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: QNNGY

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 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 196
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1365052.881397
FMO2-HF: Nuclear repulsion 1285333.353773
FMO2-HF: Total energy -79719.527624
FMO2-MP2: Total energy -79953.786335


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.
-1.7111.4550.089-1.634-1.62-0.001
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 : -0.010 / q_NPA : -0.010
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].
3N7LYS10.8360.9003.296-0.7512.3630.090-1.629-1.575-0.001
4N8LEU00.0420.0264.9340.3420.394-0.001-0.005-0.0450.000
5N9ASP-1-0.807-0.8848.736-1.036-1.0360.0000.0000.0000.000
6N10ILE00.0480.02610.8760.0800.0800.0000.0000.0000.000
7N11THR00.0050.00214.1400.0410.0410.0000.0000.0000.000
8N12GLN00.1180.04517.6000.0060.0060.0000.0000.0000.000
9N13LYS10.9640.97220.0240.2430.2430.0000.0000.0000.000
10N14GLN00.0220.00616.502-0.019-0.0190.0000.0000.0000.000
11N15LEU00.0540.03717.0750.0140.0140.0000.0000.0000.000
12N16ARG10.9310.95919.1730.2410.2410.0000.0000.0000.000
13N17PHE0-0.078-0.02422.6050.0260.0260.0000.0000.0000.000
14N18LEU00.0280.00818.1780.0120.0120.0000.0000.0000.000
15N19HIS00.0390.02022.0840.0320.0320.0000.0000.0000.000
16N20LYS10.9400.95523.3450.2150.2150.0000.0000.0000.000
17N21GLN00.0350.03023.967-0.013-0.0130.0000.0000.0000.000
18N22PHE0-0.033-0.01620.1070.0030.0030.0000.0000.0000.000
19N23LYS10.8820.94125.9650.1700.1700.0000.0000.0000.000
20N24GLU-1-0.907-0.93128.744-0.167-0.1670.0000.0000.0000.000
21N25ILE00.0040.00527.0220.0100.0100.0000.0000.0000.000
22N26ILE0-0.042-0.03226.6880.0110.0110.0000.0000.0000.000
23N27ASP-1-0.896-0.95330.928-0.124-0.1240.0000.0000.0000.000
24N28GLU-1-0.954-0.98733.649-0.137-0.1370.0000.0000.0000.000
25N29LYS10.9170.95933.4190.1180.1180.0000.0000.0000.000
26N30VAL0-0.017-0.00633.8220.0090.0090.0000.0000.0000.000
27N31ARG10.9610.99636.4540.1110.1110.0000.0000.0000.000
28N32THR0-0.130-0.05437.9670.0040.0040.0000.0000.0000.000
29N33ALA0-0.098-0.05838.5150.0050.0050.0000.0000.0000.000
30N34LEU0-0.0060.00038.8770.0050.0050.0000.0000.0000.000
31N35PRO0-0.048-0.02542.193-0.003-0.0030.0000.0000.0000.000
32N36GLU-1-0.836-0.93941.723-0.090-0.0900.0000.0000.0000.000
33N37SER0-0.111-0.04643.612-0.001-0.0010.0000.0000.0000.000
34N38SER00.0170.01341.844-0.003-0.0030.0000.0000.0000.000
35N39GLU-1-0.971-0.98542.239-0.064-0.0640.0000.0000.0000.000
36N40ASP-1-0.830-0.90742.491-0.059-0.0590.0000.0000.0000.000
37N41ASP-1-0.956-0.97142.603-0.045-0.0450.0000.0000.0000.000
38N42GLN0-0.053-0.03940.357-0.004-0.0040.0000.0000.0000.000
39N43VAL0-0.025-0.01439.696-0.001-0.0010.0000.0000.0000.000
40N44SER00.0130.00738.858-0.001-0.0010.0000.0000.0000.000
41N45GLN00.029-0.00537.159-0.005-0.0050.0000.0000.0000.000
42N46GLU-1-0.908-0.95733.925-0.079-0.0790.0000.0000.0000.000
43N47ILE00.0120.02133.277-0.005-0.0050.0000.0000.0000.000
44N48GLN0-0.001-0.00732.198-0.007-0.0070.0000.0000.0000.000
45N49LEU00.0060.00531.189-0.009-0.0090.0000.0000.0000.000
46N50GLN0-0.034-0.00929.396-0.010-0.0100.0000.0000.0000.000
47N51LEU0-0.035-0.02927.851-0.011-0.0110.0000.0000.0000.000
48N52ASP-1-0.868-0.92926.454-0.155-0.1550.0000.0000.0000.000
49N53GLN00.009-0.02825.172-0.018-0.0180.0000.0000.0000.000
50N54PHE00.0130.03323.119-0.013-0.0130.0000.0000.0000.000
51N55LEU0-0.023-0.02321.991-0.025-0.0250.0000.0000.0000.000
52N56MET0-0.097-0.03220.568-0.026-0.0260.0000.0000.0000.000
53N57ASP-1-0.827-0.90419.228-0.172-0.1720.0000.0000.0000.000
54N58VAL0-0.045-0.02617.502-0.038-0.0380.0000.0000.0000.000
55N59LEU0-0.044-0.03716.048-0.061-0.0610.0000.0000.0000.000
56N60GLU-1-1.009-1.00314.969-0.262-0.2620.0000.0000.0000.000
57N61MET00.0180.00513.475-0.038-0.0380.0000.0000.0000.000
58N62ALA0-0.0200.00111.619-0.093-0.0930.0000.0000.0000.000
59N63GLY0-0.098-0.05210.396-0.173-0.1730.0000.0000.0000.000
60N64GLU-1-0.985-0.9789.102-0.357-0.3570.0000.0000.0000.000
61N65SER0-0.043-0.0145.5830.0460.0460.0000.0000.0000.000
62N66MET0-0.056-0.0296.529-0.276-0.2760.0000.0000.0000.000
63N67ASN0-0.124-0.0647.8640.2430.2430.0000.0000.0000.000
64N68VAL00.005-0.0179.6220.0100.0100.0000.0000.0000.000
65N69VAL0-0.060-0.03012.020-0.004-0.0040.0000.0000.0000.000
66N70ASP-1-0.939-0.97514.327-0.261-0.2610.0000.0000.0000.000
67N71ALA00.0360.03016.9140.0430.0430.0000.0000.0000.000
68N72GLY00.006-0.00814.568-0.041-0.0410.0000.0000.0000.000
69N73LYS10.9380.9666.1660.8370.8370.0000.0000.0000.000
70N74GLY00.0700.03810.941-0.009-0.0090.0000.0000.0000.000
71N75THR0-0.034-0.01412.3730.0590.0590.0000.0000.0000.000
72N76THR0-0.001-0.01215.658-0.015-0.0150.0000.0000.0000.000
73N77VAL00.0550.03314.8930.0210.0210.0000.0000.0000.000
74N78LYS11.0341.00116.1140.2580.2580.0000.0000.0000.000
75N79SER0-0.0010.00619.9870.0160.0160.0000.0000.0000.000
76N80VAL0-0.046-0.02020.2630.0140.0140.0000.0000.0000.000
77N81ILE0-0.0010.00319.7520.0070.0070.0000.0000.0000.000
78N82GLN00.0370.00422.8110.0140.0140.0000.0000.0000.000
79N83GLU-1-0.974-0.97625.361-0.155-0.1550.0000.0000.0000.000
80N84VAL00.007-0.00425.0020.0060.0060.0000.0000.0000.000
81N85GLN00.0270.02126.7740.0000.0000.0000.0000.0000.000
82N86LYS10.9020.94528.6070.1050.1050.0000.0000.0000.000
83N87GLU-1-0.998-0.98130.239-0.151-0.1510.0000.0000.0000.000
84N88TYR0-0.0350.00228.6520.0030.0030.0000.0000.0000.000
85N89THR00.021-0.02433.6440.0070.0070.0000.0000.0000.000
86N90GLU-1-0.951-0.96732.840-0.088-0.0880.0000.0000.0000.000
87N91PRO0-0.039-0.01936.3160.0010.0010.0000.0000.0000.000
88N92PHE0-0.020-0.02134.6760.0040.0040.0000.0000.0000.000
89N93ASP-1-0.808-0.90640.287-0.049-0.0490.0000.0000.0000.000
90N94VAL0-0.008-0.00843.7910.0030.0030.0000.0000.0000.000
91N95GLU-1-0.945-0.95945.769-0.041-0.0410.0000.0000.0000.000
92N96LEU00.0240.00445.9200.0040.0040.0000.0000.0000.000
93N97ASN00.0030.00442.3470.0050.0050.0000.0000.0000.000
94N98GLU-1-0.894-0.94945.898-0.027-0.0270.0000.0000.0000.000
95N99LYS10.8880.93549.1900.0390.0390.0000.0000.0000.000
96N100VAL00.0100.01445.2730.0020.0020.0000.0000.0000.000
97N101ARG10.9590.97446.6990.0280.0280.0000.0000.0000.000
98N102LYS10.8970.95349.4830.0300.0300.0000.0000.0000.000
99N103LEU00.0520.01351.9260.0020.0020.0000.0000.0000.000
100N104TYR0-0.0440.00747.4360.0010.0010.0000.0000.0000.000
101N105GLN0-0.036-0.02651.1910.0010.0010.0000.0000.0000.000
102N106GLU-1-0.924-0.95453.470-0.019-0.0190.0000.0000.0000.000
103N107TRP0-0.015-0.00151.0880.0020.0020.0000.0000.0000.000
104N108GLU-1-0.916-0.94050.734-0.012-0.0120.0000.0000.0000.000
105N109ASP-1-0.880-0.94455.027-0.012-0.0120.0000.0000.0000.000
106N110GLU-1-0.932-0.97958.463-0.012-0.0120.0000.0000.0000.000
107N111THR0-0.043-0.03756.0330.0010.0010.0000.0000.0000.000
108N112VAL0-0.003-0.01057.6350.0020.0020.0000.0000.0000.000
109N113LYS10.9040.95460.0960.0110.0110.0000.0000.0000.000
110N114VAL00.0530.01561.1380.0010.0010.0000.0000.0000.000
111N115SER0-0.079-0.03060.3380.0010.0010.0000.0000.0000.000
112N116LYS10.9170.94662.9450.0080.0080.0000.0000.0000.000
113N117LEU00.0260.01965.6080.0000.0000.0000.0000.0000.000
114N118ARG10.9380.96462.7890.0070.0070.0000.0000.0000.000
115N119ARG10.9090.96961.8630.0020.0020.0000.0000.0000.000
116N120GLU-1-0.921-0.95868.447-0.004-0.0040.0000.0000.0000.000
117N121ALA00.0050.01170.6020.0000.0000.0000.0000.0000.000
118N122PRO0-0.011-0.00970.9530.0000.0000.0000.0000.0000.000
119N123GLN00.0560.00470.6040.0000.0000.0000.0000.0000.000
120N124VAL00.0250.01674.1210.0000.0000.0000.0000.0000.000
121N125ALA00.0320.05276.4160.0000.0000.0000.0000.0000.000
122N126VAL0-0.026-0.01476.6820.0000.0000.0000.0000.0000.000
123N127SER0-0.108-0.06278.0760.0000.0000.0000.0000.0000.000
124N128GLU-1-0.897-0.96879.976-0.002-0.0020.0000.0000.0000.000
125N129TYR0-0.0040.00482.3680.0000.0000.0000.0000.0000.000
126N130THR0-0.032-0.02781.7840.0000.0000.0000.0000.0000.000
127N131LYS10.8850.95182.1300.0010.0010.0000.0000.0000.000
128N132GLN00.0270.03285.7350.0000.0000.0000.0000.0000.000
129N133GLU-1-0.963-0.99187.240-0.001-0.0010.0000.0000.0000.000
130N134ASN0-0.019-0.00387.9760.0000.0000.0000.0000.0000.000
131N135GLN00.004-0.00889.9120.0000.0000.0000.0000.0000.000
132N136LEU00.0420.02892.2550.0000.0000.0000.0000.0000.000
133N137LEU0-0.028-0.01891.4660.0000.0000.0000.0000.0000.000
134N138GLU-1-0.904-0.93095.0630.0000.0000.0000.0000.0000.000
135N139GLU-1-0.905-0.88797.5100.0000.0000.0000.0000.0000.000
136N140ILE0-0.059-0.04495.9160.0000.0000.0000.0000.0000.000
137N141ASP-1-0.855-0.94495.0240.0020.0020.0000.0000.0000.000
138N142SER0-0.097-0.11298.4750.0000.0000.0000.0000.0000.000
139N143LEU0-0.077-0.051101.6100.0000.0000.0000.0000.0000.000
140N144ILE0-0.013-0.00998.1050.0000.0000.0000.0000.0000.000
141N145ALA00.0030.016100.9190.0000.0000.0000.0000.0000.000
142N146LYS10.9020.951102.514-0.001-0.0010.0000.0000.0000.000
143N147MET0-0.143-0.067103.7400.0000.0000.0000.0000.0000.000
144N148ASP-1-0.898-0.920103.9930.0030.0030.0000.0000.0000.000
145N149SER0-0.054-0.034107.1300.0000.0000.0000.0000.0000.000
146N150SER0-0.052-0.025110.7120.0000.0000.0000.0000.0000.000
147N167LYS11.0190.991143.823-0.001-0.0010.0000.0000.0000.000
148N168THR00.0510.011140.4840.0000.0000.0000.0000.0000.000
149N169GLN00.0450.021141.0950.0000.0000.0000.0000.0000.000
150N170GLU-1-0.927-0.936144.9830.0010.0010.0000.0000.0000.000
151N171TYR00.0340.014145.6070.0000.0000.0000.0000.0000.000
152N172TRP00.0030.004139.0530.0000.0000.0000.0000.0000.000
153N173ASN0-0.001-0.030146.4180.0000.0000.0000.0000.0000.000
154N174GLN00.0070.021149.6090.0000.0000.0000.0000.0000.000
155N175VAL00.0180.001146.8040.0000.0000.0000.0000.0000.000
156N176ALA0-0.0130.007149.1020.0000.0000.0000.0000.0000.000
157N177ASN00.003-0.011150.7340.0000.0000.0000.0000.0000.000
158N178GLN00.0100.028151.7950.0000.0000.0000.0000.0000.000
159N179TYR00.0210.016151.0930.0000.0000.0000.0000.0000.000
160N180GLY00.0270.002153.4330.0000.0000.0000.0000.0000.000
161N181SER0-0.013-0.023156.0460.0000.0000.0000.0000.0000.000
162N182ILE0-0.006-0.003154.1640.0000.0000.0000.0000.0000.000
163N183LEU0-0.033-0.013154.3840.0000.0000.0000.0000.0000.000
164N184THR0-0.007-0.006158.4490.0000.0000.0000.0000.0000.000
165N185SER0-0.013-0.009160.9910.0000.0000.0000.0000.0000.000
166N186LEU0-0.043-0.001158.6110.0000.0000.0000.0000.0000.000
167N187LYS10.9840.980161.969-0.002-0.0020.0000.0000.0000.000
168N188GLU-1-0.898-0.945164.2810.0020.0020.0000.0000.0000.000
169N189ILE0-0.033-0.023163.9470.0000.0000.0000.0000.0000.000
170N190ASN0-0.058-0.041163.4940.0000.0000.0000.0000.0000.000
171N191ASP-1-0.860-0.931166.9500.0020.0020.0000.0000.0000.000
172N192LYS10.8550.920169.822-0.002-0.0020.0000.0000.0000.000
173N193ILE00.0160.023168.4220.0000.0000.0000.0000.0000.000
174N194PRO0-0.0030.006170.8330.0000.0000.0000.0000.0000.000
175N195THR00.0300.005173.7370.0000.0000.0000.0000.0000.000
176N196HIS00.003-0.006174.3400.0000.0000.0000.0000.0000.000
177N197GLU-1-0.801-0.889173.5590.0020.0020.0000.0000.0000.000
178N198SER0-0.072-0.033176.6550.0000.0000.0000.0000.0000.000
179N199LYS10.9010.929179.537-0.002-0.0020.0000.0000.0000.000
180N200GLN00.0530.032175.5620.0000.0000.0000.0000.0000.000
181N201LYS10.9390.984180.460-0.002-0.0020.0000.0000.0000.000
182N202ARG10.8820.931182.488-0.002-0.0020.0000.0000.0000.000
183N203LEU00.0720.039181.0760.0000.0000.0000.0000.0000.000
184N204ARG10.9780.992180.291-0.002-0.0020.0000.0000.0000.000
185N205LEU0-0.043-0.024185.1880.0000.0000.0000.0000.0000.000
186N206LEU0-0.006-0.011187.8820.0000.0000.0000.0000.0000.000
187N207LEU0-0.007-0.004185.2960.0000.0000.0000.0000.0000.000
188N208ASP-1-0.931-0.963189.1380.0010.0010.0000.0000.0000.000
189N209LEU0-0.071-0.034190.7580.0000.0000.0000.0000.0000.000
190N210ILE0-0.051-0.029192.3400.0000.0000.0000.0000.0000.000
191N211GLU-1-0.881-0.928192.4250.0010.0010.0000.0000.0000.000
192N212LYS10.8930.959195.250-0.001-0.0010.0000.0000.0000.000
193N213GLU-1-0.914-0.962197.3570.0010.0010.0000.0000.0000.000
194N214VAL0-0.133-0.049196.1590.0000.0000.0000.0000.0000.000
195N215ALA00.0400.018198.4070.0000.0000.0000.0000.0000.000
196N216THR0-0.062-0.031202.0160.0000.0000.0000.0000.0000.000