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: VK2J1

Calculation Name: 1QR4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1QR4

Chain ID: A

ChEMBL ID:

UniProt ID: P10039

Base Structure: X-ray

Registration Date: 2023-09-26

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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1556386.738737
FMO2-HF: Nuclear repulsion 1490302.003085
FMO2-HF: Total energy -66084.735652
FMO2-MP2: Total energy -66281.704881


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:1:ASP)


Summations of interaction energy for fragment #1(A:1:ASP)
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.
-292.759-302.19148.436-21.311-17.6950.206
Interaction energy analysis for fragmet #1(A:1:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.805 / q_NPA : -0.880
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].
3A3PRO00.0550.0323.63710.96013.6930.041-1.296-1.4780.003
4A4LYS10.8570.9551.730-114.065-119.54116.086-6.206-4.4040.074
5A5ASP-1-0.833-0.9187.04129.66529.6650.0000.0000.0000.000
6A6LEU0-0.0050.01210.744-0.821-0.8210.0000.0000.0000.000
7A7GLU-1-0.855-0.91412.64318.26018.2600.0000.0000.0000.000
8A8VAL0-0.031-0.04116.2580.1070.1070.0000.0000.0000.000
9A9SER0-0.001-0.01819.591-0.361-0.3610.0000.0000.0000.000
10A10ASP-1-0.881-0.94422.21113.54313.5430.0000.0000.0000.000
11A11PRO0-0.0020.00425.525-0.094-0.0940.0000.0000.0000.000
12A12THR00.0020.01927.157-0.520-0.5200.0000.0000.0000.000
13A13GLU-1-0.835-0.88929.8209.1469.1460.0000.0000.0000.000
14A14THR0-0.031-0.03330.4270.0610.0610.0000.0000.0000.000
15A15THR0-0.021-0.02726.1110.1140.1140.0000.0000.0000.000
16A16LEU00.0100.01422.441-0.026-0.0260.0000.0000.0000.000
17A17SER00.0180.03321.5400.5010.5010.0000.0000.0000.000
18A18LEU0-0.006-0.00416.2820.4320.4320.0000.0000.0000.000
19A19ARG10.9310.94914.712-19.480-19.4800.0000.0000.0000.000
20A20TRP0-0.036-0.0108.891-0.492-0.4920.0000.0000.0000.000
21A21ARG10.8960.9347.113-31.031-31.0310.0000.0000.0000.000
22A22ARG10.9310.9616.836-27.119-27.1190.0000.0000.0000.000
23A23PRO0-0.046-0.0222.7150.9443.3080.950-1.447-1.8680.013
24A24VAL00.0250.0071.766-19.058-24.65213.528-4.178-3.7560.045
25A25ALA0-0.060-0.0222.558-15.488-13.4931.053-1.299-1.7490.008
26A26LYS10.9811.0013.948-27.172-27.0780.0020.000-0.0960.000
27A27PHE0-0.133-0.0926.0401.9191.9190.0000.0000.0000.000
28A28ASP-1-0.853-0.9198.02719.12519.1250.0000.0000.0000.000
29A29ARG10.8540.92510.612-19.938-19.9380.0000.0000.0000.000
30A30TYR0-0.026-0.0068.1414.7494.7490.0000.0000.0000.000
31A31ARG10.8270.90011.807-20.082-20.0820.0000.0000.0000.000
32A32LEU0-0.017-0.01213.3641.5151.5150.0000.0000.0000.000
33A33THR0-0.019-0.02615.846-0.875-0.8750.0000.0000.0000.000
34A34TYR00.0180.00417.7310.7080.7080.0000.0000.0000.000
35A35VAL0-0.013-0.01820.441-0.484-0.4840.0000.0000.0000.000
36A36SER00.0440.03523.2580.0730.0730.0000.0000.0000.000
37A37PRO00.0660.02426.6380.1030.1030.0000.0000.0000.000
38A38SER0-0.048-0.01528.741-0.227-0.2270.0000.0000.0000.000
39A39GLY00.003-0.00326.304-0.143-0.1430.0000.0000.0000.000
40A40LYS10.8780.95926.454-11.246-11.2460.0000.0000.0000.000
41A41LYS10.9880.98619.920-14.383-14.3830.0000.0000.0000.000
42A42ASN0-0.0270.00022.514-0.840-0.8400.0000.0000.0000.000
43A43GLU-1-0.798-0.88318.82116.45816.4580.0000.0000.0000.000
44A44MET00.0250.01918.461-0.777-0.7770.0000.0000.0000.000
45A45GLU-1-0.867-0.91116.12318.53418.5340.0000.0000.0000.000
46A46ILE0-0.033-0.01614.675-0.765-0.7650.0000.0000.0000.000
47A47PRO00.0780.03214.2481.4201.4200.0000.0000.0000.000
48A48VAL00.0240.00110.4420.9960.9960.0000.0000.0000.000
49A49ASP-1-0.941-0.97411.76820.49920.4990.0000.0000.0000.000
50A50SER0-0.0080.01413.878-0.961-0.9610.0000.0000.0000.000
51A51THR0-0.030-0.02510.6301.5281.5280.0000.0000.0000.000
52A52SER0-0.002-0.01213.026-0.344-0.3440.0000.0000.0000.000
53A53PHE00.024-0.00116.365-0.235-0.2350.0000.0000.0000.000
54A54ILE00.0270.03318.7380.1470.1470.0000.0000.0000.000
55A55LEU00.0060.00920.878-0.227-0.2270.0000.0000.0000.000
56A56ARG10.9040.92422.744-13.470-13.4700.0000.0000.0000.000
57A57GLY0-0.0090.00326.4400.1850.1850.0000.0000.0000.000
58A58LEU0-0.068-0.00824.7050.0080.0080.0000.0000.0000.000
59A59ASP-1-0.833-0.91228.98710.06010.0600.0000.0000.0000.000
60A60ALA00.0530.04030.7920.3050.3050.0000.0000.0000.000
61A61GLY0-0.0260.00032.008-0.161-0.1610.0000.0000.0000.000
62A62THR0-0.083-0.03828.640-0.217-0.2170.0000.0000.0000.000
63A63GLU-1-0.876-0.94424.72313.31613.3160.0000.0000.0000.000
64A64TYR0-0.022-0.02123.012-0.088-0.0880.0000.0000.0000.000
65A65THR0-0.035-0.00318.6570.5100.5100.0000.0000.0000.000
66A66ILE00.011-0.00916.630-0.096-0.0960.0000.0000.0000.000
67A67SER0-0.007-0.01213.6540.5320.5320.0000.0000.0000.000
68A68LEU00.0250.03010.377-0.748-0.7480.0000.0000.0000.000
69A69VAL0-0.067-0.0338.1852.4682.4680.0000.0000.0000.000
70A70ALA00.0790.0415.307-2.126-2.1260.0000.0000.0000.000
71A71GLU-1-0.798-0.8936.80922.64622.6460.0000.0000.0000.000
72A72LYS10.8980.9111.876-72.485-78.47516.772-6.752-4.0300.063
73A73GLY00.0550.0217.804-1.055-1.0550.0000.0000.0000.000
74A74ARG10.9871.00711.391-17.680-17.6800.0000.0000.0000.000
75A75HIS0-0.052-0.0247.949-0.799-0.7990.0000.0000.0000.000
76A76LYS10.8950.9388.071-18.716-18.7160.0000.0000.0000.000
77A77SER0-0.037-0.0173.9660.2100.4740.005-0.124-0.1460.000
78A78LYS10.9350.9665.132-35.887-35.709-0.001-0.009-0.1680.000
79A79PRO00.024-0.0047.0052.9872.9870.0000.0000.0000.000
80A80THR0-0.024-0.0227.6570.8060.8060.0000.0000.0000.000
81A81THR0-0.040-0.03810.265-1.180-1.1800.0000.0000.0000.000
82A82ILE00.0360.03414.0030.3120.3120.0000.0000.0000.000
83A83LYS10.8730.93716.790-14.809-14.8090.0000.0000.0000.000
84A84GLY00.0420.03220.5340.2310.2310.0000.0000.0000.000
85A85SER00.0230.00622.734-0.019-0.0190.0000.0000.0000.000
86A86THR0-0.083-0.06526.4540.1290.1290.0000.0000.0000.000
87A87VAL00.0490.03528.691-0.168-0.1680.0000.0000.0000.000
88A88VAL0-0.003-0.01731.666-0.082-0.0820.0000.0000.0000.000
89A89GLY00.0230.00735.1140.0230.0230.0000.0000.0000.000
90A90SER00.0280.00237.314-0.198-0.1980.0000.0000.0000.000
91A91PRO0-0.029-0.01939.943-0.046-0.0460.0000.0000.0000.000
92A92LYS10.8970.93040.601-7.921-7.9210.0000.0000.0000.000
93A93GLY00.0300.01844.3440.0100.0100.0000.0000.0000.000
94A94ILE0-0.0150.01847.710-0.095-0.0950.0000.0000.0000.000
95A95SER0-0.026-0.01349.950-0.093-0.0930.0000.0000.0000.000
96A96PHE00.013-0.01352.585-0.010-0.0100.0000.0000.0000.000
97A97SER0-0.029-0.04256.869-0.005-0.0050.0000.0000.0000.000
98A98ASP-1-0.822-0.87560.3065.3605.3600.0000.0000.0000.000
99A99ILE0-0.0230.00059.9390.0130.0130.0000.0000.0000.000
100A100THR0-0.035-0.01063.408-0.106-0.1060.0000.0000.0000.000
101A101GLU-1-0.896-0.94865.2274.7084.7080.0000.0000.0000.000
102A102ASN0-0.030-0.04265.100-0.033-0.0330.0000.0000.0000.000
103A103SER0-0.029-0.01562.4370.0390.0390.0000.0000.0000.000
104A104ALA00.0020.00859.174-0.040-0.0400.0000.0000.0000.000
105A105THR0-0.058-0.04458.0170.0750.0750.0000.0000.0000.000
106A106VAL00.0020.02052.4030.0200.0200.0000.0000.0000.000
107A107SER00.017-0.00953.313-0.039-0.0390.0000.0000.0000.000
108A108TRP00.000-0.00147.323-0.034-0.0340.0000.0000.0000.000
109A109THR00.0190.01346.387-0.063-0.0630.0000.0000.0000.000
110A110PRO00.0260.00845.3920.1770.1770.0000.0000.0000.000
111A111PRO00.0140.03339.952-0.019-0.0190.0000.0000.0000.000
112A112ARG10.9130.94839.323-7.954-7.9540.0000.0000.0000.000
113A113SER00.011-0.00535.9450.2660.2660.0000.0000.0000.000
114A114ARG10.9530.98737.943-8.569-8.5690.0000.0000.0000.000
115A115VAL00.0210.00538.8410.2010.2010.0000.0000.0000.000
116A116ASP-1-0.802-0.88240.4918.0238.0230.0000.0000.0000.000
117A117SER0-0.041-0.02043.144-0.238-0.2380.0000.0000.0000.000
118A118TYR00.0510.02043.8140.2170.2170.0000.0000.0000.000
119A119ARG10.8570.90140.947-7.956-7.9560.0000.0000.0000.000
120A120VAL0-0.0040.00246.2530.0750.0750.0000.0000.0000.000
121A121SER0-0.0010.00147.167-0.102-0.1020.0000.0000.0000.000
122A122TYR00.011-0.01249.6180.0000.0000.0000.0000.0000.000
123A123VAL00.0130.00550.723-0.049-0.0490.0000.0000.0000.000
124A124PRO00.0340.03653.6620.0420.0420.0000.0000.0000.000
125A125ILE00.0400.00752.4830.0760.0760.0000.0000.0000.000
126A126THR0-0.0140.00153.8210.0490.0490.0000.0000.0000.000
127A127GLY0-0.042-0.01552.8400.0160.0160.0000.0000.0000.000
128A128GLY00.008-0.00452.633-0.142-0.1420.0000.0000.0000.000
129A129THR0-0.018-0.00851.3040.1240.1240.0000.0000.0000.000
130A130PRO0-0.013-0.01948.126-0.114-0.1140.0000.0000.0000.000
131A131ASN0-0.0280.00651.346-0.135-0.1350.0000.0000.0000.000
132A132VAL0-0.006-0.00847.3610.0220.0220.0000.0000.0000.000
133A133VAL0-0.007-0.00150.697-0.097-0.0970.0000.0000.0000.000
134A134THR00.0030.00047.3000.1590.1590.0000.0000.0000.000
135A135VAL0-0.073-0.04049.106-0.192-0.1920.0000.0000.0000.000
136A136ASP-1-0.809-0.90948.6096.8146.8140.0000.0000.0000.000
137A137GLY00.0620.03546.241-0.060-0.0600.0000.0000.0000.000
138A138SER0-0.078-0.04347.059-0.001-0.0010.0000.0000.0000.000
139A139LYS10.8860.95149.648-6.124-6.1240.0000.0000.0000.000
140A140THR00.0310.01449.9410.1360.1360.0000.0000.0000.000
141A141ARG10.9100.95151.481-5.801-5.8010.0000.0000.0000.000
142A142THR0-0.035-0.02553.530-0.052-0.0520.0000.0000.0000.000
143A143LYS10.9650.99955.725-5.345-5.3450.0000.0000.0000.000
144A144LEU0-0.0060.01354.6360.0480.0480.0000.0000.0000.000
145A145VAL00.013-0.01758.724-0.111-0.1110.0000.0000.0000.000
146A146LYS10.9420.96060.849-5.143-5.1430.0000.0000.0000.000
147A147LEU0-0.0070.01558.5490.0350.0350.0000.0000.0000.000
148A148VAL00.0290.02962.298-0.105-0.1050.0000.0000.0000.000
149A149PRO00.0660.03263.6450.0670.0670.0000.0000.0000.000
150A150GLY0-0.0060.00964.810-0.006-0.0060.0000.0000.0000.000
151A151VAL0-0.009-0.01059.4230.0100.0100.0000.0000.0000.000
152A152ASP-1-0.872-0.92956.6895.6385.6380.0000.0000.0000.000
153A153TYR0-0.025-0.03255.4320.0310.0310.0000.0000.0000.000
154A154ASN00.0070.00649.2860.0580.0580.0000.0000.0000.000
155A155VAL0-0.039-0.02650.767-0.008-0.0080.0000.0000.0000.000
156A156ASN00.0280.00545.3200.1050.1050.0000.0000.0000.000
157A157ILE0-0.042-0.00945.843-0.119-0.1190.0000.0000.0000.000
158A158ILE00.0410.03440.3560.0900.0900.0000.0000.0000.000
159A159SER0-0.015-0.01539.868-0.307-0.3070.0000.0000.0000.000
160A160VAL00.0190.00739.6040.1830.1830.0000.0000.0000.000
161A161LYS10.7990.88436.009-8.745-8.7450.0000.0000.0000.000
162A162GLY0-0.037-0.01936.8820.2780.2780.0000.0000.0000.000
163A163PHE0-0.021-0.02334.766-0.229-0.2290.0000.0000.0000.000
164A164GLU-1-0.929-0.94331.91510.36210.3620.0000.0000.0000.000
165A165GLU-1-0.849-0.93535.3977.9017.9010.0000.0000.0000.000
166A166SER0-0.033-0.01236.1580.1050.1050.0000.0000.0000.000
167A167GLU-1-0.875-0.92235.1858.9778.9770.0000.0000.0000.000
168A168PRO0-0.028-0.01337.866-0.188-0.1880.0000.0000.0000.000
169A169ILE0-0.031-0.00341.3910.0390.0390.0000.0000.0000.000
170A170SER0-0.003-0.02543.983-0.084-0.0840.0000.0000.0000.000
171A171GLY00.001-0.00147.1750.0050.0050.0000.0000.0000.000
172A172ILE00.0060.01350.5880.0040.0040.0000.0000.0000.000
173A173LEU0-0.083-0.04253.719-0.062-0.0620.0000.0000.0000.000
174A174LYS11.0001.00856.668-5.707-5.7070.0000.0000.0000.000
175A175THR0-0.015-0.01060.101-0.065-0.0650.0000.0000.0000.000