# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 13:51:49 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 5-(1H-indol-3-ylmethyl)-1,3-benzodioxole-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1c(Cc2c[nH]c3ccccc23)ccc4OCOc14
#
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
 C5Q  C5Q  '5-(1H-indol-3-ylmethyl)-1,3-benzodioxole-4-carboxylic acid'  ligand  34  22  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C5Q
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
 C5Q  C1    C  CR16   0  -0.271   3.7637   2.0900  -0.1803
 C5Q  C2    C  CR16   0  -0.287   4.5837   1.3745  -1.0690
 C5Q  C3    C  CR16   0  -0.366   2.7485   1.4614   0.5150
 C5Q  C4    C  CR16   0  -0.355  -0.8662   1.4864   1.5448
 C5Q  C5    C  CR16   0  -0.307   4.4054   0.0197  -1.2764
 C5Q  C6    C  CR16   0  -0.347  -1.8888   2.2566   0.9766
 C5Q  C7    C  CR56   0   0.017   2.5413   0.0901   0.3247
 C5Q  C8    C  CR6    0   0.122  -0.6465   0.1585   1.2030
 C5Q  C9    C  CR6    0  -0.190  -1.4629  -0.4727   0.2374
 C5Q  C10   C  CR56   0   0.348   3.3802  -0.6103  -0.5722
 C5Q  C11   C  CR56   0   0.281  -2.6664   1.6303   0.0387
 C5Q  C12   C  CR56   0   0.287  -2.4434   0.3122  -0.3262
 C5Q  C13   C  CR15   0  -0.070   1.9236  -2.0586   0.2902
 C5Q  C14   C  CR5    0   0.031   1.6156  -0.8601   0.8686
 C5Q  C15   C  CH2    0  -0.625   0.5124  -0.5774   1.8385
 C5Q  C16   C  C      0   0.383  -1.3281  -1.9308  -0.1819
 C5Q  C17   C  CH2    0   0.070  -4.0716   1.1299  -1.6026
 C5Q  N18   N  NR15   0  -0.690   2.9787  -1.9134  -0.5681
 C5Q  O19   O  OC    -1  -0.588  -1.2798  -2.1433  -1.4050
 C5Q  O20   O  O      0  -0.595  -1.3125  -2.7735   0.7345
 C5Q  O21   O  O      0  -0.492  -3.7376   2.1187  -0.6394
 C5Q  O22   O  O      0  -0.482  -3.3833  -0.0550  -1.2401
 C5Q  H1    H  HCR6   0   0.243   3.9340   3.1498  -0.0406
 C5Q  H2    H  HCR6   0   0.246   5.3711   1.8948  -1.5990
 C5Q  H3    H  HCR6   0   0.234   2.1224   2.0254   1.1955
 C5Q  H5    H  HCR6   0   0.256   5.0400  -0.5317  -1.9591
 C5Q  H13   H  HCR5   0   0.272   1.4514  -3.0183   0.4240
 C5Q  H15   H  HCH2   0   0.244   0.8952   0.0326   2.6616
 C5Q  H15A  H  HCH2   0   0.259   0.1658  -1.5125   2.2767
 C5Q  H17   H  HCH2   0   0.239  -5.1475   0.9524  -1.5918
 C5Q  H17A  H  HCH2   0   0.225  -3.7513   1.4585  -2.5982
 C5Q  HN18  H  HNR5   0   0.405   3.3748  -2.6518  -1.1242
 C5Q  H4    H  HCR6   0   0.241  -0.2232   1.9496   2.2835
 C5Q  H6    H  HCR6   0   0.264  -2.0536   3.2846   1.2697

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
 C5Q  C3   C1    aromatic  1.382  0.020  1.382
 C5Q  C1   C2    aromatic  1.405  0.020  1.405
 C5Q  C1   H1    single    0.930  0.020  1.080
 C5Q  C2   C5    aromatic  1.382  0.020  1.382
 C5Q  C2   H2    single    0.930  0.020  1.080
 C5Q  C3   C7    aromatic  1.400  0.020  1.400
 C5Q  C3   H3    single    0.930  0.020  1.080
 C5Q  C6   C4    aromatic  1.401  0.020  1.401
 C5Q  C4   C8    aromatic  1.389  0.020  1.389
 C5Q  C4   H4    single    0.930  0.020  1.080
 C5Q  C10  C5    aromatic  1.394  0.020  1.394
 C5Q  C5   H5    single    0.930  0.020  1.080
 C5Q  C11  C6    aromatic  1.370  0.020  1.370
 C5Q  C6   H6    single    0.930  0.020  1.080
 C5Q  C14  C7    aromatic  1.434  0.020  1.434
 C5Q  C7   C10   aromatic  1.414  0.020  1.414
 C5Q  C9   C8    aromatic  1.413  0.020  1.413
 C5Q  C8   C15   single    1.513  0.020  1.513
 C5Q  C12  C9    aromatic  1.377  0.020  1.377
 C5Q  C9   C16   single    1.523  0.020  1.523
 C5Q  N18  C10   aromatic  1.364  0.020  1.364
 C5Q  O21  C11   single    1.359  0.020  1.359
 C5Q  C11  C12   aromatic  1.386  0.020  1.386
 C5Q  O22  C12   single    1.361  0.020  1.361
 C5Q  C14  C13   aromatic  1.366  0.020  1.366
 C5Q  C13  N18   aromatic  1.368  0.020  1.368
 C5Q  C13  H13   single    0.930  0.020  1.080
 C5Q  C15  C14   single    1.496  0.020  1.496
 C5Q  C15  H15   single    0.970  0.020  1.090
 C5Q  C15  H15A  single    0.970  0.020  1.090
 C5Q  O20  C16   deloc     1.245  0.020  1.245
 C5Q  C16  O19   deloc     1.242  0.020  1.242
 C5Q  C17  O21   single    1.420  0.020  1.420
 C5Q  C17  O22   single    1.417  0.020  1.417
 C5Q  C17  H17   single    0.970  0.020  1.090
 C5Q  C17  H17A  single    0.970  0.020  1.090
 C5Q  N18  HN18  single    0.860  0.020  1.020

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
 C5Q  H1    C1   C3   119.74  3.000
 C5Q  H1    C1   C2   119.24  3.000
 C5Q  C3    C1   C2   121.03  3.000
 C5Q  H2    C2   C5   119.44  3.000
 C5Q  H2    C2   C1   119.31  3.000
 C5Q  C5    C2   C1   121.25  3.000
 C5Q  H3    C3   C7   120.67  3.000
 C5Q  H3    C3   C1   120.26  3.000
 C5Q  C7    C3   C1   119.08  3.000
 C5Q  H4    C4   C8   118.86  3.000
 C5Q  H4    C4   C6   118.35  3.000
 C5Q  C8    C4   C6   122.79  3.000
 C5Q  H5    C5   C10  121.28  3.000
 C5Q  H5    C5   C2   121.21  3.000
 C5Q  C10   C5   C2   117.51  3.000
 C5Q  H6    C6   C11  122.25  3.000
 C5Q  H6    C6   C4   121.60  3.000
 C5Q  C11   C6   C4   116.15  3.000
 C5Q  C14   C7   C10  107.18  3.000
 C5Q  C10   C7   C3   118.93  3.000
 C5Q  C14   C7   C3   133.89  3.000
 C5Q  C15   C8   C9   120.81  3.000
 C5Q  C15   C8   C4   118.88  3.000
 C5Q  C9    C8   C4   120.26  3.000
 C5Q  C16   C9   C12  119.74  3.000
 C5Q  C16   C9   C8   124.37  3.000
 C5Q  C12   C9   C8   115.88  3.000
 C5Q  N18   C10  C7   107.26  3.000
 C5Q  N18   C10  C5   130.53  3.000
 C5Q  C7    C10  C5   122.20  3.000
 C5Q  O21   C11  C12  109.72  3.000
 C5Q  C12   C11  C6   121.59  3.000
 C5Q  O21   C11  C6   128.68  3.000
 C5Q  O22   C12  C11  108.79  3.000
 C5Q  O22   C12  C9   127.79  3.000
 C5Q  C11   C12  C9   123.31  3.000
 C5Q  H13   C13  N18  120.68  3.000
 C5Q  H13   C13  C14  129.04  3.000
 C5Q  N18   C13  C14  110.27  3.000
 C5Q  C15   C14  C13  127.35  3.000
 C5Q  C15   C14  C7   126.64  3.000
 C5Q  C13   C14  C7   105.98  3.000
 C5Q  H15A  C15  H15  106.70  3.000
 C5Q  H15A  C15  C14  109.46  3.000
 C5Q  H15   C15  C14  109.59  3.000
 C5Q  H15A  C15  C8   110.05  3.000
 C5Q  H15   C15  C8   108.24  3.000
 C5Q  C14   C15  C8   112.62  3.000
 C5Q  O20   C16  O19  127.47  3.000
 C5Q  O19   C16  C9   115.99  3.000
 C5Q  O20   C16  C9   116.51  3.000
 C5Q  H17A  C17  H17  110.24  3.000
 C5Q  H17A  C17  O22  109.94  3.000
 C5Q  H17   C17  O22  109.91  3.000
 C5Q  H17A  C17  O21  109.78  3.000
 C5Q  H17   C17  O21  109.79  3.000
 C5Q  O22   C17  O21  107.12  3.000
 C5Q  HN18  N18  C13  124.95  3.000
 C5Q  HN18  N18  C10  125.73  3.000
 C5Q  C13   N18  C10  109.30  3.000
 C5Q  C17   O21  C11  105.88  3.000
 C5Q  C17   O22  C12  106.35  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
 C5Q  CONST_01  C14   C7   C3   C1    180.00   0.0  0
 C5Q  CONST_02  C10   C7   C3   C1      0.00   0.0  0
 C5Q  CONST_03  C10   C5   C2   C1      0.00   0.0  0
 C5Q  CONST_04  C7    C3   C1   C2      0.00   0.0  0
 C5Q  CONST_05  C7    C10  C5   C2      0.00   0.0  0
 C5Q  CONST_06  N18   C10  C5   C2    180.00   0.0  0
 C5Q  CONST_07  C5    C2   C1   C3      0.00   0.0  0
 C5Q  CONST_08  C13   C14  C7   C3    180.00   0.0  0
 C5Q  CONST_09  C5    C10  C7   C3      0.00   0.0  0
 C5Q  CONST_10  N18   C10  C7   C3    180.00   0.0  0
 C5Q  CONST_11  C12   C11  C6   C4      0.00   0.0  0
 C5Q  CONST_12  C12   C9   C8   C4      0.00   0.0  0
 C5Q  CONST_13  C14   C7   C10  C5    180.00   0.0  0
 C5Q  CONST_14  C13   N18  C10  C5    180.00   0.0  0
 C5Q  CONST_15  C9    C8   C4   C6      0.00   0.0  0
 C5Q  CONST_16  C9    C12  C11  C6      0.00   0.0  0
 C5Q  CONST_17  N18   C13  C14  C7      0.00   0.0  0
 C5Q  CONST_18  C13   N18  C10  C7      0.00   0.0  0
 C5Q  CONST_19  C11   C6   C4   C8      0.00   0.0  0
 C5Q  CONST_20  C11   C12  C9   C8      0.00   0.0  0
 C5Q  CONST_21  C13   C14  C7   C10     0.00   0.0  0
 C5Q  CONST_22  C14   C13  N18  C10     0.00   0.0  0
 C5Q  CONST_23  N18   C10  C7   C14     0.00   0.0  0
 C5Q  CONST_24  C15   C14  C7   C3      0.00   0.0  0
 C5Q  CONST_25  C16   C9   C8   C4    180.00   0.0  0
 C5Q  CONST_26  C15   C8   C4   C6    180.00   0.0  0
 C5Q  CONST_27  C15   C14  C7   C10   180.00   0.0  0
 C5Q  CONST_28  C16   C9   C12  C11   180.00   0.0  0
 C5Q  CONST_29  C15   C8   C9   C12   180.00   0.0  0
 C5Q  CONST_30  N18   C13  C14  C15   180.00   0.0  0
 C5Q  CONST_31  O22   C12  C9   C16     0.00   0.0  0
 C5Q  CONST_32  H5    C5   C2   C1    180.00   0.0  0
 C5Q  CONST_33  H3    C3   C1   C2    180.00   0.0  0
 C5Q  CONST_34  H2    C2   C1   C3    180.00   0.0  0
 C5Q  CONST_35  H1    C1   C2   C5    180.00   0.0  0
 C5Q  CONST_36  HN18  N18  C10  C5      0.00   0.0  0
 C5Q  CONST_37  H13   C13  C14  C7    180.00   0.0  0
 C5Q  CONST_38  H6    C6   C4   C8    180.00   0.0  0
 C5Q  CONST_39  H4    C4   C8   C9    180.00   0.0  0
 C5Q  Var_01    O22   C17  O21  C11    14.08  30.0  1
 C5Q  Var_02    O21   C17  O22  C12   -14.39  30.0  1
 C5Q  Var_03    C14   C15  C8   C4   -109.61  30.0  2
 C5Q  Var_04    C8    C15  C14  C7     73.00  30.0  2
 C5Q  Var_05    O20   C16  C9   C8     51.49  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
 C5Q  plan-1  C1    0.020
 C5Q  plan-1  C2    0.020
 C5Q  plan-1  C3    0.020
 C5Q  plan-1  C5    0.020
 C5Q  plan-1  C7    0.020
 C5Q  plan-1  C10   0.020
 C5Q  plan-1  C13   0.020
 C5Q  plan-1  C14   0.020
 C5Q  plan-1  C15   0.020
 C5Q  plan-1  N18   0.020
 C5Q  plan-1  H1    0.020
 C5Q  plan-1  H2    0.020
 C5Q  plan-1  H3    0.020
 C5Q  plan-1  H5    0.020
 C5Q  plan-1  H13   0.020
 C5Q  plan-1  HN18  0.020
 C5Q  plan-2  C4    0.020
 C5Q  plan-2  C6    0.020
 C5Q  plan-2  C8    0.020
 C5Q  plan-2  C9    0.020
 C5Q  plan-2  C11   0.020
 C5Q  plan-2  C12   0.020
 C5Q  plan-2  C15   0.020
 C5Q  plan-2  C16   0.020
 C5Q  plan-2  O21   0.020
 C5Q  plan-2  O22   0.020
 C5Q  plan-2  H4    0.020
 C5Q  plan-2  H6    0.020
 C5Q  plan-3  C9    0.020
 C5Q  plan-3  C16   0.020
 C5Q  plan-3  O19   0.020
 C5Q  plan-3  O20   0.020

