Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 94N32

Calculation Name: 4QT4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4QT4

Chain ID: A

ChEMBL ID:

UniProt ID: B5XIP6

Base Structure: X-ray

Registration Date: 2023-06-21

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 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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2155035.787879
FMO2-HF: Nuclear repulsion 2080387.898135
FMO2-HF: Total energy -74647.889743
FMO2-MP2: Total energy -74864.441718


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-15.429-13.76511.964-6.877-6.752-0.05
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : 0.014
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].
3A3LYS10.8260.9143.1073.6856.201-0.002-1.327-1.1870.004
4A4MET0-0.011-0.0026.4780.6060.6060.0000.0000.0000.000
5A5ILE00.0150.0149.9560.2450.2450.0000.0000.0000.000
6A6VAL00.006-0.00512.8260.1120.1120.0000.0000.0000.000
7A7GLY00.012-0.00116.1530.0390.0390.0000.0000.0000.000
8A8LEU0-0.054-0.03819.7590.0300.0300.0000.0000.0000.000
9A9GLY00.030-0.00822.6670.0140.0140.0000.0000.0000.000
10A10ASN0-0.040-0.01226.0480.0020.0020.0000.0000.0000.000
11A11PRO00.0540.04627.370-0.002-0.0020.0000.0000.0000.000
12A12GLY00.0530.01729.0560.0170.0170.0000.0000.0000.000
13A13SER00.0730.02532.392-0.007-0.0070.0000.0000.0000.000
14A14LYS10.9040.95634.8740.1840.1840.0000.0000.0000.000
15A15TYR0-0.021-0.02531.4350.0100.0100.0000.0000.0000.000
16A16GLU-1-0.842-0.88530.579-0.227-0.2270.0000.0000.0000.000
17A17LYS10.9070.94230.8320.1880.1880.0000.0000.0000.000
18A18THR0-0.087-0.04231.9700.0040.0040.0000.0000.0000.000
19A19LYS10.8920.94131.0790.1740.1740.0000.0000.0000.000
20A20HIS10.7510.83428.7740.2560.2560.0000.0000.0000.000
21A21ASN00.0120.00227.174-0.019-0.0190.0000.0000.0000.000
22A22ILE00.0450.02325.356-0.018-0.0180.0000.0000.0000.000
23A23GLY00.0050.00722.364-0.019-0.0190.0000.0000.0000.000
24A24PHE0-0.040-0.02221.750-0.039-0.0390.0000.0000.0000.000
25A25MET00.0160.02223.181-0.017-0.0170.0000.0000.0000.000
26A26ALA00.0130.00720.964-0.001-0.0010.0000.0000.0000.000
27A27ILE0-0.0080.00816.561-0.024-0.0240.0000.0000.0000.000
28A28ASP-1-0.789-0.89119.740-0.435-0.4350.0000.0000.0000.000
29A29ASN0-0.052-0.03322.5030.0270.0270.0000.0000.0000.000
30A30ILE0-0.023-0.01915.6830.0040.0040.0000.0000.0000.000
31A31VAL00.000-0.00517.007-0.009-0.0090.0000.0000.0000.000
32A32LYS10.8840.95719.0460.3560.3560.0000.0000.0000.000
33A33ASN0-0.085-0.05120.5650.0570.0570.0000.0000.0000.000
34A34LEU0-0.082-0.04314.460-0.017-0.0170.0000.0000.0000.000
35A35ASP-1-0.917-0.93617.263-0.350-0.3500.0000.0000.0000.000
36A36VAL0-0.039-0.00714.878-0.026-0.0260.0000.0000.0000.000
37A37THR00.0100.00217.7760.0200.0200.0000.0000.0000.000
38A38PHE0-0.029-0.02618.431-0.041-0.0410.0000.0000.0000.000
39A39THR0-0.040-0.01218.0310.0510.0510.0000.0000.0000.000
40A40ASP-1-0.815-0.90920.242-0.388-0.3880.0000.0000.0000.000
41A41ASP-1-0.810-0.89816.244-0.460-0.4600.0000.0000.0000.000
42A42LYS10.9430.95018.8560.2580.2580.0000.0000.0000.000
43A43ASN0-0.0140.02214.9500.0700.0700.0000.0000.0000.000
44A44PHE0-0.005-0.00613.1630.0050.0050.0000.0000.0000.000
45A45LYS10.7960.88618.9590.3600.3600.0000.0000.0000.000
46A46ALA00.0330.00118.391-0.005-0.0050.0000.0000.0000.000
47A47GLN0-0.040-0.00520.0470.0110.0110.0000.0000.0000.000
48A48ILE0-0.016-0.01914.029-0.068-0.0680.0000.0000.0000.000
49A49GLY00.0910.06115.7900.0910.0910.0000.0000.0000.000
50A50SER0-0.064-0.04210.323-0.134-0.1340.0000.0000.0000.000
51A51THR00.0360.02110.6830.1970.1970.0000.0000.0000.000
52A52PHE00.0300.0094.834-0.434-0.4340.0000.0000.0000.000
53A53ILE0-0.017-0.0097.6820.2630.2630.0000.0000.0000.000
54A54ASN0-0.010-0.0087.180-0.207-0.2070.0000.0000.0000.000
55A55HIS00.0340.0203.349-0.917-0.3200.024-0.146-0.4750.000
56A56GLU-1-0.851-0.9131.827-16.495-18.77711.939-5.105-4.553-0.055
57A57LYS10.8460.9363.8042.1302.8310.004-0.280-0.4240.001
58A58VAL00.0180.0055.655-0.980-0.9800.0000.0000.0000.000
59A59TYR00.014-0.0037.2160.5750.5750.0000.0000.0000.000
60A60PHE00.0250.00611.117-0.060-0.0600.0000.0000.0000.000
61A61VAL00.017-0.00214.3130.1100.1100.0000.0000.0000.000
62A62LYS10.8010.89917.0780.4440.4440.0000.0000.0000.000
63A63PRO0-0.008-0.00919.4530.0320.0320.0000.0000.0000.000
64A64THR00.013-0.00321.7740.0270.0270.0000.0000.0000.000
65A65THR00.0160.01322.7570.0210.0210.0000.0000.0000.000
66A66PHE00.0080.00525.5050.0240.0240.0000.0000.0000.000
67A67MET00.0570.05425.887-0.021-0.0210.0000.0000.0000.000
68A68ASN0-0.037-0.01225.698-0.021-0.0210.0000.0000.0000.000
69A69ASN0-0.018-0.00225.8270.0140.0140.0000.0000.0000.000
70A70SER0-0.004-0.01621.398-0.022-0.0220.0000.0000.0000.000
71A71GLY0-0.006-0.00520.296-0.053-0.0530.0000.0000.0000.000
72A72ILE00.0280.01719.907-0.030-0.0300.0000.0000.0000.000
73A73ALA00.0020.00319.089-0.023-0.0230.0000.0000.0000.000
74A74VAL00.0160.00414.903-0.055-0.0550.0000.0000.0000.000
75A75LYS10.9430.97315.1000.2800.2800.0000.0000.0000.000
76A76ALA00.0010.01715.308-0.025-0.0250.0000.0000.0000.000
77A77LEU0-0.005-0.00512.820-0.018-0.0180.0000.0000.0000.000
78A78LEU0-0.013-0.00910.130-0.123-0.1230.0000.0000.0000.000
79A79THR0-0.026-0.02910.373-0.027-0.0270.0000.0000.0000.000
80A80TYR0-0.041-0.02210.1620.0540.0540.0000.0000.0000.000
81A81TYR0-0.030-0.0156.4290.0990.0990.0000.0000.0000.000
82A82ASN0-0.047-0.0126.133-0.213-0.2130.0000.0000.0000.000
83A83ILE0-0.0180.0066.032-0.004-0.0040.0000.0000.0000.000
84A84ASP-1-0.734-0.8517.003-0.347-0.3470.0000.0000.0000.000
85A85ILE0-0.050-0.0388.896-0.245-0.2450.0000.0000.0000.000
86A86THR0-0.087-0.0728.671-0.074-0.0740.0000.0000.0000.000
87A87ASP-1-0.831-0.8974.458-3.773-3.641-0.001-0.019-0.1130.000
88A88LEU0-0.064-0.0177.298-0.171-0.1710.0000.0000.0000.000
89A89ILE0-0.015-0.00910.6950.1550.1550.0000.0000.0000.000
90A90VAL0-0.026-0.00313.2610.0220.0220.0000.0000.0000.000
91A91ILE00.003-0.00516.2080.0600.0600.0000.0000.0000.000
92A92TYR00.002-0.02119.5380.0180.0180.0000.0000.0000.000
93A93ASP-1-0.695-0.81923.270-0.300-0.3000.0000.0000.0000.000
94A94ASP-1-0.862-0.94726.318-0.266-0.2660.0000.0000.0000.000
95A95LEU0-0.001-0.01827.7530.0130.0130.0000.0000.0000.000
96A96ASP-1-0.793-0.86130.909-0.157-0.1570.0000.0000.0000.000
97A97MET0-0.0920.02325.9760.0040.0040.0000.0000.0000.000
98A98GLU-1-0.793-0.90831.436-0.170-0.1700.0000.0000.0000.000
99A99VAL00.0160.00331.923-0.019-0.0190.0000.0000.0000.000
100A100SER0-0.020-0.00429.6560.0060.0060.0000.0000.0000.000
101A101LYS10.8670.95427.7140.2230.2230.0000.0000.0000.000
102A102LEU00.0500.02621.825-0.009-0.0090.0000.0000.0000.000
103A103ARG10.8270.88724.2510.2660.2660.0000.0000.0000.000
104A104LEU00.0500.04617.435-0.017-0.0170.0000.0000.0000.000
105A105ARG10.8280.89819.7170.3360.3360.0000.0000.0000.000
106A106SER00.1540.07017.034-0.040-0.0400.0000.0000.0000.000
107A107LYS10.8910.95418.1000.2350.2350.0000.0000.0000.000
108A108GLY0-0.009-0.00220.7720.0040.0040.0000.0000.0000.000
109A109SER00.0560.03023.787-0.020-0.0200.0000.0000.0000.000
110A110ALA00.0440.00826.124-0.011-0.0110.0000.0000.0000.000
111A111GLY0-0.0080.00327.052-0.004-0.0040.0000.0000.0000.000
112A112GLY00.0130.00930.1900.0110.0110.0000.0000.0000.000
113A113HIS0-0.021-0.02125.2460.0060.0060.0000.0000.0000.000
114A114ASN00.0540.00927.273-0.020-0.0200.0000.0000.0000.000
115A115GLY00.0570.03624.7990.0000.0000.0000.0000.0000.000
116A116ILE00.0270.01121.306-0.020-0.0200.0000.0000.0000.000
117A117LYS10.9220.95323.3500.2000.2000.0000.0000.0000.000
118A118SER0-0.024-0.00824.045-0.002-0.0020.0000.0000.0000.000
119A119ILE00.0480.01618.2240.0050.0050.0000.0000.0000.000
120A120ILE0-0.013-0.00320.396-0.004-0.0040.0000.0000.0000.000
121A121ALA0-0.039-0.01622.0200.0090.0090.0000.0000.0000.000
122A122HIS0-0.049-0.01820.4480.0260.0260.0000.0000.0000.000
123A123ILE0-0.034-0.02515.474-0.006-0.0060.0000.0000.0000.000
124A124GLY00.0250.02918.0450.0030.0030.0000.0000.0000.000
125A125THR00.0450.02116.8450.0390.0390.0000.0000.0000.000
126A126GLN0-0.020-0.01920.005-0.027-0.0270.0000.0000.0000.000
127A127GLU-1-0.860-0.93218.080-0.287-0.2870.0000.0000.0000.000
128A128PHE00.0640.02314.775-0.023-0.0230.0000.0000.0000.000
129A129ASN0-0.034-0.01511.1470.2040.2040.0000.0000.0000.000
130A130ARG10.7740.89915.1260.3880.3880.0000.0000.0000.000
131A131ILE00.0320.01215.3440.0480.0480.0000.0000.0000.000
132A132LYS10.8450.92019.2640.3280.3280.0000.0000.0000.000
133A133VAL00.0500.02122.9820.0140.0140.0000.0000.0000.000
134A134GLY00.000-0.00425.9610.0020.0020.0000.0000.0000.000
135A135ILE0-0.034-0.01129.522-0.001-0.0010.0000.0000.0000.000
136A136GLY00.0610.03432.1520.0110.0110.0000.0000.0000.000
137A137ARG10.7820.85834.7890.1580.1580.0000.0000.0000.000
138A138PRO0-0.0160.01235.7310.0050.0050.0000.0000.0000.000
139A139LEU00.0540.01538.5640.0060.0060.0000.0000.0000.000
140A140LYS10.9550.96242.1960.1110.1110.0000.0000.0000.000
141A141GLY00.0370.02143.1990.0050.0050.0000.0000.0000.000
142A142MET0-0.0550.00539.659-0.003-0.0030.0000.0000.0000.000
143A143THR0-0.024-0.02339.470-0.005-0.0050.0000.0000.0000.000
144A144VAL00.043-0.00332.738-0.004-0.0040.0000.0000.0000.000
145A145ILE00.0320.01635.219-0.009-0.0090.0000.0000.0000.000
146A146ASN00.0580.02636.489-0.009-0.0090.0000.0000.0000.000
147A147HIS00.0370.03934.2950.0040.0040.0000.0000.0000.000
148A148VAL0-0.017-0.01731.504-0.004-0.0040.0000.0000.0000.000
149A149MET0-0.050-0.03032.385-0.010-0.0100.0000.0000.0000.000
150A150GLY00.0380.04235.7280.0060.0060.0000.0000.0000.000
151A151GLN00.005-0.00835.444-0.017-0.0170.0000.0000.0000.000
152A152PHE00.012-0.00930.0440.0000.0000.0000.0000.0000.000
153A153ASN0-0.039-0.01435.9570.0110.0110.0000.0000.0000.000
154A154THR00.011-0.00337.950-0.007-0.0070.0000.0000.0000.000
155A155GLU-1-0.869-0.94239.192-0.141-0.1410.0000.0000.0000.000
156A156ASP-1-0.799-0.89434.824-0.178-0.1780.0000.0000.0000.000
157A157ASN0-0.057-0.03333.922-0.021-0.0210.0000.0000.0000.000
158A158ILE00.0440.03932.926-0.015-0.0150.0000.0000.0000.000
159A159ALA00.0420.02232.285-0.011-0.0110.0000.0000.0000.000
160A160ILE00.003-0.01029.148-0.019-0.0190.0000.0000.0000.000
161A161SER0-0.013-0.01428.299-0.025-0.0250.0000.0000.0000.000
162A162LEU00.0210.01527.513-0.020-0.0200.0000.0000.0000.000
163A163THR0-0.054-0.04325.221-0.018-0.0180.0000.0000.0000.000
164A164LEU00.0020.00223.875-0.038-0.0380.0000.0000.0000.000
165A165ASP-1-0.771-0.88222.667-0.366-0.3660.0000.0000.0000.000
166A166ARG10.8430.92722.4090.2740.2740.0000.0000.0000.000
167A167VAL0-0.022-0.01319.017-0.033-0.0330.0000.0000.0000.000
168A168VAL00.0110.01318.146-0.074-0.0740.0000.0000.0000.000
169A169ASN0-0.034-0.02417.259-0.066-0.0660.0000.0000.0000.000
170A170ALA0-0.0070.00417.247-0.016-0.0160.0000.0000.0000.000
171A171VAL00.0170.00312.605-0.063-0.0630.0000.0000.0000.000
172A172LYS10.9020.94112.5490.3610.3610.0000.0000.0000.000
173A173PHE00.0050.00213.206-0.025-0.0250.0000.0000.0000.000
174A174TYR00.0500.0187.582-0.146-0.1460.0000.0000.0000.000
175A175LEU0-0.009-0.0177.801-0.119-0.1190.0000.0000.0000.000
176A176GLN0-0.102-0.0408.813-0.045-0.0450.0000.0000.0000.000
177A177GLU-1-0.837-0.90910.835-0.234-0.2340.0000.0000.0000.000
178A178ASN00.0150.0175.001-0.628-0.6280.0000.0000.0000.000
179A179ASP-1-0.763-0.8657.972-0.278-0.2780.0000.0000.0000.000
180A180PHE00.0240.00111.0200.0190.0190.0000.0000.0000.000
181A181GLU-1-0.917-0.95513.192-0.237-0.2370.0000.0000.0000.000
182A182LYS10.8270.90212.3860.3470.3470.0000.0000.0000.000
183A183THR0-0.022-0.02613.6040.0270.0270.0000.0000.0000.000
184A184MET0-0.067-0.04016.3340.0290.0290.0000.0000.0000.000
185A185GLN0-0.0070.00319.0400.0290.0290.0000.0000.0000.000
186A186LYS10.9360.99618.8330.2850.2850.0000.0000.0000.000
187A187PHE0-0.014-0.00718.2990.0110.0110.0000.0000.0000.000
188A188ASN0-0.068-0.03621.7580.0190.0190.0000.0000.0000.000
189A189GLY00.0300.02424.2670.0130.0130.0000.0000.0000.000