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: 857KY

Calculation Name: 2V3C-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2V3C

Chain ID: D

ChEMBL ID:

UniProt ID: Q58440

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 401
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6507178.803072
FMO2-HF: Nuclear repulsion 6352243.962824
FMO2-HF: Total energy -154934.840249
FMO2-MP2: Total energy -155391.468228


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(D:2:MET)


Summations of interaction energy for fragment #1(D:2:MET)
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.
-16.716-12.04626.194-10.431-20.436-0.035
Interaction energy analysis for fragmet #1(D:2:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.031 / q_NPA : 0.034
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].
3D4LYN0-0.046-0.0391.9860.406-2.64110.801-4.256-3.499-0.011
4D5LEU0-0.0220.0193.0960.7361.8330.115-0.314-0.8980.001
5D6GLY00.046-0.0054.0030.6541.2450.000-0.297-0.2940.001
6D7GLU-1-0.828-0.9085.145-1.005-0.841-0.001-0.010-0.1520.000
7D8ASN0-0.047-0.0477.6020.6040.6040.0000.0000.0000.000
8D9LEU0-0.050-0.0077.2580.3140.3140.0000.0000.0000.000
9D10ASN00.0250.0009.4020.3190.3190.0000.0000.0000.000
10D11LYS10.8570.92111.3291.0931.0930.0000.0000.0000.000
11D12ALA00.012-0.00813.1130.0950.0950.0000.0000.0000.000
12D13LEU00.022-0.00313.3590.0680.0680.0000.0000.0000.000
13D14ASN0-0.040-0.03215.0320.0160.0160.0000.0000.0000.000
14D15LYN0-0.057-0.00316.841-0.003-0.0030.0000.0000.0000.000
15D16LEU0-0.030-0.01819.5510.0400.0400.0000.0000.0000.000
16D17LYN0-0.0040.01615.3730.0500.0500.0000.0000.0000.000
17D18ALA0-0.002-0.01219.6510.0170.0170.0000.0000.0000.000
18D19ALA0-0.0110.01423.0130.0180.0180.0000.0000.0000.000
19D20ALA00.0550.02225.6200.0120.0120.0000.0000.0000.000
20D21PHE00.0470.01627.310-0.003-0.0030.0000.0000.0000.000
21D22VAL0-0.0180.00025.0210.0090.0090.0000.0000.0000.000
22D23ASP-1-0.847-0.92527.5150.0020.0020.0000.0000.0000.000
23D24LYS10.9300.96227.5530.0050.0050.0000.0000.0000.000
24D25LYS10.9570.98326.6940.0190.0190.0000.0000.0000.000
25D26LEU00.0440.01423.5540.0090.0090.0000.0000.0000.000
26D27ILE00.0290.03221.938-0.014-0.0140.0000.0000.0000.000
27D28LYS10.8380.88821.450-0.060-0.0600.0000.0000.0000.000
28D29GLU-1-0.928-0.96120.691-0.132-0.1320.0000.0000.0000.000
29D30VAL00.0560.03716.294-0.012-0.0120.0000.0000.0000.000
30D31ILE0-0.031-0.00516.9420.0110.0110.0000.0000.0000.000
31D32LYS10.7770.87418.2710.0690.0690.0000.0000.0000.000
32D33ASP-1-0.834-0.90815.660-0.055-0.0550.0000.0000.0000.000
33D34ILE00.0570.01111.816-0.020-0.0200.0000.0000.0000.000
34D35GLN00.0020.00312.5180.0600.0600.0000.0000.0000.000
35D36ARG10.9630.96811.3340.0710.0710.0000.0000.0000.000
36D37ALA0-0.047-0.0149.2900.0450.0450.0000.0000.0000.000
37D38LEU00.0380.0188.4040.0790.0790.0000.0000.0000.000
38D39ILE00.0150.0059.3510.1900.1900.0000.0000.0000.000
39D40GLN0-0.077-0.0417.4950.2790.2790.0000.0000.0000.000
40D41ALA00.0440.0305.3530.0070.0070.0000.0000.0000.000
41D42ASP-1-0.857-0.9136.8091.6141.6140.0000.0000.0000.000
42D43VAL00.0140.0148.4660.0500.0500.0000.0000.0000.000
43D44ASN0-0.027-0.01310.980-0.207-0.2070.0000.0000.0000.000
44D45VAL00.0520.01114.774-0.028-0.0280.0000.0000.0000.000
45D46LYS10.9500.97216.555-0.356-0.3560.0000.0000.0000.000
46D47LEU00.0210.01413.280-0.054-0.0540.0000.0000.0000.000
47D48VAL00.0280.03112.967-0.033-0.0330.0000.0000.0000.000
48D49LEU0-0.0300.00015.393-0.062-0.0620.0000.0000.0000.000
49D50LYS10.8080.91717.181-0.561-0.5610.0000.0000.0000.000
50D51MET00.1340.08213.189-0.015-0.0150.0000.0000.0000.000
51D52SER0-0.088-0.06917.438-0.053-0.0530.0000.0000.0000.000
52D53LYS10.8550.91819.103-0.261-0.2610.0000.0000.0000.000
53D54GLU-1-0.798-0.86620.5720.1680.1680.0000.0000.0000.000
54D55ILE00.0320.01115.941-0.027-0.0270.0000.0000.0000.000
55D56GLU-1-0.828-0.90820.5400.0540.0540.0000.0000.0000.000
56D57ARG10.7730.88423.033-0.152-0.1520.0000.0000.0000.000
57D58ARG10.8800.92822.502-0.130-0.1300.0000.0000.0000.000
58D59ALA0-0.046-0.03823.428-0.017-0.0170.0000.0000.0000.000
59D60LEU0-0.094-0.07225.514-0.020-0.0200.0000.0000.0000.000
60D61GLU-1-0.916-0.94928.0910.0910.0910.0000.0000.0000.000
61D62GLU-1-0.825-0.88827.8250.0840.0840.0000.0000.0000.000
62D63LYS10.7530.89926.780-0.011-0.0110.0000.0000.0000.000
63D64THR00.0160.00129.198-0.005-0.0050.0000.0000.0000.000
64D65PRO0-0.009-0.03030.785-0.003-0.0030.0000.0000.0000.000
65D66LYS10.9190.97530.996-0.001-0.0010.0000.0000.0000.000
66D67GLY00.0560.02828.543-0.005-0.0050.0000.0000.0000.000
67D68LEU00.0000.01425.606-0.003-0.0030.0000.0000.0000.000
68D69SER0-0.014-0.03127.484-0.010-0.0100.0000.0000.0000.000
69D70LYS10.8260.91323.8350.1190.1190.0000.0000.0000.000
70D71LYS10.8820.93322.6080.1450.1450.0000.0000.0000.000
71D72GLU-1-0.691-0.84721.202-0.110-0.1100.0000.0000.0000.000
72D73HIS0-0.032-0.00321.8890.0190.0190.0000.0000.0000.000
73D74ILE00.0270.01020.6490.0190.0190.0000.0000.0000.000
74D75ILE00.0310.02016.3860.0240.0240.0000.0000.0000.000
75D76LYS10.9270.96717.397-0.060-0.0600.0000.0000.0000.000
76D77ILE0-0.0070.00018.7070.0340.0340.0000.0000.0000.000
77D78VAL0-0.020-0.01214.4430.0320.0320.0000.0000.0000.000
78D79TYR0-0.056-0.05613.1310.0860.0860.0000.0000.0000.000
79D80GLU-1-0.809-0.90014.8710.2110.2110.0000.0000.0000.000
80D81GLU-1-0.827-0.92616.7170.3880.3880.0000.0000.0000.000
81D82LEU0-0.066-0.0279.7510.0560.0560.0000.0000.0000.000
82D83VAL00.0110.00311.2740.1900.1900.0000.0000.0000.000
83D84LYS10.8410.92312.889-0.261-0.2610.0000.0000.0000.000
84D85LEU0-0.077-0.04010.307-0.024-0.0240.0000.0000.0000.000
85D86LEU0-0.060-0.0268.9250.0960.0960.0000.0000.0000.000
86D87GLY00.0300.00612.578-0.054-0.0540.0000.0000.0000.000
87D88GLU-1-0.892-0.94614.8130.5370.5370.0000.0000.0000.000
88D89GLU-1-0.708-0.83416.0060.3080.3080.0000.0000.0000.000
89D90ALA0-0.061-0.03914.9000.0410.0410.0000.0000.0000.000
90D91LYS10.7750.91614.899-0.380-0.3800.0000.0000.0000.000
91D92LYS10.7730.87216.595-0.325-0.3250.0000.0000.0000.000
92D93LEU0-0.035-0.02918.4510.0300.0300.0000.0000.0000.000
93D94GLU-1-0.891-0.92321.5820.2050.2050.0000.0000.0000.000
94D95LEU00.042-0.00722.0010.0010.0010.0000.0000.0000.000
95D96ASN0-0.0100.00725.728-0.004-0.0040.0000.0000.0000.000
96D97PRO00.0230.01528.505-0.011-0.0110.0000.0000.0000.000
97D98LYS10.9210.96531.528-0.097-0.0970.0000.0000.0000.000
98D99LYS10.8900.92633.134-0.075-0.0750.0000.0000.0000.000
99D100GLN00.0740.06131.5390.0020.0020.0000.0000.0000.000
100D101ASN0-0.077-0.06028.258-0.011-0.0110.0000.0000.0000.000
101D102VAL0-0.0050.00927.8600.0040.0040.0000.0000.0000.000
102D103ILE00.0690.05021.5750.0100.0100.0000.0000.0000.000
103D104LEU0-0.006-0.01324.412-0.015-0.0150.0000.0000.0000.000
104D105LEU0-0.013-0.00718.1540.0290.0290.0000.0000.0000.000
105D106VAL00.024-0.00220.382-0.019-0.0190.0000.0000.0000.000
106D107GLY00.0720.00518.6090.0540.0540.0000.0000.0000.000
107D108ILE00.0060.01917.281-0.058-0.0580.0000.0000.0000.000
108D109GLN00.0650.01819.095-0.079-0.0790.0000.0000.0000.000
109D110GLY0-0.046-0.01316.5260.0430.0430.0000.0000.0000.000
110D111SER00.017-0.00614.142-0.040-0.0400.0000.0000.0000.000
111D112GLY0-0.0110.00014.397-0.029-0.0290.0000.0000.0000.000
112D113LYS10.7570.90816.591-0.238-0.2380.0000.0000.0000.000
113D114THR00.0290.00918.411-0.013-0.0130.0000.0000.0000.000
114D115THR00.015-0.00815.775-0.013-0.0130.0000.0000.0000.000
115D116THR00.005-0.00414.141-0.026-0.0260.0000.0000.0000.000
116D117ALA00.0210.01415.996-0.020-0.0200.0000.0000.0000.000
117D118ALA0-0.0070.00019.005-0.021-0.0210.0000.0000.0000.000
118D119LYS10.7460.85911.5110.1770.1770.0000.0000.0000.000
119D120LEU00.0130.00315.660-0.030-0.0300.0000.0000.0000.000
120D121ALA00.0060.01017.354-0.006-0.0060.0000.0000.0000.000
121D122ARG10.9120.93618.7670.0800.0800.0000.0000.0000.000
122D123TYR00.0580.04515.695-0.003-0.0030.0000.0000.0000.000
123D124ILE00.0150.00318.315-0.006-0.0060.0000.0000.0000.000
124D125GLN00.0360.01321.478-0.014-0.0140.0000.0000.0000.000
125D126LYS10.8760.94417.9800.0590.0590.0000.0000.0000.000
126D127ARG10.8920.95319.242-0.134-0.1340.0000.0000.0000.000
127D128GLY00.001-0.00121.896-0.004-0.0040.0000.0000.0000.000
128D129LEU0-0.051-0.01225.1760.0030.0030.0000.0000.0000.000
129D130LYS10.8460.88825.870-0.044-0.0440.0000.0000.0000.000
130D131PRO0-0.0010.01523.7850.0060.0060.0000.0000.0000.000
131D132ALA00.003-0.01926.735-0.012-0.0120.0000.0000.0000.000
132D133LEU00.0200.02122.8400.0120.0120.0000.0000.0000.000
133D134ILE0-0.053-0.02227.163-0.014-0.0140.0000.0000.0000.000
134D135ALA00.0340.02227.4870.0130.0130.0000.0000.0000.000
135D136ALA00.000-0.00227.9240.0010.0010.0000.0000.0000.000
136D137ASP-1-0.822-0.89426.0450.1910.1910.0000.0000.0000.000
137D138THR0-0.0160.00428.804-0.012-0.0120.0000.0000.0000.000
138D139TYR00.0560.02224.6040.0090.0090.0000.0000.0000.000
139D140ARG10.8800.91624.304-0.179-0.1790.0000.0000.0000.000
140D141PRO00.0370.01528.451-0.004-0.0040.0000.0000.0000.000
141D142ALA00.0290.02426.476-0.009-0.0090.0000.0000.0000.000
142D143ALA0-0.020-0.00724.0850.0000.0000.0000.0000.0000.000
143D144TYR0-0.076-0.06624.645-0.007-0.0070.0000.0000.0000.000
144D145GLU-1-0.797-0.89225.320-0.017-0.0170.0000.0000.0000.000
145D146GLN00.000-0.00320.257-0.026-0.0260.0000.0000.0000.000
146D147LEU0-0.015-0.01421.5320.0160.0160.0000.0000.0000.000
147D148LYS10.8200.90224.258-0.001-0.0010.0000.0000.0000.000
148D149GLN00.0530.01826.8170.0040.0040.0000.0000.0000.000
149D150LEU0-0.027-0.00619.111-0.014-0.0140.0000.0000.0000.000
150D151ALA00.0140.01723.531-0.001-0.0010.0000.0000.0000.000
151D152GLU-1-0.911-0.96126.004-0.003-0.0030.0000.0000.0000.000
152D153LYS10.8540.95421.7310.0810.0810.0000.0000.0000.000
153D154ILE0-0.047-0.03722.160-0.021-0.0210.0000.0000.0000.000
154D155HIS00.0300.02725.8170.0020.0020.0000.0000.0000.000
155D156VAL00.0050.00224.5090.0060.0060.0000.0000.0000.000
156D157PRO00.0380.02327.7910.0050.0050.0000.0000.0000.000
157D158ILE00.0370.03827.1160.0100.0100.0000.0000.0000.000
158D159TYR00.014-0.02329.937-0.005-0.0050.0000.0000.0000.000
159D160GLY0-0.003-0.00730.8730.0090.0090.0000.0000.0000.000
160D161ASP-1-0.739-0.87032.9340.0690.0690.0000.0000.0000.000
161D162GLU-1-0.883-0.92631.2540.1080.1080.0000.0000.0000.000
162D163THR0-0.106-0.04035.475-0.005-0.0050.0000.0000.0000.000
163D164ARG10.8680.92938.906-0.088-0.0880.0000.0000.0000.000
164D165THR00.0470.01134.557-0.001-0.0010.0000.0000.0000.000
165D166LYS10.8970.93536.158-0.115-0.1150.0000.0000.0000.000
166D167SER00.1320.05531.351-0.007-0.0070.0000.0000.0000.000
167D168PRO0-0.050-0.03633.411-0.004-0.0040.0000.0000.0000.000
168D169VAL0-0.052-0.02235.668-0.006-0.0060.0000.0000.0000.000
169D170ASP-1-0.780-0.85133.6770.0930.0930.0000.0000.0000.000
170D171ILE0-0.004-0.01131.435-0.005-0.0050.0000.0000.0000.000
171D172VAL0-0.026-0.01733.580-0.005-0.0050.0000.0000.0000.000
172D173LYS10.7860.88837.095-0.071-0.0710.0000.0000.0000.000
173D174GLU-1-0.823-0.90834.2570.0630.0630.0000.0000.0000.000
174D175GLY0-0.025-0.01632.716-0.003-0.0030.0000.0000.0000.000
175D176MET0-0.0150.00033.4030.0010.0010.0000.0000.0000.000
176D177GLU-1-0.829-0.89036.5390.0520.0520.0000.0000.0000.000
177D178LYS10.7950.87430.967-0.076-0.0760.0000.0000.0000.000
178D179PHE0-0.005-0.00534.791-0.003-0.0030.0000.0000.0000.000
179D180LYS10.8470.91435.795-0.052-0.0520.0000.0000.0000.000
180D181LYS10.8880.93835.530-0.036-0.0360.0000.0000.0000.000
181D182ALA00.0090.01631.027-0.007-0.0070.0000.0000.0000.000
182D183ASP-1-0.845-0.87929.0830.0550.0550.0000.0000.0000.000
183D184VAL00.0470.01526.1210.0040.0040.0000.0000.0000.000
184D185LEU0-0.047-0.01427.155-0.004-0.0040.0000.0000.0000.000
185D186ILE00.009-0.00122.1240.0120.0120.0000.0000.0000.000
186D187ILE00.0120.00625.222-0.016-0.0160.0000.0000.0000.000
187D188ASP-1-0.669-0.81822.1270.2290.2290.0000.0000.0000.000
188D189THR00.002-0.01324.477-0.001-0.0010.0000.0000.0000.000
189D190ALA00.0230.02722.884-0.006-0.0060.0000.0000.0000.000
190D191GLY00.0040.01522.893-0.014-0.0140.0000.0000.0000.000
191D192ARG10.7840.87523.413-0.159-0.1590.0000.0000.0000.000
192D193HIS00.0050.01323.733-0.020-0.0200.0000.0000.0000.000
193D194LYS10.8760.90617.958-0.501-0.5010.0000.0000.0000.000
194D195GLU-1-0.812-0.89121.9480.3860.3860.0000.0000.0000.000
195D196GLU-1-0.821-0.93120.5830.5070.5070.0000.0000.0000.000
196D197LYS10.8550.91023.549-0.346-0.3460.0000.0000.0000.000
197D198GLY0-0.0130.00626.633-0.014-0.0140.0000.0000.0000.000
198D199LEU0-0.004-0.01221.096-0.024-0.0240.0000.0000.0000.000
199D200LEU00.0390.02723.895-0.008-0.0080.0000.0000.0000.000
200D201GLU-1-0.757-0.86627.0350.1790.1790.0000.0000.0000.000
201D202GLU-1-0.923-0.95827.5840.1780.1780.0000.0000.0000.000
202D203MET0-0.0120.00023.4270.0060.0060.0000.0000.0000.000
203D204LYS10.8240.90028.581-0.203-0.2030.0000.0000.0000.000
204D205GLN0-0.054-0.02731.252-0.019-0.0190.0000.0000.0000.000
205D206ILE0-0.019-0.00530.438-0.011-0.0110.0000.0000.0000.000
206D207LYS10.8840.92630.313-0.196-0.1960.0000.0000.0000.000
207D208GLU-1-0.861-0.90932.6740.1610.1610.0000.0000.0000.000
208D209ILE0-0.083-0.02935.079-0.010-0.0100.0000.0000.0000.000
209D210THR0-0.020-0.01830.888-0.008-0.0080.0000.0000.0000.000
210D211ASN0-0.070-0.03332.9490.0020.0020.0000.0000.0000.000
211D212PRO0-0.0090.00227.315-0.010-0.0100.0000.0000.0000.000
212D213ASP-1-0.851-0.92825.9910.1810.1810.0000.0000.0000.000
213D214GLU-1-0.755-0.83921.0360.3630.3630.0000.0000.0000.000
214D215ILE0-0.035-0.03523.201-0.018-0.0180.0000.0000.0000.000
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