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: 82V6Y

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 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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2691491.859574
FMO2-HF: Nuclear repulsion 2606361.576054
FMO2-HF: Total energy -85130.283519
FMO2-MP2: Total energy -85379.695599


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.
-12.229-1.7298.699-6.313-12.884-0.018
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 : -0.010 / 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].
3B7SER0-0.031-0.0572.693-4.486-1.5390.534-1.628-1.853-0.010
4B8HIS0-0.037-0.0224.7790.5830.768-0.001-0.006-0.1770.000
5B9PHE00.0060.0017.7020.2160.2160.0000.0000.0000.000
6B10GLN00.0360.0359.823-0.020-0.0200.0000.0000.0000.000
7B11TYR0-0.070-0.05711.2530.0110.0110.0000.0000.0000.000
8B12SER00.0050.00415.0780.0250.0250.0000.0000.0000.000
9B13THR0-0.027-0.03418.322-0.011-0.0110.0000.0000.0000.000
10B14LEU0-0.040-0.02820.8540.0050.0050.0000.0000.0000.000
11B15GLU-1-0.943-0.97022.499-0.046-0.0460.0000.0000.0000.000
12B16ASN00.0060.00326.1640.0060.0060.0000.0000.0000.000
13B17ILE0-0.015-0.00624.255-0.005-0.0050.0000.0000.0000.000
14B18PRO00.0230.00924.5310.0050.0050.0000.0000.0000.000
15B19LYS11.0821.03327.6940.0260.0260.0000.0000.0000.000
16B20ALA0-0.045-0.00227.8080.0010.0010.0000.0000.0000.000
17B21PHE0-0.007-0.02822.412-0.001-0.0010.0000.0000.0000.000
18B22ASP-1-0.851-0.93127.896-0.033-0.0330.0000.0000.0000.000
19B23ILE0-0.068-0.02029.5060.0020.0020.0000.0000.0000.000
20B24LEU0-0.093-0.04125.1600.0010.0010.0000.0000.0000.000
21B25LYS10.9050.94929.2250.0240.0240.0000.0000.0000.000
22B26ASP-1-0.906-0.95426.444-0.025-0.0250.0000.0000.0000.000
23B27PRO00.0240.02725.671-0.006-0.0060.0000.0000.0000.000
24B28PRO0-0.0130.00721.9200.0010.0010.0000.0000.0000.000
25B29LYS10.9690.96923.6370.0390.0390.0000.0000.0000.000
26B30LYS10.9360.97220.8620.0780.0780.0000.0000.0000.000
27B31LEU00.0040.01319.173-0.008-0.0080.0000.0000.0000.000
28B32TYR00.0360.02715.7090.0170.0170.0000.0000.0000.000
29B33CYS0-0.032-0.01216.700-0.004-0.0040.0000.0000.0000.000
30B34VAL00.0620.02012.004-0.017-0.0170.0000.0000.0000.000
31B35GLY00.0600.03715.3520.0120.0120.0000.0000.0000.000
32B36ASP-1-0.848-0.94717.288-0.043-0.0430.0000.0000.0000.000
33B37THR0-0.012-0.02320.8730.0040.0040.0000.0000.0000.000
34B38LYS10.9971.00222.7120.0420.0420.0000.0000.0000.000
35B39LEU0-0.0310.00020.6130.0040.0040.0000.0000.0000.000
36B40LEU0-0.019-0.01922.3870.0020.0020.0000.0000.0000.000
37B41ASP-1-0.915-0.94925.609-0.036-0.0360.0000.0000.0000.000
38B42THR0-0.130-0.06726.6700.0030.0030.0000.0000.0000.000
39B43PRO00.0110.01029.458-0.001-0.0010.0000.0000.0000.000
40B44LEU00.0370.02429.8150.0000.0000.0000.0000.0000.000
41B45LYS10.8330.93125.0900.0350.0350.0000.0000.0000.000
42B46VAL00.0380.00725.9730.0000.0000.0000.0000.0000.000
43B47ALA00.0070.01023.1450.0000.0000.0000.0000.0000.000
44B48ILE0-0.0170.00121.9210.0030.0030.0000.0000.0000.000
45B49ILE00.0070.01619.8300.0000.0000.0000.0000.0000.000
46B50GLY00.021-0.01820.1130.0030.0030.0000.0000.0000.000
47B51THR0-0.0180.00819.687-0.005-0.0050.0000.0000.0000.000
48B52ARG10.9580.96613.7170.1010.1010.0000.0000.0000.000
49B53ARG10.9310.95416.6790.0430.0430.0000.0000.0000.000
50B54PRO0-0.0150.02518.2660.0000.0000.0000.0000.0000.000
51B55THR00.0740.04021.392-0.001-0.0010.0000.0000.0000.000
52B56PRO00.037-0.00723.4580.0020.0020.0000.0000.0000.000
53B57TYR00.0030.00024.4200.0020.0020.0000.0000.0000.000
54B58SER00.046-0.03324.1890.0010.0010.0000.0000.0000.000
55B59LYS10.9170.97717.2930.0060.0060.0000.0000.0000.000
56B60GLN00.0370.01322.5800.0020.0020.0000.0000.0000.000
57B61HIS00.0280.00925.2060.0020.0020.0000.0000.0000.000
58B62THR0-0.036-0.02421.098-0.001-0.0010.0000.0000.0000.000
59B63ILE0-0.034-0.01120.7600.0010.0010.0000.0000.0000.000
60B64THR0-0.049-0.01723.2570.0010.0010.0000.0000.0000.000
61B65LEU00.0070.00026.2560.0000.0000.0000.0000.0000.000
62B66ALA00.0140.01622.152-0.001-0.0010.0000.0000.0000.000
63B67ARG10.9700.98724.2030.0010.0010.0000.0000.0000.000
64B68GLU-1-0.907-0.97025.095-0.008-0.0080.0000.0000.0000.000
65B69LEU0-0.0010.00026.883-0.001-0.0010.0000.0000.0000.000
66B70ALA0-0.0020.01523.965-0.001-0.0010.0000.0000.0000.000
67B71LYS10.8140.92425.9720.0060.0060.0000.0000.0000.000
68B72ASN0-0.040-0.03628.2990.0000.0000.0000.0000.0000.000
69B73GLY00.0370.01429.456-0.001-0.0010.0000.0000.0000.000
70B74ALA0-0.0120.01127.755-0.002-0.0020.0000.0000.0000.000
71B75VAL0-0.026-0.01522.6580.0020.0020.0000.0000.0000.000
72B76ILE0-0.0040.00520.226-0.002-0.0020.0000.0000.0000.000
73B77VAL00.0070.01920.3320.0000.0000.0000.0000.0000.000
74B78SER0-0.012-0.02917.3080.0030.0030.0000.0000.0000.000
75B79GLY00.0260.02215.276-0.014-0.0140.0000.0000.0000.000
76B80GLY00.0980.05812.088-0.035-0.0350.0000.0000.0000.000
77B81ALA0-0.046-0.02611.3020.0490.0490.0000.0000.0000.000
78B82LEU00.005-0.0189.3980.0230.0230.0000.0000.0000.000
79B83GLY00.0020.01012.950-0.017-0.0170.0000.0000.0000.000
80B84VAL00.0360.00616.1250.0120.0120.0000.0000.0000.000
81B85ASP-1-0.824-0.91215.576-0.034-0.0340.0000.0000.0000.000
82B86ILE0-0.033-0.01711.0540.0020.0020.0000.0000.0000.000
83B87ILE0-0.0130.00214.4640.0060.0060.0000.0000.0000.000
84B88ALA00.0190.00917.0410.0000.0000.0000.0000.0000.000
85B89GLN0-0.014-0.04315.1480.0010.0010.0000.0000.0000.000
86B90GLU-1-0.914-0.95914.5260.0820.0820.0000.0000.0000.000
87B91ASN0-0.080-0.06316.324-0.011-0.0110.0000.0000.0000.000
88B92ALA00.0090.01319.453-0.007-0.0070.0000.0000.0000.000
89B93LEU0-0.0480.02914.743-0.010-0.0100.0000.0000.0000.000
90B94PRO00.008-0.02018.996-0.002-0.0020.0000.0000.0000.000
91B95LYS10.9550.97620.0780.0090.0090.0000.0000.0000.000
92B96THR0-0.010-0.02416.9300.0030.0030.0000.0000.0000.000
93B97ILE00.0300.01218.357-0.002-0.0020.0000.0000.0000.000
94B98MET0-0.048-0.0139.5710.0220.0220.0000.0000.0000.000
95B99LEU0-0.001-0.00315.635-0.024-0.0240.0000.0000.0000.000
96B100SER00.033-0.00110.3120.0050.0050.0000.0000.0000.000
97B101PRO0-0.048-0.0169.9730.0260.0260.0000.0000.0000.000
98B102CYS0-0.020-0.0077.384-0.020-0.0200.0000.0000.0000.000
99B103SER00.0110.0159.0320.0880.0880.0000.0000.0000.000
100B104LEU00.0310.0148.354-0.259-0.2590.0000.0000.0000.000
101B105ASP-1-0.720-0.7828.400-0.631-0.6310.0000.0000.0000.000
102B106PHE0-0.043-0.0163.663-0.847-0.2280.003-0.162-0.4590.000
103B107ILE0-0.0060.0102.293-0.5921.6471.781-1.081-2.9400.001
104B108TYR0-0.033-0.0013.282-1.948-0.8970.054-0.563-0.542-0.004
105B109PRO0-0.009-0.0225.8530.1010.1010.0000.0000.0000.000
106B110THR00.1060.0202.261-1.364-0.2723.242-1.206-3.1290.000
107B111ASN0-0.012-0.0173.465-0.7030.1560.072-0.247-0.683-0.003
108B112ASN0-0.0160.0025.526-0.151-0.1510.0000.0000.0000.000
109B113HIS0-0.018-0.0122.734-2.372-1.1993.016-1.336-2.854-0.002
110B114LYS10.9550.9874.935-0.602-0.4880.000-0.072-0.0420.000
111B115VAL00.1130.0577.785-0.072-0.0720.0000.0000.0000.000
112B116ILE0-0.003-0.0117.164-0.108-0.1080.0000.0000.0000.000
113B117GLN0-0.024-0.0205.5900.4080.550-0.001-0.003-0.1370.000
114B118GLU-1-0.894-0.9429.2090.0210.0210.0000.0000.0000.000
115B119ILE0-0.047-0.02512.069-0.057-0.0570.0000.0000.0000.000
116B120ALA0-0.036-0.01110.868-0.042-0.0420.0000.0000.0000.000
117B121GLN0-0.063-0.02312.311-0.020-0.0200.0000.0000.0000.000
118B122ASN0-0.006-0.01115.036-0.027-0.0270.0000.0000.0000.000
119B123GLY00.0190.02716.443-0.001-0.0010.0000.0000.0000.000
120B124LEU0-0.030-0.00217.109-0.014-0.0140.0000.0000.0000.000
121B125ILE0-0.024-0.00111.0690.0030.0030.0000.0000.0000.000
122B126LEU00.0130.00514.967-0.013-0.0130.0000.0000.0000.000
123B127SER00.009-0.02212.4300.0020.0020.0000.0000.0000.000
124B128GLU-1-0.755-0.86215.201-0.066-0.0660.0000.0000.0000.000
125B129TYR0-0.062-0.03212.5630.0320.0320.0000.0000.0000.000
126B130GLU-1-0.922-0.96313.482-0.130-0.1300.0000.0000.0000.000
127B131LYS10.9290.95811.222-0.021-0.0210.0000.0000.0000.000
128B132ASP-1-0.910-0.9579.1210.1900.1900.0000.0000.0000.000
129B133PHE0-0.063-0.0309.6740.1140.1140.0000.0000.0000.000
130B134MET00.0350.0054.313-0.162-0.083-0.001-0.009-0.0680.000
131B135PRO0-0.028-0.0026.9830.0560.0560.0000.0000.0000.000
132B136ILE00.0600.02110.0120.0650.0650.0000.0000.0000.000
133B137LYS10.9590.97513.2870.0100.0100.0000.0000.0000.000
134B138GLY00.017-0.01116.526-0.006-0.0060.0000.0000.0000.000
135B139SER00.0370.02412.3740.0170.0170.0000.0000.0000.000
136B140PHE0-0.016-0.00710.897-0.008-0.0080.0000.0000.0000.000
137B141LEU0-0.060-0.03315.6090.0100.0100.0000.0000.0000.000
138B142ALA00.0330.02317.9820.0060.0060.0000.0000.0000.000
139B143ARG10.9010.95113.4390.1320.1320.0000.0000.0000.000
140B144ASN0-0.014-0.01417.9040.0010.0010.0000.0000.0000.000
141B145ARG10.7380.83120.1830.0740.0740.0000.0000.0000.000
142B146LEU0-0.0180.00418.7060.0060.0060.0000.0000.0000.000
143B147VAL00.0250.01418.6850.0040.0040.0000.0000.0000.000
144B148ILE0-0.040-0.01321.4580.0060.0060.0000.0000.0000.000
145B149ALA0-0.003-0.00625.0080.0040.0040.0000.0000.0000.000
146B150LEU0-0.028-0.01122.1370.0030.0030.0000.0000.0000.000
147B151SER0-0.024-0.01924.2410.0030.0030.0000.0000.0000.000
148B152ASP-1-0.806-0.88526.723-0.026-0.0260.0000.0000.0000.000
149B153VAL0-0.006-0.00829.1590.0010.0010.0000.0000.0000.000
150B154VAL0-0.038-0.01325.647-0.002-0.0020.0000.0000.0000.000
151B155ILE00.0120.00726.4030.0020.0020.0000.0000.0000.000
152B156ILE0-0.035-0.03224.886-0.001-0.0010.0000.0000.0000.000
153B157PRO0-0.0060.00323.6800.0010.0010.0000.0000.0000.000
154B158GLN00.1460.10624.3650.0020.0020.0000.0000.0000.000
155B159ALA0-0.070-0.04824.410-0.002-0.0020.0000.0000.0000.000
156B160ASP-1-0.859-0.89624.972-0.025-0.0250.0000.0000.0000.000
157B161LEU00.0770.02526.799-0.002-0.0020.0000.0000.0000.000
158B162LYS10.8940.94126.7570.0140.0140.0000.0000.0000.000
159B163SER00.0440.03122.627-0.003-0.0030.0000.0000.0000.000
160B164GLY00.024-0.00720.6220.0010.0010.0000.0000.0000.000
161B165SER00.0720.03221.678-0.001-0.0010.0000.0000.0000.000
162B166MET00.0280.05523.4800.0010.0010.0000.0000.0000.000
163B167SER0-0.094-0.05523.3910.0020.0020.0000.0000.0000.000
164B168SER00.004-0.00922.429-0.001-0.0010.0000.0000.0000.000
165B169ALA00.0790.04325.0440.0010.0010.0000.0000.0000.000
166B170ARG10.9340.96927.1540.0250.0250.0000.0000.0000.000
167B171LEU0-0.050-0.01424.6760.0010.0010.0000.0000.0000.000
168B172ALA00.0550.02428.4130.0010.0010.0000.0000.0000.000
169B173GLN0-0.0010.00829.8060.0020.0020.0000.0000.0000.000
170B174LYS10.8950.96030.2750.0250.0250.0000.0000.0000.000
171B175TYR0-0.042-0.03528.3220.0010.0010.0000.0000.0000.000
172B176GLN0-0.0060.00132.6620.0000.0000.0000.0000.0000.000
173B177LYS10.8570.94029.1040.0310.0310.0000.0000.0000.000
174B178PRO00.0110.00932.2150.0000.0000.0000.0000.0000.000
175B179LEU00.0140.00728.699-0.001-0.0010.0000.0000.0000.000
176B180PHE00.0060.00430.5640.0010.0010.0000.0000.0000.000
177B181VAL00.0020.00329.800-0.001-0.0010.0000.0000.0000.000
178B182LEU0-0.0160.00127.3020.0010.0010.0000.0000.0000.000
179B183PRO00.0260.02031.158-0.001-0.0010.0000.0000.0000.000
180B184GLN0-0.027-0.02327.7840.0000.0000.0000.0000.0000.000
181B185ARG10.9870.99732.8020.0140.0140.0000.0000.0000.000
182B186LEU00.0650.01833.707-0.001-0.0010.0000.0000.0000.000
183B187ASN0-0.021-0.01333.2240.0000.0000.0000.0000.0000.000
184B188GLU-1-0.949-0.95929.422-0.018-0.0180.0000.0000.0000.000
185B189SER0-0.031-0.05728.131-0.002-0.0020.0000.0000.0000.000
186B190ASP-1-0.853-0.92929.468-0.015-0.0150.0000.0000.0000.000
187B191GLY0-0.033-0.03028.8040.0010.0010.0000.0000.0000.000
188B192THR00.0530.03128.2240.0000.0000.0000.0000.0000.000
189B193ASN00.003-0.00130.8540.0010.0010.0000.0000.0000.000
190B194GLU-1-0.878-0.92233.204-0.014-0.0140.0000.0000.0000.000
191B195LEU0-0.080-0.04829.7880.0000.0000.0000.0000.0000.000
192B196LEU0-0.031-0.02034.3180.0010.0010.0000.0000.0000.000
193B197GLU-1-0.962-0.96436.779-0.011-0.0110.0000.0000.0000.000
194B198LYS10.8710.93336.1960.0140.0140.0000.0000.0000.000
195B199GLY00.0210.01939.2720.0000.0000.0000.0000.0000.000
196B200GLN0-0.062-0.03534.888-0.001-0.0010.0000.0000.0000.000
197B201ALA0-0.025-0.01633.007-0.001-0.0010.0000.0000.0000.000
198B202GLN00.0210.02034.9490.0010.0010.0000.0000.0000.000
199B203GLY00.0210.01634.589-0.001-0.0010.0000.0000.0000.000
200B204ILE0-0.027-0.02130.6570.0000.0000.0000.0000.0000.000
201B205PHE00.022-0.00734.5300.0000.0000.0000.0000.0000.000
202B206ASN0-0.006-0.00536.7890.0000.0000.0000.0000.0000.000
203B207ILE00.0450.02630.4040.0000.0000.0000.0000.0000.000
204B208GLN00.0480.01933.8930.0000.0000.0000.0000.0000.000
205B209ASN00.0250.00835.8010.0000.0000.0000.0000.0000.000
206B210PHE00.0150.01430.7170.0000.0000.0000.0000.0000.000
207B211ILE00.0310.01130.7990.0000.0000.0000.0000.0000.000
208B212ASN00.0460.01434.019-0.001-0.0010.0000.0000.0000.000
209B213THR0-0.051-0.03137.2860.0000.0000.0000.0000.0000.000
210B214LEU00.0170.02431.4300.0000.0000.0000.0000.0000.000
211B215LEU0-0.014-0.01932.560-0.001-0.0010.0000.0000.0000.000
212B216LYS10.9090.96035.8800.0110.0110.0000.0000.0000.000
213B217ASP-1-0.923-0.93737.501-0.014-0.0140.0000.0000.0000.000
214B218TYR0-0.078-0.03834.017-0.001-0.0010.0000.0000.0000.000
215B219HIS0-0.042-0.01936.9510.0000.0000.0000.0000.0000.000
216B220LEU0-0.040-0.00132.4920.0000.0000.0000.0000.0000.000
217B221LYS10.9070.94637.0360.0120.0120.0000.0000.0000.000
218B222GLU-1-0.905-0.95836.614-0.010-0.0100.0000.0000.0000.000
219B223MET0-0.060-0.02133.7330.0000.0000.0000.0000.0000.000