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: MMK1Z

Calculation Name: 1VAJ-A-Xray315

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VAJ

Chain ID: A

ChEMBL ID:

UniProt ID: O57770

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 205
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2421280.685523
FMO2-HF: Nuclear repulsion 2340406.18711
FMO2-HF: Total energy -80874.498413
FMO2-MP2: Total energy -81113.698111


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:ACE )


Summations of interaction energy for fragment #1(A:2:ACE )
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.
-0.3190.378-0.004-0.281-0.4120
Interaction energy analysis for fragmet #1(A:2:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.028 / q_NPA : -0.025
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].
3A4LYS 10.8580.9383.8791.5042.201-0.004-0.281-0.4120.000
4A5ILE 0-0.032-0.0136.6250.4140.4140.0000.0000.0000.000
5A6LYS 10.8950.9608.6550.1120.1120.0000.0000.0000.000
6A7ASP -1-0.762-0.8839.601-0.802-0.8020.0000.0000.0000.000
7A8GLU -1-0.818-0.92311.597-0.308-0.3080.0000.0000.0000.000
8A9TRP 0-0.021-0.02910.8900.0220.0220.0000.0000.0000.000
9A10GLY 00.0620.03713.3070.0360.0360.0000.0000.0000.000
10A11GLU -1-0.937-0.98514.474-0.253-0.2530.0000.0000.0000.000
11A12PHE 0-0.062-0.04217.2350.0410.0410.0000.0000.0000.000
12A13LEU 00.013-0.00215.2630.0320.0320.0000.0000.0000.000
13A14VAL 00.0370.02717.7390.0280.0280.0000.0000.0000.000
14A15ARG 10.9430.97419.6590.2330.2330.0000.0000.0000.000
15A16LEU 0-0.070-0.02222.1770.0230.0230.0000.0000.0000.000
16A17ALA 00.0480.02022.4560.0170.0170.0000.0000.0000.000
17A18ARG 10.7620.85524.2400.1540.1540.0000.0000.0000.000
18A19ARG 10.9350.96526.5250.1280.1280.0000.0000.0000.000
19A20ALA 0-0.006-0.01027.2600.0110.0110.0000.0000.0000.000
20A21ILE 00.0330.02527.2320.0100.0100.0000.0000.0000.000
21A22GLU -1-0.847-0.92830.405-0.099-0.0990.0000.0000.0000.000
22A23GLU -1-0.928-0.96832.068-0.068-0.0680.0000.0000.0000.000
23A24TYR 00.0200.02432.9520.0070.0070.0000.0000.0000.000
24A25LEU 0-0.026-0.01433.9620.0070.0070.0000.0000.0000.000
25A26LYS 10.8600.95434.7170.0860.0860.0000.0000.0000.000
26A27THR 0-0.072-0.06037.2960.0050.0050.0000.0000.0000.000
27A28GLY 0-0.0050.01237.9900.0040.0040.0000.0000.0000.000
28A29LYS 10.8740.93336.3210.0580.0580.0000.0000.0000.000
29A30GLU -1-0.841-0.90630.389-0.096-0.0960.0000.0000.0000.000
30A31ILE 0-0.082-0.04127.4180.0030.0030.0000.0000.0000.000
31A32GLU -1-0.881-0.94129.620-0.073-0.0730.0000.0000.0000.000
32A33PRO 0-0.003-0.00224.622-0.006-0.0060.0000.0000.0000.000
33A34PRO 0-0.058-0.00724.2830.0120.0120.0000.0000.0000.000
34A35LYS 10.9550.97925.4780.0870.0870.0000.0000.0000.000
35A36ASP -1-0.937-0.97524.067-0.118-0.1180.0000.0000.0000.000
36A37THR 00.019-0.02020.707-0.016-0.0160.0000.0000.0000.000
37A38PRO 0-0.0150.00516.9260.0140.0140.0000.0000.0000.000
38A39PRO 00.0440.01718.472-0.009-0.0090.0000.0000.0000.000
39A40GLU -1-0.858-0.94413.577-0.144-0.1440.0000.0000.0000.000
40A41LEU 0-0.036-0.01514.595-0.022-0.0220.0000.0000.0000.000
41A42TRP 0-0.004-0.00317.3400.0050.0050.0000.0000.0000.000
42A43GLU -1-0.905-0.94314.082-0.150-0.1500.0000.0000.0000.000
43A44LYS 10.8740.95218.0440.0570.0570.0000.0000.0000.000
44A45MET 0-0.001-0.00211.554-0.017-0.0170.0000.0000.0000.000
45A46GLY 00.0270.03916.5420.0190.0190.0000.0000.0000.000
46A47VAL 0-0.023-0.02316.541-0.047-0.0470.0000.0000.0000.000
47A48PHE 00.0280.00918.4920.0370.0370.0000.0000.0000.000
48A49VAL 0-0.0290.00519.677-0.032-0.0320.0000.0000.0000.000
49A50THR 00.024-0.00121.4960.0260.0260.0000.0000.0000.000
50A51LEU 0-0.0090.00923.615-0.008-0.0080.0000.0000.0000.000
51A52ASN 00.0250.01223.1270.0210.0210.0000.0000.0000.000
52A53ARG 10.8930.92227.0070.0940.0940.0000.0000.0000.000
53A54TYR 00.028-0.00226.4110.0010.0010.0000.0000.0000.000
54A55ASN 0-0.046-0.02628.9750.0060.0060.0000.0000.0000.000
55A56VAL 0-0.0280.00929.9840.0100.0100.0000.0000.0000.000
56A57PRO 00.001-0.00429.424-0.008-0.0080.0000.0000.0000.000
57A58PRO 00.0870.04525.2280.0020.0020.0000.0000.0000.000
58A59GLN 00.0300.03227.0800.0040.0040.0000.0000.0000.000
59A60THR 0-0.126-0.07928.6730.0080.0080.0000.0000.0000.000
60A61ALA 0-0.012-0.00627.1630.0050.0050.0000.0000.0000.000
61A62LEU 00.0250.03925.7030.0000.0000.0000.0000.0000.000
62A63ARG 10.7450.85128.4120.1020.1020.0000.0000.0000.000
63A64GLY 00.0300.02228.3940.0090.0090.0000.0000.0000.000
64A65CYS 0-0.103-0.04623.276-0.012-0.0120.0000.0000.0000.000
65A66ILE 00.0330.02725.3450.0100.0100.0000.0000.0000.000
66A67GLY 00.045-0.00522.615-0.017-0.0170.0000.0000.0000.000
67A68PHE 0-0.066-0.01321.9660.0200.0200.0000.0000.0000.000
68A69PRO 00.0400.01720.310-0.018-0.0180.0000.0000.0000.000
69A70THR 00.0190.01019.600-0.008-0.0080.0000.0000.0000.000
70A71PRO 00.0300.02418.228-0.007-0.0070.0000.0000.0000.000
71A72ILE 0-0.038-0.03220.2750.0150.0150.0000.0000.0000.000
72A73TYR 0-0.016-0.00622.5090.0130.0130.0000.0000.0000.000
73A74PRO 0-0.006-0.00220.765-0.014-0.0140.0000.0000.0000.000
74A75LEU 00.0420.01914.878-0.001-0.0010.0000.0000.0000.000
75A76VAL 00.0130.00518.970-0.006-0.0060.0000.0000.0000.000
76A77GLU -1-0.899-0.96821.162-0.090-0.0900.0000.0000.0000.000
77A78ALA 0-0.005-0.00220.8670.0060.0060.0000.0000.0000.000
78A79THR 0-0.001-0.01519.847-0.009-0.0090.0000.0000.0000.000
79A80ILE 0-0.034-0.00822.1000.0040.0040.0000.0000.0000.000
80A81LYS 10.8960.93725.5820.1010.1010.0000.0000.0000.000
81A82ALA 00.0120.01423.3640.0060.0060.0000.0000.0000.000
82A83ALA 00.0090.01224.6480.0020.0020.0000.0000.0000.000
83A84ILE 00.0240.01726.0420.0060.0060.0000.0000.0000.000
84A85TYR 00.014-0.00428.2470.0050.0050.0000.0000.0000.000
85A86SER 0-0.078-0.03726.4420.0030.0030.0000.0000.0000.000
86A87ALA 00.010-0.00128.5970.0030.0030.0000.0000.0000.000
87A88VAL 0-0.067-0.04331.1750.0070.0070.0000.0000.0000.000
88A89ASP -1-0.912-0.94432.393-0.075-0.0750.0000.0000.0000.000
89A90ASP -1-0.712-0.83029.982-0.108-0.1080.0000.0000.0000.000
90A91PRO 0-0.021-0.02732.4900.0040.0040.0000.0000.0000.000
91A92ARG 10.7830.87127.9980.1120.1120.0000.0000.0000.000
92A93PHE 0-0.030-0.01630.6030.0020.0020.0000.0000.0000.000
93A94PRO 0-0.0320.00635.7360.0010.0010.0000.0000.0000.000
94A95PRO 00.0610.01935.649-0.004-0.0040.0000.0000.0000.000
95A96VAL 0-0.020-0.00831.8720.0030.0030.0000.0000.0000.000
96A97LYS 10.9390.97335.2080.0630.0630.0000.0000.0000.000
97A98LEU 00.0350.00334.911-0.004-0.0040.0000.0000.0000.000
98A99GLU -1-0.900-0.96435.606-0.071-0.0710.0000.0000.0000.000
99A100GLU -1-0.785-0.87733.863-0.090-0.0900.0000.0000.0000.000
100A101MET 0-0.0270.00028.561-0.006-0.0060.0000.0000.0000.000
101A102ASP -1-0.865-0.91131.206-0.094-0.0940.0000.0000.0000.000
102A103ASN 0-0.116-0.07432.4540.0000.0000.0000.0000.0000.000
103A104LEU 00.0220.02128.788-0.001-0.0010.0000.0000.0000.000
104A105VAL 0-0.018-0.00123.9660.0020.0020.0000.0000.0000.000
105A106VAL 0-0.011-0.01921.9590.0010.0010.0000.0000.0000.000
106A107GLU -1-0.848-0.93718.437-0.296-0.2960.0000.0000.0000.000
107A108VAL 0-0.012-0.00216.5260.0200.0200.0000.0000.0000.000
108A109SER 00.001-0.00615.185-0.066-0.0660.0000.0000.0000.000
109A110VAL 00.010-0.00212.3250.0560.0560.0000.0000.0000.000
110A111LEU 0-0.012-0.00912.497-0.086-0.0860.0000.0000.0000.000
111A112THR 0-0.024-0.0079.3170.0320.0320.0000.0000.0000.000
112A113PRO 0-0.032-0.03712.5400.0210.0210.0000.0000.0000.000
113A114PRO 00.0170.01114.9940.0050.0050.0000.0000.0000.000
114A115GLU -1-0.959-0.97214.2030.0090.0090.0000.0000.0000.000
115A116LEU 0-0.039-0.02717.948-0.006-0.0060.0000.0000.0000.000
116A117ILE 0-0.024-0.00619.9630.0110.0110.0000.0000.0000.000
117A118GLU -1-0.954-0.97521.7620.0350.0350.0000.0000.0000.000
118A119GLY 0-0.049-0.04024.0280.0000.0000.0000.0000.0000.000
119A120PRO 00.0050.00026.843-0.004-0.0040.0000.0000.0000.000
120A121PRO 00.0740.03728.302-0.001-0.0010.0000.0000.0000.000
121A122GLU -1-0.836-0.93228.830-0.007-0.0070.0000.0000.0000.000
122A123GLU -1-1.012-1.01726.6210.0130.0130.0000.0000.0000.000
123A124ARG 10.7760.88424.3910.0260.0260.0000.0000.0000.000
124A125PRO 00.0680.03223.044-0.004-0.0040.0000.0000.0000.000
125A126ARG 10.9390.97022.402-0.009-0.0090.0000.0000.0000.000
126A127LYS 10.8740.95519.703-0.003-0.0030.0000.0000.0000.000
127A128ILE 0-0.0050.02318.042-0.005-0.0050.0000.0000.0000.000
128A129LYS 10.9190.95412.8280.0720.0720.0000.0000.0000.000
129A130VAL 00.0610.04216.200-0.039-0.0390.0000.0000.0000.000
130A131GLY 0-0.012-0.00515.3960.0090.0090.0000.0000.0000.000
131A132ARG 10.6880.80410.7490.0430.0430.0000.0000.0000.000
132A133ASP -1-0.774-0.86613.088-0.181-0.1810.0000.0000.0000.000
133A134GLY 00.0350.03615.448-0.001-0.0010.0000.0000.0000.000
134A135LEU 0-0.010-0.02017.6670.0180.0180.0000.0000.0000.000
135A136ILE 00.002-0.00720.473-0.007-0.0070.0000.0000.0000.000
136A137VAL 00.0120.01023.0980.0090.0090.0000.0000.0000.000
137A138GLU -1-0.895-0.95826.461-0.067-0.0670.0000.0000.0000.000
138A139LYS 10.9540.98028.9110.0340.0340.0000.0000.0000.000
139A140GLY 0-0.0210.00032.438-0.001-0.0010.0000.0000.0000.000
140A141ILE 0-0.022-0.02333.623-0.001-0.0010.0000.0000.0000.000
141A142TYR 0-0.055-0.01033.168-0.003-0.0030.0000.0000.0000.000
142A143SER 00.015-0.01027.297-0.001-0.0010.0000.0000.0000.000
143A144GLY 00.0180.01727.579-0.001-0.0010.0000.0000.0000.000
144A145LEU 0-0.032-0.00320.4640.0000.0000.0000.0000.0000.000
145A146LEU 0-0.026-0.00922.506-0.001-0.0010.0000.0000.0000.000
146A147LEU 0-0.003-0.00818.155-0.006-0.0060.0000.0000.0000.000
147A148PRO 00.0420.01514.6200.0170.0170.0000.0000.0000.000
148A149GLN 00.010-0.01217.2060.0050.0050.0000.0000.0000.000
149A150VAL 0-0.0060.01218.5400.0180.0180.0000.0000.0000.000
150A151PRO 00.0290.01919.6870.0110.0110.0000.0000.0000.000
151A152VAL 0-0.034-0.01117.1280.0070.0070.0000.0000.0000.000
152A153GLU -1-0.944-0.97320.578-0.135-0.1350.0000.0000.0000.000
153A154TRP 0-0.057-0.04323.0960.0170.0170.0000.0000.0000.000
154A155GLY 0-0.058-0.00624.1360.0100.0100.0000.0000.0000.000
155A156TRP 00.0190.01224.2070.0020.0020.0000.0000.0000.000
156A157ASP -1-0.835-0.91223.293-0.064-0.0640.0000.0000.0000.000
157A158GLU -1-0.851-0.96620.259-0.077-0.0770.0000.0000.0000.000
158A159GLU -1-0.943-0.97423.355-0.033-0.0330.0000.0000.0000.000
159A160GLU -1-0.878-0.93926.985-0.063-0.0630.0000.0000.0000.000
160A161PHE 0-0.020-0.01519.447-0.005-0.0050.0000.0000.0000.000
161A162LEU 0-0.010-0.00523.936-0.004-0.0040.0000.0000.0000.000
162A163ALA 00.0150.01726.1990.0010.0010.0000.0000.0000.000
163A164GLU -1-0.894-0.95527.110-0.073-0.0730.0000.0000.0000.000
164A165THR 0-0.062-0.04524.304-0.007-0.0070.0000.0000.0000.000
165A166CYS 0-0.092-0.02926.9640.0030.0030.0000.0000.0000.000
166A167TRP 00.0380.02430.0020.0040.0040.0000.0000.0000.000
167A168LYS 10.8800.95327.1380.1040.1040.0000.0000.0000.000
168A169ALA 0-0.013-0.00929.302-0.001-0.0010.0000.0000.0000.000
169A170GLY 0-0.052-0.01230.9630.0040.0040.0000.0000.0000.000
170A171LEU 0-0.063-0.04131.5670.0050.0050.0000.0000.0000.000
171A172PRO 0-0.006-0.00734.542-0.002-0.0020.0000.0000.0000.000
172A173PRO 00.0520.00832.900-0.001-0.0010.0000.0000.0000.000
173A174ASP -1-0.878-0.93232.131-0.033-0.0330.0000.0000.0000.000
174A175CYS 0-0.0060.01232.2790.0030.0030.0000.0000.0000.000
175A176TRP 00.0540.01028.1870.0030.0030.0000.0000.0000.000
176A177LEU 00.0090.01429.9530.0030.0030.0000.0000.0000.000
177A178ASP -1-0.911-0.94232.494-0.017-0.0170.0000.0000.0000.000
178A179GLU -1-0.922-0.96831.785-0.011-0.0110.0000.0000.0000.000
179A180ASP -1-0.959-0.97931.589-0.015-0.0150.0000.0000.0000.000
180A181THR 0-0.117-0.05628.993-0.004-0.0040.0000.0000.0000.000
181A182LYS 10.8790.94026.3730.0390.0390.0000.0000.0000.000
182A183VAL 00.0400.01622.677-0.007-0.0070.0000.0000.0000.000
183A184TYR 00.0060.00020.0980.0100.0100.0000.0000.0000.000
184A185LYS 10.8930.95615.5610.0190.0190.0000.0000.0000.000
185A186PHE 0-0.013-0.00114.4120.0100.0100.0000.0000.0000.000
186A187THR 00.0440.0269.179-0.001-0.0010.0000.0000.0000.000
187A188ALA 00.037-0.00511.5350.0290.0290.0000.0000.0000.000
188A189GLU -1-0.806-0.8706.556-2.223-2.2230.0000.0000.0000.000
189A190ILE 0-0.0050.00210.4430.1090.1090.0000.0000.0000.000
190A191PHE 0-0.0270.00110.141-0.063-0.0630.0000.0000.0000.000
191A192GLU -1-0.805-0.91715.235-0.198-0.1980.0000.0000.0000.000
192A193GLU -1-0.774-0.84818.776-0.174-0.1740.0000.0000.0000.000
193A194GLU -1-0.876-0.95420.589-0.195-0.1950.0000.0000.0000.000
194A195TYR 0-0.019-0.02122.5650.0150.0150.0000.0000.0000.000
195A196PRO 0-0.0150.00225.730-0.009-0.0090.0000.0000.0000.000
196A197ARG 10.7590.86626.6260.1130.1130.0000.0000.0000.000
197A198GLY 00.0050.01625.5060.0080.0080.0000.0000.0000.000
198A199PRO 0-0.072-0.03521.320-0.012-0.0120.0000.0000.0000.000
199A200ILE 0-0.0150.01116.861-0.003-0.0030.0000.0000.0000.000
200A201LYS 10.8830.94715.5270.2450.2450.0000.0000.0000.000
201A202ARG 10.8180.9027.8251.3901.3900.0000.0000.0000.000
202A203LYS 10.8450.91912.8570.3240.3240.0000.0000.0000.000
203A204PRO 0-0.045-0.01510.538-0.046-0.0460.0000.0000.0000.000
204A205LEU 00.0050.00412.0720.0840.0840.0000.0000.0000.000
205A206NME 00.0000.00213.563-0.004-0.0040.0000.0000.0000.000