# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 13:12:22 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: N-[2-(2-iodo-5-methoxy-1H-indol-3-yl)ethyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2[nH]c(I)c(CCNC(C)=O)c2c1
#
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
 ML2  ML2  N-[2-(2-iodo-5-methoxy-1H-indol-3-yl)ethyl]acetamide  ligand  33  18  .  2021-08-14  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ML2
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
 ML2  C2    C  CR5   0  -0.037   0.1435  -1.3991   0.0994
 ML2  C4    C  CR56  0   0.332  -2.0397  -1.4179  -0.2815
 ML2  C5    C  CR16  0  -0.283  -3.3507  -1.7334  -0.6129
 ML2  C6    C  CR16  0  -0.405  -4.3220  -0.7652  -0.4292
 ML2  C9    C  CH3   0  -0.434  -6.2601   1.2256  -0.0326
 ML2  C12   C  CR5   0   0.054  -0.2826  -0.1550   0.4766
 ML2  C13   C  CH2   0  -0.584   0.5271   0.9859   0.9888
 ML2  N15   N  NH1   0  -0.636   1.7458   3.0144   0.3942
 ML2  C16   C  C     0   0.521   2.0202   4.1262  -0.3058
 ML2  C18   C  CH3   0  -0.778   2.8465   5.1622   0.4149
 ML2  I1    I  I     0   0.107   2.0688  -2.1570   0.1519
 ML2  N3    N  NR15  0  -0.703  -0.8932  -2.1627  -0.3511
 ML2  C7    C  CR6   0   0.391  -3.9937   0.5071   0.0785
 ML2  O8    O  O2    0  -0.482  -4.9079   1.4879   0.2727
 ML2  C10   C  CR16  0  -0.484  -2.6842   0.8174   0.4095
 ML2  C11   C  CR56  0   0.071  -1.6945  -0.1516   0.2306
 ML2  C14   C  CH2   0  -0.229   0.9829   1.9078  -0.1402
 ML2  O17   O  O     0  -0.511   1.6184   4.3009  -1.4495
 ML2  H5    H  HCR6  0   0.268  -3.6190  -2.7056  -1.0051
 ML2  H6    H  HCR6  0   0.277  -5.3426  -1.0120  -0.6868
 ML2  H91   H  HCH3  0   0.256  -6.8123   2.1324   0.2038
 ML2  H92   H  HCH3  0   0.224  -6.4074   0.9930  -1.0909
 ML2  H93   H  HCH3  0   0.224  -6.6666   0.4053   0.5656
 ML2  H131  H  HCH2  0   0.260  -0.0637   1.5625   1.7062
 ML2  H132  H  HCH2  0   0.258   1.4009   0.6180   1.5345
 ML2  H15   H  HNH1  0   0.401   2.1619   2.8999   1.3040
 ML2  H181  H  HCH3  0   0.248   3.1717   4.8510   1.4057
 ML2  H182  H  HCH3  0   0.264   3.7286   5.4017  -0.1784
 ML2  H183  H  HCH3  0   0.266   2.2670   6.0800   0.5164
 ML2  H3    H  HNR5  0   0.417  -0.8255  -3.1083  -0.6889
 ML2  H10   H  HCR6  0   0.249  -2.4400   1.7992   0.7981
 ML2  H141  H  HCH2  0   0.235   1.5770   1.3387  -0.8626
 ML2  H142  H  HCH2  0   0.243   0.1135   2.2932  -0.6754

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
 ML2  C18  C16   single    1.508  0.020  1.508
 ML2  C16  N15   single    1.342  0.020  1.342
 ML2  C16  O17   double    1.225  0.020  1.225
 ML2  N15  C14   single    1.446  0.020  1.446
 ML2  C13  C14   single    1.527  0.020  1.527
 ML2  C13  C12   single    1.490  0.020  1.490
 ML2  C12  C2    aromatic  1.368  0.020  1.368
 ML2  C12  C11   aromatic  1.433  0.020  1.433
 ML2  I1   C2    single    2.070  0.020  2.070
 ML2  C2   N3    aromatic  1.364  0.020  1.364
 ML2  C10  C11   aromatic  1.397  0.020  1.397
 ML2  C10  C7    aromatic  1.386  0.020  1.386
 ML2  C11  C4    aromatic  1.409  0.020  1.409
 ML2  O8   C7    single    1.355  0.020  1.355
 ML2  O8   C9    single    1.411  0.020  1.411
 ML2  C7   C6    aromatic  1.409  0.020  1.409
 ML2  N3   C4    aromatic  1.369  0.020  1.369
 ML2  C4   C5    aromatic  1.389  0.020  1.389
 ML2  C6   C5    aromatic  1.384  0.020  1.384
 ML2  C5   H5    single    0.930  0.020  1.080
 ML2  C6   H6    single    0.930  0.020  1.080
 ML2  C9   H91   single    0.970  0.020  1.090
 ML2  C9   H92   single    0.970  0.020  1.090
 ML2  C9   H93   single    0.970  0.020  1.090
 ML2  C13  H131  single    0.970  0.020  1.090
 ML2  C13  H132  single    0.970  0.020  1.090
 ML2  N15  H15   single    0.860  0.020  1.020
 ML2  C18  H181  single    0.970  0.020  1.090
 ML2  C18  H182  single    0.970  0.020  1.090
 ML2  C18  H183  single    0.970  0.020  1.090
 ML2  N3   H3    single    0.860  0.020  1.020
 ML2  C10  H10   single    0.930  0.020  1.080
 ML2  C14  H141  single    0.970  0.020  1.090
 ML2  C14  H142  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
 ML2  N3    C2   I1    120.69  3.000
 ML2  N3    C2   C12   111.31  3.000
 ML2  I1    C2   C12   128.00  3.000
 ML2  C11   C4   N3    107.59  3.000
 ML2  N3    C4   C5    130.92  3.000
 ML2  C11   C4   C5    121.48  3.000
 ML2  H5    C5   C6    120.18  3.000
 ML2  H5    C5   C4    121.65  3.000
 ML2  C6    C5   C4    118.17  3.000
 ML2  H6    C6   C7    120.80  3.000
 ML2  H6    C6   C5    118.12  3.000
 ML2  C7    C6   C5    121.08  3.000
 ML2  H93   C9   H92   108.65  3.000
 ML2  H93   C9   H91   108.53  3.000
 ML2  H92   C9   H91   108.62  3.000
 ML2  H93   C9   O8    112.17  3.000
 ML2  H92   C9   O8    112.21  3.000
 ML2  H91   C9   O8    106.53  3.000
 ML2  C11   C12  C13   126.34  3.000
 ML2  C11   C12  C2    105.17  3.000
 ML2  C13   C12  C2    128.45  3.000
 ML2  H132  C13  H131  106.35  3.000
 ML2  H132  C13  C14   109.48  3.000
 ML2  H131  C13  C14   109.14  3.000
 ML2  H132  C13  C12   110.37  3.000
 ML2  H131  C13  C12   109.61  3.000
 ML2  C14   C13  C12   111.74  3.000
 ML2  H15   N15  C14   117.69  3.000
 ML2  H15   N15  C16   118.74  3.000
 ML2  C14   N15  C16   123.29  3.000
 ML2  O17   C16  C18   121.86  3.000
 ML2  O17   C16  N15   122.56  3.000
 ML2  C18   C16  N15   115.58  3.000
 ML2  H183  C18  H182  107.21  3.000
 ML2  H183  C18  H181  108.35  3.000
 ML2  H182  C18  H181  108.47  3.000
 ML2  H183  C18  C16   109.36  3.000
 ML2  H182  C18  C16   109.53  3.000
 ML2  H181  C18  C16   113.72  3.000
 ML2  H3    N3   C4    125.77  3.000
 ML2  H3    N3   C2    125.85  3.000
 ML2  C4    N3   C2    108.37  3.000
 ML2  C10   C7   O8    116.19  3.000
 ML2  O8    C7   C6    123.25  3.000
 ML2  C10   C7   C6    120.56  3.000
 ML2  C7    O8   C9    118.76  3.000
 ML2  H10   C10  C11   120.98  3.000
 ML2  H10   C10  C7    120.09  3.000
 ML2  C11   C10  C7    118.93  3.000
 ML2  C10   C11  C12   132.67  3.000
 ML2  C10   C11  C4    119.77  3.000
 ML2  C12   C11  C4    107.56  3.000
 ML2  H142  C14  H141  106.99  3.000
 ML2  H142  C14  N15   109.35  3.000
 ML2  H141  C14  N15   110.81  3.000
 ML2  H142  C14  C13   109.75  3.000
 ML2  H141  C14  C13   109.63  3.000
 ML2  N15   C14  C13   110.25  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
 ML2  CONST_01  C10   C11  C12  C2    180.00   0.0  0
 ML2  CONST_02  C4    C11  C12  C2      0.00   0.0  0
 ML2  CONST_03  C11   C4   N3   C2      0.00   0.0  0
 ML2  CONST_04  C5    C4   N3   C2    180.00   0.0  0
 ML2  CONST_05  C7    C10  C11  C4      0.00   0.0  0
 ML2  CONST_06  C12   C2   N3   C4      0.00   0.0  0
 ML2  CONST_07  C7    C6   C5   C4      0.00   0.0  0
 ML2  CONST_08  C12   C11  C4   C5    180.00   0.0  0
 ML2  CONST_09  C10   C11  C4   C5      0.00   0.0  0
 ML2  CONST_10  C10   C7   C6   C5      0.00   0.0  0
 ML2  CONST_11  C11   C10  C7   C6      0.00   0.0  0
 ML2  CONST_12  C11   C4   C5   C6      0.00   0.0  0
 ML2  CONST_13  N3    C4   C5   C6    180.00   0.0  0
 ML2  CONST_14  C7    C10  C11  C12   180.00   0.0  0
 ML2  CONST_15  N3    C4   C11  C12     0.00   0.0  0
 ML2  CONST_16  C11   C12  C2   N3      0.00   0.0  0
 ML2  CONST_17  C10   C11  C4   N3    180.00   0.0  0
 ML2  CONST_18  C13   C12  C11  C4    180.00   0.0  0
 ML2  CONST_19  I1    C2   N3   C4    180.00   0.0  0
 ML2  CONST_20  O8    C7   C6   C5    180.00   0.0  0
 ML2  CONST_21  N3    C2   C12  C13   180.00   0.0  0
 ML2  CONST_22  C10   C11  C12  C13     0.00   0.0  0
 ML2  CONST_23  C11   C12  C2   I1    180.00   0.0  0
 ML2  CONST_24  C11   C10  C7   O8    180.00   0.0  0
 ML2  CONST_25  H10   C10  C11  C4    180.00   0.0  0
 ML2  CONST_26  H6    C6   C5   C4    180.00   0.0  0
 ML2  CONST_27  H3    N3   C4   C5      0.00   0.0  0
 ML2  CONST_28  H5    C5   C4   N3      0.00   0.0  0
 ML2  CONST_29  C14   N15  C16  C18   180.00   0.0  0
 ML2  CONST_30  O17   C16  N15  C14     0.00   0.0  0
 ML2  CONST_31  H15   N15  C16  C18     0.00   0.0  0
 ML2  Var_01    C14   C13  C12  C2     91.73  30.0  2
 ML2  Var_02    C10   C7   O8   C9   -179.31  30.0  2
 ML2  Var_03    N15   C14  C13  C12   179.04  30.0  3
 ML2  Var_04    H91   C9   O8   C7    179.47  30.0  3
 ML2  Var_05    C16   N15  C14  C13  -164.76  30.0  1
 ML2  Var_06    H181  C18  C16  N15     3.44  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
 ML2  plan-1  C2   0.020
 ML2  plan-1  C4   0.020
 ML2  plan-1  C5   0.020
 ML2  plan-1  C6   0.020
 ML2  plan-1  C12  0.020
 ML2  plan-1  C13  0.020
 ML2  plan-1  I1   0.020
 ML2  plan-1  N3   0.020
 ML2  plan-1  C7   0.020
 ML2  plan-1  O8   0.020
 ML2  plan-1  C10  0.020
 ML2  plan-1  C11  0.020
 ML2  plan-1  H5   0.020
 ML2  plan-1  H6   0.020
 ML2  plan-1  H3   0.020
 ML2  plan-1  H10  0.020
 ML2  plan-2  N15  0.020
 ML2  plan-2  C16  0.020
 ML2  plan-2  C18  0.020
 ML2  plan-2  C14  0.020
 ML2  plan-2  O17  0.020
 ML2  plan-2  H15  0.020

