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: YQKM2

Calculation Name: 1VRR-A-Xray310

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VRR

Chain ID: A

ChEMBL ID:

UniProt ID: Q84AF2

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 203
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2300784.664515
FMO2-HF: Nuclear repulsion 2220189.893353
FMO2-HF: Total energy -80594.771162
FMO2-MP2: Total energy -80832.50624


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:MET )


Summations of interaction energy for fragment #1(A:1: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.
-22.405-34.34162.925-20.472-30.513-0.101
Interaction energy analysis for fragmet #1(A:1:MET )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.064 / q_NPA : -0.062
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].
3A3ILE 00.030-0.0013.815-0.8401.398-0.015-1.124-1.0990.003
4A4VAL 0-0.068-0.0225.9270.0160.0160.0000.0000.0000.000
5A5GLU -1-0.895-0.9478.1110.0130.0130.0000.0000.0000.000
6A6VAL 0-0.015-0.00710.0430.0370.0370.0000.0000.0000.000
7A7TYR 0-0.030-0.01012.507-0.020-0.0200.0000.0000.0000.000
8A8SER 0-0.051-0.06715.9280.0120.0120.0000.0000.0000.000
9A9HIS 0-0.027-0.01818.506-0.001-0.0010.0000.0000.0000.000
10A10LEU 0-0.026-0.02521.176-0.006-0.0060.0000.0000.0000.000
11A11ASN 0-0.014-0.01822.741-0.006-0.0060.0000.0000.0000.000
12A12GLY 00.0710.04420.123-0.008-0.0080.0000.0000.0000.000
13A13LEU 00.015-0.00315.193-0.010-0.0100.0000.0000.0000.000
14A14GLU -1-0.822-0.86718.583-0.069-0.0690.0000.0000.0000.000
15A15TYR 0-0.069-0.05121.512-0.010-0.0100.0000.0000.0000.000
16A16ILE 00.0450.01416.382-0.007-0.0070.0000.0000.0000.000
17A17GLN 0-0.025-0.01717.5500.0050.0050.0000.0000.0000.000
18A18VAL 0-0.024-0.00320.325-0.006-0.0060.0000.0000.0000.000
19A19HIS 0-0.069-0.03023.0760.0070.0070.0000.0000.0000.000
20A20LEU 0-0.049-0.02619.6630.0000.0000.0000.0000.0000.000
21A21PRO 00.0260.02918.786-0.027-0.0270.0000.0000.0000.000
22A22HIS 00.0710.02417.321-0.037-0.0370.0000.0000.0000.000
23A23ILE 0-0.016-0.00215.224-0.062-0.0620.0000.0000.0000.000
24A24TRP 00.0330.01111.552-0.064-0.0640.0000.0000.0000.000
25A25GLU -1-0.914-0.94212.335-0.453-0.4530.0000.0000.0000.000
26A26GLU -1-0.806-0.89910.962-0.508-0.5080.0000.0000.0000.000
27A27ILE 0-0.013-0.0149.230-0.205-0.2050.0000.0000.0000.000
28A28GLN 0-0.051-0.0357.820-0.274-0.2740.0000.0000.0000.000
29A29GLU -1-0.942-0.9836.296-1.624-1.6240.0000.0000.0000.000
30A30ILE 0-0.021-0.0225.802-0.925-0.9250.0000.0000.0000.000
31A31ILE 0-0.031-0.0132.648-1.514-0.5270.416-0.365-1.037-0.001
32A32VAL 00.020-0.0062.131-11.778-11.0727.000-3.711-3.996-0.045
33A33SER 0-0.143-0.0562.5522.8833.2761.918-0.602-1.709-0.010
34A34ILE 0-0.0230.0022.409-0.4961.9061.219-0.997-2.624-0.001
35A35ASP -1-0.804-0.8841.651-8.821-19.80023.922-8.565-4.378-0.056
36A36ALA 00.046-0.0092.0451.588-0.2416.863-1.833-3.2000.000
37A37GLU -1-0.911-0.9483.8220.0500.2370.0290.005-0.2200.000
38A38ALA 0-0.033-0.0096.9810.1280.1280.0000.0000.0000.000
39A39CYS 0-0.078-0.0395.5880.3480.3480.0000.0000.0000.000
40A40ARG 10.8360.9447.734-0.010-0.0100.0000.0000.0000.000
41A41THR 00.014-0.0029.084-0.037-0.0370.0000.0000.0000.000
42A42LYS 10.9120.97111.236-0.235-0.2350.0000.0000.0000.000
43A43GLU -1-0.876-0.94113.0880.0940.0940.0000.0000.0000.000
44A44SER 0-0.051-0.02815.2370.0010.0010.0000.0000.0000.000
45A45LYS 10.9640.96916.608-0.131-0.1310.0000.0000.0000.000
46A46GLU -1-0.898-0.94416.4970.1540.1540.0000.0000.0000.000
47A47LYS 11.0050.99020.775-0.083-0.0830.0000.0000.0000.000
48A48THR 0-0.064-0.04320.355-0.003-0.0030.0000.0000.0000.000
49A49LYS 10.9560.99414.464-0.145-0.1450.0000.0000.0000.000
50A50GLN 0-0.0020.00018.7730.0030.0030.0000.0000.0000.000
51A51GLY 00.0200.01620.404-0.004-0.0040.0000.0000.0000.000
52A52GLN 00.0220.02514.177-0.005-0.0050.0000.0000.0000.000
53A53ILE 00.0210.00112.1480.0100.0100.0000.0000.0000.000
54A54LEU 0-0.084-0.03810.440-0.016-0.0160.0000.0000.0000.000
55A55TYR 00.0690.0354.8800.0600.0600.0000.0000.0000.000
56A56SER 0-0.049-0.0287.4620.0140.0140.0000.0000.0000.000
57A57PRO 00.0300.0167.3840.1960.1960.0000.0000.0000.000
58A58VAL 0-0.014-0.0188.4130.1070.1070.0000.0000.0000.000
59A59ALA 00.0440.0328.299-0.014-0.0140.0000.0000.0000.000
60A60LEU 00.021-0.0132.634-0.845-0.1931.002-0.255-1.3990.000
61A61ASN 0-0.010-0.0106.1770.2490.2490.0000.0000.0000.000
62A62GLU -1-0.955-0.9699.1740.1200.1200.0000.0000.0000.000
63A63ALA 0-0.0030.0076.331-0.185-0.1850.0000.0000.0000.000
64A64PHE 00.007-0.0213.862-1.155-0.4480.106-0.200-0.6120.000
65A65LYS 10.9030.9618.349-0.436-0.4360.0000.0000.0000.000
66A66GLU -1-0.931-0.94511.530-0.356-0.3560.0000.0000.0000.000
67A67LYS 10.9300.9637.4271.2761.2760.0000.0000.0000.000
68A68LEU 00.0090.00010.283-0.051-0.0510.0000.0000.0000.000
69A69GLU -1-0.866-0.94612.5920.0350.0350.0000.0000.0000.000
70A70ALA 0-0.049-0.00414.126-0.007-0.0070.0000.0000.0000.000
71A71LYS 10.8830.94712.5520.4830.4830.0000.0000.0000.000
72A72GLY 0-0.025-0.00715.8570.0110.0110.0000.0000.0000.000
73A73TRP 0-0.101-0.04914.3170.0640.0640.0000.0000.0000.000
74A74LYS 10.9921.00217.4320.0190.0190.0000.0000.0000.000
75A75GLU -1-0.879-0.93619.7370.0900.0900.0000.0000.0000.000
76A76SER 0-0.076-0.03620.644-0.021-0.0210.0000.0000.0000.000
77A77ARG 10.9170.96222.922-0.063-0.0630.0000.0000.0000.000
78A78THR 00.005-0.00225.552-0.014-0.0140.0000.0000.0000.000
79A79ASN 00.004-0.00528.4110.0130.0130.0000.0000.0000.000
80A80TYR 00.0160.00428.040-0.005-0.0050.0000.0000.0000.000
81A81TYR 0-0.0010.00133.7350.0040.0040.0000.0000.0000.000
82A82VAL 0-0.0160.00433.207-0.001-0.0010.0000.0000.0000.000
83A83THR 00.021-0.00536.425-0.002-0.0020.0000.0000.0000.000
84A84ALA 00.0190.00039.0390.0010.0010.0000.0000.0000.000
85A85ASP -1-0.914-0.94340.7960.0290.0290.0000.0000.0000.000
86A86PRO 00.0510.01440.2930.0000.0000.0000.0000.0000.000
87A87LYS 10.9280.93041.262-0.025-0.0250.0000.0000.0000.000
88A88LEU 00.0740.05942.789-0.001-0.0010.0000.0000.0000.000
89A89ILE 0-0.0040.00336.7850.0000.0000.0000.0000.0000.000
90A90ARG 10.8950.93838.619-0.032-0.0320.0000.0000.0000.000
91A91GLU -1-0.948-0.96540.7330.0220.0220.0000.0000.0000.000
92A92THR 0-0.040-0.01839.824-0.001-0.0010.0000.0000.0000.000
93A93LEU 0-0.039-0.01735.1960.0010.0010.0000.0000.0000.000
94A94SER 0-0.019-0.00536.7160.0010.0010.0000.0000.0000.000
95A95LEU 0-0.0160.01238.966-0.002-0.0020.0000.0000.0000.000
96A96GLU -1-0.854-0.92937.0470.0210.0210.0000.0000.0000.000
97A97PRO 0-0.003-0.01434.7480.0010.0010.0000.0000.0000.000
98A98GLU -1-0.928-0.96237.3890.0280.0280.0000.0000.0000.000
99A99GLU -1-0.901-0.96540.5420.0160.0160.0000.0000.0000.000
100A100GLN 0-0.017-0.02636.0120.0030.0030.0000.0000.0000.000
101A101LYS 10.9480.97640.262-0.030-0.0300.0000.0000.0000.000
102A102LYS 10.9380.98341.758-0.016-0.0160.0000.0000.0000.000
103A103VAL 0-0.004-0.01344.452-0.001-0.0010.0000.0000.0000.000
104A104ILE 0-0.054-0.02440.0540.0000.0000.0000.0000.0000.000
105A105GLU -1-0.824-0.92944.4270.0280.0280.0000.0000.0000.000
106A106ALA 0-0.0590.00346.580-0.001-0.0010.0000.0000.0000.000
107A107ALA 0-0.059-0.04847.945-0.001-0.0010.0000.0000.0000.000
108A108GLY 0-0.067-0.03249.6440.0000.0000.0000.0000.0000.000
109A109LYS 10.8510.94244.323-0.027-0.0270.0000.0000.0000.000
110A110GLU -1-0.888-0.94041.1920.0400.0400.0000.0000.0000.000
111A111ALA 00.0180.00640.2940.0010.0010.0000.0000.0000.000
112A112LEU 0-0.016-0.00135.6970.0010.0010.0000.0000.0000.000
113A113LYS 10.8530.92931.090-0.057-0.0570.0000.0000.0000.000
114A114SER 00.0150.01529.6710.0070.0070.0000.0000.0000.000
115A115TYR 0-0.043-0.05124.382-0.011-0.0110.0000.0000.0000.000
116A116ASN 00.0200.03824.127-0.002-0.0020.0000.0000.0000.000
117A117GLN 00.0270.00220.414-0.022-0.0220.0000.0000.0000.000
118A118THR 00.0280.00617.7100.0070.0070.0000.0000.0000.000
119A119ASP -1-0.917-0.96415.2590.2100.2100.0000.0000.0000.000
120A120PHE 0-0.0010.01512.093-0.028-0.0280.0000.0000.0000.000
121A121VAL 0-0.009-0.01416.6190.0050.0050.0000.0000.0000.000
122A122LYS 10.8130.88916.7760.1850.1850.0000.0000.0000.000
123A123ASP -1-0.899-0.94320.235-0.098-0.0980.0000.0000.0000.000
124A124ARG 10.7770.88622.5290.0140.0140.0000.0000.0000.000
125A125VAL 00.0230.03116.7750.0060.0060.0000.0000.0000.000
126A126ALA 00.024-0.01018.1290.0010.0010.0000.0000.0000.000
127A127ILE 00.0040.00611.3990.0070.0070.0000.0000.0000.000
128A128GLU -1-0.859-0.93813.5210.2610.2610.0000.0000.0000.000
129A129VAL 0-0.0130.0107.3920.0740.0740.0000.0000.0000.000
130A130GLN 0-0.018-0.01010.037-0.024-0.0240.0000.0000.0000.000
131A131PHE 00.003-0.0123.938-0.338-0.1230.002-0.029-0.1880.000
132A132GLY 00.0210.0059.621-0.067-0.0670.0000.0000.0000.000
133A133LYS 10.8100.90013.293-0.194-0.1940.0000.0000.0000.000
134A134TYR 00.0990.01415.090-0.008-0.0080.0000.0000.0000.000
135A135SER 0-0.046-0.00916.0120.0010.0010.0000.0000.0000.000
136A136PHE 0-0.009-0.02016.043-0.022-0.0220.0000.0000.0000.000
137A137VAL 00.0820.07513.668-0.001-0.0010.0000.0000.0000.000
138A138ALA 00.0060.01016.472-0.020-0.0200.0000.0000.0000.000
139A139TYR 0-0.030-0.01419.916-0.020-0.0200.0000.0000.0000.000
140A140ASP -1-0.728-0.87115.6550.2640.2640.0000.0000.0000.000
141A141LEU 0-0.049-0.03317.011-0.026-0.0260.0000.0000.0000.000
142A142PHE 0-0.063-0.04820.042-0.020-0.0200.0000.0000.0000.000
143A143VAL 0-0.053-0.01522.856-0.013-0.0130.0000.0000.0000.000
144A144LYS 10.8390.93118.382-0.211-0.2110.0000.0000.0000.000
145A145HIS 00.0430.03316.302-0.051-0.0510.0000.0000.0000.000
146A146MET 0-0.0240.00721.782-0.020-0.0200.0000.0000.0000.000
147A147ALA 00.0150.01725.107-0.011-0.0110.0000.0000.0000.000
148A148PHE 0-0.010-0.01921.271-0.013-0.0130.0000.0000.0000.000
149A149TYR 00.036-0.00325.060-0.009-0.0090.0000.0000.0000.000
150A150VAL 0-0.022-0.01926.654-0.008-0.0080.0000.0000.0000.000
151A151SER 0-0.121-0.05728.987-0.004-0.0040.0000.0000.0000.000
152A152ASP -1-0.881-0.91429.545-0.004-0.0040.0000.0000.0000.000
153A153LYS 10.8940.95026.498-0.037-0.0370.0000.0000.0000.000
154A154ILE 0-0.122-0.01019.977-0.004-0.0040.0000.0000.0000.000
155A155ASP -1-0.746-0.86023.026-0.018-0.0180.0000.0000.0000.000
156A156VAL 0-0.058-0.04018.558-0.001-0.0010.0000.0000.0000.000
157A157GLY 00.015-0.00218.805-0.001-0.0010.0000.0000.0000.000
158A158VAL 0-0.050-0.03012.364-0.011-0.0110.0000.0000.0000.000
159A159GLU -1-0.815-0.93012.5060.3460.3460.0000.0000.0000.000
160A160ILE 0-0.014-0.0036.646-0.015-0.0150.0000.0000.0000.000
161A161LEU 0-0.019-0.0248.3270.0410.0410.0000.0000.0000.000
162A162PRO 00.0070.0225.2130.0810.0810.0000.0000.0000.000
163A163MET 00.0530.0316.101-0.140-0.1400.0000.0000.0000.000
164A164LYS 10.8970.9438.185-0.165-0.1650.0000.0000.0000.000
165A165GLU -1-0.954-0.9967.7200.1360.1360.0000.0000.0000.000
166A166LEU 00.0930.0752.734-0.448-0.0110.455-0.133-0.7580.000
167A167SER 00.0090.0006.8840.0060.0060.0000.0000.0000.000
168A168LYS 10.8360.9369.100-0.117-0.1170.0000.0000.0000.000
169A169GLU -1-0.919-0.9748.4430.0380.0380.0000.0000.0000.000
170A170MET 00.0170.0275.6010.0070.0070.0000.0000.0000.000
171A171SER 0-0.032-0.0289.785-0.024-0.0240.0000.0000.0000.000
172A172SER 0-0.030-0.01812.9030.0140.0140.0000.0000.0000.000
173A173GLY 0-0.083-0.04215.3670.0110.0110.0000.0000.0000.000
174A174ILE 00.0750.0339.483-0.011-0.0110.0000.0000.0000.000
175A175SER 0-0.0180.00912.307-0.019-0.0190.0000.0000.0000.000
176A176TYR 0-0.017-0.01010.2800.0220.0220.0000.0000.0000.000
177A177TYR 00.0740.0339.606-0.037-0.0370.0000.0000.0000.000
178A178GLU -1-0.784-0.90411.4270.1590.1590.0000.0000.0000.000
179A179GLY 0-0.033-0.02114.279-0.020-0.0200.0000.0000.0000.000
180A180GLU -1-0.850-0.94414.2220.1750.1750.0000.0000.0000.000
181A181LEU 00.0190.01815.202-0.019-0.0190.0000.0000.0000.000
182A182TYR 0-0.015-0.00316.857-0.023-0.0230.0000.0000.0000.000
183A183ASN 0-0.039-0.01818.848-0.032-0.0320.0000.0000.0000.000
184A184VAL 00.0130.03518.958-0.009-0.0090.0000.0000.0000.000
185A185ILE 00.001-0.00120.488-0.012-0.0120.0000.0000.0000.000
186A186ARG 10.8290.91222.862-0.094-0.0940.0000.0000.0000.000
187A187GLN 0-0.118-0.05923.751-0.011-0.0110.0000.0000.0000.000
188A188GLY 00.0200.00927.230-0.002-0.0020.0000.0000.0000.000
189A189ARG 10.9880.97625.713-0.008-0.0080.0000.0000.0000.000
190A190GLY 00.0160.00126.703-0.006-0.0060.0000.0000.0000.000
191A191VAL 0-0.0660.00926.453-0.001-0.0010.0000.0000.0000.000
192A192PRO 00.0570.01022.4990.0020.0020.0000.0000.0000.000
193A193ALA 00.018-0.00225.361-0.004-0.0040.0000.0000.0000.000
194A194VAL 00.006-0.00922.378-0.003-0.0030.0000.0000.0000.000
195A195PRO 00.0070.02022.8510.0080.0080.0000.0000.0000.000
196A196LEU 0-0.022-0.01518.1470.0120.0120.0000.0000.0000.000
197A197VAL 00.0260.01913.602-0.021-0.0210.0000.0000.0000.000
198A198LEU 0-0.0230.00513.3940.0400.0400.0000.0000.0000.000
199A199ILE 00.0220.0037.629-0.066-0.0660.0000.0000.0000.000
200A200GLY 00.021-0.0108.0580.1690.1690.0000.0000.0000.000
201A201ILE 0-0.002-0.0072.627-1.628-1.2032.734-0.570-2.5890.005
202A202ALA 0-0.049-0.0673.488-0.814-0.1630.025-0.205-0.471-0.001
203A203PRO -1-0.915-0.8701.8013.858-5.27017.249-1.888-6.2330.005