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: 2JMYR

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 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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1993945.258656
FMO2-HF: Nuclear repulsion 1921377.198149
FMO2-HF: Total energy -72568.060507
FMO2-MP2: Total energy -72780.880323


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.
-7.987-5.05812.542-5.174-10.296-0.006
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 : -0.023 / q_NPA : -0.015
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].
3M3ILE0-0.0110.0033.726-0.2221.130-0.004-0.673-0.6760.002
4M4MET00.0680.0456.360-0.025-0.0250.0000.0000.0000.000
5M5GLU-1-0.646-0.7977.644-0.519-0.5190.0000.0000.0000.000
6M6GLY0-0.031-0.01211.3210.0860.0860.0000.0000.0000.000
7M7TYR0-0.0050.0059.8140.1190.1190.0000.0000.0000.000
8M8LEU00.0020.00611.3910.0810.0810.0000.0000.0000.000
9M9PRO00.0290.03613.984-0.027-0.0270.0000.0000.0000.000
10M10VAL00.0690.01017.763-0.030-0.0300.0000.0000.0000.000
11M11THR00.0130.00319.984-0.023-0.0230.0000.0000.0000.000
12M12HIS00.0470.01416.235-0.030-0.0300.0000.0000.0000.000
13M13ALA0-0.0190.01215.787-0.045-0.0450.0000.0000.0000.000
14M14ILE00.0300.00616.834-0.048-0.0480.0000.0000.0000.000
15M15GLY00.0170.01519.704-0.011-0.0110.0000.0000.0000.000
16M16TRP00.0230.00714.204-0.027-0.0270.0000.0000.0000.000
17M17SER0-0.004-0.00616.240-0.065-0.0650.0000.0000.0000.000
18M18LEU0-0.047-0.02617.5350.0000.0000.0000.0000.0000.000
19M19ALA0-0.0060.00217.0630.0110.0110.0000.0000.0000.000
20M20ALA00.0160.00114.729-0.007-0.0070.0000.0000.0000.000
21M21ALA00.0140.00716.614-0.004-0.0040.0000.0000.0000.000
22M22PRO00.0130.01219.6860.0110.0110.0000.0000.0000.000
23M23PHE00.0070.00117.1800.0120.0120.0000.0000.0000.000
24M24VAL00.0140.00316.0850.0010.0010.0000.0000.0000.000
25M25VAL00.009-0.00118.5860.0170.0170.0000.0000.0000.000
26M26ALA00.0050.01121.2900.0250.0250.0000.0000.0000.000
27M27GLY0-0.008-0.01219.8970.0230.0230.0000.0000.0000.000
28M28ALA00.0040.00620.9810.0130.0130.0000.0000.0000.000
29M29LEU0-0.015-0.01822.4740.0270.0270.0000.0000.0000.000
30M30LYS10.9350.97722.1330.3020.3020.0000.0000.0000.000
31M31ILE00.0380.01919.7820.0210.0210.0000.0000.0000.000
32M32ARG10.9430.96724.3140.2480.2480.0000.0000.0000.000
33M33LYS10.9490.98227.4370.2030.2030.0000.0000.0000.000
34M34ILE00.0360.01024.7000.0070.0070.0000.0000.0000.000
35M35VAL0-0.047-0.01126.0680.0090.0090.0000.0000.0000.000
36M36ALA0-0.035-0.01628.8320.0100.0100.0000.0000.0000.000
37M37GLU-1-0.961-0.97131.469-0.159-0.1590.0000.0000.0000.000
38M38ARG10.9130.96029.9380.1670.1670.0000.0000.0000.000
39M39PRO00.0440.03229.782-0.015-0.0150.0000.0000.0000.000
40M40GLU-1-0.818-0.94029.413-0.178-0.1780.0000.0000.0000.000
41M41ALA0-0.024-0.02525.712-0.011-0.0110.0000.0000.0000.000
42M42ARG10.9250.96124.6270.1800.1800.0000.0000.0000.000
43M43MET00.0170.01923.964-0.022-0.0220.0000.0000.0000.000
44M44THR0-0.012-0.00623.324-0.023-0.0230.0000.0000.0000.000
45M45LEU00.0250.01020.003-0.023-0.0230.0000.0000.0000.000
46M46ALA0-0.0040.00319.050-0.046-0.0460.0000.0000.0000.000
47M47ALA00.0040.00218.988-0.024-0.0240.0000.0000.0000.000
48M48ALA0-0.0020.00317.303-0.017-0.0170.0000.0000.0000.000
49M49GLY00.0200.00514.503-0.055-0.0550.0000.0000.0000.000
50M50ALA00.0100.00213.783-0.079-0.0790.0000.0000.0000.000
51M51PHE0-0.008-0.00314.715-0.013-0.0130.0000.0000.0000.000
52M52ALA0-0.007-0.00410.828-0.004-0.0040.0000.0000.0000.000
53M53PHE00.0280.0199.831-0.128-0.1280.0000.0000.0000.000
54M54VAL00.0370.04210.468-0.032-0.0320.0000.0000.0000.000
55M55LEU00.0050.0058.8970.0540.0540.0000.0000.0000.000
56M56SER0-0.100-0.0746.2060.0500.0500.0000.0000.0000.000
57M57ALA00.0200.0046.700-0.059-0.0590.0000.0000.0000.000
58M58LEU0-0.045-0.0059.0990.1370.1370.0000.0000.0000.000
59M59LYS10.8850.9609.2160.0510.0510.0000.0000.0000.000
60M60ILE00.0870.0249.253-0.070-0.0700.0000.0000.0000.000
61M61PRO0-0.0090.01010.4410.1400.1400.0000.0000.0000.000
62M62SER0-0.005-0.0089.7840.0440.0440.0000.0000.0000.000
63M63VAL00.0190.01311.591-0.128-0.1280.0000.0000.0000.000
64M64THR00.0280.00611.558-0.088-0.0880.0000.0000.0000.000
65M65GLY00.0170.01113.884-0.030-0.0300.0000.0000.0000.000
66M66SER0-0.0210.0027.956-0.110-0.1100.0000.0000.0000.000
67M67CYS0-0.046-0.0419.032-0.166-0.1660.0000.0000.0000.000
68M68SER00.0130.0266.0350.0680.0680.0000.0000.0000.000
69M69HIS10.8100.8824.760-0.514-0.431-0.001-0.006-0.0750.000
70M70PRO00.0040.0184.8520.5430.716-0.001-0.007-0.1650.000
71M71THR00.017-0.0162.313-2.020-1.4032.213-0.801-2.029-0.006
72M72GLY00.0660.0244.772-0.208-0.132-0.001-0.004-0.0720.000
73M73THR0-0.0310.0175.2950.0740.0740.0000.0000.0000.000
74M74GLY00.014-0.0167.9130.1950.1950.0000.0000.0000.000
75M75LEU00.0300.01910.5580.0590.0590.0000.0000.0000.000
76M76GLY00.0300.01811.3180.0640.0640.0000.0000.0000.000
77M77ALA00.0030.01212.2210.0690.0690.0000.0000.0000.000
78M78VAL00.018-0.01313.9970.0620.0620.0000.0000.0000.000
79M79VAL0-0.063-0.01915.7440.0460.0460.0000.0000.0000.000
80M80PHE0-0.075-0.04814.9800.0320.0320.0000.0000.0000.000
81M81GLY00.0290.01816.436-0.044-0.0440.0000.0000.0000.000
82M82PRO00.007-0.02315.5290.0010.0010.0000.0000.0000.000
83M83SER0-0.019-0.00116.251-0.027-0.0270.0000.0000.0000.000
84M84VAL0-0.019-0.01117.357-0.018-0.0180.0000.0000.0000.000
85M85MET00.0530.04311.7130.0090.0090.0000.0000.0000.000
86M86ALA00.0110.02213.656-0.086-0.0860.0000.0000.0000.000
87M87VAL0-0.009-0.02014.656-0.045-0.0450.0000.0000.0000.000
88M88LEU0-0.008-0.00114.548-0.010-0.0100.0000.0000.0000.000
89M89GLY00.0110.01210.914-0.059-0.0590.0000.0000.0000.000
90M90VAL00.0460.02010.887-0.136-0.1360.0000.0000.0000.000
91M91ILE0-0.037-0.01113.140-0.022-0.0220.0000.0000.0000.000
92M92VAL0-0.013-0.0078.4070.0240.0240.0000.0000.0000.000
93M93LEU00.0050.0086.688-0.038-0.0380.0000.0000.0000.000
94M94LEU00.0220.0089.6400.0230.0230.0000.0000.0000.000
95M95PHE00.0100.00712.7160.0520.0520.0000.0000.0000.000
96M96GLN00.0590.0305.860-0.185-0.1850.0000.0000.0000.000
97M97ALA0-0.030-0.0019.067-0.011-0.0110.0000.0000.0000.000
98M98LEU0-0.046-0.03510.5730.1000.1000.0000.0000.0000.000
99M99LEU0-0.068-0.02812.5960.0810.0810.0000.0000.0000.000
100M100LEU0-0.049-0.0248.2540.0470.0470.0000.0000.0000.000
101M101ALA0-0.0070.0159.9710.0300.0300.0000.0000.0000.000
102M102HIS0-0.065-0.0511.971-0.369-0.7803.386-0.986-1.989-0.003
103M103GLY0-0.035-0.0265.829-0.318-0.3180.0000.0000.0000.000
104M104GLY00.0480.0147.509-0.078-0.0780.0000.0000.0000.000
105M105LEU0-0.093-0.06110.405-0.070-0.0700.0000.0000.0000.000
106M106THR0-0.073-0.08513.8210.0210.0210.0000.0000.0000.000
107M107THR00.005-0.0019.4120.0730.0730.0000.0000.0000.000
108M108LEU0-0.0190.01010.633-0.172-0.1720.0000.0000.0000.000
109M109GLY00.0300.00311.3740.1430.1430.0000.0000.0000.000
110M110ALA00.001-0.00310.7380.0330.0330.0000.0000.0000.000
111M111ASN00.0610.0177.048-0.199-0.1990.0000.0000.0000.000
112M112ALA0-0.015-0.0088.137-0.135-0.1350.0000.0000.0000.000
113M113PHE0-0.015-0.00610.6880.0290.0290.0000.0000.0000.000
114M114SER00.0260.0256.756-0.069-0.0690.0000.0000.0000.000
115M115MET00.0590.0233.051-0.6540.1230.110-0.147-0.7400.000
116M116ALA00.0120.0146.9510.3330.3330.0000.0000.0000.000
117M117ILE0-0.068-0.03010.1910.1290.1290.0000.0000.0000.000
118M118VAL0-0.0180.00210.3200.0990.0990.0000.0000.0000.000
119M119GLY00.0110.0058.1770.1060.1060.0000.0000.0000.000
120M120PRO0-0.028-0.0459.0710.1960.1960.0000.0000.0000.000
121M121TRP0-0.042-0.00411.7910.1130.1130.0000.0000.0000.000
122M122VAL00.0260.01811.7580.0770.0770.0000.0000.0000.000
123M123ALA00.0290.02511.0160.0760.0760.0000.0000.0000.000
124M124PHE00.0200.00013.0020.0800.0800.0000.0000.0000.000
125M125GLY0-0.029-0.01016.2770.0450.0450.0000.0000.0000.000
126M126VAL00.009-0.00915.1400.0330.0330.0000.0000.0000.000
127M127TYR0-0.0050.00816.8100.0270.0270.0000.0000.0000.000
128M128LYS10.9380.95818.2980.1990.1990.0000.0000.0000.000
129M129LEU0-0.076-0.03520.7730.0180.0180.0000.0000.0000.000
130M130ALA00.0510.03120.2960.0150.0150.0000.0000.0000.000
131M131GLY00.0300.02022.2150.0110.0110.0000.0000.0000.000
132M132LYS10.9150.96124.1390.0640.0640.0000.0000.0000.000
133M133ALA0-0.066-0.02825.3990.0050.0050.0000.0000.0000.000
134M134GLY00.0240.01327.2290.0110.0110.0000.0000.0000.000
135M135ALA0-0.040-0.00722.8140.0070.0070.0000.0000.0000.000
136M136SER00.0370.01624.767-0.012-0.0120.0000.0000.0000.000
137M137MET00.0470.01621.504-0.007-0.0070.0000.0000.0000.000
138M138ALA00.0750.02920.320-0.010-0.0100.0000.0000.0000.000
139M139VAL00.0070.00519.1220.0110.0110.0000.0000.0000.000
140M140ALA00.0160.00718.6390.0040.0040.0000.0000.0000.000
141M141VAL00.010-0.00315.352-0.022-0.0220.0000.0000.0000.000
142M142PHE0-0.0100.00914.286-0.031-0.0310.0000.0000.0000.000
143M143LEU0-0.018-0.00913.9520.0280.0280.0000.0000.0000.000
144M144ALA0-0.016-0.00713.784-0.018-0.0180.0000.0000.0000.000
145M145ALA0-0.002-0.01410.114-0.096-0.0960.0000.0000.0000.000
146M146PHE00.0080.0238.890-0.068-0.0680.0000.0000.0000.000
147M147LEU0-0.004-0.0179.9800.0650.0650.0000.0000.0000.000
148M148GLY0-0.004-0.0029.518-0.025-0.0250.0000.0000.0000.000
149M149ASP-1-0.833-0.9235.460-0.789-0.7890.0000.0000.0000.000
150M150LEU0-0.011-0.0086.088-0.085-0.0850.0000.0000.0000.000
151M151ALA00.0260.0268.4770.1140.1140.0000.0000.0000.000
152M152THR0-0.038-0.0024.369-0.451-0.326-0.001-0.013-0.1100.000
153M153TYR0-0.029-0.0645.563-0.150-0.1500.0000.0000.0000.000
154M154VAL0-0.0070.0026.5770.2820.2820.0000.0000.0000.000
155M155THR0-0.049-0.0618.9600.0220.0220.0000.0000.0000.000
156M156THR0-0.001-0.0064.946-0.217-0.2170.0000.0000.0000.000
157M157SER0-0.012-0.0177.9020.2310.2310.0000.0000.0000.000
158M158LEU0-0.0060.0019.589-0.023-0.0230.0000.0000.0000.000
159M159GLN0-0.046-0.01710.137-0.072-0.0720.0000.0000.0000.000
160M160LEU00.0010.0077.898-0.022-0.0220.0000.0000.0000.000
161M161ALA00.0110.01312.193-0.003-0.0030.0000.0000.0000.000
162M162LEU0-0.075-0.03615.007-0.027-0.0270.0000.0000.0000.000
163M163ALA0-0.037-0.02214.552-0.019-0.0190.0000.0000.0000.000
164M164TYR0-0.090-0.04913.4650.0030.0030.0000.0000.0000.000
165M165PRO00.0170.01717.1370.0500.0500.0000.0000.0000.000
166M166ASP-1-0.824-0.88519.5480.2400.2400.0000.0000.0000.000
167M167PRO00.0070.00620.778-0.018-0.0180.0000.0000.0000.000
168M168ALA0-0.029-0.02024.216-0.014-0.0140.0000.0000.0000.000
169M169SER00.0110.02522.653-0.002-0.0020.0000.0000.0000.000
170M170GLY00.0270.08023.069-0.008-0.0080.0000.0000.0000.000
171M171PHE00.016-0.00919.1710.0280.0280.0000.0000.0000.000
172M172LEU00.0220.00918.4000.0370.0370.0000.0000.0000.000
173M173GLY00.170-0.00319.3420.0370.0370.0000.0000.0000.000
174M174ALA0-0.102-0.05116.0700.0530.0530.0000.0000.0000.000
175M175ALA00.005-0.00114.4850.0900.0900.0000.0000.0000.000
176M176LEU0-0.0020.00614.2470.1110.1110.0000.0000.0000.000
177M177LYS10.8370.94215.423-0.256-0.2560.0000.0000.0000.000
178M178PHE00.021-0.00110.0850.0910.0910.0000.0000.0000.000
179M179GLY00.0550.03410.3510.3280.3280.0000.0000.0000.000
180M180SER0-0.014-0.00511.3800.1840.1840.0000.0000.0000.000
181M181VAL0-0.007-0.0029.8170.0510.0510.0000.0000.0000.000
182M182PHE00.0120.0035.2980.2710.374-0.001-0.005-0.0960.000
183M183ALA00.0120.0117.7100.5000.5000.0000.0000.0000.000
184M184LEU0-0.029-0.01310.215-0.011-0.0110.0000.0000.0000.000
185M185THR0-0.007-0.0105.8870.2320.2320.0000.0000.0000.000
186M186GLN0-0.002-0.0062.546-3.561-3.4604.838-2.107-2.8310.001
187M187ILE00.0400.0366.554-0.453-0.4530.0000.0000.0000.000
188M188PRO0-0.001-0.0099.467-0.240-0.2400.0000.0000.0000.000
189M189LEU00.0150.0073.249-0.189-0.2562.004-0.425-1.5130.000
190M190ALA00.0290.0137.320-0.454-0.4540.0000.0000.0000.000
191M191ILE0-0.041-0.0138.077-0.319-0.3190.0000.0000.0000.000
192M192ALA00.0000.0039.972-0.169-0.1690.0000.0000.0000.000
193M193GLU-1-0.785-0.8725.998-0.336-0.3360.0000.0000.0000.000
194M194GLY00.0400.0049.438-0.206-0.2060.0000.0000.0000.000
195M195PHE0-0.035-0.03212.099-0.065-0.0650.0000.0000.0000.000
196M196LEU0-0.010-0.00810.759-0.069-0.0690.0000.0000.0000.000
197M197THR0-0.036-0.03410.682-0.079-0.0790.0000.0000.0000.000
198M198VAL00.0140.01113.621-0.038-0.0380.0000.0000.0000.000
199M199ILE00.0350.02216.922-0.019-0.0190.0000.0000.0000.000
200M200VAL0-0.038-0.01515.179-0.020-0.0200.0000.0000.0000.000
201M201VAL00.007-0.01116.752-0.015-0.0150.0000.0000.0000.000
202M202ASP-1-0.912-0.93819.222-0.003-0.0030.0000.0000.0000.000
203M203ALA0-0.033-0.01921.144-0.003-0.0030.0000.0000.0000.000
204M204LEU0-0.095-0.06018.634-0.008-0.0080.0000.0000.0000.000
205M205ALA0-0.0180.01122.598-0.003-0.0030.0000.0000.0000.000
206M206GLY0-0.027-0.00225.0730.0040.0040.0000.0000.0000.000
207M207LYS10.9090.95722.6500.1300.1300.0000.0000.0000.000