Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

tag_button

FMODB ID: NNKGQ

Calculation Name: 1K7K-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1K7K

Chain ID: A

ChEMBL ID:

UniProt ID: P52061

Base Structure: X-ray

Registration Date: 2023-09-23

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 209
LigandCharge DGL=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2201199.174042
FMO2-HF: Nuclear repulsion 2123047.385739
FMO2-HF: Total energy -78151.788303
FMO2-MP2: Total energy -78382.095953


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:-11:SER)


Summations of interaction energy for fragment #1(A:-11:SER)
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.
-4.84-15.97126.456-8.347-6.98-0.039
Interaction energy analysis for fragmet #1(A:-11:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : 0.005
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].
3A-9GLY00.0530.0243.821-2.909-1.4550.006-0.790-0.6710.003
4A-8ARG10.8200.8646.3940.5560.5560.0000.0000.0000.000
5A-7DGL-1-0.782-0.8639.300-0.367-0.3670.0000.0000.0000.000
6A-6ASN00.0160.0197.0840.1350.1350.0000.0000.0000.000
7A-5LEU00.0290.0288.1720.0660.0660.0000.0000.0000.000
8A-4TYR00.0020.00711.610-0.035-0.0350.0000.0000.0000.000
9A-3PHE00.0210.0019.2750.0090.0090.0000.0000.0000.000
10A-2GLN0-0.032-0.02115.0310.0030.0030.0000.0000.0000.000
11A-1GLY0-0.014-0.01418.0650.0200.0200.0000.0000.0000.000
12A0HIS0-0.0090.02220.4340.0010.0010.0000.0000.0000.000
13A1MET0-0.002-0.00718.959-0.005-0.0050.0000.0000.0000.000
14A2GLN0-0.067-0.03316.187-0.013-0.0130.0000.0000.0000.000
15A3LYS10.8930.95018.3800.0410.0410.0000.0000.0000.000
16A4VAL0-0.0050.00415.552-0.014-0.0140.0000.0000.0000.000
17A5VAL00.0090.02518.8500.0140.0140.0000.0000.0000.000
18A6LEU00.001-0.00618.6430.0030.0030.0000.0000.0000.000
19A7ALA00.0120.00420.662-0.001-0.0010.0000.0000.0000.000
20A8THR0-0.072-0.05022.6700.0060.0060.0000.0000.0000.000
21A9GLY00.1360.06225.318-0.004-0.0040.0000.0000.0000.000
22A10ASN0-0.093-0.03826.1980.0030.0030.0000.0000.0000.000
23A11VAL00.1230.05226.5810.0020.0020.0000.0000.0000.000
24A12GLY00.0040.00327.0850.0010.0010.0000.0000.0000.000
25A13LYS10.9690.97322.718-0.048-0.0480.0000.0000.0000.000
26A14VAL00.0510.03722.2230.0050.0050.0000.0000.0000.000
27A15ARG10.9270.95922.752-0.035-0.0350.0000.0000.0000.000
28A16GLU-1-0.875-0.93320.4360.0920.0920.0000.0000.0000.000
29A17LEU00.022-0.00215.5060.0100.0100.0000.0000.0000.000
30A18ALA00.006-0.00618.444-0.002-0.0020.0000.0000.0000.000
31A19SER0-0.036-0.02520.120-0.004-0.0040.0000.0000.0000.000
32A20LEU0-0.012-0.00716.4310.0030.0030.0000.0000.0000.000
33A21LEU00.010-0.01212.9350.0100.0100.0000.0000.0000.000
34A22SER0-0.035-0.00416.025-0.019-0.0190.0000.0000.0000.000
35A23ASP-1-0.965-0.96515.0880.0690.0690.0000.0000.0000.000
36A24PHE0-0.003-0.00210.901-0.004-0.0040.0000.0000.0000.000
37A25GLY0-0.010-0.00614.244-0.040-0.0400.0000.0000.0000.000
38A26LEU0-0.054-0.02312.588-0.014-0.0140.0000.0000.0000.000
39A27ASP-1-0.856-0.92816.969-0.004-0.0040.0000.0000.0000.000
40A28ILE0-0.022-0.00316.785-0.005-0.0050.0000.0000.0000.000
41A29VAL00.040-0.00220.6740.0050.0050.0000.0000.0000.000
42A30ALA0-0.0060.01223.3220.0000.0000.0000.0000.0000.000
43A31GLN00.0520.00824.687-0.006-0.0060.0000.0000.0000.000
44A32THR00.0300.00626.249-0.001-0.0010.0000.0000.0000.000
45A33ASP-1-0.955-0.95528.2110.0010.0010.0000.0000.0000.000
46A34LEU0-0.103-0.06225.056-0.003-0.0030.0000.0000.0000.000
47A35GLY0-0.0020.01029.358-0.003-0.0030.0000.0000.0000.000
48A36VAL0-0.046-0.01526.467-0.002-0.0020.0000.0000.0000.000
49A37ASP-1-0.900-0.94429.682-0.006-0.0060.0000.0000.0000.000
50A38SER0-0.069-0.06328.618-0.001-0.0010.0000.0000.0000.000
51A39ALA0-0.0020.00826.126-0.002-0.0020.0000.0000.0000.000
52A40GLU-1-0.877-0.92728.0510.0020.0020.0000.0000.0000.000
53A41GLU-1-0.962-0.99625.1140.0170.0170.0000.0000.0000.000
54A42THR0-0.038-0.02625.7860.0000.0000.0000.0000.0000.000
55A43GLY00.0120.01323.420-0.003-0.0030.0000.0000.0000.000
56A44LEU0-0.002-0.00823.7630.0030.0030.0000.0000.0000.000
57A45THR0-0.035-0.05019.6270.0060.0060.0000.0000.0000.000
58A46PHE00.0040.00618.9140.0000.0000.0000.0000.0000.000
59A47ILE00.0150.01012.8010.0040.0040.0000.0000.0000.000
60A48GLU-1-0.865-0.91317.022-0.009-0.0090.0000.0000.0000.000
61A49ASN00.0270.00319.439-0.010-0.0100.0000.0000.0000.000
62A50ALA0-0.0140.00517.067-0.004-0.0040.0000.0000.0000.000
63A51ILE00.005-0.01014.310-0.006-0.0060.0000.0000.0000.000
64A52LEU0-0.028-0.00417.772-0.012-0.0120.0000.0000.0000.000
65A53LYS10.8240.91721.237-0.037-0.0370.0000.0000.0000.000
66A54ALA00.0020.00117.630-0.005-0.0050.0000.0000.0000.000
67A55ARG10.9480.97217.9480.0300.0300.0000.0000.0000.000
68A56HIS0-0.035-0.01620.630-0.011-0.0110.0000.0000.0000.000
69A57ALA00.0560.02821.788-0.004-0.0040.0000.0000.0000.000
70A58ALA00.0080.01619.715-0.005-0.0050.0000.0000.0000.000
71A59LYS10.9050.95521.8080.0490.0490.0000.0000.0000.000
72A60VAL0-0.043-0.02624.586-0.003-0.0030.0000.0000.0000.000
73A61THR0-0.022-0.02723.628-0.002-0.0020.0000.0000.0000.000
74A62ALA0-0.057-0.01523.522-0.002-0.0020.0000.0000.0000.000
75A63LEU0-0.045-0.00820.645-0.010-0.0100.0000.0000.0000.000
76A64PRO00.0150.01315.4390.0050.0050.0000.0000.0000.000
77A65ALA00.0050.00316.7070.0130.0130.0000.0000.0000.000
78A66ILE00.0050.00714.1070.0070.0070.0000.0000.0000.000
79A67ALA0-0.0040.00216.420-0.008-0.0080.0000.0000.0000.000
80A68ASP-1-0.898-0.93116.8600.0880.0880.0000.0000.0000.000
81A69ASP-1-0.747-0.87618.8610.0230.0230.0000.0000.0000.000
82A70SER0-0.054-0.04220.0190.0160.0160.0000.0000.0000.000
83A71GLY0-0.012-0.00322.453-0.009-0.0090.0000.0000.0000.000
84A72LEU0-0.0230.00024.2340.0070.0070.0000.0000.0000.000
85A73ALA0-0.031-0.01124.157-0.005-0.0050.0000.0000.0000.000
86A74VAL00.029-0.00826.1550.0040.0040.0000.0000.0000.000
87A75ASP-1-0.879-0.93526.2980.0350.0350.0000.0000.0000.000
88A76VAL00.000-0.00628.595-0.004-0.0040.0000.0000.0000.000
89A77LEU0-0.048-0.02131.156-0.003-0.0030.0000.0000.0000.000
90A78GLY0-0.008-0.00328.744-0.002-0.0020.0000.0000.0000.000
91A79GLY0-0.010-0.00326.140-0.002-0.0020.0000.0000.0000.000
92A80ALA0-0.0080.01526.9440.0030.0030.0000.0000.0000.000
93A81PRO00.039-0.01129.6230.0020.0020.0000.0000.0000.000
94A82GLY00.0600.04225.720-0.004-0.0040.0000.0000.0000.000
95A83ILE00.0170.02423.7900.0040.0040.0000.0000.0000.000
96A84TYR0-0.029-0.01626.341-0.002-0.0020.0000.0000.0000.000
97A85SER0-0.022-0.03027.5090.0010.0010.0000.0000.0000.000
98A86ALA00.0490.02829.5670.0000.0000.0000.0000.0000.000
99A87ARG11.0071.00529.289-0.011-0.0110.0000.0000.0000.000
100A88TYR00.0230.02933.145-0.003-0.0030.0000.0000.0000.000
101A89SER0-0.096-0.08034.618-0.002-0.0020.0000.0000.0000.000
102A90GLY0-0.019-0.00237.162-0.001-0.0010.0000.0000.0000.000
103A91GLU-1-0.902-0.95238.4710.0050.0050.0000.0000.0000.000
104A92ASP-1-0.912-0.95940.4950.0080.0080.0000.0000.0000.000
105A93ALA0-0.073-0.02736.9350.0010.0010.0000.0000.0000.000
106A94THR00.0220.00138.1130.0000.0000.0000.0000.0000.000
107A95ASP-1-0.793-0.91334.4410.0310.0310.0000.0000.0000.000
108A96GLN00.0420.02236.6190.0020.0020.0000.0000.0000.000
109A97LYS10.9150.96239.718-0.013-0.0130.0000.0000.0000.000
110A98ASN00.0290.02934.313-0.003-0.0030.0000.0000.0000.000
111A99LEU00.0270.00636.0970.0000.0000.0000.0000.0000.000
112A100GLN0-0.012-0.01037.0690.0010.0010.0000.0000.0000.000
113A101LYS10.9010.97037.472-0.014-0.0140.0000.0000.0000.000
114A102LEU0-0.038-0.01132.709-0.001-0.0010.0000.0000.0000.000
115A103LEU00.0320.00436.8490.0000.0000.0000.0000.0000.000
116A104GLU-1-0.848-0.90439.3920.0140.0140.0000.0000.0000.000
117A105THR0-0.094-0.05036.462-0.001-0.0010.0000.0000.0000.000
118A106MET00.0030.00733.6420.0000.0000.0000.0000.0000.000
119A107LYS10.8480.93338.489-0.012-0.0120.0000.0000.0000.000
120A108ASP-1-0.908-0.95341.8300.0140.0140.0000.0000.0000.000
121A109VAL0-0.072-0.02035.808-0.001-0.0010.0000.0000.0000.000
122A110PRO00.0390.01338.4700.0010.0010.0000.0000.0000.000
123A111ASP-1-0.779-0.90237.7700.0280.0280.0000.0000.0000.000
124A112ASP-1-0.980-0.97935.8640.0290.0290.0000.0000.0000.000
125A113GLN0-0.024-0.01133.7910.0000.0000.0000.0000.0000.000
126A114ARG10.7920.87433.600-0.029-0.0290.0000.0000.0000.000
127A115GLN0-0.0130.00828.1500.0010.0010.0000.0000.0000.000
128A116ALA00.0340.01327.478-0.004-0.0040.0000.0000.0000.000
129A117ARG10.9190.95318.757-0.076-0.0760.0000.0000.0000.000
130A118PHE00.0100.02623.799-0.007-0.0070.0000.0000.0000.000
131A119HIS00.0470.02619.4510.0200.0200.0000.0000.0000.000
132A120CYS0-0.071-0.02418.335-0.007-0.0070.0000.0000.0000.000
133A121VAL00.0160.01214.1410.0240.0240.0000.0000.0000.000
134A122LEU00.0340.02112.576-0.025-0.0250.0000.0000.0000.000
135A123VAL0-0.036-0.03112.4870.0460.0460.0000.0000.0000.000
136A124TYR00.002-0.02710.631-0.028-0.0280.0000.0000.0000.000
137A125LEU0-0.027-0.00111.7720.0090.0090.0000.0000.0000.000
138A126ARG10.8280.8927.7300.3540.3540.0000.0000.0000.000
139A127HIS00.0440.01214.6060.0160.0160.0000.0000.0000.000
140A128ALA0-0.011-0.00917.5390.0060.0060.0000.0000.0000.000
141A129GLU-1-0.904-0.95619.144-0.073-0.0730.0000.0000.0000.000
142A130ASP-1-0.857-0.90212.623-0.167-0.1670.0000.0000.0000.000
143A131PRO00.017-0.00113.0290.0270.0270.0000.0000.0000.000
144A132THR0-0.088-0.0398.705-0.031-0.0310.0000.0000.0000.000
145A133PRO00.0270.0309.3320.0320.0320.0000.0000.0000.000
146A134LEU00.0090.0035.3600.1680.1680.0000.0000.0000.000
147A135VAL00.003-0.0097.925-0.172-0.1720.0000.0000.0000.000
148A136CYS0-0.0460.0068.5770.1570.1570.0000.0000.0000.000
149A137HIS0-0.035-0.04610.847-0.064-0.0640.0000.0000.0000.000
150A138GLY00.0190.02913.4970.0170.0170.0000.0000.0000.000
151A139SER0-0.049-0.03716.031-0.033-0.0330.0000.0000.0000.000
152A140TRP00.0490.02218.9610.0100.0100.0000.0000.0000.000
153A141PRO0-0.010-0.00421.884-0.009-0.0090.0000.0000.0000.000
154A142GLY00.0340.01224.7130.0040.0040.0000.0000.0000.000
155A143VAL0-0.036-0.01228.421-0.003-0.0030.0000.0000.0000.000
156A144ILE0-0.038-0.01530.8390.0010.0010.0000.0000.0000.000
157A145THR0-0.0020.00033.893-0.001-0.0010.0000.0000.0000.000
158A146ARG10.8320.89837.284-0.026-0.0260.0000.0000.0000.000
159A147GLU-1-0.860-0.93140.5810.0270.0270.0000.0000.0000.000
160A148PRO0-0.042-0.02039.1190.0020.0020.0000.0000.0000.000
161A149ALA00.0150.01838.589-0.001-0.0010.0000.0000.0000.000
162A150GLY00.0460.02337.6220.0030.0030.0000.0000.0000.000
163A151THR0-0.045-0.03738.415-0.001-0.0010.0000.0000.0000.000
164A152GLY0-0.0030.00834.923-0.001-0.0010.0000.0000.0000.000
165A153GLY0-0.064-0.03631.4560.0010.0010.0000.0000.0000.000
166A154PHE0-0.025-0.01927.083-0.002-0.0020.0000.0000.0000.000
167A155GLY00.0030.00631.6670.0030.0030.0000.0000.0000.000
168A156TYR0-0.056-0.06130.372-0.002-0.0020.0000.0000.0000.000
169A157ASP-1-0.743-0.85729.6610.0580.0580.0000.0000.0000.000
170A158PRO00.019-0.00632.2330.0010.0010.0000.0000.0000.000
171A159ILE00.0040.01534.080-0.001-0.0010.0000.0000.0000.000
172A160PHE0-0.0330.00526.295-0.001-0.0010.0000.0000.0000.000
173A161PHE00.0660.02531.9920.0030.0030.0000.0000.0000.000
174A162VAL00.0420.01327.9600.0020.0020.0000.0000.0000.000
175A163PRO0-0.006-0.01329.6700.0010.0010.0000.0000.0000.000
176A164SER0-0.064-0.03028.136-0.002-0.0020.0000.0000.0000.000
177A165GLU-1-0.904-0.95428.5430.0910.0910.0000.0000.0000.000
178A166GLY0-0.055-0.01831.919-0.003-0.0030.0000.0000.0000.000
179A167LYS10.9200.96533.740-0.060-0.0600.0000.0000.0000.000
180A168THR0-0.014-0.01433.1890.0040.0040.0000.0000.0000.000
181A169ALA00.0080.00329.5460.0020.0020.0000.0000.0000.000
182A170ALA0-0.062-0.01531.1730.0020.0020.0000.0000.0000.000
183A171GLU-1-0.865-0.94334.1040.0420.0420.0000.0000.0000.000
184A172LEU0-0.0130.03128.8210.0010.0010.0000.0000.0000.000
185A173THR00.0080.00731.871-0.003-0.0030.0000.0000.0000.000
186A174ARG10.8520.89929.481-0.052-0.0520.0000.0000.0000.000
187A175GLU-1-0.891-0.93627.5550.0820.0820.0000.0000.0000.000
188A176GLU-1-0.843-0.92226.7390.0770.0770.0000.0000.0000.000
189A177LYS10.8370.90426.143-0.059-0.0590.0000.0000.0000.000
190A178SER0-0.037-0.05223.8850.0060.0060.0000.0000.0000.000
191A179ALA0-0.0260.00722.1770.0130.0130.0000.0000.0000.000
192A180ILE0-0.0020.00421.8100.0170.0170.0000.0000.0000.000
193A181SER0-0.0310.00122.1980.0020.0020.0000.0000.0000.000
194A182HIS00.0320.01219.6140.0220.0220.0000.0000.0000.000
195A183ARG10.8330.87918.209-0.071-0.0710.0000.0000.0000.000
196A184GLY00.0640.04217.7460.0120.0120.0000.0000.0000.000
197A185GLN0-0.100-0.06716.0330.0410.0410.0000.0000.0000.000
198A186ALA00.012-0.00113.7820.0440.0440.0000.0000.0000.000
199A187LEU00.000-0.00112.8550.0350.0350.0000.0000.0000.000
200A188LYS10.9640.99812.771-0.298-0.2980.0000.0000.0000.000
201A189LEU0-0.034-0.0199.5280.0600.0600.0000.0000.0000.000
202A190LEU00.016-0.0028.4760.1030.1030.0000.0000.0000.000
203A191LEU0-0.024-0.0178.942-0.050-0.0500.0000.0000.0000.000
204A192ASP-1-0.936-0.9646.2421.6841.6840.0000.0000.0000.000
205A193ALA00.0260.0034.0230.2000.351-0.001-0.017-0.1330.000
206A194LEU0-0.037-0.0153.689-1.473-1.2320.002-0.127-0.117-0.001
207A195ARG10.8930.9666.146-0.665-0.6650.0000.0000.0000.000
208A196ASN0-0.064-0.0394.595-0.340-0.235-0.001-0.063-0.0400.000
209A197GLY00.0320.0192.090-2.270-15.35226.450-7.350-6.019-0.041