# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 13:24:10 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  54  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   3.3085  -1.2392   5.4836
 YPA  C2    C  CR16   0  -0.370   2.0366  -1.3133   6.0256
 YPA  C3    C  CR56   0   0.067   0.9960  -0.6344   5.3970
 YPA  C4    C  CR56   0   0.352   1.2526   0.1128   4.2306
 YPA  C5    C  CR16   0  -0.319   2.5282   0.1894   3.6790
 YPA  C6    C  CR16   0  -0.271   3.5464  -0.4943   4.3226
 YPA  C11   C  CR56   0   0.064  -0.4121  -0.4979   5.6669
 YPA  C12   C  CR56   0   0.353  -0.9362   0.3234   4.6487
 YPA  N13   N  NR5    0  -0.635   0.0823   0.6956   3.8007
 YPA  C14   C  CR16   0  -0.369  -1.2544  -0.9910   6.6601
 YPA  C15   C  CR16   0  -0.271  -2.5989  -0.6635   6.6215
 YPA  C16   C  CR16   0  -0.270  -3.1051   0.1493   5.6005
 YPA  C17   C  CR16   0  -0.319  -2.2879   0.6526   4.6018
 YPA  C22   C  CH2    0  -0.370  -0.0628   1.4900   2.6092
 YPA  C23   C  CH2    0  -0.171  -0.3368   0.6161   1.3940
 YPA  O26   O  O2     0  -0.478  -0.4537   1.4825   0.2873
 YPA  C29   C  C      0   0.365  -0.6730   0.9491  -0.9363
 YPA  C30   C  C1     0  -0.338  -0.7652   1.8500  -1.9977
 YPA  C31   C  C1     0  -0.272  -0.9832   1.3910  -3.2841
 YPA  C32   C  C      0   0.124  -1.1266   0.0302  -3.5579
 YPA  C33   C  C1     0  -0.304  -1.0363  -0.8501  -2.4878
 YPA  C34   C  C1     0  -0.368  -0.8121  -0.4115  -1.1863
 YPA  C39   C  CH2    0  -0.546  -1.3320  -0.4753  -4.9569
 YPA  C40   C  CH1    0  -0.021  -0.0145  -0.7011  -5.7045
 YPA  C43   C  C      0   0.369  -0.2908  -1.3815  -7.0668
 YPA  O44   O  OC    -1  -0.622  -0.6688  -2.5687  -6.9897
 YPA  O45   O  O      0  -0.596  -0.1408  -0.7057  -8.0991
 YPA  O47   O  O2     0  -0.479   0.6317   0.5388  -5.8004
 YPA  C49   C  CH2    0  -0.134   2.0049   0.4603  -6.0857
 YPA  C50   C  CH3    0  -0.687   2.6093   1.8438  -5.9819
 YPA  H1    H  HCR6   0   0.253   4.1272  -1.7643   5.9573
 YPA  H2    H  HCR6   0   0.246   1.8559  -1.8927   6.9225
 YPA  H5    H  HCR6   0   0.264   2.7267   0.7561   2.7781
 YPA  H6    H  HCR6   0   0.257   4.5480  -0.4522   3.9149
 YPA  H14   H  HCR6   0   0.246  -0.8655  -1.6204   7.4511
 YPA  H15   H  HCR6   0   0.252  -3.2673  -1.0397   7.3846
 YPA  H16   H  HCR6   0   0.257  -4.1600   0.3908   5.5880
 YPA  H17   H  HCR6   0   0.264  -2.6988   1.2746   3.8170
 YPA  H221  H  HCH2   0   0.278   0.8479   2.0720   2.4590
 YPA  H222  H  HCH2   0   0.280  -0.8741   2.2043   2.7542
 YPA  H231  H  HCH2   0   0.230  -1.2574   0.0404   1.5446
 YPA  H232  H  HCH2   0   0.231   0.4823  -0.0988   1.2510
 YPA  H30   H  H      0   0.255  -0.6617   2.9113  -1.8063
 YPA  H31   H  H      0   0.238  -1.0479   2.1096  -4.0910
 YPA  H33   H  H      0   0.245  -1.1454  -1.9148  -2.6606
 YPA  H34   H  H      0   0.274  -0.7559  -1.1440  -0.3925
 YPA  H391  H  HCH2   0   0.237  -1.9473   0.2285  -5.5264
 YPA  H392  H  HCH2   0   0.248  -1.8737  -1.4218  -4.9348
 YPA  H40   H  HCH1   0   0.188   0.5959  -1.3961  -5.1040
 YPA  H491  H  HCH2   0   0.192   2.1795   0.0506  -7.0875
 YPA  H492  H  HCH2   0   0.180   2.5043  -0.2154  -5.3756
 YPA  H501  H  HCH3   0   0.223   3.6781   1.8009  -6.1927
 YPA  H502  H  HCH3   0   0.222   2.1566   2.5316  -6.6976
 YPA  H503  H  HCH3   0   0.224   2.4794   2.2573  -4.9810

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  1.385  0.020  1.385
 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    1.410  0.020  1.410
 YPA  C23  H231  single    0.970  0.020  1.090
 YPA  C23  H232  single    0.970  0.020  1.090
 YPA  O26  C29   single    1.353  0.020  1.353
 YPA  C29  C30   aromatic  1.395  0.020  1.395
 YPA  C29  C34   aromatic  1.390  0.020  1.390
 YPA  C30  C31   aromatic  1.383  0.020  1.383
 YPA  C30  H30   single    0.930  0.020  1.080
 YPA  C31  C32   aromatic  1.396  0.020  1.396
 YPA  C31  H31   single    0.930  0.020  1.080
 YPA  C32  C33   aromatic  1.389  0.020  1.389
 YPA  C32  C39   single    1.502  0.020  1.502
 YPA  C33  C34   aromatic  1.392  0.020  1.392
 YPA  C33  H33   single    0.930  0.020  1.080
 YPA  C34  H34   single    0.930  0.020  1.080
 YPA  C39  C40   single    1.532  0.020  1.532
 YPA  C39  H391  single    0.970  0.020  1.090
 YPA  C39  H392  single    0.970  0.020  1.090
 YPA  C40  C43   single    1.548  0.020  1.548
 YPA  C40  O47   single    1.401  0.020  1.401
 YPA  C40  H40   single    0.970  0.020  1.090
 YPA  C43  O44   deloc     1.248  0.020  1.248
 YPA  C43  O45   deloc     1.243  0.020  1.243
 YPA  O47  C49   single    1.405  0.020  1.405
 YPA  C49  C50   single    1.513  0.020  1.513
 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    119.86  3.000
 YPA  C6    C1   C2    120.62  3.000
 YPA  H2    C2   C3    120.66  3.000
 YPA  H2    C2   C1    120.41  3.000
 YPA  C3    C2   C1    118.93  3.000
 YPA  C11   C3   C4    106.44  3.000
 YPA  C11   C3   C2    133.81  3.000
 YPA  C4    C3   C2    119.75  3.000
 YPA  N13   C4   C5    129.22  3.000
 YPA  N13   C4   C3    109.17  3.000
 YPA  C5    C4   C3    121.62  3.000
 YPA  H5    C5   C6    120.68  3.000
 YPA  H5    C5   C4    121.78  3.000
 YPA  C6    C5   C4    117.55  3.000
 YPA  H6    C6   C5    119.09  3.000
 YPA  H6    C6   C1    119.38  3.000
 YPA  C5    C6   C1    121.54  3.000
 YPA  C14   C11  C12   119.79  3.000
 YPA  C14   C11  C3    133.75  3.000
 YPA  C12   C11  C3    106.46  3.000
 YPA  C17   C12  N13   129.33  3.000
 YPA  C17   C12  C11   121.55  3.000
 YPA  N13   C12  C11   109.12  3.000
 YPA  C22   N13  C12   125.78  3.000
 YPA  C22   N13  C4    125.31  3.000
 YPA  C12   N13  C4    108.79  3.000
 YPA  H14   C14  C15   120.43  3.000
 YPA  H14   C14  C11   120.63  3.000
 YPA  C15   C14  C11   118.93  3.000
 YPA  H15   C15  C16   119.54  3.000
 YPA  H15   C15  C14   119.87  3.000
 YPA  C16   C15  C14   120.59  3.000
 YPA  H16   C16  C17   119.06  3.000
 YPA  H16   C16  C15   119.37  3.000
 YPA  C17   C16  C15   121.57  3.000
 YPA  H17   C17  C16   120.50  3.000
 YPA  H17   C17  C12   121.93  3.000
 YPA  C16   C17  C12   117.57  3.000
 YPA  H222  C22  H221  106.85  3.000
 YPA  H222  C22  C23   110.39  3.000
 YPA  H221  C22  C23   110.28  3.000
 YPA  H222  C22  N13   109.05  3.000
 YPA  H221  C22  N13   108.92  3.000
 YPA  C23   C22  N13   111.24  3.000
 YPA  H232  C23  H231  107.62  3.000
 YPA  H232  C23  O26   111.11  3.000
 YPA  H231  C23  O26   111.15  3.000
 YPA  H232  C23  C22   110.13  3.000
 YPA  H231  C23  C22   110.07  3.000
 YPA  O26   C23  C22   106.79  3.000
 YPA  C29   O26  C23   118.75  3.000
 YPA  C34   C29  C30   119.24  3.000
 YPA  C34   C29  O26   124.39  3.000
 YPA  C30   C29  O26   116.37  3.000
 YPA  H30   C30  C31   120.30  3.000
 YPA  H30   C30  C29   119.46  3.000
 YPA  C31   C30  C29   120.24  3.000
 YPA  H31   C31  C32   119.67  3.000
 YPA  H31   C31  C30   118.84  3.000
 YPA  C32   C31  C30   121.49  3.000
 YPA  C39   C32  C33   120.90  3.000
 YPA  C39   C32  C31   121.68  3.000
 YPA  C33   C32  C31   117.41  3.000
 YPA  H33   C33  C34   118.35  3.000
 YPA  H33   C33  C32   119.55  3.000
 YPA  C34   C33  C32   122.10  3.000
 YPA  H34   C34  C33   118.77  3.000
 YPA  H34   C34  C29   121.71  3.000
 YPA  C33   C34  C29   119.52  3.000
 YPA  H392  C39  H391  106.82  3.000
 YPA  H392  C39  C40   108.01  3.000
 YPA  H391  C39  C40   108.93  3.000
 YPA  H392  C39  C32   109.95  3.000
 YPA  H391  C39  C32   110.19  3.000
 YPA  C40   C39  C32   112.75  3.000
 YPA  H40   C40  O47   109.85  3.000
 YPA  H40   C40  C43   107.52  3.000
 YPA  O47   C40  C43   114.27  3.000
 YPA  H40   C40  C39   107.65  3.000
 YPA  O47   C40  C39   107.43  3.000
 YPA  C43   C40  C39   109.93  3.000
 YPA  O45   C43  O44   127.22  3.000
 YPA  O45   C43  C40   118.07  3.000
 YPA  O44   C43  C40   114.70  3.000
 YPA  C49   O47  C40   114.53  3.000
 YPA  H492  C49  H491  106.74  3.000
 YPA  H492  C49  C50   109.63  3.000
 YPA  H491  C49  C50   109.92  3.000
 YPA  H492  C49  O47   110.31  3.000
 YPA  H491  C49  O47   111.23  3.000
 YPA  C50   C49  O47   108.99  3.000
 YPA  H503  C50  H502  108.27  3.000
 YPA  H503  C50  H501  108.01  3.000
 YPA  H502  C50  H501  107.75  3.000
 YPA  H503  C50  C49   111.22  3.000
 YPA  H502  C50  C49   111.45  3.000
 YPA  H501  C50  C49   110.01  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  Var_01    C23   C22  N13  C4     86.23  30.0  2
 YPA  Var_02    C30   C29  O26  C23  -179.28  30.0  2
 YPA  Var_03    C40   C39  C32  C31    86.21  30.0  2
 YPA  Var_04    O26   C23  C22  N13  -179.66  30.0  3
 YPA  Var_05    C50   C49  O47  C40  -172.66  30.0  3
 YPA  Var_06    H501  C50  C49  O47   179.55  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

