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: N1VKQ

Calculation Name: 1VJN-A-Xray319

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 1VJN

Chain ID: A

ChEMBL ID:
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UniProt ID: Q9WY50

Base Structure: X-ray

Registration Date: 2021-09-07

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 -2401213.993208
FMO2-HF: Nuclear repulsion 2321860.309351
FMO2-HF: Total energy -79353.683858
FMO2-MP2: Total energy -79586.895392


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:ACE )


Summations of interaction energy for fragment #1(A:-1: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.
-1.673-0.0340.297-0.937-0.998-0.003
Interaction energy analysis for fragmet #1(A:-1:ACE )
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 : -0.025
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].
3A1MET 00.0320.0463.8540.9401.739-0.006-0.384-0.409-0.001
4A2LYS 10.9350.9806.9870.4760.4760.0000.0000.0000.000
5A3ILE 0-0.0090.00310.7100.1150.1150.0000.0000.0000.000
6A4THR 0-0.0010.00013.531-0.014-0.0140.0000.0000.0000.000
7A5TRP 0-0.060-0.01717.1020.0250.0250.0000.0000.0000.000
8A6PHE 00.028-0.01619.739-0.003-0.0030.0000.0000.0000.000
9A7GLY 00.0300.01123.3560.0120.0120.0000.0000.0000.000
10A8HIS 0-0.035-0.01725.1270.0030.0030.0000.0000.0000.000
11A9ALA 00.0360.02223.640-0.005-0.0050.0000.0000.0000.000
12A10CYS 0-0.0300.03322.396-0.003-0.0030.0000.0000.0000.000
13A11PHE 00.025-0.00517.194-0.013-0.0130.0000.0000.0000.000
14A12ALA 0-0.0090.00116.9310.0210.0210.0000.0000.0000.000
15A13LEU 0-0.028-0.01812.231-0.042-0.0420.0000.0000.0000.000
16A14GLU -1-0.937-0.97311.263-0.344-0.3440.0000.0000.0000.000
17A15MET 00.0410.0187.668-0.137-0.1370.0000.0000.0000.000
18A16GLU -1-0.848-0.9266.9440.7530.7530.0000.0000.0000.000
19A17GLY 0-0.074-0.0298.4250.0360.0360.0000.0000.0000.000
20A18LYS 10.8190.91811.0420.0790.0790.0000.0000.0000.000
21A19THR 00.0270.00912.410-0.067-0.0670.0000.0000.0000.000
22A20ILE 0-0.014-0.01213.2830.0430.0430.0000.0000.0000.000
23A21VAL 00.015-0.00516.633-0.030-0.0300.0000.0000.0000.000
24A22THR 00.001-0.00418.2790.0140.0140.0000.0000.0000.000
25A23ASP -1-0.794-0.87120.973-0.051-0.0510.0000.0000.0000.000
26A24PRO 0-0.020-0.01724.114-0.007-0.0070.0000.0000.0000.000
27A25PHE 0-0.033-0.02225.8630.0090.0090.0000.0000.0000.000
28A26ASP -1-0.816-0.92429.375-0.054-0.0540.0000.0000.0000.000
29A27GLU -1-0.989-0.99632.073-0.053-0.0530.0000.0000.0000.000
30A28SER 0-0.018-0.02133.9160.0060.0060.0000.0000.0000.000
31A29VAL 00.0080.01334.877-0.005-0.0050.0000.0000.0000.000
32A30GLY 0-0.031-0.02135.0220.0020.0020.0000.0000.0000.000
33A31TYR 0-0.029-0.02030.219-0.002-0.0020.0000.0000.0000.000
34A32PRO 0-0.023-0.00628.4450.0030.0030.0000.0000.0000.000
35A33ILE 00.0350.01628.147-0.006-0.0060.0000.0000.0000.000
36A34PRO 00.0390.02623.714-0.008-0.0080.0000.0000.0000.000
37A35ASN 0-0.041-0.00924.8170.0120.0120.0000.0000.0000.000
38A36VAL 00.022-0.00519.522-0.015-0.0150.0000.0000.0000.000
39A37THR 0-0.049-0.02820.2450.0180.0180.0000.0000.0000.000
40A38ALA 00.0080.00618.956-0.015-0.0150.0000.0000.0000.000
41A39ASP -1-0.838-0.91116.296-0.068-0.0680.0000.0000.0000.000
42A40VAL 0-0.039-0.02917.6880.0220.0220.0000.0000.0000.000
43A41VAL 00.0200.02419.811-0.019-0.0190.0000.0000.0000.000
44A42THR 0-0.008-0.01119.6980.0110.0110.0000.0000.0000.000
45A43GLU -1-0.823-0.91622.491-0.047-0.0470.0000.0000.0000.000
46A44SER 0-0.042-0.03724.7710.0100.0100.0000.0000.0000.000
47A45HIS 10.8840.93826.2160.0350.0350.0000.0000.0000.000
48A46GLN 0-0.010-0.01829.972-0.001-0.0010.0000.0000.0000.000
49A47HIS 00.039-0.01929.1580.0000.0000.0000.0000.0000.000
50A48PHE 0-0.0360.00832.0110.0020.0020.0000.0000.0000.000
51A49ASP -1-0.901-0.95534.900-0.025-0.0250.0000.0000.0000.000
52A50HIS 0-0.040-0.03235.5670.0040.0040.0000.0000.0000.000
53A51ASN 0-0.069-0.02731.578-0.001-0.0010.0000.0000.0000.000
54A52ALA 00.0750.04128.948-0.002-0.0020.0000.0000.0000.000
55A53HIS 0-0.035-0.00326.863-0.003-0.0030.0000.0000.0000.000
56A54HIS 0-0.081-0.04028.5000.0000.0000.0000.0000.0000.000
57A55LEU 00.0010.00929.8180.0000.0000.0000.0000.0000.000
58A56VAL 0-0.0290.00823.180-0.008-0.0080.0000.0000.0000.000
59A57LYS 10.9390.96724.4530.0950.0950.0000.0000.0000.000
60A58GLY 00.0400.02222.922-0.006-0.0060.0000.0000.0000.000
61A59ASN 0-0.078-0.03023.4660.0040.0040.0000.0000.0000.000
62A60PHE 0-0.0010.00622.1400.0070.0070.0000.0000.0000.000
63A61ARG 10.8880.95321.799-0.013-0.0130.0000.0000.0000.000
64A62VAL 00.0520.02222.864-0.004-0.0040.0000.0000.0000.000
65A63ILE 0-0.077-0.04620.7250.0090.0090.0000.0000.0000.000
66A64ASP -1-0.828-0.91124.607-0.006-0.0060.0000.0000.0000.000
67A65ARG 10.9160.93826.557-0.010-0.0100.0000.0000.0000.000
68A66PRO 00.0420.03625.5680.0030.0030.0000.0000.0000.000
69A67GLY 0-0.0040.00824.8380.0000.0000.0000.0000.0000.000
70A68ALA 0-0.016-0.00821.4590.0030.0030.0000.0000.0000.000
71A69TYR 0-0.047-0.04320.352-0.005-0.0050.0000.0000.0000.000
72A70THR 0-0.042-0.02116.7610.0250.0250.0000.0000.0000.000
73A71VAL 0-0.0110.00217.116-0.009-0.0090.0000.0000.0000.000
74A72ASN 0-0.017-0.02015.788-0.008-0.0080.0000.0000.0000.000
75A73GLY 00.0220.01013.239-0.005-0.0050.0000.0000.0000.000
76A74VAL 00.0590.05410.9720.0600.0600.0000.0000.0000.000
77A75LYS 10.8920.95213.197-0.310-0.3100.0000.0000.0000.000
78A76ILE 00.0340.00814.662-0.007-0.0070.0000.0000.0000.000
79A77LYS 10.8660.94317.311-0.089-0.0890.0000.0000.0000.000
80A78GLY 00.0250.02219.841-0.011-0.0110.0000.0000.0000.000
81A79VAL 0-0.004-0.00622.3700.0050.0050.0000.0000.0000.000
82A80GLU -1-0.878-0.94324.8500.0070.0070.0000.0000.0000.000
83A81THR 0-0.035-0.02726.5350.0020.0020.0000.0000.0000.000
84A82PHE 0-0.018-0.01029.279-0.001-0.0010.0000.0000.0000.000
85A83HIS 00.0360.01532.2100.0000.0000.0000.0000.0000.000
86A84ASP -1-0.948-0.94334.9450.0010.0010.0000.0000.0000.000
87A85NME 00.0150.00938.6900.0010.0010.0000.0000.0000.000
88A91ACE 0-0.006-0.00939.4890.0000.0000.0000.0000.0000.000
89A92GLY 0-0.042-0.02535.622-0.003-0.0030.0000.0000.0000.000
90A93LYS 10.8920.95929.9670.0030.0030.0000.0000.0000.000
91A94ASN 0-0.021-0.00926.374-0.009-0.0090.0000.0000.0000.000
92A95ILE 0-0.076-0.02824.1330.0060.0060.0000.0000.0000.000
93A96VAL 00.0230.03221.115-0.007-0.0070.0000.0000.0000.000
94A97PHE 00.002-0.00918.9980.0110.0110.0000.0000.0000.000
95A98VAL 00.001-0.00915.132-0.010-0.0100.0000.0000.0000.000
96A99PHE 00.028-0.00512.8200.0120.0120.0000.0000.0000.000
97A100GLU -1-0.907-0.96510.8450.3310.3310.0000.0000.0000.000
98A101GLY 00.007-0.0238.357-0.017-0.0170.0000.0000.0000.000
99A102GLU -1-0.809-0.9092.795-0.641-0.3780.284-0.252-0.296-0.001
100A103GLY 0-0.111-0.0493.7120.1560.5350.007-0.150-0.236-0.001
101A104ILE 0-0.023-0.0084.139-0.184-0.1390.000-0.013-0.0330.000
102A105LYS 10.8700.9377.207-0.342-0.3420.0000.0000.0000.000
103A106VAL 00.0280.01010.136-0.050-0.0500.0000.0000.0000.000
104A107CYS 0-0.040-0.00712.6720.0270.0270.0000.0000.0000.000
105A108HIS 00.0370.01816.478-0.011-0.0110.0000.0000.0000.000
106A109LEU 00.018-0.02319.1670.0140.0140.0000.0000.0000.000
107A110GLY 00.0210.01822.4040.0070.0070.0000.0000.0000.000
108A111ASP -1-0.860-0.94224.844-0.042-0.0420.0000.0000.0000.000
109A112LEU 0-0.046-0.01325.4100.0040.0040.0000.0000.0000.000
110A113GLY 00.0760.02328.143-0.003-0.0030.0000.0000.0000.000
111A114HIS 10.7310.84430.066-0.006-0.0060.0000.0000.0000.000
112A115VAL 00.0680.02728.5710.0000.0000.0000.0000.0000.000
113A116LEU 0-0.0100.01923.3910.0020.0020.0000.0000.0000.000
114A117THR 00.0250.01427.9330.0020.0020.0000.0000.0000.000
115A118PRO 00.0680.00828.0760.0030.0030.0000.0000.0000.000
116A119ALA 00.0390.03827.5630.0050.0050.0000.0000.0000.000
117A120GLN 00.0730.02526.0740.0030.0030.0000.0000.0000.000
118A121VAL 00.0060.00723.1000.0030.0030.0000.0000.0000.000
119A122GLU -1-0.988-0.98222.5790.0780.0780.0000.0000.0000.000
120A123GLU -1-0.987-0.99422.7370.0700.0700.0000.0000.0000.000
121A124ILE 0-0.030-0.02718.9070.0080.0080.0000.0000.0000.000
122A125GLY 0-0.0020.00718.2990.0160.0160.0000.0000.0000.000
123A126GLU -1-0.940-0.99115.8480.1140.1140.0000.0000.0000.000
124A127ILE 0-0.031-0.01614.2120.0170.0170.0000.0000.0000.000
125A128ASP -1-0.852-0.9139.7260.2410.2410.0000.0000.0000.000
126A129VAL 00.005-0.00910.236-0.052-0.0520.0000.0000.0000.000
127A130LEU 0-0.017-0.01012.9920.0240.0240.0000.0000.0000.000
128A131LEU 00.0120.01915.877-0.017-0.0170.0000.0000.0000.000
129A132VAL 0-0.001-0.01418.8800.0170.0170.0000.0000.0000.000
130A133PRO 00.0140.02622.343-0.008-0.0080.0000.0000.0000.000
131A134VAL 0-0.006-0.02425.4110.0050.0050.0000.0000.0000.000
132A135GLY 00.0200.00828.1760.0010.0010.0000.0000.0000.000
133A136GLY 0-0.039-0.03031.4190.0010.0010.0000.0000.0000.000
134A137THR 0-0.049-0.00433.6070.0040.0040.0000.0000.0000.000
135A138TYR 0-0.019-0.02933.5450.0030.0030.0000.0000.0000.000
136A139THR 00.0090.01029.227-0.001-0.0010.0000.0000.0000.000
137A140ILE 0-0.0050.02426.3110.0010.0010.0000.0000.0000.000
138A141GLY 00.0450.02530.460-0.005-0.0050.0000.0000.0000.000
139A142PRO 00.0080.00328.8970.0010.0010.0000.0000.0000.000
140A143LYS 10.9550.95128.6140.0180.0180.0000.0000.0000.000
141A144GLU -1-0.826-0.90929.525-0.010-0.0100.0000.0000.0000.000
142A145ALA 00.0100.01425.2230.0030.0030.0000.0000.0000.000
143A146LYS 10.8750.94424.6860.0180.0180.0000.0000.0000.000
144A147GLU -1-0.920-0.95125.0340.0070.0070.0000.0000.0000.000
145A148VAL 00.0110.00522.8830.0070.0070.0000.0000.0000.000
146A149ALA 00.010-0.01220.8700.0060.0060.0000.0000.0000.000
147A150ASP -1-0.883-0.94520.8100.0030.0030.0000.0000.0000.000
148A151LEU 0-0.059-0.02122.7010.0100.0100.0000.0000.0000.000
149A152LEU 0-0.0120.00118.8540.0090.0090.0000.0000.0000.000
150A153ASN 0-0.038-0.01417.411-0.005-0.0050.0000.0000.0000.000
151A154ALA 00.0120.02416.1110.0050.0050.0000.0000.0000.000
152A155LYS 10.8900.95012.773-0.054-0.0540.0000.0000.0000.000
153A156VAL 00.0390.02611.834-0.015-0.0150.0000.0000.0000.000
154A157ILE 0-0.024-0.00914.5730.0200.0200.0000.0000.0000.000
155A158ILE 00.0150.00114.876-0.012-0.0120.0000.0000.0000.000
156A159PRO 0-0.0350.00118.9860.0140.0140.0000.0000.0000.000
157A160MET 0-0.017-0.00922.458-0.016-0.0160.0000.0000.0000.000
158A161HIS 00.012-0.00624.5190.0050.0050.0000.0000.0000.000
159A162TYR 00.0080.00624.4600.0080.0080.0000.0000.0000.000
160A163LYS 10.7940.91430.0040.0420.0420.0000.0000.0000.000
161A164THR 00.0490.02830.040-0.005-0.0050.0000.0000.0000.000
162A165LYS 10.9160.94832.7420.0620.0620.0000.0000.0000.000
163A166TYR 00.015-0.02135.0390.0040.0040.0000.0000.0000.000
164A167LEU 00.0780.07432.4080.0040.0040.0000.0000.0000.000
165A168LYS 10.9920.97734.5580.0400.0400.0000.0000.0000.000
166A169PHE 0-0.006-0.01237.0410.0010.0010.0000.0000.0000.000
167A170ASN 00.0000.00338.0930.0000.0000.0000.0000.0000.000
168A171LEU 00.0140.02432.6290.0010.0010.0000.0000.0000.000
169A172LEU 0-0.031-0.02133.087-0.001-0.0010.0000.0000.0000.000
170A173PRO 0-0.012-0.01132.384-0.004-0.0040.0000.0000.0000.000
171A174VAL 00.1000.04825.8120.0030.0030.0000.0000.0000.000
172A175ASP -1-0.878-0.94928.675-0.067-0.0670.0000.0000.0000.000
173A176ASP -1-0.920-0.96930.744-0.037-0.0370.0000.0000.0000.000
174A177PHE 0-0.020-0.02322.9830.0040.0040.0000.0000.0000.000
175A178LEU 0-0.008-0.00624.8620.0020.0020.0000.0000.0000.000
176A179LYS 10.9140.96927.4420.0350.0350.0000.0000.0000.000
177A180LEU 0-0.108-0.04227.9540.0050.0050.0000.0000.0000.000
178A181PHE 0-0.017-0.01823.0390.0060.0060.0000.0000.0000.000
179A182ASP -1-0.895-0.93925.248-0.035-0.0350.0000.0000.0000.000
180A183SER 0-0.080-0.03722.607-0.007-0.0070.0000.0000.0000.000
181A184TYR 0-0.024-0.01821.6330.0030.0030.0000.0000.0000.000
182A185GLU -1-0.878-0.93317.508-0.247-0.2470.0000.0000.0000.000
183A186ARG 10.9050.95721.2140.1040.1040.0000.0000.0000.000
184A187VAL 00.0130.01117.204-0.010-0.0100.0000.0000.0000.000
185A188GLY 00.0550.03720.1750.0200.0200.0000.0000.0000.000
186A189ASN 00.0500.02020.496-0.014-0.0140.0000.0000.0000.000
187A190ILE 00.000-0.01114.745-0.008-0.0080.0000.0000.0000.000
188A191LEU 0-0.018-0.00312.2450.0150.0150.0000.0000.0000.000
189A192GLU -1-0.920-0.9659.914-0.787-0.7870.0000.0000.0000.000
190A193LEU 0-0.054-0.0276.8830.1630.1630.0000.0000.0000.000
191A194PHE 00.025-0.0045.285-0.562-0.5590.000-0.0170.0150.000
192A195GLU -1-0.945-0.9663.811-1.026-0.9120.012-0.114-0.0110.000
193A196LYS 10.9390.9784.817-0.484-0.4480.000-0.007-0.0280.000
194A197PRO 00.003-0.0016.275-0.013-0.0130.0000.0000.0000.000
195A198LYS 10.9560.9849.8150.0190.0190.0000.0000.0000.000
196A199GLU -1-0.948-0.98212.315-0.029-0.0290.0000.0000.0000.000
197A200ARG 10.7780.89114.646-0.001-0.0010.0000.0000.0000.000
198A201LYS 10.8890.94514.0550.2670.2670.0000.0000.0000.000
199A202VAL 00.0080.01817.186-0.008-0.0080.0000.0000.0000.000
200A203VAL 00.007-0.00515.671-0.007-0.0070.0000.0000.0000.000
201A204VAL 0-0.024-0.02118.9070.0090.0090.0000.0000.0000.000
202A205MET 0-0.0110.00416.964-0.006-0.0060.0000.0000.0000.000
203A206GLU -1-0.964-0.99621.165-0.104-0.1040.0000.0000.0000.000
204A207VAL 0-0.057-0.02123.351-0.012-0.0120.0000.0000.0000.000
205A208GLN -1-0.941-0.96324.337-0.152-0.1520.0000.0000.0000.000