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

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FMODB ID: J39R9

Calculation Name: 4LJL-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4LJL

Chain ID: B

ChEMBL ID:

UniProt ID: O25100

Base Structure: X-ray

Registration Date: 2023-06-19

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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2696801.189574
FMO2-HF: Nuclear repulsion 2611669.651022
FMO2-HF: Total energy -85131.538552
FMO2-MP2: Total energy -85380.940858


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:5:MET)


Summations of interaction energy for fragment #1(B:5: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.
-14.632-5.81610.455-5.962-13.305-0.011
Interaction energy analysis for fragmet #1(B:5:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.016 / q_NPA : -0.011
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].
3B7SER0-0.051-0.0552.723-4.392-1.8230.702-1.512-1.758-0.009
4B8HIS0-0.036-0.0254.5300.6820.921-0.001-0.011-0.2270.000
5B9PHE00.0060.0047.4520.2170.2170.0000.0000.0000.000
6B10GLN00.0080.0159.695-0.022-0.0220.0000.0000.0000.000
7B11TYR0-0.077-0.06010.9300.0200.0200.0000.0000.0000.000
8B12SER00.0270.01114.6350.0050.0050.0000.0000.0000.000
9B13THR00.010-0.00817.621-0.004-0.0040.0000.0000.0000.000
10B14LEU0-0.035-0.02320.218-0.001-0.0010.0000.0000.0000.000
11B15GLU-1-0.953-0.97121.868-0.024-0.0240.0000.0000.0000.000
12B16ASN00.0110.00325.5630.0050.0050.0000.0000.0000.000
13B17ILE0-0.0010.00024.695-0.001-0.0010.0000.0000.0000.000
14B18PRO00.0270.00624.3460.0020.0020.0000.0000.0000.000
15B19LYS11.0451.02027.520-0.006-0.0060.0000.0000.0000.000
16B20ALA0-0.0320.00027.6700.0010.0010.0000.0000.0000.000
17B21PHE0-0.018-0.02822.5340.0030.0030.0000.0000.0000.000
18B22ASP-1-0.864-0.93628.1370.0100.0100.0000.0000.0000.000
19B23ILE0-0.027-0.00429.9860.0010.0010.0000.0000.0000.000
20B24LEU0-0.081-0.03325.6800.0020.0020.0000.0000.0000.000
21B25LYS10.8520.90929.739-0.030-0.0300.0000.0000.0000.000
22B26ASP-1-0.863-0.91726.5290.0270.0270.0000.0000.0000.000
23B27PRO00.0760.05026.0140.0010.0010.0000.0000.0000.000
24B28PRO0-0.0110.00122.4710.0010.0010.0000.0000.0000.000
25B29LYS10.9230.94524.280-0.017-0.0170.0000.0000.0000.000
26B30LYS10.8770.95320.6150.0310.0310.0000.0000.0000.000
27B31LEU0-0.0010.00519.8460.0030.0030.0000.0000.0000.000
28B32TYR00.0040.00915.784-0.002-0.0020.0000.0000.0000.000
29B33CYS0-0.023-0.01616.1820.0130.0130.0000.0000.0000.000
30B34VAL00.0430.01711.320-0.026-0.0260.0000.0000.0000.000
31B35GLY00.0840.04914.8230.0300.0300.0000.0000.0000.000
32B36ASP-1-0.819-0.89416.807-0.018-0.0180.0000.0000.0000.000
33B37THR00.0460.00220.5430.0090.0090.0000.0000.0000.000
34B38LYS10.9010.93622.1590.0140.0140.0000.0000.0000.000
35B39LEU0-0.040-0.00920.0530.0040.0040.0000.0000.0000.000
36B40LEU0-0.009-0.01121.6390.0050.0050.0000.0000.0000.000
37B41ASP-1-0.881-0.93325.0920.0010.0010.0000.0000.0000.000
38B42THR0-0.108-0.05826.2110.0010.0010.0000.0000.0000.000
39B43PRO00.0230.01329.0190.0010.0010.0000.0000.0000.000
40B44LEU00.0330.02829.8190.0000.0000.0000.0000.0000.000
41B45LYS10.7700.89325.074-0.018-0.0180.0000.0000.0000.000
42B46VAL00.0290.00125.665-0.002-0.0020.0000.0000.0000.000
43B47ALA0-0.0090.01023.1430.0080.0080.0000.0000.0000.000
44B48ILE0-0.0140.00221.713-0.004-0.0040.0000.0000.0000.000
45B49ILE0-0.0020.01019.3220.0150.0150.0000.0000.0000.000
46B50GLY00.003-0.02419.882-0.013-0.0130.0000.0000.0000.000
47B51THR0-0.046-0.03419.5840.0160.0160.0000.0000.0000.000
48B52ARG10.9460.95913.653-0.145-0.1450.0000.0000.0000.000
49B53ARG10.9090.95117.151-0.061-0.0610.0000.0000.0000.000
50B54PRO00.0110.02518.799-0.010-0.0100.0000.0000.0000.000
51B55THR00.0440.02421.825-0.001-0.0010.0000.0000.0000.000
52B56PRO00.037-0.00223.5990.0050.0050.0000.0000.0000.000
53B57TYR0-0.025-0.00824.6100.0010.0010.0000.0000.0000.000
54B58SER00.0630.00524.393-0.001-0.0010.0000.0000.0000.000
55B59LYS10.8310.93216.777-0.113-0.1130.0000.0000.0000.000
56B60GLN00.0200.00822.5720.0030.0030.0000.0000.0000.000
57B61HIS00.0460.01825.4230.0000.0000.0000.0000.0000.000
58B62THR0-0.034-0.02921.0420.0000.0000.0000.0000.0000.000
59B63ILE0-0.032-0.01720.9580.0030.0030.0000.0000.0000.000
60B64THR0-0.050-0.02123.044-0.003-0.0030.0000.0000.0000.000
61B65LEU0-0.005-0.00726.230-0.003-0.0030.0000.0000.0000.000
62B66ALA00.0150.00921.896-0.003-0.0030.0000.0000.0000.000
63B67ARG10.8960.93223.761-0.041-0.0410.0000.0000.0000.000
64B68GLU-1-0.808-0.88524.7980.0220.0220.0000.0000.0000.000
65B69LEU0-0.009-0.00326.769-0.004-0.0040.0000.0000.0000.000
66B70ALA00.0090.01023.861-0.004-0.0040.0000.0000.0000.000
67B71LYS10.7550.86425.893-0.028-0.0280.0000.0000.0000.000
68B72ASN0-0.036-0.03028.335-0.003-0.0030.0000.0000.0000.000
69B73GLY0-0.0030.01129.107-0.003-0.0030.0000.0000.0000.000
70B74ALA0-0.0080.01527.847-0.001-0.0010.0000.0000.0000.000
71B75VAL0-0.033-0.02322.4520.0020.0020.0000.0000.0000.000
72B76ILE0-0.0170.00220.0900.0000.0000.0000.0000.0000.000
73B77VAL00.0080.02420.2660.0120.0120.0000.0000.0000.000
74B78SER00.000-0.02816.9770.0110.0110.0000.0000.0000.000
75B79GLY00.0370.02115.517-0.014-0.0140.0000.0000.0000.000
76B80GLY00.0840.05012.4800.0090.0090.0000.0000.0000.000
77B81ALA0-0.031-0.02311.4020.1230.1230.0000.0000.0000.000
78B82LEU00.008-0.01110.0730.0150.0150.0000.0000.0000.000
79B83GLY00.0080.00913.410-0.041-0.0410.0000.0000.0000.000
80B84VAL00.0100.00016.5970.0150.0150.0000.0000.0000.000
81B85ASP-1-0.813-0.91315.6830.1480.1480.0000.0000.0000.000
82B86ILE0-0.029-0.00711.050-0.008-0.0080.0000.0000.0000.000
83B87ILE0-0.0240.00114.431-0.014-0.0140.0000.0000.0000.000
84B88ALA00.0420.02317.295-0.018-0.0180.0000.0000.0000.000
85B89GLN0-0.002-0.03114.8010.0170.0170.0000.0000.0000.000
86B90GLU-1-0.827-0.90914.7230.1450.1450.0000.0000.0000.000
87B91ASN0-0.108-0.06916.111-0.036-0.0360.0000.0000.0000.000
88B92ALA00.0340.01319.135-0.017-0.0170.0000.0000.0000.000
89B93LEU0-0.0110.02214.320-0.011-0.0110.0000.0000.0000.000
90B94PRO00.008-0.00418.924-0.010-0.0100.0000.0000.0000.000
91B95LYS10.9400.98120.125-0.023-0.0230.0000.0000.0000.000
92B96THR0-0.003-0.01216.8340.0130.0130.0000.0000.0000.000
93B97ILE00.0320.00917.856-0.004-0.0040.0000.0000.0000.000
94B98MET0-0.0380.0049.5320.0210.0210.0000.0000.0000.000
95B99LEU00.001-0.00615.463-0.034-0.0340.0000.0000.0000.000
96B100SER00.0410.00010.7480.0420.0420.0000.0000.0000.000
97B101PRO0-0.053-0.02110.059-0.003-0.0030.0000.0000.0000.000
98B102CYS0-0.026-0.0077.9930.0050.0050.0000.0000.0000.000
99B103SER0-0.0030.0069.5230.0700.0700.0000.0000.0000.000
100B104LEU00.0350.0188.987-0.162-0.1620.0000.0000.0000.000
101B105ASP-1-0.714-0.7918.263-0.447-0.4470.0000.0000.0000.000
102B106PHE0-0.038-0.0113.348-1.137-0.4920.009-0.177-0.4770.000
103B107ILE0-0.0090.0062.486-1.0040.9572.830-1.137-3.6540.000
104B108TYR0-0.016-0.0013.167-1.503-0.1990.090-0.691-0.702-0.006
105B109PRO0-0.011-0.0095.879-0.072-0.0720.0000.0000.0000.000
106B110THR00.0800.0072.439-1.975-1.8533.936-1.023-3.0350.007
107B111ASN00.001-0.0053.775-0.4970.1780.056-0.173-0.558-0.002
108B112ASN0-0.016-0.0076.103-0.317-0.3170.0000.0000.0000.000
109B113HIS0-0.015-0.0042.885-3.313-2.3312.834-1.152-2.663-0.001
110B114LYS10.9270.9794.885-0.289-0.1680.001-0.068-0.0540.000
111B115VAL00.1380.0707.766-0.033-0.0330.0000.0000.0000.000
112B116ILE0-0.007-0.0066.530-0.099-0.0990.0000.0000.0000.000
113B117GLN0-0.016-0.0245.8640.0830.183-0.001-0.003-0.0950.000
114B118GLU-1-0.907-0.9488.8170.0430.0430.0000.0000.0000.000
115B119ILE0-0.009-0.01411.804-0.076-0.0760.0000.0000.0000.000
116B120ALA0-0.039-0.01410.399-0.058-0.0580.0000.0000.0000.000
117B121GLN0-0.052-0.01811.245-0.071-0.0710.0000.0000.0000.000
118B122ASN0-0.058-0.03514.705-0.039-0.0390.0000.0000.0000.000
119B123GLY00.0110.01716.241-0.004-0.0040.0000.0000.0000.000
120B124LEU0-0.058-0.01716.518-0.022-0.0220.0000.0000.0000.000
121B125ILE0-0.028-0.00410.2590.0270.0270.0000.0000.0000.000
122B126LEU00.0240.01314.340-0.033-0.0330.0000.0000.0000.000
123B127SER0-0.004-0.02713.0000.0200.0200.0000.0000.0000.000
124B128GLU-1-0.781-0.85915.7300.0140.0140.0000.0000.0000.000
125B129TYR0-0.037-0.03013.1370.0220.0220.0000.0000.0000.000
126B130GLU-1-0.813-0.90114.069-0.075-0.0750.0000.0000.0000.000
127B131LYS10.8790.93611.614-0.042-0.0420.0000.0000.0000.000
128B132ASP-1-0.890-0.95710.0280.1620.1620.0000.0000.0000.000
129B133PHE0-0.055-0.01910.3310.1020.1020.0000.0000.0000.000
130B134MET00.0360.0094.288-0.236-0.138-0.001-0.015-0.0820.000
131B135PRO0-0.0270.0067.2100.0150.0150.0000.0000.0000.000
132B136ILE00.0440.01310.1610.0470.0470.0000.0000.0000.000
133B137LYS10.9440.96213.405-0.086-0.0860.0000.0000.0000.000
134B138GLY00.0260.00916.635-0.004-0.0040.0000.0000.0000.000
135B139SER00.0580.02212.7970.0070.0070.0000.0000.0000.000
136B140PHE0-0.033-0.01910.776-0.006-0.0060.0000.0000.0000.000
137B141LEU0-0.017-0.01015.7840.0010.0010.0000.0000.0000.000
138B142ALA00.0240.01718.456-0.002-0.0020.0000.0000.0000.000
139B143ARG10.8650.92713.314-0.117-0.1170.0000.0000.0000.000
140B144ASN0-0.028-0.01718.2820.0080.0080.0000.0000.0000.000
141B145ARG10.7380.82220.280-0.023-0.0230.0000.0000.0000.000
142B146LEU0-0.0120.00919.047-0.002-0.0020.0000.0000.0000.000
143B147VAL00.0180.00818.770-0.002-0.0020.0000.0000.0000.000
144B148ILE0-0.033-0.00621.580-0.001-0.0010.0000.0000.0000.000
145B149ALA00.0030.00325.070-0.002-0.0020.0000.0000.0000.000
146B150LEU0-0.010-0.00621.794-0.003-0.0030.0000.0000.0000.000
147B151SER00.004-0.00724.3170.0000.0000.0000.0000.0000.000
148B152ASP-1-0.784-0.86126.8410.0230.0230.0000.0000.0000.000
149B153VAL0-0.002-0.00329.192-0.001-0.0010.0000.0000.0000.000
150B154VAL0-0.030-0.02325.7330.0050.0050.0000.0000.0000.000
151B155ILE00.0260.01626.102-0.003-0.0030.0000.0000.0000.000
152B156ILE0-0.025-0.02524.6260.0080.0080.0000.0000.0000.000
153B157PRO00.0040.00023.828-0.004-0.0040.0000.0000.0000.000
154B158GLN00.0850.05424.478-0.002-0.0020.0000.0000.0000.000
155B159ALA0-0.004-0.00724.1650.0100.0100.0000.0000.0000.000
156B160ASP-1-0.812-0.86823.8510.0660.0660.0000.0000.0000.000
157B161LEU00.0890.04626.6530.0020.0020.0000.0000.0000.000
158B162LYS10.8980.93727.084-0.048-0.0480.0000.0000.0000.000
159B163SER00.0110.00922.7350.0040.0040.0000.0000.0000.000
160B164GLY00.0400.00620.810-0.003-0.0030.0000.0000.0000.000
161B165SER00.0640.05121.821-0.003-0.0030.0000.0000.0000.000
162B166MET00.0520.05523.500-0.004-0.0040.0000.0000.0000.000
163B167SER0-0.091-0.05123.678-0.004-0.0040.0000.0000.0000.000
164B168SER0-0.022-0.03122.810-0.002-0.0020.0000.0000.0000.000
165B169ALA00.0880.04325.195-0.003-0.0030.0000.0000.0000.000
166B170ARG10.9520.98627.840-0.049-0.0490.0000.0000.0000.000
167B171LEU0-0.043-0.01924.918-0.003-0.0030.0000.0000.0000.000
168B172ALA00.0380.01328.280-0.003-0.0030.0000.0000.0000.000
169B173GLN0-0.005-0.00129.831-0.004-0.0040.0000.0000.0000.000
170B174LYS10.8880.95530.868-0.031-0.0310.0000.0000.0000.000
171B175TYR0-0.033-0.02428.046-0.002-0.0020.0000.0000.0000.000
172B176GLN0-0.015-0.01332.589-0.002-0.0020.0000.0000.0000.000
173B177LYS10.8300.92429.190-0.030-0.0300.0000.0000.0000.000
174B178PRO00.0100.00232.2980.0020.0020.0000.0000.0000.000
175B179LEU00.0010.01428.9680.0030.0030.0000.0000.0000.000
176B180PHE00.003-0.00330.551-0.003-0.0030.0000.0000.0000.000
177B181VAL0-0.0030.00329.5890.0050.0050.0000.0000.0000.000
178B182LEU0-0.0120.00827.319-0.003-0.0030.0000.0000.0000.000
179B183PRO00.0300.02131.2180.0000.0000.0000.0000.0000.000
180B184GLN0-0.043-0.02328.017-0.001-0.0010.0000.0000.0000.000
181B185ARG10.8840.93532.601-0.030-0.0300.0000.0000.0000.000
182B186LEU00.0600.02833.7820.0020.0020.0000.0000.0000.000
183B187ASN0-0.061-0.04833.001-0.002-0.0020.0000.0000.0000.000
184B188GLU-1-0.858-0.90229.5640.0360.0360.0000.0000.0000.000
185B189SER0-0.022-0.04728.3700.0080.0080.0000.0000.0000.000
186B190ASP-1-0.741-0.86529.6570.0360.0360.0000.0000.0000.000
187B191GLY0-0.029-0.01728.919-0.002-0.0020.0000.0000.0000.000
188B192THR00.0320.01928.256-0.001-0.0010.0000.0000.0000.000
189B193ASN0-0.021-0.02430.894-0.002-0.0020.0000.0000.0000.000
190B194GLU-1-0.840-0.91333.2820.0350.0350.0000.0000.0000.000
191B195LEU0-0.043-0.03029.675-0.001-0.0010.0000.0000.0000.000
192B196LEU0-0.023-0.00634.197-0.002-0.0020.0000.0000.0000.000
193B197GLU-1-0.942-0.97136.8730.0270.0270.0000.0000.0000.000
194B198LYS10.7930.89236.051-0.034-0.0340.0000.0000.0000.000
195B199GLY00.0120.01639.175-0.001-0.0010.0000.0000.0000.000
196B200GLN0-0.035-0.00634.5520.0020.0020.0000.0000.0000.000
197B201ALA0-0.028-0.02132.6920.0020.0020.0000.0000.0000.000
198B202GLN00.0110.01434.659-0.003-0.0030.0000.0000.0000.000
199B203GLY00.0340.01734.3350.0030.0030.0000.0000.0000.000
200B204ILE0-0.026-0.01830.313-0.002-0.0020.0000.0000.0000.000
201B205PHE00.003-0.02334.4730.0010.0010.0000.0000.0000.000
202B206ASN0-0.0070.00636.709-0.001-0.0010.0000.0000.0000.000
203B207ILE00.0440.02030.6500.0000.0000.0000.0000.0000.000
204B208GLN00.0590.03233.6880.0010.0010.0000.0000.0000.000
205B209ASN00.013-0.00535.4730.0000.0000.0000.0000.0000.000
206B210PHE00.0160.02630.2820.0000.0000.0000.0000.0000.000
207B211ILE00.0150.01230.5060.0000.0000.0000.0000.0000.000
208B212ASN00.015-0.03333.7500.0010.0010.0000.0000.0000.000
209B213THR0-0.068-0.02037.107-0.002-0.0020.0000.0000.0000.000
210B214LEU00.0370.02331.125-0.001-0.0010.0000.0000.0000.000
211B215LEU0-0.040-0.03431.8970.0000.0000.0000.0000.0000.000
212B216LYS10.8320.89535.620-0.016-0.0160.0000.0000.0000.000
213B217ASP-1-0.912-0.94837.4230.0180.0180.0000.0000.0000.000
214B218TYR0-0.103-0.06833.8030.0000.0000.0000.0000.0000.000
215B219HIS0-0.050-0.01936.832-0.001-0.0010.0000.0000.0000.000
216B220LEU0-0.0200.00132.016-0.001-0.0010.0000.0000.0000.000
217B221LYS10.9310.95836.603-0.008-0.0080.0000.0000.0000.000
218B222GLU-1-0.764-0.85636.0080.0150.0150.0000.0000.0000.000
219B223MET0-0.0520.00732.943-0.001-0.0010.0000.0000.0000.000