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: NNKLQ

Calculation Name: 5XI8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5XI8

Chain ID: A

ChEMBL ID:

UniProt ID: P66948

Base Structure: X-ray

Registration Date: 2023-09-23

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 OptHSide
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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1670386.630444
FMO2-HF: Nuclear repulsion 1603035.683079
FMO2-HF: Total energy -67350.947365
FMO2-MP2: Total energy -67550.333265


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(A:308:GLY)


Summations of interaction energy for fragment #1(A:308:GLY)
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.
-1.2881.3430.751-1.286-2.0970.004
Interaction energy analysis for fragmet #1(A:308:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.042 / q_NPA : 0.009
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].
3A310ALA00.0410.0263.5060.3561.5030.009-0.494-0.6620.001
4A311ALA0-0.0020.0012.536-1.253-0.4150.741-0.627-0.9520.003
5A312GLN00.0280.0163.517-0.4550.1090.002-0.156-0.4100.000
6A313TYR00.0480.0055.6320.3880.3880.0000.0000.0000.000
7A314GLY00.0380.0237.7800.1060.1060.0000.0000.0000.000
8A315ARG10.8980.9344.1180.1410.223-0.001-0.009-0.0730.000
9A316ALA00.0020.0029.6550.0150.0150.0000.0000.0000.000
10A317LEU00.0200.00811.7090.0360.0360.0000.0000.0000.000
11A318GLN00.0020.01012.8560.0070.0070.0000.0000.0000.000
12A319ALA0-0.038-0.02013.8860.0020.0020.0000.0000.0000.000
13A320MET0-0.019-0.00515.686-0.004-0.0040.0000.0000.0000.000
14A321GLU-1-0.943-0.95617.5310.0550.0550.0000.0000.0000.000
15A322ALA0-0.064-0.02518.7340.0090.0090.0000.0000.0000.000
16A323ASN0-0.023-0.02820.5260.0040.0040.0000.0000.0000.000
17A324LYS10.9280.97618.1080.0310.0310.0000.0000.0000.000
18A325TYR00.0610.02517.945-0.024-0.0240.0000.0000.0000.000
19A326ASP-1-0.851-0.92018.201-0.226-0.2260.0000.0000.0000.000
20A327GLU-1-0.871-0.93513.984-0.294-0.2940.0000.0000.0000.000
21A328ALA00.0330.01713.831-0.061-0.0610.0000.0000.0000.000
22A329ARG10.7910.87713.6110.1300.1300.0000.0000.0000.000
23A330LYS10.7780.87113.8510.1840.1840.0000.0000.0000.000
24A331THR0-0.055-0.0178.406-0.100-0.1000.0000.0000.0000.000
25A332LEU00.0010.0039.562-0.233-0.2330.0000.0000.0000.000
26A333GLN0-0.007-0.01111.724-0.010-0.0100.0000.0000.0000.000
27A334PRO0-0.009-0.0119.0900.0420.0420.0000.0000.0000.000
28A335LEU0-0.025-0.0016.093-0.116-0.1160.0000.0000.0000.000
29A336LEU00.003-0.0019.8430.1130.1130.0000.0000.0000.000
30A337ALA0-0.021-0.01513.4340.0610.0610.0000.0000.0000.000
31A338ALA0-0.0120.00610.6760.0610.0610.0000.0000.0000.000
32A339GLU-1-0.842-0.89910.031-0.497-0.4970.0000.0000.0000.000
33A340PRO0-0.012-0.01213.9550.0180.0180.0000.0000.0000.000
34A341GLY0-0.040-0.03216.8790.0290.0290.0000.0000.0000.000
35A342ASN0-0.007-0.00111.9270.0810.0810.0000.0000.0000.000
36A343ALA00.0310.00415.765-0.009-0.0090.0000.0000.0000.000
37A344TRP00.0710.03814.2120.0090.0090.0000.0000.0000.000
38A345TYR0-0.077-0.0458.840-0.083-0.0830.0000.0000.0000.000
39A346LEU0-0.022-0.01414.2640.0070.0070.0000.0000.0000.000
40A347ASP-1-0.868-0.89817.681-0.083-0.0830.0000.0000.0000.000
41A348LEU00.0510.02313.3340.0010.0010.0000.0000.0000.000
42A349ALA0-0.033-0.03116.9510.0060.0060.0000.0000.0000.000
43A350THR0-0.054-0.03918.1880.0150.0150.0000.0000.0000.000
44A351ASP-1-0.825-0.91320.263-0.072-0.0720.0000.0000.0000.000
45A352ILE0-0.026-0.02315.7170.0050.0050.0000.0000.0000.000
46A353ASP-1-0.805-0.87620.332-0.175-0.1750.0000.0000.0000.000
47A354LEU0-0.0220.00223.1120.0110.0110.0000.0000.0000.000
48A355GLY00.0290.03523.8560.0100.0100.0000.0000.0000.000
49A356GLN0-0.033-0.02221.976-0.010-0.0100.0000.0000.0000.000
50A357ASN0-0.026-0.00325.6730.0020.0020.0000.0000.0000.000
51A358LYS10.8320.90723.7370.1440.1440.0000.0000.0000.000
52A359ALA00.0970.04326.666-0.008-0.0080.0000.0000.0000.000
53A360ASN00.0060.00028.4490.0000.0000.0000.0000.0000.000
54A361GLU-1-0.847-0.91324.759-0.123-0.1230.0000.0000.0000.000
55A362ALA00.0120.01023.985-0.010-0.0100.0000.0000.0000.000
56A363ILE0-0.0010.00125.021-0.003-0.0030.0000.0000.0000.000
57A364ASN0-0.018-0.01827.4450.0060.0060.0000.0000.0000.000
58A365ARG10.8380.91419.3550.2040.2040.0000.0000.0000.000
59A366LEU00.0310.02222.286-0.004-0.0040.0000.0000.0000.000
60A367LYS10.8850.93924.6730.0920.0920.0000.0000.0000.000
61A368ASN0-0.064-0.02023.5670.0160.0160.0000.0000.0000.000
62A369ALA00.0280.03122.393-0.008-0.0080.0000.0000.0000.000
63A370ARG10.9740.97220.9970.1600.1600.0000.0000.0000.000
64A371ASP-1-0.887-0.94722.147-0.096-0.0960.0000.0000.0000.000
65A372LEU00.0040.00524.5300.0090.0090.0000.0000.0000.000
66A373ARG10.8600.91826.2960.0860.0860.0000.0000.0000.000
67A374THR00.0110.00626.5770.0040.0040.0000.0000.0000.000
68A375ASN00.0320.03020.7760.0100.0100.0000.0000.0000.000
69A376PRO00.0610.01625.000-0.006-0.0060.0000.0000.0000.000
70A377VAL00.0660.04420.0740.0000.0000.0000.0000.0000.000
71A378LEU0-0.0160.00520.597-0.007-0.0070.0000.0000.0000.000
72A379GLN0-0.015-0.00524.0040.0040.0040.0000.0000.0000.000
73A380LEU00.0400.02726.091-0.001-0.0010.0000.0000.0000.000
74A381ASN0-0.035-0.04221.931-0.005-0.0050.0000.0000.0000.000
75A382LEU0-0.026-0.01125.410-0.002-0.0020.0000.0000.0000.000
76A383ALA0-0.005-0.00127.7350.0020.0020.0000.0000.0000.000
77A384ASN00.0680.03726.1500.0070.0070.0000.0000.0000.000
78A385ALA00.0260.00426.7440.0000.0000.0000.0000.0000.000
79A386TYR0-0.017-0.03028.780-0.002-0.0020.0000.0000.0000.000
80A387LEU0-0.012-0.00532.2370.0020.0020.0000.0000.0000.000
81A388GLN0-0.030-0.01529.7020.0040.0040.0000.0000.0000.000
82A389GLY0-0.048-0.02632.348-0.001-0.0010.0000.0000.0000.000
83A390GLY0-0.0300.00033.2130.0010.0010.0000.0000.0000.000
84A391GLN0-0.051-0.03434.5220.0030.0030.0000.0000.0000.000
85A392PRO00.0710.02636.252-0.001-0.0010.0000.0000.0000.000
86A393GLN00.0190.01638.0010.0020.0020.0000.0000.0000.000
87A394GLU-1-0.850-0.93935.035-0.047-0.0470.0000.0000.0000.000
88A395ALA0-0.017-0.00333.841-0.001-0.0010.0000.0000.0000.000
89A396ALA00.0750.03634.8390.0020.0020.0000.0000.0000.000
90A397ASN0-0.065-0.02236.8880.0050.0050.0000.0000.0000.000
91A398ILE0-0.087-0.04230.7040.0020.0020.0000.0000.0000.000
92A399LEU00.0190.00732.1350.0020.0020.0000.0000.0000.000
93A400ASN0-0.031-0.00834.9340.0060.0060.0000.0000.0000.000
94A401ARG10.8800.95032.8060.0440.0440.0000.0000.0000.000
95A402TYR0-0.072-0.05527.9350.0010.0010.0000.0000.0000.000
96A403THR00.0410.00033.1990.0030.0030.0000.0000.0000.000
97A404PHE0-0.061-0.01435.4950.0040.0040.0000.0000.0000.000
98A405ASN0-0.098-0.06532.8440.0040.0040.0000.0000.0000.000
99A406ASN0-0.071-0.03229.7220.0040.0040.0000.0000.0000.000
100A407LYS10.8850.93132.712-0.008-0.0080.0000.0000.0000.000
101A408ASP-1-0.826-0.89632.8690.0100.0100.0000.0000.0000.000
102A409ASP-1-0.788-0.86229.217-0.008-0.0080.0000.0000.0000.000
103A410SER00.0400.00531.868-0.002-0.0020.0000.0000.0000.000
104A411ASN0-0.010-0.00428.375-0.003-0.0030.0000.0000.0000.000
105A412GLY00.0180.01131.273-0.005-0.0050.0000.0000.0000.000
106A413TRP0-0.015-0.03132.643-0.004-0.0040.0000.0000.0000.000
107A414ASP-1-0.900-0.94033.918-0.009-0.0090.0000.0000.0000.000
108A415LEU0-0.007-0.00929.698-0.003-0.0030.0000.0000.0000.000
109A416LEU0-0.031-0.01534.406-0.002-0.0020.0000.0000.0000.000
110A417ALA00.005-0.00237.2230.0000.0000.0000.0000.0000.000
111A418GLN0-0.026-0.01634.4840.0000.0000.0000.0000.0000.000
112A419ALA0-0.008-0.00736.839-0.001-0.0010.0000.0000.0000.000
113A420GLU-1-0.790-0.91438.740-0.025-0.0250.0000.0000.0000.000
114A421ALA0-0.044-0.01241.7960.0010.0010.0000.0000.0000.000
115A422ALA0-0.057-0.02740.4290.0000.0000.0000.0000.0000.000
116A423LEU0-0.068-0.02740.705-0.001-0.0010.0000.0000.0000.000
117A424ASN0-0.083-0.02544.1870.0020.0020.0000.0000.0000.000
118A425ASN0-0.039-0.01444.0600.0020.0020.0000.0000.0000.000
119A426ARG10.9200.94346.3010.0130.0130.0000.0000.0000.000
120A427ASP-1-0.804-0.89247.915-0.012-0.0120.0000.0000.0000.000
121A428GLN00.0820.03543.9280.0020.0020.0000.0000.0000.000
122A429GLU-1-0.804-0.87143.225-0.014-0.0140.0000.0000.0000.000
123A430LEU0-0.082-0.04343.8650.0010.0010.0000.0000.0000.000
124A431ALA00.0320.01044.8110.0020.0020.0000.0000.0000.000
125A432ALA00.0090.01439.7580.0020.0020.0000.0000.0000.000
126A433ARG10.9040.92640.6090.0120.0120.0000.0000.0000.000
127A434ALA0-0.051-0.01642.4280.0020.0020.0000.0000.0000.000
128A435GLU-1-0.776-0.85339.8120.0010.0010.0000.0000.0000.000
129A436GLY00.0500.03038.3360.0020.0020.0000.0000.0000.000
130A437TYR0-0.050-0.04539.3210.0020.0020.0000.0000.0000.000
131A438ALA0-0.016-0.00941.7730.0020.0020.0000.0000.0000.000
132A439LEU0-0.0200.00135.3240.0030.0030.0000.0000.0000.000
133A440ALA0-0.0350.00037.8680.0030.0030.0000.0000.0000.000
134A441GLY00.0080.00339.5050.0010.0010.0000.0000.0000.000
135A442ARG10.8410.91842.489-0.006-0.0060.0000.0000.0000.000
136A443LEU00.0400.00844.181-0.002-0.0020.0000.0000.0000.000
137A444ASP-1-0.831-0.91846.9550.0060.0060.0000.0000.0000.000
138A445GLN00.0160.01347.1400.0000.0000.0000.0000.0000.000
139A446ALA00.0240.01345.128-0.001-0.0010.0000.0000.0000.000
140A447ILE00.0180.01147.003-0.001-0.0010.0000.0000.0000.000
141A448SER0-0.0030.01950.276-0.001-0.0010.0000.0000.0000.000
142A449LEU0-0.035-0.02046.101-0.001-0.0010.0000.0000.0000.000
143A450MET00.0140.02245.105-0.002-0.0020.0000.0000.0000.000
144A451SER0-0.018-0.03249.5970.0000.0000.0000.0000.0000.000
145A452SER0-0.059-0.02751.859-0.001-0.0010.0000.0000.0000.000
146A453ALA00.0090.01849.159-0.001-0.0010.0000.0000.0000.000
147A454SER0-0.029-0.05851.210-0.001-0.0010.0000.0000.0000.000
148A455SER0-0.113-0.06353.4450.0000.0000.0000.0000.0000.000
149A456GLN0-0.005-0.00752.406-0.001-0.0010.0000.0000.0000.000
150A457VAL0-0.0040.02751.490-0.001-0.0010.0000.0000.0000.000
151A458LYS10.9410.96954.8310.0110.0110.0000.0000.0000.000
152A459LEU00.0620.02957.3670.0000.0000.0000.0000.0000.000
153A460GLY0-0.013-0.00958.9840.0000.0000.0000.0000.0000.000
154A461SER0-0.077-0.03754.8570.0000.0000.0000.0000.0000.000
155A462LEU00.0380.00550.1520.0000.0000.0000.0000.0000.000
156A463GLN00.012-0.00146.4900.0010.0010.0000.0000.0000.000
157A464GLN00.0470.01851.1130.0000.0000.0000.0000.0000.000
158A465ALA00.0260.01553.3070.0010.0010.0000.0000.0000.000
159A466ARG10.9030.95546.5110.0120.0120.0000.0000.0000.000
160A467TYR0-0.011-0.03746.4770.0010.0010.0000.0000.0000.000
161A468ASP-1-0.772-0.85850.031-0.002-0.0020.0000.0000.0000.000
162A469ALA0-0.013-0.00349.7090.0010.0010.0000.0000.0000.000
163A470ARG10.7720.83343.0830.0010.0010.0000.0000.0000.000
164A471ILE0-0.015-0.00148.0280.0010.0010.0000.0000.0000.000
165A472ASP-1-0.890-0.94350.6640.0030.0030.0000.0000.0000.000
166A473GLN0-0.034-0.01445.6980.0010.0010.0000.0000.0000.000
167A474LEU0-0.026-0.01544.5580.0020.0020.0000.0000.0000.000
168A475ARG10.9710.98847.902-0.002-0.0020.0000.0000.0000.000
169A476GLN0-0.015-0.00549.9780.0010.0010.0000.0000.0000.000
170A477LEU0-0.035-0.01543.1520.0020.0020.0000.0000.0000.000
171A478GLN0-0.002-0.01847.5520.0010.0010.0000.0000.0000.000
172A479GLU-1-0.818-0.87449.4250.0110.0110.0000.0000.0000.000
173A480ARG10.8660.94243.328-0.018-0.0180.0000.0000.0000.000
174A481PHE0-0.044-0.02642.8110.0020.0020.0000.0000.0000.000
175A482LYS10.8010.90248.787-0.009-0.0090.0000.0000.0000.000