FMODB

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

Last updated: 2024-04-25

All entries: 37426

Number of unique PDB entries: 7782

tag_button

FMODB ID: JM8V9

Calculation Name: 4PON-A-Xray313

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4PON

Chain ID: A

ChEMBL ID:

UniProt ID: E0TY72

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 178
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1754620.671958
FMO2-HF: Nuclear repulsion 1687963.135234
FMO2-HF: Total energy -66657.536723
FMO2-MP2: Total energy -66852.725223


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:ACE )


Summations of interaction energy for fragment #1(A:0:ACE )
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.
1.9282.864-0.005-0.443-0.488-0.001
Interaction energy analysis for fragmet #1(A:0:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.031 / q_NPA : 0.007
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].
3A2ILE 00.0240.0263.8700.7391.675-0.005-0.443-0.488-0.001
4A3LEU 00.0290.0226.7390.2850.2850.0000.0000.0000.000
5A4LYS 10.8760.9269.5120.0700.0700.0000.0000.0000.000
6A5LYS 10.9820.9948.5620.8150.8150.0000.0000.0000.000
7A6ILE 00.0820.04212.6310.0410.0410.0000.0000.0000.000
8A7LEU 00.0730.04516.2560.0240.0240.0000.0000.0000.000
9A8PRO 0-0.038-0.01612.1500.0250.0250.0000.0000.0000.000
10A9TYR 00.0250.02214.9690.0260.0260.0000.0000.0000.000
11A10SER 0-0.004-0.02216.1250.0320.0320.0000.0000.0000.000
12A11LYS 10.9670.97917.3930.1450.1450.0000.0000.0000.000
13A12GLU -1-0.856-0.91514.963-0.148-0.1480.0000.0000.0000.000
14A13LEU 00.006-0.00318.3950.0150.0150.0000.0000.0000.000
15A14LEU 00.0090.00021.4210.0130.0130.0000.0000.0000.000
16A15LYS 10.9280.96417.5260.0520.0520.0000.0000.0000.000
17A16MET 0-0.060-0.01821.3300.0030.0030.0000.0000.0000.000
18A17ALA 0-0.0140.01223.8590.0050.0050.0000.0000.0000.000
19A18ALA 0-0.042-0.01626.3980.0050.0050.0000.0000.0000.000
20A19GLY 00.010-0.01026.290-0.002-0.0020.0000.0000.0000.000
21A20GLU -1-0.954-0.98228.0200.0030.0030.0000.0000.0000.000
22A21GLY 0-0.040-0.01730.4550.0000.0000.0000.0000.0000.000
23A22ASP -1-0.859-0.92231.090-0.026-0.0260.0000.0000.0000.000
24A23ILE 0-0.022-0.01433.2480.0000.0000.0000.0000.0000.000
25A24VAL 0-0.0070.00329.230-0.003-0.0030.0000.0000.0000.000
26A25ILE 0-0.013-0.02531.7030.0030.0030.0000.0000.0000.000
27A26ASP -1-0.770-0.86729.432-0.066-0.0660.0000.0000.0000.000
28A27ALA 0-0.004-0.00631.0730.0050.0050.0000.0000.0000.000
29A28THR 0-0.034-0.01429.4610.0000.0000.0000.0000.0000.000
30A29MET 0-0.0040.02730.038-0.003-0.0030.0000.0000.0000.000
31A30GLY 00.0250.01029.869-0.003-0.0030.0000.0000.0000.000
32A31ASN 0-0.036-0.04126.5080.0040.0040.0000.0000.0000.000
33A32GLY 00.0980.06029.0170.0050.0050.0000.0000.0000.000
34A33HIS 0-0.105-0.05923.2090.0080.0080.0000.0000.0000.000
35A34ASP -1-0.842-0.92323.329-0.095-0.0950.0000.0000.0000.000
36A35THR 0-0.019-0.04325.3300.0050.0050.0000.0000.0000.000
37A36GLN 00.0100.00725.4990.0000.0000.0000.0000.0000.000
38A37PHE 0-0.022-0.00720.1720.0020.0020.0000.0000.0000.000
39A38LEU 00.005-0.00524.2530.0050.0050.0000.0000.0000.000
40A39ALA 00.0360.01626.9770.0050.0050.0000.0000.0000.000
41A40GLU -1-0.957-0.98423.132-0.016-0.0160.0000.0000.0000.000
42A41LEU 0-0.105-0.04223.7110.0040.0040.0000.0000.0000.000
43A42VAL 0-0.0150.01326.0040.0040.0040.0000.0000.0000.000
44A43GLY 00.0450.02729.1820.0040.0040.0000.0000.0000.000
45A44GLU -1-1.003-1.03130.5820.0030.0030.0000.0000.0000.000
46A45ASN 0-0.028-0.01133.938-0.001-0.0010.0000.0000.0000.000
47A46GLY 00.0410.04133.329-0.001-0.0010.0000.0000.0000.000
48A47HIS 0-0.068-0.06734.2420.0020.0020.0000.0000.0000.000
49A48VAL 00.0050.00830.565-0.003-0.0030.0000.0000.0000.000
50A49TYR 0-0.001-0.00733.5380.0020.0020.0000.0000.0000.000
51A50ALA 00.0370.01633.273-0.004-0.0040.0000.0000.0000.000
52A51PHE 0-0.060-0.02734.4330.0040.0040.0000.0000.0000.000
53A52ASP -1-0.744-0.87633.895-0.056-0.0560.0000.0000.0000.000
54A53ILE 0-0.010-0.01536.5280.0030.0030.0000.0000.0000.000
55A54GLN 0-0.055-0.02434.7030.0040.0040.0000.0000.0000.000
56A55GLU -1-0.895-0.95038.237-0.026-0.0260.0000.0000.0000.000
57A56SER 0-0.003-0.01337.4460.0010.0010.0000.0000.0000.000
58A57ALA 00.0120.02434.0170.0000.0000.0000.0000.0000.000
59A58VAL 00.0210.00834.6230.0010.0010.0000.0000.0000.000
60A59ALA 0-0.025-0.00936.6030.0020.0020.0000.0000.0000.000
61A60ASN 00.0490.01332.5550.0040.0040.0000.0000.0000.000
62A61THR 00.0070.00431.5170.0000.0000.0000.0000.0000.000
63A62LYS 10.9500.96632.9080.0200.0200.0000.0000.0000.000
64A63GLU -1-0.989-0.98433.589-0.020-0.0200.0000.0000.0000.000
65A64ARG 10.8730.94824.8300.0420.0420.0000.0000.0000.000
66A65LEU 0-0.049-0.02529.8460.0020.0020.0000.0000.0000.000
67A66GLY 00.0410.02231.8590.0030.0030.0000.0000.0000.000
68A67GLU -1-0.939-0.98834.525-0.003-0.0030.0000.0000.0000.000
69A68ALA 0-0.035-0.00731.9800.0000.0000.0000.0000.0000.000
70A69TYR 0-0.024-0.02526.7550.0010.0010.0000.0000.0000.000
71A70GLN 00.0180.02233.365-0.003-0.0030.0000.0000.0000.000
72A71ALA 0-0.015-0.01136.825-0.001-0.0010.0000.0000.0000.000
73A72ARG 10.9120.98430.0850.0080.0080.0000.0000.0000.000
74A73THR 0-0.024-0.01632.736-0.004-0.0040.0000.0000.0000.000
75A74THR 0-0.0190.02335.8720.0020.0020.0000.0000.0000.000
76A75LEU 0-0.012-0.00134.739-0.003-0.0030.0000.0000.0000.000
77A76PHE 0-0.014-0.01638.0100.0030.0030.0000.0000.0000.000
78A77HIS 0-0.0030.00538.969-0.001-0.0010.0000.0000.0000.000
79A78LYS 10.9000.94840.0090.0290.0290.0000.0000.0000.000
80A79SER 00.0170.01739.088-0.003-0.0030.0000.0000.0000.000
81A80HIS 00.0710.02434.2020.0020.0020.0000.0000.0000.000
82A81ASP -1-0.832-0.89937.975-0.039-0.0390.0000.0000.0000.000
83A82LYS 10.8060.88940.9190.0380.0380.0000.0000.0000.000
84A83ILE 00.0750.04735.9790.0020.0020.0000.0000.0000.000
85A84ALA 00.019-0.00640.4540.0020.0020.0000.0000.0000.000
86A85LYS 10.8920.93943.1970.0300.0300.0000.0000.0000.000
87A86SER 0-0.086-0.04641.8300.0020.0020.0000.0000.0000.000
88A87LEU 00.0020.00937.9000.0010.0010.0000.0000.0000.000
89A88PRO 00.0570.04141.8480.0000.0000.0000.0000.0000.000
90A89PRO 00.0510.03143.962-0.001-0.0010.0000.0000.0000.000
91A90GLU -1-0.900-0.94644.356-0.017-0.0170.0000.0000.0000.000
92A91THR 0-0.057-0.05239.7940.0000.0000.0000.0000.0000.000
93A92HIS 0-0.070-0.03340.357-0.002-0.0020.0000.0000.0000.000
94A93GLY 00.000-0.00340.6510.0020.0020.0000.0000.0000.000
95A94LYS 10.9150.94638.4030.0170.0170.0000.0000.0000.000
96A95VAL 0-0.043-0.00334.1300.0000.0000.0000.0000.0000.000
97A96ALA 00.0440.01931.095-0.002-0.0020.0000.0000.0000.000
98A97ALA 00.029-0.00228.073-0.004-0.0040.0000.0000.0000.000
99A98ALA 0-0.011-0.01029.5020.0040.0040.0000.0000.0000.000
100A99VAL 00.0070.01724.843-0.006-0.0060.0000.0000.0000.000
101A100PHE 00.011-0.00127.6600.0080.0080.0000.0000.0000.000
102A101ASN 0-0.009-0.01524.451-0.022-0.0220.0000.0000.0000.000
103A102LEU 0-0.026-0.02127.3680.0090.0090.0000.0000.0000.000
104A103GLY 00.0610.02527.920-0.009-0.0090.0000.0000.0000.000
105A104NME 0-0.022-0.00630.0310.0010.0010.0000.0000.0000.000
106A114ACE 00.0250.00337.2000.0000.0000.0000.0000.0000.000
107A115ASN 00.008-0.02737.9650.0000.0000.0000.0000.0000.000
108A116GLY 00.0690.05036.933-0.003-0.0030.0000.0000.0000.000
109A117SER 00.0240.01038.0050.0000.0000.0000.0000.0000.000
110A118SER 0-0.050-0.04339.2310.0020.0020.0000.0000.0000.000
111A119THR 00.0210.00633.4700.0000.0000.0000.0000.0000.000
112A120ILE 00.0240.02836.5550.0000.0000.0000.0000.0000.000
113A121LYS 10.9560.98438.2400.0410.0410.0000.0000.0000.000
114A122ALA 0-0.031-0.01036.4410.0020.0020.0000.0000.0000.000
115A123ILE 00.0050.00233.3510.0010.0010.0000.0000.0000.000
116A124GLU -1-0.909-0.96136.373-0.042-0.0420.0000.0000.0000.000
117A125GLN 0-0.027-0.01739.7230.0030.0030.0000.0000.0000.000
118A126LEU 00.0170.01733.4930.0020.0020.0000.0000.0000.000
119A127LEU 00.0550.03134.7810.0020.0020.0000.0000.0000.000
120A128SER 0-0.091-0.03437.7990.0030.0030.0000.0000.0000.000
121A129ILE 0-0.018-0.00938.6250.0020.0020.0000.0000.0000.000
122A130MET 0-0.0520.00331.7090.0010.0010.0000.0000.0000.000
123A131LYS 10.9591.00732.1730.0340.0340.0000.0000.0000.000
124A132ASP -1-0.897-0.96735.703-0.034-0.0340.0000.0000.0000.000
125A133GLU -1-0.979-0.99830.857-0.038-0.0380.0000.0000.0000.000
126A134GLY 0-0.0350.00430.881-0.002-0.0020.0000.0000.0000.000
127A135LEU 0-0.012-0.01924.835-0.005-0.0050.0000.0000.0000.000
128A136ILE 0-0.019-0.00929.2360.0010.0010.0000.0000.0000.000
129A137VAL 0-0.010-0.00622.976-0.008-0.0080.0000.0000.0000.000
130A138LEU 0-0.028-0.02026.2900.0040.0040.0000.0000.0000.000
131A139VAL 0-0.003-0.00621.846-0.015-0.0150.0000.0000.0000.000
132A140VAL 0-0.012-0.00824.3690.0110.0110.0000.0000.0000.000
133A141TYR 0-0.014-0.01721.588-0.025-0.0250.0000.0000.0000.000
134A142HIS 0-0.0050.00025.6540.0070.0070.0000.0000.0000.000
135A143GLY 00.0580.04126.6570.0090.0090.0000.0000.0000.000
136A144NME 0-0.036-0.01528.3010.0010.0010.0000.0000.0000.000
137A151ACE 00.017-0.00431.765-0.002-0.0020.0000.0000.0000.000
138A152ASN 0-0.004-0.01632.2300.0010.0010.0000.0000.0000.000
139A153ASP -1-0.849-0.92135.267-0.061-0.0610.0000.0000.0000.000
140A154VAL 0-0.0080.00532.4550.0020.0020.0000.0000.0000.000
141A155LEU 00.0050.00529.0520.0000.0000.0000.0000.0000.000
142A156ASP -1-0.862-0.93332.712-0.072-0.0720.0000.0000.0000.000
143A157PHE 0-0.028-0.02635.9990.0020.0020.0000.0000.0000.000
144A158CYS 0-0.044-0.02732.1880.0010.0010.0000.0000.0000.000
145A159ARG 10.8780.92931.3740.0870.0870.0000.0000.0000.000
146A160ASN 0-0.049-0.03034.4970.0050.0050.0000.0000.0000.000
147A161LEU 0-0.0220.02234.3760.0040.0040.0000.0000.0000.000
148A162ASP -1-0.834-0.91137.362-0.044-0.0440.0000.0000.0000.000
149A163GLN 00.0240.00736.378-0.003-0.0030.0000.0000.0000.000
150A164GLN 0-0.094-0.06436.9500.0010.0010.0000.0000.0000.000
151A165ALA 00.0270.01738.7560.0010.0010.0000.0000.0000.000
152A166ALA 0-0.004-0.01133.8410.0000.0000.0000.0000.0000.000
153A167ARG 10.8280.91928.3970.0650.0650.0000.0000.0000.000
154A168VAL 00.0250.01029.435-0.002-0.0020.0000.0000.0000.000
155A169LEU 0-0.0290.00222.172-0.002-0.0020.0000.0000.0000.000
156A170THR 00.003-0.01324.4880.0000.0000.0000.0000.0000.000
157A171TYR 0-0.033-0.02813.9960.0000.0000.0000.0000.0000.000
158A172GLY 00.0630.01318.9430.0070.0070.0000.0000.0000.000
159A173PHE 0-0.073-0.02112.321-0.021-0.0210.0000.0000.0000.000
160A174ILE 00.0650.02217.5650.0190.0190.0000.0000.0000.000
161A175ASN 0-0.012-0.00215.3590.0040.0040.0000.0000.0000.000
162A176GLN 0-0.038-0.01113.7420.0250.0250.0000.0000.0000.000
163A177GLN 0-0.029-0.03118.2450.0380.0380.0000.0000.0000.000
164A178ASN 0-0.016-0.02217.6920.0210.0210.0000.0000.0000.000
165A179ASP -1-0.902-0.93322.039-0.141-0.1410.0000.0000.0000.000
166A180PRO 0-0.0190.00418.7120.0050.0050.0000.0000.0000.000
167A181PRO 0-0.002-0.00319.5080.0080.0080.0000.0000.0000.000
168A182PHE 0-0.062-0.02720.373-0.027-0.0270.0000.0000.0000.000
169A183ILE 0-0.043-0.01918.8380.0100.0100.0000.0000.0000.000
170A184VAL 00.0160.00022.855-0.002-0.0020.0000.0000.0000.000
171A185ALA 0-0.024-0.00524.3240.0030.0030.0000.0000.0000.000
172A186ILE 00.003-0.00426.4160.0010.0010.0000.0000.0000.000
173A187GLU -1-0.835-0.90228.879-0.060-0.0600.0000.0000.0000.000
174A188LYS 10.8450.91430.7700.0370.0370.0000.0000.0000.000
175A189LYS 10.8950.96034.1870.0500.0500.0000.0000.0000.000
176A190ALA 00.0510.02436.0640.0020.0020.0000.0000.0000.000
177A191GLN 0-0.035-0.01638.7020.0000.0000.0000.0000.0000.000
178A192NME 0-0.0270.00340.442-0.001-0.0010.0000.0000.0000.000