Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: K9893

Calculation Name: 1VK0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VK0

Chain ID: A

ChEMBL ID:

UniProt ID: Q9FNG3

Base Structure: X-ray

Registration Date: 2023-06-22

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 OptAll
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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2383373.835863
FMO2-HF: Nuclear repulsion 2303459.450878
FMO2-HF: Total energy -79914.384986
FMO2-MP2: Total energy -80152.637667


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:1:SER)


Summations of interaction energy for fragment #1(A:1: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.
-0.2350.757-0.004-0.383-0.6060.002
Interaction energy analysis for fragmet #1(A:1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.020
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].
3A3SER0-0.008-0.0193.858-0.7470.245-0.004-0.383-0.6060.002
4A4PHE00.0420.0056.1610.3670.3670.0000.0000.0000.000
5A5ASP-1-0.804-0.8706.936-1.193-1.1930.0000.0000.0000.000
6A6GLY00.0230.0299.5780.0280.0280.0000.0000.0000.000
7A7PRO00.0000.01613.070-0.061-0.0610.0000.0000.0000.000
8A8LYS10.8640.93414.1340.4750.4750.0000.0000.0000.000
9A9PHE00.0410.02217.552-0.008-0.0080.0000.0000.0000.000
10A10LYS10.8370.92821.2330.1610.1610.0000.0000.0000.000
11A11MET00.0250.03422.3160.0170.0170.0000.0000.0000.000
12A12THR00.015-0.00825.629-0.008-0.0080.0000.0000.0000.000
13A13ASP-1-0.783-0.85525.707-0.048-0.0480.0000.0000.0000.000
14A14GLY0-0.057-0.03126.471-0.003-0.0030.0000.0000.0000.000
15A15SER0-0.072-0.06421.706-0.023-0.0230.0000.0000.0000.000
16A16TYR00.014-0.02018.942-0.007-0.0070.0000.0000.0000.000
17A17VAL00.0610.05718.215-0.011-0.0110.0000.0000.0000.000
18A18GLN0-0.031-0.02710.908-0.017-0.0170.0000.0000.0000.000
19A19THR0-0.018-0.02714.6800.0840.0840.0000.0000.0000.000
20A20LYS10.7870.8817.8080.3080.3080.0000.0000.0000.000
21A21THR00.0380.02213.4120.0690.0690.0000.0000.0000.000
22A22ILE0-0.049-0.02211.404-0.010-0.0100.0000.0000.0000.000
23A23ASP-1-0.805-0.85214.9950.0780.0780.0000.0000.0000.000
24A24VAL0-0.036-0.02515.8640.0510.0510.0000.0000.0000.000
25A25GLY00.0630.02316.976-0.054-0.0540.0000.0000.0000.000
26A26SER00.011-0.01118.0480.0430.0430.0000.0000.0000.000
27A27SER0-0.060-0.02515.851-0.002-0.0020.0000.0000.0000.000
28A28THR0-0.0110.01312.6650.0690.0690.0000.0000.0000.000
29A29ASP-1-0.782-0.8679.1621.7321.7320.0000.0000.0000.000
30A30ILE00.0300.00710.5270.0780.0780.0000.0000.0000.000
31A31SER0-0.032-0.02511.0270.0390.0390.0000.0000.0000.000
32A32PRO00.0050.0086.308-0.073-0.0730.0000.0000.0000.000
33A33TYR00.0280.0066.820-0.270-0.2700.0000.0000.0000.000
34A34LEU00.0250.01310.378-0.167-0.1670.0000.0000.0000.000
35A35SER0-0.064-0.05910.270-0.203-0.2030.0000.0000.0000.000
36A36LEU00.0180.0226.657-0.156-0.1560.0000.0000.0000.000
37A37ILE00.0120.01911.088-0.153-0.1530.0000.0000.0000.000
38A38ARG10.8830.94113.331-0.944-0.9440.0000.0000.0000.000
39A39GLU-1-0.939-0.96910.6660.7980.7980.0000.0000.0000.000
40A40ASP-1-0.751-0.83013.9410.0670.0670.0000.0000.0000.000
41A41SER00.024-0.01215.553-0.049-0.0490.0000.0000.0000.000
42A42ILE0-0.093-0.05518.016-0.034-0.0340.0000.0000.0000.000
43A43LEU0-0.074-0.02714.883-0.027-0.0270.0000.0000.0000.000
44A44ASN0-0.053-0.04615.623-0.040-0.0400.0000.0000.0000.000
45A45GLY00.0160.02319.687-0.029-0.0290.0000.0000.0000.000
46A46ASN00.0160.00621.5970.0110.0110.0000.0000.0000.000
47A47ARG10.8510.92122.199-0.278-0.2780.0000.0000.0000.000
48A48ALA00.0590.04623.2350.0100.0100.0000.0000.0000.000
49A49VAL0-0.044-0.01619.7180.0210.0210.0000.0000.0000.000
50A50ILE0-0.0010.01622.204-0.005-0.0050.0000.0000.0000.000
51A51PHE0-0.048-0.04422.3700.0220.0220.0000.0000.0000.000
52A52ASP-1-0.767-0.86324.2870.0660.0660.0000.0000.0000.000
53A53VAL0-0.026-0.01724.7250.0250.0250.0000.0000.0000.000
54A54TYR0-0.062-0.04523.966-0.017-0.0170.0000.0000.0000.000
55A55TRP0-0.022-0.03727.8010.0140.0140.0000.0000.0000.000
56A56ASP-1-0.867-0.91830.3380.0690.0690.0000.0000.0000.000
57A57VAL0-0.011-0.00931.7890.0060.0060.0000.0000.0000.000
58A58GLY00.0110.02235.572-0.007-0.0070.0000.0000.0000.000
59A59PHE00.003-0.02237.4330.0000.0000.0000.0000.0000.000
60A60PRO0-0.070-0.04339.436-0.001-0.0010.0000.0000.0000.000
61A61GLU-1-0.774-0.85240.0890.0640.0640.0000.0000.0000.000
62A62THR00.007-0.00339.167-0.004-0.0040.0000.0000.0000.000
63A63GLU-1-0.816-0.89241.4770.0860.0860.0000.0000.0000.000
64A64THR0-0.048-0.05342.525-0.004-0.0040.0000.0000.0000.000
65A65LYS10.7640.88244.907-0.063-0.0630.0000.0000.0000.000
66A66THR00.0520.03841.093-0.005-0.0050.0000.0000.0000.000
67A67LYS10.8630.91141.973-0.055-0.0550.0000.0000.0000.000
68A68THR00.0300.01938.420-0.003-0.0030.0000.0000.0000.000
69A69SER0-0.019-0.01237.3740.0030.0030.0000.0000.0000.000
70A70GLY0-0.0170.00436.2810.0050.0050.0000.0000.0000.000
71A71TRP0-0.0250.00334.392-0.002-0.0020.0000.0000.0000.000
72A72SER0-0.0060.00730.2130.0090.0090.0000.0000.0000.000
73A73LEU00.0240.00025.110-0.006-0.0060.0000.0000.0000.000
74A74SER0-0.0030.00725.8360.0090.0090.0000.0000.0000.000
75A75SER0-0.047-0.04022.4190.0010.0010.0000.0000.0000.000
76A76VAL00.0090.01820.489-0.003-0.0030.0000.0000.0000.000
77A77LYS10.8260.91820.348-0.066-0.0660.0000.0000.0000.000
78A78LEU0-0.022-0.00917.5820.0160.0160.0000.0000.0000.000
79A79SER00.026-0.00418.494-0.018-0.0180.0000.0000.0000.000
80A80THR0-0.047-0.04117.0710.0160.0160.0000.0000.0000.000
81A81ARG10.8470.90919.712-0.044-0.0440.0000.0000.0000.000
82A82ASN0-0.030-0.03216.024-0.057-0.0570.0000.0000.0000.000
83A83LEU0-0.031-0.00112.473-0.053-0.0530.0000.0000.0000.000
84A84CYS0-0.031-0.01015.8140.0260.0260.0000.0000.0000.000
85A85LEU0-0.027-0.01212.786-0.025-0.0250.0000.0000.0000.000
86A86PHE00.0270.00915.9440.0200.0200.0000.0000.0000.000
87A87LEU0-0.020-0.02014.8200.0320.0320.0000.0000.0000.000
88A88ARG10.8730.88918.316-0.064-0.0640.0000.0000.0000.000
89A89LEU0-0.017-0.00319.6170.0410.0410.0000.0000.0000.000
90A90PRO0-0.0140.00820.585-0.029-0.0290.0000.0000.0000.000
91A91LYS10.8880.91523.351-0.108-0.1080.0000.0000.0000.000
92A92PRO0-0.044-0.00725.763-0.002-0.0020.0000.0000.0000.000
93A93PHE00.0650.01823.8470.0200.0200.0000.0000.0000.000
94A94HIS00.0300.00521.3620.0000.0000.0000.0000.0000.000
95A95ASP-1-0.796-0.89321.2410.3700.3700.0000.0000.0000.000
96A96ASN0-0.013-0.02315.969-0.034-0.0340.0000.0000.0000.000
97A97LEU00.0400.02117.4680.0570.0570.0000.0000.0000.000
98A98LYS10.8040.89119.585-0.362-0.3620.0000.0000.0000.000
99A99ASP-1-0.820-0.88216.0680.7120.7120.0000.0000.0000.000
100A100LEU00.0290.02218.1320.0110.0110.0000.0000.0000.000
101A101TYR0-0.045-0.03319.511-0.019-0.0190.0000.0000.0000.000
102A102ARG10.7900.85217.927-0.588-0.5880.0000.0000.0000.000
103A103PHE0-0.028-0.00916.858-0.002-0.0020.0000.0000.0000.000
104A104PHE00.0900.03120.035-0.020-0.0200.0000.0000.0000.000
105A105ALA0-0.0110.01123.372-0.030-0.0300.0000.0000.0000.000
106A106SER0-0.0080.00221.380-0.021-0.0210.0000.0000.0000.000
107A107LYS10.9850.97823.745-0.232-0.2320.0000.0000.0000.000
108A108PHE0-0.075-0.02719.870-0.011-0.0110.0000.0000.0000.000
109A109VAL00.0360.03020.3210.0020.0020.0000.0000.0000.000
110A110THR00.0100.01523.6960.0050.0050.0000.0000.0000.000
111A111PHE0-0.013-0.00421.455-0.001-0.0010.0000.0000.0000.000
112A112VAL00.0210.01926.052-0.014-0.0140.0000.0000.0000.000
113A113GLY00.0510.02226.9140.0060.0060.0000.0000.0000.000
114A114VAL0-0.004-0.01129.364-0.007-0.0070.0000.0000.0000.000
115A115GLN0-0.039-0.04732.4450.0050.0050.0000.0000.0000.000
116A116ILE00.0030.01429.7980.0010.0010.0000.0000.0000.000
117A117GLU-1-0.834-0.90433.0580.0930.0930.0000.0000.0000.000
118A118GLU-1-0.881-0.93136.2820.0820.0820.0000.0000.0000.000
119A119ASP-1-0.826-0.91031.0650.1110.1110.0000.0000.0000.000
120A120LEU0-0.038-0.03530.5690.0140.0140.0000.0000.0000.000
121A121ASP-1-0.803-0.86432.9220.1210.1210.0000.0000.0000.000
122A122LEU00.0480.02633.6460.0050.0050.0000.0000.0000.000
123A123LEU0-0.046-0.02827.5390.0090.0090.0000.0000.0000.000
124A124ARG10.7400.85430.918-0.119-0.1190.0000.0000.0000.000
125A125GLU-1-0.929-0.96233.2000.1040.1040.0000.0000.0000.000
126A126ASN0-0.035-0.03632.9830.0000.0000.0000.0000.0000.000
127A127HIS00.0000.01227.459-0.009-0.0090.0000.0000.0000.000
128A128GLY00.0210.04029.0980.0190.0190.0000.0000.0000.000
129A129LEU0-0.076-0.03624.2970.0180.0180.0000.0000.0000.000
130A130VAL0-0.013-0.02028.134-0.016-0.0160.0000.0000.0000.000
131A131ILE00.0280.01925.9740.0200.0200.0000.0000.0000.000
132A132ARG10.7770.87426.386-0.280-0.2800.0000.0000.0000.000
133A133ASN0-0.059-0.03627.112-0.024-0.0240.0000.0000.0000.000
134A134ALA00.0210.01727.9750.0120.0120.0000.0000.0000.000
135A135ILE00.0220.01530.030-0.008-0.0080.0000.0000.0000.000
136A136ASN0-0.003-0.00431.4810.0000.0000.0000.0000.0000.000
137A137VAL00.018-0.00831.159-0.005-0.0050.0000.0000.0000.000
138A138GLY00.0530.02833.700-0.006-0.0060.0000.0000.0000.000
139A139LYS10.7990.89136.712-0.081-0.0810.0000.0000.0000.000
140A140LEU00.0340.01733.996-0.003-0.0030.0000.0000.0000.000
141A141ALA00.0220.00736.391-0.004-0.0040.0000.0000.0000.000
142A142ALA0-0.051-0.01638.151-0.005-0.0050.0000.0000.0000.000
143A143GLU-1-0.958-0.98540.8870.0680.0680.0000.0000.0000.000
144A144ALA0-0.016-0.00238.932-0.003-0.0030.0000.0000.0000.000
145A145ARG10.7330.80836.604-0.039-0.0390.0000.0000.0000.000
146A146GLY00.0000.02342.309-0.004-0.0040.0000.0000.0000.000
147A147THR0-0.102-0.05543.305-0.004-0.0040.0000.0000.0000.000
148A148LEU00.043-0.00543.7580.0010.0010.0000.0000.0000.000
149A149VAL00.004-0.00443.9310.0020.0020.0000.0000.0000.000
150A150LEU00.003-0.00639.4440.0000.0000.0000.0000.0000.000
151A151GLU-1-0.834-0.90039.2810.0650.0650.0000.0000.0000.000
152A152PHE0-0.062-0.01339.9180.0030.0030.0000.0000.0000.000
153A153LEU0-0.0450.00038.285-0.004-0.0040.0000.0000.0000.000
154A154GLY00.0630.03335.8270.0060.0060.0000.0000.0000.000
155A155THR0-0.006-0.03929.820-0.002-0.0020.0000.0000.0000.000
156A156ARG10.8460.89132.7600.0020.0020.0000.0000.0000.000
157A157GLU-1-0.795-0.87833.9300.0070.0070.0000.0000.0000.000
158A158LEU00.0100.00333.609-0.001-0.0010.0000.0000.0000.000
159A159ALA00.0440.01631.9940.0000.0000.0000.0000.0000.000
160A160HIS0-0.106-0.06233.921-0.006-0.0060.0000.0000.0000.000
161A161ARG10.8430.90736.955-0.017-0.0170.0000.0000.0000.000
162A162VAL00.0070.01734.8390.0010.0010.0000.0000.0000.000
163A163LEU0-0.019-0.01231.243-0.001-0.0010.0000.0000.0000.000
164A164TRP0-0.093-0.03435.586-0.006-0.0060.0000.0000.0000.000
165A165SER0-0.0090.00333.171-0.002-0.0020.0000.0000.0000.000
166A166ASP-1-0.912-0.95633.996-0.039-0.0390.0000.0000.0000.000
167A167LEU00.011-0.00132.3960.0020.0020.0000.0000.0000.000
168A168GLY00.0430.02834.1260.0010.0010.0000.0000.0000.000
169A169GLN0-0.047-0.04128.1220.0040.0040.0000.0000.0000.000
170A170LEU0-0.0190.00029.285-0.002-0.0020.0000.0000.0000.000
171A171ASP-1-0.784-0.86331.669-0.011-0.0110.0000.0000.0000.000
172A172SER0-0.061-0.02433.4760.0030.0030.0000.0000.0000.000
173A173ILE0-0.033-0.00828.0850.0000.0000.0000.0000.0000.000
174A174GLH0-0.054-0.07031.7660.0030.0030.0000.0000.0000.000
175A175ALA0-0.033-0.01434.1360.0040.0040.0000.0000.0000.000
176A176LYS10.7560.86931.9670.0560.0560.0000.0000.0000.000
177A177TRP00.0960.04628.068-0.007-0.0070.0000.0000.0000.000
178A178GLU-1-0.835-0.90732.705-0.018-0.0180.0000.0000.0000.000
179A179LYS10.7820.86734.8590.0230.0230.0000.0000.0000.000
180A180ALA0-0.0410.00630.430-0.008-0.0080.0000.0000.0000.000
181A181GLY00.0110.01228.0760.0040.0040.0000.0000.0000.000
182A182PRO00.010-0.01423.9840.0020.0020.0000.0000.0000.000
183A183GLU-1-0.870-0.94620.434-0.176-0.1760.0000.0000.0000.000
184A184GLU-1-0.764-0.86823.494-0.068-0.0680.0000.0000.0000.000
185A185GLN0-0.029-0.01326.3620.0110.0110.0000.0000.0000.000
186A186LEU0-0.031-0.00518.5770.0140.0140.0000.0000.0000.000
187A187GLU-1-0.818-0.90622.896-0.094-0.0940.0000.0000.0000.000
188A188ALA00.010-0.00123.7920.0090.0090.0000.0000.0000.000
189A189ALA00.0040.00924.0190.0110.0110.0000.0000.0000.000
190A190ALA00.031-0.00720.9230.0200.0200.0000.0000.0000.000
191A191ILE0-0.022-0.01122.6390.0080.0080.0000.0000.0000.000
192A192GLU-1-0.787-0.86825.5220.0340.0340.0000.0000.0000.000
193A193GLY00.0070.01223.1700.0120.0120.0000.0000.0000.000
194A194TRP00.023-0.00122.8450.0120.0120.0000.0000.0000.000
195A195LEU0-0.0210.00724.3190.0040.0040.0000.0000.0000.000
196A196ILE00.007-0.00627.2230.0040.0040.0000.0000.0000.000
197A197VAL0-0.042-0.01522.6270.0110.0110.0000.0000.0000.000
198A198ASN0-0.003-0.00825.9480.0000.0000.0000.0000.0000.000
199A199VAL0-0.031-0.00428.638-0.001-0.0010.0000.0000.0000.000
200A200TRP00.015-0.00227.3680.0030.0030.0000.0000.0000.000
201A201ASP-1-0.836-0.92826.1120.0720.0720.0000.0000.0000.000
202A202GLN0-0.0160.02029.173-0.004-0.0040.0000.0000.0000.000
203A203LEU00.006-0.01333.0120.0020.0020.0000.0000.0000.000
204A204SER0-0.060-0.02130.4830.0080.0080.0000.0000.0000.000
205A205ASP-1-1.012-0.99831.4830.0750.0750.0000.0000.0000.000
206A206GLU-1-0.833-0.86234.5620.0390.0390.0000.0000.0000.000