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: Z6ZJN

Calculation Name: 5X3X-M-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5X3X

Chain ID: M

ChEMBL ID:

UniProt ID: D5AUZ9

Base Structure: X-ray

Registration Date: 2023-06-22

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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1995965.264433
FMO2-HF: Nuclear repulsion 1923394.867436
FMO2-HF: Total energy -72570.396997
FMO2-MP2: Total energy -72783.117485


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(M:1:MET)


Summations of interaction energy for fragment #1(M:1:MET)
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.
-13.663-16.10324.056-9.012-12.6010.017
Interaction energy analysis for fragmet #1(M:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : 0.019
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].
3M3ILE0-0.023-0.0083.8510.3231.702-0.013-0.700-0.6660.002
4M4MET00.0640.0416.5890.0660.0660.0000.0000.0000.000
5M5GLU-1-0.686-0.8388.029-0.300-0.3000.0000.0000.0000.000
6M6GLY0-0.027-0.00311.8390.0690.0690.0000.0000.0000.000
7M7TYR0-0.022-0.0019.7700.0200.0200.0000.0000.0000.000
8M8LEU00.0090.01011.663-0.081-0.0810.0000.0000.0000.000
9M9PRO00.0360.03913.9030.0290.0290.0000.0000.0000.000
10M10VAL00.0630.00917.777-0.045-0.0450.0000.0000.0000.000
11M11THR00.015-0.00519.968-0.012-0.0120.0000.0000.0000.000
12M12HIS00.0100.01716.330-0.008-0.0080.0000.0000.0000.000
13M13ALA00.0050.01915.767-0.069-0.0690.0000.0000.0000.000
14M14ILE00.0180.01916.806-0.043-0.0430.0000.0000.0000.000
15M15GLY00.0210.01219.910-0.017-0.0170.0000.0000.0000.000
16M16TRP00.023-0.00314.493-0.059-0.0590.0000.0000.0000.000
17M17SER0-0.003-0.01516.360-0.062-0.0620.0000.0000.0000.000
18M18LEU0-0.058-0.02817.4400.0010.0010.0000.0000.0000.000
19M19ALA0-0.013-0.00117.4140.0080.0080.0000.0000.0000.000
20M20ALA0-0.001-0.00715.076-0.017-0.0170.0000.0000.0000.000
21M21ALA00.0300.01317.0370.0110.0110.0000.0000.0000.000
22M22PRO00.0150.00520.0770.0170.0170.0000.0000.0000.000
23M23PHE00.0040.00417.9070.0190.0190.0000.0000.0000.000
24M24VAL00.0230.01716.4050.0110.0110.0000.0000.0000.000
25M25VAL00.0110.00419.1110.0350.0350.0000.0000.0000.000
26M26ALA0-0.0010.00222.4780.0270.0270.0000.0000.0000.000
27M27GLY00.0220.00820.5830.0210.0210.0000.0000.0000.000
28M28ALA00.002-0.00121.6650.0260.0260.0000.0000.0000.000
29M29LEU0-0.041-0.02623.2130.0320.0320.0000.0000.0000.000
30M30LYS10.8850.94722.0140.3890.3890.0000.0000.0000.000
31M31ILE00.0240.00420.6240.0200.0200.0000.0000.0000.000
32M32ARG10.9380.95625.1530.2270.2270.0000.0000.0000.000
33M33LYS10.9390.99528.1260.2160.2160.0000.0000.0000.000
34M34ILE00.0690.03925.5580.0110.0110.0000.0000.0000.000
35M35VAL0-0.022-0.01826.4820.0130.0130.0000.0000.0000.000
36M36ALA0-0.031-0.01629.5610.0140.0140.0000.0000.0000.000
37M37GLU-1-0.931-0.97031.991-0.175-0.1750.0000.0000.0000.000
38M38ARG10.8590.92130.4640.1580.1580.0000.0000.0000.000
39M39PRO00.0110.01730.762-0.010-0.0100.0000.0000.0000.000
40M40GLU-1-0.763-0.89230.178-0.150-0.1500.0000.0000.0000.000
41M41ALA00.002-0.00426.734-0.005-0.0050.0000.0000.0000.000
42M42ARG10.8390.92625.5540.1300.1300.0000.0000.0000.000
43M43MET00.0330.02024.931-0.013-0.0130.0000.0000.0000.000
44M44THR00.0010.00324.071-0.010-0.0100.0000.0000.0000.000
45M45LEU00.0200.00621.143-0.026-0.0260.0000.0000.0000.000
46M46ALA00.0120.01319.886-0.035-0.0350.0000.0000.0000.000
47M47ALA00.0030.00219.555-0.011-0.0110.0000.0000.0000.000
48M48ALA00.0020.00617.882-0.007-0.0070.0000.0000.0000.000
49M49GLY00.0150.00415.457-0.059-0.0590.0000.0000.0000.000
50M50ALA0-0.0020.00114.618-0.039-0.0390.0000.0000.0000.000
51M51PHE0-0.012-0.00814.9980.0070.0070.0000.0000.0000.000
52M52ALA00.0270.00711.5180.0000.0000.0000.0000.0000.000
53M53PHE00.0240.01310.449-0.107-0.1070.0000.0000.0000.000
54M54VAL00.0150.01610.4650.0400.0400.0000.0000.0000.000
55M55LEU0-0.021-0.0159.0280.0930.0930.0000.0000.0000.000
56M56SER0-0.035-0.0206.2810.0910.0910.0000.0000.0000.000
57M57ALA00.0230.0126.6700.1560.1560.0000.0000.0000.000
58M58LEU0-0.074-0.0249.2970.1990.1990.0000.0000.0000.000
59M59LYS10.9430.9789.086-0.238-0.2380.0000.0000.0000.000
60M60ILE00.0370.0119.100-0.210-0.2100.0000.0000.0000.000
61M61PRO00.0070.02210.1220.3310.3310.0000.0000.0000.000
62M62SER0-0.019-0.0178.7050.0210.0210.0000.0000.0000.000
63M63VAL00.002-0.00610.620-0.149-0.1490.0000.0000.0000.000
64M64THR00.0070.00911.661-0.046-0.0460.0000.0000.0000.000
65M65GLY00.0360.02312.9160.0800.0800.0000.0000.0000.000
66M66SER0-0.015-0.0088.7770.0040.0040.0000.0000.0000.000
67M67CYS0-0.051-0.0229.795-0.252-0.2520.0000.0000.0000.000
68M68SER0-0.011-0.0095.5650.3440.445-0.001-0.012-0.0870.000
69M69HIS10.8760.9164.599-2.024-1.890-0.001-0.009-0.1240.000
70M70PRO0-0.0050.0234.8230.3720.526-0.001-0.006-0.1460.000
71M71THR0-0.007-0.0332.561-2.711-1.7591.446-0.747-1.650-0.010
72M72GLY00.0010.0024.3590.1950.263-0.001-0.016-0.0510.000
73M73THR0-0.067-0.0405.8680.2470.2470.0000.0000.0000.000
74M74GLY00.0150.0048.4230.2440.2440.0000.0000.0000.000
75M75LEU00.0260.01210.9830.1260.1260.0000.0000.0000.000
76M76GLY00.0450.00711.5560.0980.0980.0000.0000.0000.000
77M77ALA0-0.067-0.03012.7180.0910.0910.0000.0000.0000.000
78M78VAL0-0.020-0.01414.6220.0750.0750.0000.0000.0000.000
79M79VAL0-0.035-0.00216.2710.0630.0630.0000.0000.0000.000
80M80PHE0-0.022-0.01915.0740.0520.0520.0000.0000.0000.000
81M81GLY00.0520.01917.780-0.026-0.0260.0000.0000.0000.000
82M82PRO00.0090.00115.8250.0250.0250.0000.0000.0000.000
83M83SER00.0100.01616.989-0.029-0.0290.0000.0000.0000.000
84M84VAL0-0.030-0.00318.3900.0230.0230.0000.0000.0000.000
85M85MET00.0320.03111.5810.0300.0300.0000.0000.0000.000
86M86ALA00.0330.02114.200-0.078-0.0780.0000.0000.0000.000
87M87VAL0-0.033-0.01115.240-0.014-0.0140.0000.0000.0000.000
88M88LEU00.000-0.01715.4610.0030.0030.0000.0000.0000.000
89M89GLY00.0360.02411.417-0.011-0.0110.0000.0000.0000.000
90M90VAL00.0250.01011.041-0.069-0.0690.0000.0000.0000.000
91M91ILE0-0.012-0.00113.2390.0530.0530.0000.0000.0000.000
92M92VAL0-0.010-0.0038.9000.0820.0820.0000.0000.0000.000
93M93LEU0-0.0040.0016.6750.0870.0870.0000.0000.0000.000
94M94LEU00.001-0.0019.5930.1590.1590.0000.0000.0000.000
95M95PHE00.0010.00112.5040.1030.1030.0000.0000.0000.000
96M96GLN00.0450.0056.359-0.071-0.0710.0000.0000.0000.000
97M97ALA0-0.040-0.0068.7340.2490.2490.0000.0000.0000.000
98M98LEU0-0.030-0.02410.4560.1130.1130.0000.0000.0000.000
99M99LEU0-0.052-0.02012.6110.0230.0230.0000.0000.0000.000
100M100LEU0-0.051-0.0248.8030.0260.0260.0000.0000.0000.000
101M101ALA0-0.0120.0079.7950.1970.1970.0000.0000.0000.000
102M102HIS0-0.051-0.0172.563-2.210-0.8090.430-0.569-1.2620.003
103M103GLY0-0.011-0.0045.3910.3740.3740.0000.0000.0000.000
104M104GLY00.006-0.0037.006-0.012-0.0120.0000.0000.0000.000
105M105LEU0-0.037-0.04210.438-0.156-0.1560.0000.0000.0000.000
106M106THR0-0.066-0.06513.606-0.059-0.0590.0000.0000.0000.000
107M107THR0-0.006-0.0129.376-0.034-0.0340.0000.0000.0000.000
108M108LEU0-0.0380.00110.836-0.256-0.2560.0000.0000.0000.000
109M109GLY00.019-0.01211.9850.0830.0830.0000.0000.0000.000
110M110ALA0-0.0080.00310.964-0.054-0.0540.0000.0000.0000.000
111M111ASN00.0840.0436.739-0.748-0.7480.0000.0000.0000.000
112M112ALA00.0040.0108.322-0.195-0.1950.0000.0000.0000.000
113M113PHE00.002-0.01410.986-0.031-0.0310.0000.0000.0000.000
114M114SER00.0170.0097.3760.0640.0640.0000.0000.0000.000
115M115MET00.0190.0052.482-0.3170.2390.876-0.254-1.177-0.001
116M116ALA0-0.022-0.0027.6600.1800.1800.0000.0000.0000.000
117M117ILE0-0.056-0.01611.0390.1770.1770.0000.0000.0000.000
118M118VAL00.003-0.00311.1210.0800.0800.0000.0000.0000.000
119M119GLY00.0530.0339.0650.0920.0920.0000.0000.0000.000
120M120PRO00.017-0.0129.9370.2040.2040.0000.0000.0000.000
121M121TRP0-0.038-0.00712.6810.1450.1450.0000.0000.0000.000
122M122VAL00.001-0.00212.3320.1100.1100.0000.0000.0000.000
123M123ALA00.0350.03011.5970.1070.1070.0000.0000.0000.000
124M124PHE00.041-0.00313.5890.1270.1270.0000.0000.0000.000
125M125GLY0-0.027-0.01217.0690.0750.0750.0000.0000.0000.000
126M126VAL00.002-0.00415.0330.0640.0640.0000.0000.0000.000
127M127TYR0-0.004-0.00517.0480.0530.0530.0000.0000.0000.000
128M128LYS10.8960.95718.5340.4270.4270.0000.0000.0000.000
129M129LEU0-0.048-0.02020.2970.0370.0370.0000.0000.0000.000
130M130ALA00.0320.02119.8750.0300.0300.0000.0000.0000.000
131M131GLY00.0310.01421.9320.0260.0260.0000.0000.0000.000
132M132LYS10.8960.94524.2190.2290.2290.0000.0000.0000.000
133M133ALA0-0.043-0.01624.7820.0150.0150.0000.0000.0000.000
134M134GLY00.0190.01926.7720.0140.0140.0000.0000.0000.000
135M135ALA0-0.054-0.01922.2730.0120.0120.0000.0000.0000.000
136M136SER00.0380.01324.374-0.011-0.0110.0000.0000.0000.000
137M137MET00.0370.02521.215-0.030-0.0300.0000.0000.0000.000
138M138ALA00.0800.03919.536-0.032-0.0320.0000.0000.0000.000
139M139VAL00.0080.00518.350-0.021-0.0210.0000.0000.0000.000
140M140ALA00.0200.00418.230-0.030-0.0300.0000.0000.0000.000
141M141VAL0-0.006-0.01715.121-0.060-0.0600.0000.0000.0000.000
142M142PHE00.0050.01813.639-0.091-0.0910.0000.0000.0000.000
143M143LEU0-0.011-0.00913.102-0.066-0.0660.0000.0000.0000.000
144M144ALA0-0.013-0.00813.331-0.076-0.0760.0000.0000.0000.000
145M145ALA00.0310.00210.121-0.160-0.1600.0000.0000.0000.000
146M146PHE0-0.0090.0138.771-0.259-0.2590.0000.0000.0000.000
147M147LEU0-0.005-0.0218.867-0.145-0.1450.0000.0000.0000.000
148M148GLY00.0230.0219.643-0.058-0.0580.0000.0000.0000.000
149M149ASP-1-0.736-0.8483.951-4.097-3.8800.002-0.062-0.1570.000
150M150LEU0-0.0240.0115.491-0.449-0.4490.0000.0000.0000.000
151M151ALA00.0210.0117.6660.0230.0230.0000.0000.0000.000
152M152THR0-0.050-0.0174.393-0.548-0.430-0.001-0.012-0.1060.000
153M153TYR00.0190.0004.970-0.044-0.0440.0000.0000.0000.000
154M154VAL00.0040.0116.1020.3110.3110.0000.0000.0000.000
155M155THR0-0.032-0.0339.2200.2050.2050.0000.0000.0000.000
156M156THR00.013-0.0094.9600.2020.2020.0000.0000.0000.000
157M157SER0-0.043-0.0317.9680.3450.3450.0000.0000.0000.000
158M158LEU0-0.006-0.0079.7740.1900.1900.0000.0000.0000.000
159M159GLN0-0.069-0.0419.877-0.076-0.0760.0000.0000.0000.000
160M160LEU00.0050.0057.2730.1480.1480.0000.0000.0000.000
161M161ALA0-0.016-0.00811.8060.1200.1200.0000.0000.0000.000
162M162LEU0-0.018-0.01214.8680.0640.0640.0000.0000.0000.000
163M163ALA0-0.039-0.01314.0560.0440.0440.0000.0000.0000.000
164M164TYR0-0.076-0.05412.6140.0690.0690.0000.0000.0000.000
165M165PRO00.0080.00016.6590.0070.0070.0000.0000.0000.000
166M166ASP-1-0.788-0.88318.886-0.023-0.0230.0000.0000.0000.000
167M167PRO0-0.004-0.00620.218-0.006-0.0060.0000.0000.0000.000
168M168ALA0-0.0180.00023.2270.0040.0040.0000.0000.0000.000
169M169SER0-0.011-0.01122.4350.0030.0030.0000.0000.0000.000
170M170GLY00.0300.02922.539-0.017-0.0170.0000.0000.0000.000
171M171PHE00.011-0.01518.9910.0020.0020.0000.0000.0000.000
172M172LEU00.0300.02018.208-0.030-0.0300.0000.0000.0000.000
173M173GLY00.0480.02918.892-0.001-0.0010.0000.0000.0000.000
174M174ALA0-0.009-0.00215.7060.0190.0190.0000.0000.0000.000
175M175ALA00.0140.00114.247-0.016-0.0160.0000.0000.0000.000
176M176LEU0-0.0140.00414.051-0.014-0.0140.0000.0000.0000.000
177M177LYS10.8430.92414.9930.0670.0670.0000.0000.0000.000
178M178PHE00.0230.00510.0160.0520.0520.0000.0000.0000.000
179M179GLY00.0470.02710.1160.0460.0460.0000.0000.0000.000
180M180SER0-0.037-0.02911.1410.1040.1040.0000.0000.0000.000
181M181VAL00.0190.0109.2440.1100.1100.0000.0000.0000.000
182M182PHE00.013-0.0035.1610.0710.0710.0000.0000.0000.000
183M183ALA00.0010.0067.8810.4930.4930.0000.0000.0000.000
184M184LEU0-0.010-0.0089.7080.1230.1230.0000.0000.0000.000
185M185THR0-0.031-0.0165.9540.5220.5220.0000.0000.0000.000
186M186GLN0-0.011-0.0322.161-5.864-12.02216.685-5.731-4.7970.025
187M187ILE00.0180.0195.314-0.853-0.817-0.001-0.004-0.0310.000
188M188PRO0-0.034-0.0218.119-0.169-0.1690.0000.0000.0000.000
189M189LEU00.0320.0272.4030.574-0.8244.636-0.890-2.347-0.002
190M190ALA00.0250.0135.741-0.487-0.4870.0000.0000.0000.000
191M191ILE0-0.010-0.0076.544-0.088-0.0880.0000.0000.0000.000
192M192ALA00.0090.0138.751-0.056-0.0560.0000.0000.0000.000
193M193GLU-1-0.822-0.9166.474-1.077-1.0770.0000.0000.0000.000
194M194GLY00.0240.0178.619-0.053-0.0530.0000.0000.0000.000
195M195PHE0-0.021-0.02911.4050.0010.0010.0000.0000.0000.000
196M196LEU00.0000.00710.172-0.004-0.0040.0000.0000.0000.000
197M197THR0-0.022-0.04010.564-0.005-0.0050.0000.0000.0000.000
198M198VAL0-0.0060.01013.3660.0030.0030.0000.0000.0000.000
199M199ILE00.0250.02516.6020.0080.0080.0000.0000.0000.000
200M200VAL0-0.030-0.01214.3540.0090.0090.0000.0000.0000.000
201M201VAL0-0.001-0.01216.4290.0010.0010.0000.0000.0000.000
202M202ASP-1-0.888-0.94218.876-0.120-0.1200.0000.0000.0000.000
203M203ALA0-0.017-0.00920.4830.0140.0140.0000.0000.0000.000
204M204LEU0-0.088-0.05218.6780.0080.0080.0000.0000.0000.000
205M205ALA0-0.025-0.00822.3230.0070.0070.0000.0000.0000.000
206M206GLY0-0.0150.00024.8660.0090.0090.0000.0000.0000.000
207M207LYS10.8690.94721.9690.1350.1350.0000.0000.0000.000