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: RY918

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 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 332
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5178302.38787
FMO2-HF: Nuclear repulsion 5050245.453741
FMO2-HF: Total energy -128056.934129
FMO2-MP2: Total energy -128428.964806


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.
-1.7380.0670000000000010.214-0.783-1.2360.002
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 : 0.036 / q_NPA : 0.015
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-1-0.792-0.8983.878-1.469-0.244-0.006-0.537-0.6820.003
4A136ALA0-0.075-0.0616.3180.4910.4910.0000.0000.0000.000
5A137ALA0-0.061-0.0259.4490.2600.2600.0000.0000.0000.000
6A138ASP-1-0.835-0.9136.836-3.225-3.2250.0000.0000.0000.000
7A139ILE0-0.062-0.0298.1220.3290.3290.0000.0000.0000.000
8A140ARG10.8910.94111.1330.8440.8440.0000.0000.0000.000
9A141VAL0-0.007-0.01414.7900.0940.0940.0000.0000.0000.000
10A142LEU00.0080.03216.7030.0580.0580.0000.0000.0000.000
11A143ARG10.8800.91819.9480.3240.3240.0000.0000.0000.000
12A144GLY00.017-0.00723.1160.0080.0080.0000.0000.0000.000
13A145HIS00.0280.04724.1710.0070.0070.0000.0000.0000.000
14A146GLN0-0.033-0.02226.671-0.001-0.0010.0000.0000.0000.000
15A147LEU0-0.057-0.03528.2000.0020.0020.0000.0000.0000.000
16A148SER0-0.020-0.04924.575-0.019-0.0190.0000.0000.0000.000
17A149ILE00.0020.01621.2540.0170.0170.0000.0000.0000.000
18A150THR0-0.088-0.06923.4920.0030.0030.0000.0000.0000.000
19A151CYS0-0.047-0.00522.8530.0150.0150.0000.0000.0000.000
20A152LEU00.0130.00918.031-0.011-0.0110.0000.0000.0000.000
21A153VAL0-0.024-0.00221.4850.0200.0200.0000.0000.0000.000
22A154VAL00.0560.03317.542-0.024-0.0240.0000.0000.0000.000
23A155THR0-0.059-0.05321.0050.0200.0200.0000.0000.0000.000
24A156PRO00.0260.00522.109-0.011-0.0110.0000.0000.0000.000
25A157ASP-1-0.777-0.83022.641-0.145-0.1450.0000.0000.0000.000
26A158ASP-1-0.782-0.88318.138-0.204-0.2040.0000.0000.0000.000
27A159SER0-0.047-0.04519.574-0.043-0.0430.0000.0000.0000.000
28A160ALA0-0.007-0.01722.249-0.021-0.0210.0000.0000.0000.000
29A161ILE0-0.0120.00617.8760.0030.0030.0000.0000.0000.000
30A162PHE00.0140.00122.3280.0070.0070.0000.0000.0000.000
31A163SER00.004-0.02222.504-0.009-0.0090.0000.0000.0000.000
32A164ALA00.0540.02224.4080.0080.0080.0000.0000.0000.000
33A165ALA00.0450.03025.560-0.008-0.0080.0000.0000.0000.000
34A166LYS10.7910.87927.4270.1080.1080.0000.0000.0000.000
35A167ASP-1-0.771-0.85329.254-0.138-0.1380.0000.0000.0000.000
36A168CYS0-0.132-0.05831.5530.0090.0090.0000.0000.0000.000
37A169SER0-0.046-0.02930.3910.0020.0020.0000.0000.0000.000
38A170ILE00.015-0.01628.410-0.001-0.0010.0000.0000.0000.000
39A171ILE0-0.054-0.01326.2750.0040.0040.0000.0000.0000.000
40A172LYS10.9060.96626.3140.1390.1390.0000.0000.0000.000
41A173TRP0-0.035-0.04522.356-0.011-0.0110.0000.0000.0000.000
42A174SER00.0140.00023.1930.0070.0070.0000.0000.0000.000
43A175VAL00.0260.01616.885-0.034-0.0340.0000.0000.0000.000
44A176GLU-1-0.697-0.79318.271-0.348-0.3480.0000.0000.0000.000
45A177SER0-0.091-0.07119.489-0.038-0.0380.0000.0000.0000.000
46A178GLY00.005-0.00420.846-0.018-0.0180.0000.0000.0000.000
47A179ARG10.8510.90921.3760.2860.2860.0000.0000.0000.000
48A180LYS10.8410.91425.1390.2400.2400.0000.0000.0000.000
49A181LEU0-0.005-0.00925.9070.0070.0070.0000.0000.0000.000
50A182HIS00.0330.01329.1380.0100.0100.0000.0000.0000.000
51A183VAL0-0.023-0.01929.951-0.013-0.0130.0000.0000.0000.000
52A184ILE00.0020.03332.1150.0080.0080.0000.0000.0000.000
53A185PRO00.0160.00033.274-0.005-0.0050.0000.0000.0000.000
54A186ARG10.9320.96935.5750.0890.0890.0000.0000.0000.000
55A187ALA00.0460.02536.7990.0010.0010.0000.0000.0000.000
56A188LYS10.8220.89840.0410.0570.0570.0000.0000.0000.000
57A189LYS10.8570.94442.5050.0620.0620.0000.0000.0000.000
58A190GLY00.0250.00845.6140.0010.0010.0000.0000.0000.000
59A191ALA00.009-0.00349.1780.0020.0020.0000.0000.0000.000
60A192GLU-1-0.878-0.93749.449-0.056-0.0560.0000.0000.0000.000
61A193GLY00.0810.04048.830-0.003-0.0030.0000.0000.0000.000
62A194LYS10.8660.92545.8440.0470.0470.0000.0000.0000.000
63A195PRO00.0450.02241.7170.0020.0020.0000.0000.0000.000
64A196PRO00.0010.03039.5210.0010.0010.0000.0000.0000.000
65A197GLY00.0710.02136.998-0.006-0.0060.0000.0000.0000.000
66A198HIS00.0110.02234.0470.0030.0030.0000.0000.0000.000
67A199SER0-0.046-0.03036.896-0.002-0.0020.0000.0000.0000.000
68A200SER0-0.037-0.04636.5440.0020.0020.0000.0000.0000.000
69A201HIS00.0640.02531.1550.0000.0000.0000.0000.0000.000
70A202VAL00.0700.04529.3260.0080.0080.0000.0000.0000.000
71A203LEU0-0.061-0.01728.622-0.008-0.0080.0000.0000.0000.000
72A204CYS0-0.0350.01427.1290.0020.0020.0000.0000.0000.000
73A205MET00.010-0.00325.723-0.002-0.0020.0000.0000.0000.000
74A206ALA0-0.0140.01526.3170.0020.0020.0000.0000.0000.000
75A207ILE0-0.009-0.01425.453-0.007-0.0070.0000.0000.0000.000
76A208SER0-0.007-0.00428.0130.0050.0050.0000.0000.0000.000
77A209SER00.0430.00427.278-0.005-0.0050.0000.0000.0000.000
78A210ASP-1-0.790-0.85527.827-0.054-0.0540.0000.0000.0000.000
79A211GLY0-0.0010.00128.375-0.007-0.0070.0000.0000.0000.000
80A212LYS10.8120.90429.1010.0510.0510.0000.0000.0000.000
81A213TYR00.0290.00132.299-0.005-0.0050.0000.0000.0000.000
82A214LEU0-0.0300.00328.3340.0000.0000.0000.0000.0000.000
83A215ALA00.0230.00530.7070.0060.0060.0000.0000.0000.000
84A216SER00.004-0.01930.477-0.005-0.0050.0000.0000.0000.000
85A217GLY00.0640.03331.4470.0050.0050.0000.0000.0000.000
86A218ASP-1-0.756-0.84932.009-0.061-0.0610.0000.0000.0000.000
87A219ARG10.8870.91631.8260.0610.0610.0000.0000.0000.000
88A220SER0-0.057-0.03736.5480.0030.0030.0000.0000.0000.000
89A221LYS10.8480.94538.2100.0340.0340.0000.0000.0000.000
90A222LEU0-0.0240.00038.1610.0030.0030.0000.0000.0000.000
91A223ILE00.0390.00934.420-0.002-0.0020.0000.0000.0000.000
92A224LEU0-0.074-0.01535.8850.0030.0030.0000.0000.0000.000
93A225ILE00.0140.01335.107-0.003-0.0030.0000.0000.0000.000
94A226TRP00.024-0.02733.530-0.001-0.0010.0000.0000.0000.000
95A227GLU-1-0.790-0.86534.424-0.067-0.0670.0000.0000.0000.000
96A228ALA0-0.012-0.00329.800-0.007-0.0070.0000.0000.0000.000
97A229GLN00.0370.01730.786-0.010-0.0100.0000.0000.0000.000
98A230SER00.0350.00232.278-0.010-0.0100.0000.0000.0000.000
99A231CYS0-0.056-0.02131.965-0.007-0.0070.0000.0000.0000.000
100A232GLN0-0.0170.00034.3650.0000.0000.0000.0000.0000.000
101A233HIS0-0.043-0.02837.7450.0010.0010.0000.0000.0000.000
102A234LEU0-0.020-0.00338.0640.0020.0020.0000.0000.0000.000
103A235TYR00.0160.01240.0140.0040.0040.0000.0000.0000.000
104A236THR0-0.011-0.02139.781-0.006-0.0060.0000.0000.0000.000
105A237PHE00.0480.04738.4150.0030.0030.0000.0000.0000.000
106A238THR0-0.024-0.02640.935-0.002-0.0020.0000.0000.0000.000
107A239GLY00.0840.03243.1130.0020.0020.0000.0000.0000.000
108A240HIS0-0.034-0.00537.3760.0020.0020.0000.0000.0000.000
109A241ARG10.9010.92741.2030.0050.0050.0000.0000.0000.000
110A242ASP-1-0.842-0.91839.266-0.022-0.0220.0000.0000.0000.000
111A243ALA0-0.067-0.04334.921-0.002-0.0020.0000.0000.0000.000
112A244VAL0-0.0290.00133.1980.0050.0050.0000.0000.0000.000
113A245SER0-0.039-0.05230.726-0.008-0.0080.0000.0000.0000.000
114A246GLY00.013-0.01228.772-0.002-0.0020.0000.0000.0000.000
115A247LEU0-0.038-0.03028.6640.0020.0020.0000.0000.0000.000
116A248ALA00.0330.02028.018-0.003-0.0030.0000.0000.0000.000
117A249PHE00.0220.00829.2600.0030.0030.0000.0000.0000.000
118A250ARG10.7950.90229.678-0.010-0.0100.0000.0000.0000.000
119A251ARG10.9450.96623.2700.0030.0030.0000.0000.0000.000
120A252GLY00.0250.00029.6460.0070.0070.0000.0000.0000.000
121A253THR0-0.057-0.02332.1300.0000.0000.0000.0000.0000.000
122A254HIS0-0.015-0.03633.474-0.002-0.0020.0000.0000.0000.000
123A255GLN00.0510.04035.8940.0000.0000.0000.0000.0000.000
124A256LEU0-0.053-0.02432.675-0.002-0.0020.0000.0000.0000.000
125A257TYR00.0310.00232.1910.0040.0040.0000.0000.0000.000
126A258SER0-0.003-0.02032.858-0.006-0.0060.0000.0000.0000.000
127A259THR00.003-0.00931.6830.0060.0060.0000.0000.0000.000
128A260SER00.016-0.00133.916-0.006-0.0060.0000.0000.0000.000
129A261HIS00.0550.02032.2220.0070.0070.0000.0000.0000.000
130A262ASP-1-0.815-0.86436.641-0.005-0.0050.0000.0000.0000.000
131A263ARG10.8670.94237.652-0.008-0.0080.0000.0000.0000.000
132A264SER0-0.080-0.05138.6590.0040.0040.0000.0000.0000.000
133A265VAL00.0250.01435.048-0.002-0.0020.0000.0000.0000.000
134A266LYS10.8300.92237.0350.0090.0090.0000.0000.0000.000
135A267VAL00.0340.02537.144-0.001-0.0010.0000.0000.0000.000
136A268TRP0-0.010-0.02537.058-0.001-0.0010.0000.0000.0000.000
137A269ASN00.0200.01038.732-0.001-0.0010.0000.0000.0000.000
138A270VAL0-0.004-0.00836.057-0.002-0.0020.0000.0000.0000.000
139A271ALA0-0.033-0.00939.122-0.003-0.0030.0000.0000.0000.000
140A272GLU-1-0.886-0.94140.902-0.014-0.0140.0000.0000.0000.000
141A273ASN0-0.062-0.02941.504-0.001-0.0010.0000.0000.0000.000
142A274SER00.0120.01243.1440.0000.0000.0000.0000.0000.000
143A275TYR0-0.050-0.04642.6000.0000.0000.0000.0000.0000.000
144A276VAL0-0.0120.00342.2810.0010.0010.0000.0000.0000.000
145A277GLU-1-0.842-0.93141.8200.0120.0120.0000.0000.0000.000
146A278THR0-0.089-0.05741.635-0.004-0.0040.0000.0000.0000.000
147A279LEU00.0640.06939.1130.0020.0020.0000.0000.0000.000
148A280PHE00.025-0.01640.587-0.003-0.0030.0000.0000.0000.000
149A281GLY00.0520.02040.1590.0030.0030.0000.0000.0000.000
150A282HIS0-0.0320.01332.8700.0020.0020.0000.0000.0000.000
151A283GLN00.0200.00037.792-0.006-0.0060.0000.0000.0000.000
152A284ASP-1-0.844-0.91136.0020.0070.0070.0000.0000.0000.000
153A285ALA0-0.036-0.01134.9360.0000.0000.0000.0000.0000.000
154A286VAL0-0.0030.02231.3540.0030.0030.0000.0000.0000.000
155A287ALA0-0.0020.02727.926-0.009-0.0090.0000.0000.0000.000
156A288ALA0-0.023-0.02325.790-0.011-0.0110.0000.0000.0000.000
157A289LEU0-0.028-0.02027.5620.0080.0080.0000.0000.0000.000
158A290ASP-1-0.824-0.89523.7240.0110.0110.0000.0000.0000.000
159A291ALA0-0.014-0.02726.7920.0070.0070.0000.0000.0000.000
160A292LEU00.0080.00324.072-0.003-0.0030.0000.0000.0000.000
161A293SER0-0.043-0.03628.241-0.007-0.0070.0000.0000.0000.000
162A294ARG10.7900.86030.713-0.073-0.0730.0000.0000.0000.000
163A295GLU-1-0.817-0.87233.6350.0080.0080.0000.0000.0000.000
164A296CYS0-0.083-0.05733.0840.0050.0050.0000.0000.0000.000
165A297CYS0-0.0070.01330.845-0.004-0.0040.0000.0000.0000.000
166A298VAL00.0130.00426.6050.0060.0060.0000.0000.0000.000
167A299THR00.003-0.02429.270-0.008-0.0080.0000.0000.0000.000
168A300ALA00.0420.02326.9850.0110.0110.0000.0000.0000.000
169A301GLY00.0160.00129.061-0.010-0.0100.0000.0000.0000.000
170A302GLY00.0590.03429.563-0.004-0.0040.0000.0000.0000.000
171A303ARG10.8640.89630.612-0.004-0.0040.0000.0000.0000.000
172A304ASP-1-0.782-0.83633.3020.0420.0420.0000.0000.0000.000
173A305GLY00.0320.03531.8270.0030.0030.0000.0000.0000.000
174A306THR0-0.099-0.07732.2380.0070.0070.0000.0000.0000.000
175A307VAL00.0240.01327.029-0.005-0.0050.0000.0000.0000.000
176A308ARG10.7930.88830.338-0.036-0.0360.0000.0000.0000.000
177A309VAL00.0090.00230.706-0.001-0.0010.0000.0000.0000.000
178A310TRP0-0.015-0.02433.200-0.001-0.0010.0000.0000.0000.000
179A311LYS10.8200.89235.867-0.052-0.0520.0000.0000.0000.000
180A312ILE00.0450.02736.8110.0000.0000.0000.0000.0000.000
181A313PRO0-0.0150.00339.405-0.001-0.0010.0000.0000.0000.000
182A314GLU-1-0.834-0.91839.7020.0450.0450.0000.0000.0000.000
183A315GLU-1-0.952-0.96343.3010.0220.0220.0000.0000.0000.000
184A316SER0-0.0150.00340.8440.0020.0020.0000.0000.0000.000
185A317GLN0-0.004-0.01537.6570.0000.0000.0000.0000.0000.000
186A318LEU0-0.042-0.00634.3760.0030.0030.0000.0000.0000.000
187A319VAL00.002-0.00235.035-0.001-0.0010.0000.0000.0000.000
188A320PHE0-0.058-0.02929.9290.0040.0040.0000.0000.0000.000
189A321TYR00.0680.02532.411-0.005-0.0050.0000.0000.0000.000
190A322GLY00.015-0.02828.8860.0090.0090.0000.0000.0000.000
191A323HIS0-0.0640.00222.891-0.013-0.0130.0000.0000.0000.000
192A324GLN0-0.037-0.01727.424-0.015-0.0150.0000.0000.0000.000
193A325GLY00.0330.02727.9550.0010.0010.0000.0000.0000.000
194A326SER0-0.067-0.06028.4720.0000.0000.0000.0000.0000.000
195A327ILE0-0.014-0.00625.7770.0030.0030.0000.0000.0000.000
196A328ASP-1-0.835-0.92324.543-0.002-0.0020.0000.0000.0000.000
197A329CYS0-0.131-0.02821.147-0.011-0.0110.0000.0000.0000.000
198A330ILE00.005-0.01422.5150.0210.0210.0000.0000.0000.000
199A331HIS0-0.0100.00719.149-0.045-0.0450.0000.0000.0000.000
200A332LEU0-0.024-0.01021.4640.0300.0300.0000.0000.0000.000
201A333ILE0-0.0010.01018.411-0.009-0.0090.0000.0000.0000.000
202A334ASN00.0610.02620.650-0.009-0.0090.0000.0000.0000.000
203A335GLU-1-0.712-0.84023.6410.0490.0490.0000.0000.0000.000
204A336GLU-1-0.852-0.88826.6920.0900.0900.0000.0000.0000.000
205A337HIS10.8360.91123.471-0.157-0.1570.0000.0000.0000.000
206A338MET00.0160.03322.377-0.006-0.0060.0000.0000.0000.000
207A339VAL00.0390.02117.3730.0200.0200.0000.0000.0000.000
208A340SER0-0.005-0.00720.668-0.024-0.0240.0000.0000.0000.000
209A341GLY00.033-0.00920.6470.0300.0300.0000.0000.0000.000
210A342ALA0-0.0050.00721.426-0.019-0.0190.0000.0000.0000.000
211A343ASP-1-0.863-0.94923.1040.0440.0440.0000.0000.0000.000
212A344ASP-1-0.750-0.83724.7090.1160.1160.0000.0000.0000.000
213A345GLY0-0.013-0.01321.3980.0110.0110.0000.0000.0000.000
214A346SER0-0.075-0.06620.0250.0300.0300.0000.0000.0000.000
215A347VAL0-0.006-0.01616.721-0.024-0.0240.0000.0000.0000.000
216A348ALA0-0.030-0.01019.7820.0260.0260.0000.0000.0000.000
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