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: 17YVZ

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 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 401
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6514146.743627
FMO2-HF: Nuclear repulsion 6359228.027516
FMO2-HF: Total energy -154918.716111
FMO2-MP2: Total energy -155377.566299


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.
-10.307-47.5180.126-18.783-24.1420.011
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 : -0.046 / q_NPA : 0.001
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].
3D4LYN00.023-0.0271.7831.535-15.23128.608-7.119-4.7230.036
4D5LEU0-0.053-0.0113.049-2.059-1.1880.182-0.254-0.7990.000
5D6GLY00.0840.0073.729-0.358-0.1530.001-0.044-0.1620.000
6D7GLU-1-0.886-0.9295.682-0.099-0.0990.0000.0000.0000.000
7D8ASN00.032-0.0407.2650.2180.2180.0000.0000.0000.000
8D9LEU0-0.0100.0547.3590.0220.0220.0000.0000.0000.000
9D10ASN0-0.005-0.0219.2170.1880.1880.0000.0000.0000.000
10D11LYS10.8620.95810.7940.1180.1180.0000.0000.0000.000
11D12ALA0-0.029-0.03112.205-0.007-0.0070.0000.0000.0000.000
12D13LEU00.008-0.00513.419-0.021-0.0210.0000.0000.0000.000
13D14ASN00.063-0.04414.380-0.069-0.0690.0000.0000.0000.000
14D15LYN0-0.084-0.01715.982-0.059-0.0590.0000.0000.0000.000
15D16LEU0-0.073-0.03118.7880.0020.0020.0000.0000.0000.000
16D17LYN00.0140.09615.2090.0140.0140.0000.0000.0000.000
17D18ALA0-0.039-0.08619.527-0.005-0.0050.0000.0000.0000.000
18D19ALA00.0190.02522.717-0.002-0.0020.0000.0000.0000.000
19D20ALA00.0220.01125.8690.0030.0030.0000.0000.0000.000
20D21PHE00.0320.02126.9410.0080.0080.0000.0000.0000.000
21D22VAL0-0.045-0.01324.8520.0010.0010.0000.0000.0000.000
22D23ASP-1-0.910-0.97426.9740.1280.1280.0000.0000.0000.000
23D24LYS11.0421.00227.025-0.121-0.1210.0000.0000.0000.000
24D25LYS10.9790.97025.774-0.147-0.1470.0000.0000.0000.000
25D26LEU00.0360.02622.7340.0170.0170.0000.0000.0000.000
26D27ILE00.0100.03721.6500.0050.0050.0000.0000.0000.000
27D28LYS10.9470.95520.944-0.219-0.2190.0000.0000.0000.000
28D29GLU-1-0.942-0.98619.9550.1790.1790.0000.0000.0000.000
29D30VAL00.0770.06315.2180.0220.0220.0000.0000.0000.000
30D31ILE0-0.0330.01016.4300.0660.0660.0000.0000.0000.000
31D32LYS10.9250.97418.065-0.300-0.3000.0000.0000.0000.000
32D33ASP-1-0.927-0.98315.1390.4240.4240.0000.0000.0000.000
33D34ILE00.022-0.01511.3530.1130.1130.0000.0000.0000.000
34D35GLN00.0700.00411.7070.1590.1590.0000.0000.0000.000
35D36ARG10.9370.97310.690-1.011-1.0110.0000.0000.0000.000
36D37ALA0-0.057-0.0348.7370.1520.1520.0000.0000.0000.000
37D38LEU00.0440.0288.5700.2770.2770.0000.0000.0000.000
38D39ILE0-0.024-0.0149.1290.1580.1580.0000.0000.0000.000
39D40GLN0-0.062-0.0177.8270.2780.2780.0000.0000.0000.000
40D41ALA00.0310.0135.5290.4830.4830.0000.0000.0000.000
41D42ASP-1-0.917-0.9317.1520.9780.9780.0000.0000.0000.000
42D43VAL00.0300.0488.582-0.075-0.0750.0000.0000.0000.000
43D44ASN0-0.001-0.01111.144-0.143-0.1430.0000.0000.0000.000
44D45VAL00.0390.00114.925-0.008-0.0080.0000.0000.0000.000
45D46LYS10.9490.97515.945-0.457-0.4570.0000.0000.0000.000
46D47LEU00.0910.04713.939-0.070-0.0700.0000.0000.0000.000
47D48VAL0-0.0090.03413.117-0.023-0.0230.0000.0000.0000.000
48D49LEU0-0.0290.03515.460-0.068-0.0680.0000.0000.0000.000
49D50LYS10.8570.92917.912-0.555-0.5550.0000.0000.0000.000
50D51MET00.1640.07313.5110.0050.0050.0000.0000.0000.000
51D52SER0-0.144-0.11517.160-0.046-0.0460.0000.0000.0000.000
52D53LYS10.8960.95018.764-0.421-0.4210.0000.0000.0000.000
53D54GLU-1-0.902-0.94520.5410.2690.2690.0000.0000.0000.000
54D55ILE00.0520.04116.104-0.032-0.0320.0000.0000.0000.000
55D56GLU-1-0.931-0.98220.5720.2620.2620.0000.0000.0000.000
56D57ARG10.8390.90322.825-0.266-0.2660.0000.0000.0000.000
57D58ARG10.9370.98022.137-0.224-0.2240.0000.0000.0000.000
58D59ALA0-0.017-0.07623.331-0.023-0.0230.0000.0000.0000.000
59D60LEU0-0.080-0.03424.620-0.022-0.0220.0000.0000.0000.000
60D61GLU-1-0.966-1.00127.5060.1880.1880.0000.0000.0000.000
61D62GLU-1-0.813-0.86827.1570.1810.1810.0000.0000.0000.000
62D63LYS10.7941.00425.563-0.148-0.1480.0000.0000.0000.000
63D64THR0-0.007-0.01128.638-0.005-0.0050.0000.0000.0000.000
64D65PRO0-0.050-0.03630.2020.0010.0010.0000.0000.0000.000
65D66LYS10.9370.95631.112-0.076-0.0760.0000.0000.0000.000
66D67GLY00.0170.00328.6920.0020.0020.0000.0000.0000.000
67D68LEU00.0130.02825.039-0.005-0.0050.0000.0000.0000.000
68D69SER0-0.028-0.02626.769-0.011-0.0110.0000.0000.0000.000
69D70LYS10.9370.95523.648-0.066-0.0660.0000.0000.0000.000
70D71LYS10.8830.98122.1200.0610.0610.0000.0000.0000.000
71D72GLU-1-0.716-0.89220.7710.0240.0240.0000.0000.0000.000
72D73HIS0-0.0290.02921.7680.0230.0230.0000.0000.0000.000
73D74ILE00.014-0.02319.8190.0140.0140.0000.0000.0000.000
74D75ILE00.0940.03016.2490.0360.0360.0000.0000.0000.000
75D76LYS10.9731.02517.057-0.111-0.1110.0000.0000.0000.000
76D77ILE0-0.039-0.01818.1150.0390.0390.0000.0000.0000.000
77D78VAL0-0.0490.00214.1140.0340.0340.0000.0000.0000.000
78D79TYR0-0.011-0.02312.6240.1070.1070.0000.0000.0000.000
79D80GLU-1-0.897-0.96214.1900.2870.2870.0000.0000.0000.000
80D81GLU-1-0.833-0.93216.1520.5980.5980.0000.0000.0000.000
81D82LEU0-0.129-0.0259.4700.0760.0760.0000.0000.0000.000
82D83VAL00.011-0.00610.6170.1630.1630.0000.0000.0000.000
83D84LYS10.9830.98712.323-0.370-0.3700.0000.0000.0000.000
84D85LEU0-0.103-0.05410.382-0.019-0.0190.0000.0000.0000.000
85D86LEU0-0.037-0.0188.9300.0740.0740.0000.0000.0000.000
86D87GLY00.050-0.00112.770-0.118-0.1180.0000.0000.0000.000
87D88GLU-1-0.928-0.96914.4320.6540.6540.0000.0000.0000.000
88D89GLU-1-0.703-0.82515.8680.2310.2310.0000.0000.0000.000
89D90ALA0-0.070-0.06115.2620.0520.0520.0000.0000.0000.000
90D91LYS10.8390.93714.256-0.470-0.4700.0000.0000.0000.000
91D92LYS10.8340.90516.493-0.291-0.2910.0000.0000.0000.000
92D93LEU0-0.060-0.00818.2610.0060.0060.0000.0000.0000.000
93D94GLU-1-0.866-0.91621.2380.1260.1260.0000.0000.0000.000
94D95LEU00.024-0.01121.912-0.010-0.0100.0000.0000.0000.000
95D96ASN0-0.019-0.00925.713-0.004-0.0040.0000.0000.0000.000
96D97PRO00.0070.01028.565-0.005-0.0050.0000.0000.0000.000
97D98LYS10.9700.97731.365-0.027-0.0270.0000.0000.0000.000
98D99LYS10.8570.90233.3750.0060.0060.0000.0000.0000.000
99D100GLN00.0730.06831.345-0.001-0.0010.0000.0000.0000.000
100D101ASN0-0.025-0.02429.435-0.005-0.0050.0000.0000.0000.000
101D102VAL00.0240.01426.8750.0050.0050.0000.0000.0000.000
102D103ILE00.0440.06321.3030.0100.0100.0000.0000.0000.000
103D104LEU0-0.024-0.00624.188-0.019-0.0190.0000.0000.0000.000
104D105LEU0-0.026-0.00118.4110.0180.0180.0000.0000.0000.000
105D106VAL00.0320.01220.365-0.016-0.0160.0000.0000.0000.000
106D107GLY00.063-0.01718.6840.0340.0340.0000.0000.0000.000
107D108ILE00.0480.02116.827-0.029-0.0290.0000.0000.0000.000
108D109GLN0-0.028-0.00919.608-0.021-0.0210.0000.0000.0000.000
109D110GLY0-0.087-0.04717.2770.0300.0300.0000.0000.0000.000
110D111SER00.0900.05614.193-0.008-0.0080.0000.0000.0000.000
111D112GLY0-0.046-0.05014.396-0.103-0.1030.0000.0000.0000.000
112D113LYS10.8390.99315.9820.0400.0400.0000.0000.0000.000
113D114THR00.0070.02718.1180.0000.0000.0000.0000.0000.000
114D115THR00.0680.03514.6420.0150.0150.0000.0000.0000.000
115D116THR0-0.045-0.05513.037-0.048-0.0480.0000.0000.0000.000
116D117ALA00.0800.02915.5370.0230.0230.0000.0000.0000.000
117D118ALA0-0.052-0.03817.9420.0060.0060.0000.0000.0000.000
118D119LYS10.8140.93510.7320.7300.7300.0000.0000.0000.000
119D120LEU0-0.0190.01015.596-0.020-0.0200.0000.0000.0000.000
120D121ALA00.0230.01216.8370.0340.0340.0000.0000.0000.000
121D122ARG10.9320.94718.8580.3070.3070.0000.0000.0000.000
122D123TYR00.0170.01614.6570.0250.0250.0000.0000.0000.000
123D124ILE00.0570.01618.3240.0100.0100.0000.0000.0000.000
124D125GLN00.1050.02921.091-0.007-0.0070.0000.0000.0000.000
125D126LYS10.8190.92118.4870.2690.2690.0000.0000.0000.000
126D127ARG10.8940.95819.2730.0290.0290.0000.0000.0000.000
127D128GLY00.013-0.00421.6970.0020.0020.0000.0000.0000.000
128D129LEU0-0.025-0.00225.1170.0160.0160.0000.0000.0000.000
129D130LYS10.9100.99425.4780.0620.0620.0000.0000.0000.000
130D131PRO00.0580.03424.0530.0140.0140.0000.0000.0000.000
131D132ALA00.008-0.04826.263-0.002-0.0020.0000.0000.0000.000
132D133LEU0-0.0310.01221.9340.0120.0120.0000.0000.0000.000
133D134ILE0-0.0180.01626.367-0.005-0.0050.0000.0000.0000.000
134D135ALA00.0350.02626.8480.0040.0040.0000.0000.0000.000
135D136ALA00.0620.01627.7020.0100.0100.0000.0000.0000.000
136D137ASP-1-0.797-0.85625.270-0.021-0.0210.0000.0000.0000.000
137D138THR0-0.036-0.01028.025-0.005-0.0050.0000.0000.0000.000
138D139TYR0-0.005-0.01323.697-0.016-0.0160.0000.0000.0000.000
139D140ARG10.9330.94024.0840.0780.0780.0000.0000.0000.000
140D141PRO00.0620.03428.054-0.012-0.0120.0000.0000.0000.000
141D142ALA0-0.0180.00425.938-0.003-0.0030.0000.0000.0000.000
142D143ALA00.003-0.00123.646-0.018-0.0180.0000.0000.0000.000
143D144TYR0-0.030-0.03824.181-0.022-0.0220.0000.0000.0000.000
144D145GLU-1-0.840-0.93924.736-0.183-0.1830.0000.0000.0000.000
145D146GLN0-0.075-0.00519.641-0.010-0.0100.0000.0000.0000.000
146D147LEU00.004-0.01620.963-0.004-0.0040.0000.0000.0000.000
147D148LYS10.9430.97823.5170.1700.1700.0000.0000.0000.000
148D149GLN00.0510.01825.8650.0110.0110.0000.0000.0000.000
149D150LEU0-0.025-0.00118.680-0.008-0.0080.0000.0000.0000.000
150D151ALA00.0330.01223.106-0.004-0.0040.0000.0000.0000.000
151D152GLU-1-0.960-0.97625.740-0.134-0.1340.0000.0000.0000.000
152D153LYS10.8820.97521.3560.3230.3230.0000.0000.0000.000
153D154ILE0-0.117-0.08122.304-0.021-0.0210.0000.0000.0000.000
154D155HIS00.0260.03325.6070.0040.0040.0000.0000.0000.000
155D156VAL0-0.0230.01424.7040.0080.0080.0000.0000.0000.000
156D157PRO00.0480.03527.862-0.002-0.0020.0000.0000.0000.000
157D158ILE0-0.003-0.01526.9180.0060.0060.0000.0000.0000.000
158D159TYR0-0.018-0.03329.8320.0030.0030.0000.0000.0000.000
159D160GLY0-0.0140.00730.575-0.004-0.0040.0000.0000.0000.000
160D161ASP-1-0.861-0.94432.670-0.030-0.0300.0000.0000.0000.000
161D162GLU-1-0.926-0.95731.111-0.064-0.0640.0000.0000.0000.000
162D163THR0-0.071-0.02035.2620.0000.0000.0000.0000.0000.000
163D164ARG10.9210.95438.4320.0040.0040.0000.0000.0000.000
164D165THR00.0500.02334.3060.0020.0020.0000.0000.0000.000
165D166LYS10.8610.90835.681-0.018-0.0180.0000.0000.0000.000
166D167SER00.1410.04930.9390.0000.0000.0000.0000.0000.000
167D168PRO0-0.012-0.04933.140-0.004-0.0040.0000.0000.0000.000
168D169VAL0-0.046-0.04435.2760.0030.0030.0000.0000.0000.000
169D170ASP-1-0.825-0.86133.605-0.022-0.0220.0000.0000.0000.000
170D171ILE0-0.0050.05030.907-0.005-0.0050.0000.0000.0000.000
171D172VAL0-0.012-0.02533.511-0.002-0.0020.0000.0000.0000.000
172D173LYS10.9550.97136.7810.0190.0190.0000.0000.0000.000
173D174GLU-1-0.830-0.91533.426-0.037-0.0370.0000.0000.0000.000
174D175GLY0-0.032-0.04031.910-0.002-0.0020.0000.0000.0000.000
175D176MET0-0.097-0.04132.7040.0010.0010.0000.0000.0000.000
176D177GLU-1-0.907-0.93835.964-0.022-0.0220.0000.0000.0000.000
177D178LYS10.8040.92230.2810.0590.0590.0000.0000.0000.000
178D179PHE0-0.023-0.02734.473-0.004-0.0040.0000.0000.0000.000
179D180LYS10.9710.97736.0150.0380.0380.0000.0000.0000.000
180D181LYS10.8870.91035.2220.0570.0570.0000.0000.0000.000
181D182ALA0-0.030-0.01230.581-0.007-0.0070.0000.0000.0000.000
182D183ASP-1-0.913-0.95328.630-0.049-0.0490.0000.0000.0000.000
183D184VAL00.0690.05026.0540.0080.0080.0000.0000.0000.000
184D185LEU0-0.043-0.02026.192-0.008-0.0080.0000.0000.0000.000
185D186ILE00.0280.00221.7130.0060.0060.0000.0000.0000.000
186D187ILE0-0.016-0.00124.901-0.014-0.0140.0000.0000.0000.000
187D188ASP-1-0.740-0.87021.796-0.056-0.0560.0000.0000.0000.000
188D189THR0-0.023-0.04723.976-0.002-0.0020.0000.0000.0000.000
189D190ALA00.0460.04622.2800.0000.0000.0000.0000.0000.000
190D191GLY00.0100.00622.486-0.012-0.0120.0000.0000.0000.000
191D192ARG10.8600.91522.4930.0060.0060.0000.0000.0000.000
192D193HIS00.0100.01023.4950.0100.0100.0000.0000.0000.000
193D194LYS10.9380.93818.813-0.120-0.1200.0000.0000.0000.000
194D195GLU-1-0.933-0.96922.0970.2450.2450.0000.0000.0000.000
195D196GLU-1-0.795-0.88920.1990.2870.2870.0000.0000.0000.000
196D197LYS10.9320.97723.452-0.205-0.2050.0000.0000.0000.000
197D198GLY00.0340.01526.797-0.005-0.0050.0000.0000.0000.000
198D199LEU00.1320.06020.773-0.012-0.0120.0000.0000.0000.000
199D200LEU00.020-0.01823.259-0.009-0.0090.0000.0000.0000.000
200D201GLU-1-0.836-0.99426.4310.0870.0870.0000.0000.0000.000
201D202GLU-1-0.882-0.88426.5590.0370.0370.0000.0000.0000.000
202D203MET0-0.111-0.10024.384-0.004-0.0040.0000.0000.0000.000
203D204LYS10.9341.03928.333-0.108-0.1080.0000.0000.0000.000
204D205GLN0-0.092-0.04230.626-0.011-0.0110.0000.0000.0000.000
205D206ILE0-0.0540.00229.785-0.006-0.0060.0000.0000.0000.000
206D207LYS10.9520.98929.640-0.122-0.1220.0000.0000.0000.000
207D208GLU-1-0.955-0.96631.8340.0670.0670.0000.0000.0000.000
208D209ILE0-0.078-0.01834.133-0.006-0.0060.0000.0000.0000.000
209D210THR0-0.068-0.05230.316-0.012-0.0120.0000.0000.0000.000
210D211ASN0-0.064-0.03132.7420.0040.0040.0000.0000.0000.000
211D212PRO0-0.060-0.04127.343-0.006-0.0060.0000.0000.0000.000
212D213ASP-1-0.843-0.94524.7150.0990.0990.0000.0000.0000.000
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