# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 21:23:58 2022
#   Inital geometry file: a 98 line input string
#   Ligand name: (phenylmethyl) (2~{S})-2-(hydroxymethyl)-2,3-dihydroindole-1-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1Cc2ccccc2N1C(=O)OCc3ccccc3
#
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
 DJO  DJO  '(phenylmethyl) (2~{S})-2-(hydroxymethyl)-2,3-dihydroindole-1-carboxylate'  ligand  38  21  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DJO
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
 DJO  CAE  C  CR15  0  -0.150   2.8765  -1.1508  -0.3653
 DJO  CAF  C  CH2   0  -0.487   3.6375   0.1024  -0.8157
 DJO  CAG  C  CR56  0   0.006   2.7861   1.2114  -0.2713
 DJO  CAH  C  CR56  0   0.386   1.5224   0.7171   0.0575
 DJO  CAI  C  CH2   0  -0.123   3.4423  -1.6556   0.9523
 DJO  CAJ  C  CR16  0  -0.334   3.0896   2.5458  -0.0926
 DJO  CAK  C  CR16  0  -0.286   0.5501   1.5554   0.5855
 DJO  CAM  C  CR16  0  -0.261   2.1190   3.4000   0.4261
 DJO  CAN  C  CR16  0  -0.266   0.8679   2.9010   0.7581
 DJO  CAO  C  CH2   0  -0.237  -1.9197  -1.5733  -0.5340
 DJO  CAP  C  CR6   0   0.080  -3.0586  -0.6334  -0.2838
 DJO  CAQ  C  CR16  0  -0.288  -3.6246  -0.5350   0.9836
 DJO  CAR  C  CR16  0  -0.289  -3.5415   0.1778  -1.3063
 DJO  CAS  C  CR16  0  -0.243  -4.6593   0.3579   1.2267
 DJO  CAT  C  CR16  0  -0.243  -4.5754   1.0723  -1.0672
 DJO  CAU  C  CR16  0  -0.261  -5.1358   1.1637   0.2005
 DJO  NAD  N  NR5   0  -0.612   1.4998  -0.6669  -0.1960
 DJO  OAA  O  OH1   0  -0.659   2.6400  -2.6914   1.4557
 DJO  OAB  O  O2    0  -0.472  -0.7169  -0.8397  -0.2662
 DJO  OAC  O  O     0  -0.506   0.5263  -2.6272  -0.8069
 DJO  H1   H  HCR5  0   0.275   2.9021  -1.9397  -1.1150
 DJO  H2   H  HCH2  0   0.268   4.6599   0.1197  -0.4356
 DJO  H3   H  HCH2  0   0.275   3.6979   0.1596  -1.9055
 DJO  H4   H  HCH2  0   0.207   4.4725  -1.9859   0.7624
 DJO  H5   H  HCH2  0   0.196   3.5042  -0.8140   1.6565
 DJO  H6   H  HCR6  0   0.253   4.0715   2.9219  -0.3528
 DJO  H7   H  HCR6  0   0.266  -0.4276   1.1991   0.8681
 DJO  H8   H  HCR6  0   0.253   2.3421   4.4481   0.5758
 DJO  H9   H  HCR6  0   0.256   0.1173   3.5639   1.1694
 DJO  H10  H  HCH2  0   0.250  -1.9783  -2.4439   0.1222
 DJO  H11  H  HCH2  0   0.249  -1.9203  -1.9235  -1.5679
 DJO  H12  H  HCR6  0   0.254  -3.2583  -1.1656   1.7852
 DJO  H13  H  HCR6  0   0.255  -3.1103   0.1069  -2.2980
 DJO  H14  H  HCR6  0   0.258  -5.0953   0.4222   2.2151
 DJO  H15  H  HCR6  0   0.258  -4.9452   1.6967  -1.8701
 DJO  H16  H  HCR6  0   0.259  -5.9451   1.8581   0.3856
 DJO  H17  H  HOH1  0   0.456   2.9584  -2.9108   2.3359
 DJO  CAL  C  C     0   0.759   0.4374  -1.4744  -0.4460

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
 DJO  CAJ  CAM  aromatic  1.393  0.020  1.393
 DJO  CAJ  CAG  aromatic  1.380  0.020  1.380
 DJO  CAM  CAN  aromatic  1.387  0.020  1.387
 DJO  CAG  CAF  single    1.500  0.020  1.500
 DJO  CAG  CAH  aromatic  1.396  0.020  1.396
 DJO  CAN  CAK  aromatic  1.393  0.020  1.393
 DJO  CAF  CAE  single    1.534  0.020  1.534
 DJO  CAH  CAK  aromatic  1.388  0.020  1.388
 DJO  CAH  NAD  single    1.407  0.020  1.407
 DJO  CAE  NAD  single    1.469  0.020  1.469
 DJO  CAE  CAI  single    1.520  0.020  1.520
 DJO  OAA  CAI  single    1.404  0.020  1.404
 DJO  NAD  CAL  single    1.358  0.020  1.358
 DJO  CAS  CAQ  aromatic  1.388  0.020  1.388
 DJO  CAS  CAU  aromatic  1.389  0.020  1.389
 DJO  CAQ  CAP  aromatic  1.392  0.020  1.392
 DJO  CAL  OAB  single    1.330  0.020  1.330
 DJO  CAL  OAC  double    1.211  0.020  1.211
 DJO  OAB  CAO  single    1.434  0.020  1.434
 DJO  CAU  CAT  aromatic  1.389  0.020  1.389
 DJO  CAP  CAO  single    1.498  0.020  1.498
 DJO  CAP  CAR  aromatic  1.392  0.020  1.392
 DJO  CAT  CAR  aromatic  1.388  0.020  1.388
 DJO  CAE  H1   single    0.970  0.020  1.090
 DJO  CAF  H2   single    0.970  0.020  1.090
 DJO  CAF  H3   single    0.970  0.020  1.090
 DJO  CAI  H4   single    0.970  0.020  1.090
 DJO  CAI  H5   single    0.970  0.020  1.090
 DJO  CAJ  H6   single    0.930  0.020  1.080
 DJO  CAK  H7   single    0.930  0.020  1.080
 DJO  CAM  H8   single    0.930  0.020  1.080
 DJO  CAN  H9   single    0.930  0.020  1.080
 DJO  CAO  H10  single    0.970  0.020  1.090
 DJO  CAO  H11  single    0.970  0.020  1.090
 DJO  CAQ  H12  single    0.930  0.020  1.080
 DJO  CAR  H13  single    0.930  0.020  1.080
 DJO  CAS  H14  single    0.930  0.020  1.080
 DJO  CAT  H15  single    0.930  0.020  1.080
 DJO  CAU  H16  single    0.930  0.020  1.080
 DJO  OAA  H17  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
 DJO  H1   CAE  NAD  109.89  3.000
 DJO  H1   CAE  CAI  110.34  3.000
 DJO  NAD  CAE  CAI  110.99  3.000
 DJO  H1   CAE  CAF  112.22  3.000
 DJO  CAI  CAE  CAF  109.95  3.000
 DJO  NAD  CAE  CAF  103.27  3.000
 DJO  H3   CAF  H2   107.14  3.000
 DJO  H3   CAF  CAG  110.76  3.000
 DJO  H2   CAF  CAG  113.19  3.000
 DJO  H3   CAF  CAE  111.28  3.000
 DJO  H2   CAF  CAE  112.06  3.000
 DJO  CAG  CAF  CAE  102.47  3.000
 DJO  CAJ  CAG  CAH  120.72  3.000
 DJO  CAH  CAG  CAF  109.72  3.000
 DJO  CAJ  CAG  CAF  129.56  3.000
 DJO  NAD  CAH  CAK  130.63  3.000
 DJO  NAD  CAH  CAG  108.68  3.000
 DJO  CAK  CAH  CAG  120.65  3.000
 DJO  H5   CAI  H4   106.75  3.000
 DJO  H5   CAI  OAA  111.57  3.000
 DJO  H4   CAI  OAA  112.10  3.000
 DJO  H5   CAI  CAE  108.79  3.000
 DJO  H4   CAI  CAE  107.40  3.000
 DJO  OAA  CAI  CAE  110.07  3.000
 DJO  H6   CAJ  CAM  120.54  3.000
 DJO  H6   CAJ  CAG  120.26  3.000
 DJO  CAM  CAJ  CAG  119.20  3.000
 DJO  H7   CAK  CAN  119.57  3.000
 DJO  H7   CAK  CAH  122.36  3.000
 DJO  CAN  CAK  CAH  118.07  3.000
 DJO  H8   CAM  CAN  120.08  3.000
 DJO  H8   CAM  CAJ  120.12  3.000
 DJO  CAN  CAM  CAJ  119.79  3.000
 DJO  H9   CAN  CAM  119.74  3.000
 DJO  H9   CAN  CAK  118.70  3.000
 DJO  CAM  CAN  CAK  121.56  3.000
 DJO  H11  CAO  H10  108.26  3.000
 DJO  H11  CAO  OAB  109.97  3.000
 DJO  H10  CAO  OAB  109.92  3.000
 DJO  H11  CAO  CAP  111.05  3.000
 DJO  H10  CAO  CAP  111.05  3.000
 DJO  OAB  CAO  CAP  106.59  3.000
 DJO  CAR  CAP  CAQ  119.13  3.000
 DJO  CAR  CAP  CAO  120.46  3.000
 DJO  CAQ  CAP  CAO  120.39  3.000
 DJO  H12  CAQ  CAS  119.79  3.000
 DJO  H12  CAQ  CAP  119.67  3.000
 DJO  CAS  CAQ  CAP  120.54  3.000
 DJO  H13  CAR  CAT  119.75  3.000
 DJO  H13  CAR  CAP  119.75  3.000
 DJO  CAT  CAR  CAP  120.50  3.000
 DJO  H14  CAS  CAU  120.14  3.000
 DJO  H14  CAS  CAQ  119.90  3.000
 DJO  CAU  CAS  CAQ  119.97  3.000
 DJO  H15  CAT  CAU  120.08  3.000
 DJO  H15  CAT  CAR  119.90  3.000
 DJO  CAU  CAT  CAR  120.01  3.000
 DJO  H16  CAU  CAT  120.00  3.000
 DJO  H16  CAU  CAS  120.15  3.000
 DJO  CAT  CAU  CAS  119.84  3.000
 DJO  CAL  NAD  CAH  129.11  3.000
 DJO  CAL  NAD  CAE  121.07  3.000
 DJO  CAH  NAD  CAE  109.25  3.000
 DJO  H17  OAA  CAI  107.91  3.000
 DJO  CAO  OAB  CAL  117.30  3.000
 DJO  OAC  CAL  OAB  123.95  3.000
 DJO  OAC  CAL  NAD  124.30  3.000
 DJO  OAB  CAL  NAD  111.75  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
 DJO  CONST_01  CAN  CAM  CAJ  CAG     0.00   0.0  0
 DJO  CONST_02  CAN  CAK  CAH  CAG     0.00   0.0  0
 DJO  CONST_03  CAM  CAJ  CAG  CAH     0.00   0.0  0
 DJO  CONST_04  CAM  CAN  CAK  CAH     0.00   0.0  0
 DJO  CONST_05  CAK  CAN  CAM  CAJ     0.00   0.0  0
 DJO  CONST_06  CAK  CAH  CAG  CAJ     0.00   0.0  0
 DJO  CONST_07  CAU  CAS  CAQ  CAP     0.00   0.0  0
 DJO  CONST_08  CAU  CAT  CAR  CAP     0.00   0.0  0
 DJO  CONST_09  CAT  CAU  CAS  CAQ     0.00   0.0  0
 DJO  CONST_10  CAT  CAR  CAP  CAQ     0.00   0.0  0
 DJO  CONST_11  CAS  CAQ  CAP  CAR     0.00   0.0  0
 DJO  CONST_12  CAS  CAU  CAT  CAR     0.00   0.0  0
 DJO  CONST_13  CAS  CAQ  CAP  CAO   180.00   0.0  0
 DJO  CONST_14  CAT  CAR  CAP  CAO   180.00   0.0  0
 DJO  CONST_15  H6   CAJ  CAG  CAF     0.00   0.0  0
 DJO  CONST_16  H8   CAM  CAJ  CAG   180.00   0.0  0
 DJO  CONST_17  H7   CAK  CAH  CAG   180.00   0.0  0
 DJO  CONST_18  H9   CAN  CAK  CAH   180.00   0.0  0
 DJO  CONST_19  H14  CAS  CAQ  CAP   180.00   0.0  0
 DJO  CONST_20  H15  CAT  CAR  CAP   180.00   0.0  0
 DJO  CONST_21  H16  CAU  CAS  CAQ   180.00   0.0  0
 DJO  CONST_22  H13  CAR  CAP  CAQ   180.00   0.0  0
 DJO  CONST_23  H12  CAQ  CAP  CAR   180.00   0.0  0
 DJO  Var_01    CAJ  CAG  CAF  CAE   164.00  30.0  1
 DJO  Var_02    CAG  CAH  NAD  CAE    14.89  30.0  1
 DJO  Var_03    OAB  CAL  NAD  CAE  -178.41  30.0  2
 DJO  Var_04    OAB  CAO  CAP  CAQ   -89.34  30.0  2
 DJO  Var_05    CAP  CAO  OAB  CAL  -178.88  30.0  3
 DJO  Var_06    NAD  CAL  OAB  CAO   178.33  30.0  1

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
 DJO  chir_01  CAE  CAF  NAD  CAI  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
 DJO  plan-1  CAO  0.020
 DJO  plan-1  CAP  0.020
 DJO  plan-1  CAQ  0.020
 DJO  plan-1  CAR  0.020
 DJO  plan-1  CAS  0.020
 DJO  plan-1  CAT  0.020
 DJO  plan-1  CAU  0.020
 DJO  plan-1  H12  0.020
 DJO  plan-1  H13  0.020
 DJO  plan-1  H14  0.020
 DJO  plan-1  H15  0.020
 DJO  plan-1  H16  0.020
 DJO  plan-2  CAF  0.020
 DJO  plan-2  CAG  0.020
 DJO  plan-2  CAH  0.020
 DJO  plan-2  CAJ  0.020
 DJO  plan-2  CAK  0.020
 DJO  plan-2  CAM  0.020
 DJO  plan-2  CAN  0.020
 DJO  plan-2  NAD  0.020
 DJO  plan-2  H6   0.020
 DJO  plan-2  H7   0.020
 DJO  plan-2  H8   0.020
 DJO  plan-2  H9   0.020
 DJO  plan-3  NAD  0.020
 DJO  plan-3  OAB  0.020
 DJO  plan-3  OAC  0.020
 DJO  plan-3  CAL  0.020

