Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: G6GM1

Calculation Name: 1VGW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VGW

Chain ID: A

ChEMBL ID:

UniProt ID: Q5F829

Base Structure: X-ray

Registration Date: 2023-09-20

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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2337212.973744
FMO2-HF: Nuclear repulsion 2257240.489168
FMO2-HF: Total energy -79972.484576
FMO2-MP2: Total energy -80210.591529


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:LYS)


Summations of interaction energy for fragment #1(A:2:LYS)
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.
-112.515-110.5620.004-0.727-1.2310
Interaction energy analysis for fragmet #1(A:2:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.986 / q_NPA : 0.970
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].
3A4LYS10.9310.9773.50941.57843.3950.005-0.710-1.1130.000
4A5ASN0-0.029-0.0156.0620.4970.4970.0000.0000.0000.000
5A6ILE00.0190.0119.3541.0781.0780.0000.0000.0000.000
6A7ALA00.0110.01912.2740.5070.5070.0000.0000.0000.000
7A8LEU00.002-0.00215.7790.0220.0220.0000.0000.0000.000
8A9ILE0-0.029-0.02018.8030.4570.4570.0000.0000.0000.000
9A10PRO0-0.0160.01422.3710.1690.1690.0000.0000.0000.000
10A11ALA0-0.012-0.01725.4800.2980.2980.0000.0000.0000.000
11A12ALA00.0060.01128.2600.3070.3070.0000.0000.0000.000
12A23PRO00.0460.01135.7780.0410.0410.0000.0000.0000.000
13A24LYS10.9010.94635.2297.8287.8280.0000.0000.0000.000
14A25GLN00.0510.04630.2370.0670.0670.0000.0000.0000.000
15A26TYR0-0.084-0.12030.647-0.118-0.1180.0000.0000.0000.000
16A27VAL0-0.033-0.01234.1550.2320.2320.0000.0000.0000.000
17A28GLU-1-0.867-0.93234.795-8.480-8.4800.0000.0000.0000.000
18A29ILE0-0.024-0.01834.5610.2660.2660.0000.0000.0000.000
19A30GLY00.0290.02734.426-0.217-0.2170.0000.0000.0000.000
20A31SER0-0.060-0.03833.3360.0600.0600.0000.0000.0000.000
21A32LYS10.9800.99828.5689.3399.3390.0000.0000.0000.000
22A33THR00.0370.03030.767-0.006-0.0060.0000.0000.0000.000
23A34VAL0-0.009-0.01729.693-0.184-0.1840.0000.0000.0000.000
24A35LEU00.0300.01025.302-0.242-0.2420.0000.0000.0000.000
25A36GLU-1-0.865-0.93325.986-9.966-9.9660.0000.0000.0000.000
26A37HIS0-0.064-0.02825.830-0.506-0.5060.0000.0000.0000.000
27A38VAL0-0.042-0.00623.077-0.262-0.2620.0000.0000.0000.000
28A39LEU0-0.011-0.01221.438-0.492-0.4920.0000.0000.0000.000
29A40GLY00.0200.01520.680-0.461-0.4610.0000.0000.0000.000
30A41ILE0-0.081-0.04520.066-0.170-0.1700.0000.0000.0000.000
31A42PHE0-0.017-0.01816.264-0.304-0.3040.0000.0000.0000.000
32A43GLU-1-0.911-0.95016.155-15.087-15.0870.0000.0000.0000.000
33A44ARG10.8970.96216.81011.46911.4690.0000.0000.0000.000
34A45HIS0-0.041-0.02814.316-0.335-0.3350.0000.0000.0000.000
35A46GLU-1-0.917-0.96412.289-16.160-16.1600.0000.0000.0000.000
36A47ALA0-0.044-0.0109.592-1.051-1.0510.0000.0000.0000.000
37A48VAL0-0.051-0.0229.377-1.564-1.5640.0000.0000.0000.000
38A49ASP-1-0.798-0.8916.874-28.439-28.4390.0000.0000.0000.000
39A50LEU0-0.049-0.0389.7210.5370.5370.0000.0000.0000.000
40A51THR00.0410.01812.946-0.083-0.0830.0000.0000.0000.000
41A52VAL0-0.024-0.00316.3970.3650.3650.0000.0000.0000.000
42A53VAL00.0180.00018.9610.2090.2090.0000.0000.0000.000
43A54VAL0-0.036-0.00822.5030.0170.0170.0000.0000.0000.000
44A55VAL00.015-0.00124.8850.2930.2930.0000.0000.0000.000
45A56SER00.020-0.01228.599-0.153-0.1530.0000.0000.0000.000
46A57PRO00.008-0.00830.7860.0340.0340.0000.0000.0000.000
47A58GLU-1-0.912-0.94032.543-8.691-8.6910.0000.0000.0000.000
48A59ASP-1-0.880-0.89531.880-9.242-9.2420.0000.0000.0000.000
49A60THR00.0140.00233.425-0.026-0.0260.0000.0000.0000.000
50A61PHE0-0.041-0.03532.6150.0180.0180.0000.0000.0000.000
51A62ALA00.0530.03429.322-0.147-0.1470.0000.0000.0000.000
52A63ASP-1-0.829-0.91329.281-9.824-9.8240.0000.0000.0000.000
53A64LYS10.9090.93730.1118.0538.0530.0000.0000.0000.000
54A65VAL00.0260.02226.138-0.067-0.0670.0000.0000.0000.000
55A66GLN0-0.034-0.02822.629-0.346-0.3460.0000.0000.0000.000
56A67THR0-0.058-0.02525.705-0.180-0.1800.0000.0000.0000.000
57A68ALA0-0.0210.00027.360-0.037-0.0370.0000.0000.0000.000
58A69PHE0-0.028-0.01621.788-0.089-0.0890.0000.0000.0000.000
59A70PRO00.0200.00822.636-0.370-0.3700.0000.0000.0000.000
60A71GLN0-0.027-0.01717.087-0.556-0.5560.0000.0000.0000.000
61A72VAL00.0140.03717.563-0.898-0.8980.0000.0000.0000.000
62A73ARG10.9260.96815.40117.20817.2080.0000.0000.0000.000
63A74VAL00.0370.01520.067-0.060-0.0600.0000.0000.0000.000
64A75TRP0-0.030-0.01616.8810.3090.3090.0000.0000.0000.000
65A76LYS10.9260.96924.29610.24810.2480.0000.0000.0000.000
66A77ASN00.007-0.00522.9370.2500.2500.0000.0000.0000.000
67A78GLY00.0330.00926.584-0.322-0.3220.0000.0000.0000.000
68A79GLY00.010-0.01228.4190.1300.1300.0000.0000.0000.000
69A80GLN00.0060.00230.0950.2380.2380.0000.0000.0000.000
70A81THR00.0110.01830.2560.0960.0960.0000.0000.0000.000
71A82ARG10.8970.93824.96911.59011.5900.0000.0000.0000.000
72A83ALA00.0500.01126.555-0.419-0.4190.0000.0000.0000.000
73A84GLU-1-0.897-0.95525.741-10.706-10.7060.0000.0000.0000.000
74A85THR0-0.055-0.01825.799-0.508-0.5080.0000.0000.0000.000
75A86VAL00.0270.02721.221-0.445-0.4450.0000.0000.0000.000
76A87ARG10.9330.97521.17710.97110.9710.0000.0000.0000.000
77A88ASN0-0.036-0.02621.322-0.708-0.7080.0000.0000.0000.000
78A89GLY0-0.0090.00420.594-0.387-0.3870.0000.0000.0000.000
79A90VAL00.0320.00815.694-0.784-0.7840.0000.0000.0000.000
80A91ALA00.0180.01016.386-0.978-0.9780.0000.0000.0000.000
81A92LYS10.9310.98217.47613.34913.3490.0000.0000.0000.000
82A93LEU00.001-0.01413.586-0.376-0.3760.0000.0000.0000.000
83A94LEU00.0160.00411.392-1.453-1.4530.0000.0000.0000.000
84A95GLU-1-1.004-0.99313.733-16.651-16.6510.0000.0000.0000.000
85A96THR0-0.034-0.00514.3050.0610.0610.0000.0000.0000.000
86A97GLY00.0220.01611.738-0.071-0.0710.0000.0000.0000.000
87A98LEU0-0.126-0.07110.205-1.872-1.8720.0000.0000.0000.000
88A99ALA0-0.046-0.0168.839-1.715-1.7150.0000.0000.0000.000
89A100ALA00.0130.0145.5371.5131.5130.0000.0000.0000.000
90A101GLU-1-0.921-0.9717.546-24.538-24.5380.0000.0000.0000.000
91A102THR0-0.043-0.0174.369-1.928-1.792-0.001-0.017-0.1180.000
92A103ASP-1-0.769-0.8855.589-48.625-48.6250.0000.0000.0000.000
93A104ASN0-0.073-0.0387.1952.9682.9680.0000.0000.0000.000
94A105ILE00.0020.01210.5800.0600.0600.0000.0000.0000.000
95A106LEU00.001-0.00912.8370.7080.7080.0000.0000.0000.000
96A107VAL00.0160.01916.4260.4940.4940.0000.0000.0000.000
97A108HIS00.0680.01020.051-0.003-0.0030.0000.0000.0000.000
98A109ASP-1-0.852-0.93622.066-10.979-10.9790.0000.0000.0000.000
99A110ALA00.0360.00425.6990.0530.0530.0000.0000.0000.000
100A111ALA0-0.013-0.00926.8740.2010.2010.0000.0000.0000.000
101A112ARG10.8460.93825.92011.07611.0760.0000.0000.0000.000
102A113CYS00.003-0.01625.880-0.351-0.3510.0000.0000.0000.000
103A114CYS00.0070.01427.4160.2520.2520.0000.0000.0000.000
104A115LEU0-0.0100.01620.2000.1260.1260.0000.0000.0000.000
105A116PRO00.0100.00523.698-0.129-0.1290.0000.0000.0000.000
106A117SER00.0530.02519.466-0.309-0.3090.0000.0000.0000.000
107A118GLU-1-0.894-0.95318.952-11.880-11.8800.0000.0000.0000.000
108A119ALA0-0.046-0.03320.212-0.246-0.2460.0000.0000.0000.000
109A120LEU00.0090.00915.729-0.347-0.3470.0000.0000.0000.000
110A121ALA00.0180.00615.293-0.879-0.8790.0000.0000.0000.000
111A122ARG10.9040.96515.57211.58511.5850.0000.0000.0000.000
112A123LEU0-0.0180.00116.347-0.460-0.4600.0000.0000.0000.000
113A124ILE00.001-0.00510.627-0.688-0.6880.0000.0000.0000.000
114A125GLU-1-0.961-0.98712.674-19.801-19.8010.0000.0000.0000.000
115A126GLN0-0.043-0.02414.014-0.240-0.2400.0000.0000.0000.000
116A127ALA00.0060.00015.322-0.047-0.0470.0000.0000.0000.000
117A128GLY00.0190.02811.315-1.019-1.0190.0000.0000.0000.000
118A129ASN0-0.074-0.0478.639-5.773-5.7730.0000.0000.0000.000
119A130ALA00.0360.03010.8640.1410.1410.0000.0000.0000.000
120A131ALA0-0.056-0.03312.592-0.725-0.7250.0000.0000.0000.000
121A132GLU-1-0.909-0.96513.582-17.711-17.7110.0000.0000.0000.000
122A133GLY00.0060.00315.3040.7730.7730.0000.0000.0000.000
123A134GLY00.0330.00116.1370.6750.6750.0000.0000.0000.000
124A135ILE0-0.0030.01319.019-0.351-0.3510.0000.0000.0000.000
125A136LEU0-0.0130.00120.7210.2010.2010.0000.0000.0000.000
126A137ALA00.007-0.00823.2060.2910.2910.0000.0000.0000.000
127A138VAL0-0.021-0.00526.967-0.057-0.0570.0000.0000.0000.000
128A139PRO00.0210.01430.0940.1520.1520.0000.0000.0000.000
129A140VAL00.0180.01232.9090.1740.1740.0000.0000.0000.000
130A141ALA00.000-0.00436.2170.0900.0900.0000.0000.0000.000
131A142ASP-1-0.902-0.93838.469-7.306-7.3060.0000.0000.0000.000
132A143THR0-0.081-0.06041.565-0.064-0.0640.0000.0000.0000.000
133A144LEU00.0700.04139.0640.0440.0440.0000.0000.0000.000
134A145LYS10.8820.93843.6676.6466.6460.0000.0000.0000.000
135A146ARG10.9811.00642.7097.0307.0300.0000.0000.0000.000
136A147ALA00.001-0.01346.8470.1510.1510.0000.0000.0000.000
137A148GLU-1-0.917-0.95548.916-6.138-6.1380.0000.0000.0000.000
138A149SER0-0.030-0.03151.597-0.007-0.0070.0000.0000.0000.000
139A150GLY00.0080.01152.3040.1020.1020.0000.0000.0000.000
140A151GLN0-0.020-0.00353.5300.0390.0390.0000.0000.0000.000
141A152ILE0-0.014-0.01150.475-0.122-0.1220.0000.0000.0000.000
142A153SER00.0520.03350.2290.0750.0750.0000.0000.0000.000
143A154ALA0-0.007-0.01448.5910.0150.0150.0000.0000.0000.000
144A155THR0-0.009-0.00246.756-0.053-0.0530.0000.0000.0000.000
145A156VAL0-0.055-0.03041.6850.0260.0260.0000.0000.0000.000
146A157ASP-1-0.840-0.93142.071-7.591-7.5910.0000.0000.0000.000
147A158ARG10.9160.96339.2887.6047.6040.0000.0000.0000.000
148A159SER0-0.011-0.01537.967-0.290-0.2900.0000.0000.0000.000
149A160GLY0-0.0220.00034.393-0.095-0.0950.0000.0000.0000.000
150A161LEU0-0.0140.01033.416-0.271-0.2710.0000.0000.0000.000
151A162TRP0-0.007-0.01527.8420.0040.0040.0000.0000.0000.000
152A163GLN0-0.033-0.01231.9780.0920.0920.0000.0000.0000.000
153A164ALA00.0470.02927.317-0.157-0.1570.0000.0000.0000.000
154A165GLN0-0.037-0.03025.8260.1050.1050.0000.0000.0000.000
155A166THR0-0.0300.01423.010-0.064-0.0640.0000.0000.0000.000
156A167PRO00.028-0.02218.5590.4650.4650.0000.0000.0000.000
157A168GLN0-0.062-0.03520.3700.0730.0730.0000.0000.0000.000
158A169LEU0-0.0070.00712.719-0.240-0.2400.0000.0000.0000.000
159A170PHE00.0490.01314.6750.1540.1540.0000.0000.0000.000
160A171GLN00.0310.0159.085-1.508-1.5080.0000.0000.0000.000
161A172ALA00.0330.01210.5971.8571.8570.0000.0000.0000.000
162A173GLY00.0360.01211.0161.7501.7500.0000.0000.0000.000
163A174LEU0-0.068-0.03312.7601.5271.5270.0000.0000.0000.000
164A175LEU00.0260.01014.8731.4061.4060.0000.0000.0000.000
165A176HIS00.0340.00715.8961.1821.1820.0000.0000.0000.000
166A177ARG10.9400.96814.37420.01420.0140.0000.0000.0000.000
167A178ALA00.0100.00319.0730.8270.8270.0000.0000.0000.000
168A179LEU0-0.038-0.01720.2970.8160.8160.0000.0000.0000.000
169A180ALA0-0.030-0.00821.7630.5550.5550.0000.0000.0000.000
170A181ALA0-0.024-0.00223.4920.5180.5180.0000.0000.0000.000
171A182GLU-1-0.844-0.91825.987-9.575-9.5750.0000.0000.0000.000
172A183ASN0-0.036-0.02326.209-0.040-0.0400.0000.0000.0000.000
173A184LEU0-0.004-0.01329.6770.1140.1140.0000.0000.0000.000
174A185GLY0-0.024-0.00832.1220.2310.2310.0000.0000.0000.000
175A186GLY0-0.037-0.01532.613-0.003-0.0030.0000.0000.0000.000
176A187ILE0-0.030-0.00626.878-0.031-0.0310.0000.0000.0000.000
177A188THR0-0.036-0.02129.1140.2500.2500.0000.0000.0000.000
178A189ASP-1-0.839-0.91525.961-11.891-11.8910.0000.0000.0000.000
179A190GLU-1-0.828-0.92621.073-13.081-13.0810.0000.0000.0000.000
180A191ALA00.0280.00722.134-0.396-0.3960.0000.0000.0000.000
181A192SER00.0220.02823.1390.1120.1120.0000.0000.0000.000
182A193ALA0-0.028-0.02023.2120.2000.2000.0000.0000.0000.000
183A194VAL0-0.018-0.01418.908-0.168-0.1680.0000.0000.0000.000
184A195GLU-1-0.896-0.95821.689-11.951-11.9510.0000.0000.0000.000
185A196LYS10.8310.92724.52710.83610.8360.0000.0000.0000.000
186A197LEU0-0.067-0.02919.7220.1730.1730.0000.0000.0000.000
187A198GLY0-0.039-0.00523.196-0.158-0.1580.0000.0000.0000.000
188A199VAL0-0.049-0.00718.346-0.113-0.1130.0000.0000.0000.000
189A200ARG10.9400.95821.49412.19512.1950.0000.0000.0000.000
190A201PRO00.0320.02620.033-0.298-0.2980.0000.0000.0000.000
191A202LEU00.0130.01717.8430.8100.8100.0000.0000.0000.000
192A203LEU0-0.020-0.01721.5900.0180.0180.0000.0000.0000.000
193A204ILE0-0.0080.01318.9800.1570.1570.0000.0000.0000.000
194A205GLN00.0070.00022.9670.1790.1790.0000.0000.0000.000
195A206GLY00.0370.02124.113-0.332-0.3320.0000.0000.0000.000
196A207ASP-1-0.851-0.94725.635-9.984-9.9840.0000.0000.0000.000
197A208ALA00.0370.01728.0630.0000.0000.0000.0000.0000.000
198A209ARG10.9320.96527.09710.11710.1170.0000.0000.0000.000
199A210ASN0-0.067-0.02124.7330.0110.0110.0000.0000.0000.000
200A211LEU0-0.0020.00128.289-0.150-0.1500.0000.0000.0000.000
201A212LYS10.9390.96230.3439.4279.4270.0000.0000.0000.000
202A213LEU00.0300.02431.7800.2960.2960.0000.0000.0000.000
203A214THR0-0.061-0.03734.170-0.158-0.1580.0000.0000.0000.000
204A215GLN0-0.009-0.00636.7640.2630.2630.0000.0000.0000.000
205A216PRO00.0410.02239.459-0.126-0.1260.0000.0000.0000.000
206A217GLN0-0.007-0.00539.0150.0070.0070.0000.0000.0000.000
207A218ASP-1-0.767-0.88936.182-8.230-8.2300.0000.0000.0000.000
208A219ALA0-0.036-0.02837.148-0.113-0.1130.0000.0000.0000.000
209A220TYR0-0.040-0.01838.080-0.024-0.0240.0000.0000.0000.000
210A221ILE00.0520.02935.610-0.009-0.0090.0000.0000.0000.000
211A222VAL0-0.009-0.01632.750-0.120-0.1200.0000.0000.0000.000
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