# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jun  4 04:54:28 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: (2S)-3-{4-[2-(9H-carbazol-9-yl)ethoxy]phenyl}-2-ethoxypropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCO[C@@H](Cc1ccc(OCCn2c3ccccc3c4ccccc24)cc1)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
 YPA  YPA  '(2S)-3-{4-[2-(9H-carbazol-9-yl)ethoxy]phenyl}-2-ethoxypropanoic acid'  ligand  55  30  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YPA
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
 YPA  C1    C  CR16  0  -0.270   3.2974  -1.2244   5.6260
 YPA  C2    C  CR16  0  -0.370   2.0111  -1.2984   6.1326
 YPA  C3    C  CR56  0   0.066   0.9868  -0.6261   5.4709
 YPA  C4    C  CR56  0   0.352   1.2740   0.1141   4.3071
 YPA  C5    C  CR16  0  -0.319   2.5642   0.1898   3.7905
 YPA  C6    C  CR16  0  -0.271   3.5658  -0.4866   4.4671
 YPA  C11   C  CR56  0   0.063  -0.4288  -0.4928   5.6999
 YPA  C12   C  CR56  0   0.352  -0.9264   0.3201   4.6620
 YPA  N13   N  NR5   0  -0.636   0.1146   0.6907   3.8408
 YPA  C14   C  CR16  0  -0.369  -1.2969  -0.9807   6.6731
 YPA  C15   C  CR16  0  -0.271  -2.6408  -0.6575   6.5947
 YPA  C16   C  CR16  0  -0.270  -3.1207   0.1461   5.5540
 YPA  C17   C  CR16  0  -0.319  -2.2772   0.6451   4.5751
 YPA  C22   C  CH2   0  -0.369  -0.0013   1.4770   2.6408
 YPA  C23   C  CH2   0  -0.173  -0.2406   0.5941   1.4250
 YPA  O26   O  O2    0  -0.476  -0.3594   1.4552   0.3134
 YPA  C29   C  CR6   0   0.371  -0.5927   0.9191  -0.9042
 YPA  C30   C  CR16  0  -0.336  -0.7277   1.8197  -1.9616
 YPA  C31   C  CR16  0  -0.275  -0.9702   1.3585  -3.2424
 YPA  C32   C  CR6   0   0.117  -1.0935  -0.0047  -3.5107
 YPA  C33   C  CR16  0  -0.296  -0.9561  -0.8868  -2.4476
 YPA  C34   C  CR16  0  -0.367  -0.7079  -0.4445  -1.1525
 YPA  C39   C  CH2   0  -0.554  -1.3421  -0.5131  -4.9019
 YPA  C40   C  CH1   0  -0.021  -0.0319  -0.7106  -5.6774
 YPA  C43   C  C     0   0.503  -0.3221  -1.3588  -7.0256
 YPA  O44   O  OH1   0  -0.593  -0.6349  -2.6406  -6.8872
 YPA  O45   O  O     0  -0.430  -0.2955  -0.7823  -8.0810
 YPA  O47   O  O2    0  -0.473   0.5714   0.5292  -5.8471
 YPA  C49   C  CH2   0  -0.153   1.9643   0.4823  -6.0852
 YPA  C50   C  CH3   0  -0.689   2.4723   1.8936  -6.2670
 YPA  H1    H  HCR6  0   0.252   4.1039  -1.7441   6.1258
 YPA  H2    H  HCR6  0   0.248   1.8066  -1.8721   7.0280
 YPA  H5    H  HCR6  0   0.265   2.7868   0.7503   2.8913
 YPA  H6    H  HCR6  0   0.257   4.5782  -0.4442   4.0871
 YPA  H14   H  HCR6  0   0.248  -0.9288  -1.6026   7.4799
 YPA  H15   H  HCR6  0   0.252  -3.3292  -1.0294   7.3418
 YPA  H16   H  HCR6  0   0.257  -4.1755   0.3845   5.5102
 YPA  H17   H  HCR6  0   0.265  -2.6677   1.2603   3.7747
 YPA  H221  H  HCH2  0   0.279   0.9103   2.0626   2.5118
 YPA  H222  H  HCH2  0   0.281  -0.8198   2.1877   2.7598
 YPA  H231  H  HCH2  0   0.233  -1.1523   0.0019   1.5643
 YPA  H232  H  HCH2  0   0.232   0.5938  -0.1052   1.2950
 YPA  H30   H  HCR6  0   0.260  -0.6422   2.8825  -1.7711
 YPA  H31   H  HCR6  0   0.245  -1.0737   2.0767  -4.0456
 YPA  H33   H  HCR6  0   0.251  -1.0491  -1.9530  -2.6195
 YPA  H34   H  HCR6  0   0.278  -0.6161  -1.1765  -0.3617
 YPA  H391  H  HCH2  0   0.264  -1.9775   0.1828  -5.4563
 YPA  H392  H  HCH2  0   0.272  -1.8757  -1.4639  -4.8581
 YPA  H40   H  HCH1  0   0.252   0.6086  -1.3963  -5.1023
 YPA  H44   H  HOH1  0   0.484  -0.8636  -3.0265  -7.7464
 YPA  H491  H  HCH2  0   0.205   2.1941  -0.1114  -6.9784
 YPA  H492  H  HCH2  0   0.206   2.4746   0.0009  -5.2408
 YPA  H501  H  HCH3  0   0.232   3.5474   1.8777  -6.4448
 YPA  H502  H  HCH3  0   0.229   1.9994   2.3780  -7.1219
 YPA  H503  H  HCH3  0   0.230   2.2874   2.5008  -5.3804

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
 YPA  C1   C2    aromatic  1.384  0.020  1.384
 YPA  C1   C6    aromatic  1.400  0.020  1.400
 YPA  C1   H1    single    0.930  0.020  1.080
 YPA  C2   C3    aromatic  1.392  0.020  1.392
 YPA  C2   H2    single    0.930  0.020  1.080
 YPA  C3   C4    aromatic  1.409  0.020  1.409
 YPA  C3   C11   aromatic  1.440  0.020  1.440
 YPA  C4   C5    aromatic  1.392  0.020  1.392
 YPA  C4   N13   aromatic  1.376  0.020  1.376
 YPA  C5   C6    aromatic  1.385  0.020  1.385
 YPA  C5   H5    single    0.930  0.020  1.080
 YPA  C6   H6    single    0.930  0.020  1.080
 YPA  C11  C12   aromatic  1.409  0.020  1.409
 YPA  C11  C14   aromatic  1.392  0.020  1.392
 YPA  C12  N13   aromatic  1.377  0.020  1.377
 YPA  C12  C17   aromatic  1.392  0.020  1.392
 YPA  N13  C22   single    1.439  0.020  1.439
 YPA  C14  C15   aromatic  1.384  0.020  1.384
 YPA  C14  H14   single    0.930  0.020  1.080
 YPA  C15  C16   aromatic  1.400  0.020  1.400
 YPA  C15  H15   single    0.930  0.020  1.080
 YPA  C16  C17   aromatic  1.385  0.020  1.385
 YPA  C16  H16   single    0.930  0.020  1.080
 YPA  C17  H17   single    0.930  0.020  1.080
 YPA  C22  C23   single    1.522  0.020  1.522
 YPA  C22  H221  single    0.970  0.020  1.090
 YPA  C22  H222  single    0.970  0.020  1.090
 YPA  C23  O26   single    1.411  0.020  1.411
 YPA  C23  H231  single    0.970  0.020  1.090
 YPA  C23  H232  single    0.970  0.020  1.090
 YPA  O26  C29   single    1.351  0.020  1.351
 YPA  C29  C30   aromatic  1.395  0.020  1.395
 YPA  C29  C34   aromatic  1.391  0.020  1.391
 YPA  C30  C31   aromatic  1.383  0.020  1.383
 YPA  C30  H30   single    0.930  0.020  1.080
 YPA  C31  C32   aromatic  1.395  0.020  1.395
 YPA  C31  H31   single    0.930  0.020  1.080
 YPA  C32  C33   aromatic  1.388  0.020  1.388
 YPA  C32  C39   single    1.502  0.020  1.502
 YPA  C33  C34   aromatic  1.391  0.020  1.391
 YPA  C33  H33   single    0.930  0.020  1.080
 YPA  C34  H34   single    0.930  0.020  1.080
 YPA  C39  C40   single    1.535  0.020  1.535
 YPA  C39  H391  single    0.970  0.020  1.090
 YPA  C39  H392  single    0.970  0.020  1.090
 YPA  C40  C43   single    1.524  0.020  1.524
 YPA  C40  O47   single    1.389  0.020  1.389
 YPA  C40  H40   single    0.970  0.020  1.090
 YPA  C43  O44   single    1.327  0.020  1.327
 YPA  C43  O45   double    1.203  0.020  1.203
 YPA  O44  H44   single    0.850  0.020  0.980
 YPA  O47  C49   single    1.414  0.020  1.414
 YPA  C49  C50   single    1.511  0.020  1.511
 YPA  C49  H491  single    0.970  0.020  1.090
 YPA  C49  H492  single    0.970  0.020  1.090
 YPA  C50  H501  single    0.970  0.020  1.090
 YPA  C50  H502  single    0.970  0.020  1.090
 YPA  C50  H503  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
 YPA  H1    C1   C6    119.52  3.000
 YPA  H1    C1   C2    119.87  3.000
 YPA  C6    C1   C2    120.61  3.000
 YPA  H2    C2   C3    120.65  3.000
 YPA  H2    C2   C1    120.42  3.000
 YPA  C3    C2   C1    118.93  3.000
 YPA  C11   C3   C4    106.44  3.000
 YPA  C11   C3   C2    133.80  3.000
 YPA  C4    C3   C2    119.76  3.000
 YPA  N13   C4   C5    129.23  3.000
 YPA  N13   C4   C3    109.16  3.000
 YPA  C5    C4   C3    121.61  3.000
 YPA  H5    C5   C6    120.66  3.000
 YPA  H5    C5   C4    121.80  3.000
 YPA  C6    C5   C4    117.54  3.000
 YPA  H6    C6   C5    119.06  3.000
 YPA  H6    C6   C1    119.39  3.000
 YPA  C5    C6   C1    121.55  3.000
 YPA  C14   C11  C12   119.78  3.000
 YPA  C14   C11  C3    133.75  3.000
 YPA  C12   C11  C3    106.47  3.000
 YPA  C17   C12  N13   129.32  3.000
 YPA  C17   C12  C11   121.56  3.000
 YPA  N13   C12  C11   109.12  3.000
 YPA  C22   N13  C12   125.70  3.000
 YPA  C22   N13  C4    125.39  3.000
 YPA  C12   N13  C4    108.79  3.000
 YPA  H14   C14  C15   120.41  3.000
 YPA  H14   C14  C11   120.66  3.000
 YPA  C15   C14  C11   118.93  3.000
 YPA  H15   C15  C16   119.51  3.000
 YPA  H15   C15  C14   119.88  3.000
 YPA  C16   C15  C14   120.60  3.000
 YPA  H16   C16  C17   119.05  3.000
 YPA  H16   C16  C15   119.39  3.000
 YPA  C17   C16  C15   121.56  3.000
 YPA  H17   C17  C16   120.50  3.000
 YPA  H17   C17  C12   121.94  3.000
 YPA  C16   C17  C12   117.56  3.000
 YPA  H222  C22  H221  106.87  3.000
 YPA  H222  C22  C23   110.32  3.000
 YPA  H221  C22  C23   110.39  3.000
 YPA  H222  C22  N13   109.00  3.000
 YPA  H221  C22  N13   108.94  3.000
 YPA  C23   C22  N13   111.21  3.000
 YPA  H232  C23  H231  107.67  3.000
 YPA  H232  C23  O26   111.09  3.000
 YPA  H231  C23  O26   111.09  3.000
 YPA  H232  C23  C22   110.20  3.000
 YPA  H231  C23  C22   110.05  3.000
 YPA  O26   C23  C22   106.77  3.000
 YPA  C29   O26  C23   118.84  3.000
 YPA  C34   C29  C30   119.30  3.000
 YPA  C34   C29  O26   124.36  3.000
 YPA  C30   C29  O26   116.34  3.000
 YPA  H30   C30  C31   120.27  3.000
 YPA  H30   C30  C29   119.49  3.000
 YPA  C31   C30  C29   120.24  3.000
 YPA  H31   C31  C32   119.82  3.000
 YPA  H31   C31  C30   118.87  3.000
 YPA  C32   C31  C30   121.31  3.000
 YPA  C39   C32  C33   120.71  3.000
 YPA  C39   C32  C31   121.58  3.000
 YPA  C33   C32  C31   117.71  3.000
 YPA  H33   C33  C34   118.41  3.000
 YPA  H33   C33  C32   119.67  3.000
 YPA  C34   C33  C32   121.92  3.000
 YPA  H34   C34  C33   118.74  3.000
 YPA  H34   C34  C29   121.73  3.000
 YPA  C33   C34  C29   119.53  3.000
 YPA  H392  C39  H391  106.91  3.000
 YPA  H392  C39  C40   109.00  3.000
 YPA  H391  C39  C40   108.76  3.000
 YPA  H392  C39  C32   109.80  3.000
 YPA  H391  C39  C32   110.51  3.000
 YPA  C40   C39  C32   111.72  3.000
 YPA  H40   C40  O47   111.54  3.000
 YPA  H40   C40  C43   107.94  3.000
 YPA  O47   C40  C43   110.75  3.000
 YPA  H40   C40  C39   108.23  3.000
 YPA  O47   C40  C39   108.52  3.000
 YPA  C43   C40  C39   109.82  3.000
 YPA  O45   C43  O44   124.04  3.000
 YPA  O45   C43  C40   124.62  3.000
 YPA  O44   C43  C40   111.32  3.000
 YPA  H44   O44  C43   110.36  3.000
 YPA  C49   O47  C40   114.76  3.000
 YPA  H492  C49  H491  106.95  3.000
 YPA  H492  C49  C50   110.24  3.000
 YPA  H491  C49  C50   109.71  3.000
 YPA  H492  C49  O47   110.06  3.000
 YPA  H491  C49  O47   111.19  3.000
 YPA  C50   C49  O47   108.70  3.000
 YPA  H503  C50  H502  108.45  3.000
 YPA  H503  C50  H501  107.94  3.000
 YPA  H502  C50  H501  107.84  3.000
 YPA  H503  C50  C49   111.43  3.000
 YPA  H502  C50  C49   111.32  3.000
 YPA  H501  C50  C49   109.74  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
 YPA  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 YPA  CONST_02  C11   C3   C2   C1   180.00   0.0  0
 YPA  CONST_03  C4    C5   C6   C1     0.00   0.0  0
 YPA  CONST_04  C5    C6   C1   C2     0.00   0.0  0
 YPA  CONST_05  C5    C4   C3   C2     0.00   0.0  0
 YPA  CONST_06  N13   C4   C3   C2   180.00   0.0  0
 YPA  CONST_07  C12   C11  C3   C2   180.00   0.0  0
 YPA  CONST_08  C14   C11  C3   C2     0.00   0.0  0
 YPA  CONST_09  C6    C1   C2   C3     0.00   0.0  0
 YPA  CONST_10  C6    C5   C4   C3     0.00   0.0  0
 YPA  CONST_11  C12   N13  C4   C3     0.00   0.0  0
 YPA  CONST_12  N13   C12  C11  C3     0.00   0.0  0
 YPA  CONST_13  C17   C12  C11  C3   180.00   0.0  0
 YPA  CONST_14  C15   C14  C11  C3   180.00   0.0  0
 YPA  CONST_15  C12   C11  C3   C4     0.00   0.0  0
 YPA  CONST_16  C14   C11  C3   C4   180.00   0.0  0
 YPA  CONST_17  C11   C12  N13  C4     0.00   0.0  0
 YPA  CONST_18  C17   C12  N13  C4   180.00   0.0  0
 YPA  CONST_19  C11   C3   C4   C5   180.00   0.0  0
 YPA  CONST_20  C12   N13  C4   C5   180.00   0.0  0
 YPA  CONST_21  N13   C4   C5   C6   180.00   0.0  0
 YPA  CONST_22  N13   C4   C3   C11    0.00   0.0  0
 YPA  CONST_23  C16   C17  C12  C11    0.00   0.0  0
 YPA  CONST_24  C16   C15  C14  C11    0.00   0.0  0
 YPA  CONST_25  C15   C14  C11  C12    0.00   0.0  0
 YPA  CONST_26  C15   C16  C17  C12    0.00   0.0  0
 YPA  CONST_27  C14   C11  C12  N13  180.00   0.0  0
 YPA  CONST_28  C16   C17  C12  N13  180.00   0.0  0
 YPA  CONST_29  C17   C12  C11  C14    0.00   0.0  0
 YPA  CONST_30  C17   C16  C15  C14    0.00   0.0  0
 YPA  CONST_31  C32   C31  C30  C29    0.00   0.0  0
 YPA  CONST_32  C32   C33  C34  C29    0.00   0.0  0
 YPA  CONST_33  C33   C34  C29  C30    0.00   0.0  0
 YPA  CONST_34  C33   C32  C31  C30    0.00   0.0  0
 YPA  CONST_35  C34   C29  C30  C31    0.00   0.0  0
 YPA  CONST_36  C34   C33  C32  C31    0.00   0.0  0
 YPA  CONST_37  C22   N13  C4   C3   180.00   0.0  0
 YPA  CONST_38  C22   N13  C4   C5     0.00   0.0  0
 YPA  CONST_39  C22   N13  C12  C11  180.00   0.0  0
 YPA  CONST_40  C22   N13  C12  C17    0.00   0.0  0
 YPA  CONST_41  C31   C30  C29  O26  180.00   0.0  0
 YPA  CONST_42  C33   C34  C29  O26  180.00   0.0  0
 YPA  CONST_43  C39   C32  C31  C30  180.00   0.0  0
 YPA  CONST_44  C39   C32  C33  C34  180.00   0.0  0
 YPA  CONST_45  H5    C5   C6   C1   180.00   0.0  0
 YPA  CONST_46  H6    C6   C1   C2   180.00   0.0  0
 YPA  CONST_47  H1    C1   C2   C3   180.00   0.0  0
 YPA  CONST_48  H14   C14  C11  C3     0.00   0.0  0
 YPA  CONST_49  H2    C2   C3   C4   180.00   0.0  0
 YPA  CONST_50  H17   C17  C12  C11  180.00   0.0  0
 YPA  CONST_51  H15   C15  C14  C11  180.00   0.0  0
 YPA  CONST_52  H16   C16  C17  C12  180.00   0.0  0
 YPA  CONST_53  H31   C31  C30  C29  180.00   0.0  0
 YPA  CONST_54  H33   C33  C34  C29  180.00   0.0  0
 YPA  CONST_55  H34   C34  C29  C30  180.00   0.0  0
 YPA  CONST_56  H30   C30  C31  C32  180.00   0.0  0
 YPA  CONST_57  H44   O44  C43  C40  180.00   0.0  0
 YPA  Var_01    C23   C22  N13  C4    86.27  30.0  2
 YPA  Var_02    C30   C29  O26  C23  178.75  30.0  2
 YPA  Var_03    C40   C39  C32  C31   86.64  30.0  2
 YPA  Var_04    O26   C23  C22  N13  179.12  30.0  3
 YPA  Var_05    C50   C49  O47  C40  179.24  30.0  3
 YPA  Var_06    H501  C50  C49  O47  179.60  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
 YPA  chir_01  C40  C39  C43  O47  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
 YPA  plan-1  O26  0.020
 YPA  plan-1  C29  0.020
 YPA  plan-1  C30  0.020
 YPA  plan-1  C31  0.020
 YPA  plan-1  C32  0.020
 YPA  plan-1  C33  0.020
 YPA  plan-1  C34  0.020
 YPA  plan-1  C39  0.020
 YPA  plan-1  H30  0.020
 YPA  plan-1  H31  0.020
 YPA  plan-1  H33  0.020
 YPA  plan-1  H34  0.020
 YPA  plan-2  C1   0.020
 YPA  plan-2  C2   0.020
 YPA  plan-2  C3   0.020
 YPA  plan-2  C4   0.020
 YPA  plan-2  C5   0.020
 YPA  plan-2  C6   0.020
 YPA  plan-2  C11  0.020
 YPA  plan-2  C12  0.020
 YPA  plan-2  N13  0.020
 YPA  plan-2  C14  0.020
 YPA  plan-2  C15  0.020
 YPA  plan-2  C16  0.020
 YPA  plan-2  C17  0.020
 YPA  plan-2  C22  0.020
 YPA  plan-2  H1   0.020
 YPA  plan-2  H2   0.020
 YPA  plan-2  H5   0.020
 YPA  plan-2  H6   0.020
 YPA  plan-2  H14  0.020
 YPA  plan-2  H15  0.020
 YPA  plan-2  H16  0.020
 YPA  plan-2  H17  0.020
 YPA  plan-3  C40  0.020
 YPA  plan-3  C43  0.020
 YPA  plan-3  O44  0.020
 YPA  plan-3  O45  0.020
 YPA  plan-3  H44  0.020

