FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: YVG42

Calculation Name: 2P4H-X-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2P4H

Chain ID: X

ChEMBL ID:

UniProt ID: Q40316

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 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 314
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4650682.205252
FMO2-HF: Nuclear repulsion 4529363.183839
FMO2-HF: Total energy -121319.021413
FMO2-MP2: Total energy -121674.086536


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(X:5:LYS)


Summations of interaction energy for fragment #1(X:5:LYS)
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.
-157.977-145.38812.165-10.376-14.377-0.111
Interaction energy analysis for fragmet #1(X:5:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.908 / q_NPA : 0.957
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].
3X7ARG10.9010.9523.78616.61518.621-0.034-1.123-0.8490.004
4X8VAL00.0310.0235.8940.6440.6440.0000.0000.0000.000
5X9CYS0-0.0090.0008.5181.1811.1810.0000.0000.0000.000
6X10VAL00.0160.01611.339-0.031-0.0310.0000.0000.0000.000
7X11THR00.021-0.00813.9170.7360.7360.0000.0000.0000.000
8X12GLY0-0.019-0.00417.716-0.274-0.2740.0000.0000.0000.000
9X13GLY00.0530.01217.137-0.198-0.1980.0000.0000.0000.000
10X14THR0-0.008-0.01618.043-0.347-0.3470.0000.0000.0000.000
11X15GLY00.0070.01020.6220.5640.5640.0000.0000.0000.000
12X16PHE00.0330.00920.161-0.736-0.7360.0000.0000.0000.000
13X17LEU00.0400.02316.751-0.600-0.6000.0000.0000.0000.000
14X18GLY00.0410.02316.347-1.207-1.2070.0000.0000.0000.000
15X19SER0-0.021-0.03115.327-1.246-1.2460.0000.0000.0000.000
16X20TRP0-0.012-0.01913.285-0.200-0.2000.0000.0000.0000.000
17X21ILE00.0230.00311.173-1.851-1.8510.0000.0000.0000.000
18X22ILE0-0.0250.00110.634-2.630-2.6300.0000.0000.0000.000
19X23LYS10.8560.92710.66621.53021.5300.0000.0000.0000.000
20X24SER00.0190.0168.665-2.888-2.8880.0000.0000.0000.000
21X25LEU00.003-0.0066.154-5.449-5.4490.0000.0000.0000.000
22X26LEU0-0.042-0.0145.707-6.460-6.4600.0000.0000.0000.000
23X27GLU-1-0.882-0.9257.428-30.878-30.8780.0000.0000.0000.000
24X28ASN0-0.074-0.0372.686-9.126-8.2020.073-0.267-0.730-0.002
25X29GLY0-0.017-0.0172.156-39.044-35.8655.721-4.152-4.748-0.061
26X30TYR0-0.103-0.0802.129-5.352-0.5936.340-4.109-6.990-0.046
27X31SER0-0.052-0.0203.5565.7625.9920.0080.029-0.2670.000
28X32VAL00.000-0.0256.092-1.100-1.1000.0000.0000.0000.000
29X33ASN00.0730.0419.4031.0511.0510.0000.0000.0000.000
30X34THR0-0.020-0.01612.657-0.255-0.2550.0000.0000.0000.000
31X35THR00.0390.02515.6270.7310.7310.0000.0000.0000.000
32X36ILE0-0.017-0.01519.226-0.265-0.2650.0000.0000.0000.000
33X37ARG10.9720.98421.69511.64111.6410.0000.0000.0000.000
34X38ALA0-0.016-0.00525.204-0.063-0.0630.0000.0000.0000.000
35X39ASP-1-0.893-0.95027.954-10.001-10.0010.0000.0000.0000.000
36X40PRO0-0.009-0.02130.3000.1730.1730.0000.0000.0000.000
37X41GLU-1-0.830-0.90433.505-8.024-8.0240.0000.0000.0000.000
38X42ARG10.8050.89330.8158.5368.5360.0000.0000.0000.000
39X43LYS10.8840.94523.43711.66211.6620.0000.0000.0000.000
40X44ARG10.9180.96926.9909.7309.7300.0000.0000.0000.000
41X45ASP-1-0.826-0.92826.084-11.627-11.6270.0000.0000.0000.000
42X46VAL0-0.0090.00120.547-0.152-0.1520.0000.0000.0000.000
43X47SER00.0440.03120.668-0.779-0.7790.0000.0000.0000.000
44X48PHE0-0.0120.00120.184-0.452-0.4520.0000.0000.0000.000
45X49LEU0-0.046-0.03016.479-0.808-0.8080.0000.0000.0000.000
46X50THR00.007-0.01516.382-0.994-0.9940.0000.0000.0000.000
47X51ASN0-0.015-0.00617.5200.1920.1920.0000.0000.0000.000
48X52LEU0-0.0330.00114.297-0.263-0.2630.0000.0000.0000.000
49X53PRO00.0520.00812.6650.0080.0080.0000.0000.0000.000
50X54GLY00.0290.02010.501-1.918-1.9180.0000.0000.0000.000
51X55ALA00.000-0.00610.793-0.343-0.3430.0000.0000.0000.000
52X56SER0-0.059-0.06912.9200.6570.6570.0000.0000.0000.000
53X57GLU-1-0.873-0.89411.216-18.899-18.8990.0000.0000.0000.000
54X58LYS10.8750.9415.39432.82632.8260.0000.0000.0000.000
55X59LEU0-0.0100.0229.470-1.107-1.1070.0000.0000.0000.000
56X60HIS0-0.0090.00811.0261.9351.9350.0000.0000.0000.000
57X61PHE00.014-0.00814.418-0.312-0.3120.0000.0000.0000.000
58X62PHE00.0130.01414.5280.4920.4920.0000.0000.0000.000
59X63ASN0-0.055-0.03919.573-0.006-0.0060.0000.0000.0000.000
60X64ALA00.0440.01521.949-0.148-0.1480.0000.0000.0000.000
61X65ASP-1-0.906-0.95423.977-10.005-10.0050.0000.0000.0000.000
62X66LEU0-0.035-0.03023.114-0.043-0.0430.0000.0000.0000.000
63X67SER00.0120.01025.539-0.077-0.0770.0000.0000.0000.000
64X68ASN00.0020.01027.3670.1710.1710.0000.0000.0000.000
65X69PRO00.0040.00724.416-0.307-0.3070.0000.0000.0000.000
66X70ASP-1-0.851-0.92923.594-11.065-11.0650.0000.0000.0000.000
67X71SER0-0.085-0.03124.282-0.263-0.2630.0000.0000.0000.000
68X72PHE0-0.023-0.02719.433-0.447-0.4470.0000.0000.0000.000
69X73ALA00.0300.02419.175-0.742-0.7420.0000.0000.0000.000
70X74ALA00.0190.00118.735-0.468-0.4680.0000.0000.0000.000
71X75ALA0-0.017-0.01116.297-0.587-0.5870.0000.0000.0000.000
72X76ILE00.019-0.01114.396-1.298-1.2980.0000.0000.0000.000
73X77GLU-1-0.912-0.94014.248-15.132-15.1320.0000.0000.0000.000
74X78GLY0-0.034-0.01612.131-0.590-0.5900.0000.0000.0000.000
75X79CYS0-0.119-0.0279.594-1.668-1.6680.0000.0000.0000.000
76X80VAL00.0420.0215.3230.8890.8890.0000.0000.0000.000
77X81GLY00.0240.0148.7500.0320.0320.0000.0000.0000.000
78X82ILE00.0030.01310.1040.3290.3290.0000.0000.0000.000
79X83PHE00.0190.0028.8910.1880.1880.0000.0000.0000.000
80X84HIS00.0460.03013.922-0.060-0.0600.0000.0000.0000.000
81X85THR0-0.035-0.03516.3470.5220.5220.0000.0000.0000.000
82X86ALA0-0.0150.00219.0840.6460.6460.0000.0000.0000.000
83X87SER0-0.011-0.02621.9310.2690.2690.0000.0000.0000.000
84X88PRO0-0.018-0.00225.5290.0460.0460.0000.0000.0000.000
85X89ILE0-0.0060.00528.6130.2030.2030.0000.0000.0000.000
86X98GLU-1-0.904-0.95840.161-7.190-7.1900.0000.0000.0000.000
87X99ILE00.0460.01438.492-0.236-0.2360.0000.0000.0000.000
88X100VAL00.015-0.00135.898-0.240-0.2400.0000.0000.0000.000
89X101THR00.0230.00234.831-0.324-0.3240.0000.0000.0000.000
90X102LYS10.9590.99333.8578.3368.3360.0000.0000.0000.000
91X103ARG10.9861.00031.7808.8048.8040.0000.0000.0000.000
92X104THR0-0.085-0.03930.217-0.379-0.3790.0000.0000.0000.000
93X105VAL00.0260.00829.013-0.394-0.3940.0000.0000.0000.000
94X106ASP-1-0.852-0.93128.413-9.713-9.7130.0000.0000.0000.000
95X107GLY0-0.037-0.01626.797-0.315-0.3150.0000.0000.0000.000
96X108ALA0-0.025-0.01524.442-0.550-0.5500.0000.0000.0000.000
97X109LEU00.022-0.00523.471-0.473-0.4730.0000.0000.0000.000
98X110GLY00.0100.02924.353-0.132-0.1320.0000.0000.0000.000
99X111ILE0-0.009-0.01616.8920.0180.0180.0000.0000.0000.000
100X112LEU00.0150.01620.031-0.408-0.4080.0000.0000.0000.000
101X113LYS10.9240.95021.24810.29110.2910.0000.0000.0000.000
102X114ALA0-0.032-0.00720.5690.1380.1380.0000.0000.0000.000
103X115CYS0-0.029-0.00917.105-0.508-0.5080.0000.0000.0000.000
104X116VAL00.0270.02119.221-0.329-0.3290.0000.0000.0000.000
105X117ASN0-0.013-0.00721.260-0.002-0.0020.0000.0000.0000.000
106X118SER0-0.0040.01915.458-0.219-0.2190.0000.0000.0000.000
107X119LYS10.9660.96516.22412.73312.7330.0000.0000.0000.000
108X120THR0-0.044-0.03910.9540.1450.1450.0000.0000.0000.000
109X121VAL0-0.047-0.00511.218-1.572-1.5720.0000.0000.0000.000
110X122LYS10.9170.9635.60834.52334.5230.0000.0000.0000.000
111X123ARG10.7760.86811.36420.98020.9800.0000.0000.0000.000
112X124PHE00.0020.01412.531-0.702-0.7020.0000.0000.0000.000
113X125ILE0-0.019-0.01412.0400.5040.5040.0000.0000.0000.000
114X126TYR0-0.015-0.01515.8060.1820.1820.0000.0000.0000.000
115X127THR0-0.008-0.00718.668-0.486-0.4860.0000.0000.0000.000
116X128SER0-0.024-0.03320.2610.8150.8150.0000.0000.0000.000
117X129SER0-0.032-0.04023.537-0.274-0.2740.0000.0000.0000.000
118X130GLY00.1380.08126.1610.2280.2280.0000.0000.0000.000
119X131SER0-0.050-0.01228.4760.2900.2900.0000.0000.0000.000
120X132ALA00.0130.00828.5540.4370.4370.0000.0000.0000.000
121X133VAL00.0210.01328.9230.1620.1620.0000.0000.0000.000
122X134SER00.016-0.01331.5180.2730.2730.0000.0000.0000.000
123X135PHE0-0.063-0.02333.8740.2320.2320.0000.0000.0000.000
124X136ASN00.0270.00335.5860.3370.3370.0000.0000.0000.000
125X137GLY0-0.010-0.00838.0550.1350.1350.0000.0000.0000.000
126X138LYS10.9130.97937.6678.6648.6640.0000.0000.0000.000
127X139ASP-1-0.913-0.94939.952-7.674-7.6740.0000.0000.0000.000
128X140LYS10.7880.87735.5409.1109.1100.0000.0000.0000.000
129X141ASP-1-0.901-0.95836.382-8.947-8.9470.0000.0000.0000.000
130X142VAL00.0180.02531.230-0.318-0.3180.0000.0000.0000.000
131X143LEU0-0.078-0.04230.8860.2560.2560.0000.0000.0000.000
132X144ASP-1-0.799-0.89028.322-10.855-10.8550.0000.0000.0000.000
133X145GLU-1-0.842-0.93524.064-12.857-12.8570.0000.0000.0000.000
134X146SER0-0.105-0.05827.7180.1390.1390.0000.0000.0000.000
135X147ASP-1-0.816-0.88431.087-9.239-9.2390.0000.0000.0000.000
136X148TRP00.012-0.01327.998-0.350-0.3500.0000.0000.0000.000
137X149SER0-0.060-0.04533.3410.3240.3240.0000.0000.0000.000
138X150ASP-1-0.822-0.91035.354-7.932-7.9320.0000.0000.0000.000
139X151VAL0-0.018-0.03835.9780.0690.0690.0000.0000.0000.000
140X152ASP-1-0.890-0.93838.577-7.523-7.5230.0000.0000.0000.000
141X153LEU0-0.0030.00441.6020.1690.1690.0000.0000.0000.000
142X154LEU0-0.055-0.03136.3570.0890.0890.0000.0000.0000.000
143X155ARG10.9280.95338.2608.1028.1020.0000.0000.0000.000
144X156SER0-0.054-0.00942.7550.1600.1600.0000.0000.0000.000
145X157VAL00.009-0.00244.3520.1300.1300.0000.0000.0000.000
146X158LYS10.8720.95242.7256.9436.9430.0000.0000.0000.000
147X159PRO00.0410.03739.9750.0510.0510.0000.0000.0000.000
148X160PHE00.045-0.00237.514-0.105-0.1050.0000.0000.0000.000
149X161GLY00.0260.01236.611-0.182-0.1820.0000.0000.0000.000
150X162TRP00.0360.01436.046-0.318-0.3180.0000.0000.0000.000
151X163ASN0-0.006-0.00336.907-0.109-0.1090.0000.0000.0000.000
152X164TYR00.0380.01127.517-0.158-0.1580.0000.0000.0000.000
153X165ALA00.0580.02632.135-0.329-0.3290.0000.0000.0000.000
154X166VAL0-0.0070.01233.058-0.166-0.1660.0000.0000.0000.000
155X167SER0-0.057-0.02331.000-0.263-0.2630.0000.0000.0000.000
156X168LYS10.9330.95625.99311.50011.5000.0000.0000.0000.000
157X169THR00.0330.01428.740-0.315-0.3150.0000.0000.0000.000
158X170LEU0-0.055-0.03330.623-0.065-0.0650.0000.0000.0000.000
159X171ALA0-0.007-0.00126.804-0.046-0.0460.0000.0000.0000.000
160X172GLU-1-0.726-0.81424.642-12.742-12.7420.0000.0000.0000.000
161X173LYS10.9410.97726.4579.2459.2450.0000.0000.0000.000
162X174ALA00.0010.01028.3820.0130.0130.0000.0000.0000.000
163X175VAL0-0.009-0.00921.906-0.063-0.0630.0000.0000.0000.000
164X176LEU0-0.043-0.02523.242-0.243-0.2430.0000.0000.0000.000
165X177GLU-1-0.878-0.92225.242-10.083-10.0830.0000.0000.0000.000
166X178PHE0-0.003-0.00823.8870.1230.1230.0000.0000.0000.000
167X179GLY00.010-0.01422.754-0.054-0.0540.0000.0000.0000.000
168X180GLU-1-0.934-0.95323.388-10.919-10.9190.0000.0000.0000.000
169X181GLN0-0.051-0.03125.6100.1340.1340.0000.0000.0000.000
170X182ASN0-0.120-0.06824.5030.4300.4300.0000.0000.0000.000
171X183GLY00.0000.01722.968-0.236-0.2360.0000.0000.0000.000
172X184ILE0-0.048-0.01818.089-0.545-0.5450.0000.0000.0000.000
173X185ASP-1-0.853-0.90615.624-17.309-17.3090.0000.0000.0000.000
174X186VAL0-0.009-0.01316.355-1.060-1.0600.0000.0000.0000.000
175X187VAL00.0220.02315.9020.2740.2740.0000.0000.0000.000
176X188THR0-0.076-0.05018.273-0.294-0.2940.0000.0000.0000.000
177X189LEU00.0250.00415.607-0.113-0.1130.0000.0000.0000.000
178X190ILE0-0.022-0.00920.2500.3040.3040.0000.0000.0000.000
179X191LEU0-0.028-0.01718.948-0.257-0.2570.0000.0000.0000.000
180X192PRO0-0.0110.01922.4400.6220.6220.0000.0000.0000.000
181X193PHE0-0.060-0.03424.777-0.130-0.1300.0000.0000.0000.000
182X194ILE0-0.0040.00519.855-0.350-0.3500.0000.0000.0000.000
183X195VAL00.0330.00421.9440.4360.4360.0000.0000.0000.000
184X196GLY00.0810.04520.027-0.759-0.7590.0000.0000.0000.000
185X197ARG10.8340.91818.45415.59115.5910.0000.0000.0000.000
186X198PHE00.002-0.03619.626-0.537-0.5370.0000.0000.0000.000
187X199VAL00.027-0.00217.6550.3200.3200.0000.0000.0000.000
188X200CYS0-0.067-0.00620.5540.1920.1920.0000.0000.0000.000
189X201PRO00.005-0.01422.9120.2610.2610.0000.0000.0000.000
190X202LYS10.9440.97926.47810.64710.6470.0000.0000.0000.000
191X203LEU00.0710.04626.598-0.553-0.5530.0000.0000.0000.000
192X204PRO0-0.032-0.01223.7570.2520.2520.0000.0000.0000.000
193X205ASP-1-0.819-0.91526.769-10.125-10.1250.0000.0000.0000.000
194X206SER0-0.050-0.04024.6790.2640.2640.0000.0000.0000.000
195X207ILE00.0130.00623.0910.0710.0710.0000.0000.0000.000
196X208GLU-1-0.936-0.96527.407-9.352-9.3520.0000.0000.0000.000
197X209LYS10.8500.91430.8449.8929.8920.0000.0000.0000.000
198X210ALA0-0.0040.00628.2400.2290.2290.0000.0000.0000.000
199X211LEU00.0030.00228.3470.0810.0810.0000.0000.0000.000
200X212VAL00.0440.02031.7260.2840.2840.0000.0000.0000.000
201X213LEU0-0.040-0.02934.9680.2450.2450.0000.0000.0000.000
202X214VAL00.0210.01432.4030.1570.1570.0000.0000.0000.000
203X215LEU0-0.052-0.01831.1830.0580.0580.0000.0000.0000.000
204X216GLY0-0.0140.00335.7270.1500.1500.0000.0000.0000.000
205X217LYS10.9420.97038.4197.3877.3870.0000.0000.0000.000
206X218LYS11.0411.01241.2596.7786.7780.0000.0000.0000.000
207X219GLU-1-0.934-0.97943.227-7.139-7.1390.0000.0000.0000.000
208X220GLN0-0.072-0.02838.7250.0140.0140.0000.0000.0000.000
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