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: 945J2

Calculation Name: 1JN5-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JN5

Chain ID: B

ChEMBL ID:

UniProt ID: Q9UBU9

Base Structure: X-ray

Registration Date: 2023-09-20

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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1945930.893267
FMO2-HF: Nuclear repulsion 1873287.261301
FMO2-HF: Total energy -72643.631966
FMO2-MP2: Total energy -72855.675242


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(B:370:ALA)


Summations of interaction energy for fragment #1(B:370:ALA)
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.
-0.4210.619-0.007-0.433-0.60.002
Interaction energy analysis for fragmet #1(B:370:ALA)
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 : -0.013
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].
3B372PRO00.0170.0133.893-1.106-0.066-0.007-0.433-0.6000.002
4B373CYS0-0.010-0.0036.0640.4640.4640.0000.0000.0000.000
5B374LYS10.9370.9717.7840.2570.2570.0000.0000.0000.000
6B375GLY00.0330.01911.4880.0210.0210.0000.0000.0000.000
7B376SER00.0170.00414.827-0.001-0.0010.0000.0000.0000.000
8B377TYR0-0.0160.01315.343-0.008-0.0080.0000.0000.0000.000
9B378PHE00.0740.01217.4720.0100.0100.0000.0000.0000.000
10B379GLY00.0110.02319.3220.0120.0120.0000.0000.0000.000
11B380THR00.001-0.01420.6060.0010.0010.0000.0000.0000.000
12B381GLU-1-0.793-0.91424.006-0.036-0.0360.0000.0000.0000.000
13B382ASN0-0.0160.01526.3840.0000.0000.0000.0000.0000.000
14B383LEU00.0570.03224.100-0.002-0.0020.0000.0000.0000.000
15B384LYS10.8620.93722.9820.0580.0580.0000.0000.0000.000
16B385SER0-0.022-0.02525.458-0.004-0.0040.0000.0000.0000.000
17B386LEU00.0200.01829.137-0.003-0.0030.0000.0000.0000.000
18B387VAL00.0240.00524.790-0.001-0.0010.0000.0000.0000.000
19B388LEU0-0.013-0.00824.312-0.004-0.0040.0000.0000.0000.000
20B389HIS00.0080.01028.118-0.005-0.0050.0000.0000.0000.000
21B390PHE00.008-0.00229.8840.0000.0000.0000.0000.0000.000
22B391LEU0-0.018-0.01025.672-0.001-0.0010.0000.0000.0000.000
23B392GLN0-0.002-0.00829.6460.0000.0000.0000.0000.0000.000
24B393GLN0-0.015-0.00232.1900.0010.0010.0000.0000.0000.000
25B394TYR00.019-0.00731.973-0.001-0.0010.0000.0000.0000.000
26B395TYR0-0.024-0.03128.2830.0000.0000.0000.0000.0000.000
27B396ALA00.0060.01733.214-0.001-0.0010.0000.0000.0000.000
28B397ILE00.0110.01936.3300.0010.0010.0000.0000.0000.000
29B398TYR0-0.027-0.00933.1660.0010.0010.0000.0000.0000.000
30B399ASP-1-0.739-0.84833.254-0.042-0.0420.0000.0000.0000.000
31B400SER0-0.050-0.02836.725-0.001-0.0010.0000.0000.0000.000
32B401GLY0-0.024-0.01340.3150.0000.0000.0000.0000.0000.000
33B402ASP-1-0.835-0.90442.247-0.011-0.0110.0000.0000.0000.000
34B403ARG10.7320.83535.7430.0240.0240.0000.0000.0000.000
35B404GLN0-0.028-0.02140.2610.0030.0030.0000.0000.0000.000
36B405GLY00.0260.00542.0750.0020.0020.0000.0000.0000.000
37B406LEU0-0.034-0.02035.6640.0010.0010.0000.0000.0000.000
38B407LEU0-0.014-0.00538.7320.0030.0030.0000.0000.0000.000
39B408ASP-1-0.886-0.92741.0540.0040.0040.0000.0000.0000.000
40B409ALA0-0.035-0.00735.4410.0010.0010.0000.0000.0000.000
41B410TYR0-0.052-0.04532.6410.0010.0010.0000.0000.0000.000
42B411HIS00.0820.03136.701-0.001-0.0010.0000.0000.0000.000
43B412ASP-1-0.797-0.88538.5880.0110.0110.0000.0000.0000.000
44B413GLY0-0.020-0.00839.880-0.001-0.0010.0000.0000.0000.000
45B414ALA0-0.041-0.01335.3100.0030.0030.0000.0000.0000.000
46B415CYS0-0.066-0.02732.8960.0000.0000.0000.0000.0000.000
47B416CYS0-0.026-0.01732.231-0.001-0.0010.0000.0000.0000.000
48B417SER0-0.034-0.01729.8370.0030.0030.0000.0000.0000.000
49B418LEU00.0430.04329.490-0.002-0.0020.0000.0000.0000.000
50B419SER0-0.054-0.04726.2540.0030.0030.0000.0000.0000.000
51B420ILE00.0310.02626.562-0.005-0.0050.0000.0000.0000.000
52B421PRO0-0.032-0.02023.4910.0060.0060.0000.0000.0000.000
53B422PHE00.035-0.00625.3230.0020.0020.0000.0000.0000.000
54B423ILE0-0.0270.00422.6280.0010.0010.0000.0000.0000.000
55B424PRO00.0160.02726.6660.0000.0000.0000.0000.0000.000
56B425GLN00.051-0.01628.384-0.007-0.0070.0000.0000.0000.000
57B426ASN00.0230.01327.844-0.002-0.0020.0000.0000.0000.000
58B427PRO00.0310.01925.2140.0000.0000.0000.0000.0000.000
59B428ALA00.0340.02728.149-0.004-0.0040.0000.0000.0000.000
60B429ARG10.8410.92227.2560.0580.0580.0000.0000.0000.000
61B430SER00.0630.03630.8220.0060.0060.0000.0000.0000.000
62B431SER00.0350.01931.585-0.001-0.0010.0000.0000.0000.000
63B432LEU00.0420.03227.873-0.001-0.0010.0000.0000.0000.000
64B433ALA0-0.006-0.00732.5380.0040.0040.0000.0000.0000.000
65B434GLU-1-0.823-0.91635.905-0.020-0.0200.0000.0000.0000.000
66B435TYR0-0.017-0.02831.7500.0020.0020.0000.0000.0000.000
67B436PHE0-0.059-0.04032.8830.0030.0030.0000.0000.0000.000
68B437LYS10.8940.95234.1700.0100.0100.0000.0000.0000.000
69B438ASP-1-0.783-0.87835.3820.0000.0000.0000.0000.0000.000
70B439SER0-0.0320.00130.2190.0030.0030.0000.0000.0000.000
71B440ARG10.9130.95130.911-0.024-0.0240.0000.0000.0000.000
72B441ASN00.0260.00126.1620.0100.0100.0000.0000.0000.000
73B442VAL00.0330.01227.7160.0000.0000.0000.0000.0000.000
74B443LYN00.0940.08524.1380.0000.0000.0000.0000.0000.000
75B444LYS10.7830.89526.852-0.013-0.0130.0000.0000.0000.000
76B445LEU00.0560.03130.8710.0010.0010.0000.0000.0000.000
77B446LYS10.8910.93030.597-0.031-0.0310.0000.0000.0000.000
78B447ASP-1-0.711-0.83735.1840.0230.0230.0000.0000.0000.000
79B448PRO00.015-0.00637.283-0.001-0.0010.0000.0000.0000.000
80B449THR0-0.003-0.00938.3200.0000.0000.0000.0000.0000.000
81B450LEU0-0.008-0.02338.264-0.001-0.0010.0000.0000.0000.000
82B451ARG10.8410.91731.511-0.038-0.0380.0000.0000.0000.000
83B452PHE0-0.0160.01035.3750.0000.0000.0000.0000.0000.000
84B453ARG10.9700.97337.883-0.012-0.0120.0000.0000.0000.000
85B454LEU00.0140.01734.804-0.002-0.0020.0000.0000.0000.000
86B455LEU0-0.094-0.03932.789-0.002-0.0020.0000.0000.0000.000
87B456LYS10.8320.92435.743-0.003-0.0030.0000.0000.0000.000
88B457HIS00.010-0.01736.5230.0010.0010.0000.0000.0000.000
89B458THR00.0100.00938.917-0.002-0.0020.0000.0000.0000.000
90B459ARG10.8030.86239.420-0.009-0.0090.0000.0000.0000.000
91B460LEU00.0380.03140.455-0.002-0.0020.0000.0000.0000.000
92B461ASN0-0.016-0.02241.161-0.003-0.0030.0000.0000.0000.000
93B462VAL0-0.051-0.02335.841-0.002-0.0020.0000.0000.0000.000
94B463VAL00.0190.00337.993-0.002-0.0020.0000.0000.0000.000
95B464ALA0-0.0060.00639.584-0.002-0.0020.0000.0000.0000.000
96B465PHE00.0340.01234.178-0.002-0.0020.0000.0000.0000.000
97B466LEU0-0.032-0.02633.478-0.003-0.0030.0000.0000.0000.000
98B467ASN0-0.011-0.01137.138-0.005-0.0050.0000.0000.0000.000
99B468GLU-1-0.958-0.96240.231-0.007-0.0070.0000.0000.0000.000
100B469LEU0-0.062-0.01333.594-0.002-0.0020.0000.0000.0000.000
101B470PRO00.0110.00735.282-0.001-0.0010.0000.0000.0000.000
102B471LYS10.9180.96636.3660.0240.0240.0000.0000.0000.000
103B472THR0-0.087-0.07932.721-0.002-0.0020.0000.0000.0000.000
104B473GLN00.0170.00931.6020.0020.0020.0000.0000.0000.000
105B474HIS10.8310.91027.7340.0430.0430.0000.0000.0000.000
106B475ASP-1-0.828-0.88226.752-0.092-0.0920.0000.0000.0000.000
107B476VAL00.009-0.01126.300-0.006-0.0060.0000.0000.0000.000
108B477ASN0-0.017-0.00426.1460.0020.0020.0000.0000.0000.000
109B478SER0-0.040-0.03222.828-0.014-0.0140.0000.0000.0000.000
110B479PHE0-0.080-0.02921.735-0.007-0.0070.0000.0000.0000.000
111B480VAL00.0070.01015.670-0.005-0.0050.0000.0000.0000.000
112B481VAL0-0.051-0.03019.1140.0160.0160.0000.0000.0000.000
113B482ASP-1-0.852-0.93215.946-0.095-0.0950.0000.0000.0000.000
114B483ILE0-0.038-0.02318.2900.0160.0160.0000.0000.0000.000
115B484SER0-0.010-0.00918.0520.0110.0110.0000.0000.0000.000
116B485ALA0-0.004-0.00419.0760.0260.0260.0000.0000.0000.000
117B486GLN0-0.009-0.00822.032-0.014-0.0140.0000.0000.0000.000
118B487THR00.0270.02125.1680.0090.0090.0000.0000.0000.000
119B488SER00.0230.00628.402-0.005-0.0050.0000.0000.0000.000
120B489THR0-0.030-0.02431.320-0.004-0.0040.0000.0000.0000.000
121B490LEU00.0020.01125.965-0.003-0.0030.0000.0000.0000.000
122B491LEU00.0070.00225.0390.0050.0050.0000.0000.0000.000
123B492CYS0-0.022-0.01221.844-0.007-0.0070.0000.0000.0000.000
124B493PHE0-0.002-0.01021.5130.0030.0030.0000.0000.0000.000
125B494SER00.0130.00918.9340.0060.0060.0000.0000.0000.000
126B495VAL0-0.005-0.00521.035-0.009-0.0090.0000.0000.0000.000
127B496ASN0-0.034-0.02217.6570.0140.0140.0000.0000.0000.000
128B497GLY00.0280.02120.484-0.011-0.0110.0000.0000.0000.000
129B498VAL00.0090.00022.2160.0030.0030.0000.0000.0000.000
130B499PHE0-0.040-0.02425.0900.0050.0050.0000.0000.0000.000
131B500LYS10.8820.95628.8720.0530.0530.0000.0000.0000.000
132B501GLU-1-0.706-0.80931.829-0.037-0.0370.0000.0000.0000.000
133B502VAL00.019-0.00634.781-0.002-0.0020.0000.0000.0000.000
134B503ASP-1-0.868-0.92538.144-0.027-0.0270.0000.0000.0000.000
135B504GLY00.0790.04539.175-0.001-0.0010.0000.0000.0000.000
136B505LYS10.8180.87639.7000.0220.0220.0000.0000.0000.000
137B506SER00.0010.00334.8810.0000.0000.0000.0000.0000.000
138B507ARG10.8880.94535.6490.0380.0380.0000.0000.0000.000
139B508ASP-1-0.825-0.90035.262-0.051-0.0510.0000.0000.0000.000
140B509SER0-0.0150.00231.152-0.006-0.0060.0000.0000.0000.000
141B510LEU0-0.0160.00025.8260.0030.0030.0000.0000.0000.000
142B511ARG10.7050.81727.4700.0440.0440.0000.0000.0000.000
143B512ALA00.015-0.00322.051-0.006-0.0060.0000.0000.0000.000
144B513PHE0-0.065-0.03323.0930.0080.0080.0000.0000.0000.000
145B514THR00.017-0.00118.593-0.012-0.0120.0000.0000.0000.000
146B515ARG10.7880.87521.8090.0220.0220.0000.0000.0000.000
147B516THR00.0050.00321.902-0.004-0.0040.0000.0000.0000.000
148B517PHE00.0020.01123.9820.0010.0010.0000.0000.0000.000
149B518ILE00.002-0.00925.4910.0060.0060.0000.0000.0000.000
150B519ALA00.0020.00027.778-0.004-0.0040.0000.0000.0000.000
151B520VAL00.0200.01730.3900.0060.0060.0000.0000.0000.000
152B521PRO00.008-0.00532.713-0.005-0.0050.0000.0000.0000.000
153B522ALA00.0010.01934.8780.0010.0010.0000.0000.0000.000
154B523SER0-0.011-0.02037.8710.0000.0000.0000.0000.0000.000
155B524ASN00.0220.00439.3710.0010.0010.0000.0000.0000.000
156B525SER0-0.026-0.01035.924-0.001-0.0010.0000.0000.0000.000
157B526GLY00.0230.02835.274-0.001-0.0010.0000.0000.0000.000
158B527LEU0-0.045-0.02529.6320.0040.0040.0000.0000.0000.000
159B528CYS0-0.0080.00733.822-0.003-0.0030.0000.0000.0000.000
160B529ILE0-0.0020.00430.9550.0050.0050.0000.0000.0000.000
161B530VAL00.012-0.00531.552-0.001-0.0010.0000.0000.0000.000
162B531ASN0-0.029-0.02529.1830.0030.0030.0000.0000.0000.000
163B532ASP-1-0.692-0.78428.658-0.003-0.0030.0000.0000.0000.000
164B533GLU-1-0.868-0.90825.3460.0060.0060.0000.0000.0000.000
165B534LEU00.0240.01926.207-0.005-0.0050.0000.0000.0000.000
166B535PHE00.0660.04021.148-0.002-0.0020.0000.0000.0000.000
167B536VAL0-0.009-0.01524.688-0.009-0.0090.0000.0000.0000.000
168B537ARG10.7610.82718.7860.1160.1160.0000.0000.0000.000
169B538ASN00.0080.00325.4600.0010.0010.0000.0000.0000.000
170B539ALA00.0320.02222.937-0.004-0.0040.0000.0000.0000.000
171B540SER0-0.040-0.05419.4060.0090.0090.0000.0000.0000.000
172B541SER00.0350.00622.2280.0040.0040.0000.0000.0000.000
173B542GLU-1-0.820-0.89418.190-0.170-0.1700.0000.0000.0000.000
174B543GLU-1-0.799-0.85019.094-0.149-0.1490.0000.0000.0000.000
175B544ILE0-0.013-0.00721.3900.0050.0050.0000.0000.0000.000
176B545GLN0-0.002-0.00323.3330.0040.0040.0000.0000.0000.000
177B546ARG10.9220.95417.8050.2210.2210.0000.0000.0000.000
178B547ALA0-0.024-0.00723.0020.0030.0030.0000.0000.0000.000
179B548PHE0-0.015-0.01625.4620.0090.0090.0000.0000.0000.000
180B549ALA0-0.0070.01225.6220.0050.0050.0000.0000.0000.000
181B550MET0-0.024-0.00727.5950.0010.0010.0000.0000.0000.000
182B551PRO0-0.023-0.00227.7780.0060.0060.0000.0000.0000.000
183B552ALA00.0290.01031.0500.0010.0010.0000.0000.0000.000
184B553PRO0-0.0060.00030.730-0.007-0.0070.0000.0000.0000.000
185B554THR0-0.001-0.00829.0770.0050.0050.0000.0000.0000.000
186B555PRO0-0.0120.00328.440-0.009-0.0090.0000.0000.0000.000