQG  C16  O17   single  1.441  0.020  1.441
 JQG  O17  P18   single  1.576  0.020  1.576
 JQG  O21  P18   double  1.573  0.020  1.573
 JQG  P18  O19   double  1.494  0.020  1.494
 JQG  C04  H041  single  0.970  0.020  1.090
 JQG  C04  H042  single  0.970  0.020  1.090
 JQG  C05  H052  single  0.970  0.020  1.090
 JQG  C05  H051  single  0.970  0.020  1.090
 JQG  C08  H081  single  0.970  0.020  1.090
 JQG  C08  H082  single  0.970  0.020  1.090
 JQG  C09  H092  single  0.970  0.020  1.090
 JQG  C09  H091  single  0.970  0.020  1.090
 JQG  C12  H121  single  0.970  0.020  1.090
 JQG  C15  H153  single  0.970  0.020  1.090
 JQG  C15  H152  single  0.970  0.020  1.090
 JQG  C15  H151  single  0.970  0.020  1.090
 JQG  C16  H162  single  0.970  0.020  1.090
 JQG  C16  H161  single  0.970  0.020  1.090
 JQG  C22  H223  single  0.970  0.020  1.090
 JQG  C22  H222  single  0.970  0.020  1.090
 JQG  C22  H221  single  0.970  0.020  1.090
 JQG  C25  H251  single  0.970  0.020  1.090
 JQG  C26  H261  single  0.970  0.020  1.090
 JQG  C27  H273  single  0.970  0.020  1.090
 JQG  C27  H272  single  0.970  0.020  1.090
 JQG  C27  H271  single  0.970  0.020  1.090
 JQG  C28  H283  single  0.970  0.020  1.090
 JQG  C28  H282  single  0.970  0.020  1.090
 JQG  C28  H281  single  0.970  0.020  1.090
 JQG  C30  H301  single  0.930  0.020  1.080
 JQG  N03  H031  single  0.860  0.020  1.020
 JQG  N06  H061  single  0.860  0.020  1.020
 JQG  N10  H101  single  0.860  0.020  1.020
 JQG  N29  H291  single  0.860  0.020  1.020
 JQG  O13  H131  single  0.850  0.020  0.980
 JQG  P18  O1    single  1.579  0.020  1.579
 JQG  O1   H1    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
 JQG  O01   C02  N03   123.45  3.000
 JQG  N03   C02  C25   114.49  3.000
 JQG  O01   C02  C25   122.02  3.000
 JQG  H042  C04  H041  107.34  3.000
 JQG  H042  C04  N03   107.76  3.000
 JQG  H041  C04  N03   109.57  3.000
 JQG  H042  C04  C05   109.90  3.000
 JQG  H041  C04  C05   110.05  3.000
 JQG  N03   C04  C05   112.08  3.000
 JQG  H051  C05  H052  107.30  3.000
 JQG  H051  C05  N06   109.54  3.000
 JQG  H052  C05  N06   108.02  3.000
 JQG  H051  C05  C04   109.83  3.000
 JQG  H052  C05  C04   109.88  3.000
 JQG  N06   C05  C04   112.13  3.000
 JQG  O24   C07  N06   122.93  3.000
 JQG  O24   C07  C08   122.51  3.000
 JQG  N06   C07  C08   114.55  3.000
 JQG  H082  C08  H081  106.25  3.000
 JQG  H082  C08  C09   110.34  3.000
 JQG  H081  C08  C09   110.04  3.000
 JQG  H082  C08  C07   108.67  3.000
 JQG  H081  C08  C07   109.11  3.000
 JQG  C09   C08  C07   112.23  3.000
 JQG  H091  C09  H092  107.38  3.000
 JQG  H091  C09  N10   108.67  3.000
 JQG  H092  C09  N10   110.26  3.000
 JQG  H091  C09  C08   110.31  3.000
 JQG  H092  C09  C08   110.55  3.000
 JQG  N10   C09  C08   109.63  3.000
 JQG  O23   C11  N10   123.84  3.000
 JQG  N10   C11  C12   116.59  3.000
 JQG  O23   C11  C12   119.57  3.000
 JQG  H121  C12  O13   107.61  3.000
 JQG  H121  C12  C14   106.12  3.000
 JQG  O13   C12  C14   112.39  3.000
 JQG  H121  C12  C11   109.00  3.000
 JQG  O13   C12  C11   108.28  3.000
 JQG  C14   C12  C11   113.24  3.000
 JQG  C22   C14  C16   110.43  3.000
 JQG  C16   C14  C15   110.15  3.000
 JQG  C22   C14  C15   109.34  3.000
 JQG  C16   C14  C12   109.29  3.000
 JQG  C22   C14  C12   107.57  3.000
 JQG  C15   C14  C12   110.02  3.000
 JQG  H151  C15  H152  107.03  3.000
 JQG  H151  C15  H153  108.06  3.000
 JQG  H152  C15  H153  107.40  3.000
 JQG  H151  C15  C14   110.86  3.000
 JQG  H152  C15  C14   110.72  3.000
 JQG  H153  C15  C14   112.54  3.000
 JQG  H161  C16  H162  108.72  3.000
 JQG  H161  C16  O17   109.21  3.000
 JQG  H162  C16  O17   108.53  3.000
 JQG  H161  C16  C14   110.75  3.000
 JQG  H162  C16  C14   111.30  3.000
 JQG  O17   C16  C14   108.27  3.000
 JQG  H221  C22  H222  107.93  3.000
 JQG  H221  C22  H223  108.03  3.000
 JQG  H222  C22  H223  107.37  3.000
 JQG  H221  C22  C14   111.86  3.000
 JQG  H222  C22  C14   111.14  3.000
 JQG  H223  C22  C14   110.35  3.000
 JQG  H251  C25  N29   107.64  3.000
 JQG  H251  C25  C26   107.80  3.000
 JQG  N29   C25  C26   112.99  3.000
 JQG  H251  C25  C02   108.60  3.000
 JQG  N29   C25  C02   108.85  3.000
 JQG  C26   C25  C02   110.82  3.000
 JQG  H261  C26  C28   108.19  3.000
 JQG  H261  C26  C27   107.73  3.000
 JQG  C28   C26  C27   110.80  3.000
 JQG  H261  C26  C25   106.41  3.000
 JQG  C28   C26  C25   112.67  3.000
 JQG  C27   C26  C25   110.79  3.000
 JQG  H271  C27  H272  107.78  3.000
 JQG  H271  C27  H273  107.95  3.000
 JQG  H272  C27  H273  107.40  3.000
 JQG  H271  C27  C26   111.85  3.000
 JQG  H272  C27  C26   110.21  3.000
 JQG  H273  C27  C26   111.47  3.000
 JQG  H281  C28  H282  107.18  3.000
 JQG  H281  C28  H283  108.05  3.000
 JQG  H282  C28  H283  107.27  3.000
 JQG  H281  C28  C26   111.47  3.000
 JQG  H282  C28  C26   109.96  3.000
 JQG  H283  C28  C26   112.68  3.000
 JQG  H031  N03  C04   117.54  3.000
 JQG  H031  N03  C02   118.76  3.000
 JQG  C04   N03  C02   123.43  3.000
 JQG  H061  N06  C07   118.72  3.000
 JQG  H061  N06  C05   117.78  3.000
 JQG  C07   N06  C05   123.32  3.000
 JQG  H101  N10  C11   118.35  3.000
 JQG  H101  N10  C09   117.92  3.000
 JQG  C11   N10  C09   123.54  3.000
 JQG  H291  N29  C30   117.33  3.000
 JQG  H291  N29  C25   117.76  3.000
 JQG  C30   N29  C25   124.56  3.000
 JQG  H131  O13  C12   107.60  3.000
 JQG  P18   O17  C16   120.88  3.000
 JQG  O1    P18  O21   111.53  3.000
 JQG  O1    P18  O19   118.42  3.000
 JQG  O21   P18  O19   101.09  3.000
 JQG  O1    P18  O17    97.79  3.000
 JQG  O19   P18  O17   117.81  3.000
 JQG  O21   P18  O17   110.57  3.000
 JQG  H1    O1   P18   114.82  3.000
 JQG  H301  C30  O31   122.56  3.000
 JQG  H301  C30  N29   111.44  3.000
 JQG  O31   C30  N29   125.99  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
 JQG  CONST_01  C25   C02  N03  C04   180.00   0.0  0
 JQG  CONST_02  O01   C02  N03  C04     0.00   0.0  0
 JQG  CONST_03  O24   C07  N06  C05     0.00   0.0  0
 JQG  CONST_04  C08   C07  N06  C05   180.00   0.0  0
 JQG  CONST_05  O23   C11  N10  C09     0.00   0.0  0
 JQG  CONST_06  C12   C11  N10  C09   180.00   0.0  0
 JQG  CONST_07  O31   C30  N29  C25     0.00   0.0  0
 JQG  CONST_08  H061  N06  C07  C08     0.00   0.0  0
 JQG  CONST_09  H101  N10  C11  C12     0.00   0.0  0
 JQG  CONST_10  H031  N03  C02  C25     0.00   0.0  0
 JQG  CONST_11  H291  N29  C30  O31   180.00   0.0  0
 JQG  Var_01    C05   C04  N03  C02    83.50  30.0  3
 JQG  Var_02    C07   N06  C05  C04   -85.18  30.0  3
 JQG  Var_03    N10   C09  C08  C07   178.79  30.0  3
 JQG  Var_04    C11   N10  C09  C08  -155.92  30.0  3
 JQG  Var_05    N06   C07  C08  C09  -175.01  30.0  2
 JQG  Var_06    O17   C16  C14  C12   176.67  30.0  3
 JQG  Var_07    O21   P18  O17  C16    63.44  30.0  3
 JQG  Var_08    N06   C05  C04  N03   178.89  30.0  3
 JQG  Var_09    H153  C15  C14  C12    69.32  30.0  3
 JQG  Var_10    H223  C22  C14  C12    59.92  30.0  3
 JQG  Var_11    H273  C27  C26  C25    67.62  30.0  3
 JQG  Var_12    H283  C28  C26  C25    60.81  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
 JQG  chir_01  C12  C11  C14  O13  negativ
 JQG  chir_02  C25  C26  N29  C02  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
 JQG  plan-1  C02   0.020
 JQG  plan-1  C04   0.020
 JQG  plan-1  C25   0.020
 JQG  plan-1  N03   0.020
 JQG  plan-1  O01   0.020
 JQG  plan-1  H031  0.020
 JQG  plan-2  C05   0.020
 JQG  plan-2  C07   0.020
 JQG  plan-2  C08   0.020
 JQG  plan-2  N06   0.020
 JQG  plan-2  O24   0.020
 JQG  plan-2  H061  0.020
 JQG  plan-3  C09   0.020
 JQG  plan-3  C11   0.020
 JQG  plan-3  C12   0.020
 JQG  plan-3  N10   0.020
 JQG  plan-3  O23   0.020
 JQG  plan-3  H101  0.020
 JQG  plan-4  C25   0.020
 JQG  plan-4  N29   0.020
 JQG  plan-4  O31   0.020
 JQG  plan-4  H301  0.020
 JQG  plan-4  H291  0.020
 JQG  plan-4  C30   0.020

