Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 4LLVN

Calculation Name: 5T58-N-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5T58

Chain ID: N

ChEMBL ID:

UniProt ID: Q6CLK3

Base Structure: X-ray

Registration Date: 2023-09-27

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 196
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1365360.547564
FMO2-HF: Nuclear repulsion 1285637.852556
FMO2-HF: Total energy -79722.695007
FMO2-MP2: Total energy -79956.479084


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(N:5:VAL)


Summations of interaction energy for fragment #1(N:5:VAL)
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.
-1.8481.2430.118-1.699-1.508-0.001
Interaction energy analysis for fragmet #1(N:5:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / q_NPA : -0.004
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].
3N7LYS10.8160.8713.208-1.0741.9560.119-1.697-1.451-0.001
4N8LEU00.0250.0315.2640.4620.523-0.001-0.002-0.0570.000
5N9ASP-1-0.798-0.8809.026-1.152-1.1520.0000.0000.0000.000
6N10ILE00.0200.01011.1940.0780.0780.0000.0000.0000.000
7N11THR00.0010.00314.5770.0250.0250.0000.0000.0000.000
8N12GLN00.0680.00617.939-0.008-0.0080.0000.0000.0000.000
9N13LYS10.9330.96620.1420.2390.2390.0000.0000.0000.000
10N14GLN00.0230.01317.263-0.002-0.0020.0000.0000.0000.000
11N15LEU00.0480.03216.8920.0080.0080.0000.0000.0000.000
12N16ARG10.8150.89119.4560.2110.2110.0000.0000.0000.000
13N17PHE0-0.068-0.02123.0850.0220.0220.0000.0000.0000.000
14N18LEU00.0060.00518.1320.0090.0090.0000.0000.0000.000
15N19HIS00.0680.04421.9240.0300.0300.0000.0000.0000.000
16N20LYS10.8050.87923.1880.1900.1900.0000.0000.0000.000
17N21GLN00.0450.02424.153-0.010-0.0100.0000.0000.0000.000
18N22PHE0-0.044-0.02919.7420.0010.0010.0000.0000.0000.000
19N23LYS10.8630.91725.7200.1490.1490.0000.0000.0000.000
20N24GLU-1-0.943-0.95828.492-0.163-0.1630.0000.0000.0000.000
21N25ILE00.0280.01427.1280.0090.0090.0000.0000.0000.000
22N26ILE0-0.046-0.02026.8060.0110.0110.0000.0000.0000.000
23N27ASP-1-0.848-0.92330.960-0.105-0.1050.0000.0000.0000.000
24N28GLU-1-0.963-0.97533.517-0.128-0.1280.0000.0000.0000.000
25N29LYS10.9190.95432.4690.1190.1190.0000.0000.0000.000
26N30VAL0-0.003-0.01134.0400.0080.0080.0000.0000.0000.000
27N31ARG10.8010.87436.5940.1020.1020.0000.0000.0000.000
28N32THR0-0.086-0.03937.7880.0030.0030.0000.0000.0000.000
29N33ALA0-0.103-0.04638.1430.0030.0030.0000.0000.0000.000
30N34LEU0-0.028-0.00739.0580.0050.0050.0000.0000.0000.000
31N35PRO0-0.014-0.01741.974-0.003-0.0030.0000.0000.0000.000
32N36GLU-1-0.805-0.89041.890-0.084-0.0840.0000.0000.0000.000
33N37SER0-0.088-0.03543.4090.0000.0000.0000.0000.0000.000
34N38SER00.0160.01241.476-0.003-0.0030.0000.0000.0000.000
35N39GLU-1-0.947-0.96241.793-0.059-0.0590.0000.0000.0000.000
36N40ASP-1-0.846-0.90442.002-0.049-0.0490.0000.0000.0000.000
37N41ASP-1-0.913-0.95641.963-0.038-0.0380.0000.0000.0000.000
38N42GLN0-0.084-0.04340.1860.0000.0000.0000.0000.0000.000
39N43VAL0-0.047-0.02139.5420.0000.0000.0000.0000.0000.000
40N44SER00.012-0.01238.420-0.002-0.0020.0000.0000.0000.000
41N45GLN0-0.021-0.03636.865-0.003-0.0030.0000.0000.0000.000
42N46GLU-1-0.850-0.91233.771-0.065-0.0650.0000.0000.0000.000
43N47ILE00.0330.01632.871-0.005-0.0050.0000.0000.0000.000
44N48GLN0-0.011-0.00532.024-0.007-0.0070.0000.0000.0000.000
45N49LEU00.0190.01931.002-0.009-0.0090.0000.0000.0000.000
46N50GLN0-0.079-0.05129.310-0.010-0.0100.0000.0000.0000.000
47N51LEU0-0.013-0.01227.637-0.009-0.0090.0000.0000.0000.000
48N52ASP-1-0.829-0.89526.300-0.147-0.1470.0000.0000.0000.000
49N53GLN0-0.021-0.04325.145-0.006-0.0060.0000.0000.0000.000
50N54PHE00.0080.01322.545-0.013-0.0130.0000.0000.0000.000
51N55LEU0-0.014-0.01621.812-0.024-0.0240.0000.0000.0000.000
52N56MET0-0.063-0.00920.589-0.024-0.0240.0000.0000.0000.000
53N57ASP-1-0.874-0.92719.056-0.139-0.1390.0000.0000.0000.000
54N58VAL0-0.031-0.01917.290-0.032-0.0320.0000.0000.0000.000
55N59LEU0-0.043-0.03216.001-0.062-0.0620.0000.0000.0000.000
56N60GLU-1-0.911-0.95015.094-0.228-0.2280.0000.0000.0000.000
57N61MET00.0090.00613.214-0.022-0.0220.0000.0000.0000.000
58N62ALA0-0.0100.00311.423-0.087-0.0870.0000.0000.0000.000
59N63GLY0-0.072-0.03610.409-0.181-0.1810.0000.0000.0000.000
60N64GLU-1-0.983-0.9868.728-0.206-0.2060.0000.0000.0000.000
61N65SER0-0.047-0.0444.8520.1950.1950.0000.0000.0000.000
62N66MET0-0.091-0.0306.229-0.372-0.3720.0000.0000.0000.000
63N67ASN0-0.086-0.0447.8660.1590.1590.0000.0000.0000.000
64N68VAL00.008-0.00510.130-0.026-0.0260.0000.0000.0000.000
65N69VAL0-0.061-0.03511.877-0.003-0.0030.0000.0000.0000.000
66N70ASP-1-0.871-0.93614.405-0.276-0.2760.0000.0000.0000.000
67N71ALA00.0240.01916.9010.0460.0460.0000.0000.0000.000
68N72GLY00.0290.00514.693-0.040-0.0400.0000.0000.0000.000
69N73LYS10.9030.9505.7410.9660.9660.0000.0000.0000.000
70N74GLY00.1000.05711.402-0.057-0.0570.0000.0000.0000.000
71N75THR0-0.052-0.03812.3280.0620.0620.0000.0000.0000.000
72N76THR0-0.019-0.01815.821-0.029-0.0290.0000.0000.0000.000
73N77VAL00.0300.02214.4170.0170.0170.0000.0000.0000.000
74N78LYS10.9280.94415.5670.2040.2040.0000.0000.0000.000
75N79SER00.0050.00519.4440.0100.0100.0000.0000.0000.000
76N80VAL00.000-0.00220.3690.0130.0130.0000.0000.0000.000
77N81ILE0-0.0070.01119.7080.0050.0050.0000.0000.0000.000
78N82GLN00.0290.01022.3670.0190.0190.0000.0000.0000.000
79N83GLU-1-0.847-0.90625.285-0.157-0.1570.0000.0000.0000.000
80N84VAL0-0.035-0.02524.9270.0070.0070.0000.0000.0000.000
81N85GLN00.0450.02526.9510.0010.0010.0000.0000.0000.000
82N86LYS10.7260.83228.6970.0940.0940.0000.0000.0000.000
83N87GLU-1-0.822-0.88429.730-0.150-0.1500.0000.0000.0000.000
84N88TYR0-0.0170.00227.5390.0020.0020.0000.0000.0000.000
85N89THR00.013-0.01433.4220.0070.0070.0000.0000.0000.000
86N90GLU-1-0.847-0.90032.835-0.075-0.0750.0000.0000.0000.000
87N91PRO00.0080.01835.9840.0000.0000.0000.0000.0000.000
88N92PHE00.008-0.01033.9090.0030.0030.0000.0000.0000.000
89N93ASP-1-0.808-0.90839.846-0.038-0.0380.0000.0000.0000.000
90N94VAL00.0180.00143.5070.0030.0030.0000.0000.0000.000
91N95GLU-1-0.895-0.92945.854-0.031-0.0310.0000.0000.0000.000
92N96LEU00.014-0.00345.4390.0030.0030.0000.0000.0000.000
93N97ASN00.0050.01242.7130.0040.0040.0000.0000.0000.000
94N98GLU-1-0.802-0.87445.656-0.018-0.0180.0000.0000.0000.000
95N99LYS10.8260.90249.0370.0330.0330.0000.0000.0000.000
96N100VAL00.0330.02245.1550.0020.0020.0000.0000.0000.000
97N101ARG10.8580.90546.3010.0200.0200.0000.0000.0000.000
98N102LYS10.8370.90649.1240.0220.0220.0000.0000.0000.000
99N103LEU00.0470.01951.5750.0010.0010.0000.0000.0000.000
100N104TYR0-0.090-0.05047.6670.0010.0010.0000.0000.0000.000
101N105GLN0-0.045-0.03650.8950.0010.0010.0000.0000.0000.000
102N106GLU-1-0.930-0.96253.263-0.012-0.0120.0000.0000.0000.000
103N107TRP0-0.010-0.00150.1810.0010.0010.0000.0000.0000.000
104N108GLU-1-0.842-0.87950.441-0.002-0.0020.0000.0000.0000.000
105N109ASP-1-0.852-0.92754.584-0.004-0.0040.0000.0000.0000.000
106N110GLU-1-0.816-0.89557.994-0.006-0.0060.0000.0000.0000.000
107N111THR0-0.036-0.02155.3870.0010.0010.0000.0000.0000.000
108N112VAL0-0.016-0.00256.9660.0010.0010.0000.0000.0000.000
109N113LYS10.8120.88459.5020.0060.0060.0000.0000.0000.000
110N114VAL00.0100.00060.6740.0010.0010.0000.0000.0000.000
111N115SER0-0.083-0.04759.5470.0010.0010.0000.0000.0000.000
112N116LYS10.7980.87962.1590.0000.0000.0000.0000.0000.000
113N117LEU00.027-0.00364.8820.0010.0010.0000.0000.0000.000
114N118ARG10.9290.95562.8650.0010.0010.0000.0000.0000.000
115N119ARG10.9110.96860.919-0.004-0.0040.0000.0000.0000.000
116N120GLU-1-0.809-0.87968.0570.0010.0010.0000.0000.0000.000
117N121ALA00.0210.01570.1670.0000.0000.0000.0000.0000.000
118N122PRO0-0.006-0.00670.3130.0000.0000.0000.0000.0000.000
119N123GLN00.0440.01969.7200.0000.0000.0000.0000.0000.000
120N124VAL0-0.0010.00173.7300.0000.0000.0000.0000.0000.000
121N125ALA00.0330.03576.0540.0000.0000.0000.0000.0000.000
122N126VAL00.010-0.00276.2190.0000.0000.0000.0000.0000.000
123N127SER0-0.065-0.01177.5720.0000.0000.0000.0000.0000.000
124N128GLU-1-0.779-0.88479.4990.0020.0020.0000.0000.0000.000
125N129TYR00.0030.00681.2470.0000.0000.0000.0000.0000.000
126N130THR0-0.043-0.03781.2870.0000.0000.0000.0000.0000.000
127N131LYS10.7600.85981.529-0.002-0.0020.0000.0000.0000.000
128N132GLN0-0.048-0.01585.2300.0000.0000.0000.0000.0000.000
129N133GLU-1-0.855-0.93786.6660.0020.0020.0000.0000.0000.000
130N134ASN0-0.105-0.04786.7570.0000.0000.0000.0000.0000.000
131N135GLN0-0.021-0.03389.3420.0000.0000.0000.0000.0000.000
132N136LEU00.0300.02791.5620.0000.0000.0000.0000.0000.000
133N137LEU0-0.039-0.02490.7060.0000.0000.0000.0000.0000.000
134N138GLU-1-0.859-0.90094.4720.0030.0030.0000.0000.0000.000
135N139GLU-1-0.970-0.96796.8690.0030.0030.0000.0000.0000.000
136N140ILE0-0.033-0.03195.9150.0000.0000.0000.0000.0000.000
137N141ASP-1-0.846-0.94094.5440.0050.0050.0000.0000.0000.000
138N142SER0-0.052-0.03498.0520.0000.0000.0000.0000.0000.000
139N143LEU0-0.069-0.039101.2240.0000.0000.0000.0000.0000.000
140N144ILE0-0.018-0.01297.3950.0000.0000.0000.0000.0000.000
141N145ALA0-0.017-0.004100.4750.0000.0000.0000.0000.0000.000
142N146LYS10.8860.948102.197-0.004-0.0040.0000.0000.0000.000
143N147MET0-0.084-0.036103.4040.0000.0000.0000.0000.0000.000
144N148ASP-1-0.902-0.922103.3870.0060.0060.0000.0000.0000.000
145N149SER0-0.047-0.048106.5690.0000.0000.0000.0000.0000.000
146N150SER0-0.057-0.020110.1150.0000.0000.0000.0000.0000.000
147N167LYS10.9270.924142.451-0.002-0.0020.0000.0000.0000.000
148N168THR00.0390.012139.8170.0000.0000.0000.0000.0000.000
149N169GLN00.0340.005140.4570.0000.0000.0000.0000.0000.000
150N170GLU-1-0.823-0.865144.4260.0030.0030.0000.0000.0000.000
151N171TYR00.0200.002145.2200.0000.0000.0000.0000.0000.000
152N172TRP00.0140.014138.3460.0000.0000.0000.0000.0000.000
153N173ASN0-0.005-0.013145.8710.0000.0000.0000.0000.0000.000
154N174GLN0-0.0110.000149.1700.0000.0000.0000.0000.0000.000
155N175VAL00.0210.010146.1760.0000.0000.0000.0000.0000.000
156N176ALA00.0110.012148.6410.0000.0000.0000.0000.0000.000
157N177ASN0-0.021-0.015150.3670.0000.0000.0000.0000.0000.000
158N178GLN00.0200.022151.5610.0000.0000.0000.0000.0000.000
159N179TYR00.0210.012150.7480.0000.0000.0000.0000.0000.000
160N180GLY00.0460.018153.0640.0000.0000.0000.0000.0000.000
161N181SER0-0.005-0.004155.6480.0000.0000.0000.0000.0000.000
162N182ILE0-0.0090.012153.7300.0000.0000.0000.0000.0000.000
163N183LEU0-0.010-0.004153.6200.0000.0000.0000.0000.0000.000
164N184THR0-0.018-0.022157.7670.0000.0000.0000.0000.0000.000
165N185SER0-0.026-0.029160.5540.0000.0000.0000.0000.0000.000
166N186LEU0-0.036-0.006157.9200.0000.0000.0000.0000.0000.000
167N187LYS10.8590.904161.424-0.003-0.0030.0000.0000.0000.000
168N188GLU-1-0.822-0.897163.3900.0030.0030.0000.0000.0000.000
169N189ILE00.007-0.003163.8000.0000.0000.0000.0000.0000.000
170N190ASN0-0.040-0.030162.6690.0000.0000.0000.0000.0000.000
171N191ASP-1-0.777-0.865166.3970.0030.0030.0000.0000.0000.000
172N192LYS10.7730.867169.335-0.003-0.0030.0000.0000.0000.000
173N193ILE00.0240.025167.7320.0000.0000.0000.0000.0000.000
174N194PRO00.0160.009170.2190.0000.0000.0000.0000.0000.000
175N195THR0-0.004-0.001173.1240.0000.0000.0000.0000.0000.000
176N196HIS00.0220.017173.5720.0000.0000.0000.0000.0000.000
177N197GLU-1-0.743-0.859173.9740.0030.0030.0000.0000.0000.000
178N198SER0-0.058-0.025176.2380.0000.0000.0000.0000.0000.000
179N199LYS10.9200.945178.849-0.002-0.0020.0000.0000.0000.000
180N200GLN00.0180.018175.5570.0000.0000.0000.0000.0000.000
181N201LYS10.9730.985179.945-0.003-0.0030.0000.0000.0000.000
182N202ARG10.9100.950181.739-0.002-0.0020.0000.0000.0000.000
183N203LEU00.0260.017180.6020.0000.0000.0000.0000.0000.000
184N204ARG10.8420.892177.523-0.003-0.0030.0000.0000.0000.000
185N205LEU0-0.022-0.009184.4020.0000.0000.0000.0000.0000.000
186N206LEU0-0.032-0.024187.3640.0000.0000.0000.0000.0000.000
187N207LEU00.0030.001184.7870.0000.0000.0000.0000.0000.000
188N208ASP-1-0.915-0.944188.7550.0020.0020.0000.0000.0000.000
189N209LEU0-0.023-0.031190.4630.0000.0000.0000.0000.0000.000
190N210ILE0-0.043-0.014191.5140.0000.0000.0000.0000.0000.000
191N211GLU-1-0.900-0.940191.4580.0020.0020.0000.0000.0000.000
192N212LYS10.8700.949194.455-0.002-0.0020.0000.0000.0000.000
193N213GLU-1-0.907-0.962196.8680.0020.0020.0000.0000.0000.000
194N214VAL0-0.106-0.049195.1180.0000.0000.0000.0000.0000.000
195N215ALA00.0340.039197.7170.0000.0000.0000.0000.0000.000
196N216THR0-0.093-0.052201.4230.0000.0000.0000.0000.0000.000