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: YVVQ2

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 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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1921149.223605
FMO2-HF: Nuclear repulsion 1847015.468679
FMO2-HF: Total energy -74133.754926
FMO2-MP2: Total energy -74353.235755


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.
61.4868.3895.47-5.239-7.1380.051
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 : -0.931 / q_NPA : -0.978
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].
3A51GLN00.0150.0082.042-36.057-30.9405.098-4.730-5.4840.052
4A52ARG10.9891.0072.669-42.673-41.3100.371-0.416-1.317-0.001
5A53VAL0-0.0070.0013.918-4.512-4.0830.001-0.093-0.3370.000
6A54GLY00.0350.0126.135-3.013-3.0130.0000.0000.0000.000
7A55ASP-1-0.941-0.9717.38131.95131.9510.0000.0000.0000.000
8A56ILE0-0.037-0.0257.387-2.189-2.1890.0000.0000.0000.000
9A57LEU00.0380.02810.188-1.702-1.7020.0000.0000.0000.000
10A58GLN0-0.059-0.02111.874-2.549-2.5490.0000.0000.0000.000
11A59SER0-0.066-0.05513.228-0.889-0.8890.0000.0000.0000.000
12A60GLU-1-0.885-0.93814.36215.51915.5190.0000.0000.0000.000
13A61LEU0-0.026-0.01615.645-0.904-0.9040.0000.0000.0000.000
14A62LYS10.8340.91117.572-17.189-17.1890.0000.0000.0000.000
15A63ILE00.0350.02018.415-0.551-0.5510.0000.0000.0000.000
16A64GLU-1-0.823-0.91319.93812.40312.4030.0000.0000.0000.000
17A65LYS10.8490.93620.823-14.241-14.2410.0000.0000.0000.000
18A66GLU-1-1.001-0.98524.31811.33011.3300.0000.0000.0000.000
19A67THR0-0.042-0.01626.261-0.019-0.0190.0000.0000.0000.000
20A68LEU00.0440.00325.627-0.299-0.2990.0000.0000.0000.000
21A69PRO0-0.0130.00727.613-0.212-0.2120.0000.0000.0000.000
22A70GLU-1-0.926-0.95030.4148.9208.9200.0000.0000.0000.000
23A71SER0-0.069-0.02533.541-0.023-0.0230.0000.0000.0000.000
24A72THR00.0240.00232.547-0.341-0.3410.0000.0000.0000.000
25A73SER00.008-0.00535.157-0.039-0.0390.0000.0000.0000.000
26A74LEU00.011-0.00434.867-0.083-0.0830.0000.0000.0000.000
27A75ASP-1-0.946-0.97738.3267.2467.2460.0000.0000.0000.000
28A76SER00.0980.05640.483-0.205-0.2050.0000.0000.0000.000
29A77PHE0-0.027-0.00534.850-0.132-0.1320.0000.0000.0000.000
30A78ASN0-0.041-0.03040.716-0.099-0.0990.0000.0000.0000.000
31A79ASP-1-0.914-0.95543.3286.5016.5010.0000.0000.0000.000
32A80PHE00.0020.00443.017-0.174-0.1740.0000.0000.0000.000
33A81LEU00.001-0.00740.465-0.147-0.1470.0000.0000.0000.000
34A82ASN0-0.0090.00045.061-0.146-0.1460.0000.0000.0000.000
35A83LYS10.7940.90648.058-6.150-6.1500.0000.0000.0000.000
36A84TYR0-0.062-0.04347.944-0.199-0.1990.0000.0000.0000.000
37A85LYS10.8900.93549.441-5.692-5.6920.0000.0000.0000.000
38A86PHE00.010-0.00344.317-0.039-0.0390.0000.0000.0000.000
39A87SER0-0.058-0.02343.9270.0100.0100.0000.0000.0000.000
40A88LEU0-0.0020.00336.589-0.052-0.0520.0000.0000.0000.000
41A89VAL0-0.040-0.02537.7880.0090.0090.0000.0000.0000.000
42A90GLU-1-0.760-0.84031.5569.2959.2950.0000.0000.0000.000
43A91THR0-0.041-0.03031.407-0.045-0.0450.0000.0000.0000.000
44A92PRO0-0.005-0.01028.4560.1860.1860.0000.0000.0000.000
45A93GLY0-0.072-0.04025.4010.0510.0510.0000.0000.0000.000
46A94LYS10.8680.93426.161-9.053-9.0530.0000.0000.0000.000
47A95ASN00.0540.01026.3800.1910.1910.0000.0000.0000.000
48A96GLU-1-0.960-0.96329.1088.0268.0260.0000.0000.0000.000
49A97ALA0-0.0090.00632.9150.1060.1060.0000.0000.0000.000
50A98GLU-1-0.774-0.89335.1097.1007.1000.0000.0000.0000.000
51A99ILE0-0.0290.00338.7990.0370.0370.0000.0000.0000.000
52A100VAL0-0.017-0.01441.775-0.123-0.1230.0000.0000.0000.000
53A101ARG10.8740.94845.223-6.015-6.0150.0000.0000.0000.000
54A102ARG10.8510.90348.700-5.671-5.6710.0000.0000.0000.000
55A103THR0-0.028-0.01452.355-0.048-0.0480.0000.0000.0000.000
56A104GLU-1-0.926-0.97754.8235.1675.1670.0000.0000.0000.000
57A105SER0-0.074-0.03157.868-0.083-0.0830.0000.0000.0000.000
58A106GLY0-0.023-0.01057.367-0.046-0.0460.0000.0000.0000.000
59A107GLU-1-0.830-0.89254.0525.4935.4930.0000.0000.0000.000
60A108THR0-0.043-0.01448.9220.0480.0480.0000.0000.0000.000
61A109VAL00.004-0.00247.313-0.018-0.0180.0000.0000.0000.000
62A110HIS10.8220.90243.721-6.603-6.6030.0000.0000.0000.000
63A111VAL00.0380.01941.077-0.092-0.0920.0000.0000.0000.000
64A112PHE00.006-0.00238.1350.0400.0400.0000.0000.0000.000
65A113PHE00.0270.00534.776-0.128-0.1280.0000.0000.0000.000
66A114ASP-1-0.812-0.91030.0499.5809.5800.0000.0000.0000.000
67A115VAL00.0030.00128.673-0.005-0.0050.0000.0000.0000.000
68A116ALA0-0.0170.00126.0250.1320.1320.0000.0000.0000.000
69A117GLN0-0.064-0.02327.6950.0150.0150.0000.0000.0000.000
70A118ILE0-0.059-0.02630.216-0.119-0.1190.0000.0000.0000.000
71A119ALA0-0.0090.00325.671-0.007-0.0070.0000.0000.0000.000
72A150PHE0-0.073-0.05335.8620.0070.0070.0000.0000.0000.000
73A151ALA00.0100.02535.0250.1870.1870.0000.0000.0000.000
74A152ASN00.0140.00836.011-0.057-0.0570.0000.0000.0000.000
75A153VAL0-0.017-0.00537.3550.1430.1430.0000.0000.0000.000
76A154ASN00.0940.06640.020-0.339-0.3390.0000.0000.0000.000
77A155VAL00.003-0.00342.0650.0480.0480.0000.0000.0000.000
78A156VAL0-0.011-0.00144.377-0.127-0.1270.0000.0000.0000.000
79A157ILE00.0010.00547.0810.0210.0210.0000.0000.0000.000
80A158SER0-0.006-0.01450.597-0.011-0.0110.0000.0000.0000.000
81A159LYS10.9880.98652.777-5.185-5.1850.0000.0000.0000.000
82A160GLU-1-0.819-0.85054.8765.5475.5470.0000.0000.0000.000
83A161SER00.009-0.03651.4600.1020.1020.0000.0000.0000.000
84A162ALA00.002-0.00951.0130.0150.0150.0000.0000.0000.000
85A163SER0-0.068-0.03452.0690.0680.0680.0000.0000.0000.000
86A164GLU-1-0.939-0.95654.6535.1055.1050.0000.0000.0000.000
87A165PRO0-0.042-0.03154.3620.0910.0910.0000.0000.0000.000
88A166ALA00.0010.00650.408-0.017-0.0170.0000.0000.0000.000
89A167VAL0-0.037-0.00250.956-0.027-0.0270.0000.0000.0000.000
90A168SER0-0.069-0.03445.2270.0640.0640.0000.0000.0000.000
91A169PHE00.028-0.00547.310-0.108-0.1080.0000.0000.0000.000
92A170GLU-1-0.890-0.93041.4477.2447.2440.0000.0000.0000.000
93A171LEU0-0.010-0.01743.063-0.142-0.1420.0000.0000.0000.000
94A172LEU00.0140.01139.7570.2110.2110.0000.0000.0000.000
95A173MET0-0.0040.00337.899-0.188-0.1880.0000.0000.0000.000
96A174ASN0-0.002-0.01339.1340.3490.3490.0000.0000.0000.000
97A175LEU00.0310.00433.692-0.083-0.0830.0000.0000.0000.000
98A176GLN0-0.042-0.01936.0030.2160.2160.0000.0000.0000.000
99A177GLU-1-0.997-1.00239.2176.4996.4990.0000.0000.0000.000
100A178GLY00.0070.02241.470-0.098-0.0980.0000.0000.0000.000
101A179SER00.0040.00042.618-0.091-0.0910.0000.0000.0000.000
102A180PHE00.021-0.00942.0980.1790.1790.0000.0000.0000.000
103A181TYR0-0.0020.00244.458-0.109-0.1090.0000.0000.0000.000
104A182VAL00.0060.00245.5100.1320.1320.0000.0000.0000.000
105A183ASP-1-0.938-0.95143.2956.6276.6270.0000.0000.0000.000
106A184SER0-0.053-0.03745.743-0.112-0.1120.0000.0000.0000.000
107A185ALA00.0480.01947.9230.0530.0530.0000.0000.0000.000
108A186THR0-0.0310.00248.488-0.088-0.0880.0000.0000.0000.000
109A187PRO0-0.027-0.00450.4670.0560.0560.0000.0000.0000.000
110A188TYR00.0650.01346.022-0.021-0.0210.0000.0000.0000.000
111A189PRO0-0.019-0.02051.519-0.069-0.0690.0000.0000.0000.000
112A190SER00.0250.01450.949-0.034-0.0340.0000.0000.0000.000
113A191VAL00.0650.03646.9760.0710.0710.0000.0000.0000.000
114A192ASP-1-0.881-0.92446.1556.6716.6710.0000.0000.0000.000
115A193ALA0-0.001-0.00345.9210.1370.1370.0000.0000.0000.000
116A194ALA0-0.017-0.00846.2620.0850.0850.0000.0000.0000.000
117A195LEU00.003-0.00142.1300.0910.0910.0000.0000.0000.000
118A196ASN0-0.077-0.04141.3420.3600.3600.0000.0000.0000.000
119A197GLN00.0550.01535.3150.0690.0690.0000.0000.0000.000
120A198SER0-0.075-0.01637.7630.1570.1570.0000.0000.0000.000
121A199ALA00.0500.01037.725-0.035-0.0350.0000.0000.0000.000
122A200GLU-1-0.915-0.97139.2476.8226.8220.0000.0000.0000.000
123A201ALA0-0.040-0.00742.369-0.149-0.1490.0000.0000.0000.000
124A202GLU-1-0.839-0.91638.2007.2677.2670.0000.0000.0000.000
125A203ILE00.0280.02340.675-0.102-0.1020.0000.0000.0000.000
126A204THR0-0.089-0.05443.178-0.194-0.1940.0000.0000.0000.000
127A205ARG10.7890.88540.508-7.210-7.2100.0000.0000.0000.000
128A206GLU-1-0.918-0.95939.7187.1817.1810.0000.0000.0000.000
129A207LEU0-0.081-0.03644.412-0.116-0.1160.0000.0000.0000.000
130A208VAL0-0.052-0.00847.791-0.173-0.1730.0000.0000.0000.000
131A209TYR0-0.033-0.01549.2270.0710.0710.0000.0000.0000.000
132A210HIS10.8800.92246.357-6.365-6.3650.0000.0000.0000.000
133A211GLY00.0290.02050.0970.0070.0070.0000.0000.0000.000
134A212PRO0-0.053-0.02351.6370.0640.0640.0000.0000.0000.000
135A213PRO00.0470.01250.2320.0510.0510.0000.0000.0000.000
136A214PHE00.0740.04350.311-0.126-0.1260.0000.0000.0000.000
137A215SER00.0350.00751.323-0.060-0.0600.0000.0000.0000.000
138A216ASN0-0.090-0.05353.134-0.116-0.1160.0000.0000.0000.000
139A217LEU0-0.092-0.01754.614-0.117-0.1170.0000.0000.0000.000
140A218ASP-1-0.894-0.95457.4064.8194.8190.0000.0000.0000.000
141A219GLU-1-0.907-0.96158.5875.1095.1090.0000.0000.0000.000
142A220GLU-1-0.883-0.92559.1294.9164.9160.0000.0000.0000.000
143A221LEU0-0.080-0.04157.7910.0250.0250.0000.0000.0000.000
144A222GLN0-0.068-0.04754.6200.1290.1290.0000.0000.0000.000
145A223GLU-1-0.826-0.91055.4425.1445.1440.0000.0000.0000.000
146A224SER0-0.076-0.03557.1140.0530.0530.0000.0000.0000.000
147A225LEU0-0.056-0.03854.0150.0390.0390.0000.0000.0000.000
148A226GLU-1-0.878-0.94251.8245.7715.7710.0000.0000.0000.000
149A227ALA00.0460.02253.4160.0620.0620.0000.0000.0000.000
150A228TYR0-0.103-0.05753.4530.0240.0240.0000.0000.0000.000
151A229LEU00.0350.01949.2750.0390.0390.0000.0000.0000.000
152A230GLU-1-0.912-0.93351.5045.6915.6910.0000.0000.0000.000
153A231SER0-0.124-0.06852.7190.0040.0040.0000.0000.0000.000
154A232ARG10.7850.86751.696-5.436-5.4360.0000.0000.0000.000
155A233GLY0-0.046-0.01749.9980.0960.0960.0000.0000.0000.000
156A234VAL0-0.0210.00446.1040.1530.1530.0000.0000.0000.000
157A235ASN00.0470.01047.3200.0230.0230.0000.0000.0000.000
158A236GLU-1-0.838-0.93545.8756.2446.2440.0000.0000.0000.000
159A237GLU-1-0.835-0.89144.6476.3196.3190.0000.0000.0000.000
160A238LEU0-0.0090.00542.7510.1610.1610.0000.0000.0000.000
161A239ALA00.0430.02441.3930.1910.1910.0000.0000.0000.000
162A240SER0-0.026-0.01639.8930.2250.2250.0000.0000.0000.000
163A241PHE0-0.007-0.00538.6810.2140.2140.0000.0000.0000.000
164A242ILE00.0050.00536.8490.2140.2140.0000.0000.0000.000
165A243SER00.0120.00935.3900.2850.2850.0000.0000.0000.000
166A244ALA00.0430.02334.0920.2600.2600.0000.0000.0000.000
167A245TYR0-0.080-0.08833.8590.2430.2430.0000.0000.0000.000
168A246SER0-0.008-0.02531.7430.2810.2810.0000.0000.0000.000
169A247GLU-1-0.898-0.94629.3179.6739.6730.0000.0000.0000.000
170A248PHE0-0.030-0.01628.7970.3590.3590.0000.0000.0000.000
171A249LYS10.7680.87328.868-9.368-9.3680.0000.0000.0000.000
172A250GLU-1-0.903-0.95823.57711.94311.9430.0000.0000.0000.000
173A251ASN00.0460.03323.7400.3780.3780.0000.0000.0000.000
174A252ASN0-0.002-0.01023.8720.7150.7150.0000.0000.0000.000
175A253GLU-1-0.823-0.90024.13911.32111.3210.0000.0000.0000.000
176A254TYR00.0040.00316.9631.0791.0790.0000.0000.0000.000
177A255ILE00.0320.01519.4060.9960.9960.0000.0000.0000.000
178A256SER0-0.051-0.03519.8540.6410.6410.0000.0000.0000.000
179A257TRP0-0.025-0.01313.6970.8460.8460.0000.0000.0000.000
180A258LEU00.0200.01614.8371.2091.2090.0000.0000.0000.000
181A259GLU-1-0.945-0.97415.18416.73716.7370.0000.0000.0000.000
182A260LYS10.8760.92516.531-12.636-12.6360.0000.0000.0000.000
183A261MET00.0240.02011.1650.7950.7950.0000.0000.0000.000
184A262LYS10.9480.98111.887-16.844-16.8440.0000.0000.0000.000
185A263LYS10.8830.92711.882-13.832-13.8320.0000.0000.0000.000
186A264PHE0-0.049-0.0039.3930.2340.2340.0000.0000.0000.000
187A265PHE0-0.013-0.0196.2541.5041.5040.0000.0000.0000.000
188A266HIS0-0.0440.0017.4923.2533.2530.0000.0000.0000.000