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

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FMODB ID: 2LNZR

Calculation Name: 3EVT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EVT

Chain ID: A

ChEMBL ID:

UniProt ID: F9URQ7

Base Structure: X-ray

Registration Date: 2023-09-27

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 OptHSide
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 310
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3955289.486184
FMO2-HF: Nuclear repulsion 3838472.82358
FMO2-HF: Total energy -116816.662604
FMO2-MP2: Total energy -117160.186426


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:2:SER)


Summations of interaction energy for fragment #1(A:2: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.
-15.385-6.0913.221-4.933-7.582-0.006
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : 0.016
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].
3A4VAL00.0050.0043.844-1.8240.462-0.026-1.281-0.9780.003
4A5LEU0-0.036-0.0096.959-0.014-0.0140.0000.0000.0000.000
5A6MET0-0.016-0.01210.014-0.080-0.0800.0000.0000.0000.000
6A7ALA00.0020.00612.751-0.004-0.0040.0000.0000.0000.000
7A8GLN0-0.092-0.04115.800-0.022-0.0220.0000.0000.0000.000
8A9ALA00.0270.01216.8050.0080.0080.0000.0000.0000.000
9A10THR00.0260.01015.825-0.009-0.0090.0000.0000.0000.000
10A11LYS10.8250.89618.932-0.030-0.0300.0000.0000.0000.000
11A12PRO00.0300.01119.1640.0010.0010.0000.0000.0000.000
12A13GLU-1-0.759-0.89718.5420.0370.0370.0000.0000.0000.000
13A14GLN0-0.052-0.00417.420-0.002-0.0020.0000.0000.0000.000
14A15LEU00.0330.01812.647-0.012-0.0120.0000.0000.0000.000
15A16GLN00.0420.01313.699-0.034-0.0340.0000.0000.0000.000
16A17GLN0-0.0150.00214.683-0.025-0.0250.0000.0000.0000.000
17A18LEU0-0.0120.01510.706-0.023-0.0230.0000.0000.0000.000
18A19GLN00.009-0.00610.020-0.063-0.0630.0000.0000.0000.000
19A20THR0-0.050-0.02910.784-0.051-0.0510.0000.0000.0000.000
20A21THR0-0.052-0.02612.375-0.015-0.0150.0000.0000.0000.000
21A22TYR0-0.021-0.0217.1770.0160.0160.0000.0000.0000.000
22A23PRO00.0150.0207.645-0.098-0.0980.0000.0000.0000.000
23A24ASP-1-0.924-0.9655.599-1.195-1.1950.0000.0000.0000.000
24A25TRP0-0.016-0.0023.025-2.1430.3731.081-0.916-2.681-0.005
25A26THR0-0.055-0.0273.8040.5401.4000.001-0.400-0.4620.001
26A27PHE00.002-0.0095.6960.1380.1380.0000.0000.0000.000
27A28LYS10.8170.8958.383-1.032-1.0320.0000.0000.0000.000
28A29ASP-1-0.860-0.92710.1500.2470.2470.0000.0000.0000.000
29A30ALA00.006-0.01713.5820.0590.0590.0000.0000.0000.000
30A31ALA0-0.044-0.01314.7160.0020.0020.0000.0000.0000.000
31A32ALA0-0.018-0.01014.038-0.002-0.0020.0000.0000.0000.000
32A33VAL0-0.068-0.01410.2080.0980.0980.0000.0000.0000.000
33A34THR00.013-0.01811.407-0.105-0.1050.0000.0000.0000.000
34A35ALA00.008-0.02311.5720.0880.0880.0000.0000.0000.000
35A36ALA0-0.018-0.00410.935-0.042-0.0420.0000.0000.0000.000
36A37ASP-1-0.753-0.8637.3771.6141.6140.0000.0000.0000.000
37A38TYR00.0090.0136.9420.0890.0890.0000.0000.0000.000
38A39ASP-1-0.721-0.8087.6700.0670.0670.0000.0000.0000.000
39A40GLN0-0.014-0.0113.119-3.949-2.4580.173-0.639-1.0260.004
40A41ILE0-0.071-0.0343.106-3.638-2.4830.096-0.718-0.533-0.006
41A42GLU-1-0.785-0.8712.043-3.943-3.0431.897-0.975-1.822-0.003
42A43VAL00.0050.0144.990-0.090-0.004-0.001-0.004-0.0800.000
43A44MET0-0.051-0.0077.6510.0130.0130.0000.0000.0000.000
44A45TYR00.0460.02710.794-0.058-0.0580.0000.0000.0000.000
45A46GLY00.009-0.00613.3830.0060.0060.0000.0000.0000.000
46A47ASN0-0.005-0.01215.3870.0200.0200.0000.0000.0000.000
47A48HIS00.1130.04315.5930.0080.0080.0000.0000.0000.000
48A49PRO00.001-0.00917.670-0.014-0.0140.0000.0000.0000.000
49A50LEU00.0340.01413.489-0.016-0.0160.0000.0000.0000.000
50A51LEU00.0040.02713.966-0.006-0.0060.0000.0000.0000.000
51A52LYS10.8770.92315.342-0.122-0.1220.0000.0000.0000.000
52A53THR00.0070.00715.702-0.021-0.0210.0000.0000.0000.000
53A54ILE00.015-0.00410.497-0.006-0.0060.0000.0000.0000.000
54A55LEU0-0.010-0.00913.503-0.036-0.0360.0000.0000.0000.000
55A56ALA0-0.038-0.00715.162-0.022-0.0220.0000.0000.0000.000
56A57ARG10.7970.87711.795-0.238-0.2380.0000.0000.0000.000
57A58PRO0-0.021-0.00414.286-0.034-0.0340.0000.0000.0000.000
58A59THR0-0.035-0.03911.952-0.034-0.0340.0000.0000.0000.000
59A60ASN0-0.0190.0039.669-0.075-0.0750.0000.0000.0000.000
60A61GLN0-0.010-0.0215.077-0.247-0.2470.0000.0000.0000.000
61A62LEU0-0.023-0.0076.611-0.159-0.1590.0000.0000.0000.000
62A63LYS10.8320.9025.3331.6461.6460.0000.0000.0000.000
63A64PHE00.0070.0069.1240.0120.0120.0000.0000.0000.000
64A65VAL0-0.023-0.00910.4490.0700.0700.0000.0000.0000.000
65A66GLN00.0270.02213.168-0.031-0.0310.0000.0000.0000.000
66A67VAL0-0.012-0.00415.3220.0190.0190.0000.0000.0000.000
67A68ILE0-0.001-0.02018.196-0.008-0.0080.0000.0000.0000.000
68A69SER0-0.027-0.01820.782-0.004-0.0040.0000.0000.0000.000
69A70ALA00.0360.00723.300-0.001-0.0010.0000.0000.0000.000
70A71GLY00.0200.02325.606-0.005-0.0050.0000.0000.0000.000
71A72VAL00.025-0.00921.8540.0070.0070.0000.0000.0000.000
72A73ASP-1-0.892-0.93723.9720.0170.0170.0000.0000.0000.000
73A74TYR0-0.047-0.02022.9840.0020.0020.0000.0000.0000.000
74A75LEU0-0.0090.00019.4760.0090.0090.0000.0000.0000.000
75A76PRO00.0180.01518.611-0.007-0.0070.0000.0000.0000.000
76A77LEU00.0520.01120.207-0.010-0.0100.0000.0000.0000.000
77A78LYS10.9080.94821.1070.0360.0360.0000.0000.0000.000
78A79ALA00.0230.00718.556-0.010-0.0100.0000.0000.0000.000
79A80LEU00.0140.01015.223-0.015-0.0150.0000.0000.0000.000
80A81GLN00.1030.06016.832-0.016-0.0160.0000.0000.0000.000
81A82ALA0-0.081-0.03218.867-0.016-0.0160.0000.0000.0000.000
82A83ALA0-0.034-0.01614.078-0.014-0.0140.0000.0000.0000.000
83A84GLY0-0.006-0.00214.165-0.042-0.0420.0000.0000.0000.000
84A85VAL0-0.088-0.03912.106-0.010-0.0100.0000.0000.0000.000
85A86VAL00.0370.03312.8450.0200.0200.0000.0000.0000.000
86A87VAL00.023-0.00414.1200.0310.0310.0000.0000.0000.000
87A88ALA00.0610.04816.662-0.012-0.0120.0000.0000.0000.000
88A89ASN00.0010.00618.3770.0130.0130.0000.0000.0000.000
89A90THR0-0.026-0.01421.020-0.002-0.0020.0000.0000.0000.000
90A91SER0-0.007-0.00623.301-0.002-0.0020.0000.0000.0000.000
91A92GLY00.0950.03626.262-0.002-0.0020.0000.0000.0000.000
92A93ILE00.0060.01924.802-0.002-0.0020.0000.0000.0000.000
93A94HIS0-0.013-0.01228.7100.0000.0000.0000.0000.0000.000
94A95ALA00.0160.01132.280-0.001-0.0010.0000.0000.0000.000
95A96ASP-1-0.746-0.84528.732-0.015-0.0150.0000.0000.0000.000
96A97ALA00.0170.01331.446-0.002-0.0020.0000.0000.0000.000
97A98ILE00.0560.03333.100-0.001-0.0010.0000.0000.0000.000
98A99SER0-0.020-0.02534.060-0.002-0.0020.0000.0000.0000.000
99A100GLU-1-0.853-0.91630.422-0.017-0.0170.0000.0000.0000.000
100A101SER0-0.013-0.00635.114-0.001-0.0010.0000.0000.0000.000
101A102VAL00.0170.01138.3590.0000.0000.0000.0000.0000.000
102A103LEU00.007-0.00434.949-0.001-0.0010.0000.0000.0000.000
103A104ALA0-0.0020.01137.943-0.001-0.0010.0000.0000.0000.000
104A105ALA00.0230.02639.6160.0000.0000.0000.0000.0000.000
105A106MET0-0.0040.00941.0280.0000.0000.0000.0000.0000.000
106A107LEU0-0.006-0.01637.732-0.001-0.0010.0000.0000.0000.000
107A108SER0-0.074-0.04442.1080.0000.0000.0000.0000.0000.000
108A109VAL00.0690.03243.7140.0000.0000.0000.0000.0000.000
109A110VAL00.0130.01744.4470.0000.0000.0000.0000.0000.000
110A111ARG10.8220.88841.6760.0230.0230.0000.0000.0000.000
111A112GLY00.0400.02245.0660.0000.0000.0000.0000.0000.000
112A113TYR0-0.032-0.00641.3800.0010.0010.0000.0000.0000.000
113A114HIS00.005-0.00246.0050.0000.0000.0000.0000.0000.000
114A115ALA00.0400.00848.4660.0010.0010.0000.0000.0000.000
115A116ALA0-0.003-0.01247.8450.0000.0000.0000.0000.0000.000
116A117TRP0-0.0070.00047.2610.0000.0000.0000.0000.0000.000
117A118LEU00.0380.02249.9040.0010.0010.0000.0000.0000.000
118A119ASN0-0.008-0.00252.7190.0010.0010.0000.0000.0000.000
119A120GLN00.008-0.00347.6970.0000.0000.0000.0000.0000.000
120A121ARG10.8250.91150.0510.0070.0070.0000.0000.0000.000
121A122GLY00.0630.04354.5310.0010.0010.0000.0000.0000.000
122A123ALA0-0.019-0.01957.5810.0000.0000.0000.0000.0000.000
123A124ARG10.8480.94354.4740.0080.0080.0000.0000.0000.000
124A125GLN0-0.013-0.00656.0120.0000.0000.0000.0000.0000.000
125A126TRP0-0.012-0.00349.2270.0000.0000.0000.0000.0000.000
126A127ALA00.019-0.00154.045-0.001-0.0010.0000.0000.0000.000
127A128LEU0-0.0080.00349.8600.0010.0010.0000.0000.0000.000
128A129PRO0-0.0190.00454.5790.0000.0000.0000.0000.0000.000
129A130MET00.0020.00449.8220.0000.0000.0000.0000.0000.000
130A131THR0-0.0010.00252.556-0.001-0.0010.0000.0000.0000.000
131A132THR0-0.013-0.00847.5270.0000.0000.0000.0000.0000.000
132A133SER00.0420.01947.7330.0000.0000.0000.0000.0000.000
133A134THR0-0.0030.00042.9440.0000.0000.0000.0000.0000.000
134A135LEU00.0510.02039.5690.0010.0010.0000.0000.0000.000
135A136THR0-0.0160.00640.3400.0000.0000.0000.0000.0000.000
136A137GLY00.010-0.00642.0080.0010.0010.0000.0000.0000.000
137A138GLN0-0.050-0.02744.4890.0020.0020.0000.0000.0000.000
138A139GLN0-0.014-0.00344.822-0.001-0.0010.0000.0000.0000.000
139A140LEU0-0.022-0.02141.0320.0010.0010.0000.0000.0000.000
140A141LEU00.0330.02244.9790.0000.0000.0000.0000.0000.000
141A142ILE0-0.030-0.02840.6510.0010.0010.0000.0000.0000.000
142A143TYR00.0710.03944.8900.0000.0000.0000.0000.0000.000
143A144GLY00.0330.00843.8660.0010.0010.0000.0000.0000.000
144A145THR00.0210.01340.9950.0000.0000.0000.0000.0000.000
145A146GLY0-0.0090.00239.2630.0000.0000.0000.0000.0000.000
146A147GLN00.030-0.00232.210-0.001-0.0010.0000.0000.0000.000
147A148ILE00.0410.01235.139-0.001-0.0010.0000.0000.0000.000
148A149GLY00.0410.03636.943-0.001-0.0010.0000.0000.0000.000
149A150GLN0-0.021-0.01834.986-0.002-0.0020.0000.0000.0000.000
150A151SER00.006-0.00332.387-0.002-0.0020.0000.0000.0000.000
151A152LEU0-0.028-0.01533.828-0.002-0.0020.0000.0000.0000.000
152A153ALA00.0320.00936.642-0.002-0.0020.0000.0000.0000.000
153A154ALA00.0190.01331.901-0.002-0.0020.0000.0000.0000.000
154A155LYS10.7360.84629.7900.0160.0160.0000.0000.0000.000
155A156ALA00.0410.01533.939-0.002-0.0020.0000.0000.0000.000
156A157SER00.0170.01835.843-0.002-0.0020.0000.0000.0000.000
157A158ALA0-0.031-0.00532.147-0.002-0.0020.0000.0000.0000.000
158A159LEU0-0.089-0.04034.167-0.002-0.0020.0000.0000.0000.000
159A160GLY0-0.009-0.01036.5810.0010.0010.0000.0000.0000.000
160A161MET0-0.094-0.02339.1490.0010.0010.0000.0000.0000.000
161A162HIS0-0.026-0.02040.749-0.003-0.0030.0000.0000.0000.000
162A163VAL0-0.036-0.03239.4370.0020.0020.0000.0000.0000.000
163A164ILE00.0470.02842.6470.0000.0000.0000.0000.0000.000
164A165GLY00.0160.00043.8680.0010.0010.0000.0000.0000.000
165A166VAL0-0.023-0.00444.7840.0000.0000.0000.0000.0000.000
166A167ASN0-0.051-0.04643.9030.0010.0010.0000.0000.0000.000
167A168THR00.014-0.00647.2120.0000.0000.0000.0000.0000.000
168A169THR0-0.024-0.03947.9350.0000.0000.0000.0000.0000.000
169A170GLY00.0110.02848.1320.0000.0000.0000.0000.0000.000
170A171HIS00.0160.02942.926-0.001-0.0010.0000.0000.0000.000
171A172PRO00.0290.03041.1610.0000.0000.0000.0000.0000.000
172A173ALA0-0.027-0.01939.2220.0020.0020.0000.0000.0000.000
173A174ASP-1-0.879-0.93533.264-0.024-0.0240.0000.0000.0000.000
174A175HIS0-0.025-0.03630.9390.0000.0000.0000.0000.0000.000
175A176PHE0-0.0310.00436.2090.0000.0000.0000.0000.0000.000
176A177HIS00.0270.03139.3230.0010.0010.0000.0000.0000.000
177A178GLU-1-0.879-0.92441.802-0.021-0.0210.0000.0000.0000.000
178A179THR0-0.066-0.06943.1040.0000.0000.0000.0000.0000.000
179A180VAL00.0240.01845.8950.0000.0000.0000.0000.0000.000
180A181ALA00.0360.01549.0040.0010.0010.0000.0000.0000.000
181A182PHE00.0370.00148.8360.0000.0000.0000.0000.0000.000
182A183THR0-0.057-0.02353.0600.0000.0000.0000.0000.0000.000
183A184ALA0-0.041-0.02653.5170.0000.0000.0000.0000.0000.000
184A185THR00.0310.01351.786-0.001-0.0010.0000.0000.0000.000
185A186ALA00.0070.01554.2670.0000.0000.0000.0000.0000.000
186A187ASP-1-0.875-0.93854.751-0.014-0.0140.0000.0000.0000.000
187A188ALA00.005-0.00150.4550.0000.0000.0000.0000.0000.000
188A189LEU0-0.010-0.01952.2450.0000.0000.0000.0000.0000.000
189A190ALA00.0100.02254.2480.0000.0000.0000.0000.0000.000
190A191THR0-0.018-0.01852.2420.0000.0000.0000.0000.0000.000
191A192ALA00.0030.01050.064-0.001-0.0010.0000.0000.0000.000
192A193ASN00.0530.03948.2460.0000.0000.0000.0000.0000.000
193A194PHE0-0.014-0.00846.0110.0010.0010.0000.0000.0000.000
194A195ILE00.0270.01947.6450.0000.0000.0000.0000.0000.000
195A196VAL00.0190.01142.7180.0010.0010.0000.0000.0000.000
196A197ASN0-0.014-0.01846.1060.0000.0000.0000.0000.0000.000
197A198ALA00.009-0.00142.0050.0010.0010.0000.0000.0000.000
198A199LEU0-0.032-0.00843.7050.0010.0010.0000.0000.0000.000
199A200PRO0-0.031-0.01445.0970.0010.0010.0000.0000.0000.000
200A201LEU00.0260.00746.951-0.001-0.0010.0000.0000.0000.000
201A202THR0-0.041-0.01150.3860.0010.0010.0000.0000.0000.000
202A203PRO00.0510.00452.8520.0000.0000.0000.0000.0000.000
203A204THR0-0.006-0.00255.0370.0000.0000.0000.0000.0000.000
204A205THR0-0.026-0.01751.311-0.001-0.0010.0000.0000.0000.000
205A206HIS0-0.023-0.00253.9150.0000.0000.0000.0000.0000.000
206A207HIS0-0.094-0.07356.1850.0000.0000.0000.0000.0000.000
207A208LEU00.0040.02252.1630.0000.0000.0000.0000.0000.000
208A209PHE0-0.058-0.04050.243-0.001-0.0010.0000.0000.0000.000
209A210SER00.0590.00255.6190.0000.0000.0000.0000.0000.000
210A211THR0-0.002-0.00559.269-0.001-0.0010.0000.0000.0000.000
211A212GLU-1-0.928-0.96161.634-0.007-0.0070.0000.0000.0000.000
212A213LEU00.0050.00654.023-0.001-0.0010.0000.0000.0000.000
213A214PHE00.025-0.00755.003-0.001-0.0010.0000.0000.0000.000
214A215GLN00.0160.02358.7910.0000.0000.0000.0000.0000.000
215A216GLN0-0.017-0.00758.4370.0000.0000.0000.0000.0000.000
216A217THR0-0.069-0.02255.448-0.001-0.0010.0000.0000.0000.000
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