# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 22:04:10 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 3-[(2-aminocarbonyl-1~{H}-indol-5-yl)oxymethyl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1[nH]c2ccc(OCc3cccc(c3)C(O)=O)cc2c1
#
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
 5WD  5WD  '3-[(2-aminocarbonyl-1~{H}-indol-5-yl)oxymethyl]benzoic acid'  ligand  37  23  .  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_5WD
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
 5WD  C1   C  CR6   0   0.386   0.6092   0.4979   0.2601
 5WD  C2   C  CR16  0  -0.396   1.1041   1.1957   1.3816
 5WD  C3   C  CR16  0  -0.290   2.4527   1.2030   1.6806
 5WD  C14  C  CH2   0  -0.266  -1.6295   1.1972   0.7142
 5WD  C15  C  CR6   0   0.120  -2.9811   1.0111   0.0934
 5WD  C16  C  CR16  0  -0.282  -3.4448   1.9003  -0.8710
 5WD  C17  C  CR16  0  -0.228  -4.6830   1.7113  -1.4676
 5WD  C18  C  CR16  0  -0.269  -5.4696   0.6272  -1.1114
 5WD  C19  C  CR6   0  -0.064  -5.0139  -0.2733  -0.1495
 5WD  C20  C  CR16  0  -0.302  -3.7709  -0.0742   0.4455
 5WD  C21  C  C     0   0.535  -5.8137  -1.4488   0.2770
 5WD  C4   C  CR16  0  -0.451   1.4653  -0.2070  -0.5668
 5WD  C5   C  CR56  0   0.086   2.8328  -0.2152  -0.2738
 5WD  C6   C  CR56  0   0.333   3.3132   0.5010   0.8436
 5WD  N7   N  NR15  0  -0.741   4.6692   0.3469   0.8886
 5WD  C8   C  CR5   0   0.227   5.0604  -0.4643  -0.1453
 5WD  C9   C  CR15  0  -0.400   3.9648  -0.8280  -0.8823
 5WD  C10  C  C     0   0.466   6.4605  -0.8486  -0.4202
 5WD  N11  N  NH2   0  -0.815   7.4099  -0.1068   0.1750
 5WD  O12  O  O     0  -0.474   6.7078  -1.8003  -1.1471
 5WD  O13  O  O2    0  -0.478  -0.7053   0.4692  -0.0765
 5WD  O22  O  OH1   0  -0.593  -6.9671  -1.5536  -0.3668
 5WD  O23  O  O     0  -0.438  -5.4553  -2.2327   1.1232
 5WD  H1   H  HCR6  0   0.282   0.4359   1.7448   2.0305
 5WD  H2   H  HCR6  0   0.269   2.8181   1.7442   2.5436
 5WD  H3   H  HCH2  0   0.242  -1.3663   2.2602   0.7389
 5WD  H4   H  HCH2  0   0.241  -1.6320   0.8302   1.7461
 5WD  H5   H  HCR6  0   0.265  -2.8367   2.7511  -1.1545
 5WD  H6   H  HCR6  0   0.269  -5.0386   2.4121  -2.2109
 5WD  H7   H  HCR6  0   0.272  -6.4339   0.4961  -1.5819
 5WD  H8   H  HCR6  0   0.264  -3.4167  -0.7697   1.1963
 5WD  H9   H  HCR6  0   0.255   1.0757  -0.7408  -1.4251
 5WD  H10  H  HNR5  0   0.411   5.2474   0.6524   1.6538
 5WD  H11  H  HCR5  0   0.259   3.9760  -1.4426  -1.7681
 5WD  H12  H  HNH2  0   0.407   7.2159   0.7852   0.5969
 5WD  H13  H  HNH2  0   0.410   8.3787  -0.3041  -0.0188
 5WD  H14  H  HOH1  0   0.489  -7.4538  -2.3273  -0.0459

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
 5WD  C17  C16  aromatic  1.387  0.020  1.387
 5WD  C17  C18  aromatic  1.386  0.020  1.386
 5WD  C16  C15  aromatic  1.391  0.020  1.391
 5WD  C18  C19  aromatic  1.394  0.020  1.394
 5WD  N11  C10  single    1.344  0.020  1.344
 5WD  C9   C8   aromatic  1.370  0.020  1.370
 5WD  C9   C5   aromatic  1.424  0.020  1.424
 5WD  C10  C8   single    1.478  0.020  1.478
 5WD  C10  O12  double    1.223  0.020  1.223
 5WD  C4   C5   aromatic  1.399  0.020  1.399
 5WD  C4   C1   aromatic  1.383  0.020  1.383
 5WD  C15  C14  single    1.499  0.020  1.499
 5WD  C15  C20  aromatic  1.388  0.020  1.388
 5WD  C8   N7   aromatic  1.371  0.020  1.371
 5WD  C5   C6   aromatic  1.411  0.020  1.411
 5WD  O13  C1   single    1.357  0.020  1.357
 5WD  O13  C14  single    1.418  0.020  1.418
 5WD  C1   C2   aromatic  1.411  0.020  1.411
 5WD  N7   C6   aromatic  1.365  0.020  1.365
 5WD  C6   C3   aromatic  1.391  0.020  1.391
 5WD  C19  C20  aromatic  1.392  0.020  1.392
 5WD  C19  C21  single    1.484  0.020  1.484
 5WD  C2   C3   aromatic  1.381  0.020  1.381
 5WD  O23  C21  double    1.208  0.020  1.208
 5WD  C21  O22  single    1.325  0.020  1.325
 5WD  C2   H1   single    0.930  0.020  1.080
 5WD  C3   H2   single    0.930  0.020  1.080
 5WD  C14  H3   single    0.970  0.020  1.090
 5WD  C14  H4   single    0.970  0.020  1.090
 5WD  C16  H5   single    0.930  0.020  1.080
 5WD  C17  H6   single    0.930  0.020  1.080
 5WD  C18  H7   single    0.930  0.020  1.080
 5WD  C20  H8   single    0.930  0.020  1.080
 5WD  C4   H9   single    0.930  0.020  1.080
 5WD  N7   H10  single    0.860  0.020  1.020
 5WD  C9   H11  single    0.930  0.020  1.080
 5WD  N11  H12  single    0.860  0.020  1.020
 5WD  N11  H13  single    0.860  0.020  1.020
 5WD  O22  H14  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
 5WD  O13  C1   C4   116.13  3.000
 5WD  O13  C1   C2   123.20  3.000
 5WD  C4   C1   C2   120.68  3.000
 5WD  H1   C2   C3   118.09  3.000
 5WD  H1   C2   C1   120.76  3.000
 5WD  C3   C2   C1   121.15  3.000
 5WD  H2   C3   C6   121.57  3.000
 5WD  H2   C3   C2   120.32  3.000
 5WD  C6   C3   C2   118.11  3.000
 5WD  H4   C14  H3   107.73  3.000
 5WD  H4   C14  O13  110.79  3.000
 5WD  H3   C14  O13  110.75  3.000
 5WD  H4   C14  C15  110.28  3.000
 5WD  H3   C14  C15  110.28  3.000
 5WD  O13  C14  C15  107.04  3.000
 5WD  C20  C15  C16  119.08  3.000
 5WD  C20  C15  C14  120.35  3.000
 5WD  C16  C15  C14  120.55  3.000
 5WD  H5   C16  C17  119.69  3.000
 5WD  H5   C16  C15  119.75  3.000
 5WD  C17  C16  C15  120.56  3.000
 5WD  H6   C17  C18  119.79  3.000
 5WD  H6   C17  C16  120.04  3.000
 5WD  C18  C17  C16  120.17  3.000
 5WD  H7   C18  C19  120.90  3.000
 5WD  H7   C18  C17  119.29  3.000
 5WD  C19  C18  C17  119.80  3.000
 5WD  C21  C19  C20  118.13  3.000
 5WD  C21  C19  C18  122.25  3.000
 5WD  C20  C19  C18  119.62  3.000
 5WD  H8   C20  C19  119.76  3.000
 5WD  H8   C20  C15  119.47  3.000
 5WD  C19  C20  C15  120.76  3.000
 5WD  O23  C21  O22  123.18  3.000
 5WD  O22  C21  C19  113.08  3.000
 5WD  O23  C21  C19  123.73  3.000
 5WD  H9   C4   C5   120.98  3.000
 5WD  H9   C4   C1   120.14  3.000
 5WD  C5   C4   C1   118.88  3.000
 5WD  C9   C5   C6   106.63  3.000
 5WD  C6   C5   C4   119.71  3.000
 5WD  C9   C5   C4   133.66  3.000
 5WD  N7   C6   C5   107.87  3.000
 5WD  N7   C6   C3   130.66  3.000
 5WD  C5   C6   C3   121.47  3.000
 5WD  H10  N7   C8   126.08  3.000
 5WD  H10  N7   C6   124.14  3.000
 5WD  C8   N7   C6   108.98  3.000
 5WD  C10  C8   C9   126.07  3.000
 5WD  C10  C8   N7   124.37  3.000
 5WD  C9   C8   N7   109.55  3.000
 5WD  H11  C9   C8   125.81  3.000
 5WD  H11  C9   C5   127.21  3.000
 5WD  C8   C9   C5   106.96  3.000
 5WD  O12  C10  N11  123.37  3.000
 5WD  O12  C10  C8   120.31  3.000
 5WD  N11  C10  C8   116.32  3.000
 5WD  H13  N11  H12  116.10  3.000
 5WD  H13  N11  C10  119.08  3.000
 5WD  H12  N11  C10  122.62  3.000
 5WD  C14  O13  C1   118.83  3.000
 5WD  H14  O22  C21  109.85  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
 5WD  CONST_01  C9   C5   C4   C1    180.00   0.0  0
 5WD  CONST_02  C6   C5   C4   C1      0.00   0.0  0
 5WD  CONST_03  C6   C3   C2   C1      0.00   0.0  0
 5WD  CONST_04  C5   C4   C1   C2      0.00   0.0  0
 5WD  CONST_05  C5   C6   C3   C2      0.00   0.0  0
 5WD  CONST_06  N7   C6   C3   C2    180.00   0.0  0
 5WD  CONST_07  C9   C5   C6   C3    180.00   0.0  0
 5WD  CONST_08  C4   C5   C6   C3      0.00   0.0  0
 5WD  CONST_09  C8   N7   C6   C3    180.00   0.0  0
 5WD  CONST_10  C4   C1   C2   C3      0.00   0.0  0
 5WD  CONST_11  C18  C17  C16  C15     0.00   0.0  0
 5WD  CONST_12  C18  C19  C20  C15     0.00   0.0  0
 5WD  CONST_13  C19  C18  C17  C16     0.00   0.0  0
 5WD  CONST_14  C19  C20  C15  C16     0.00   0.0  0
 5WD  CONST_15  C20  C15  C16  C17     0.00   0.0  0
 5WD  CONST_16  C20  C19  C18  C17     0.00   0.0  0
 5WD  CONST_17  C8   C9   C5   C4    180.00   0.0  0
 5WD  CONST_18  N7   C6   C5   C4    180.00   0.0  0
 5WD  CONST_19  N7   C8   C9   C5      0.00   0.0  0
 5WD  CONST_20  C8   N7   C6   C5      0.00   0.0  0
 5WD  CONST_21  C8   C9   C5   C6      0.00   0.0  0
 5WD  CONST_22  C9   C8   N7   C6      0.00   0.0  0
 5WD  CONST_23  C9   C5   C6   N7      0.00   0.0  0
 5WD  CONST_24  O13  C1   C2   C3    180.00   0.0  0
 5WD  CONST_25  C17  C16  C15  C14   180.00   0.0  0
 5WD  CONST_26  C19  C20  C15  C14   180.00   0.0  0
 5WD  CONST_27  C21  C19  C20  C15   180.00   0.0  0
 5WD  CONST_28  C21  C19  C18  C17   180.00   0.0  0
 5WD  CONST_29  C10  C8   C9   C5    180.00   0.0  0
 5WD  CONST_30  O13  C1   C4   C5    180.00   0.0  0
 5WD  CONST_31  C10  C8   N7   C6    180.00   0.0  0
 5WD  CONST_32  H2   C3   C2   C1    180.00   0.0  0
 5WD  CONST_33  H9   C4   C1   C2    180.00   0.0  0
 5WD  CONST_34  H10  N7   C6   C3      0.00   0.0  0
 5WD  CONST_35  H6   C17  C16  C15   180.00   0.0  0
 5WD  CONST_36  H7   C18  C17  C16   180.00   0.0  0
 5WD  CONST_37  H8   C20  C15  C16   180.00   0.0  0
 5WD  CONST_38  H5   C16  C17  C18   180.00   0.0  0
 5WD  CONST_39  H11  C9   C5   C4      0.00   0.0  0
 5WD  CONST_40  H1   C2   C1   C4    180.00   0.0  0
 5WD  CONST_41  H12  N11  C10  C8      0.00   0.0  0
 5WD  CONST_42  H13  N11  C10  C8    180.00   0.0  0
 5WD  CONST_43  H14  O22  C21  C19   180.00   0.0  0
 5WD  Var_01    C15  C14  O13  C1    178.60  30.0  3
 5WD  Var_02    C4   C1   O13  C14  -178.59  30.0  2
 5WD  Var_03    O13  C14  C15  C16   -90.70  30.0  2
 5WD  Var_04    O23  C21  C19  C18  -178.71  30.0  2
 5WD  Var_05    N11  C10  C8   N7    -16.52  30.0  2

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
 5WD  plan-1  C14  0.020
 5WD  plan-1  C15  0.020
 5WD  plan-1  C16  0.020
 5WD  plan-1  C17  0.020
 5WD  plan-1  C18  0.020
 5WD  plan-1  C19  0.020
 5WD  plan-1  C20  0.020
 5WD  plan-1  C21  0.020
 5WD  plan-1  H5   0.020
 5WD  plan-1  H6   0.020
 5WD  plan-1  H7   0.020
 5WD  plan-1  H8   0.020
 5WD  plan-2  C1   0.020
 5WD  plan-2  C2   0.020
 5WD  plan-2  C3   0.020
 5WD  plan-2  C4   0.020
 5WD  plan-2  C5   0.020
 5WD  plan-2  C6   0.020
 5WD  plan-2  N7   0.020
 5WD  plan-2  C8   0.020
 5WD  plan-2  C9   0.020
 5WD  plan-2  C10  0.020
 5WD  plan-2  O13  0.020
 5WD  plan-2  H1   0.020
 5WD  plan-2  H2   0.020
 5WD  plan-2  H9   0.020
 5WD  plan-2  H10  0.020
 5WD  plan-2  H11  0.020
 5WD  plan-3  C8   0.020
 5WD  plan-3  C10  0.020
 5WD  plan-3  N11  0.020
 5WD  plan-3  O12  0.020
 5WD  plan-3  H12  0.020
 5WD  plan-3  H13  0.020
 5WD  plan-4  C19  0.020
 5WD  plan-4  C21  0.020
 5WD  plan-4  O22  0.020
 5WD  plan-4  O23  0.020
 5WD  plan-4  H14  0.020

