# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 13:05:26 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: N-[2-(5-methoxy-1H-indol-3-yl)ethyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2[nH]cc(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
 ML1  ML1  N-[2-(5-methoxy-1H-indol-3-yl)ethyl]acetamide  ligand  33  17  .  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_ML1
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
 ML1  C1    C  CH2   0  -0.232   2.2238   0.2850  -0.1128
 ML1  C2    C  CR15  0  -0.079  -0.1723   2.8281   0.1605
 ML1  C3    C  CH3   0  -0.433  -4.1144  -2.8736  -0.0979
 ML1  C4    C  C     0   0.520   4.2738  -1.0494  -0.2799
 ML1  C5    C  CH3   0  -0.776   5.5477  -1.4607   0.4155
 ML1  C6    C  CH2   0  -0.586   1.4632   1.0353   0.9775
 ML1  C8    C  CR56  0   0.052  -1.0330   0.7642   0.2420
 ML1  C9    C  CR16  0  -0.489  -1.3379  -0.5913   0.3893
 ML1  C12   C  CR16  0  -0.291  -3.2933   1.2102  -0.5685
 ML1  C13   C  CR56  0   0.339  -2.0199   1.6535  -0.2364
 ML1  C7    C  CR5   0   0.003   0.1462   1.5398   0.4916
 ML1  C10   C  CR6   0   0.386  -2.6095  -1.0351   0.0603
 ML1  C11   C  CR16  0  -0.405  -3.5808  -0.1360  -0.4192
 ML1  N1    N  NH1   0  -0.635   3.4873  -0.2019   0.3987
 ML1  N2    N  NR15  0  -0.690  -1.4627   2.9021  -0.2750
 ML1  O1    O  O2    0  -0.484  -2.8418  -2.3614   0.2287
 ML1  O2    O  O     0  -0.513   3.9756  -1.4754  -1.3896
 ML1  H11   H  HCH2  0   0.237   1.6275  -0.5565  -0.4732
 ML1  H12A  H  HCH2  0   0.234   2.3838   0.9495  -0.9666
 ML1  H2    H  HCR5  0   0.281   0.4422   3.7138   0.2111
 ML1  H31   H  HCH3  0   0.255  -4.0824  -3.9408   0.1108
 ML1  H32   H  HCH3  0   0.222  -4.9088  -2.4260   0.5061
 ML1  H33   H  HCH3  0   0.222  -4.3584  -2.7342  -1.1550
 ML1  H51   H  HCH3  0   0.266   5.5042  -2.5252   0.6488
 ML1  H52   H  HCH3  0   0.262   6.3926  -1.3102  -0.2556
 ML1  H53   H  HCH3  0   0.247   5.7388  -0.9174   1.3393
 ML1  H61   H  HCH2  0   0.245   1.3206   0.3691   1.8343
 ML1  H62   H  HCH2  0   0.255   2.0690   1.8742   1.3309
 ML1  H9    H  HCR6  0   0.244  -0.5986  -1.2948   0.7559
 ML1  H12   H  HCR6  0   0.262  -4.0519   1.8903  -0.9350
 ML1  H111  H  HCR6  0   0.272  -4.5715  -0.4794  -0.6828
 ML1  HN1   H  HNH1  0   0.401   3.7907   0.1282   1.3001
 ML1  H16   H  HNR5  0   0.407  -1.9282   3.7462  -0.5610

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
 ML1  C1   C6    single    1.526  0.020  1.526
 ML1  C1   N1    single    1.447  0.020  1.447
 ML1  C1   H11   single    0.970  0.020  1.090
 ML1  C1   H12A  single    0.970  0.020  1.090
 ML1  C2   C7    aromatic  1.368  0.020  1.368
 ML1  C2   H2    single    0.930  0.020  1.080
 ML1  C3   H31   single    0.970  0.020  1.090
 ML1  C3   H32   single    0.970  0.020  1.090
 ML1  C3   H33   single    0.970  0.020  1.090
 ML1  C4   N1    single    1.341  0.020  1.341
 ML1  C5   C4    single    1.509  0.020  1.509
 ML1  C5   H51   single    0.970  0.020  1.090
 ML1  C5   H52   single    0.970  0.020  1.090
 ML1  C5   H53   single    0.970  0.020  1.090
 ML1  C6   H61   single    0.970  0.020  1.090
 ML1  C6   H62   single    0.970  0.020  1.090
 ML1  C8   C9    aromatic  1.397  0.020  1.397
 ML1  C8   C7    aromatic  1.433  0.020  1.433
 ML1  C9   H9    single    0.930  0.020  1.080
 ML1  C12  C11   aromatic  1.385  0.020  1.385
 ML1  C12  C13   aromatic  1.389  0.020  1.389
 ML1  C12  H12   single    0.930  0.020  1.080
 ML1  C13  C8    aromatic  1.412  0.020  1.412
 ML1  C7   C6    single    1.492  0.020  1.492
 ML1  C10  O1    single    1.357  0.020  1.357
 ML1  C10  C9    aromatic  1.386  0.020  1.386
 ML1  C11  C10   aromatic  1.408  0.020  1.408
 ML1  C11  H111  single    0.930  0.020  1.080
 ML1  N1   HN1   single    0.860  0.020  1.020
 ML1  N2   C13   aromatic  1.368  0.020  1.368
 ML1  N2   C2    aromatic  1.364  0.020  1.364
 ML1  O1   C3    single    1.410  0.020  1.410
 ML1  O2   C4    double    1.225  0.020  1.225
 ML1  N2   H16   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
 ML1  H12A  C1   H11  106.87  3.000
 ML1  H12A  C1   N1   110.65  3.000
 ML1  H11   C1   N1   109.51  3.000
 ML1  H12A  C1   C6   109.38  3.000
 ML1  H11   C1   C6   110.01  3.000
 ML1  N1    C1   C6   110.36  3.000
 ML1  H2    C2   N2   120.61  3.000
 ML1  N2    C2   C7   110.41  3.000
 ML1  H2    C2   C7   128.99  3.000
 ML1  H33   C3   H32  108.63  3.000
 ML1  H33   C3   H31  108.49  3.000
 ML1  H32   C3   H31  108.47  3.000
 ML1  H33   C3   O1   112.26  3.000
 ML1  H32   C3   O1   112.26  3.000
 ML1  H31   C3   O1   106.58  3.000
 ML1  O2    C4   N1   122.37  3.000
 ML1  O2    C4   C5   121.88  3.000
 ML1  N1    C4   C5   115.75  3.000
 ML1  H53   C5   H52  108.52  3.000
 ML1  H53   C5   H51  108.22  3.000
 ML1  H52   C5   H51  107.32  3.000
 ML1  H53   C5   C4   113.78  3.000
 ML1  H52   C5   C4   109.46  3.000
 ML1  H51   C5   C4   109.33  3.000
 ML1  H62   C6   H61  106.62  3.000
 ML1  H62   C6   C7   109.57  3.000
 ML1  H61   C6   C7   110.23  3.000
 ML1  C7    C6   C1   111.93  3.000
 ML1  H62   C6   C1   109.38  3.000
 ML1  H61   C6   C1   108.96  3.000
 ML1  C7    C8   C13  107.05  3.000
 ML1  C13   C8   C9   119.62  3.000
 ML1  C7    C8   C9   133.33  3.000
 ML1  H9    C9   C10  119.86  3.000
 ML1  C10   C9   C8   119.06  3.000
 ML1  H9    C9   C8   121.08  3.000
 ML1  H12   C12  C11  120.11  3.000
 ML1  H12   C12  C13  121.53  3.000
 ML1  C11   C12  C13  118.36  3.000
 ML1  N2    C13  C12  131.16  3.000
 ML1  N2    C13  C8   107.44  3.000
 ML1  C12   C13  C8   121.39  3.000
 ML1  C8    C7   C6   126.87  3.000
 ML1  C6    C7   C2   127.09  3.000
 ML1  C8    C7   C2   106.02  3.000
 ML1  O1    C10  C11  123.25  3.000
 ML1  C11   C10  C9   120.61  3.000
 ML1  O1    C10  C9   116.14  3.000
 ML1  H111  C11  C10  120.82  3.000
 ML1  H111  C11  C12  118.22  3.000
 ML1  C10   C11  C12  120.96  3.000
 ML1  HN1   N1   C4   118.93  3.000
 ML1  HN1   N1   C1   117.98  3.000
 ML1  C4    N1   C1   123.08  3.000
 ML1  H16   N2   C13  125.85  3.000
 ML1  H16   N2   C2   125.06  3.000
 ML1  C13   N2   C2   109.08  3.000
 ML1  C10   O1   C3   118.74  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
 ML1  CONST_01  C9    C8   C7   C2    180.00   0.0  0
 ML1  CONST_02  C13   C8   C7   C2      0.00   0.0  0
 ML1  CONST_03  C12   C13  N2   C2    180.00   0.0  0
 ML1  CONST_04  C8    C13  N2   C2      0.00   0.0  0
 ML1  CONST_05  C11   C10  C9   C8      0.00   0.0  0
 ML1  CONST_06  N2    C2   C7   C8      0.00   0.0  0
 ML1  CONST_07  C11   C12  C13  C8      0.00   0.0  0
 ML1  CONST_08  C12   C13  C8   C9      0.00   0.0  0
 ML1  CONST_09  N2    C13  C8   C9    180.00   0.0  0
 ML1  CONST_10  C12   C11  C10  C9      0.00   0.0  0
 ML1  CONST_11  C7    C8   C13  C12   180.00   0.0  0
 ML1  CONST_12  C10   C11  C12  C13     0.00   0.0  0
 ML1  CONST_13  C10   C9   C8   C13     0.00   0.0  0
 ML1  CONST_14  C7    C2   N2   C13     0.00   0.0  0
 ML1  CONST_15  C10   C9   C8   C7    180.00   0.0  0
 ML1  CONST_16  N2    C13  C8   C7      0.00   0.0  0
 ML1  CONST_17  N2    C13  C12  C11   180.00   0.0  0
 ML1  CONST_18  N2    C2   C7   C6    180.00   0.0  0
 ML1  CONST_19  C9    C8   C7   C6      0.00   0.0  0
 ML1  CONST_20  C13   C8   C7   C6    180.00   0.0  0
 ML1  CONST_21  O1    C10  C9   C8    180.00   0.0  0
 ML1  CONST_22  O1    C10  C11  C12   180.00   0.0  0
 ML1  CONST_23  H2    C2   C7   C8    180.00   0.0  0
 ML1  CONST_24  H12   C12  C13  C8    180.00   0.0  0
 ML1  CONST_25  H16   N2   C13  C8    180.00   0.0  0
 ML1  CONST_26  H111  C11  C10  C9    180.00   0.0  0
 ML1  CONST_27  H9    C9   C8   C13   180.00   0.0  0
 ML1  CONST_28  C5    C4   N1   C1    180.00   0.0  0
 ML1  CONST_29  O2    C4   N1   C1      0.00   0.0  0
 ML1  CONST_30  HN1   N1   C4   C5      0.00   0.0  0
 ML1  Var_01    C2    C7   C6   C1   -104.15  30.0  2
 ML1  Var_02    C9    C10  O1   C3   -179.57  30.0  1
 ML1  Var_03    N1    C1   C6   C7   -179.35  30.0  1
 ML1  Var_04    H31   C3   O1   C10  -179.96  30.0  3
 ML1  Var_05    C6    C1   N1   C4    170.45  30.0  1
 ML1  Var_06    H51   C5   C4   N1    113.69  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
 ML1  plan-1  C2    0.020
 ML1  plan-1  C6    0.020
 ML1  plan-1  C8    0.020
 ML1  plan-1  C9    0.020
 ML1  plan-1  C12   0.020
 ML1  plan-1  C13   0.020
 ML1  plan-1  C7    0.020
 ML1  plan-1  C10   0.020
 ML1  plan-1  C11   0.020
 ML1  plan-1  N2    0.020
 ML1  plan-1  O1    0.020
 ML1  plan-1  H2    0.020
 ML1  plan-1  H9    0.020
 ML1  plan-1  H12   0.020
 ML1  plan-1  H111  0.020
 ML1  plan-1  H16   0.020
 ML1  plan-2  C1    0.020
 ML1  plan-2  C4    0.020
 ML1  plan-2  C5    0.020
 ML1  plan-2  N1    0.020
 ML1  plan-2  O2    0.020
 ML1  plan-2  HN1   0.020

