# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 10:16:02 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 4-{[3-(2-amino-2-oxoethyl)-1-benzyl-2-methyl-1H-indol-5-yl]oxy}butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1n(Cc2ccccc2)c3ccc(OCCCC(O)=O)cc3c1CC(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
 6IN  6IN  '4-{[3-(2-amino-2-oxoethyl)-1-benzyl-2-methyl-1H-indol-5-yl]oxy}butanoic acid'  ligand  52  28  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6IN
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
 6IN  C1    C  CR6   0   0.388  -0.3519   0.6782  -1.5056
 6IN  C2    C  CR16  0  -0.408   0.9134   1.1365  -1.0998
 6IN  C3    C  CR16  0  -0.299   1.1722   1.4220   0.2324
 6IN  C4    C  CR56  0   0.326   0.1511   1.2491   1.1535
 6IN  C5    C  CR56  0   0.108  -1.1213   0.7873   0.7633
 6IN  C6    C  CR16  0  -0.501  -1.3712   0.5033  -0.5794
 6IN  N10   N  NR5   0  -0.572   0.1274   1.4503   2.5124
 6IN  C7    C  CR5   0   0.291  -1.1130   1.0923   2.9912
 6IN  C12   C  CR5   0  -0.000  -1.9112   0.6980   1.9517
 6IN  C13   C  CH2   0  -0.378   1.2963   1.6928   3.3125
 6IN  C14   C  CR6   0   0.081   2.0945   0.4454   3.6206
 6IN  C17   C  CR16  0  -0.297   1.5722  -0.8324   3.4481
 6IN  C18   C  CR16  0  -0.241   2.3326  -1.9506   3.7725
 6IN  C19   C  CR16  0  -0.267   3.6188  -1.8064   4.2721
 6IN  C20   C  CR16  0  -0.244   4.1452  -0.5321   4.4463
 6IN  C21   C  CR16  0  -0.291   3.3877   0.5829   4.1202
 6IN  C27   C  CH3   0  -0.747  -1.4190   1.1388   4.4441
 6IN  C32   C  CH2   0  -0.738  -3.2946   0.1620   2.0375
 6IN  C34   C  C     0   0.528  -3.3138  -1.3554   2.1744
 6IN  N37   N  NH2   0  -0.804  -4.3883  -1.9543   1.6382
 6IN  O40   O  O     0  -0.477  -2.4282  -1.9640   2.7533
 6IN  O41   O  O2    0  -0.489  -0.6578   0.3765  -2.7929
 6IN  C42   C  CH2   0  -0.163   0.3589   0.4451  -3.7728
 6IN  C43   C  CH2   0  -0.461  -0.2193  -0.0383  -5.0870
 6IN  C46   C  CH2   0  -0.588   0.8424  -0.0003  -6.1741
 6IN  C49   C  C     0   0.554   0.3481  -0.4886  -7.5073
 6IN  O52   O  OH1   0  -0.597   1.3147  -0.4869  -8.4201
 6IN  O54   O  O     0  -0.443  -0.7802  -0.8404  -7.7441
 6IN  H2    H  HCR6  0   0.272   1.7123   1.2706  -1.8154
 6IN  H3    H  HCR6  0   0.261   2.1560   1.7637   0.5284
 6IN  H6    H  HCR6  0   0.241  -2.3396   0.1417  -0.9065
 6IN  H131  H  HCH2  0   0.279   1.9283   2.4215   2.8007
 6IN  H132  H  HCH2  0   0.291   0.9895   2.1739   4.2432
 6IN  H17   H  HCR6  0   0.262   0.5687  -0.9757   3.0630
 6IN  H18   H  HCR6  0   0.256   1.9144  -2.9389   3.6312
 6IN  H19   H  HCR6  0   0.255   4.2077  -2.6795   4.5214
 6IN  H20   H  HCR6  0   0.256   5.1481  -0.4056   4.8335
 6IN  H21   H  HCR6  0   0.251   3.8074   1.5732   4.2565
 6IN  H271  H  HCH3  0   0.255  -1.2464   2.1307   4.8651
 6IN  H272  H  HCH3  0   0.262  -2.4595   0.8780   4.6211
 6IN  H273  H  HCH3  0   0.252  -0.8053   0.4328   5.0082
 6IN  H321  H  HCH2  0   0.292  -3.8130   0.5611   2.9153
 6IN  H322  H  HCH2  0   0.270  -3.8921   0.4759   1.1777
 6IN  H371  H  HNH2  0   0.398  -4.5284  -2.9461   1.7417
 6IN  H372  H  HNH2  0   0.406  -5.1114  -1.4319   1.1752
 6IN  H421  H  HCH2  0   0.217   0.7281   1.4732  -3.8755
 6IN  H422  H  HCH2  0   0.217   1.2135  -0.1803  -3.4863
 6IN  H431  H  HCH2  0   0.243  -0.5930  -1.0573  -4.9652
 6IN  H432  H  HCH2  0   0.244  -1.0680   0.5884  -5.3691
 6IN  H461  H  HCH2  0   0.283   1.2251   1.0166  -6.3091
 6IN  H462  H  HCH2  0   0.281   1.7107  -0.6027  -5.8894
 6IN  HXT   H  HOH1  0   0.480   0.9712  -0.8053  -9.2683

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
 6IN  C1   C2    aromatic  1.406  0.020  1.406
 6IN  C1   C6    aromatic  1.388  0.020  1.388
 6IN  C1   O41   single    1.357  0.020  1.357
 6IN  C2   C3    aromatic  1.387  0.020  1.387
 6IN  C2   H2    single    0.930  0.020  1.080
 6IN  C3   C4    aromatic  1.386  0.020  1.386
 6IN  C3   H3    single    0.930  0.020  1.080
 6IN  C4   C5    aromatic  1.409  0.020  1.409
 6IN  C4   N10   aromatic  1.374  0.020  1.374
 6IN  C5   C6    aromatic  1.395  0.020  1.395
 6IN  C5   C12   aromatic  1.430  0.020  1.430
 6IN  C6   H6    single    0.930  0.020  1.080
 6IN  N10  C7    aromatic  1.377  0.020  1.377
 6IN  N10  C13   single    1.437  0.020  1.437
 6IN  C7   C12   aromatic  1.369  0.020  1.369
 6IN  C7   C27   single    1.485  0.020  1.485
 6IN  C12  C32   single    1.486  0.020  1.486
 6IN  C13  C14   single    1.513  0.020  1.513
 6IN  C13  H131  single    0.970  0.020  1.090
 6IN  C13  H132  single    0.970  0.020  1.090
 6IN  C14  C17   aromatic  1.391  0.020  1.391
 6IN  C14  C21   aromatic  1.393  0.020  1.393
 6IN  C17  C18   aromatic  1.391  0.020  1.391
 6IN  C17  H17   single    0.930  0.020  1.080
 6IN  C18  C19   aromatic  1.387  0.020  1.387
 6IN  C18  H18   single    0.930  0.020  1.080
 6IN  C19  C20   aromatic  1.390  0.020  1.390
 6IN  C19  H19   single    0.930  0.020  1.080
 6IN  C20  C21   aromatic  1.387  0.020  1.387
 6IN  C20  H20   single    0.930  0.020  1.080
 6IN  C21  H21   single    0.930  0.020  1.080
 6IN  C27  H271  single    0.970  0.020  1.090
 6IN  C27  H272  single    0.970  0.020  1.090
 6IN  C27  H273  single    0.970  0.020  1.090
 6IN  C32  C34   single    1.524  0.020  1.524
 6IN  C32  H321  single    0.970  0.020  1.090
 6IN  C32  H322  single    0.970  0.020  1.090
 6IN  C34  N37   single    1.342  0.020  1.342
 6IN  C34  O40   double    1.221  0.020  1.221
 6IN  N37  H371  single    0.860  0.020  1.020
 6IN  N37  H372  single    0.860  0.020  1.020
 6IN  O41  C42   single    1.414  0.020  1.414
 6IN  C42  C43   single    1.515  0.020  1.515
 6IN  C42  H421  single    0.970  0.020  1.090
 6IN  C42  H422  single    0.970  0.020  1.090
 6IN  C43  C46   single    1.520  0.020  1.520
 6IN  C43  H431  single    0.970  0.020  1.090
 6IN  C43  H432  single    0.970  0.020  1.090
 6IN  C46  C49   single    1.503  0.020  1.503
 6IN  C46  H461  single    0.970  0.020  1.090
 6IN  C46  H462  single    0.970  0.020  1.090
 6IN  C49  O52   single    1.330  0.020  1.330
 6IN  C49  O54   double    1.205  0.020  1.205
 6IN  O52  HXT   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
 6IN  O41   C1   C6    116.06  3.000
 6IN  O41   C1   C2    123.31  3.000
 6IN  C6    C1   C2    120.62  3.000
 6IN  H2    C2   C3    118.20  3.000
 6IN  H2    C2   C1    120.97  3.000
 6IN  C3    C2   C1    120.83  3.000
 6IN  H3    C3   C4    121.81  3.000
 6IN  H3    C3   C2    119.81  3.000
 6IN  C4    C3   C2    118.37  3.000
 6IN  N10   C4   C5    107.85  3.000
 6IN  N10   C4   C3    130.67  3.000
 6IN  C5    C4   C3    121.48  3.000
 6IN  C12   C5   C6    133.50  3.000
 6IN  C12   C5   C4    106.81  3.000
 6IN  C6    C5   C4    119.68  3.000
 6IN  H6    C6   C5    121.21  3.000
 6IN  H6    C6   C1    119.77  3.000
 6IN  C5    C6   C1    119.01  3.000
 6IN  C13   N10  C7    125.65  3.000
 6IN  C13   N10  C4    124.15  3.000
 6IN  C7    N10  C4    108.75  3.000
 6IN  C27   C7   C12   129.18  3.000
 6IN  C27   C7   N10   121.17  3.000
 6IN  C12   C7   N10   109.64  3.000
 6IN  C32   C12  C7    127.08  3.000
 6IN  C32   C12  C5    125.79  3.000
 6IN  C7    C12  C5    106.93  3.000
 6IN  H132  C13  H131  105.55  3.000
 6IN  H132  C13  C14   109.76  3.000
 6IN  H131  C13  C14   109.90  3.000
 6IN  H132  C13  N10   108.69  3.000
 6IN  H131  C13  N10   108.81  3.000
 6IN  C14   C13  N10   113.80  3.000
 6IN  C21   C14  C17   118.92  3.000
 6IN  C21   C14  C13   118.79  3.000
 6IN  C17   C14  C13   122.28  3.000
 6IN  H17   C17  C18   118.86  3.000
 6IN  H17   C17  C14   120.85  3.000
 6IN  C18   C17  C14   120.29  3.000
 6IN  H18   C18  C19   120.01  3.000
 6IN  H18   C18  C17   119.50  3.000
 6IN  C19   C18  C17   120.49  3.000
 6IN  H19   C19  C20   120.31  3.000
 6IN  H19   C19  C18   120.24  3.000
 6IN  C20   C19  C18   119.45  3.000
 6IN  H20   C20  C21   119.75  3.000
 6IN  H20   C20  C19   120.20  3.000
 6IN  C21   C20  C19   120.05  3.000
 6IN  H21   C21  C20   119.56  3.000
 6IN  H21   C21  C14   119.64  3.000
 6IN  C20   C21  C14   120.80  3.000
 6IN  H273  C27  H272  107.37  3.000
 6IN  H273  C27  H271  107.42  3.000
 6IN  H272  C27  H271  107.85  3.000
 6IN  H273  C27  C7    111.66  3.000
 6IN  H272  C27  C7    110.42  3.000
 6IN  H271  C27  C7    111.91  3.000
 6IN  H322  C32  H321  105.50  3.000
 6IN  H322  C32  C34   110.47  3.000
 6IN  H321  C32  C34   106.56  3.000
 6IN  H322  C32  C12   111.09  3.000
 6IN  H321  C32  C12   110.83  3.000
 6IN  C34   C32  C12   112.09  3.000
 6IN  O40   C34  N37   123.23  3.000
 6IN  O40   C34  C32   122.01  3.000
 6IN  N37   C34  C32   114.75  3.000
 6IN  H372  N37  H371  117.33  3.000
 6IN  H372  N37  C34   121.89  3.000
 6IN  H371  N37  C34   120.65  3.000
 6IN  C42   O41  C1    118.98  3.000
 6IN  H422  C42  H421  107.25  3.000
 6IN  H422  C42  C43   110.00  3.000
 6IN  H421  C42  C43   110.26  3.000
 6IN  H422  C42  O41   110.59  3.000
 6IN  H421  C42  O41   110.63  3.000
 6IN  C43   C42  O41   108.14  3.000
 6IN  H432  C43  H431  107.35  3.000
 6IN  H432  C43  C46   110.11  3.000
 6IN  H431  C43  C46   110.00  3.000
 6IN  H432  C43  C42   109.73  3.000
 6IN  H431  C43  C42   109.36  3.000
 6IN  C46   C43  C42   110.23  3.000
 6IN  H462  C46  H461  105.42  3.000
 6IN  H462  C46  C49   108.23  3.000
 6IN  H461  C46  C49   107.89  3.000
 6IN  H462  C46  C43   110.75  3.000
 6IN  H461  C46  C43   110.82  3.000
 6IN  C49   C46  C43   113.36  3.000
 6IN  O54   C49  O52   123.10  3.000
 6IN  O54   C49  C46   125.22  3.000
 6IN  O52   C49  C46   111.68  3.000
 6IN  HXT   O52  C49   110.05  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
 6IN  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 6IN  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 6IN  CONST_03  C12   C5   C6   C1    180.00   0.0  0
 6IN  CONST_04  C5    C6   C1   C2      0.00   0.0  0
 6IN  CONST_05  C5    C4   C3   C2      0.00   0.0  0
 6IN  CONST_06  N10   C4   C3   C2    180.00   0.0  0
 6IN  CONST_07  C6    C1   C2   C3      0.00   0.0  0
 6IN  CONST_08  C6    C5   C4   C3      0.00   0.0  0
 6IN  CONST_09  C12   C5   C4   C3    180.00   0.0  0
 6IN  CONST_10  C7    N10  C4   C3    180.00   0.0  0
 6IN  CONST_11  C7    C12  C5   C4      0.00   0.0  0
 6IN  CONST_12  C12   C7   N10  C4      0.00   0.0  0
 6IN  CONST_13  C7    N10  C4   C5      0.00   0.0  0
 6IN  CONST_14  N10   C7   C12  C5      0.00   0.0  0
 6IN  CONST_15  N10   C4   C5   C6    180.00   0.0  0
 6IN  CONST_16  C7    C12  C5   C6    180.00   0.0  0
 6IN  CONST_17  C12   C5   C4   N10     0.00   0.0  0
 6IN  CONST_18  C19   C18  C17  C14     0.00   0.0  0
 6IN  CONST_19  C19   C20  C21  C14     0.00   0.0  0
 6IN  CONST_20  C20   C21  C14  C17     0.00   0.0  0
 6IN  CONST_21  C20   C19  C18  C17     0.00   0.0  0
 6IN  CONST_22  C21   C14  C17  C18     0.00   0.0  0
 6IN  CONST_23  C21   C20  C19  C18     0.00   0.0  0
 6IN  CONST_24  O41   C1   C2   C3    180.00   0.0  0
 6IN  CONST_25  C13   N10  C4   C3      0.00   0.0  0
 6IN  CONST_26  C32   C12  C5   C4    180.00   0.0  0
 6IN  CONST_27  C27   C7   N10  C4    180.00   0.0  0
 6IN  CONST_28  C13   N10  C4   C5    180.00   0.0  0
 6IN  CONST_29  O41   C1   C6   C5    180.00   0.0  0
 6IN  CONST_30  C27   C7   C12  C5    180.00   0.0  0
 6IN  CONST_31  C32   C12  C5   C6      0.00   0.0  0
 6IN  CONST_32  C32   C12  C7   N10   180.00   0.0  0
 6IN  CONST_33  C13   N10  C7   C12   180.00   0.0  0
 6IN  CONST_34  C18   C17  C14  C13   180.00   0.0  0
 6IN  CONST_35  C20   C21  C14  C13   180.00   0.0  0
 6IN  CONST_36  H3    C3   C2   C1    180.00   0.0  0
 6IN  CONST_37  H6    C6   C1   C2    180.00   0.0  0
 6IN  CONST_38  H2    C2   C3   C4    180.00   0.0  0
 6IN  CONST_39  H18   C18  C17  C14   180.00   0.0  0
 6IN  CONST_40  H20   C20  C21  C14   180.00   0.0  0
 6IN  CONST_41  H21   C21  C14  C17   180.00   0.0  0
 6IN  CONST_42  H19   C19  C18  C17   180.00   0.0  0
 6IN  CONST_43  H17   C17  C18  C19   180.00   0.0  0
 6IN  CONST_44  H371  N37  C34  C32   180.00   0.0  0
 6IN  CONST_45  H372  N37  C34  C32     0.00   0.0  0
 6IN  CONST_46  HXT   O52  C49  C46   180.00   0.0  0
 6IN  Var_01    C14   C13  N10  C4    -78.19  30.0  2
 6IN  Var_02    C17   C14  C13  N10   -15.66  30.0  2
 6IN  Var_03    C34   C32  C12  C5     84.19  30.0  2
 6IN  Var_04    H271  C27  C7   N10    56.53  30.0  2
 6IN  Var_05    C43   C42  O41  C1    175.73  30.0  3
 6IN  Var_06    N37   C34  C32  C12  -149.60  30.0  3
 6IN  Var_07    C46   C43  C42  O41  -179.31  30.0  3
 6IN  Var_08    C49   C46  C43  C42   179.06  30.0  3
 6IN  Var_09    O52   C49  C46  C43  -177.73  30.0  3

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
 6IN  plan-1  C13   0.020
 6IN  plan-1  C14   0.020
 6IN  plan-1  C17   0.020
 6IN  plan-1  C18   0.020
 6IN  plan-1  C19   0.020
 6IN  plan-1  C20   0.020
 6IN  plan-1  C21   0.020
 6IN  plan-1  H17   0.020
 6IN  plan-1  H18   0.020
 6IN  plan-1  H19   0.020
 6IN  plan-1  H20   0.020
 6IN  plan-1  H21   0.020
 6IN  plan-2  C1    0.020
 6IN  plan-2  C2    0.020
 6IN  plan-2  C3    0.020
 6IN  plan-2  C4    0.020
 6IN  plan-2  C5    0.020
 6IN  plan-2  C6    0.020
 6IN  plan-2  N10   0.020
 6IN  plan-2  C7    0.020
 6IN  plan-2  C12   0.020
 6IN  plan-2  C13   0.020
 6IN  plan-2  C27   0.020
 6IN  plan-2  C32   0.020
 6IN  plan-2  O41   0.020
 6IN  plan-2  H2    0.020
 6IN  plan-2  H3    0.020
 6IN  plan-2  H6    0.020
 6IN  plan-3  C32   0.020
 6IN  plan-3  C34   0.020
 6IN  plan-3  N37   0.020
 6IN  plan-3  O40   0.020
 6IN  plan-3  H371  0.020
 6IN  plan-3  H372  0.020
 6IN  plan-4  C46   0.020
 6IN  plan-4  C49   0.020
 6IN  plan-4  O52   0.020
 6IN  plan-4  O54   0.020
 6IN  plan-4  HXT   0.020

