FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

tag_button

FMODB ID: KG343

Calculation Name: 1YQF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YQF

Chain ID: A

ChEMBL ID:

UniProt ID: Q4Q7K6

Base Structure: X-ray

Registration Date: 2023-09-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1809265.567645
FMO2-HF: Nuclear repulsion 1736353.743869
FMO2-HF: Total energy -72911.823775
FMO2-MP2: Total energy -73123.123142


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:14:ALA)


Summations of interaction energy for fragment #1(A:14:ALA)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-8.533-4.1332.84-2.903-4.336-0.023
Interaction energy analysis for fragmet #1(A:14:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : -0.008
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A16ASP-1-0.902-0.9592.427-8.832-5.5601.618-2.118-2.771-0.019
4A17ALA00.0500.0312.3380.0720.9391.218-0.746-1.339-0.004
5A18ALA00.0190.0083.8411.1331.3940.004-0.039-0.2260.000
6A19LEU0-0.014-0.0016.1850.6900.6900.0000.0000.0000.000
7A20ALA00.0320.0187.1360.3980.3980.0000.0000.0000.000
8A21ASP-1-0.936-0.9797.541-1.301-1.3010.0000.0000.0000.000
9A22ALA0-0.045-0.02310.0800.2300.2300.0000.0000.0000.000
10A23THR00.0370.01611.4400.1230.1230.0000.0000.0000.000
11A24ARG10.8710.94811.3670.8090.8090.0000.0000.0000.000
12A25ARG10.9220.95810.6910.6900.6900.0000.0000.0000.000
13A26GLU-1-0.858-0.91815.998-0.290-0.2900.0000.0000.0000.000
14A27LEU0-0.023-0.01316.7660.0440.0440.0000.0000.0000.000
15A28GLU-1-0.953-0.98016.983-0.406-0.4060.0000.0000.0000.000
16A29GLU-1-0.968-0.97620.002-0.215-0.2150.0000.0000.0000.000
17A30GLU-1-0.807-0.91621.779-0.199-0.1990.0000.0000.0000.000
18A31MET0-0.086-0.04822.3850.0330.0330.0000.0000.0000.000
19A32GLY0-0.039-0.01224.5910.0160.0160.0000.0000.0000.000
20A33ARG10.8150.93226.2350.1870.1870.0000.0000.0000.000
21A34SER0-0.068-0.04528.4460.0040.0040.0000.0000.0000.000
22A35ASP-1-0.886-0.94930.771-0.127-0.1270.0000.0000.0000.000
23A36LYS10.8870.96426.8940.1980.1980.0000.0000.0000.000
24A37PRO00.0120.00131.1200.0090.0090.0000.0000.0000.000
25A38GLU-1-0.914-0.95333.806-0.104-0.1040.0000.0000.0000.000
26A39GLN0-0.059-0.02836.2060.0040.0040.0000.0000.0000.000
27A40PRO0-0.0040.01837.5140.0040.0040.0000.0000.0000.000
28A41THR0-0.007-0.01641.007-0.001-0.0010.0000.0000.0000.000
29A42PRO0-0.019-0.00243.3310.0020.0020.0000.0000.0000.000
30A43PRO00.0310.00545.6630.0020.0020.0000.0000.0000.000
31A44ALA00.006-0.00249.312-0.001-0.0010.0000.0000.0000.000
32A45GLY0-0.045-0.02451.9840.0010.0010.0000.0000.0000.000
33A46TRP0-0.0080.00047.748-0.001-0.0010.0000.0000.0000.000
34A47GLN0-0.0010.00244.339-0.002-0.0020.0000.0000.0000.000
35A48VAL00.0240.01640.0860.0010.0010.0000.0000.0000.000
36A49VAL0-0.012-0.00141.053-0.002-0.0020.0000.0000.0000.000
37A50ARG10.9660.99730.7950.1560.1560.0000.0000.0000.000
38A51LYS10.9650.99136.7950.1080.1080.0000.0000.0000.000
39A52PRO0-0.003-0.00535.394-0.008-0.0080.0000.0000.0000.000
40A53GLY0-0.008-0.00731.1040.0000.0000.0000.0000.0000.000
41A54THR0-0.079-0.04530.428-0.005-0.0050.0000.0000.0000.000
42A55CYS00.0710.03930.582-0.004-0.0040.0000.0000.0000.000
43A56THR0-0.052-0.01433.0660.0080.0080.0000.0000.0000.000
44A57PHE0-0.015-0.02134.181-0.004-0.0040.0000.0000.0000.000
45A58ASP-1-0.781-0.87539.393-0.081-0.0810.0000.0000.0000.000
46A59LEU0-0.018-0.00243.137-0.001-0.0010.0000.0000.0000.000
47A60THR0-0.025-0.01945.6560.0040.0040.0000.0000.0000.000
48A61LYS10.9380.96248.6760.0540.0540.0000.0000.0000.000
49A62SER0-0.0100.01052.1830.0000.0000.0000.0000.0000.000
50A63PHE0-0.040-0.03255.8160.0000.0000.0000.0000.0000.000
51A64GLU-1-0.905-0.94758.580-0.040-0.0400.0000.0000.0000.000
52A65GLY0-0.082-0.04260.9430.0010.0010.0000.0000.0000.000
53A66GLU-1-0.834-0.89057.763-0.045-0.0450.0000.0000.0000.000
54A67ASP-1-0.926-0.96553.411-0.055-0.0550.0000.0000.0000.000
55A68LEU0-0.024-0.02152.5680.0000.0000.0000.0000.0000.000
56A69VAL0-0.033-0.02946.545-0.002-0.0020.0000.0000.0000.000
57A70VAL00.0160.02445.3410.0020.0020.0000.0000.0000.000
58A71ARG10.8000.89441.5500.0770.0770.0000.0000.0000.000
59A72TYR00.0260.01138.3190.0040.0040.0000.0000.0000.000
60A73SER0-0.005-0.01834.665-0.006-0.0060.0000.0000.0000.000
61A74THR00.0320.00832.0940.0050.0050.0000.0000.0000.000
62A75ASN0-0.0240.00229.916-0.013-0.0130.0000.0000.0000.000
63A76GLN00.0210.01229.6490.0000.0000.0000.0000.0000.000
64A77ASP-1-0.920-0.96331.079-0.100-0.1000.0000.0000.0000.000
65A78SER0-0.074-0.03529.441-0.002-0.0020.0000.0000.0000.000
66A79ASP-1-0.881-0.93730.856-0.074-0.0740.0000.0000.0000.000
67A80LYS10.8990.94434.1050.0680.0680.0000.0000.0000.000
68A81ALA00.0100.01032.927-0.004-0.0040.0000.0000.0000.000
69A82ASN0-0.057-0.04534.8740.0020.0020.0000.0000.0000.000
70A83SER00.0060.01938.4480.0010.0010.0000.0000.0000.000
71A84HIS00.0620.02836.576-0.006-0.0060.0000.0000.0000.000
72A85ASN0-0.019-0.00840.3460.0070.0070.0000.0000.0000.000
73A86ILE0-0.019-0.01241.645-0.005-0.0050.0000.0000.0000.000
74A87PHE0-0.043-0.01041.6200.0030.0030.0000.0000.0000.000
75A88VAL00.0070.00646.305-0.002-0.0020.0000.0000.0000.000
76A89TYR0-0.025-0.02745.9060.0010.0010.0000.0000.0000.000
77A90ILE0-0.011-0.00651.1630.0000.0000.0000.0000.0000.000
78A91THR0-0.046-0.03953.8340.0000.0000.0000.0000.0000.000
79A92GLN00.0400.02355.9540.0000.0000.0000.0000.0000.000
80A93LYS11.0090.99058.8810.0380.0380.0000.0000.0000.000
81A94ASN0-0.084-0.05760.760-0.001-0.0010.0000.0000.0000.000
82A95GLY00.0500.03957.4840.0000.0000.0000.0000.0000.000
83A96GLN00.0310.02256.731-0.001-0.0010.0000.0000.0000.000
84A97THR0-0.037-0.01052.481-0.001-0.0010.0000.0000.0000.000
85A98MET0-0.0190.00255.0660.0010.0010.0000.0000.0000.000
86A99GLN0-0.024-0.02147.654-0.002-0.0020.0000.0000.0000.000
87A100ALA00.001-0.00751.2480.0020.0020.0000.0000.0000.000
88A101ASP-1-0.798-0.89247.267-0.061-0.0610.0000.0000.0000.000
89A102LEU0-0.016-0.02947.3850.0030.0030.0000.0000.0000.000
90A103SER0-0.0060.00444.799-0.003-0.0030.0000.0000.0000.000
91A104ILE0-0.070-0.01943.2420.0030.0030.0000.0000.0000.000
92A105GLU-1-0.888-0.95643.682-0.057-0.0570.0000.0000.0000.000
93A106GLU-1-0.931-0.96844.901-0.052-0.0520.0000.0000.0000.000
94A107GLY0-0.066-0.02845.8290.0020.0020.0000.0000.0000.000
95A108GLU-1-0.928-0.94847.363-0.042-0.0420.0000.0000.0000.000
96A109LEU0-0.053-0.03548.316-0.002-0.0020.0000.0000.0000.000
97A110VAL00.0350.03349.1750.0030.0030.0000.0000.0000.000
98A111LEU0-0.035-0.02749.803-0.002-0.0020.0000.0000.0000.000
99A112ASN00.002-0.01547.4060.0040.0040.0000.0000.0000.000
100A113ASN0-0.080-0.04650.5540.0010.0010.0000.0000.0000.000
101A114ILE00.0460.02852.245-0.002-0.0020.0000.0000.0000.000
102A115ARG10.9100.97849.4710.0520.0520.0000.0000.0000.000
103A116PHE0-0.011-0.02254.976-0.001-0.0010.0000.0000.0000.000
104A117TYR0-0.004-0.01549.7640.0010.0010.0000.0000.0000.000
105A118ASP-1-0.908-0.95855.822-0.039-0.0390.0000.0000.0000.000
106A119GLU-1-0.973-0.98353.865-0.048-0.0480.0000.0000.0000.000
107A120ALA00.021-0.00252.460-0.001-0.0010.0000.0000.0000.000
108A121ALA00.0020.00449.697-0.002-0.0020.0000.0000.0000.000
109A122LEU00.0330.02948.955-0.002-0.0020.0000.0000.0000.000
110A123ALA0-0.0010.00549.456-0.001-0.0010.0000.0000.0000.000
111A124LYS10.9360.96846.7490.0600.0600.0000.0000.0000.000
112A125ASP-1-0.891-0.92745.132-0.070-0.0700.0000.0000.0000.000
113A126THR0-0.036-0.02839.736-0.002-0.0020.0000.0000.0000.000
114A127GLY00.001-0.01939.3070.0010.0010.0000.0000.0000.000
115A128ALA00.0250.00738.7240.0020.0020.0000.0000.0000.000
116A129GLU-1-0.885-0.95740.632-0.056-0.0560.0000.0000.0000.000
117A130ALA0-0.062-0.02043.7540.0030.0030.0000.0000.0000.000
118A131GLU-1-0.869-0.93642.238-0.068-0.0680.0000.0000.0000.000
119A132ALA00.000-0.00644.4850.0030.0030.0000.0000.0000.000
120A133LYS10.9550.97446.0290.0610.0610.0000.0000.0000.000
121A134ARG10.8530.93644.1650.0680.0680.0000.0000.0000.000
122A135ASN0-0.049-0.02444.3970.0020.0020.0000.0000.0000.000
123A136GLU-1-0.976-0.96848.862-0.040-0.0400.0000.0000.0000.000
124A137LEU0-0.066-0.02452.1390.0020.0020.0000.0000.0000.000
125A138TYR0-0.013-0.00553.7820.0000.0000.0000.0000.0000.000
126A139THR0-0.006-0.01250.9690.0000.0000.0000.0000.0000.000
127A140GLY00.0420.02553.873-0.001-0.0010.0000.0000.0000.000
128A141PRO0-0.062-0.02556.4120.0000.0000.0000.0000.0000.000
129A142LEU00.0310.00654.209-0.002-0.0020.0000.0000.0000.000
130A143VAL00.0390.01354.2950.0010.0010.0000.0000.0000.000
131A144HIS0-0.010-0.00755.5440.0000.0000.0000.0000.0000.000
132A145GLU-1-0.972-0.98957.221-0.028-0.0280.0000.0000.0000.000
133A146LEU0-0.078-0.02058.8700.0010.0010.0000.0000.0000.000
134A147ASP-1-0.888-0.94061.766-0.026-0.0260.0000.0000.0000.000
135A148TYR0-0.016-0.01961.825-0.001-0.0010.0000.0000.0000.000
136A149ASP-1-0.902-0.95563.477-0.028-0.0280.0000.0000.0000.000
137A150LEU0-0.011-0.01062.029-0.001-0.0010.0000.0000.0000.000
138A151LEU00.0580.02456.919-0.001-0.0010.0000.0000.0000.000
139A152ASN00.0430.02659.578-0.003-0.0030.0000.0000.0000.000
140A153CYS0-0.059-0.03761.392-0.001-0.0010.0000.0000.0000.000
141A154VAL0-0.022-0.00757.183-0.001-0.0010.0000.0000.0000.000
142A155MET00.0530.03553.618-0.002-0.0020.0000.0000.0000.000
143A156THR00.0140.01857.613-0.001-0.0010.0000.0000.0000.000
144A157TYR0-0.082-0.04757.9090.0000.0000.0000.0000.0000.000
145A158LEU00.008-0.00553.570-0.001-0.0010.0000.0000.0000.000
146A159GLU-1-0.894-0.93455.828-0.044-0.0440.0000.0000.0000.000
147A160LYS10.8800.93456.8920.0360.0360.0000.0000.0000.000
148A161ARG10.7530.87055.8340.0440.0440.0000.0000.0000.000
149A162GLY0-0.044-0.02453.724-0.002-0.0020.0000.0000.0000.000
150A163VAL0-0.0080.00550.521-0.003-0.0030.0000.0000.0000.000
151A164ASP-1-0.812-0.92351.567-0.053-0.0530.0000.0000.0000.000
152A165GLU-1-0.889-0.95749.943-0.051-0.0510.0000.0000.0000.000
153A166LYS10.8890.94848.6480.0500.0500.0000.0000.0000.000
154A167LEU0-0.029-0.00246.072-0.004-0.0040.0000.0000.0000.000
155A168GLY00.0440.01045.607-0.004-0.0040.0000.0000.0000.000
156A169GLU-1-0.906-0.95543.885-0.070-0.0700.0000.0000.0000.000
157A170PHE00.0140.00441.734-0.005-0.0050.0000.0000.0000.000
158A171VAL00.0160.00740.536-0.006-0.0060.0000.0000.0000.000
159A172VAL00.0050.01539.297-0.007-0.0070.0000.0000.0000.000
160A173LEU00.0160.00137.972-0.007-0.0070.0000.0000.0000.000
161A174TYR0-0.049-0.03736.531-0.008-0.0080.0000.0000.0000.000
162A175SER0-0.016-0.02335.256-0.009-0.0090.0000.0000.0000.000
163A176PHE00.0030.01033.342-0.008-0.0080.0000.0000.0000.000
164A177TRP0-0.029-0.00632.104-0.010-0.0100.0000.0000.0000.000
165A178ALA0-0.017-0.02831.460-0.011-0.0110.0000.0000.0000.000
166A179GLU-1-0.915-0.94927.330-0.193-0.1930.0000.0000.0000.000
167A180GLN0-0.088-0.05825.739-0.005-0.0050.0000.0000.0000.000
168A181GLN0-0.067-0.03426.439-0.024-0.0240.0000.0000.0000.000
169A182ASP-1-0.901-0.95525.962-0.211-0.2110.0000.0000.0000.000
170A183TYR00.0080.01620.491-0.043-0.0430.0000.0000.0000.000
171A184GLU-1-0.808-0.91421.682-0.267-0.2670.0000.0000.0000.000
172A185ALA0-0.017-0.01321.093-0.038-0.0380.0000.0000.0000.000
173A186TRP0-0.029-0.01617.809-0.053-0.0530.0000.0000.0000.000
174A187LEU00.0150.01417.295-0.064-0.0640.0000.0000.0000.000
175A188THR0-0.023-0.00515.984-0.084-0.0840.0000.0000.0000.000
176A189THR0-0.074-0.04516.137-0.051-0.0510.0000.0000.0000.000
177A190MET00.0050.00812.837-0.058-0.0580.0000.0000.0000.000
178A191ASN0-0.045-0.02011.741-0.090-0.0900.0000.0000.0000.000
179A192LYS10.9390.96511.2880.3140.3140.0000.0000.0000.000
180A193PHE0-0.089-0.05011.487-0.016-0.0160.0000.0000.0000.000
181A194ALA0-0.040-0.0067.773-0.035-0.0350.0000.0000.0000.000
182A195SER0-0.060-0.0116.922-0.317-0.3170.0000.0000.0000.000