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: 16J8Z

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 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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1558666.516877
FMO2-HF: Nuclear repulsion 1492580.915824
FMO2-HF: Total energy -66085.601054
FMO2-MP2: Total energy -66282.573093


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.
-287.283-296.59241.464-15.823-16.3320.167
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 : -0.757 / q_NPA : -0.879
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].
3A3PRO00.0790.0563.54811.64514.4320.068-1.376-1.4790.002
4A4LYS10.8120.9171.712-110.815-117.88716.534-5.496-3.9660.065
5A5ASP-1-0.804-0.9067.29929.91629.9160.0000.0000.0000.000
6A6LEU0-0.035-0.00410.941-1.047-1.0470.0000.0000.0000.000
7A7GLU-1-0.839-0.90112.56718.08718.0870.0000.0000.0000.000
8A8VAL0-0.041-0.04516.2660.1720.1720.0000.0000.0000.000
9A9SER00.010-0.01019.734-0.355-0.3550.0000.0000.0000.000
10A10ASP-1-0.856-0.91122.77113.48213.4820.0000.0000.0000.000
11A11PRO00.0020.00825.878-0.111-0.1110.0000.0000.0000.000
12A12THR0-0.0060.00327.551-0.543-0.5430.0000.0000.0000.000
13A13GLU-1-0.833-0.89429.9339.1339.1330.0000.0000.0000.000
14A14THR0-0.031-0.03630.5370.0230.0230.0000.0000.0000.000
15A15THR0-0.007-0.02726.5350.0950.0950.0000.0000.0000.000
16A16LEU00.0030.00622.790-0.098-0.0980.0000.0000.0000.000
17A17SER0-0.0220.00321.9970.7390.7390.0000.0000.0000.000
18A18LEU00.0150.00516.7830.3340.3340.0000.0000.0000.000
19A19ARG10.8970.94215.122-19.669-19.6690.0000.0000.0000.000
20A20TRP0-0.024-0.0049.161-0.681-0.6810.0000.0000.0000.000
21A21ARG10.8860.9347.643-30.556-30.5560.0000.0000.0000.000
22A22ARG10.9290.9506.693-29.119-29.1190.0000.0000.0000.000
23A23PRO0-0.061-0.0272.787-0.1682.1031.133-1.473-1.9310.017
24A24VAL00.0300.0171.781-18.283-24.77012.956-3.296-3.1730.039
25A25ALA0-0.041-0.0162.283-18.955-17.0062.919-2.004-2.8640.023
26A26LYS10.8670.9263.858-28.517-28.4240.0010.009-0.1040.000
27A27PHE0-0.095-0.0625.8852.2162.2160.0000.0000.0000.000
28A28ASP-1-0.826-0.9177.78822.54422.5440.0000.0000.0000.000
29A29ARG10.8330.88310.635-21.273-21.2730.0000.0000.0000.000
30A30TYR0-0.020-0.0148.1504.6044.6040.0000.0000.0000.000
31A31ARG10.8500.91711.669-20.489-20.4890.0000.0000.0000.000
32A32LEU00.0040.00613.3151.6411.6410.0000.0000.0000.000
33A33THR0-0.027-0.02515.976-0.928-0.9280.0000.0000.0000.000
34A34TYR00.0100.00618.0120.7290.7290.0000.0000.0000.000
35A35VAL00.003-0.00220.796-0.496-0.4960.0000.0000.0000.000
36A36SER00.0760.05723.6730.1140.1140.0000.0000.0000.000
37A37PRO00.036-0.00227.0620.0510.0510.0000.0000.0000.000
38A38SER0-0.031-0.00829.190-0.174-0.1740.0000.0000.0000.000
39A39GLY00.0160.01626.591-0.183-0.1830.0000.0000.0000.000
40A40LYS10.8740.94226.311-11.070-11.0700.0000.0000.0000.000
41A41LYS10.8930.94219.660-14.396-14.3960.0000.0000.0000.000
42A42ASN0-0.027-0.00522.782-0.972-0.9720.0000.0000.0000.000
43A43GLU-1-0.800-0.89619.60716.37516.3750.0000.0000.0000.000
44A44MET00.0190.02218.947-0.724-0.7240.0000.0000.0000.000
45A45GLU-1-0.823-0.88316.16319.27319.2730.0000.0000.0000.000
46A46ILE0-0.006-0.00614.762-0.941-0.9410.0000.0000.0000.000
47A47PRO00.0500.02714.2351.7131.7130.0000.0000.0000.000
48A48VAL00.0400.01310.8990.9470.9470.0000.0000.0000.000
49A49ASP-1-0.886-0.93111.23321.94521.9450.0000.0000.0000.000
50A50SER0-0.027-0.00313.724-0.174-0.1740.0000.0000.0000.000
51A51THR0-0.006-0.01610.7911.9151.9150.0000.0000.0000.000
52A52SER0-0.013-0.02213.091-0.361-0.3610.0000.0000.0000.000
53A53PHE0-0.006-0.01416.313-0.304-0.3040.0000.0000.0000.000
54A54ILE00.0520.04318.8200.0500.0500.0000.0000.0000.000
55A55LEU00.0190.02120.820-0.214-0.2140.0000.0000.0000.000
56A56ARG10.8900.91622.791-13.747-13.7470.0000.0000.0000.000
57A57GLY0-0.0140.01126.4720.2070.2070.0000.0000.0000.000
58A58LEU0-0.063-0.00825.0380.0920.0920.0000.0000.0000.000
59A59ASP-1-0.796-0.87129.22910.11510.1150.0000.0000.0000.000
60A60ALA00.0720.05330.8510.2940.2940.0000.0000.0000.000
61A61GLY0-0.0290.00532.689-0.225-0.2250.0000.0000.0000.000
62A62THR0-0.094-0.03529.015-0.187-0.1870.0000.0000.0000.000
63A63GLU-1-0.841-0.91224.73913.37913.3790.0000.0000.0000.000
64A64TYR0-0.026-0.04423.256-0.107-0.1070.0000.0000.0000.000
65A65THR0-0.023-0.00219.2900.4010.4010.0000.0000.0000.000
66A66ILE00.009-0.00116.970-0.178-0.1780.0000.0000.0000.000
67A67SER0-0.008-0.01013.7840.4520.4520.0000.0000.0000.000
68A68LEU00.0260.02910.525-0.719-0.7190.0000.0000.0000.000
69A69VAL0-0.068-0.0338.6082.2032.2030.0000.0000.0000.000
70A70ALA00.0510.0225.867-1.241-1.2410.0000.0000.0000.000
71A71GLU-1-0.764-0.8687.99123.29523.2950.0000.0000.0000.000
72A72LYS10.8800.9212.214-72.022-75.1897.855-2.110-2.5780.021
73A73GLY00.0580.0448.925-0.775-0.7750.0000.0000.0000.000
74A74ARG10.9410.97112.430-18.185-18.1850.0000.0000.0000.000
75A75HIS0-0.022-0.0068.388-1.241-1.2410.0000.0000.0000.000
76A76LYS10.8740.9278.902-19.640-19.6400.0000.0000.0000.000
77A77SER0-0.038-0.0144.4890.4170.558-0.001-0.067-0.0730.000
78A78LYS10.9400.9634.580-34.337-34.161-0.001-0.010-0.1640.000
79A79PRO00.0210.0076.5303.6683.6680.0000.0000.0000.000
80A80THR0-0.049-0.0317.4800.4800.4800.0000.0000.0000.000
81A81THR00.001-0.01410.367-0.448-0.4480.0000.0000.0000.000
82A82ILE00.0160.02314.1040.2330.2330.0000.0000.0000.000
83A83LYS10.8210.88116.876-14.029-14.0290.0000.0000.0000.000
84A84GLY00.0390.02520.6710.3700.3700.0000.0000.0000.000
85A85SER00.0140.00322.9260.0000.0000.0000.0000.0000.000
86A86THR0-0.049-0.03526.6110.0690.0690.0000.0000.0000.000
87A87VAL00.0450.04128.987-0.178-0.1780.0000.0000.0000.000
88A88VAL0-0.014-0.01931.947-0.069-0.0690.0000.0000.0000.000
89A89GLY0-0.0040.00235.344-0.021-0.0210.0000.0000.0000.000
90A90SER00.048-0.01637.258-0.219-0.2190.0000.0000.0000.000
91A91PRO0-0.044-0.02439.881-0.061-0.0610.0000.0000.0000.000
92A92LYS10.8970.93840.350-8.006-8.0060.0000.0000.0000.000
93A93GLY00.0370.02544.0950.0010.0010.0000.0000.0000.000
94A94ILE0-0.0100.00147.435-0.031-0.0310.0000.0000.0000.000
95A95SER0-0.040-0.02450.153-0.088-0.0880.0000.0000.0000.000
96A96PHE00.034-0.00453.0320.0130.0130.0000.0000.0000.000
97A97SER0-0.034-0.04857.124-0.010-0.0100.0000.0000.0000.000
98A98ASP-1-0.802-0.85860.5065.3625.3620.0000.0000.0000.000
99A99ILE0-0.018-0.00360.219-0.011-0.0110.0000.0000.0000.000
100A100THR0-0.023-0.00663.717-0.106-0.1060.0000.0000.0000.000
101A101GLU-1-0.905-0.95265.1054.7254.7250.0000.0000.0000.000
102A102ASN0-0.028-0.02365.229-0.031-0.0310.0000.0000.0000.000
103A103SER0-0.029-0.02962.4800.0330.0330.0000.0000.0000.000
104A104ALA00.0110.02159.585-0.034-0.0340.0000.0000.0000.000
105A105THR0-0.088-0.06757.8050.0610.0610.0000.0000.0000.000
106A106VAL00.0130.01752.4730.0090.0090.0000.0000.0000.000
107A107SER00.026-0.00953.344-0.028-0.0280.0000.0000.0000.000
108A108TRP00.0060.01747.405-0.058-0.0580.0000.0000.0000.000
109A109THR00.0060.00646.302-0.096-0.0960.0000.0000.0000.000
110A110PRO00.0100.00445.2590.1690.1690.0000.0000.0000.000
111A111PRO00.0130.03939.6930.0050.0050.0000.0000.0000.000
112A112ARG10.9110.94439.241-7.937-7.9370.0000.0000.0000.000
113A113SER0-0.011-0.02235.6390.2420.2420.0000.0000.0000.000
114A114ARG10.8770.94037.566-8.347-8.3470.0000.0000.0000.000
115A115VAL00.0290.01538.5810.1930.1930.0000.0000.0000.000
116A116ASP-1-0.810-0.88840.3388.0098.0090.0000.0000.0000.000
117A117SER0-0.048-0.02543.180-0.217-0.2170.0000.0000.0000.000
118A118TYR00.024-0.00343.7290.2330.2330.0000.0000.0000.000
119A119ARG10.8330.88940.853-7.935-7.9350.0000.0000.0000.000
120A120VAL00.0160.01946.2910.0690.0690.0000.0000.0000.000
121A121SER00.002-0.00347.645-0.022-0.0220.0000.0000.0000.000
122A122TYR0-0.010-0.01350.0150.0110.0110.0000.0000.0000.000
123A123VAL00.0150.01651.164-0.032-0.0320.0000.0000.0000.000
124A124PRO00.0270.03054.0800.0240.0240.0000.0000.0000.000
125A125ILE00.031-0.00552.8050.1000.1000.0000.0000.0000.000
126A126THR0-0.023-0.00354.4950.0380.0380.0000.0000.0000.000
127A127GLY0-0.0130.01053.1240.0350.0350.0000.0000.0000.000
128A128GLY00.013-0.01352.964-0.150-0.1500.0000.0000.0000.000
129A129THR0-0.005-0.00551.7320.1210.1210.0000.0000.0000.000
130A130PRO0-0.018-0.01048.530-0.120-0.1200.0000.0000.0000.000
131A131ASN0-0.0260.00551.699-0.106-0.1060.0000.0000.0000.000
132A132VAL00.008-0.01147.7090.0940.0940.0000.0000.0000.000
133A133VAL0-0.019-0.00850.686-0.115-0.1150.0000.0000.0000.000
134A134THR00.0210.01347.0120.1560.1560.0000.0000.0000.000
135A135VAL0-0.073-0.04048.789-0.198-0.1980.0000.0000.0000.000
136A136ASP-1-0.770-0.87348.3396.7816.7810.0000.0000.0000.000
137A137GLY00.0490.03146.055-0.035-0.0350.0000.0000.0000.000
138A138SER0-0.067-0.04546.8430.0060.0060.0000.0000.0000.000
139A139LYS10.8800.94549.671-6.092-6.0920.0000.0000.0000.000
140A140THR00.0250.01150.2970.1010.1010.0000.0000.0000.000
141A141ARG10.8960.95251.363-5.764-5.7640.0000.0000.0000.000
142A142THR0-0.032-0.02153.551-0.061-0.0610.0000.0000.0000.000
143A143LYS10.9710.99755.656-5.285-5.2850.0000.0000.0000.000
144A144LEU0-0.0060.00854.5470.0620.0620.0000.0000.0000.000
145A145VAL00.011-0.01558.700-0.102-0.1020.0000.0000.0000.000
146A146LYS10.9440.96761.068-5.142-5.1420.0000.0000.0000.000
147A147LEU0-0.0070.02458.8650.0250.0250.0000.0000.0000.000
148A148VAL00.0390.01862.332-0.106-0.1060.0000.0000.0000.000
149A149PRO00.0590.03363.8620.0700.0700.0000.0000.0000.000
150A150GLY00.0000.01165.754-0.007-0.0070.0000.0000.0000.000
151A151VAL0-0.019-0.01959.8320.0210.0210.0000.0000.0000.000
152A152ASP-1-0.859-0.93857.0865.6265.6260.0000.0000.0000.000
153A153TYR0-0.009-0.00555.7550.0380.0380.0000.0000.0000.000
154A154ASN00.0120.00949.0890.0490.0490.0000.0000.0000.000
155A155VAL0-0.027-0.02351.188-0.027-0.0270.0000.0000.0000.000
156A156ASN00.017-0.01045.8010.1110.1110.0000.0000.0000.000
157A157ILE0-0.061-0.03446.056-0.131-0.1310.0000.0000.0000.000
158A158ILE00.0330.04340.4620.0790.0790.0000.0000.0000.000
159A159SER0-0.030-0.02839.970-0.303-0.3030.0000.0000.0000.000
160A160VAL00.0230.01239.7070.1910.1910.0000.0000.0000.000
161A161LYS10.8550.90235.770-8.751-8.7510.0000.0000.0000.000
162A162GLY0-0.029-0.02036.9410.2760.2760.0000.0000.0000.000
163A163PHE0-0.040-0.02534.983-0.195-0.1950.0000.0000.0000.000
164A164GLU-1-0.885-0.92132.02610.31310.3130.0000.0000.0000.000
165A165GLU-1-0.837-0.92435.4227.7807.7800.0000.0000.0000.000
166A166SER0-0.020-0.01436.1720.1500.1500.0000.0000.0000.000
167A167GLU-1-0.855-0.92335.6158.9238.9230.0000.0000.0000.000
168A168PRO0-0.038-0.00438.169-0.195-0.1950.0000.0000.0000.000
169A169ILE0-0.0120.01341.9250.0270.0270.0000.0000.0000.000
170A170SER0-0.009-0.02444.144-0.076-0.0760.0000.0000.0000.000
171A171GLY0-0.004-0.00347.3540.0090.0090.0000.0000.0000.000
172A172ILE0-0.0090.00450.802-0.011-0.0110.0000.0000.0000.000
173A173LEU0-0.064-0.03154.194-0.070-0.0700.0000.0000.0000.000
174A174LYS10.9700.99557.297-5.719-5.7190.0000.0000.0000.000
175A175THR0-0.042-0.01960.568-0.047-0.0470.0000.0000.0000.000