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: LJMR9

Calculation Name: 4LJL-B-Xray319

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: 2021-09-07

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 220
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2693866.485578
FMO2-HF: Nuclear repulsion 2608717.138136
FMO2-HF: Total energy -85149.347441
FMO2-MP2: Total energy -85398.852487


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.
-12.224-1.7528.705-6.338-12.839-0.019
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 : -0.013 / q_NPA : -0.016
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].
3B7SER 0-0.030-0.0572.693-4.508-1.5810.534-1.630-1.831-0.011
4B8HIS 0-0.038-0.0224.7790.6170.7980.000-0.007-0.1730.000
5B9PHE 00.0050.0017.7020.2210.2210.0000.0000.0000.000
6B10GLN 00.0360.0359.823-0.014-0.0140.0000.0000.0000.000
7B11TYR 0-0.069-0.05711.2530.0110.0110.0000.0000.0000.000
8B12SER 00.0040.00315.0780.0280.0280.0000.0000.0000.000
9B13THR 0-0.027-0.03518.322-0.011-0.0110.0000.0000.0000.000
10B14LEU 0-0.039-0.02820.8450.0050.0050.0000.0000.0000.000
11B15GLU -1-0.942-0.96922.499-0.048-0.0480.0000.0000.0000.000
12B16ASN 00.0060.00326.1640.0060.0060.0000.0000.0000.000
13B17ILE 0-0.015-0.00624.250-0.006-0.0060.0000.0000.0000.000
14B18PRO 00.0220.00824.5310.0060.0060.0000.0000.0000.000
15B19LYS 11.0841.03427.6940.0280.0280.0000.0000.0000.000
16B20ALA 0-0.044-0.00127.8090.0010.0010.0000.0000.0000.000
17B21PHE 0-0.011-0.03022.412-0.001-0.0010.0000.0000.0000.000
18B22ASP -1-0.848-0.93027.894-0.036-0.0360.0000.0000.0000.000
19B23ILE 0-0.069-0.01929.5060.0020.0020.0000.0000.0000.000
20B24LEU 0-0.093-0.04225.1590.0010.0010.0000.0000.0000.000
21B25LYS 10.9050.94929.2240.0270.0270.0000.0000.0000.000
22B26ASP -1-0.905-0.95326.441-0.027-0.0270.0000.0000.0000.000
23B27PRO 00.0230.02725.668-0.007-0.0070.0000.0000.0000.000
24B28PRO 0-0.0150.00621.9160.0010.0010.0000.0000.0000.000
25B29LYS 10.9690.97023.6310.0420.0420.0000.0000.0000.000
26B30LYS 10.9380.97320.8520.0810.0810.0000.0000.0000.000
27B31LEU 00.0010.01119.169-0.009-0.0090.0000.0000.0000.000
28B32TYR 00.0370.02715.7020.0170.0170.0000.0000.0000.000
29B33CYS 0-0.027-0.01016.700-0.005-0.0050.0000.0000.0000.000
30B34VAL 00.0600.01812.004-0.018-0.0180.0000.0000.0000.000
31B35GLY 00.0640.04015.3520.0120.0120.0000.0000.0000.000
32B36ASP -1-0.849-0.94817.288-0.047-0.0470.0000.0000.0000.000
33B37THR 00.021-0.01320.8730.0030.0030.0000.0000.0000.000
34B38LYS 10.9540.98622.7120.0470.0470.0000.0000.0000.000
35B39LEU 0-0.0290.00220.6120.0050.0050.0000.0000.0000.000
36B40LEU 0-0.015-0.01722.3880.0020.0020.0000.0000.0000.000
37B41ASP -1-0.914-0.94825.609-0.040-0.0400.0000.0000.0000.000
38B42THR 0-0.131-0.06726.6690.0030.0030.0000.0000.0000.000
39B43PRO 00.0140.01129.458-0.001-0.0010.0000.0000.0000.000
40B44LEU 00.0370.02429.8150.0000.0000.0000.0000.0000.000
41B45LYS 10.8350.93125.0900.0390.0390.0000.0000.0000.000
42B46VAL 00.0320.00525.9730.0000.0000.0000.0000.0000.000
43B47ALA 00.0110.01123.1450.0000.0000.0000.0000.0000.000
44B48ILE 0-0.0150.00321.9210.0040.0040.0000.0000.0000.000
45B49ILE 00.0070.01619.830-0.001-0.0010.0000.0000.0000.000
46B50GLY 00.017-0.01920.1130.0040.0040.0000.0000.0000.000
47B51THR 0-0.0180.00719.687-0.006-0.0060.0000.0000.0000.000
48B52ARG 10.9620.96813.7260.1050.1050.0000.0000.0000.000
49B53ARG 10.9290.95316.6790.0450.0450.0000.0000.0000.000
50B54PRO 0-0.0180.02318.2660.0010.0010.0000.0000.0000.000
51B55THR 00.0770.04121.392-0.001-0.0010.0000.0000.0000.000
52B56PRO 00.035-0.00723.4580.0010.0010.0000.0000.0000.000
53B57TYR 00.0030.00124.4200.0020.0020.0000.0000.0000.000
54B58SER 00.046-0.03324.1890.0010.0010.0000.0000.0000.000
55B59LYS 10.9210.97817.2930.0130.0130.0000.0000.0000.000
56B60GLN 00.0320.01222.5800.0020.0020.0000.0000.0000.000
57B61HIS 00.0250.00825.2060.0020.0020.0000.0000.0000.000
58B62THR 0-0.029-0.02221.098-0.001-0.0010.0000.0000.0000.000
59B63ILE 0-0.035-0.01120.7600.0010.0010.0000.0000.0000.000
60B64THR 0-0.051-0.01723.2570.0010.0010.0000.0000.0000.000
61B65LEU 00.0100.00126.2560.0000.0000.0000.0000.0000.000
62B66ALA 00.0120.01522.152-0.001-0.0010.0000.0000.0000.000
63B67ARG 10.9690.98724.2030.0060.0060.0000.0000.0000.000
64B68GLU -1-0.906-0.97025.095-0.011-0.0110.0000.0000.0000.000
65B69LEU 0-0.002-0.00226.882-0.001-0.0010.0000.0000.0000.000
66B70ALA 0-0.0060.01523.965-0.001-0.0010.0000.0000.0000.000
67B71LYS 10.8220.92725.9720.0100.0100.0000.0000.0000.000
68B72ASN 0-0.045-0.03728.2990.0000.0000.0000.0000.0000.000
69B73GLY 00.0380.01429.4570.0000.0000.0000.0000.0000.000
70B74ALA 0-0.0130.01027.755-0.002-0.0020.0000.0000.0000.000
71B75VAL 0-0.025-0.01622.6590.0010.0010.0000.0000.0000.000
72B76ILE 0-0.0030.00620.226-0.002-0.0020.0000.0000.0000.000
73B77VAL 00.0090.02120.332-0.001-0.0010.0000.0000.0000.000
74B78SER 0-0.015-0.03017.3080.0030.0030.0000.0000.0000.000
75B79GLY 00.0280.02315.276-0.015-0.0150.0000.0000.0000.000
76B80GLY 00.1000.05812.088-0.036-0.0360.0000.0000.0000.000
77B81ALA 0-0.051-0.02711.3020.0470.0470.0000.0000.0000.000
78B82LEU 00.009-0.0169.3980.0240.0240.0000.0000.0000.000
79B83GLY 00.0060.01112.950-0.016-0.0160.0000.0000.0000.000
80B84VAL 00.0300.00416.1250.0110.0110.0000.0000.0000.000
81B85ASP -1-0.825-0.91215.576-0.044-0.0440.0000.0000.0000.000
82B86ILE 0-0.030-0.01511.0540.0030.0030.0000.0000.0000.000
83B87ILE 0-0.0140.00114.4640.0060.0060.0000.0000.0000.000
84B88ALA 00.0210.01017.0410.0000.0000.0000.0000.0000.000
85B89GLN 0-0.014-0.04215.1480.0010.0010.0000.0000.0000.000
86B90GLU -1-0.917-0.96014.5260.0700.0700.0000.0000.0000.000
87B91ASN 0-0.079-0.06216.324-0.010-0.0100.0000.0000.0000.000
88B92ALA 00.0090.01319.453-0.006-0.0060.0000.0000.0000.000
89B93LEU 0-0.0440.03114.743-0.009-0.0090.0000.0000.0000.000
90B94PRO 00.006-0.02118.996-0.002-0.0020.0000.0000.0000.000
91B95LYS 10.9570.97720.0780.0150.0150.0000.0000.0000.000
92B96THR 0-0.012-0.02416.9290.0020.0020.0000.0000.0000.000
93B97ILE 00.0280.01118.357-0.003-0.0030.0000.0000.0000.000
94B98MET 0-0.050-0.0169.5710.0220.0220.0000.0000.0000.000
95B99LEU 00.004-0.00115.635-0.025-0.0250.0000.0000.0000.000
96B100SER 00.031-0.00110.3070.0020.0020.0000.0000.0000.000
97B101PRO 0-0.048-0.0169.9760.0280.0280.0000.0000.0000.000
98B102CYS 0-0.020-0.0077.383-0.021-0.0210.0000.0000.0000.000
99B103SER 00.0080.0149.0230.0880.0880.0000.0000.0000.000
100B104LEU 00.0350.0168.347-0.270-0.2700.0000.0000.0000.000
101B105ASP -1-0.720-0.7818.389-0.652-0.6520.0000.0000.0000.000
102B106PHE 0-0.040-0.0143.650-0.879-0.2610.004-0.163-0.4590.000
103B107ILE 0-0.0060.0102.293-0.5791.6441.784-1.083-2.9240.001
104B108TYR 0-0.038-0.0033.282-1.945-0.8880.054-0.568-0.543-0.004
105B109PRO 0-0.010-0.0245.8530.1200.1200.0000.0000.0000.000
106B110THR 00.1080.0212.261-1.342-0.2583.240-1.205-3.1190.000
107B111ASN 0-0.016-0.0183.465-0.7520.1160.073-0.252-0.688-0.003
108B112ASN 0-0.0110.0045.526-0.138-0.1380.0000.0000.0000.000
109B113HIS 0-0.016-0.0122.734-2.332-1.1553.015-1.342-2.850-0.002
110B114LYS 10.9520.9874.935-0.600-0.4870.001-0.073-0.0420.000
111B115VAL 00.1130.0577.785-0.076-0.0760.0000.0000.0000.000
112B116ILE 0-0.005-0.0127.164-0.105-0.1050.0000.0000.0000.000
113B117GLN 0-0.017-0.0185.5900.3940.5330.000-0.005-0.1340.000
114B118GLU -1-0.899-0.9449.2090.0040.0040.0000.0000.0000.000
115B119ILE 0-0.044-0.02412.069-0.055-0.0550.0000.0000.0000.000
116B120ALA 0-0.041-0.01110.868-0.041-0.0410.0000.0000.0000.000
117B121GLN 0-0.061-0.02312.311-0.016-0.0160.0000.0000.0000.000
118B122ASN 0-0.004-0.01115.036-0.024-0.0240.0000.0000.0000.000
119B123GLY 00.0180.02616.4430.0000.0000.0000.0000.0000.000
120B124LEU 0-0.032-0.00217.109-0.014-0.0140.0000.0000.0000.000
121B125ILE 0-0.0210.00011.0690.0020.0020.0000.0000.0000.000
122B126LEU 00.0120.00514.967-0.013-0.0130.0000.0000.0000.000
123B127SER 00.009-0.02212.4250.0010.0010.0000.0000.0000.000
124B128GLU -1-0.755-0.86115.197-0.069-0.0690.0000.0000.0000.000
125B129TYR 0-0.063-0.03212.5570.0330.0330.0000.0000.0000.000
126B130GLU -1-0.924-0.96413.473-0.135-0.1350.0000.0000.0000.000
127B131LYS 10.9310.96011.210-0.022-0.0220.0000.0000.0000.000
128B132ASP -1-0.911-0.9589.1070.1930.1930.0000.0000.0000.000
129B133PHE 0-0.062-0.0309.6650.1140.1140.0000.0000.0000.000
130B134MET 00.0370.0054.314-0.182-0.0970.000-0.010-0.0760.000
131B135PRO 0-0.035-0.0036.9840.0590.0590.0000.0000.0000.000
132B136ILE 00.0640.02210.0120.0720.0720.0000.0000.0000.000
133B137LYS 10.9600.97613.2870.0110.0110.0000.0000.0000.000
134B138GLY 00.018-0.01016.528-0.006-0.0060.0000.0000.0000.000
135B139SER 00.0340.02212.3740.0170.0170.0000.0000.0000.000
136B140PHE 0-0.015-0.00710.903-0.009-0.0090.0000.0000.0000.000
137B141LEU 0-0.060-0.03215.6120.0100.0100.0000.0000.0000.000
138B142ALA 00.0330.02317.9820.0060.0060.0000.0000.0000.000
139B143ARG 10.9010.95213.4400.1420.1420.0000.0000.0000.000
140B144ASN 0-0.014-0.01417.9050.0010.0010.0000.0000.0000.000
141B145ARG 10.7370.83020.1860.0790.0790.0000.0000.0000.000
142B146LEU 0-0.0170.00418.7040.0060.0060.0000.0000.0000.000
143B147VAL 00.0250.01418.6850.0050.0050.0000.0000.0000.000
144B148ILE 0-0.042-0.01421.4580.0070.0070.0000.0000.0000.000
145B149ALA 0-0.004-0.00725.0080.0040.0040.0000.0000.0000.000
146B150LEU 0-0.029-0.01022.1370.0030.0030.0000.0000.0000.000
147B151SER 0-0.023-0.01924.2410.0030.0030.0000.0000.0000.000
148B152ASP -1-0.803-0.88326.723-0.029-0.0290.0000.0000.0000.000
149B153VAL 0-0.007-0.00829.1590.0020.0020.0000.0000.0000.000
150B154VAL 0-0.034-0.01325.647-0.002-0.0020.0000.0000.0000.000
151B155ILE 00.0120.00726.4030.0020.0020.0000.0000.0000.000
152B156ILE 0-0.035-0.03324.886-0.002-0.0020.0000.0000.0000.000
153B157PRO 0-0.0070.00323.6800.0010.0010.0000.0000.0000.000
154B158GLN 00.1510.10824.3650.0020.0020.0000.0000.0000.000
155B159ALA 0-0.078-0.05124.410-0.003-0.0030.0000.0000.0000.000
156B160ASP -1-0.854-0.89524.972-0.027-0.0270.0000.0000.0000.000
157B161LEU 00.0780.02626.799-0.002-0.0020.0000.0000.0000.000
158B162LYS 10.8930.94226.7660.0150.0150.0000.0000.0000.000
159B163SER 00.0420.03022.627-0.003-0.0030.0000.0000.0000.000
160B164GLY 00.026-0.00720.6300.0010.0010.0000.0000.0000.000
161B165SER 00.0690.03121.686-0.001-0.0010.0000.0000.0000.000
162B166MET 00.0310.05623.4800.0010.0010.0000.0000.0000.000
163B167SER 0-0.094-0.05423.3970.0020.0020.0000.0000.0000.000
164B168SER 00.003-0.01022.433-0.002-0.0020.0000.0000.0000.000
165B169ALA 00.0790.04325.0440.0010.0010.0000.0000.0000.000
166B170ARG 10.9360.97027.1600.0280.0280.0000.0000.0000.000
167B171LEU 0-0.051-0.01524.6790.0010.0010.0000.0000.0000.000
168B172ALA 00.0530.02328.4130.0010.0010.0000.0000.0000.000
169B173GLN 00.0020.01029.8060.0030.0030.0000.0000.0000.000
170B174LYS 10.8960.96130.2760.0280.0280.0000.0000.0000.000
171B175TYR 0-0.045-0.03628.3220.0010.0010.0000.0000.0000.000
172B176GLN 0-0.0050.00232.6620.0000.0000.0000.0000.0000.000
173B177LYS 10.8590.94129.1050.0340.0340.0000.0000.0000.000
174B178PRO 00.0090.00832.2150.0000.0000.0000.0000.0000.000
175B179LEU 00.0160.00828.699-0.002-0.0020.0000.0000.0000.000
176B180PHE 00.0030.00330.5650.0020.0020.0000.0000.0000.000
177B181VAL 00.0060.00429.800-0.001-0.0010.0000.0000.0000.000
178B182LEU 0-0.0180.00027.3020.0010.0010.0000.0000.0000.000
179B183PRO 00.0230.02031.1580.0000.0000.0000.0000.0000.000
180B184GLN 0-0.027-0.02327.7840.0000.0000.0000.0000.0000.000
181B185ARG 10.9870.99632.8020.0160.0160.0000.0000.0000.000
182B186LEU 00.0690.02033.707-0.001-0.0010.0000.0000.0000.000
183B187ASN 0-0.025-0.01433.2240.0000.0000.0000.0000.0000.000
184B188GLU -1-0.949-0.95929.421-0.020-0.0200.0000.0000.0000.000
185B189SER 0-0.030-0.05728.131-0.002-0.0020.0000.0000.0000.000
186B190ASP -1-0.853-0.92829.468-0.017-0.0170.0000.0000.0000.000
187B191GLY 0-0.034-0.03128.8050.0010.0010.0000.0000.0000.000
188B192THR 00.0540.03128.2240.0000.0000.0000.0000.0000.000
189B193ASN 00.0050.00030.8540.0010.0010.0000.0000.0000.000
190B194GLU -1-0.880-0.92333.204-0.016-0.0160.0000.0000.0000.000
191B195LEU 0-0.077-0.04729.7880.0000.0000.0000.0000.0000.000
192B196LEU 0-0.034-0.02034.3180.0010.0010.0000.0000.0000.000
193B197GLU -1-0.962-0.96436.779-0.012-0.0120.0000.0000.0000.000
194B198LYS 10.8730.93436.1960.0150.0150.0000.0000.0000.000
195B199GLY 00.0190.01839.2720.0000.0000.0000.0000.0000.000
196B200GLN 0-0.062-0.03534.888-0.001-0.0010.0000.0000.0000.000
197B201ALA 0-0.025-0.01733.007-0.001-0.0010.0000.0000.0000.000
198B202GLN 00.0230.02034.9490.0020.0020.0000.0000.0000.000
199B203GLY 00.0220.01634.589-0.001-0.0010.0000.0000.0000.000
200B204ILE 0-0.030-0.02130.6570.0000.0000.0000.0000.0000.000
201B205PHE 00.022-0.00734.5300.0000.0000.0000.0000.0000.000
202B206ASN 0-0.005-0.00536.7890.0000.0000.0000.0000.0000.000
203B207ILE 00.0440.02630.4030.0000.0000.0000.0000.0000.000
204B208GLN 00.0510.02133.8930.0000.0000.0000.0000.0000.000
205B209ASN 00.0250.00735.8010.0000.0000.0000.0000.0000.000
206B210PHE 00.0150.01430.7170.0000.0000.0000.0000.0000.000
207B211ILE 00.0330.01230.800-0.001-0.0010.0000.0000.0000.000
208B212ASN 00.0480.01234.019-0.001-0.0010.0000.0000.0000.000
209B213THR 0-0.048-0.02937.2860.0000.0000.0000.0000.0000.000
210B214LEU 00.0140.02331.4300.0000.0000.0000.0000.0000.000
211B215LEU 0-0.013-0.01932.560-0.001-0.0010.0000.0000.0000.000
212B216LYS 10.9090.96135.8800.0130.0130.0000.0000.0000.000
213B217ASP -1-0.921-0.93637.501-0.016-0.0160.0000.0000.0000.000
214B218TYR 0-0.079-0.03934.017-0.001-0.0010.0000.0000.0000.000
215B219HIS 0-0.041-0.01936.9510.0000.0000.0000.0000.0000.000
216B220LEU 0-0.038-0.00132.4920.0000.0000.0000.0000.0000.000
217B221LYS 10.9080.94737.0350.0150.0150.0000.0000.0000.000
218B222GLU -1-0.904-0.96336.614-0.012-0.0120.0000.0000.0000.000
219B223MET 0-0.097-0.04833.7330.0000.0000.0000.0000.0000.000
220B1NME 00.0230.02737.4150.0000.0000.0000.0000.0000.000