# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 19:45:15 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: methyl (R)-(2-carbamoyl-5-chloro-1H-indol-3-yl)[3-(2-cyanoethyl)-5-methylphenyl]phosphinate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[P@](=O)(c1cc(C)cc(CCC#N)c1)c2c([nH]c3ccc(Cl)cc23)C(N)=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
 5DV  5DV  'methyl (R)-(2-carbamoyl-5-chloro-1H-indol-3-yl)[3-(2-cyanoethyl)-5-methylphenyl]phosphinate'  ligand  47  28  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5DV
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
 5DV  NBB  N   NS    0  -0.274  -7.8492   0.4967  -0.7275
 5DV  CBA  C   CSP   0   0.120  -6.7251   0.2572  -0.7835
 5DV  CAZ  C   CH2   0  -0.532  -5.3069  -0.0606  -0.8409
 5DV  CAY  C   CH2   0  -0.522  -4.9382  -1.2153   0.1037
 5DV  CAT  C   CR6   0   0.164  -3.4680  -1.5114   0.0079
 5DV  CAS  C   CR16  0  -0.353  -2.5512  -0.7482   0.7231
 5DV  CAU  C   CR16  0  -0.358  -2.9988  -2.5163  -0.8291
 5DV  CAV  C   CR6   0   0.136  -1.6371  -2.7788  -0.9705
 5DV  CAX  C   CH3   0  -0.722  -1.1542  -3.8498  -1.9042
 5DV  CAW  C   CR16  0  -0.334  -0.7378  -2.0051  -0.2467
 5DV  CAR  C   CR6   0  -0.158  -1.1903  -0.9932   0.5975
 5DV  PAO  P   P     0   1.303  -0.0527   0.0534   1.5146
 5DV  OAQ  O   O2    0  -0.595   0.9609  -1.0553   2.1080
 5DV  CBC  C   CH3   0  -0.430   1.9791  -0.6458   3.0249
 5DV  OAP  O   O     0  -0.699  -0.6986   0.9195   2.5391
 5DV  CAI  C   CR5   0  -0.340   0.9385   0.9573   0.3355
 5DV  CAE  C   CR56  0   0.055   2.1660   0.5783  -0.3056
 5DV  CAF  C   CR16  0  -0.334   2.9580  -0.5775  -0.3022
 5DV  CAA  C   CR6   0  -0.035   4.0935  -0.5825  -1.0799
 5DV  CL   CL  CL    0  -0.132   5.0915  -2.0040  -1.1025
 5DV  CAB  C   CR16  0  -0.240   4.4837   0.5140  -1.8631
 5DV  CAC  C   CR16  0  -0.298   3.7168   1.6582  -1.8789
 5DV  CAD  C   CR56  0   0.363   2.5651   1.6751  -1.0968
 5DV  NAG  N   NR15  0  -0.715   1.6341   2.6601  -0.9377
 5DV  CAH  C   CR5   0   0.203   0.6568   2.2320  -0.1015
 5DV  CAL  C   C     0   0.455  -0.5615   3.0490   0.1611
 5DV  OAN  O   O     0  -0.445  -1.6613   2.5258   0.1462
 5DV  NAM  N   NH2   0  -0.801  -0.3381   4.3548   0.3541
 5DV  H1   H   HCH2  0   0.315  -5.0555  -0.3126  -1.8727
 5DV  H2   H   HCH2  0   0.311  -4.7469   0.8410  -0.5842
 5DV  H3   H   HCH2  0   0.275  -5.2049  -0.9420   1.1255
 5DV  H4   H   HCH2  0   0.275  -5.5206  -2.0986  -0.1610
 5DV  H5   H   HCR6  0   0.255  -2.9022   0.0400   1.3773
 5DV  H6   H   HCR6  0   0.252  -3.7128  -3.1122  -1.3880
 5DV  H7   H   HCH3  0   0.253  -1.0105  -3.4490  -2.9095
 5DV  H8   H   HCH3  0   0.247  -0.1998  -4.2642  -1.5811
 5DV  H9   H   HCH3  0   0.247  -1.8698  -4.6676  -1.9808
 5DV  H10  H   HCR6  0   0.256   0.3228  -2.2040  -0.3507
 5DV  H11  H   HCH3  0   0.256   2.4978  -1.5453   3.3464
 5DV  H12  H   HCH3  0   0.233   2.6993   0.0258   2.5539
 5DV  H14  H   HCR6  0   0.276   2.6903  -1.4471   0.2812
 5DV  H15  H   HCR6  0   0.281   5.3853   0.4592  -2.4571
 5DV  H16  H   HCR6  0   0.281   4.0039   2.5092  -2.4823
 5DV  H17  H   HNR5  0   0.426   1.6256   3.5336  -1.4424
 5DV  H18  H   HNH2  0   0.418   0.5852   4.7231   0.5112
 5DV  H19  H   HNH2  0   0.415  -1.1130   4.9716   0.5412
 5DV  H21  H   HCH3  0   0.246   1.5506  -0.1516   3.8968

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
 5DV  NBB  CBA  triple    1.151  0.020  1.151
 5DV  CBA  CAZ  single    1.454  0.020  1.454
 5DV  CAZ  CAY  single    1.537  0.020  1.537
 5DV  CAY  CAT  single    1.503  0.020  1.503
 5DV  CAT  CAS  aromatic  1.391  0.020  1.391
 5DV  CAT  CAU  aromatic  1.389  0.020  1.389
 5DV  CAS  CAR  aromatic  1.389  0.020  1.389
 5DV  CAU  CAV  aromatic  1.394  0.020  1.394
 5DV  CAV  CAX  single    1.501  0.020  1.501
 5DV  CAV  CAW  aromatic  1.390  0.020  1.390
 5DV  CAW  CAR  aromatic  1.393  0.020  1.393
 5DV  CAR  PAO  single    1.797  0.020  1.797
 5DV  PAO  OAQ  single    1.615  0.020  1.615
 5DV  PAO  OAP  double    1.489  0.020  1.489
 5DV  PAO  CAI  single    1.786  0.020  1.786
 5DV  OAQ  CBC  single    1.430  0.020  1.430
 5DV  CAI  CAE  aromatic  1.436  0.020  1.436
 5DV  CAI  CAH  aromatic  1.377  0.020  1.377
 5DV  CAE  CAF  aromatic  1.401  0.020  1.401
 5DV  CAE  CAD  aromatic  1.410  0.020  1.410
 5DV  CAF  CAA  aromatic  1.376  0.020  1.376
 5DV  CAA  CL   single    1.737  0.020  1.737
 5DV  CAA  CAB  aromatic  1.403  0.020  1.403
 5DV  CAB  CAC  aromatic  1.377  0.020  1.377
 5DV  CAC  CAD  aromatic  1.392  0.020  1.392
 5DV  CAD  NAG  aromatic  1.365  0.020  1.365
 5DV  NAG  CAH  aromatic  1.356  0.020  1.356
 5DV  CAH  CAL  single    1.490  0.020  1.490
 5DV  CAL  OAN  double    1.218  0.020  1.218
 5DV  CAL  NAM  single    1.339  0.020  1.339
 5DV  CAZ  H1   single    0.970  0.020  1.090
 5DV  CAZ  H2   single    0.970  0.020  1.090
 5DV  CAY  H3   single    0.970  0.020  1.090
 5DV  CAY  H4   single    0.970  0.020  1.090
 5DV  CAS  H5   single    0.930  0.020  1.080
 5DV  CAU  H6   single    0.930  0.020  1.080
 5DV  CAX  H7   single    0.970  0.020  1.090
 5DV  CAX  H8   single    0.970  0.020  1.090
 5DV  CAX  H9   single    0.970  0.020  1.090
 5DV  CAW  H10  single    0.930  0.020  1.080
 5DV  CBC  H11  single    0.970  0.020  1.090
 5DV  CBC  H12  single    0.970  0.020  1.090
 5DV  CAF  H14  single    0.930  0.020  1.080
 5DV  CAB  H15  single    0.930  0.020  1.080
 5DV  CAC  H16  single    0.930  0.020  1.080
 5DV  NAG  H17  single    0.860  0.020  1.020
 5DV  NAM  H18  single    0.860  0.020  1.020
 5DV  NAM  H19  single    0.860  0.020  1.020
 5DV  CBC  H21  single    0.970  0.020  1.090

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
 5DV  CAZ  CBA  NBB  180.00  3.000
 5DV  H2   CAZ  H1   107.13  3.000
 5DV  H2   CAZ  CAY  110.66  3.000
 5DV  H1   CAZ  CAY  110.63  3.000
 5DV  H2   CAZ  CBA  108.08  3.000
 5DV  H1   CAZ  CBA  108.20  3.000
 5DV  CAY  CAZ  CBA  111.96  3.000
 5DV  H4   CAY  H3   107.44  3.000
 5DV  H4   CAY  CAT  110.33  3.000
 5DV  H3   CAY  CAT  110.38  3.000
 5DV  H4   CAY  CAZ  109.35  3.000
 5DV  H3   CAY  CAZ  109.20  3.000
 5DV  CAT  CAY  CAZ  110.10  3.000
 5DV  CAU  CAT  CAS  118.95  3.000
 5DV  CAU  CAT  CAY  120.75  3.000
 5DV  CAS  CAT  CAY  120.26  3.000
 5DV  H5   CAS  CAR  120.05  3.000
 5DV  H5   CAS  CAT  119.77  3.000
 5DV  CAR  CAS  CAT  120.18  3.000
 5DV  H6   CAU  CAV  119.15  3.000
 5DV  H6   CAU  CAT  119.04  3.000
 5DV  CAV  CAU  CAT  121.81  3.000
 5DV  CAW  CAV  CAX  120.88  3.000
 5DV  CAW  CAV  CAU  118.32  3.000
 5DV  CAX  CAV  CAU  120.79  3.000
 5DV  H9   CAX  H8   108.11  3.000
 5DV  H9   CAX  H7   107.29  3.000
 5DV  H8   CAX  H7   107.30  3.000
 5DV  H9   CAX  CAV  111.60  3.000
 5DV  H8   CAX  CAV  111.64  3.000
 5DV  H7   CAX  CAV  110.69  3.000
 5DV  H10  CAW  CAR  120.61  3.000
 5DV  H10  CAW  CAV  118.75  3.000
 5DV  CAR  CAW  CAV  120.65  3.000
 5DV  PAO  CAR  CAW  121.77  3.000
 5DV  PAO  CAR  CAS  118.13  3.000
 5DV  CAW  CAR  CAS  120.09  3.000
 5DV  CAI  PAO  OAP  113.62  3.000
 5DV  CAI  PAO  OAQ  103.99  3.000
 5DV  OAP  PAO  OAQ  114.75  3.000
 5DV  CAI  PAO  CAR  108.01  3.000
 5DV  OAP  PAO  CAR  114.53  3.000
 5DV  OAQ  PAO  CAR  100.66  3.000
 5DV  CBC  OAQ  PAO  119.07  3.000
 5DV  H21  CBC  H12  109.00  3.000
 5DV  H21  CBC  H11  109.04  3.000
 5DV  H12  CBC  H11  108.78  3.000
 5DV  H21  CBC  OAQ  111.27  3.000
 5DV  H12  CBC  OAQ  111.67  3.000
 5DV  H11  CBC  OAQ  107.01  3.000
 5DV  CAH  CAI  CAE  106.12  3.000
 5DV  CAH  CAI  PAO  124.38  3.000
 5DV  CAE  CAI  PAO  129.47  3.000
 5DV  CAD  CAE  CAF  118.88  3.000
 5DV  CAD  CAE  CAI  106.69  3.000
 5DV  CAF  CAE  CAI  134.42  3.000
 5DV  H14  CAF  CAA  120.43  3.000
 5DV  H14  CAF  CAE  121.67  3.000
 5DV  CAA  CAF  CAE  117.90  3.000
 5DV  CAB  CAA  CL   118.20  3.000
 5DV  CAB  CAA  CAF  122.83  3.000
 5DV  CL   CAA  CAF  118.96  3.000
 5DV  H15  CAB  CAC  120.00  3.000
 5DV  H15  CAB  CAA  119.94  3.000
 5DV  CAC  CAB  CAA  120.06  3.000
 5DV  H16  CAC  CAD  121.55  3.000
 5DV  H16  CAC  CAB  120.80  3.000
 5DV  CAD  CAC  CAB  117.65  3.000
 5DV  NAG  CAD  CAC  129.68  3.000
 5DV  NAG  CAD  CAE  107.63  3.000
 5DV  CAC  CAD  CAE  122.68  3.000
 5DV  H17  NAG  CAH  125.16  3.000
 5DV  H17  NAG  CAD  124.92  3.000
 5DV  CAH  NAG  CAD  109.62  3.000
 5DV  CAL  CAH  NAG  121.66  3.000
 5DV  CAL  CAH  CAI  128.25  3.000
 5DV  NAG  CAH  CAI  109.92  3.000
 5DV  NAM  CAL  OAN  124.85  3.000
 5DV  NAM  CAL  CAH  115.07  3.000
 5DV  OAN  CAL  CAH  120.03  3.000
 5DV  H19  NAM  H18  116.90  3.000
 5DV  H19  NAM  CAL  119.69  3.000
 5DV  H18  NAM  CAL  122.18  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
 5DV  CONST_01  CAW  CAR  CAS  CAT     0.00   0.0  0
 5DV  CONST_02  CAW  CAV  CAU  CAT     0.00   0.0  0
 5DV  CONST_03  CAV  CAU  CAT  CAS     0.00   0.0  0
 5DV  CONST_04  CAV  CAW  CAR  CAS     0.00   0.0  0
 5DV  CONST_05  CAR  CAS  CAT  CAU     0.00   0.0  0
 5DV  CONST_06  CAR  CAW  CAV  CAU     0.00   0.0  0
 5DV  CONST_07  CAA  CAF  CAE  CAI   180.00   0.0  0
 5DV  CONST_08  CAC  CAD  CAE  CAI   180.00   0.0  0
 5DV  CONST_09  NAG  CAD  CAE  CAI     0.00   0.0  0
 5DV  CONST_10  CAD  NAG  CAH  CAI     0.00   0.0  0
 5DV  CONST_11  NAG  CAH  CAI  CAE     0.00   0.0  0
 5DV  CONST_12  CAB  CAA  CAF  CAE     0.00   0.0  0
 5DV  CONST_13  CAB  CAC  CAD  CAE     0.00   0.0  0
 5DV  CONST_14  CAH  NAG  CAD  CAE     0.00   0.0  0
 5DV  CONST_15  CAH  CAI  CAE  CAF   180.00   0.0  0
 5DV  CONST_16  CAC  CAD  CAE  CAF     0.00   0.0  0
 5DV  CONST_17  NAG  CAD  CAE  CAF   180.00   0.0  0
 5DV  CONST_18  CAC  CAB  CAA  CAF     0.00   0.0  0
 5DV  CONST_19  CAD  CAE  CAF  CAA     0.00   0.0  0
 5DV  CONST_20  CAD  CAC  CAB  CAA     0.00   0.0  0
 5DV  CONST_21  NAG  CAD  CAC  CAB   180.00   0.0  0
 5DV  CONST_22  CAH  NAG  CAD  CAC   180.00   0.0  0
 5DV  CONST_23  CAH  CAI  CAE  CAD     0.00   0.0  0
 5DV  CONST_24  CAR  CAS  CAT  CAY   180.00   0.0  0
 5DV  CONST_25  CAV  CAU  CAT  CAY   180.00   0.0  0
 5DV  CONST_26  PAO  CAR  CAS  CAT   180.00   0.0  0
 5DV  CONST_27  CAX  CAV  CAU  CAT   180.00   0.0  0
 5DV  CONST_28  PAO  CAR  CAW  CAV   180.00   0.0  0
 5DV  CONST_29  CAR  CAW  CAV  CAX   180.00   0.0  0
 5DV  CONST_30  CAF  CAE  CAI  PAO     0.00   0.0  0
 5DV  CONST_31  CAD  CAE  CAI  PAO   180.00   0.0  0
 5DV  CONST_32  NAG  CAH  CAI  PAO   180.00   0.0  0
 5DV  CONST_33  CAL  CAH  CAI  CAE   180.00   0.0  0
 5DV  CONST_34  CL   CAA  CAF  CAE   180.00   0.0  0
 5DV  CONST_35  CAC  CAB  CAA  CL    180.00   0.0  0
 5DV  CONST_36  CAL  CAH  NAG  CAD   180.00   0.0  0
 5DV  CONST_37  H6   CAU  CAT  CAS   180.00   0.0  0
 5DV  CONST_38  H10  CAW  CAR  CAS   180.00   0.0  0
 5DV  CONST_39  H5   CAS  CAT  CAU   180.00   0.0  0
 5DV  CONST_40  H14  CAF  CAE  CAI     0.00   0.0  0
 5DV  CONST_41  H17  NAG  CAH  CAI   180.00   0.0  0
 5DV  CONST_42  H16  CAC  CAD  CAE   180.00   0.0  0
 5DV  CONST_43  H15  CAB  CAA  CAF   180.00   0.0  0
 5DV  CONST_44  H18  NAM  CAL  CAH     0.00   0.0  0
 5DV  CONST_45  H19  NAM  CAL  CAH   180.00   0.0  0
 5DV  Var_01    CAI  PAO  CAR  CAS  -116.07  30.0  2
 5DV  Var_02    CAE  CAI  PAO  CAR   -87.12  30.0  2
 5DV  Var_03    CAS  CAT  CAY  CAZ    82.11  30.0  2
 5DV  Var_04    OAN  CAL  CAH  CAI   -40.25  30.0  2
 5DV  Var_05    H7   CAX  CAV  CAU    88.01  30.0  2
 5DV  Var_06    CAT  CAY  CAZ  CBA   179.81  30.0  3
 5DV  Var_07    CAY  CAZ  CBA  NBB    -1.39  30.0  3
 5DV  Var_08    H11  CBC  OAQ  PAO   176.30  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
 5DV  chir_01  PAO  OAQ  OAP  CAI  both

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
 5DV  plan-1  CAY  0.020
 5DV  plan-1  CAT  0.020
 5DV  plan-1  CAS  0.020
 5DV  plan-1  CAU  0.020
 5DV  plan-1  CAV  0.020
 5DV  plan-1  CAX  0.020
 5DV  plan-1  CAW  0.020
 5DV  plan-1  CAR  0.020
 5DV  plan-1  PAO  0.020
 5DV  plan-1  H5   0.020
 5DV  plan-1  H6   0.020
 5DV  plan-1  H10  0.020
 5DV  plan-2  PAO  0.020
 5DV  plan-2  CAI  0.020
 5DV  plan-2  CAE  0.020
 5DV  plan-2  CAF  0.020
 5DV  plan-2  CAA  0.020
 5DV  plan-2  CL   0.020
 5DV  plan-2  CAB  0.020
 5DV  plan-2  CAC  0.020
 5DV  plan-2  CAD  0.020
 5DV  plan-2  NAG  0.020
 5DV  plan-2  CAH  0.020
 5DV  plan-2  CAL  0.020
 5DV  plan-2  H14  0.020
 5DV  plan-2  H15  0.020
 5DV  plan-2  H16  0.020
 5DV  plan-2  H17  0.020
 5DV  plan-3  CAH  0.020
 5DV  plan-3  CAL  0.020
 5DV  plan-3  OAN  0.020
 5DV  plan-3  NAM  0.020
 5DV  plan-3  H18  0.020
 5DV  plan-3  H19  0.020

