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: 85M1Y

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 OptHSide
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 -2339978.453308
FMO2-HF: Nuclear repulsion 2260004.76133
FMO2-HF: Total energy -79973.691978
FMO2-MP2: Total energy -80211.726604


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.
-117.966-115.8380.004-0.793-1.340
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 : 0.978 / q_NPA : 0.974
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].
3A4LYS10.8700.9313.57643.36245.2430.005-0.743-1.1430.000
4A5ASN0-0.033-0.0246.1040.3640.3640.0000.0000.0000.000
5A6ILE00.0090.0069.4021.1231.1230.0000.0000.0000.000
6A7ALA00.0020.01412.3090.5570.5570.0000.0000.0000.000
7A8LEU0-0.0030.00015.8150.0080.0080.0000.0000.0000.000
8A9ILE0-0.014-0.01518.8090.4920.4920.0000.0000.0000.000
9A10PRO0-0.0250.00922.4060.1790.1790.0000.0000.0000.000
10A11ALA0-0.012-0.01825.0320.3110.3110.0000.0000.0000.000
11A12ALA00.0170.01928.2380.2990.2990.0000.0000.0000.000
12A23PRO00.041-0.00535.8620.0490.0490.0000.0000.0000.000
13A24LYS10.9030.96135.2617.8337.8330.0000.0000.0000.000
14A25GLN00.0560.03930.2300.0460.0460.0000.0000.0000.000
15A26TYR0-0.060-0.08830.448-0.138-0.1380.0000.0000.0000.000
16A27VAL0-0.044-0.01534.1750.2440.2440.0000.0000.0000.000
17A28GLU-1-0.861-0.93334.816-8.547-8.5470.0000.0000.0000.000
18A29ILE0-0.025-0.02034.5450.2890.2890.0000.0000.0000.000
19A30GLY00.0420.04034.442-0.225-0.2250.0000.0000.0000.000
20A31SER0-0.038-0.02733.6600.0220.0220.0000.0000.0000.000
21A32LYS10.9270.97429.0969.2159.2150.0000.0000.0000.000
22A33THR00.018-0.01731.0260.0120.0120.0000.0000.0000.000
23A34VAL0-0.035-0.02829.829-0.190-0.1900.0000.0000.0000.000
24A35LEU00.0380.01125.486-0.252-0.2520.0000.0000.0000.000
25A36GLU-1-0.817-0.87126.005-10.021-10.0210.0000.0000.0000.000
26A37HIS0-0.058-0.03825.843-0.509-0.5090.0000.0000.0000.000
27A38VAL0-0.045-0.01323.124-0.269-0.2690.0000.0000.0000.000
28A39LEU0-0.011-0.01021.451-0.509-0.5090.0000.0000.0000.000
29A40GLY00.0190.01020.694-0.470-0.4700.0000.0000.0000.000
30A41ILE0-0.092-0.05220.186-0.165-0.1650.0000.0000.0000.000
31A42PHE0-0.014-0.01916.353-0.288-0.2880.0000.0000.0000.000
32A43GLU-1-0.871-0.93516.171-15.670-15.6700.0000.0000.0000.000
33A44ARG10.8920.96416.81111.58011.5800.0000.0000.0000.000
34A45HIS0-0.061-0.04014.554-0.257-0.2570.0000.0000.0000.000
35A46GLU-1-0.902-0.95612.207-16.212-16.2120.0000.0000.0000.000
36A47ALA0-0.051-0.0139.619-1.102-1.1020.0000.0000.0000.000
37A48VAL0-0.050-0.0309.411-1.644-1.6440.0000.0000.0000.000
38A49ASP-1-0.798-0.8846.579-29.403-29.4030.0000.0000.0000.000
39A50LEU0-0.048-0.0349.7270.4550.4550.0000.0000.0000.000
40A51THR00.0110.01112.953-0.241-0.2410.0000.0000.0000.000
41A52VAL0-0.027-0.00816.2130.3800.3800.0000.0000.0000.000
42A53VAL00.0290.00518.9770.2380.2380.0000.0000.0000.000
43A54VAL0-0.040-0.01021.9800.0150.0150.0000.0000.0000.000
44A55VAL00.022-0.00424.4760.3010.3010.0000.0000.0000.000
45A56SER00.004-0.03328.199-0.172-0.1720.0000.0000.0000.000
46A57PRO0-0.019-0.00930.5560.0260.0260.0000.0000.0000.000
47A58GLU-1-0.865-0.90932.176-8.975-8.9750.0000.0000.0000.000
48A59ASP-1-0.869-0.90731.823-9.407-9.4070.0000.0000.0000.000
49A60THR0-0.007-0.01433.389-0.029-0.0290.0000.0000.0000.000
50A61PHE0-0.027-0.02232.1950.0170.0170.0000.0000.0000.000
51A62ALA00.0430.03029.400-0.148-0.1480.0000.0000.0000.000
52A63ASP-1-0.809-0.88329.282-10.163-10.1630.0000.0000.0000.000
53A64LYS10.9270.95630.1408.1568.1560.0000.0000.0000.000
54A65VAL00.0190.01126.219-0.055-0.0550.0000.0000.0000.000
55A66GLN0-0.008-0.01722.625-0.419-0.4190.0000.0000.0000.000
56A67THR0-0.063-0.02925.693-0.177-0.1770.0000.0000.0000.000
57A68ALA0-0.024-0.00427.343-0.034-0.0340.0000.0000.0000.000
58A69PHE0-0.012-0.00921.754-0.091-0.0910.0000.0000.0000.000
59A70PRO00.0170.01022.311-0.388-0.3880.0000.0000.0000.000
60A71GLN0-0.031-0.01916.745-0.412-0.4120.0000.0000.0000.000
61A72VAL0-0.0050.02517.551-0.926-0.9260.0000.0000.0000.000
62A73ARG10.9270.97615.26817.85617.8560.0000.0000.0000.000
63A74VAL00.0380.01620.098-0.053-0.0530.0000.0000.0000.000
64A75TRP00.006-0.00616.5090.3470.3470.0000.0000.0000.000
65A76LYS10.8910.93023.90510.28110.2810.0000.0000.0000.000
66A77ASN00.0300.00722.5280.0910.0910.0000.0000.0000.000
67A78GLY00.0220.01625.984-0.370-0.3700.0000.0000.0000.000
68A79GLY00.011-0.00627.9340.1280.1280.0000.0000.0000.000
69A80GLN0-0.007-0.01229.5830.3580.3580.0000.0000.0000.000
70A81THR00.002-0.00829.8630.1260.1260.0000.0000.0000.000
71A82ARG10.8410.91324.68411.78611.7860.0000.0000.0000.000
72A83ALA00.0570.01326.064-0.440-0.4400.0000.0000.0000.000
73A84GLU-1-0.865-0.93025.265-10.940-10.9400.0000.0000.0000.000
74A85THR0-0.038-0.01125.304-0.491-0.4910.0000.0000.0000.000
75A86VAL00.0160.01120.746-0.503-0.5030.0000.0000.0000.000
76A87ARG10.9050.95720.67211.35111.3510.0000.0000.0000.000
77A88ASN0-0.039-0.02920.842-0.731-0.7310.0000.0000.0000.000
78A89GLY0-0.0090.00220.064-0.429-0.4290.0000.0000.0000.000
79A90VAL00.0270.00215.189-0.865-0.8650.0000.0000.0000.000
80A91ALA00.0090.01015.796-1.081-1.0810.0000.0000.0000.000
81A92LYS10.8680.95316.59913.57113.5710.0000.0000.0000.000
82A93LEU00.002-0.00813.049-0.441-0.4410.0000.0000.0000.000
83A94LEU0-0.015-0.01010.984-1.597-1.5970.0000.0000.0000.000
84A95GLU-1-1.004-0.99412.854-17.238-17.2380.0000.0000.0000.000
85A96THR0-0.024-0.01214.405-0.048-0.0480.0000.0000.0000.000
86A97GLY00.0060.01910.831-0.058-0.0580.0000.0000.0000.000
87A98LEU0-0.073-0.0439.685-2.221-2.2210.0000.0000.0000.000
88A99ALA0-0.035-0.0078.516-2.034-2.0340.0000.0000.0000.000
89A100ALA00.0280.0184.8361.5251.5250.0000.0000.0000.000
90A101GLU-1-0.898-0.9596.693-25.224-25.2240.0000.0000.0000.000
91A102THR0-0.0030.0003.808-1.252-1.0400.000-0.040-0.1730.000
92A103ASP-1-0.806-0.8864.769-52.691-52.656-0.001-0.010-0.0240.000
93A104ASN0-0.070-0.0406.6832.9032.9030.0000.0000.0000.000
94A105ILE00.0030.00910.0930.0100.0100.0000.0000.0000.000
95A106LEU00.007-0.00312.7880.8110.8110.0000.0000.0000.000
96A107VAL00.0100.01816.4250.4700.4700.0000.0000.0000.000
97A108HIS00.0780.01519.6340.0820.0820.0000.0000.0000.000
98A109ASP-1-0.831-0.92222.114-11.196-11.1960.0000.0000.0000.000
99A110ALA00.0450.00925.7400.0680.0680.0000.0000.0000.000
100A111ALA0-0.019-0.01526.9110.2130.2130.0000.0000.0000.000
101A112ARG10.8470.94526.03011.27711.2770.0000.0000.0000.000
102A113CYS0-0.013-0.02125.920-0.353-0.3530.0000.0000.0000.000
103A114CYS00.0100.01927.4560.2560.2560.0000.0000.0000.000
104A115LEU0-0.0020.01920.4330.1340.1340.0000.0000.0000.000
105A116PRO00.0030.00023.736-0.159-0.1590.0000.0000.0000.000
106A117SER00.0680.03519.467-0.249-0.2490.0000.0000.0000.000
107A118GLU-1-0.869-0.93618.993-11.873-11.8730.0000.0000.0000.000
108A119ALA0-0.014-0.01720.262-0.242-0.2420.0000.0000.0000.000
109A120LEU00.0000.00616.021-0.360-0.3600.0000.0000.0000.000
110A121ALA00.0270.00715.342-0.880-0.8800.0000.0000.0000.000
111A122ARG10.8380.93315.63011.40111.4010.0000.0000.0000.000
112A123LEU0-0.022-0.00316.627-0.455-0.4550.0000.0000.0000.000
113A124ILE00.008-0.00510.748-0.662-0.6620.0000.0000.0000.000
114A125GLU-1-0.949-0.97512.744-19.465-19.4650.0000.0000.0000.000
115A126GLN0-0.069-0.03914.079-0.025-0.0250.0000.0000.0000.000
116A127ALA0-0.003-0.00615.298-0.012-0.0120.0000.0000.0000.000
117A128GLY00.0200.03111.390-1.030-1.0300.0000.0000.0000.000
118A129ASN0-0.053-0.0388.300-5.727-5.7270.0000.0000.0000.000
119A130ALA00.0320.03710.8120.2420.2420.0000.0000.0000.000
120A131ALA0-0.053-0.03612.480-0.875-0.8750.0000.0000.0000.000
121A132GLU-1-0.905-0.96313.486-17.845-17.8450.0000.0000.0000.000
122A133GLY0-0.0010.00415.0220.7140.7140.0000.0000.0000.000
123A134GLY00.0390.00115.8590.7300.7300.0000.0000.0000.000
124A135ILE0-0.0130.01218.807-0.392-0.3920.0000.0000.0000.000
125A136LEU00.0010.00920.8870.2330.2330.0000.0000.0000.000
126A137ALA00.003-0.01223.2730.2790.2790.0000.0000.0000.000
127A138VAL0-0.025-0.00827.035-0.038-0.0380.0000.0000.0000.000
128A139PRO00.0330.01430.1610.1500.1500.0000.0000.0000.000
129A140VAL00.0110.01632.9790.1720.1720.0000.0000.0000.000
130A141ALA0-0.0030.00136.2860.0970.0970.0000.0000.0000.000
131A142ASP-1-0.895-0.94438.537-7.291-7.2910.0000.0000.0000.000
132A143THR0-0.071-0.05441.634-0.068-0.0680.0000.0000.0000.000
133A144LEU00.0670.04338.7910.0410.0410.0000.0000.0000.000
134A145LYS10.8560.92143.4856.6846.6840.0000.0000.0000.000
135A146ARG10.9901.00942.9296.9826.9820.0000.0000.0000.000
136A147ALA0-0.014-0.02546.4850.1540.1540.0000.0000.0000.000
137A148GLU-1-0.843-0.89448.529-6.283-6.2830.0000.0000.0000.000
138A149SER0-0.035-0.04051.191-0.010-0.0100.0000.0000.0000.000
139A150GLY00.0080.01251.8930.1030.1030.0000.0000.0000.000
140A151GLN0-0.028-0.00753.1080.0370.0370.0000.0000.0000.000
141A152ILE0-0.011-0.00950.039-0.119-0.1190.0000.0000.0000.000
142A153SER00.006-0.00650.2690.0750.0750.0000.0000.0000.000
143A154ALA0-0.014-0.01148.1380.0130.0130.0000.0000.0000.000
144A155THR00.0020.00746.739-0.046-0.0460.0000.0000.0000.000
145A156VAL0-0.055-0.02941.6980.0330.0330.0000.0000.0000.000
146A157ASP-1-0.797-0.89642.076-7.651-7.6510.0000.0000.0000.000
147A158ARG10.9010.95539.0557.6577.6570.0000.0000.0000.000
148A159SER0-0.037-0.04237.937-0.235-0.2350.0000.0000.0000.000
149A160GLY0-0.024-0.00634.354-0.096-0.0960.0000.0000.0000.000
150A161LEU0-0.0200.00933.279-0.284-0.2840.0000.0000.0000.000
151A162TRP00.002-0.01127.9040.0040.0040.0000.0000.0000.000
152A163GLN0-0.041-0.01831.8880.1180.1180.0000.0000.0000.000
153A164ALA00.0470.02826.920-0.153-0.1530.0000.0000.0000.000
154A165GLN0-0.057-0.03425.9340.0720.0720.0000.0000.0000.000
155A166THR0-0.042-0.00823.207-0.071-0.0710.0000.0000.0000.000
156A167PRO00.038-0.01218.5790.4530.4530.0000.0000.0000.000
157A168GLN0-0.073-0.05419.9650.0190.0190.0000.0000.0000.000
158A169LEU0-0.0070.01312.556-0.341-0.3410.0000.0000.0000.000
159A170PHE00.0640.01814.3370.2170.2170.0000.0000.0000.000
160A171GLN00.0130.0078.858-2.847-2.8470.0000.0000.0000.000
161A172ALA00.0260.00810.1401.9871.9870.0000.0000.0000.000
162A173GLY00.0350.01510.6711.8711.8710.0000.0000.0000.000
163A174LEU0-0.070-0.03312.4551.6581.6580.0000.0000.0000.000
164A175LEU00.0260.00714.5131.4971.4970.0000.0000.0000.000
165A176HIS00.0300.00615.5211.3441.3440.0000.0000.0000.000
166A177ARG10.9420.96913.80120.67320.6730.0000.0000.0000.000
167A178ALA00.0120.00618.7860.8720.8720.0000.0000.0000.000
168A179LEU0-0.012-0.00319.7890.8520.8520.0000.0000.0000.000
169A180ALA0-0.027-0.00821.4290.5940.5940.0000.0000.0000.000
170A181ALA0-0.0190.00123.1570.5360.5360.0000.0000.0000.000
171A182GLU-1-0.820-0.91125.695-9.782-9.7820.0000.0000.0000.000
172A183ASN0-0.029-0.01925.6160.0120.0120.0000.0000.0000.000
173A184LEU0-0.028-0.01029.1340.1310.1310.0000.0000.0000.000
174A185GLY00.0020.01631.0250.2870.2870.0000.0000.0000.000
175A186GLY0-0.0100.00031.522-0.106-0.1060.0000.0000.0000.000
176A187ILE0-0.034-0.02426.152-0.039-0.0390.0000.0000.0000.000
177A188THR0-0.036-0.01628.7130.2510.2510.0000.0000.0000.000
178A189ASP-1-0.811-0.88425.602-12.126-12.1260.0000.0000.0000.000
179A190GLU-1-0.797-0.88920.673-13.171-13.1710.0000.0000.0000.000
180A191ALA00.0530.01721.782-0.395-0.3950.0000.0000.0000.000
181A192SER0-0.0010.00022.7770.1570.1570.0000.0000.0000.000
182A193ALA0-0.018-0.01622.7960.2320.2320.0000.0000.0000.000
183A194VAL0-0.009-0.01118.763-0.169-0.1690.0000.0000.0000.000
184A195GLU-1-0.907-0.96121.396-12.074-12.0740.0000.0000.0000.000
185A196LYS10.7460.87724.27811.11111.1110.0000.0000.0000.000
186A197LEU0-0.057-0.02319.6080.1350.1350.0000.0000.0000.000
187A198GLY0-0.038-0.00623.018-0.145-0.1450.0000.0000.0000.000
188A199VAL0-0.057-0.01118.108-0.094-0.0940.0000.0000.0000.000
189A200ARG10.9490.96321.34012.12012.1200.0000.0000.0000.000
190A201PRO00.0370.03219.803-0.326-0.3260.0000.0000.0000.000
191A202LEU00.0000.00417.7570.8190.8190.0000.0000.0000.000
192A203LEU0-0.008-0.00921.522-0.008-0.0080.0000.0000.0000.000
193A204ILE00.0010.01519.4430.1620.1620.0000.0000.0000.000
194A205GLN0-0.019-0.01223.0380.3250.3250.0000.0000.0000.000
195A206GLY00.0570.03324.176-0.322-0.3220.0000.0000.0000.000
196A207ASP-1-0.818-0.91625.696-9.958-9.9580.0000.0000.0000.000
197A208ALA00.0460.03328.119-0.014-0.0140.0000.0000.0000.000
198A209ARG10.9060.92827.36210.08810.0880.0000.0000.0000.000
199A210ASN0-0.060-0.02424.8280.0110.0110.0000.0000.0000.000
200A211LEU0-0.009-0.00328.339-0.140-0.1400.0000.0000.0000.000
201A212LYS10.9260.96230.2759.5719.5710.0000.0000.0000.000
202A213LEU00.0160.01731.8270.2970.2970.0000.0000.0000.000
203A214THR0-0.080-0.05334.212-0.195-0.1950.0000.0000.0000.000
204A215GLN00.0250.01036.8090.3260.3260.0000.0000.0000.000
205A216PRO00.0270.01539.502-0.124-0.1240.0000.0000.0000.000
206A217GLN0-0.005-0.00739.248-0.029-0.0290.0000.0000.0000.000
207A218ASP-1-0.752-0.87136.138-8.297-8.2970.0000.0000.0000.000
208A219ALA0-0.020-0.02537.183-0.113-0.1130.0000.0000.0000.000
209A220TYR0-0.045-0.01738.116-0.030-0.0300.0000.0000.0000.000
210A221ILE00.0520.02735.677-0.008-0.0080.0000.0000.0000.000
211A222VAL00.007-0.01332.787-0.116-0.1160.0000.0000.0000.000
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