FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: VQQ21

Calculation Name: 3QV0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3QV0

Chain ID: A

ChEMBL ID:

UniProt ID: P40513

Base Structure: X-ray

Registration Date: 2023-09-21

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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1923389.303361
FMO2-HF: Nuclear repulsion 1849254.784166
FMO2-HF: Total energy -74134.519195
FMO2-MP2: Total energy -74354.042749


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:49:GLU)


Summations of interaction energy for fragment #1(A:49:GLU)
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.
59.14258.60716.298-7.602-8.160.061
Interaction energy analysis for fragmet #1(A:49:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.934 / q_NPA : -0.969
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].
3A51GLN00.012-0.0021.697-36.417-38.90015.823-7.004-6.3360.061
4A52ARG10.9901.0042.699-46.199-44.7060.473-0.493-1.4730.000
5A53VAL0-0.015-0.0033.858-5.185-4.7300.002-0.105-0.3510.000
6A54GLY00.0370.0166.177-3.343-3.3430.0000.0000.0000.000
7A55ASP-1-0.935-0.9697.38433.97633.9760.0000.0000.0000.000
8A56ILE0-0.030-0.0177.553-2.539-2.5390.0000.0000.0000.000
9A57LEU00.0420.02410.199-1.986-1.9860.0000.0000.0000.000
10A58GLN0-0.047-0.01911.879-3.050-3.0500.0000.0000.0000.000
11A59SER0-0.087-0.05613.223-1.000-1.0000.0000.0000.0000.000
12A60GLU-1-0.869-0.93814.35115.87615.8760.0000.0000.0000.000
13A61LEU0-0.039-0.02315.570-1.003-1.0030.0000.0000.0000.000
14A62LYS10.8350.91117.202-17.979-17.9790.0000.0000.0000.000
15A63ILE00.0280.01618.355-0.568-0.5680.0000.0000.0000.000
16A64GLU-1-0.850-0.92119.95512.62312.6230.0000.0000.0000.000
17A65LYS10.8270.91120.509-14.844-14.8440.0000.0000.0000.000
18A66GLU-1-1.000-0.98824.30411.45811.4580.0000.0000.0000.000
19A67THR0-0.027-0.00826.253-0.012-0.0120.0000.0000.0000.000
20A68LEU00.0410.00425.633-0.303-0.3030.0000.0000.0000.000
21A69PRO0-0.0120.00527.494-0.210-0.2100.0000.0000.0000.000
22A70GLU-1-0.937-0.95530.2989.0699.0690.0000.0000.0000.000
23A71SER0-0.049-0.02233.545-0.003-0.0030.0000.0000.0000.000
24A72THR0-0.035-0.02832.764-0.384-0.3840.0000.0000.0000.000
25A73SER0-0.025-0.02635.279-0.041-0.0410.0000.0000.0000.000
26A74LEU00.0130.00034.696-0.085-0.0850.0000.0000.0000.000
27A75ASP-1-0.902-0.94638.3747.4187.4180.0000.0000.0000.000
28A76SER00.0780.03740.397-0.239-0.2390.0000.0000.0000.000
29A77PHE0-0.026-0.01034.905-0.147-0.1470.0000.0000.0000.000
30A78ASN0-0.048-0.03140.769-0.085-0.0850.0000.0000.0000.000
31A79ASP-1-0.900-0.94843.3816.4946.4940.0000.0000.0000.000
32A80PHE0-0.0100.00143.093-0.180-0.1800.0000.0000.0000.000
33A81LEU0-0.006-0.01440.501-0.145-0.1450.0000.0000.0000.000
34A82ASN0-0.0070.00145.118-0.166-0.1660.0000.0000.0000.000
35A83LYS10.7810.89548.115-6.226-6.2260.0000.0000.0000.000
36A84TYR0-0.077-0.05747.831-0.207-0.2070.0000.0000.0000.000
37A85LYS10.8630.92749.511-5.703-5.7030.0000.0000.0000.000
38A86PHE0-0.007-0.00944.403-0.035-0.0350.0000.0000.0000.000
39A87SER0-0.051-0.01744.0020.0160.0160.0000.0000.0000.000
40A88LEU0-0.005-0.00136.682-0.049-0.0490.0000.0000.0000.000
41A89VAL0-0.040-0.02737.8410.0090.0090.0000.0000.0000.000
42A90GLU-1-0.763-0.84732.1059.3709.3700.0000.0000.0000.000
43A91THR0-0.026-0.01831.398-0.054-0.0540.0000.0000.0000.000
44A92PRO0-0.004-0.01328.4920.1890.1890.0000.0000.0000.000
45A93GLY0-0.071-0.03825.4720.0520.0520.0000.0000.0000.000
46A94LYS10.8770.94226.232-8.830-8.8300.0000.0000.0000.000
47A95ASN00.001-0.01126.6990.2780.2780.0000.0000.0000.000
48A96GLU-1-0.934-0.95729.1768.1948.1940.0000.0000.0000.000
49A97ALA0-0.0070.00632.9830.1090.1090.0000.0000.0000.000
50A98GLU-1-0.789-0.89435.1757.1487.1480.0000.0000.0000.000
51A99ILE0-0.0300.00338.8660.0380.0380.0000.0000.0000.000
52A100VAL0-0.009-0.01041.840-0.124-0.1240.0000.0000.0000.000
53A101ARG10.8710.94745.289-6.093-6.0930.0000.0000.0000.000
54A102ARG10.8340.88548.765-5.737-5.7370.0000.0000.0000.000
55A103THR0-0.043-0.02652.421-0.022-0.0220.0000.0000.0000.000
56A104GLU-1-0.887-0.96954.8885.3115.3110.0000.0000.0000.000
57A105SER0-0.063-0.04158.077-0.088-0.0880.0000.0000.0000.000
58A106GLY0-0.053-0.01857.434-0.051-0.0510.0000.0000.0000.000
59A107GLU-1-0.783-0.84654.1075.4855.4850.0000.0000.0000.000
60A108THR0-0.048-0.02248.9580.0410.0410.0000.0000.0000.000
61A109VAL0-0.004-0.00547.392-0.019-0.0190.0000.0000.0000.000
62A110HIS10.8250.89543.803-6.641-6.6410.0000.0000.0000.000
63A111VAL00.0340.01541.195-0.094-0.0940.0000.0000.0000.000
64A112PHE00.0140.00638.1590.0650.0650.0000.0000.0000.000
65A113PHE00.0310.00534.794-0.129-0.1290.0000.0000.0000.000
66A114ASP-1-0.778-0.88830.0739.7419.7410.0000.0000.0000.000
67A115VAL00.012-0.00628.5590.0000.0000.0000.0000.0000.000
68A116ALA0-0.0160.00026.0620.1370.1370.0000.0000.0000.000
69A117GLN0-0.063-0.01727.7540.0240.0240.0000.0000.0000.000
70A118ILE0-0.069-0.03130.275-0.124-0.1240.0000.0000.0000.000
71A119ALA0-0.059-0.03525.782-0.074-0.0740.0000.0000.0000.000
72A150PHE0-0.077-0.05435.9860.0160.0160.0000.0000.0000.000
73A151ALA00.0080.02235.0970.1880.1880.0000.0000.0000.000
74A152ASN00.0130.00136.073-0.083-0.0830.0000.0000.0000.000
75A153VAL0-0.023-0.01037.4180.1470.1470.0000.0000.0000.000
76A154ASN00.0200.01740.083-0.310-0.3100.0000.0000.0000.000
77A155VAL00.0160.00742.1310.0480.0480.0000.0000.0000.000
78A156VAL0-0.0060.00644.524-0.140-0.1400.0000.0000.0000.000
79A157ILE0-0.0030.00147.1500.0110.0110.0000.0000.0000.000
80A158SER0-0.006-0.02250.665-0.015-0.0150.0000.0000.0000.000
81A159LYS10.9800.98152.847-5.240-5.2400.0000.0000.0000.000
82A160GLU-1-0.786-0.82554.5065.6205.6200.0000.0000.0000.000
83A161SER0-0.009-0.03451.1490.1070.1070.0000.0000.0000.000
84A162ALA0-0.001-0.01151.1190.0260.0260.0000.0000.0000.000
85A163SER0-0.095-0.06452.1960.0710.0710.0000.0000.0000.000
86A164GLU-1-0.874-0.90354.7265.2195.2190.0000.0000.0000.000
87A165PRO0-0.051-0.03654.4340.0880.0880.0000.0000.0000.000
88A166ALA0-0.0090.00050.489-0.019-0.0190.0000.0000.0000.000
89A167VAL0-0.038-0.00351.140-0.029-0.0290.0000.0000.0000.000
90A168SER0-0.047-0.02545.3330.0850.0850.0000.0000.0000.000
91A169PHE00.027-0.00547.401-0.110-0.1100.0000.0000.0000.000
92A170GLU-1-0.845-0.90341.4647.3407.3400.0000.0000.0000.000
93A171LEU0-0.009-0.01543.117-0.146-0.1460.0000.0000.0000.000
94A172LEU00.0180.01439.7920.2140.2140.0000.0000.0000.000
95A173MET0-0.0060.00238.038-0.191-0.1910.0000.0000.0000.000
96A174ASN0-0.011-0.01439.1880.3420.3420.0000.0000.0000.000
97A175LEU00.0380.00933.761-0.080-0.0800.0000.0000.0000.000
98A176GLN0-0.038-0.01736.3190.1750.1750.0000.0000.0000.000
99A177GLU-1-0.993-1.00139.2616.5896.5890.0000.0000.0000.000
100A178GLY00.0120.02241.507-0.101-0.1010.0000.0000.0000.000
101A179SER00.0130.00142.667-0.122-0.1220.0000.0000.0000.000
102A180PHE00.011-0.01242.2050.1820.1820.0000.0000.0000.000
103A181TYR0-0.013-0.00244.323-0.161-0.1610.0000.0000.0000.000
104A182VAL00.0060.00245.5680.1380.1380.0000.0000.0000.000
105A183ASP-1-0.944-0.95143.7656.6596.6590.0000.0000.0000.000
106A184SER0-0.045-0.03545.844-0.121-0.1210.0000.0000.0000.000
107A185ALA00.0460.01947.9870.0560.0560.0000.0000.0000.000
108A186THR0-0.0280.00348.675-0.087-0.0870.0000.0000.0000.000
109A187PRO0-0.033-0.00850.5360.0570.0570.0000.0000.0000.000
110A188TYR00.0690.01945.818-0.037-0.0370.0000.0000.0000.000
111A189PRO0-0.020-0.02151.571-0.070-0.0700.0000.0000.0000.000
112A190SER00.0230.01051.118-0.034-0.0340.0000.0000.0000.000
113A191VAL00.0590.03047.0710.0740.0740.0000.0000.0000.000
114A192ASP-1-0.885-0.92646.3096.7076.7070.0000.0000.0000.000
115A193ALA00.005-0.00145.9940.1380.1380.0000.0000.0000.000
116A194ALA0-0.027-0.01546.3350.0810.0810.0000.0000.0000.000
117A195LEU00.0090.00842.3790.0910.0910.0000.0000.0000.000
118A196ASN0-0.065-0.02141.4150.3640.3640.0000.0000.0000.000
119A197GLN00.0350.00835.9210.1370.1370.0000.0000.0000.000
120A198SER0-0.073-0.03037.8370.1470.1470.0000.0000.0000.000
121A199ALA00.0380.00537.756-0.036-0.0360.0000.0000.0000.000
122A200GLU-1-0.908-0.96639.3156.8916.8910.0000.0000.0000.000
123A201ALA0-0.0270.00642.424-0.152-0.1520.0000.0000.0000.000
124A202GLU-1-0.760-0.86138.4137.3097.3090.0000.0000.0000.000
125A203ILE00.0150.01740.755-0.102-0.1020.0000.0000.0000.000
126A204THR0-0.089-0.06143.250-0.194-0.1940.0000.0000.0000.000
127A205ARG10.7420.84040.435-7.285-7.2850.0000.0000.0000.000
128A206GLU-1-0.948-0.97539.7737.2197.2190.0000.0000.0000.000
129A207LEU0-0.079-0.03444.481-0.116-0.1160.0000.0000.0000.000
130A208VAL0-0.065-0.01447.860-0.175-0.1750.0000.0000.0000.000
131A209TYR0-0.025-0.01649.2950.0530.0530.0000.0000.0000.000
132A210HIS10.8810.92646.615-6.387-6.3870.0000.0000.0000.000
133A211GLY00.0290.02450.1640.0100.0100.0000.0000.0000.000
134A212PRO0-0.063-0.03051.7010.0670.0670.0000.0000.0000.000
135A213PRO00.0490.01450.3130.0530.0530.0000.0000.0000.000
136A214PHE00.0780.04050.367-0.131-0.1310.0000.0000.0000.000
137A215SER00.0440.01751.500-0.054-0.0540.0000.0000.0000.000
138A216ASN0-0.109-0.06553.191-0.043-0.0430.0000.0000.0000.000
139A217LEU0-0.064-0.00554.457-0.121-0.1210.0000.0000.0000.000
140A218ASP-1-0.885-0.94557.4664.8524.8520.0000.0000.0000.000
141A219GLU-1-0.903-0.95958.6695.1255.1250.0000.0000.0000.000
142A220GLU-1-0.892-0.93359.1864.9184.9180.0000.0000.0000.000
143A221LEU0-0.070-0.02657.9100.0250.0250.0000.0000.0000.000
144A222GLN0-0.053-0.03754.4890.1460.1460.0000.0000.0000.000
145A223GLU-1-0.847-0.92355.5015.2045.2040.0000.0000.0000.000
146A224SER0-0.068-0.04757.1730.0560.0560.0000.0000.0000.000
147A225LEU0-0.075-0.04254.1260.0380.0380.0000.0000.0000.000
148A226GLU-1-0.877-0.94251.6735.8805.8800.0000.0000.0000.000
149A227ALA00.0370.02053.4750.0650.0650.0000.0000.0000.000
150A228TYR0-0.094-0.05653.7580.0160.0160.0000.0000.0000.000
151A229LEU00.0340.01449.3050.0380.0380.0000.0000.0000.000
152A230GLU-1-0.915-0.93351.5655.7135.7130.0000.0000.0000.000
153A231SER0-0.113-0.05952.7780.0070.0070.0000.0000.0000.000
154A232ARG10.7840.86751.737-5.477-5.4770.0000.0000.0000.000
155A233GLY0-0.042-0.01650.0580.0990.0990.0000.0000.0000.000
156A234VAL0-0.0180.00146.2990.1560.1560.0000.0000.0000.000
157A235ASN00.0420.00247.3520.0190.0190.0000.0000.0000.000
158A236GLU-1-0.831-0.92545.9406.3216.3210.0000.0000.0000.000
159A237GLU-1-0.802-0.85644.6996.3676.3670.0000.0000.0000.000
160A238LEU0-0.0150.00542.9190.1640.1640.0000.0000.0000.000
161A239ALA00.0550.03041.4500.1950.1950.0000.0000.0000.000
162A240SER0-0.034-0.02139.9460.2240.2240.0000.0000.0000.000
163A241PHE0-0.004-0.00638.8710.2200.2200.0000.0000.0000.000
164A242ILE00.0140.01137.0240.2170.2170.0000.0000.0000.000
165A243SER0-0.0010.00835.4520.2810.2810.0000.0000.0000.000
166A244ALA00.0430.02234.1440.2710.2710.0000.0000.0000.000
167A245TYR0-0.082-0.07733.8700.2460.2460.0000.0000.0000.000
168A246SER0-0.015-0.03631.7780.2730.2730.0000.0000.0000.000
169A247GLU-1-0.878-0.92229.6939.6919.6910.0000.0000.0000.000
170A248PHE00.0030.00028.8480.3930.3930.0000.0000.0000.000
171A249LYS10.7780.88328.922-9.457-9.4570.0000.0000.0000.000
172A250GLU-1-0.850-0.91124.33112.04812.0480.0000.0000.0000.000
173A251ASN00.0420.02723.9190.3810.3810.0000.0000.0000.000
174A252ASN0-0.049-0.04323.9260.6800.6800.0000.0000.0000.000
175A253GLU-1-0.804-0.88524.15911.50411.5040.0000.0000.0000.000
176A254TYR0-0.0040.00016.9381.0591.0590.0000.0000.0000.000
177A255ILE00.0360.01419.4641.0571.0570.0000.0000.0000.000
178A256SER0-0.063-0.04119.9100.6950.6950.0000.0000.0000.000
179A257TRP0-0.022-0.01313.5840.8520.8520.0000.0000.0000.000
180A258LEU00.0340.02414.8231.2421.2420.0000.0000.0000.000
181A259GLU-1-0.858-0.91615.24217.47117.4710.0000.0000.0000.000
182A260LYS10.8900.93716.466-12.783-12.7830.0000.0000.0000.000
183A261MET00.0170.01711.0280.8110.8110.0000.0000.0000.000
184A262LYS10.8750.93211.876-16.767-16.7670.0000.0000.0000.000
185A263LYS10.8810.93011.783-14.234-14.2340.0000.0000.0000.000
186A264PHE0-0.047-0.0049.4720.1990.1990.0000.0000.0000.000
187A265PHE0-0.004-0.0136.2211.4791.4790.0000.0000.0000.000
188A266HIS0-0.0450.0027.3743.6273.6270.0000.0000.0000.000