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: ZN62N

Calculation Name: 4J0W-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4J0W

Chain ID: A

ChEMBL ID:

UniProt ID: O43818

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 332
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5173265.90892
FMO2-HF: Nuclear repulsion 5045209.446964
FMO2-HF: Total energy -128056.461957
FMO2-MP2: Total energy -128428.548156


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:133:GLY)


Summations of interaction energy for fragment #1(A:133:GLY)
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.
-2.14-0.2610.09-0.802-1.1670.003
Interaction energy analysis for fragmet #1(A:133:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / q_NPA : 0.013
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].
3A135GLU-1-0.821-0.9283.815-1.972-0.549-0.009-0.646-0.7680.004
4A136ALA0-0.034-0.0376.3640.4730.4730.0000.0000.0000.000
5A137ALA0-0.062-0.0319.6570.2040.2040.0000.0000.0000.000
6A138ASP-1-0.833-0.9066.730-3.476-3.4760.0000.0000.0000.000
7A139ILE0-0.067-0.0237.6870.3450.3450.0000.0000.0000.000
8A140ARG10.8690.94010.8800.8240.8240.0000.0000.0000.000
9A141VAL00.009-0.00414.5440.0750.0750.0000.0000.0000.000
10A142LEU0-0.0080.00916.7230.0450.0450.0000.0000.0000.000
11A143ARG10.9410.96719.9070.3280.3280.0000.0000.0000.000
12A144GLY00.029-0.01022.9410.0070.0070.0000.0000.0000.000
13A145HIS00.0080.03823.9450.0080.0080.0000.0000.0000.000
14A146GLN0-0.042-0.02726.6460.0000.0000.0000.0000.0000.000
15A147LEU0-0.056-0.03627.9160.0050.0050.0000.0000.0000.000
16A148SER00.012-0.00124.354-0.018-0.0180.0000.0000.0000.000
17A149ILE00.0220.03221.1480.0160.0160.0000.0000.0000.000
18A150THR0-0.067-0.06323.2730.0030.0030.0000.0000.0000.000
19A151CYS0-0.047-0.00822.6780.0160.0160.0000.0000.0000.000
20A152LEU00.0330.01317.968-0.013-0.0130.0000.0000.0000.000
21A153VAL0-0.037-0.00721.6680.0220.0220.0000.0000.0000.000
22A154VAL00.0530.02617.536-0.026-0.0260.0000.0000.0000.000
23A155THR0-0.060-0.04921.0000.0190.0190.0000.0000.0000.000
24A156PRO00.0510.02021.885-0.010-0.0100.0000.0000.0000.000
25A157ASP-1-0.792-0.84922.261-0.126-0.1260.0000.0000.0000.000
26A158ASP-1-0.783-0.87817.946-0.161-0.1610.0000.0000.0000.000
27A159SER0-0.055-0.04319.402-0.043-0.0430.0000.0000.0000.000
28A160ALA0-0.017-0.02822.066-0.023-0.0230.0000.0000.0000.000
29A161ILE00.0000.01417.6030.0060.0060.0000.0000.0000.000
30A162PHE00.0030.00722.0990.0000.0000.0000.0000.0000.000
31A163SER00.006-0.01922.356-0.005-0.0050.0000.0000.0000.000
32A164ALA00.0450.02224.2500.0070.0070.0000.0000.0000.000
33A165ALA00.0410.02625.446-0.008-0.0080.0000.0000.0000.000
34A166LYS10.8030.88727.3410.1020.1020.0000.0000.0000.000
35A167ASP-1-0.784-0.85729.097-0.134-0.1340.0000.0000.0000.000
36A168CYS0-0.129-0.06731.3340.0080.0080.0000.0000.0000.000
37A169SER0-0.038-0.02030.1540.0020.0020.0000.0000.0000.000
38A170ILE00.034-0.00328.258-0.003-0.0030.0000.0000.0000.000
39A171ILE0-0.053-0.01726.0470.0020.0020.0000.0000.0000.000
40A172LYS10.9040.96626.0050.1250.1250.0000.0000.0000.000
41A173TRP0-0.010-0.04122.069-0.012-0.0120.0000.0000.0000.000
42A174SER00.0270.02523.0020.0010.0010.0000.0000.0000.000
43A175VAL00.0270.01716.702-0.034-0.0340.0000.0000.0000.000
44A176GLU-1-0.864-0.93518.141-0.355-0.3550.0000.0000.0000.000
45A177SER0-0.009-0.00419.475-0.030-0.0300.0000.0000.0000.000
46A178GLY0-0.008-0.00920.542-0.021-0.0210.0000.0000.0000.000
47A179ARG10.9270.96321.0570.2710.2710.0000.0000.0000.000
48A180LYS10.8300.91024.8180.2350.2350.0000.0000.0000.000
49A181LEU0-0.008-0.00925.7090.0070.0070.0000.0000.0000.000
50A182HIS00.0390.01428.8500.0090.0090.0000.0000.0000.000
51A183VAL0-0.027-0.01429.766-0.011-0.0110.0000.0000.0000.000
52A184ILE00.0060.01931.8450.0080.0080.0000.0000.0000.000
53A185PRO00.0070.00033.245-0.003-0.0030.0000.0000.0000.000
54A186ARG10.9600.98335.3210.0880.0880.0000.0000.0000.000
55A187ALA00.0320.02836.4810.0010.0010.0000.0000.0000.000
56A188LYS10.8330.87439.6320.0560.0560.0000.0000.0000.000
57A189LYS10.8570.95641.9660.0600.0600.0000.0000.0000.000
58A190GLY00.0270.00545.1900.0020.0020.0000.0000.0000.000
59A191ALA0-0.002-0.00948.8130.0020.0020.0000.0000.0000.000
60A192GLU-1-0.898-0.94849.055-0.053-0.0530.0000.0000.0000.000
61A193GLY00.0880.04548.760-0.003-0.0030.0000.0000.0000.000
62A194LYS10.8870.94545.9820.0410.0410.0000.0000.0000.000
63A195PRO00.0200.00941.8090.0020.0020.0000.0000.0000.000
64A196PRO00.0110.03039.6640.0010.0010.0000.0000.0000.000
65A197GLY00.0640.02137.054-0.006-0.0060.0000.0000.0000.000
66A198HIS00.0230.03533.9240.0030.0030.0000.0000.0000.000
67A199SER0-0.042-0.01936.906-0.004-0.0040.0000.0000.0000.000
68A200SER0-0.026-0.04236.6710.0000.0000.0000.0000.0000.000
69A201HIS00.0600.01731.2270.0010.0010.0000.0000.0000.000
70A202VAL00.0700.04829.2610.0070.0070.0000.0000.0000.000
71A203LEU0-0.062-0.02028.746-0.008-0.0080.0000.0000.0000.000
72A204CYS0-0.0280.01627.1430.0020.0020.0000.0000.0000.000
73A205MET00.018-0.00125.571-0.004-0.0040.0000.0000.0000.000
74A206ALA0-0.0080.01626.5880.0050.0050.0000.0000.0000.000
75A207ILE00.0050.00025.154-0.008-0.0080.0000.0000.0000.000
76A208SER0-0.005-0.00227.9270.0060.0060.0000.0000.0000.000
77A209SER00.0430.00527.347-0.005-0.0050.0000.0000.0000.000
78A210ASP-1-0.795-0.86527.886-0.037-0.0370.0000.0000.0000.000
79A211GLY0-0.015-0.00628.431-0.006-0.0060.0000.0000.0000.000
80A212LYS10.8110.91029.1320.0390.0390.0000.0000.0000.000
81A213TYR00.0270.00232.379-0.006-0.0060.0000.0000.0000.000
82A214LEU0-0.026-0.00827.941-0.001-0.0010.0000.0000.0000.000
83A215ALA00.0220.01130.7090.0040.0040.0000.0000.0000.000
84A216SER00.002-0.02730.481-0.004-0.0040.0000.0000.0000.000
85A217GLY00.0400.02531.3810.0040.0040.0000.0000.0000.000
86A218ASP-1-0.732-0.84832.113-0.054-0.0540.0000.0000.0000.000
87A219ARG10.9010.94331.5440.0540.0540.0000.0000.0000.000
88A220SER0-0.068-0.03736.3780.0020.0020.0000.0000.0000.000
89A221LYS10.8450.93838.2680.0280.0280.0000.0000.0000.000
90A222LEU0-0.0280.00538.2600.0030.0030.0000.0000.0000.000
91A223ILE00.0450.01734.479-0.003-0.0030.0000.0000.0000.000
92A224LEU0-0.079-0.02435.6290.0020.0020.0000.0000.0000.000
93A225ILE00.0230.01634.983-0.002-0.0020.0000.0000.0000.000
94A226TRP00.006-0.02733.420-0.002-0.0020.0000.0000.0000.000
95A227GLU-1-0.798-0.87234.598-0.054-0.0540.0000.0000.0000.000
96A228ALA00.0150.01129.707-0.008-0.0080.0000.0000.0000.000
97A229GLN00.0380.01231.009-0.009-0.0090.0000.0000.0000.000
98A230SER00.035-0.00232.438-0.008-0.0080.0000.0000.0000.000
99A231CYS0-0.054-0.01831.971-0.007-0.0070.0000.0000.0000.000
100A232GLN0-0.0190.00434.460-0.002-0.0020.0000.0000.0000.000
101A233HIS0-0.050-0.03137.7310.0010.0010.0000.0000.0000.000
102A234LEU0-0.020-0.00437.9320.0020.0020.0000.0000.0000.000
103A235TYR00.0290.01839.9250.0030.0030.0000.0000.0000.000
104A236THR0-0.014-0.01539.732-0.005-0.0050.0000.0000.0000.000
105A237PHE00.0340.03238.4310.0020.0020.0000.0000.0000.000
106A238THR0-0.019-0.01940.788-0.001-0.0010.0000.0000.0000.000
107A239GLY00.0670.01843.3350.0020.0020.0000.0000.0000.000
108A240HIS0-0.043-0.01137.6600.0020.0020.0000.0000.0000.000
109A241ARG10.9000.93241.4180.0000.0000.0000.0000.0000.000
110A242ASP-1-0.833-0.91939.232-0.017-0.0170.0000.0000.0000.000
111A243ALA0-0.082-0.04834.982-0.002-0.0020.0000.0000.0000.000
112A244VAL0-0.0130.01133.3010.0050.0050.0000.0000.0000.000
113A245SER0-0.043-0.05630.917-0.008-0.0080.0000.0000.0000.000
114A246GLY00.0150.00028.943-0.001-0.0010.0000.0000.0000.000
115A247LEU0-0.041-0.03428.7130.0000.0000.0000.0000.0000.000
116A248ALA00.0420.02627.955-0.002-0.0020.0000.0000.0000.000
117A249PHE00.0160.00429.2550.0010.0010.0000.0000.0000.000
118A250ARG10.8390.93829.851-0.020-0.0200.0000.0000.0000.000
119A251ARG10.9410.95823.620-0.029-0.0290.0000.0000.0000.000
120A252GLY00.008-0.01030.0710.0050.0050.0000.0000.0000.000
121A253THR0-0.030-0.01232.368-0.001-0.0010.0000.0000.0000.000
122A254HIS0-0.023-0.03933.775-0.002-0.0020.0000.0000.0000.000
123A255GLN00.0070.00335.936-0.001-0.0010.0000.0000.0000.000
124A256LEU0-0.045-0.02632.5230.0000.0000.0000.0000.0000.000
125A257TYR00.0490.02132.2590.0030.0030.0000.0000.0000.000
126A258SER00.005-0.01732.781-0.004-0.0040.0000.0000.0000.000
127A259THR00.000-0.00431.7640.0060.0060.0000.0000.0000.000
128A260SER00.0220.00434.092-0.006-0.0060.0000.0000.0000.000
129A261HIS00.0470.01332.1050.0070.0070.0000.0000.0000.000
130A262ASP-1-0.789-0.85036.6790.0000.0000.0000.0000.0000.000
131A263ARG10.8500.93237.843-0.011-0.0110.0000.0000.0000.000
132A264SER0-0.072-0.04738.8380.0030.0030.0000.0000.0000.000
133A265VAL00.0330.01635.155-0.002-0.0020.0000.0000.0000.000
134A266LYS10.8500.92837.1930.0020.0020.0000.0000.0000.000
135A267VAL00.0380.02937.3000.0000.0000.0000.0000.0000.000
136A268TRP0-0.026-0.04037.128-0.003-0.0030.0000.0000.0000.000
137A269ASN00.0150.00638.6890.0000.0000.0000.0000.0000.000
138A270VAL0-0.010-0.01735.904-0.002-0.0020.0000.0000.0000.000
139A271ALA0-0.023-0.00139.136-0.003-0.0030.0000.0000.0000.000
140A272GLU-1-0.914-0.95340.872-0.008-0.0080.0000.0000.0000.000
141A273ASN0-0.056-0.02041.8640.0000.0000.0000.0000.0000.000
142A274SER00.0440.01943.1300.0000.0000.0000.0000.0000.000
143A275TYR0-0.0310.00042.6490.0000.0000.0000.0000.0000.000
144A276VAL0-0.016-0.00442.1990.0000.0000.0000.0000.0000.000
145A277GLU-1-0.889-0.95242.0250.0190.0190.0000.0000.0000.000
146A278THR0-0.043-0.03941.900-0.003-0.0030.0000.0000.0000.000
147A279LEU00.0340.03738.9190.0020.0020.0000.0000.0000.000
148A280PHE00.021-0.01640.646-0.003-0.0030.0000.0000.0000.000
149A281GLY00.0600.01940.0160.0030.0030.0000.0000.0000.000
150A282HIS0-0.0450.00933.2400.0020.0020.0000.0000.0000.000
151A283GLN00.008-0.00138.132-0.006-0.0060.0000.0000.0000.000
152A284ASP-1-0.826-0.90536.2250.0110.0110.0000.0000.0000.000
153A285ALA0-0.047-0.00835.0850.0000.0000.0000.0000.0000.000
154A286VAL0-0.0140.01131.7420.0040.0040.0000.0000.0000.000
155A287ALA0-0.0150.01428.103-0.008-0.0080.0000.0000.0000.000
156A288ALA0-0.032-0.02525.892-0.009-0.0090.0000.0000.0000.000
157A289LEU0-0.027-0.01827.4730.0060.0060.0000.0000.0000.000
158A290ASP-1-0.816-0.88623.7840.0370.0370.0000.0000.0000.000
159A291ALA0-0.017-0.02626.9490.0050.0050.0000.0000.0000.000
160A292LEU00.0280.01424.040-0.001-0.0010.0000.0000.0000.000
161A293SER0-0.071-0.05328.206-0.009-0.0090.0000.0000.0000.000
162A294ARG10.8310.90330.922-0.092-0.0920.0000.0000.0000.000
163A295GLU-1-0.850-0.88733.4650.0200.0200.0000.0000.0000.000
164A296CYS0-0.089-0.06233.0250.0040.0040.0000.0000.0000.000
165A297CYS0-0.0140.01431.053-0.003-0.0030.0000.0000.0000.000
166A298VAL00.0290.01126.9960.0050.0050.0000.0000.0000.000
167A299THR00.004-0.02329.344-0.006-0.0060.0000.0000.0000.000
168A300ALA0-0.0060.00826.8550.0090.0090.0000.0000.0000.000
169A301GLY00.049-0.00428.985-0.010-0.0100.0000.0000.0000.000
170A302GLY00.0200.02229.914-0.005-0.0050.0000.0000.0000.000
171A303ARG10.8790.90430.921-0.009-0.0090.0000.0000.0000.000
172A304ASP-1-0.776-0.83433.6580.0460.0460.0000.0000.0000.000
173A305GLY00.0440.03631.7490.0030.0030.0000.0000.0000.000
174A306THR0-0.091-0.07432.5370.0070.0070.0000.0000.0000.000
175A307VAL00.0080.00627.471-0.004-0.0040.0000.0000.0000.000
176A308ARG10.8090.90530.763-0.041-0.0410.0000.0000.0000.000
177A309VAL00.0160.00431.0300.0000.0000.0000.0000.0000.000
178A310TRP0-0.029-0.03233.523-0.002-0.0020.0000.0000.0000.000
179A311LYS10.8670.91335.836-0.064-0.0640.0000.0000.0000.000
180A312ILE00.0220.01336.589-0.001-0.0010.0000.0000.0000.000
181A313PRO00.0300.03139.360-0.002-0.0020.0000.0000.0000.000
182A314GLU-1-0.877-0.94539.6070.0520.0520.0000.0000.0000.000
183A315GLU-1-0.965-0.96042.8020.0260.0260.0000.0000.0000.000
184A316SER0-0.041-0.01440.9260.0020.0020.0000.0000.0000.000
185A317GLN00.001-0.02238.1470.0010.0010.0000.0000.0000.000
186A318LEU0-0.036-0.00834.8900.0020.0020.0000.0000.0000.000
187A319VAL00.0000.00435.3100.0000.0000.0000.0000.0000.000
188A320PHE0-0.045-0.02530.3320.0040.0040.0000.0000.0000.000
189A321TYR00.0600.02732.922-0.005-0.0050.0000.0000.0000.000
190A322GLY0-0.007-0.03129.2340.0090.0090.0000.0000.0000.000
191A323HIS0-0.067-0.00223.144-0.014-0.0140.0000.0000.0000.000
192A324GLN00.0120.00727.522-0.012-0.0120.0000.0000.0000.000
193A325GLY00.0360.03828.1300.0020.0020.0000.0000.0000.000
194A326SER0-0.078-0.06528.7400.0010.0010.0000.0000.0000.000
195A327ILE0-0.021-0.01226.1000.0050.0050.0000.0000.0000.000
196A328ASP-1-0.823-0.91324.8470.0130.0130.0000.0000.0000.000
197A329CYS0-0.134-0.03721.348-0.010-0.0100.0000.0000.0000.000
198A330ILE0-0.002-0.01722.8130.0190.0190.0000.0000.0000.000
199A331HIS0-0.0150.00419.430-0.040-0.0400.0000.0000.0000.000
200A332LEU0-0.028-0.01321.8780.0270.0270.0000.0000.0000.000
201A333ILE0-0.0120.00318.752-0.005-0.0050.0000.0000.0000.000
202A334ASN00.0730.03221.008-0.011-0.0110.0000.0000.0000.000
203A335GLU-1-0.733-0.86024.0080.0660.0660.0000.0000.0000.000
204A336GLU-1-0.849-0.90526.9480.1080.1080.0000.0000.0000.000
205A337HIS10.8240.90523.585-0.179-0.1790.0000.0000.0000.000
206A338MET00.0320.04122.783-0.006-0.0060.0000.0000.0000.000
207A339VAL00.0340.02117.7930.0170.0170.0000.0000.0000.000
208A340SER0-0.009-0.02021.110-0.023-0.0230.0000.0000.0000.000
209A341GLY00.035-0.00620.9470.0270.0270.0000.0000.0000.000
210A342ALA00.0150.00921.673-0.019-0.0190.0000.0000.0000.000
211A343ASP-1-0.878-0.94923.2730.0500.0500.0000.0000.0000.000
212A344ASP-1-0.775-0.84325.1890.1120.1120.0000.0000.0000.000
213A345GLY0-0.009-0.00921.3100.0090.0090.0000.0000.0000.000
214A346SER0-0.073-0.07620.3310.0320.0320.0000.0000.0000.000
215A347VAL0-0.010-0.00617.021-0.021-0.0210.0000.0000.0000.000
216A348ALA0-0.026-0.00420.1710.0240.0240.0000.0000.0000.000
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