Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: J36K9

Calculation Name: 4LUB-B-Xray319

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4LUB

Chain ID: B

ChEMBL ID:

UniProt ID: Q8DUV6

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 194
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2158194.036249
FMO2-HF: Nuclear repulsion 2083871.925774
FMO2-HF: Total energy -74322.110476
FMO2-MP2: Total energy -74544.689365


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:4:ACE )


Summations of interaction energy for fragment #1(B:4:ACE )
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.
-3.784-0.6871.671-2.293-2.474-0.002
Interaction energy analysis for fragmet #1(B:4:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.046 / q_NPA : 0.008
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].
3B6MET 0-0.031-0.0013.875-0.3961.223-0.003-0.864-0.752-0.002
4B7LYS 10.9640.9725.995-0.327-0.3270.0000.0000.0000.000
5B8ILE 00.0250.0146.2730.0310.0310.0000.0000.0000.000
6B9ALA 00.0210.0418.5840.0570.0570.0000.0000.0000.000
7B10TYR 0-0.007-0.00911.119-0.059-0.0590.0000.0000.0000.000
8B11LEU 00.0130.01714.1540.0290.0290.0000.0000.0000.000
9B12GLY 0-0.0020.01917.643-0.015-0.0150.0000.0000.0000.000
10B13PRO 00.000-0.02119.7960.0010.0010.0000.0000.0000.000
11B14SER 00.007-0.02820.500-0.016-0.0160.0000.0000.0000.000
12B15GLY 0-0.003-0.01221.3570.0070.0070.0000.0000.0000.000
13B16SER 0-0.0230.00720.112-0.005-0.0050.0000.0000.0000.000
14B17PHE 00.048-0.00221.399-0.013-0.0130.0000.0000.0000.000
15B18THR 00.0440.01416.130-0.017-0.0170.0000.0000.0000.000
16B19HIS 00.0680.07216.789-0.014-0.0140.0000.0000.0000.000
17B20ASN 0-0.004-0.01617.295-0.035-0.0350.0000.0000.0000.000
18B21VAL 00.0000.01315.564-0.022-0.0220.0000.0000.0000.000
19B22ALA 00.0280.00312.753-0.042-0.0420.0000.0000.0000.000
20B23LEU 0-0.025-0.01113.227-0.064-0.0640.0000.0000.0000.000
21B24HIS 0-0.099-0.04915.497-0.012-0.0120.0000.0000.0000.000
22B25ALA 0-0.0150.00111.681-0.017-0.0170.0000.0000.0000.000
23B26PHE 0-0.006-0.0077.090-0.090-0.0900.0000.0000.0000.000
24B27PRO 00.0270.02611.3240.0680.0680.0000.0000.0000.000
25B28ALA 0-0.066-0.03911.7030.0610.0610.0000.0000.0000.000
26B29ALA 0-0.0100.0079.0440.0120.0120.0000.0000.0000.000
27B30ASP -1-0.914-0.95910.0540.0820.0820.0000.0000.0000.000
28B31LEU 00.0130.00810.4920.0100.0100.0000.0000.0000.000
29B32LEU 0-0.048-0.04011.3580.0470.0470.0000.0000.0000.000
30B33PRO 0-0.0210.00413.694-0.004-0.0040.0000.0000.0000.000
31B34PHE 00.018-0.00312.4860.0340.0340.0000.0000.0000.000
32B35GLU -1-0.914-0.96217.3390.0360.0360.0000.0000.0000.000
33B36ASN 00.0180.00519.441-0.005-0.0050.0000.0000.0000.000
34B37ILE 00.0470.01817.4300.0080.0080.0000.0000.0000.000
35B38THR 0-0.023-0.03716.6740.0100.0100.0000.0000.0000.000
36B39GLU -1-0.835-0.91816.6460.1410.1410.0000.0000.0000.000
37B40VAL 0-0.080-0.02512.8870.0270.0270.0000.0000.0000.000
38B41ILE 0-0.013-0.01012.1960.0250.0250.0000.0000.0000.000
39B42LYS 10.8790.92912.035-0.076-0.0760.0000.0000.0000.000
40B43ALA 00.0060.01211.5060.0630.0630.0000.0000.0000.000
41B44TYR 0-0.027-0.0194.657-0.0170.0320.000-0.005-0.0430.000
42B45GLU -1-0.828-0.8698.5830.3790.3790.0000.0000.0000.000
43B46SER 0-0.060-0.02911.1980.0340.0340.0000.0000.0000.000
44B47LYS 10.8740.9397.687-0.768-0.7680.0000.0000.0000.000
45B48GLN 0-0.038-0.0138.5720.0550.0550.0000.0000.0000.000
46B49VAL 0-0.060-0.0336.952-0.022-0.0220.0000.0000.0000.000
47B50CYS 0-0.099-0.0212.2770.6320.2441.629-0.399-0.8420.007
48B51PHE 00.0540.0333.484-1.284-0.3650.035-0.486-0.468-0.003
49B52ALA 00.0040.0036.0350.1570.1570.0000.0000.0000.000
50B53ILE 0-0.032-0.0039.727-0.064-0.0640.0000.0000.0000.000
51B54VAL 00.026-0.00212.7690.0460.0460.0000.0000.0000.000
52B55PRO 0-0.0110.00616.101-0.022-0.0220.0000.0000.0000.000
53B56VAL 00.009-0.00517.8820.0160.0160.0000.0000.0000.000
54B57GLU -1-0.809-0.89020.683-0.056-0.0560.0000.0000.0000.000
55B58ASN 00.0050.00824.108-0.006-0.0060.0000.0000.0000.000
56B59SER 00.010-0.01226.8920.0030.0030.0000.0000.0000.000
57B60ILE 0-0.087-0.02629.8360.0030.0030.0000.0000.0000.000
58B61GLU -1-0.955-0.98629.252-0.033-0.0330.0000.0000.0000.000
59B62GLY 00.0310.03429.1060.0040.0040.0000.0000.0000.000
60B63SER 0-0.021-0.01525.327-0.007-0.0070.0000.0000.0000.000
61B64VAL 0-0.013-0.01122.3130.0080.0080.0000.0000.0000.000
62B65HIS 0-0.013-0.02623.2680.0060.0060.0000.0000.0000.000
63B66GLU -1-0.806-0.87921.4500.0220.0220.0000.0000.0000.000
64B67THR 00.0050.00017.6660.0140.0140.0000.0000.0000.000
65B68PHE 00.0280.00619.2740.0080.0080.0000.0000.0000.000
66B69ASP -1-0.818-0.89821.4540.0150.0150.0000.0000.0000.000
67B70TYR 0-0.051-0.07415.676-0.003-0.0030.0000.0000.0000.000
68B71LEU 00.0390.00314.5720.0160.0160.0000.0000.0000.000
69B72PHE 0-0.033-0.00717.8950.0070.0070.0000.0000.0000.000
70B73HIS 0-0.069-0.04020.8710.0110.0110.0000.0000.0000.000
71B74GLN 0-0.037-0.01618.7960.0180.0180.0000.0000.0000.000
72B75ALA 00.0440.05214.1230.0200.0200.0000.0000.0000.000
73B76LYS 10.9350.97512.186-0.201-0.2010.0000.0000.0000.000
74B77ILE 0-0.065-0.0288.7220.0580.0580.0000.0000.0000.000
75B78GLU -1-0.917-0.95410.645-0.084-0.0840.0000.0000.0000.000
76B79ALA 0-0.015-0.01810.921-0.045-0.0450.0000.0000.0000.000
77B80VAL 0-0.016-0.0058.2400.0090.0090.0000.0000.0000.000
78B81ALA 0-0.010-0.02511.591-0.048-0.0480.0000.0000.0000.000
79B82GLU -1-0.777-0.83513.596-0.118-0.1180.0000.0000.0000.000
80B83ILE 0-0.0140.00114.900-0.009-0.0090.0000.0000.0000.000
81B84ILE 0-0.017-0.01518.3020.0230.0230.0000.0000.0000.000
82B85LEU 0-0.028-0.01221.711-0.005-0.0050.0000.0000.0000.000
83B86PRO 0-0.008-0.00923.5040.0110.0110.0000.0000.0000.000
84B87ILE 0-0.043-0.01724.928-0.003-0.0030.0000.0000.0000.000
85B88LYS 10.9180.94728.6140.0830.0830.0000.0000.0000.000
86B89NME 00.0360.03632.0060.0020.0020.0000.0000.0000.000
87B172ACE 00.007-0.00628.7410.0000.0000.0000.0000.0000.000
88B173GLU -1-0.858-0.93329.086-0.044-0.0440.0000.0000.0000.000
89B174ASN 0-0.042-0.02529.022-0.010-0.0100.0000.0000.0000.000
90B175TYR 00.0030.00826.569-0.010-0.0100.0000.0000.0000.000
91B176THR 00.0210.01822.1260.0110.0110.0000.0000.0000.000
92B177ARG 10.7240.84221.0180.0930.0930.0000.0000.0000.000
93B178PHE 00.018-0.00216.8340.0180.0180.0000.0000.0000.000
94B179TRP 0-0.019-0.01814.401-0.012-0.0120.0000.0000.0000.000
95B180VAL 00.000-0.0098.8870.0150.0150.0000.0000.0000.000
96B181LEU 0-0.020-0.01710.011-0.005-0.0050.0000.0000.0000.000
97B182GLY 00.024-0.0066.240-0.063-0.0630.0000.0000.0000.000
98B183ASP -1-0.962-0.9765.0550.4530.4530.0000.0000.0000.000
99B184GLU -1-0.926-0.9543.559-2.435-1.5370.010-0.539-0.369-0.004
100B185THR 00.019-0.0066.459-0.123-0.1230.0000.0000.0000.000
101B186PRO 0-0.0080.0197.585-0.142-0.1420.0000.0000.0000.000
102B187THR 0-0.027-0.0268.7160.2720.2720.0000.0000.0000.000
103B188ILE 00.0110.00811.724-0.006-0.0060.0000.0000.0000.000
104B189HIS 0-0.029-0.00914.3910.0510.0510.0000.0000.0000.000
105B190LEU 0-0.0080.00117.1040.0370.0370.0000.0000.0000.000
106B191LYS 10.9470.95819.8190.1340.1340.0000.0000.0000.000
107B192GLU -1-0.871-0.91819.585-0.223-0.2230.0000.0000.0000.000
108B193GLU -1-0.881-0.91121.847-0.110-0.1100.0000.0000.0000.000
109B194ASP -1-0.815-0.92322.476-0.103-0.1030.0000.0000.0000.000
110B195GLN 0-0.036-0.02218.834-0.028-0.0280.0000.0000.0000.000
111B196LYS 10.9300.99320.0850.1270.1270.0000.0000.0000.000
112B197ILE 0-0.019-0.00519.522-0.014-0.0140.0000.0000.0000.000
113B198SER 0-0.020-0.00519.4510.0030.0030.0000.0000.0000.000
114B199LEU 0-0.035-0.01920.2800.0060.0060.0000.0000.0000.000
115B200ALA 00.0050.00722.5610.0000.0000.0000.0000.0000.000
116B201LEU 0-0.018-0.00923.9960.0060.0060.0000.0000.0000.000
117B202THR 00.0210.00427.3470.0020.0020.0000.0000.0000.000
118B203LEU 0-0.019-0.00329.787-0.001-0.0010.0000.0000.0000.000
119B204PRO 00.0460.01533.2850.0030.0030.0000.0000.0000.000
120B205ASP -1-0.924-0.95735.7850.0080.0080.0000.0000.0000.000
121B206ASN 0-0.034-0.02232.799-0.001-0.0010.0000.0000.0000.000
122B207LEU 00.0370.01635.368-0.002-0.0020.0000.0000.0000.000
123B208PRO 00.023-0.00636.288-0.002-0.0020.0000.0000.0000.000
124B209GLY 0-0.0110.00537.349-0.002-0.0020.0000.0000.0000.000
125B210ALA 0-0.007-0.00837.083-0.001-0.0010.0000.0000.0000.000
126B211LEU 00.0380.02032.550-0.001-0.0010.0000.0000.0000.000
127B212TYR 00.0200.00035.309-0.002-0.0020.0000.0000.0000.000
128B213LYS 10.9450.99436.8430.0050.0050.0000.0000.0000.000
129B214ALA 00.0570.03431.649-0.001-0.0010.0000.0000.0000.000
130B215LEU 00.029-0.00231.889-0.003-0.0030.0000.0000.0000.000
131B216SER 0-0.025-0.02833.921-0.003-0.0030.0000.0000.0000.000
132B217THR 0-0.045-0.00331.420-0.001-0.0010.0000.0000.0000.000
133B218PHE 00.0120.00426.595-0.001-0.0010.0000.0000.0000.000
134B219ALA 00.0170.01531.962-0.003-0.0030.0000.0000.0000.000
135B220TRP 0-0.088-0.04135.110-0.003-0.0030.0000.0000.0000.000
136B221ARG 10.7720.87531.4090.0320.0320.0000.0000.0000.000
137B222GLY 0-0.013-0.00733.548-0.003-0.0030.0000.0000.0000.000
138B223ILE 0-0.067-0.02027.685-0.004-0.0040.0000.0000.0000.000
139B224ASP -1-0.852-0.92030.595-0.054-0.0540.0000.0000.0000.000
140B225LEU 0-0.085-0.05028.932-0.004-0.0040.0000.0000.0000.000
141B226THR 0-0.031-0.02326.664-0.001-0.0010.0000.0000.0000.000
142B227LYS 10.8280.90523.7110.0610.0610.0000.0000.0000.000
143B228ILE 0-0.001-0.00828.2110.0020.0020.0000.0000.0000.000
144B229GLU -1-0.884-0.93727.404-0.031-0.0310.0000.0000.0000.000
145B230SER 0-0.047-0.00328.5910.0020.0020.0000.0000.0000.000
146B231ARG 10.8520.91325.9590.0030.0030.0000.0000.0000.000
147B232PRO 0-0.010-0.01829.3530.0020.0020.0000.0000.0000.000
148B233LEU 00.0120.01228.5310.0020.0020.0000.0000.0000.000
149B234LYS 10.8520.93127.667-0.016-0.0160.0000.0000.0000.000
150B235THR 00.012-0.02431.5430.0030.0030.0000.0000.0000.000
151B236ILE 0-0.026-0.01534.2240.0000.0000.0000.0000.0000.000
152B237LEU 0-0.015-0.02036.547-0.001-0.0010.0000.0000.0000.000
153B238GLY 00.0010.00037.5670.0000.0000.0000.0000.0000.000
154B239GLU -1-0.857-0.86634.4450.0150.0150.0000.0000.0000.000
155B240TYR 0-0.050-0.04331.7910.0010.0010.0000.0000.0000.000
156B241PHE 0-0.0020.01424.1320.0010.0010.0000.0000.0000.000
157B242PHE 0-0.015-0.03428.423-0.002-0.0020.0000.0000.0000.000
158B243ILE 0-0.0050.00023.2210.0010.0010.0000.0000.0000.000
159B244ILE 0-0.018-0.00625.184-0.001-0.0010.0000.0000.0000.000
160B245ASP -1-0.749-0.85823.330-0.083-0.0830.0000.0000.0000.000
161B246PHE 0-0.006-0.01924.3120.0080.0080.0000.0000.0000.000
162B247GLU -1-0.869-0.93324.145-0.095-0.0950.0000.0000.0000.000
163B248ASN 0-0.104-0.07919.5550.0240.0240.0000.0000.0000.000
164B249HIS 00.0280.01822.480-0.013-0.0130.0000.0000.0000.000
165B250ASN 0-0.035-0.01624.907-0.002-0.0020.0000.0000.0000.000
166B251GLU -1-0.785-0.90419.050-0.142-0.1420.0000.0000.0000.000
167B252LYS 10.9100.96023.4010.0640.0640.0000.0000.0000.000
168B253LEU 0-0.011-0.00925.7410.0080.0080.0000.0000.0000.000
169B254VAL 00.0840.03923.3640.0080.0080.0000.0000.0000.000
170B255SER 0-0.050-0.02623.4430.0070.0070.0000.0000.0000.000
171B256PHE 0-0.004-0.00325.2720.0060.0060.0000.0000.0000.000
172B257ALA 00.0160.01627.9370.0060.0060.0000.0000.0000.000
173B258LEU 0-0.006-0.00722.6860.0050.0050.0000.0000.0000.000
174B259GLU -1-0.944-0.97427.017-0.014-0.0140.0000.0000.0000.000
175B260GLU -1-0.788-0.88828.955-0.017-0.0170.0000.0000.0000.000
176B261LEU 0-0.0160.00127.5460.0040.0040.0000.0000.0000.000
177B262THR 00.0120.00528.0340.0050.0050.0000.0000.0000.000
178B263SER 0-0.118-0.05330.4120.0030.0030.0000.0000.0000.000
179B264ILE 0-0.056-0.02333.6110.0010.0010.0000.0000.0000.000
180B265GLY 0-0.024-0.00633.3670.0010.0010.0000.0000.0000.000
181B266ILE 0-0.070-0.03629.8360.0020.0020.0000.0000.0000.000
182B267HIS 00.0140.01827.358-0.001-0.0010.0000.0000.0000.000
183B268TYR 0-0.006-0.01822.378-0.004-0.0040.0000.0000.0000.000
184B269LYS 10.8410.91917.833-0.053-0.0530.0000.0000.0000.000
185B270ILE 00.016-0.00817.172-0.009-0.0090.0000.0000.0000.000
186B271LEU 0-0.028-0.01217.1260.0090.0090.0000.0000.0000.000
187B272GLY 00.0700.03515.125-0.009-0.0090.0000.0000.0000.000
188B273LYS 10.9320.98114.9280.1240.1240.0000.0000.0000.000
189B274TYR 0-0.019-0.00914.527-0.043-0.0430.0000.0000.0000.000
190B275ALA 00.0730.04715.6240.0310.0310.0000.0000.0000.000
191B276VAL 0-0.018-0.01617.189-0.015-0.0150.0000.0000.0000.000
192B277TYR 00.0450.01315.151-0.008-0.0080.0000.0000.0000.000
193B278ARG 10.7830.86920.1670.1270.1270.0000.0000.0000.000
194B279NME 0-0.052-0.02821.651-0.001-0.0010.0000.0000.0000.000