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: 43V8N

Calculation Name: 4LUB-B-Xray372

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: 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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2139051.494491
FMO2-HF: Nuclear repulsion 2065071.227926
FMO2-HF: Total energy -73980.266565
FMO2-MP2: Total energy -74201.762258


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:THR)


Summations of interaction energy for fragment #1(B:5:THR)
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.
-8.229-4.1189.13-6.017-7.2240.012
Interaction energy analysis for fragmet #1(B:5:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.047 / q_NPA : -0.003
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].
3B7LYS10.9610.9693.849-2.193-0.386-0.017-0.912-0.8780.005
4B8ILE00.0230.0132.9790.7311.2330.080-0.134-0.4480.000
5B9ALA00.0230.0426.463-0.225-0.2250.0000.0000.0000.000
6B10TYR0-0.008-0.0099.8990.0250.0250.0000.0000.0000.000
7B11LEU00.0150.01812.395-0.020-0.0200.0000.0000.0000.000
8B12GLY0-0.0020.01816.137-0.020-0.0200.0000.0000.0000.000
9B13PRO0-0.003-0.02117.9370.0010.0010.0000.0000.0000.000
10B14SER00.008-0.02917.6810.0060.0060.0000.0000.0000.000
11B15GLY0-0.004-0.01318.174-0.002-0.0020.0000.0000.0000.000
12B16SER0-0.0250.00717.7670.0010.0010.0000.0000.0000.000
13B17PHE00.049-0.00118.3540.0000.0000.0000.0000.0000.000
14B18THR00.0490.01613.9180.0040.0040.0000.0000.0000.000
15B19HIS00.0650.07113.4200.0450.0450.0000.0000.0000.000
16B20ASN0-0.004-0.01613.766-0.009-0.0090.0000.0000.0000.000
17B21VAL00.0050.01412.7370.0050.0050.0000.0000.0000.000
18B22ALA00.0230.0029.5820.0580.0580.0000.0000.0000.000
19B23LEU0-0.021-0.0119.0850.0130.0130.0000.0000.0000.000
20B24HIS0-0.103-0.05110.125-0.028-0.0280.0000.0000.0000.000
21B25ALA0-0.0170.0008.2940.0270.0270.0000.0000.0000.000
22B26PHE0-0.005-0.0073.413-0.9050.1150.048-0.344-0.7240.001
23B27PRO00.0270.0266.035-0.493-0.4930.0000.0000.0000.000
24B28ALA0-0.066-0.0405.547-0.055-0.0550.0000.0000.0000.000
25B29ALA0-0.0110.0073.605-0.555-0.4380.001-0.034-0.0840.000
26B30ASP-1-0.912-0.9575.5530.3860.3860.0000.0000.0000.000
27B31LEU00.0130.0077.4890.1950.1950.0000.0000.0000.000
28B32LEU0-0.051-0.0409.7340.0270.0270.0000.0000.0000.000
29B33PRO0-0.0140.00611.9260.0700.0700.0000.0000.0000.000
30B34PHE00.013-0.00511.8710.0110.0110.0000.0000.0000.000
31B35GLU-1-0.912-0.96116.5140.1300.1300.0000.0000.0000.000
32B36ASN00.0150.00419.0720.0010.0010.0000.0000.0000.000
33B37ILE00.0470.01817.3970.0250.0250.0000.0000.0000.000
34B38THR0-0.021-0.03716.9790.0330.0330.0000.0000.0000.000
35B39GLU-1-0.838-0.92017.6680.2390.2390.0000.0000.0000.000
36B40VAL0-0.079-0.02512.4010.0440.0440.0000.0000.0000.000
37B41ILE0-0.014-0.01012.7230.0940.0940.0000.0000.0000.000
38B42LYS10.8810.93013.418-0.150-0.1500.0000.0000.0000.000
39B43ALA00.0050.01212.0930.0220.0220.0000.0000.0000.000
40B44TYR0-0.025-0.0196.3640.0250.0250.0000.0000.0000.000
41B45GLU-1-0.830-0.87010.3780.3160.3160.0000.0000.0000.000
42B46SER0-0.062-0.03013.135-0.061-0.0610.0000.0000.0000.000
43B47LYS10.8770.9409.630-0.398-0.3980.0000.0000.0000.000
44B48GLN0-0.041-0.0149.9090.0000.0000.0000.0000.0000.000
45B49VAL0-0.063-0.0357.192-0.014-0.0140.0000.0000.0000.000
46B50CYS0-0.075-0.0122.396-0.246-1.3724.794-1.516-2.1520.010
47B51PHE00.0410.0282.138-3.837-2.0464.224-3.077-2.938-0.004
48B52ALA00.0090.0055.866-0.067-0.0670.0000.0000.0000.000
49B53ILE0-0.039-0.0067.816-0.042-0.0420.0000.0000.0000.000
50B54VAL00.0290.00011.284-0.048-0.0480.0000.0000.0000.000
51B55PRO0-0.0100.00715.0140.0040.0040.0000.0000.0000.000
52B56VAL00.012-0.00417.229-0.001-0.0010.0000.0000.0000.000
53B57GLU-1-0.809-0.89119.9330.1030.1030.0000.0000.0000.000
54B58ASN00.0130.01322.842-0.001-0.0010.0000.0000.0000.000
55B59SER00.005-0.01425.384-0.004-0.0040.0000.0000.0000.000
56B60ILE0-0.089-0.03028.176-0.006-0.0060.0000.0000.0000.000
57B61GLU-1-0.956-0.98527.7990.0890.0890.0000.0000.0000.000
58B62GLY00.0280.03328.184-0.003-0.0030.0000.0000.0000.000
59B63SER0-0.018-0.01424.7700.0130.0130.0000.0000.0000.000
60B64VAL0-0.013-0.00921.750-0.007-0.0070.0000.0000.0000.000
61B65HIS0-0.014-0.02623.3010.0080.0080.0000.0000.0000.000
62B66GLU-1-0.809-0.88121.9430.1640.1640.0000.0000.0000.000
63B67THR00.0110.00317.9170.0090.0090.0000.0000.0000.000
64B68PHE00.0260.00520.0990.0090.0090.0000.0000.0000.000
65B69ASP-1-0.819-0.89822.2140.1070.1070.0000.0000.0000.000
66B70TYR0-0.049-0.07317.169-0.019-0.0190.0000.0000.0000.000
67B71LEU00.0350.00115.4860.0030.0030.0000.0000.0000.000
68B72PHE0-0.033-0.00719.059-0.007-0.0070.0000.0000.0000.000
69B73HIS0-0.069-0.04022.155-0.006-0.0060.0000.0000.0000.000
70B74GLN0-0.036-0.01520.504-0.002-0.0020.0000.0000.0000.000
71B75ALA00.0460.05415.6650.0050.0050.0000.0000.0000.000
72B76LYS10.9350.97414.002-0.148-0.1480.0000.0000.0000.000
73B77ILE0-0.066-0.0289.8520.0050.0050.0000.0000.0000.000
74B78GLU-1-0.917-0.95311.7680.0750.0750.0000.0000.0000.000
75B79ALA0-0.011-0.01611.5140.0560.0560.0000.0000.0000.000
76B80VAL0-0.022-0.0097.927-0.026-0.0260.0000.0000.0000.000
77B81ALA0-0.009-0.02510.5830.0200.0200.0000.0000.0000.000
78B82GLU-1-0.776-0.83512.3630.1940.1940.0000.0000.0000.000
79B83ILE0-0.017-0.00211.6610.0020.0020.0000.0000.0000.000
80B84ILE0-0.022-0.01615.871-0.016-0.0160.0000.0000.0000.000
81B85LEU0-0.036-0.01718.406-0.004-0.0040.0000.0000.0000.000
82B86PRO0-0.021-0.01620.668-0.008-0.0080.0000.0000.0000.000
83B87ILE0-0.029-0.00822.3740.0020.0020.0000.0000.0000.000
84B88LYS10.9510.97925.660-0.080-0.0800.0000.0000.0000.000
85B173GLU-1-0.856-0.93527.1940.0690.0690.0000.0000.0000.000
86B174ASN0-0.047-0.03426.7360.0100.0100.0000.0000.0000.000
87B175TYR00.0030.00623.9810.0040.0040.0000.0000.0000.000
88B176THR00.0250.02220.289-0.007-0.0070.0000.0000.0000.000
89B177ARG10.7210.84219.567-0.142-0.1420.0000.0000.0000.000
90B178PHE00.018-0.00214.876-0.010-0.0100.0000.0000.0000.000
91B179TRP0-0.017-0.01713.9570.0080.0080.0000.0000.0000.000
92B180VAL0-0.009-0.0127.4000.0290.0290.0000.0000.0000.000
93B181LEU0-0.015-0.0169.994-0.064-0.0640.0000.0000.0000.000
94B182GLY00.020-0.0086.8470.2570.2570.0000.0000.0000.000
95B183ASP-1-0.953-0.9726.434-0.150-0.1500.0000.0000.0000.000
96B184GLU-1-0.929-0.9555.768-1.775-1.7750.0000.0000.0000.000
97B185THR00.016-0.0077.0950.1420.1420.0000.0000.0000.000
98B186PRO0-0.0090.0185.044-0.007-0.0070.0000.0000.0000.000
99B187THR0-0.028-0.0276.391-0.359-0.3590.0000.0000.0000.000
100B188ILE00.0130.0107.7930.2450.2450.0000.0000.0000.000
101B189HIS0-0.029-0.00810.281-0.103-0.1030.0000.0000.0000.000
102B190LEU0-0.0110.00012.514-0.058-0.0580.0000.0000.0000.000
103B191LYS10.9450.95715.404-0.114-0.1140.0000.0000.0000.000
104B192GLU-1-0.871-0.91917.3740.1680.1680.0000.0000.0000.000
105B193GLU-1-0.882-0.91118.8310.1070.1070.0000.0000.0000.000
106B194ASP-1-0.810-0.92120.4290.0900.0900.0000.0000.0000.000
107B195GLN0-0.034-0.02117.3460.0210.0210.0000.0000.0000.000
108B196LYS10.9290.99219.455-0.135-0.1350.0000.0000.0000.000
109B197ILE0-0.020-0.00519.4730.0050.0050.0000.0000.0000.000
110B198SER0-0.020-0.00419.7790.0010.0010.0000.0000.0000.000
111B199LEU0-0.034-0.01920.8420.0010.0010.0000.0000.0000.000
112B200ALA00.0040.00723.4070.0020.0020.0000.0000.0000.000
113B201LEU0-0.018-0.00924.922-0.005-0.0050.0000.0000.0000.000
114B202THR00.0200.00428.3550.0010.0010.0000.0000.0000.000
115B203LEU0-0.016-0.00230.988-0.002-0.0020.0000.0000.0000.000
116B204PRO00.0450.01534.4610.0010.0010.0000.0000.0000.000
117B205ASP-1-0.924-0.95737.1040.0350.0350.0000.0000.0000.000
118B206ASN0-0.033-0.02234.1760.0030.0030.0000.0000.0000.000
119B207LEU00.0350.01636.6600.0010.0010.0000.0000.0000.000
120B208PRO00.025-0.00537.2140.0000.0000.0000.0000.0000.000
121B209GLY0-0.0120.00438.2810.0000.0000.0000.0000.0000.000
122B210ALA0-0.007-0.00738.097-0.002-0.0020.0000.0000.0000.000
123B211LEU00.0380.02133.1900.0000.0000.0000.0000.0000.000
124B212TYR00.0200.00035.9530.0010.0010.0000.0000.0000.000
125B213LYS10.9450.99437.718-0.033-0.0330.0000.0000.0000.000
126B214ALA00.0570.03432.392-0.001-0.0010.0000.0000.0000.000
127B215LEU00.029-0.00232.3550.0010.0010.0000.0000.0000.000
128B216SER0-0.026-0.02834.420-0.001-0.0010.0000.0000.0000.000
129B217THR0-0.045-0.00332.313-0.002-0.0020.0000.0000.0000.000
130B218PHE00.0160.00527.269-0.002-0.0020.0000.0000.0000.000
131B219ALA00.0100.01332.550-0.001-0.0010.0000.0000.0000.000
132B220TRP0-0.085-0.04135.524-0.002-0.0020.0000.0000.0000.000
133B221ARG10.7740.87632.246-0.035-0.0350.0000.0000.0000.000
134B222GLY0-0.014-0.00833.7830.0000.0000.0000.0000.0000.000
135B223ILE0-0.066-0.01928.0980.0020.0020.0000.0000.0000.000
136B224ASP-1-0.852-0.91930.1470.0550.0550.0000.0000.0000.000
137B225LEU0-0.085-0.04929.0050.0050.0050.0000.0000.0000.000
138B226THR0-0.031-0.02426.3030.0020.0020.0000.0000.0000.000
139B227LYS10.8280.90523.479-0.123-0.1230.0000.0000.0000.000
140B228ILE00.002-0.00728.359-0.001-0.0010.0000.0000.0000.000
141B229GLU-1-0.887-0.93727.7110.0900.0900.0000.0000.0000.000
142B230SER0-0.048-0.00429.1730.0020.0020.0000.0000.0000.000
143B231ARG10.8530.91426.756-0.097-0.0970.0000.0000.0000.000
144B232PRO0-0.012-0.01830.210-0.004-0.0040.0000.0000.0000.000
145B233LEU00.0130.01229.8990.0070.0070.0000.0000.0000.000
146B234LYS10.8520.93128.919-0.092-0.0920.0000.0000.0000.000
147B235THR00.012-0.02532.9240.0010.0010.0000.0000.0000.000
148B236ILE0-0.026-0.01435.717-0.002-0.0020.0000.0000.0000.000
149B237LEU0-0.015-0.02037.8220.0020.0020.0000.0000.0000.000
150B238GLY00.001-0.00138.662-0.003-0.0030.0000.0000.0000.000
151B239GLU-1-0.856-0.86635.7610.0510.0510.0000.0000.0000.000
152B240TYR0-0.052-0.04332.8210.0010.0010.0000.0000.0000.000
153B241PHE0-0.0030.01425.068-0.003-0.0030.0000.0000.0000.000
154B242PHE0-0.011-0.03229.3230.0010.0010.0000.0000.0000.000
155B243ILE0-0.010-0.00223.7320.0020.0020.0000.0000.0000.000
156B244ILE0-0.017-0.00725.722-0.005-0.0050.0000.0000.0000.000
157B245ASP-1-0.750-0.85823.4450.1320.1320.0000.0000.0000.000
158B246PHE0-0.004-0.01924.386-0.009-0.0090.0000.0000.0000.000
159B247GLU-1-0.869-0.93324.1170.0820.0820.0000.0000.0000.000
160B248ASN0-0.105-0.08019.576-0.015-0.0150.0000.0000.0000.000
161B249HIS00.0280.01922.180-0.004-0.0040.0000.0000.0000.000
162B250ASN0-0.035-0.01624.320-0.008-0.0080.0000.0000.0000.000
163B251GLU-1-0.785-0.90319.4170.0500.0500.0000.0000.0000.000
164B252LYS10.9070.95823.832-0.012-0.0120.0000.0000.0000.000
165B253LEU0-0.009-0.00826.531-0.002-0.0020.0000.0000.0000.000
166B254VAL00.0880.04024.072-0.001-0.0010.0000.0000.0000.000
167B255SER0-0.055-0.02724.6020.0000.0000.0000.0000.0000.000
168B256PHE0-0.005-0.00326.469-0.002-0.0020.0000.0000.0000.000
169B257ALA00.0260.01928.833-0.001-0.0010.0000.0000.0000.000
170B258LEU0-0.015-0.01023.7320.0010.0010.0000.0000.0000.000
171B259GLU-1-0.942-0.97328.2110.0180.0180.0000.0000.0000.000
172B260GLU-1-0.788-0.88730.4050.0300.0300.0000.0000.0000.000
173B261LEU0-0.0170.00028.5460.0000.0000.0000.0000.0000.000
174B262THR00.0110.00429.5080.0000.0000.0000.0000.0000.000
175B263SER0-0.114-0.05231.894-0.002-0.0020.0000.0000.0000.000
176B264ILE0-0.057-0.02334.980-0.001-0.0010.0000.0000.0000.000
177B265GLY0-0.024-0.00634.8410.0000.0000.0000.0000.0000.000
178B266ILE0-0.066-0.03530.8790.0020.0020.0000.0000.0000.000
179B267HIS00.0150.01828.7720.0000.0000.0000.0000.0000.000
180B268TYR0-0.009-0.01923.6940.0040.0040.0000.0000.0000.000
181B269LYS10.8420.92019.199-0.147-0.1470.0000.0000.0000.000
182B270ILE00.014-0.00818.0250.0020.0020.0000.0000.0000.000
183B271LEU0-0.027-0.01218.0460.0070.0070.0000.0000.0000.000
184B272GLY00.0770.03715.6140.0290.0290.0000.0000.0000.000
185B273LYS10.9280.97915.382-0.065-0.0650.0000.0000.0000.000
186B274TYR0-0.023-0.01014.4590.0100.0100.0000.0000.0000.000
187B275ALA00.0730.04714.465-0.024-0.0240.0000.0000.0000.000
188B276VAL0-0.017-0.01615.6710.0340.0340.0000.0000.0000.000
189B277TYR00.0400.01312.8040.0080.0080.0000.0000.0000.000
190B278ARG10.7670.85817.158-0.124-0.1240.0000.0000.0000.000