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: 5J49Z

Calculation Name: 4J9J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4J9J

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X0C6

Base Structure: X-ray

Registration Date: 2023-09-23

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 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2747400.256651
FMO2-HF: Nuclear repulsion 2660344.179006
FMO2-HF: Total energy -87056.077644
FMO2-MP2: Total energy -87312.07969


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:0:LEU)


Summations of interaction energy for fragment #1(A:0:LEU)
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.
-21.197-12.94215.44-7.773-15.923-0.048
Interaction energy analysis for fragmet #1(A:0:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : 0.006
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].
3A2ASP-1-0.792-0.8713.665-5.758-3.5910.012-1.141-1.0390.004
4A3LYS10.7540.8555.4711.6391.6390.0000.0000.0000.000
5A4VAL0-0.0260.0047.748-0.185-0.1850.0000.0000.0000.000
6A5ILE0-0.0170.0089.9380.1540.1540.0000.0000.0000.000
7A6ILE0-0.037-0.01913.1820.0150.0150.0000.0000.0000.000
8A7ASN00.0380.00215.8430.0420.0420.0000.0000.0000.000
9A8THR00.0200.00219.4250.0030.0030.0000.0000.0000.000
10A9ALA00.0160.01217.3510.0160.0160.0000.0000.0000.000
11A10ALA00.0100.01618.756-0.006-0.0060.0000.0000.0000.000
12A11VAL0-0.009-0.01120.3120.0220.0220.0000.0000.0000.000
13A12GLU-1-0.793-0.88523.147-0.202-0.2020.0000.0000.0000.000
14A13ASN00.0140.03020.5780.0300.0300.0000.0000.0000.000
15A14PRO00.0710.04621.575-0.036-0.0360.0000.0000.0000.000
16A15SER0-0.053-0.04321.984-0.023-0.0230.0000.0000.0000.000
17A16LEU0-0.016-0.00515.517-0.023-0.0230.0000.0000.0000.000
18A17ILE00.0090.00516.765-0.072-0.0720.0000.0000.0000.000
19A18THR0-0.002-0.01116.671-0.046-0.0460.0000.0000.0000.000
20A19GLN0-0.043-0.01816.493-0.043-0.0430.0000.0000.0000.000
21A20ILE0-0.0020.01011.012-0.043-0.0430.0000.0000.0000.000
22A21ALA00.0270.02212.522-0.087-0.0870.0000.0000.0000.000
23A22GLN0-0.062-0.03514.4180.0170.0170.0000.0000.0000.000
24A23THR0-0.073-0.04310.7290.1020.1020.0000.0000.0000.000
25A24PHE0-0.005-0.0156.932-0.061-0.0610.0000.0000.0000.000
26A25GLY00.0520.0519.883-0.095-0.0950.0000.0000.0000.000
27A26SER00.024-0.02712.426-0.104-0.1040.0000.0000.0000.000
28A27GLN0-0.035-0.0219.4410.1460.1460.0000.0000.0000.000
29A28ALA00.0030.0119.096-0.086-0.0860.0000.0000.0000.000
30A29VAL0-0.038-0.02510.525-0.111-0.1110.0000.0000.0000.000
31A30VAL00.0350.02113.1890.1160.1160.0000.0000.0000.000
32A31VAL00.018-0.00415.597-0.002-0.0020.0000.0000.0000.000
33A32ALA0-0.014-0.00217.4550.0350.0350.0000.0000.0000.000
34A33ILE0-0.040-0.02519.1830.0160.0160.0000.0000.0000.000
35A34ASP-1-0.833-0.91022.977-0.240-0.2400.0000.0000.0000.000
36A35ALA0-0.006-0.01425.1040.0010.0010.0000.0000.0000.000
37A36LYS10.8820.95028.7330.1490.1490.0000.0000.0000.000
38A37ARG10.7690.84632.2510.1260.1260.0000.0000.0000.000
39A38VAL0-0.068-0.05535.1720.0040.0040.0000.0000.0000.000
40A39ASP-1-0.920-0.96037.946-0.093-0.0930.0000.0000.0000.000
41A40GLY0-0.0020.01340.7260.0020.0020.0000.0000.0000.000
42A41GLU-1-0.830-0.91737.058-0.135-0.1350.0000.0000.0000.000
43A42PHE0-0.024-0.01132.591-0.002-0.0020.0000.0000.0000.000
44A43MET0-0.0150.01732.734-0.005-0.0050.0000.0000.0000.000
45A44ALA00.0640.02827.243-0.005-0.0050.0000.0000.0000.000
46A45PHE0-0.067-0.03627.3210.0170.0170.0000.0000.0000.000
47A46THR00.0630.03323.885-0.015-0.0150.0000.0000.0000.000
48A47TYR0-0.086-0.08023.3010.0190.0190.0000.0000.0000.000
49A48SER00.0300.01621.7570.0200.0200.0000.0000.0000.000
50A49GLY00.0500.02724.0090.0190.0190.0000.0000.0000.000
51A50LYS10.8030.90727.1860.1650.1650.0000.0000.0000.000
52A51LYS10.8760.93927.4280.2030.2030.0000.0000.0000.000
53A52ASN00.0410.01229.038-0.019-0.0190.0000.0000.0000.000
54A53THR0-0.022-0.03227.3650.0020.0020.0000.0000.0000.000
55A54GLY00.0080.01330.3380.0010.0010.0000.0000.0000.000
56A55ILE0-0.025-0.01028.5470.0040.0040.0000.0000.0000.000
57A56LEU00.0390.01831.652-0.003-0.0030.0000.0000.0000.000
58A57LEU0-0.034-0.02627.825-0.012-0.0120.0000.0000.0000.000
59A58ARG10.8800.91129.7440.1300.1300.0000.0000.0000.000
60A59ASP-1-0.807-0.87631.375-0.163-0.1630.0000.0000.0000.000
61A60TRP0-0.004-0.01622.582-0.009-0.0090.0000.0000.0000.000
62A61VAL00.0200.00626.231-0.023-0.0230.0000.0000.0000.000
63A62VAL00.0330.02526.233-0.015-0.0150.0000.0000.0000.000
64A63GLU-1-0.783-0.87125.887-0.256-0.2560.0000.0000.0000.000
65A64VAL0-0.023-0.02021.824-0.020-0.0200.0000.0000.0000.000
66A65GLU-1-0.699-0.80921.916-0.287-0.2870.0000.0000.0000.000
67A66LYS10.7340.84523.3020.2380.2380.0000.0000.0000.000
68A67ARG10.7760.88021.5960.2710.2710.0000.0000.0000.000
69A68GLY00.0570.04719.665-0.023-0.0230.0000.0000.0000.000
70A69ALA00.0030.00017.495-0.065-0.0650.0000.0000.0000.000
71A70GLY00.0060.00815.7310.0350.0350.0000.0000.0000.000
72A71GLU-1-0.808-0.88915.284-0.565-0.5650.0000.0000.0000.000
73A72ILE0-0.0080.00318.356-0.032-0.0320.0000.0000.0000.000
74A73LEU0-0.045-0.01316.7710.0100.0100.0000.0000.0000.000
75A74LEU00.0230.02220.0300.0100.0100.0000.0000.0000.000
76A75ALA00.004-0.01423.0230.0080.0080.0000.0000.0000.000
77A76SER0-0.055-0.04025.0210.0100.0100.0000.0000.0000.000
78A85GLY0-0.016-0.02932.8600.0000.0000.0000.0000.0000.000
79A86TYR00.0480.01624.9030.0050.0050.0000.0000.0000.000
80A87ASP-1-0.736-0.80730.006-0.135-0.1350.0000.0000.0000.000
81A88THR00.007-0.01631.500-0.009-0.0090.0000.0000.0000.000
82A89GLU-1-0.841-0.89833.089-0.115-0.1150.0000.0000.0000.000
83A90MET0-0.0120.00929.334-0.007-0.0070.0000.0000.0000.000
84A91ILE0-0.039-0.01927.994-0.009-0.0090.0000.0000.0000.000
85A92ARG10.8730.93030.3940.1150.1150.0000.0000.0000.000
86A93PHE0-0.044-0.01532.3610.0010.0010.0000.0000.0000.000
87A94VAL00.009-0.01327.055-0.002-0.0020.0000.0000.0000.000
88A95ARG10.7920.87925.2600.2230.2230.0000.0000.0000.000
89A96PRO0-0.034-0.00929.816-0.005-0.0050.0000.0000.0000.000
90A97LEU0-0.052-0.01830.3170.0040.0040.0000.0000.0000.000
91A98THR0-0.049-0.04124.975-0.020-0.0200.0000.0000.0000.000
92A99THR0-0.038-0.02225.3200.0060.0060.0000.0000.0000.000
93A100LEU0-0.0320.00220.024-0.007-0.0070.0000.0000.0000.000
94A101PRO00.0100.00218.6370.0250.0250.0000.0000.0000.000
95A102ILE0-0.026-0.01221.150-0.027-0.0270.0000.0000.0000.000
96A103ILE0-0.010-0.00816.7560.0220.0220.0000.0000.0000.000
97A104ALA00.0330.01021.3610.0030.0030.0000.0000.0000.000
98A105SER0-0.024-0.02821.568-0.004-0.0040.0000.0000.0000.000
99A106GLY00.0110.01022.2530.0210.0210.0000.0000.0000.000
100A107GLY0-0.036-0.02524.2200.0020.0020.0000.0000.0000.000
101A108ALA0-0.047-0.01126.3170.0140.0140.0000.0000.0000.000
102A109GLY00.0390.00027.257-0.006-0.0060.0000.0000.0000.000
103A110LYS10.8040.89429.3070.0790.0790.0000.0000.0000.000
104A111MET00.0600.03829.209-0.009-0.0090.0000.0000.0000.000
105A112GLU-1-0.816-0.89131.674-0.078-0.0780.0000.0000.0000.000
106A113HIS00.0140.00131.184-0.003-0.0030.0000.0000.0000.000
107A114PHE00.0270.00026.208-0.007-0.0070.0000.0000.0000.000
108A115LEU00.0000.00529.563-0.008-0.0080.0000.0000.0000.000
109A116GLU-1-0.760-0.86932.318-0.117-0.1170.0000.0000.0000.000
110A117ALA0-0.016-0.00228.055-0.005-0.0050.0000.0000.0000.000
111A118PHE0-0.017-0.01224.484-0.007-0.0070.0000.0000.0000.000
112A119LEU0-0.051-0.01029.417-0.001-0.0010.0000.0000.0000.000
113A120ALA0-0.065-0.03731.3890.0030.0030.0000.0000.0000.000
114A121GLY00.0240.00829.849-0.002-0.0020.0000.0000.0000.000
115A122ALA0-0.041-0.01325.416-0.014-0.0140.0000.0000.0000.000
116A123ASP-1-0.781-0.87022.143-0.252-0.2520.0000.0000.0000.000
117A124LYS10.7640.86115.7620.5110.5110.0000.0000.0000.000
118A125VAL0-0.0210.00822.0060.0090.0090.0000.0000.0000.000
119A126SER0-0.0060.00817.769-0.019-0.0190.0000.0000.0000.000
120A127ILE0-0.006-0.00619.5560.0280.0280.0000.0000.0000.000
121A128ASN0-0.003-0.02817.8990.0020.0020.0000.0000.0000.000
122A129THR00.024-0.00120.4050.0130.0130.0000.0000.0000.000
123A130ALA00.0430.02323.7160.0120.0120.0000.0000.0000.000
124A131ALA00.0090.01520.6650.0080.0080.0000.0000.0000.000
125A132VAL00.0200.00220.8060.0120.0120.0000.0000.0000.000
126A133GLU-1-0.806-0.87422.629-0.036-0.0360.0000.0000.0000.000
127A134ASN00.0040.02325.8420.0100.0100.0000.0000.0000.000
128A135PRO00.0720.03822.907-0.010-0.0100.0000.0000.0000.000
129A136SER0-0.056-0.03724.127-0.006-0.0060.0000.0000.0000.000
130A137LEU0-0.019-0.01125.530-0.005-0.0050.0000.0000.0000.000
131A138ILE00.0010.00819.527-0.011-0.0110.0000.0000.0000.000
132A139THR00.004-0.00723.050-0.006-0.0060.0000.0000.0000.000
133A140GLN0-0.043-0.02225.159-0.005-0.0050.0000.0000.0000.000
134A141ILE00.0110.01624.1800.0000.0000.0000.0000.0000.000
135A142ALA00.0170.01922.640-0.004-0.0040.0000.0000.0000.000
136A143GLN0-0.054-0.03124.4870.0040.0040.0000.0000.0000.000
137A144THR0-0.075-0.04427.7420.0100.0100.0000.0000.0000.000
138A145PHE0-0.009-0.01325.7520.0020.0020.0000.0000.0000.000
139A146GLY00.0540.05223.592-0.014-0.0140.0000.0000.0000.000
140A147SER00.011-0.03219.100-0.006-0.0060.0000.0000.0000.000
141A148GLN0-0.036-0.02417.721-0.015-0.0150.0000.0000.0000.000
142A149ALA00.0030.01318.726-0.040-0.0400.0000.0000.0000.000
143A150VAL0-0.022-0.01919.7970.0040.0040.0000.0000.0000.000
144A151VAL00.0310.02314.917-0.020-0.0200.0000.0000.0000.000
145A152VAL00.013-0.00615.5400.0470.0470.0000.0000.0000.000
146A153ALA00.0210.01814.478-0.045-0.0450.0000.0000.0000.000
147A154ILE00.0000.01312.3290.0620.0620.0000.0000.0000.000
148A155VAL00.001-0.00513.082-0.025-0.0250.0000.0000.0000.000
149A156ALA00.0060.00012.7480.0320.0320.0000.0000.0000.000
150A157LYS10.8970.95014.359-0.013-0.0130.0000.0000.0000.000
151A158ARG10.7510.8279.576-0.176-0.1760.0000.0000.0000.000
152A159VAL0-0.043-0.03815.933-0.030-0.0300.0000.0000.0000.000
153A160ASP-1-0.892-0.94819.5990.0890.0890.0000.0000.0000.000
154A161GLY0-0.028-0.00618.4620.0030.0030.0000.0000.0000.000
155A162GLU-1-0.879-0.93615.7270.2320.2320.0000.0000.0000.000
156A163PHE0-0.003-0.0079.880-0.033-0.0330.0000.0000.0000.000
157A164MET00.0090.02514.5410.0010.0010.0000.0000.0000.000
158A165VAL00.0410.01615.832-0.017-0.0170.0000.0000.0000.000
159A166PHE0-0.033-0.00917.6760.0040.0040.0000.0000.0000.000
160A167THR00.0350.01419.339-0.017-0.0170.0000.0000.0000.000
161A168TYR0-0.100-0.08522.0290.0020.0020.0000.0000.0000.000
162A169SER0-0.002-0.01122.0040.0020.0020.0000.0000.0000.000
163A170GLY00.0290.01220.336-0.003-0.0030.0000.0000.0000.000
164A171LYS10.8730.94121.0240.1030.1030.0000.0000.0000.000
165A172LYS10.8880.95023.9990.0440.0440.0000.0000.0000.000
166A173ASN00.0540.02821.958-0.005-0.0050.0000.0000.0000.000
167A174THR0-0.035-0.04820.7640.0040.0040.0000.0000.0000.000
168A175GLY00.0070.01122.5950.0010.0010.0000.0000.0000.000
169A176ILE0-0.0080.00419.1710.0130.0130.0000.0000.0000.000
170A177LEU00.0410.01816.894-0.007-0.0070.0000.0000.0000.000
171A178LEU0-0.046-0.03710.264-0.012-0.0120.0000.0000.0000.000
172A179ARG10.8090.87212.657-0.241-0.2410.0000.0000.0000.000
173A180ASP-1-0.778-0.86113.6780.1790.1790.0000.0000.0000.000
174A181TRP00.007-0.00715.722-0.016-0.0160.0000.0000.0000.000
175A182VAL00.0050.00010.058-0.042-0.0420.0000.0000.0000.000
176A183VAL00.0280.02213.350-0.028-0.0280.0000.0000.0000.000
177A184GLU-1-0.818-0.88615.385-0.009-0.0090.0000.0000.0000.000
178A185VAL0-0.023-0.02114.454-0.021-0.0210.0000.0000.0000.000
179A186GLU-1-0.747-0.82912.874-0.007-0.0070.0000.0000.0000.000
180A187LYS10.8830.93716.434-0.103-0.1030.0000.0000.0000.000
181A188ARG10.7710.87519.8820.0080.0080.0000.0000.0000.000
182A189GLY00.0520.04519.805-0.005-0.0050.0000.0000.0000.000
183A190ALA0-0.001-0.00516.385-0.018-0.0180.0000.0000.0000.000
184A191GLY00.0260.01716.3980.0210.0210.0000.0000.0000.000
185A192GLU-1-0.803-0.88712.376-0.853-0.8530.0000.0000.0000.000
186A193ILE00.0110.0109.9610.1160.1160.0000.0000.0000.000
187A194LEU0-0.027-0.00510.406-0.178-0.1780.0000.0000.0000.000
188A195LEU00.0160.0126.6240.1310.1310.0000.0000.0000.000
189A196THR0-0.036-0.0389.721-0.101-0.1010.0000.0000.0000.000
190A197SER00.011-0.0209.8510.0390.0390.0000.0000.0000.000
191A198ILE0-0.078-0.02112.283-0.040-0.0400.0000.0000.0000.000
192A199ASP-1-0.767-0.88813.0890.0670.0670.0000.0000.0000.000
193A200ARG10.9470.96813.3510.0200.0200.0000.0000.0000.000
194A201VAL0-0.010-0.01112.885-0.012-0.0120.0000.0000.0000.000
195A202GLY00.0430.0279.9170.0430.0430.0000.0000.0000.000
196A203THR0-0.0310.00810.605-0.057-0.0570.0000.0000.0000.000
197A204LYS10.8180.87511.6120.4090.4090.0000.0000.0000.000
198A205SER0-0.050-0.00312.304-0.049-0.0490.0000.0000.0000.000
199A206GLY00.006-0.01010.155-0.083-0.0830.0000.0000.0000.000
200A207TYR00.006-0.0046.2580.0520.0520.0000.0000.0000.000
201A208ASP-1-0.703-0.7937.3200.2860.2860.0000.0000.0000.000
202A209THR00.0220.0043.246-0.1620.2700.037-0.129-0.3400.001
203A210GLU-1-0.901-0.9283.6290.4150.8810.013-0.210-0.269-0.001
204A211MET0-0.0120.0066.2550.1460.1460.0000.0000.0000.000
205A212ILE00.007-0.0032.251-0.205-1.0484.407-0.722-2.8410.003
206A213ARG10.9180.9582.324-3.079-0.9051.419-1.336-2.257-0.001
207A214PHE0-0.034-0.0133.0790.665-0.0330.0340.897-0.2340.000
208A215VAL00.019-0.0056.004-0.077-0.0770.0000.0000.0000.000
209A216ARG10.7970.8812.496-0.4550.9521.422-0.651-2.1780.000
210A217PRO0-0.034-0.0094.640-0.337-0.252-0.001-0.013-0.0710.000
211A218LEU0-0.065-0.0247.596-0.188-0.1880.0000.0000.0000.000
212A219THR0-0.038-0.0428.162-0.177-0.1770.0000.0000.0000.000
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214A221LEU0-0.0340.00410.273-0.111-0.1110.0000.0000.0000.000
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