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: VQG91

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 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 314
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4654756.999453
FMO2-HF: Nuclear repulsion 4533436.830983
FMO2-HF: Total energy -121320.16847
FMO2-MP2: Total energy -121675.225622


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.
-195.337-184.85725.913-16.783-19.609-0.176
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 : 0.846 / q_NPA : 0.910
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].
3X7ARG10.8660.9363.78616.20618.236-0.033-1.142-0.8540.004
4X8VAL00.0280.0205.9800.3920.3920.0000.0000.0000.000
5X9CYS00.0170.0128.4631.6661.6660.0000.0000.0000.000
6X10VAL0-0.0010.00911.232-0.173-0.1730.0000.0000.0000.000
7X11THR00.006-0.01013.8610.9220.9220.0000.0000.0000.000
8X12GLY0-0.008-0.00417.661-0.322-0.3220.0000.0000.0000.000
9X13GLY00.0510.00917.080-0.218-0.2180.0000.0000.0000.000
10X14THR00.004-0.00817.966-0.364-0.3640.0000.0000.0000.000
11X15GLY0-0.0050.00620.5650.6090.6090.0000.0000.0000.000
12X16PHE00.0260.00919.714-0.754-0.7540.0000.0000.0000.000
13X17LEU00.0440.02215.631-0.604-0.6040.0000.0000.0000.000
14X18GLY00.0430.02515.790-1.299-1.2990.0000.0000.0000.000
15X19SER0-0.023-0.03115.067-1.246-1.2460.0000.0000.0000.000
16X20TRP0-0.016-0.02712.896-0.129-0.1290.0000.0000.0000.000
17X21ILE00.012-0.00210.744-1.908-1.9080.0000.0000.0000.000
18X22ILE0-0.0290.00310.376-2.762-2.7620.0000.0000.0000.000
19X23LYS10.8360.91410.50622.30322.3030.0000.0000.0000.000
20X24SER00.0170.0158.362-3.021-3.0210.0000.0000.0000.000
21X25LEU0-0.002-0.0065.736-5.168-5.1680.0000.0000.0000.000
22X26LEU0-0.045-0.0115.608-5.505-5.5050.0000.0000.0000.000
23X27GLU-1-0.861-0.9157.539-28.181-28.1810.0000.0000.0000.000
24X28ASN0-0.087-0.0482.638-8.309-7.4220.081-0.267-0.702-0.001
25X29GLY0-0.020-0.0092.580-23.844-20.6551.540-2.056-2.674-0.025
26X30TYR0-0.095-0.0712.170-2.2012.2569.166-4.837-8.785-0.043
27X31SER0-0.047-0.0203.5316.1616.3680.0120.059-0.2780.000
28X32VAL0-0.014-0.0326.015-1.471-1.4710.0000.0000.0000.000
29X33ASN00.0570.0389.3271.4371.4370.0000.0000.0000.000
30X34THR0-0.007-0.01412.566-0.368-0.3680.0000.0000.0000.000
31X35THR00.0380.02715.5361.0141.0140.0000.0000.0000.000
32X36ILE0-0.019-0.01619.143-0.287-0.2870.0000.0000.0000.000
33X37ARG10.8790.92321.61211.72711.7270.0000.0000.0000.000
34X38ALA0-0.0050.00125.127-0.036-0.0360.0000.0000.0000.000
35X39ASP-1-0.759-0.87527.866-10.412-10.4120.0000.0000.0000.000
36X40PRO0-0.014-0.00330.2130.1590.1590.0000.0000.0000.000
37X41GLU-1-0.785-0.87833.390-8.112-8.1120.0000.0000.0000.000
38X42ARG10.8180.89430.6688.5868.5860.0000.0000.0000.000
39X43LYS10.8720.93423.09612.01112.0110.0000.0000.0000.000
40X44ARG10.8570.92826.7559.7959.7950.0000.0000.0000.000
41X45ASP-1-0.775-0.87925.685-11.663-11.6630.0000.0000.0000.000
42X46VAL0-0.018-0.00520.538-0.178-0.1780.0000.0000.0000.000
43X47SER00.0410.01020.634-0.736-0.7360.0000.0000.0000.000
44X48PHE0-0.027-0.01220.229-0.417-0.4170.0000.0000.0000.000
45X49LEU0-0.041-0.02616.767-0.799-0.7990.0000.0000.0000.000
46X50THR00.010-0.01816.361-0.896-0.8960.0000.0000.0000.000
47X51ASN0-0.031-0.01117.5000.2710.2710.0000.0000.0000.000
48X52LEU0-0.0210.01114.222-0.175-0.1750.0000.0000.0000.000
49X53PRO00.0520.00613.1660.0830.0830.0000.0000.0000.000
50X54GLY00.0200.02010.512-1.847-1.8470.0000.0000.0000.000
51X55ALA00.001-0.00810.774-0.415-0.4150.0000.0000.0000.000
52X56SER0-0.037-0.04512.8960.5730.5730.0000.0000.0000.000
53X57GLU-1-0.881-0.91810.985-18.983-18.9830.0000.0000.0000.000
54X58LYS10.8980.9515.83229.98929.9890.0000.0000.0000.000
55X59LEU0-0.0130.0209.400-1.281-1.2810.0000.0000.0000.000
56X60HIS0-0.025-0.00211.0842.0222.0220.0000.0000.0000.000
57X61PHE00.021-0.00514.335-0.447-0.4470.0000.0000.0000.000
58X62PHE00.0190.02014.3640.4740.4740.0000.0000.0000.000
59X63ASN0-0.045-0.03219.477-0.114-0.1140.0000.0000.0000.000
60X64ALA00.0490.02021.845-0.158-0.1580.0000.0000.0000.000
61X65ASP-1-0.895-0.95123.899-10.351-10.3510.0000.0000.0000.000
62X66LEU0-0.036-0.03023.050-0.083-0.0830.0000.0000.0000.000
63X67SER0-0.005-0.00225.491-0.122-0.1220.0000.0000.0000.000
64X68ASN00.0100.01327.3680.1790.1790.0000.0000.0000.000
65X69PRO00.0130.01324.378-0.317-0.3170.0000.0000.0000.000
66X70ASP-1-0.866-0.93523.547-11.269-11.2690.0000.0000.0000.000
67X71SER0-0.078-0.03024.171-0.245-0.2450.0000.0000.0000.000
68X72PHE0-0.019-0.02519.399-0.419-0.4190.0000.0000.0000.000
69X73ALA00.0250.02119.115-0.780-0.7800.0000.0000.0000.000
70X74ALA00.016-0.00118.623-0.486-0.4860.0000.0000.0000.000
71X75ALA0-0.015-0.01016.191-0.581-0.5810.0000.0000.0000.000
72X76ILE00.029-0.00114.337-1.354-1.3540.0000.0000.0000.000
73X77GLU-1-0.910-0.94214.248-15.808-15.8080.0000.0000.0000.000
74X78GLY0-0.024-0.00912.131-0.557-0.5570.0000.0000.0000.000
75X79CYS0-0.127-0.0339.595-1.702-1.7020.0000.0000.0000.000
76X80VAL00.0470.0235.0100.8870.8870.0000.0000.0000.000
77X81GLY00.0170.0118.526-0.293-0.2930.0000.0000.0000.000
78X82ILE0-0.0030.0089.8620.6300.6300.0000.0000.0000.000
79X83PHE00.0210.0038.4090.2220.2220.0000.0000.0000.000
80X84HIS00.0430.03013.9130.1240.1240.0000.0000.0000.000
81X85THR0-0.029-0.03116.1980.4690.4690.0000.0000.0000.000
82X86ALA0-0.0080.01219.0620.7270.7270.0000.0000.0000.000
83X87SER0-0.019-0.02521.8940.1790.1790.0000.0000.0000.000
84X88PRO0-0.0050.00225.4980.0620.0620.0000.0000.0000.000
85X89ILE0-0.0050.01028.5720.2460.2460.0000.0000.0000.000
86X98GLU-1-0.908-0.96140.134-7.409-7.4090.0000.0000.0000.000
87X99ILE00.0460.01438.444-0.255-0.2550.0000.0000.0000.000
88X100VAL00.0230.00335.832-0.258-0.2580.0000.0000.0000.000
89X101THR00.0290.00534.813-0.343-0.3430.0000.0000.0000.000
90X102LYS10.9430.97133.8468.6828.6820.0000.0000.0000.000
91X103ARG10.9900.99531.8499.0779.0770.0000.0000.0000.000
92X104THR0-0.068-0.02830.342-0.410-0.4100.0000.0000.0000.000
93X105VAL00.0350.01329.000-0.430-0.4300.0000.0000.0000.000
94X106ASP-1-0.822-0.90628.404-10.181-10.1810.0000.0000.0000.000
95X107GLY0-0.051-0.01626.761-0.308-0.3080.0000.0000.0000.000
96X108ALA0-0.025-0.01424.427-0.583-0.5830.0000.0000.0000.000
97X109LEU00.0350.00023.464-0.531-0.5310.0000.0000.0000.000
98X110GLY0-0.0030.02524.309-0.130-0.1300.0000.0000.0000.000
99X111ILE0-0.009-0.01616.904-0.006-0.0060.0000.0000.0000.000
100X112LEU00.0120.01219.755-0.450-0.4500.0000.0000.0000.000
101X113LYS10.8970.94221.09710.84010.8400.0000.0000.0000.000
102X114ALA0-0.034-0.00820.5930.1490.1490.0000.0000.0000.000
103X115CYS0-0.029-0.01416.898-0.561-0.5610.0000.0000.0000.000
104X116VAL00.0260.02219.001-0.393-0.3930.0000.0000.0000.000
105X117ASN0-0.028-0.01121.0040.1070.1070.0000.0000.0000.000
106X118SER00.0140.02315.554-0.215-0.2150.0000.0000.0000.000
107X119LYS10.9660.96916.14013.22013.2200.0000.0000.0000.000
108X120THR0-0.043-0.04210.9510.1970.1970.0000.0000.0000.000
109X121VAL0-0.050-0.00511.043-1.803-1.8030.0000.0000.0000.000
110X122LYS10.8870.9345.64240.21140.2110.0000.0000.0000.000
111X123ARG10.7540.85711.22823.28223.2820.0000.0000.0000.000
112X124PHE00.0110.01512.315-0.723-0.7230.0000.0000.0000.000
113X125ILE0-0.021-0.01311.1440.5450.5450.0000.0000.0000.000
114X126TYR00.001-0.00315.3810.3560.3560.0000.0000.0000.000
115X127THR0-0.006-0.00917.851-0.559-0.5590.0000.0000.0000.000
116X128SER0-0.036-0.04119.4960.9690.9690.0000.0000.0000.000
117X129SER0-0.032-0.03722.362-0.298-0.2980.0000.0000.0000.000
118X130GLY00.1360.07824.8880.2300.2300.0000.0000.0000.000
119X131SER0-0.046-0.00427.0510.3040.3040.0000.0000.0000.000
120X132ALA00.0080.00927.1190.4670.4670.0000.0000.0000.000
121X133VAL00.0160.00527.3310.1560.1560.0000.0000.0000.000
122X134SER00.020-0.00530.1390.2850.2850.0000.0000.0000.000
123X135PHE0-0.053-0.02032.4200.2400.2400.0000.0000.0000.000
124X136ASN00.016-0.01033.6420.3660.3660.0000.0000.0000.000
125X137GLY0-0.004-0.00236.4650.1360.1360.0000.0000.0000.000
126X138LYS10.8600.94735.1039.2649.2640.0000.0000.0000.000
127X139ASP-1-0.918-0.95238.520-7.934-7.9340.0000.0000.0000.000
128X140LYS10.7810.88132.8069.7949.7940.0000.0000.0000.000
129X141ASP-1-0.911-0.96535.162-9.290-9.2900.0000.0000.0000.000
130X142VAL00.0370.03530.038-0.321-0.3210.0000.0000.0000.000
131X143LEU0-0.064-0.03229.4580.2860.2860.0000.0000.0000.000
132X144ASP-1-0.795-0.88526.861-11.359-11.3590.0000.0000.0000.000
133X145GLU-1-0.814-0.92122.221-13.915-13.9150.0000.0000.0000.000
134X146SER0-0.084-0.05026.0700.1400.1400.0000.0000.0000.000
135X147ASP-1-0.790-0.87829.416-9.513-9.5130.0000.0000.0000.000
136X148TRP00.017-0.01226.836-0.397-0.3970.0000.0000.0000.000
137X149SER0-0.054-0.04131.7450.3420.3420.0000.0000.0000.000
138X150ASP-1-0.822-0.91333.792-8.246-8.2460.0000.0000.0000.000
139X151VAL0-0.023-0.04035.0400.0740.0740.0000.0000.0000.000
140X152ASP-1-0.869-0.92937.557-7.800-7.8000.0000.0000.0000.000
141X153LEU00.0020.02040.1750.1880.1880.0000.0000.0000.000
142X154LEU0-0.052-0.02935.1400.0960.0960.0000.0000.0000.000
143X155ARG10.9270.95538.1188.4328.4320.0000.0000.0000.000
144X156SER0-0.054-0.02241.9660.1730.1730.0000.0000.0000.000
145X157VAL00.006-0.00743.0670.1490.1490.0000.0000.0000.000
146X158LYS10.8500.94541.6347.1327.1320.0000.0000.0000.000
147X159PRO00.0510.04138.7060.0600.0600.0000.0000.0000.000
148X160PHE00.043-0.00235.970-0.110-0.1100.0000.0000.0000.000
149X161GLY00.0270.01335.461-0.197-0.1970.0000.0000.0000.000
150X162TRP00.0340.01334.985-0.344-0.3440.0000.0000.0000.000
151X163ASN0-0.006-0.00536.136-0.163-0.1630.0000.0000.0000.000
152X164TYR00.0400.01326.564-0.167-0.1670.0000.0000.0000.000
153X165ALA00.0560.02631.395-0.352-0.3520.0000.0000.0000.000
154X166VAL0-0.0120.01232.139-0.195-0.1950.0000.0000.0000.000
155X167SER0-0.045-0.02031.151-0.287-0.2870.0000.0000.0000.000
156X168LYS10.9020.93924.79612.50112.5010.0000.0000.0000.000
157X169THR00.0310.00127.998-0.346-0.3460.0000.0000.0000.000
158X170LEU0-0.053-0.02929.839-0.087-0.0870.0000.0000.0000.000
159X171ALA0-0.016-0.00226.779-0.072-0.0720.0000.0000.0000.000
160X172GLU-1-0.724-0.80023.617-13.608-13.6080.0000.0000.0000.000
161X173LYS10.9210.97325.8929.7769.7760.0000.0000.0000.000
162X174ALA00.0030.00928.2900.0070.0070.0000.0000.0000.000
163X175VAL00.000-0.00821.828-0.076-0.0760.0000.0000.0000.000
164X176LEU0-0.034-0.01822.663-0.270-0.2700.0000.0000.0000.000
165X177GLU-1-0.852-0.89824.957-10.437-10.4370.0000.0000.0000.000
166X178PHE00.003-0.00623.6790.1240.1240.0000.0000.0000.000
167X179GLY00.020-0.00422.566-0.048-0.0480.0000.0000.0000.000
168X180GLU-1-0.945-0.96223.196-11.716-11.7160.0000.0000.0000.000
169X181GLN0-0.096-0.06225.4460.1890.1890.0000.0000.0000.000
170X182ASN0-0.115-0.06824.2710.4620.4620.0000.0000.0000.000
171X183GLY0-0.0020.01622.810-0.250-0.2500.0000.0000.0000.000
172X184ILE0-0.048-0.02017.869-0.616-0.6160.0000.0000.0000.000
173X185ASP-1-0.851-0.90515.567-19.159-19.1590.0000.0000.0000.000
174X186VAL0-0.010-0.01416.185-1.231-1.2310.0000.0000.0000.000
175X187VAL00.0200.02314.6490.2970.2970.0000.0000.0000.000
176X188THR0-0.071-0.05817.368-0.298-0.2980.0000.0000.0000.000
177X189LEU00.0200.00413.971-0.170-0.1700.0000.0000.0000.000
178X190ILE0-0.024-0.01018.6480.3900.3900.0000.0000.0000.000
179X191LEU0-0.026-0.01317.555-0.324-0.3240.0000.0000.0000.000
180X192PRO0-0.0020.01821.1980.6690.6690.0000.0000.0000.000
181X193PHE0-0.050-0.02623.580-0.151-0.1510.0000.0000.0000.000
182X194ILE0-0.0090.00218.838-0.384-0.3840.0000.0000.0000.000
183X195VAL00.0360.00221.0540.4980.4980.0000.0000.0000.000
184X196GLY00.0820.04519.513-0.822-0.8220.0000.0000.0000.000
185X197ARG10.8010.88618.49615.42015.4200.0000.0000.0000.000
186X198PHE00.005-0.03919.252-0.614-0.6140.0000.0000.0000.000
187X199VAL00.034-0.00217.6240.4200.4200.0000.0000.0000.000
188X200CYS0-0.077-0.01020.4800.2190.2190.0000.0000.0000.000
189X201PRO00.007-0.01422.6660.2870.2870.0000.0000.0000.000
190X202LYS10.8770.94526.15911.05611.0560.0000.0000.0000.000
191X203LEU00.0800.05326.196-0.579-0.5790.0000.0000.0000.000
192X204PRO0-0.028-0.00923.2520.2290.2290.0000.0000.0000.000
193X205ASP-1-0.811-0.89226.134-10.308-10.3080.0000.0000.0000.000
194X206SER0-0.026-0.03023.8130.2710.2710.0000.0000.0000.000
195X207ILE00.0140.00422.4740.0780.0780.0000.0000.0000.000
196X208GLU-1-0.940-0.97026.728-9.439-9.4390.0000.0000.0000.000
197X209LYS10.8250.88530.05110.30110.3010.0000.0000.0000.000
198X210ALA0-0.0130.00227.4580.2270.2270.0000.0000.0000.000
199X211LEU00.0060.00227.6870.0830.0830.0000.0000.0000.000
200X212VAL00.0370.01831.1240.3070.3070.0000.0000.0000.000
201X213LEU0-0.029-0.02334.3150.2580.2580.0000.0000.0000.000
202X214VAL00.0110.00732.0370.1660.1660.0000.0000.0000.000
203X215LEU0-0.051-0.00630.8380.0650.0650.0000.0000.0000.000
204X216GLY0-0.044-0.01335.2810.1510.1510.0000.0000.0000.000
205X217LYS10.8840.92937.8537.4107.4100.0000.0000.0000.000
206X218LYS10.9760.98140.5617.0027.0020.0000.0000.0000.000
207X219GLU-1-0.868-0.93842.427-7.296-7.2960.0000.0000.0000.000
208X220GLN0-0.047-0.01838.0250.0950.0950.0000.0000.0000.000
209X221ILE0-0.0140.01238.058-0.264-0.2640.0000.0000.0000.000
210X222GLY00.0380.02237.3490.1950.1950.0000.0000.0000.000
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