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: K3YZ3

Calculation Name: 1J1J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1J1J

Chain ID: A

ChEMBL ID:

UniProt ID: Q15631

Base Structure: X-ray

Registration Date: 2023-06-20

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 OptH
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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2573092.61075
FMO2-HF: Nuclear repulsion 2487036.175441
FMO2-HF: Total energy -86056.435309
FMO2-MP2: Total energy -86314.008154


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-16.742-8.90710.18-6.222-11.792-0.049
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.025 / 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].
3A3VAL00.0570.0013.195-2.030-0.1250.072-0.986-0.9910.001
4A4SER0-0.019-0.0125.6800.0650.0650.0000.0000.0000.000
5A5GLU-1-0.799-0.8902.426-6.964-4.0253.871-2.808-4.002-0.023
6A6ILE00.0170.0152.306-3.290-1.3283.461-1.469-3.953-0.001
7A7PHE0-0.013-0.0323.2901.0410.4800.0320.864-0.3360.000
8A8VAL0-0.0160.0075.7980.3860.3860.0000.0000.0000.000
9A9GLU-1-0.897-0.9562.315-7.847-6.3192.745-1.823-2.450-0.026
10A10LEU0-0.034-0.0305.1080.7550.817-0.0010.000-0.0600.000
11A11GLN0-0.0200.0057.4870.2810.2810.0000.0000.0000.000
12A12GLY00.0350.0258.8850.2170.2170.0000.0000.0000.000
13A13PHE0-0.022-0.0066.4260.2200.2200.0000.0000.0000.000
14A14LEU0-0.014-0.00610.9600.1470.1470.0000.0000.0000.000
15A15ALA0-0.033-0.02213.0070.0930.0930.0000.0000.0000.000
16A16ALA00.0480.03513.8920.0670.0670.0000.0000.0000.000
17A17GLU-1-0.925-0.98715.144-0.262-0.2620.0000.0000.0000.000
18A18GLN00.012-0.02017.0420.0700.0700.0000.0000.0000.000
19A19ASP-1-0.853-0.90518.259-0.335-0.3350.0000.0000.0000.000
20A20ILE0-0.033-0.01018.9630.0370.0370.0000.0000.0000.000
21A21ARG10.8360.92318.5740.3090.3090.0000.0000.0000.000
22A22GLU-1-0.863-0.93323.275-0.218-0.2180.0000.0000.0000.000
23A23GLU-1-0.929-0.96824.417-0.153-0.1530.0000.0000.0000.000
24A24ILE0-0.053-0.02424.5750.0200.0200.0000.0000.0000.000
25A25ARG10.9140.95524.7530.2050.2050.0000.0000.0000.000
26A26LYS10.9370.97029.0930.1620.1620.0000.0000.0000.000
27A27VAL0-0.0230.00230.5380.0100.0100.0000.0000.0000.000
28A28VAL00.0390.00631.2320.0100.0100.0000.0000.0000.000
29A29GLN0-0.0100.01033.5830.0090.0090.0000.0000.0000.000
30A30SER0-0.0200.00035.5770.0070.0070.0000.0000.0000.000
31A31LEU0-0.012-0.01435.1010.0070.0070.0000.0000.0000.000
32A32GLU-1-0.909-0.97736.198-0.091-0.0910.0000.0000.0000.000
33A33GLN0-0.068-0.02639.4270.0020.0020.0000.0000.0000.000
34A34THR00.0040.00441.3680.0050.0050.0000.0000.0000.000
35A35ALA00.0130.00741.7760.0040.0040.0000.0000.0000.000
36A36ARG10.9250.96240.5090.0830.0830.0000.0000.0000.000
37A37GLU-1-0.869-0.93845.613-0.061-0.0610.0000.0000.0000.000
38A38ILE0-0.008-0.00245.1260.0030.0030.0000.0000.0000.000
39A39LEU00.002-0.00147.7130.0020.0020.0000.0000.0000.000
40A40THR0-0.041-0.01249.4460.0020.0020.0000.0000.0000.000
41A41LEU0-0.064-0.03150.7910.0020.0020.0000.0000.0000.000
42A42LEU00.0210.01650.6810.0020.0020.0000.0000.0000.000
43A43GLN0-0.031-0.02951.8960.0010.0010.0000.0000.0000.000
44A44GLY0-0.024-0.03555.1620.0010.0010.0000.0000.0000.000
45A45VAL0-0.023-0.01357.3120.0010.0010.0000.0000.0000.000
46A46HIS0-0.077-0.03255.4560.0020.0020.0000.0000.0000.000
47A47GLN0-0.040-0.01858.9400.0000.0000.0000.0000.0000.000
48A48GLY00.0020.00863.0800.0000.0000.0000.0000.0000.000
49A49ALA00.0100.00866.4310.0000.0000.0000.0000.0000.000
50A50GLY0-0.026-0.01168.4210.0000.0000.0000.0000.0000.000
51A51PHE00.0680.02762.131-0.001-0.0010.0000.0000.0000.000
52A52GLN0-0.007-0.01564.5870.0010.0010.0000.0000.0000.000
53A53ASP-1-0.865-0.93661.824-0.032-0.0320.0000.0000.0000.000
54A54ILE00.0610.03159.326-0.001-0.0010.0000.0000.0000.000
55A55PRO00.0600.03559.099-0.001-0.0010.0000.0000.0000.000
56A56LYS10.9740.98158.8810.0310.0310.0000.0000.0000.000
57A57ARG10.7910.91256.6330.0360.0360.0000.0000.0000.000
58A58CYS00.0290.02154.790-0.002-0.0020.0000.0000.0000.000
59A59LEU0-0.022-0.00854.066-0.001-0.0010.0000.0000.0000.000
60A60LYS10.9690.98153.9130.0360.0360.0000.0000.0000.000
61A61ALA0-0.0070.00350.821-0.002-0.0020.0000.0000.0000.000
62A62ARG10.9530.96449.5270.0310.0310.0000.0000.0000.000
63A63GLU-1-0.922-0.94949.186-0.038-0.0380.0000.0000.0000.000
64A64HIS10.8650.94345.5890.0540.0540.0000.0000.0000.000
65A65PHE00.0540.00344.097-0.003-0.0030.0000.0000.0000.000
66A66GLY00.0040.01443.948-0.001-0.0010.0000.0000.0000.000
67A67THR0-0.005-0.01341.785-0.001-0.0010.0000.0000.0000.000
68A68VAL0-0.0140.00440.156-0.004-0.0040.0000.0000.0000.000
69A69LYS10.9390.97539.1830.0400.0400.0000.0000.0000.000
70A70THR0-0.0280.00138.371-0.002-0.0020.0000.0000.0000.000
71A71HIS00.018-0.01036.167-0.004-0.0040.0000.0000.0000.000
72A72LEU00.0190.01534.493-0.007-0.0070.0000.0000.0000.000
73A73THR00.0110.01033.665-0.001-0.0010.0000.0000.0000.000
74A74SER0-0.032-0.02232.444-0.006-0.0060.0000.0000.0000.000
75A75LEU00.007-0.01029.375-0.008-0.0080.0000.0000.0000.000
76A76LYS10.8590.94128.8390.0490.0490.0000.0000.0000.000
77A77THR0-0.065-0.02427.9750.0000.0000.0000.0000.0000.000
78A78LYS10.8470.92625.5990.1270.1270.0000.0000.0000.000
79A79PHE00.0090.01822.864-0.015-0.0150.0000.0000.0000.000
80A80PRO00.0460.02919.6640.0160.0160.0000.0000.0000.000
81A81ALA00.0280.01822.9310.0010.0010.0000.0000.0000.000
82A82GLU-1-0.964-0.98020.160-0.036-0.0360.0000.0000.0000.000
83A83GLN0-0.010-0.02517.330-0.012-0.0120.0000.0000.0000.000
84A84TYR00.027-0.00522.952-0.014-0.0140.0000.0000.0000.000
85A85TYR0-0.021-0.04026.417-0.007-0.0070.0000.0000.0000.000
86A86ARG10.8510.96115.4700.2260.2260.0000.0000.0000.000
87A87PHE00.0230.00919.705-0.012-0.0120.0000.0000.0000.000
88A88HIS00.015-0.01225.185-0.003-0.0030.0000.0000.0000.000
89A89GLU-1-0.929-0.98425.689-0.132-0.1320.0000.0000.0000.000
90A90HIS0-0.060-0.02624.208-0.006-0.0060.0000.0000.0000.000
91A91TRP00.0480.02228.0170.0060.0060.0000.0000.0000.000
92A92ARG10.9421.00630.2530.0990.0990.0000.0000.0000.000
93A93PHE00.015-0.00434.2030.0080.0080.0000.0000.0000.000
94A94VAL00.0300.00935.5350.0060.0060.0000.0000.0000.000
95A95LEU00.0320.03534.7320.0050.0050.0000.0000.0000.000
96A96GLN0-0.048-0.05837.6110.0050.0050.0000.0000.0000.000
97A97ARG10.8920.95240.2650.0680.0680.0000.0000.0000.000
98A98LEU0-0.025-0.01438.8560.0030.0030.0000.0000.0000.000
99A99VAL00.0130.03241.0750.0030.0030.0000.0000.0000.000
100A100PHE0-0.0030.00343.5890.0030.0030.0000.0000.0000.000
101A101LEU0-0.035-0.01944.5910.0020.0020.0000.0000.0000.000
102A102ALA00.0030.01045.8400.0020.0020.0000.0000.0000.000
103A103ALA00.0390.00547.6380.0030.0030.0000.0000.0000.000
104A104PHE0-0.013-0.00849.5240.0020.0020.0000.0000.0000.000
105A105VAL0-0.015-0.01550.5630.0020.0020.0000.0000.0000.000
106A106VAL0-0.011-0.00750.8000.0020.0020.0000.0000.0000.000
107A107TYR0-0.0090.01753.3670.0020.0020.0000.0000.0000.000
108A108LEU0-0.045-0.03155.0940.0010.0010.0000.0000.0000.000
109A109GLU-1-0.988-0.98956.283-0.026-0.0260.0000.0000.0000.000
110A110THR0-0.069-0.05356.3440.0010.0010.0000.0000.0000.000
111A111GLU-1-0.934-0.96158.400-0.022-0.0220.0000.0000.0000.000
112A112THR00.0110.01554.6920.0010.0010.0000.0000.0000.000
113A113LEU00.003-0.01349.561-0.002-0.0020.0000.0000.0000.000
114A114VAL0-0.0310.00847.7190.0010.0010.0000.0000.0000.000
115A115THR00.0550.05746.849-0.001-0.0010.0000.0000.0000.000
116A116ARG10.8810.94039.0050.0280.0280.0000.0000.0000.000
117A117GLU-1-0.813-0.94943.253-0.028-0.0280.0000.0000.0000.000
118A118ALA00.0550.02344.285-0.001-0.0010.0000.0000.0000.000
119A119VAL0-0.039-0.02542.220-0.002-0.0020.0000.0000.0000.000
120A120THR0-0.013-0.00839.829-0.004-0.0040.0000.0000.0000.000
121A121GLU-1-0.897-0.93741.525-0.028-0.0280.0000.0000.0000.000
122A122ILE0-0.103-0.04744.147-0.001-0.0010.0000.0000.0000.000
123A123LEU0-0.066-0.05039.697-0.002-0.0020.0000.0000.0000.000
124A124GLY0-0.038-0.01239.962-0.004-0.0040.0000.0000.0000.000
125A125ILE0-0.088-0.01835.674-0.003-0.0030.0000.0000.0000.000
126A126GLU-1-0.772-0.87735.018-0.045-0.0450.0000.0000.0000.000
127A127PRO00.013-0.00237.432-0.001-0.0010.0000.0000.0000.000
128A128ASP-1-0.863-0.93936.507-0.028-0.0280.0000.0000.0000.000
129A129ARG10.8130.90435.8200.0070.0070.0000.0000.0000.000
130A130GLU-1-0.842-0.94235.951-0.027-0.0270.0000.0000.0000.000
131A131LYS10.8740.92829.5420.0010.0010.0000.0000.0000.000
132A132GLY00.0770.03831.012-0.001-0.0010.0000.0000.0000.000
133A133PHE0-0.001-0.00430.234-0.001-0.0010.0000.0000.0000.000
134A134HIS00.0510.04932.0360.0050.0050.0000.0000.0000.000
135A135LEU00.0030.02434.598-0.006-0.0060.0000.0000.0000.000
136A136ASP-1-0.786-0.91133.941-0.048-0.0480.0000.0000.0000.000
137A137VAL0-0.0090.00436.6560.0010.0010.0000.0000.0000.000
138A138GLU-1-0.890-0.96036.758-0.043-0.0430.0000.0000.0000.000
139A139ASP-1-0.764-0.86335.453-0.068-0.0680.0000.0000.0000.000
140A140TYR0-0.054-0.04138.8280.0000.0000.0000.0000.0000.000
141A141LEU00.0420.00641.9250.0010.0010.0000.0000.0000.000
142A142SER0-0.041-0.03540.4370.0000.0000.0000.0000.0000.000
143A143GLY00.0280.00842.7680.0000.0000.0000.0000.0000.000
144A144VAL00.0080.00644.3460.0010.0010.0000.0000.0000.000
145A145LEU0-0.034-0.01645.0100.0010.0010.0000.0000.0000.000
146A146ILE0-0.059-0.02243.4010.0000.0000.0000.0000.0000.000
147A147LEU0-0.011-0.00447.8310.0000.0000.0000.0000.0000.000
148A148ALA00.0260.01650.3780.0010.0010.0000.0000.0000.000
149A149SER0-0.030-0.02350.7860.0000.0000.0000.0000.0000.000
150A150GLU-1-0.872-0.90551.657-0.043-0.0430.0000.0000.0000.000
151A151LEU00.006-0.00953.5300.0010.0010.0000.0000.0000.000
152A152SER0-0.007-0.01355.8170.0010.0010.0000.0000.0000.000
153A153ARG10.8680.94154.7140.0420.0420.0000.0000.0000.000
154A154LEU00.007-0.00557.7790.0010.0010.0000.0000.0000.000
155A155SER00.0090.00559.5350.0010.0010.0000.0000.0000.000
156A156VAL00.0330.01261.7190.0010.0010.0000.0000.0000.000
157A157ASN0-0.025-0.04160.0150.0010.0010.0000.0000.0000.000
158A158SER00.015-0.01163.6270.0010.0010.0000.0000.0000.000
159A159VAL00.0020.01265.2370.0010.0010.0000.0000.0000.000
160A160THR0-0.031-0.00666.5690.0010.0010.0000.0000.0000.000
161A161ALA0-0.038-0.00566.2330.0000.0000.0000.0000.0000.000
162A162GLY00.003-0.00168.3350.0010.0010.0000.0000.0000.000
163A163ASP-1-0.867-0.93266.994-0.023-0.0230.0000.0000.0000.000
164A164TYR00.006-0.01468.285-0.001-0.0010.0000.0000.0000.000
165A165SER0-0.020-0.00169.0840.0010.0010.0000.0000.0000.000
166A166ARG10.9340.97062.4080.0260.0260.0000.0000.0000.000
167A167PRO00.0000.01364.0380.0000.0000.0000.0000.0000.000
168A168LEU00.0300.01664.3120.0000.0000.0000.0000.0000.000
169A169HIS10.8880.94762.9190.0210.0210.0000.0000.0000.000
170A170ILE00.0270.01458.7750.0000.0000.0000.0000.0000.000
171A171SER00.0280.00159.819-0.001-0.0010.0000.0000.0000.000
172A172THR0-0.0090.00761.0010.0000.0000.0000.0000.0000.000
173A173PHE00.0440.01653.7020.0000.0000.0000.0000.0000.000
174A174ILE0-0.006-0.02255.5690.0000.0000.0000.0000.0000.000
175A175ASN0-0.007-0.00156.3770.0000.0000.0000.0000.0000.000
176A176GLU-1-0.949-0.96157.003-0.020-0.0200.0000.0000.0000.000
177A177LEU0-0.045-0.02751.7490.0000.0000.0000.0000.0000.000
178A178ASP-1-0.868-0.94452.740-0.027-0.0270.0000.0000.0000.000
179A179SER0-0.061-0.03753.8610.0010.0010.0000.0000.0000.000
180A180GLY00.0030.00152.3450.0010.0010.0000.0000.0000.000
181A181PHE0-0.003-0.02545.8720.0000.0000.0000.0000.0000.000
182A182ARG10.8510.94749.5490.0230.0230.0000.0000.0000.000
183A183LEU0-0.024-0.00350.6940.0010.0010.0000.0000.0000.000
184A184LEU0-0.051-0.01345.4970.0010.0010.0000.0000.0000.000
185A185ASN0-0.007-0.00144.473-0.003-0.0030.0000.0000.0000.000
186A186LEU00.007-0.00642.536-0.001-0.0010.0000.0000.0000.000
187A187LYS10.9400.96838.1490.0260.0260.0000.0000.0000.000
188A188ASN00.0680.04335.703-0.003-0.0030.0000.0000.0000.000
189A189ASP-1-0.822-0.92436.360-0.064-0.0640.0000.0000.0000.000
190A190SER0-0.0080.00036.964-0.001-0.0010.0000.0000.0000.000
191A191LEU0-0.014-0.00539.3740.0010.0010.0000.0000.0000.000
192A192ARG10.9730.98441.4930.0380.0380.0000.0000.0000.000
193A193LYS10.8910.94541.4760.0550.0550.0000.0000.0000.000
194A194ARG10.9500.97841.1700.0580.0580.0000.0000.0000.000
195A195TYR00.0140.00145.2840.0020.0020.0000.0000.0000.000
196A196ASP-1-0.917-0.94347.373-0.036-0.0360.0000.0000.0000.000
197A197GLY0-0.069-0.04448.9350.0010.0010.0000.0000.0000.000
198A198LEU00.0410.03150.7140.0000.0000.0000.0000.0000.000
199A199LYS10.9790.98852.3720.0350.0350.0000.0000.0000.000
200A200TYR0-0.060-0.02554.4010.0010.0010.0000.0000.0000.000
201A201ASP-1-0.752-0.87152.933-0.037-0.0370.0000.0000.0000.000
202A202VAL0-0.0070.00156.2050.0010.0010.0000.0000.0000.000
203A203LYS10.9590.97058.4300.0280.0280.0000.0000.0000.000
204A204LYS10.9670.99958.3050.0360.0360.0000.0000.0000.000
205A205VAL0-0.0140.00559.1530.0010.0010.0000.0000.0000.000
206A206GLU-1-0.921-0.96462.080-0.022-0.0220.0000.0000.0000.000
207A207GLU-1-0.955-0.98164.147-0.026-0.0260.0000.0000.0000.000
208A208VAL0-0.0110.01064.0910.0010.0010.0000.0000.0000.000
209A209VAL0-0.023-0.01565.8100.0010.0010.0000.0000.0000.000
210A210TYR0-0.0230.00068.3360.0010.0010.0000.0000.0000.000
211A211ASP-1-0.891-0.94869.147-0.023-0.0230.0000.0000.0000.000
212A212LEU0-0.058-0.04469.0190.0010.0010.0000.0000.0000.000
213A213SER0-0.009-0.00472.3540.0010.0010.0000.0000.0000.000
214A214ILE0-0.053-0.01574.2300.0010.0010.0000.0000.0000.000
215A215ARG10.8900.93574.3700.0210.0210.0000.0000.0000.000
216A216GLY0-0.0240.01077.6460.0000.0000.0000.0000.0000.000
217A217PHE0-0.039-0.01773.8040.0000.0000.0000.0000.0000.000