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: N9QRQ

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 OptAll
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 -2356143.408394
FMO2-HF: Nuclear repulsion 2276168.777129
FMO2-HF: Total energy -79974.631265
FMO2-MP2: Total energy -80212.700163


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.
-119.385-117.259-0.004-0.903-1.218-0.002
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 : 0.961 / q_NPA : 0.971
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].
3A4LYS10.8530.9103.85045.37247.154-0.003-0.763-1.016-0.001
4A5ASN0-0.029-0.0176.128-0.629-0.6290.0000.0000.0000.000
5A6ILE00.0020.0019.4321.1481.1480.0000.0000.0000.000
6A7ALA00.0150.02212.2660.6050.6050.0000.0000.0000.000
7A8LEU0-0.015-0.01315.7340.1330.1330.0000.0000.0000.000
8A9ILE00.0060.00418.6450.5320.5320.0000.0000.0000.000
9A10PRO0-0.035-0.00322.2400.2350.2350.0000.0000.0000.000
10A11ALA00.0240.00524.8450.3440.3440.0000.0000.0000.000
11A12ALA0-0.058-0.00727.9060.6810.6810.0000.0000.0000.000
12A23PRO00.047-0.00435.5020.0610.0610.0000.0000.0000.000
13A24LYS10.9330.97534.5827.7577.7570.0000.0000.0000.000
14A25GLN00.0420.02130.0150.0190.0190.0000.0000.0000.000
15A26TYR0-0.074-0.07530.061-0.149-0.1490.0000.0000.0000.000
16A27VAL0-0.020-0.00934.0010.2790.2790.0000.0000.0000.000
17A28GLU-1-0.845-0.92734.515-8.640-8.6400.0000.0000.0000.000
18A29ILE0-0.023-0.02733.8350.2770.2770.0000.0000.0000.000
19A30GLY00.0690.04833.960-0.229-0.2290.0000.0000.0000.000
20A31SER0-0.055-0.03233.9950.1030.1030.0000.0000.0000.000
21A32LYS10.9030.95628.9128.9708.9700.0000.0000.0000.000
22A33THR0-0.032-0.03331.0060.0640.0640.0000.0000.0000.000
23A34VAL0-0.024-0.02029.933-0.255-0.2550.0000.0000.0000.000
24A35LEU00.0360.01425.350-0.257-0.2570.0000.0000.0000.000
25A36GLU-1-0.809-0.87725.711-10.140-10.1400.0000.0000.0000.000
26A37HIS0-0.034-0.01925.540-0.500-0.5000.0000.0000.0000.000
27A38VAL0-0.044-0.01222.641-0.296-0.2960.0000.0000.0000.000
28A39LEU0-0.010-0.00821.020-0.519-0.5190.0000.0000.0000.000
29A40GLY00.0060.00120.557-0.478-0.4780.0000.0000.0000.000
30A41ILE0-0.086-0.03520.158-0.129-0.1290.0000.0000.0000.000
31A42PHE00.003-0.00816.322-0.289-0.2890.0000.0000.0000.000
32A43GLU-1-0.802-0.89216.067-16.212-16.2120.0000.0000.0000.000
33A44ARG10.8720.95217.29311.87111.8710.0000.0000.0000.000
34A45HIS0-0.035-0.03014.446-0.188-0.1880.0000.0000.0000.000
35A46GLU-1-0.912-0.96212.297-16.122-16.1220.0000.0000.0000.000
36A47ALA0-0.0420.0019.573-1.091-1.0910.0000.0000.0000.000
37A48VAL0-0.034-0.0289.710-1.427-1.4270.0000.0000.0000.000
38A49ASP-1-0.827-0.8976.051-29.863-29.8630.0000.0000.0000.000
39A50LEU0-0.049-0.0279.3760.6400.6400.0000.0000.0000.000
40A51THR00.003-0.00912.704-0.174-0.1740.0000.0000.0000.000
41A52VAL0-0.022-0.01215.9960.2470.2470.0000.0000.0000.000
42A53VAL00.0150.00618.6790.3190.3190.0000.0000.0000.000
43A54VAL0-0.0210.00221.636-0.029-0.0290.0000.0000.0000.000
44A55VAL00.0200.00224.2620.3620.3620.0000.0000.0000.000
45A56SER00.007-0.03028.023-0.227-0.2270.0000.0000.0000.000
46A57PRO00.011-0.00830.754-0.072-0.0720.0000.0000.0000.000
47A58GLU-1-0.838-0.89732.149-9.081-9.0810.0000.0000.0000.000
48A59ASP-1-0.809-0.87031.340-9.591-9.5910.0000.0000.0000.000
49A60THR00.0140.00233.124-0.067-0.0670.0000.0000.0000.000
50A61PHE0-0.060-0.03431.6930.1940.1940.0000.0000.0000.000
51A62ALA00.0280.01328.814-0.137-0.1370.0000.0000.0000.000
52A63ASP-1-0.798-0.87728.566-10.253-10.2530.0000.0000.0000.000
53A64LYS10.9220.97229.7798.3118.3110.0000.0000.0000.000
54A65VAL00.0320.01825.700-0.075-0.0750.0000.0000.0000.000
55A66GLN00.003-0.01422.247-0.469-0.4690.0000.0000.0000.000
56A67THR0-0.051-0.03825.256-0.233-0.2330.0000.0000.0000.000
57A68ALA0-0.030-0.00927.133-0.012-0.0120.0000.0000.0000.000
58A69PHE0-0.019-0.01121.738-0.103-0.1030.0000.0000.0000.000
59A70PRO00.003-0.00322.075-0.490-0.4900.0000.0000.0000.000
60A71GLN0-0.044-0.01316.566-0.378-0.3780.0000.0000.0000.000
61A72VAL0-0.0060.00417.535-0.898-0.8980.0000.0000.0000.000
62A73ARG10.8900.96015.46118.02718.0270.0000.0000.0000.000
63A74VAL00.0200.01120.056-0.113-0.1130.0000.0000.0000.000
64A75TRP00.005-0.01216.4790.3210.3210.0000.0000.0000.000
65A76LYS10.8330.90323.92110.11410.1140.0000.0000.0000.000
66A77ASN00.011-0.00222.2940.0660.0660.0000.0000.0000.000
67A78GLY00.0210.00725.607-0.432-0.4320.0000.0000.0000.000
68A79GLY00.013-0.00727.2980.1110.1110.0000.0000.0000.000
69A80GLN0-0.062-0.03329.7900.3380.3380.0000.0000.0000.000
70A81THR00.0030.00229.6670.1560.1560.0000.0000.0000.000
71A82ARG10.8480.90524.44412.02912.0290.0000.0000.0000.000
72A83ALA00.0840.04525.795-0.485-0.4850.0000.0000.0000.000
73A84GLU-1-0.815-0.89224.975-11.160-11.1600.0000.0000.0000.000
74A85THR0-0.073-0.04424.974-0.397-0.3970.0000.0000.0000.000
75A86VAL00.0390.01520.395-0.521-0.5210.0000.0000.0000.000
76A87ARG10.8600.93120.46011.29611.2960.0000.0000.0000.000
77A88ASN0-0.032-0.02820.669-0.741-0.7410.0000.0000.0000.000
78A89GLY0-0.010-0.00219.689-0.410-0.4100.0000.0000.0000.000
79A90VAL00.020-0.00315.150-0.976-0.9760.0000.0000.0000.000
80A91ALA00.0080.00815.603-1.210-1.2100.0000.0000.0000.000
81A92LYS10.8730.94916.79814.04114.0410.0000.0000.0000.000
82A93LEU0-0.017-0.01612.986-0.441-0.4410.0000.0000.0000.000
83A94LEU0-0.024-0.00511.472-1.717-1.7170.0000.0000.0000.000
84A95GLU-1-0.995-0.98812.984-17.635-17.6350.0000.0000.0000.000
85A96THR0-0.006-0.00514.859-0.118-0.1180.0000.0000.0000.000
86A97GLY0-0.0110.00110.963-0.100-0.1000.0000.0000.0000.000
87A98LEU0-0.052-0.0279.649-2.415-2.4150.0000.0000.0000.000
88A99ALA0-0.0170.0058.329-2.111-2.1110.0000.0000.0000.000
89A100ALA00.0240.0155.0961.3851.3850.0000.0000.0000.000
90A101GLU-1-0.854-0.9387.167-24.452-24.4520.0000.0000.0000.000
91A102THR00.0060.0043.842-2.942-2.5980.000-0.129-0.214-0.001
92A103ASP-1-0.798-0.8694.732-52.987-52.987-0.001-0.0110.0120.000
93A104ASN0-0.054-0.0396.9633.2073.2070.0000.0000.0000.000
94A105ILE0-0.017-0.00710.2420.4000.4000.0000.0000.0000.000
95A106LEU00.003-0.00712.5580.7110.7110.0000.0000.0000.000
96A107VAL00.0200.02116.2220.5980.5980.0000.0000.0000.000
97A108HIS00.0710.01719.5230.0980.0980.0000.0000.0000.000
98A109ASP-1-0.773-0.89222.042-11.448-11.4480.0000.0000.0000.000
99A110ALA00.0260.00425.8040.1270.1270.0000.0000.0000.000
100A111ALA0-0.019-0.01226.7500.2770.2770.0000.0000.0000.000
101A112ARG10.8170.92225.59911.52211.5220.0000.0000.0000.000
102A113CYS0-0.021-0.02725.819-0.299-0.2990.0000.0000.0000.000
103A114CYS00.0200.02727.5530.1670.1670.0000.0000.0000.000
104A115LEU00.0150.02420.1230.1000.1000.0000.0000.0000.000
105A116PRO0-0.0080.00123.501-0.156-0.1560.0000.0000.0000.000
106A117SER00.0590.02419.318-0.287-0.2870.0000.0000.0000.000
107A118GLU-1-0.787-0.86818.925-11.604-11.6040.0000.0000.0000.000
108A119ALA00.0120.00120.351-0.273-0.2730.0000.0000.0000.000
109A120LEU00.0080.00515.901-0.335-0.3350.0000.0000.0000.000
110A121ALA00.0270.00915.468-0.906-0.9060.0000.0000.0000.000
111A122ARG10.7910.88815.96511.39011.3900.0000.0000.0000.000
112A123LEU0-0.009-0.00216.671-0.378-0.3780.0000.0000.0000.000
113A124ILE00.004-0.00910.948-0.642-0.6420.0000.0000.0000.000
114A125GLU-1-0.944-0.96212.741-19.368-19.3680.0000.0000.0000.000
115A126GLN0-0.061-0.04314.302-0.196-0.1960.0000.0000.0000.000
116A127ALA00.0110.00015.3250.2300.2300.0000.0000.0000.000
117A128GLY00.0160.03011.355-0.906-0.9060.0000.0000.0000.000
118A129ASN0-0.035-0.0228.151-6.213-6.2130.0000.0000.0000.000
119A130ALA00.0110.03510.7280.1480.1480.0000.0000.0000.000
120A131ALA0-0.045-0.02812.567-1.827-1.8270.0000.0000.0000.000
121A132GLU-1-0.894-0.96413.602-18.348-18.3480.0000.0000.0000.000
122A133GLY00.0200.01315.2890.5250.5250.0000.0000.0000.000
123A134GLY00.036-0.00216.1950.8190.8190.0000.0000.0000.000
124A135ILE0-0.017-0.00319.117-0.415-0.4150.0000.0000.0000.000
125A136LEU0-0.0100.01821.0210.2820.2820.0000.0000.0000.000
126A137ALA00.003-0.00423.3170.2450.2450.0000.0000.0000.000
127A138VAL0-0.023-0.00726.984-0.025-0.0250.0000.0000.0000.000
128A139PRO00.0460.02730.1250.1270.1270.0000.0000.0000.000
129A140VAL00.0010.00432.9240.1690.1690.0000.0000.0000.000
130A141ALA00.0000.01136.3160.1520.1520.0000.0000.0000.000
131A142ASP-1-0.886-0.94238.494-7.311-7.3110.0000.0000.0000.000
132A143THR0-0.065-0.04841.600-0.090-0.0900.0000.0000.0000.000
133A144LEU00.0510.02638.8130.1600.1600.0000.0000.0000.000
134A145LYS10.8620.93143.4536.8096.8090.0000.0000.0000.000
135A146ARG10.9710.99943.8076.9196.9190.0000.0000.0000.000
136A147ALA00.021-0.00247.0980.1470.1470.0000.0000.0000.000
137A148GLU-1-0.792-0.85349.103-6.442-6.4420.0000.0000.0000.000
138A149SER0-0.050-0.04451.6890.0210.0210.0000.0000.0000.000
139A150GLY0-0.0100.01451.8130.1180.1180.0000.0000.0000.000
140A151GLN0-0.016-0.01153.003-0.029-0.0290.0000.0000.0000.000
141A152ILE0-0.019-0.01850.386-0.093-0.0930.0000.0000.0000.000
142A153SER0-0.040-0.04350.6260.0800.0800.0000.0000.0000.000
143A154ALA0-0.023-0.01548.3400.0280.0280.0000.0000.0000.000
144A155THR0-0.0020.00047.111-0.041-0.0410.0000.0000.0000.000
145A156VAL0-0.049-0.02842.3610.0440.0440.0000.0000.0000.000
146A157ASP-1-0.784-0.86642.100-7.675-7.6750.0000.0000.0000.000
147A158ARG10.8990.92738.9337.6827.6820.0000.0000.0000.000
148A159SER0-0.044-0.04337.668-0.227-0.2270.0000.0000.0000.000
149A160GLY0-0.021-0.00234.238-0.085-0.0850.0000.0000.0000.000
150A161LEU0-0.0210.00333.081-0.315-0.3150.0000.0000.0000.000
151A162TRP00.013-0.00927.7150.0010.0010.0000.0000.0000.000
152A163GLN0-0.047-0.01931.8190.1990.1990.0000.0000.0000.000
153A164ALA00.0610.03027.282-0.185-0.1850.0000.0000.0000.000
154A165GLN0-0.050-0.03725.6900.0890.0890.0000.0000.0000.000
155A166THR0-0.0260.00822.843-0.146-0.1460.0000.0000.0000.000
156A167PRO00.041-0.00218.4760.5020.5020.0000.0000.0000.000
157A168GLN0-0.085-0.05820.0580.0200.0200.0000.0000.0000.000
158A169LEU0-0.0180.00412.753-0.428-0.4280.0000.0000.0000.000
159A170PHE00.0560.01914.6910.2390.2390.0000.0000.0000.000
160A171GLN00.0330.0208.444-4.259-4.2590.0000.0000.0000.000
161A172ALA00.0380.01010.4552.0982.0980.0000.0000.0000.000
162A173GLY00.016-0.00410.5741.9221.9220.0000.0000.0000.000
163A174LEU0-0.082-0.02712.0071.6661.6660.0000.0000.0000.000
164A175LEU00.0230.00714.4111.5211.5210.0000.0000.0000.000
165A176HIS00.0270.00315.2891.4321.4320.0000.0000.0000.000
166A177ARG10.8850.94312.56422.26522.2650.0000.0000.0000.000
167A178ALA00.0070.01018.1330.8690.8690.0000.0000.0000.000
168A179LEU0-0.011-0.01619.6340.8900.8900.0000.0000.0000.000
169A180ALA0-0.027-0.00120.9740.6600.6600.0000.0000.0000.000
170A181ALA00.0020.02022.6930.4520.4520.0000.0000.0000.000
171A182GLU-1-0.848-0.93124.953-9.952-9.9520.0000.0000.0000.000
172A183ASN0-0.012-0.01625.4480.0620.0620.0000.0000.0000.000
173A184LEU0-0.032-0.01328.9100.1420.1420.0000.0000.0000.000
174A185GLY00.0020.02030.5870.3110.3110.0000.0000.0000.000
175A186GLY0-0.019-0.02130.721-0.200-0.2000.0000.0000.0000.000
176A187ILE0-0.049-0.02325.704-0.098-0.0980.0000.0000.0000.000
177A188THR0-0.065-0.03128.5170.3850.3850.0000.0000.0000.000
178A189ASP-1-0.806-0.88925.814-12.143-12.1430.0000.0000.0000.000
179A190GLU-1-0.781-0.87520.657-13.450-13.4500.0000.0000.0000.000
180A191ALA00.0420.02022.213-0.419-0.4190.0000.0000.0000.000
181A192SER0-0.0070.00223.2190.0670.0670.0000.0000.0000.000
182A193ALA0-0.008-0.00522.6900.4150.4150.0000.0000.0000.000
183A194VAL00.0280.00118.647-0.016-0.0160.0000.0000.0000.000
184A195GLU-1-0.913-0.96621.201-12.314-12.3140.0000.0000.0000.000
185A196LYS10.7550.89323.95411.37111.3710.0000.0000.0000.000
186A197LEU0-0.041-0.01318.9980.1490.1490.0000.0000.0000.000
187A198GLY0-0.042-0.01622.194-0.230-0.2300.0000.0000.0000.000
188A199VAL0-0.043-0.00618.3400.0270.0270.0000.0000.0000.000
189A200ARG10.9450.95721.11912.46912.4690.0000.0000.0000.000
190A201PRO00.0090.01920.176-0.343-0.3430.0000.0000.0000.000
191A202LEU00.0130.01317.5770.8080.8080.0000.0000.0000.000
192A203LEU0-0.020-0.01221.301-0.092-0.0920.0000.0000.0000.000
193A204ILE00.0040.01319.2170.2780.2780.0000.0000.0000.000
194A205GLN0-0.027-0.02222.8110.4390.4390.0000.0000.0000.000
195A206GLY00.0580.03124.261-0.299-0.2990.0000.0000.0000.000
196A207ASP-1-0.823-0.91125.653-9.965-9.9650.0000.0000.0000.000
197A208ALA00.0420.03128.119-0.021-0.0210.0000.0000.0000.000
198A209ARG10.8100.86826.72810.36410.3640.0000.0000.0000.000
199A210ASN0-0.056-0.04024.606-0.022-0.0220.0000.0000.0000.000
200A211LEU00.0210.02027.947-0.154-0.1540.0000.0000.0000.000
201A212LYS10.8830.92529.9879.3559.3550.0000.0000.0000.000
202A213LEU00.0130.02031.4330.2960.2960.0000.0000.0000.000
203A214THR0-0.079-0.05233.935-0.295-0.2950.0000.0000.0000.000
204A215GLN0-0.0120.01036.4910.3460.3460.0000.0000.0000.000
205A216PRO00.022-0.00839.351-0.111-0.1110.0000.0000.0000.000
206A217GLN0-0.002-0.01139.178-0.048-0.0480.0000.0000.0000.000
207A218ASP-1-0.699-0.84835.830-8.338-8.3380.0000.0000.0000.000
208A219ALA0-0.025-0.01636.967-0.124-0.1240.0000.0000.0000.000
209A220TYR0-0.024-0.00638.150-0.014-0.0140.0000.0000.0000.000
210A221ILE00.0400.02935.3900.0030.0030.0000.0000.0000.000
211A222VAL00.008-0.01132.626-0.116-0.1160.0000.0000.0000.000
212A223ARG10.9010.95734.2927.6237.6230.0000.0000.0000.000
213A224LEU00.0280.01436.375-0.006-0.0060.0000.0000.0000.000
214A225LEU0-0.034-0.01431.762-0.031-0.0310.0000.0000.0000.000
215A226LEU0-0.090-0.03729.407-0.232-0.2320.0000.0000.0000.000
216A227ASP-1-1.025-1.00132.775-7.780-7.7800.0000.0000.0000.000