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: 4J56N

Calculation Name: 5HXG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5HXG

Chain ID: A

ChEMBL ID:

UniProt ID: A0A6C8

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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2517352.664275
FMO2-HF: Nuclear repulsion 2433674.614484
FMO2-HF: Total energy -83678.049791
FMO2-MP2: Total energy -83921.134031


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:2:ARG)


Summations of interaction energy for fragment #1(A:2:ARG)
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.
-30.805-56.75648.702-17.541-5.2090.027
Interaction energy analysis for fragmet #1(A:2:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.905 / q_NPA : 0.975
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].
3A4PHE00.0450.0323.662-2.534-1.387-0.043-0.119-0.985-0.002
4A5PHE00.0200.0006.9371.1301.1300.0000.0000.0000.000
5A6MET0-0.0020.02510.4220.3590.3590.0000.0000.0000.000
6A7ALA00.0110.00012.9900.0250.0250.0000.0000.0000.000
7A8GLU-1-0.873-0.94316.550-14.024-14.0240.0000.0000.0000.000
8A9PRO0-0.017-0.00718.9080.2320.2320.0000.0000.0000.000
9A10ILE0-0.010-0.00522.5100.1930.1930.0000.0000.0000.000
10A11ARG10.8300.90425.41110.35010.3500.0000.0000.0000.000
11A12ALA00.0490.00928.6640.0950.0950.0000.0000.0000.000
12A13MET0-0.049-0.00632.3030.0250.0250.0000.0000.0000.000
13A14GLU-1-0.841-0.90834.653-7.475-7.4750.0000.0000.0000.000
14A15GLY0-0.0050.00531.6090.0420.0420.0000.0000.0000.000
15A16ASP-1-0.928-0.95030.850-8.706-8.7060.0000.0000.0000.000
16A17LEU0-0.069-0.04424.533-0.153-0.1530.0000.0000.0000.000
17A18LEU0-0.012-0.00328.0040.1950.1950.0000.0000.0000.000
18A19GLY00.0320.00725.1450.0210.0210.0000.0000.0000.000
19A20VAL0-0.049-0.00919.4610.0250.0250.0000.0000.0000.000
20A21GLU-1-0.727-0.83617.654-13.572-13.5720.0000.0000.0000.000
21A22ILE0-0.013-0.00913.175-0.365-0.3650.0000.0000.0000.000
22A23ILE0-0.026-0.00612.065-0.094-0.0940.0000.0000.0000.000
23A24THR0-0.028-0.0166.967-1.216-1.2160.0000.0000.0000.000
24A25HIS00.0140.0207.2360.8370.8370.0000.0000.0000.000
25A26PHE00.003-0.0571.549-16.048-43.14648.745-17.422-4.2240.029
26A39VAL00.0580.0138.0660.1130.1130.0000.0000.0000.000
27A40ILE00.0510.0478.309-0.537-0.5370.0000.0000.0000.000
28A41SER00.0070.00010.546-0.244-0.2440.0000.0000.0000.000
29A42SER0-0.069-0.04411.6330.7790.7790.0000.0000.0000.000
30A43TRP0-0.0040.0035.656-1.034-1.0340.0000.0000.0000.000
31A44ASP-1-0.768-0.87612.023-22.073-22.0730.0000.0000.0000.000
32A45ASN00.041-0.01812.924-1.435-1.4350.0000.0000.0000.000
33A46SER00.0170.02812.611-0.738-0.7380.0000.0000.0000.000
34A47GLN0-0.030-0.0227.9420.2490.2490.0000.0000.0000.000
35A48LYS10.8210.9049.74418.03818.0380.0000.0000.0000.000
36A49ARG10.7860.86512.28118.14218.1420.0000.0000.0000.000
37A50ARG10.8700.9147.32530.51530.5150.0000.0000.0000.000
38A51PHE00.0290.0288.057-0.161-0.1610.0000.0000.0000.000
39A52LEU00.0470.0129.8050.7860.7860.0000.0000.0000.000
40A53LEU0-0.033-0.01612.8581.0051.0050.0000.0000.0000.000
41A54ASP-1-0.851-0.8958.031-30.554-30.5540.0000.0000.0000.000
42A55LEU00.0240.03311.4221.1161.1160.0000.0000.0000.000
43A56LEU00.006-0.00912.6111.2801.2800.0000.0000.0000.000
44A57ARG10.9370.96214.25020.30220.3020.0000.0000.0000.000
45A58THR00.0120.00712.0350.6420.6420.0000.0000.0000.000
46A59ILE00.001-0.00814.5600.9470.9470.0000.0000.0000.000
47A60ALA0-0.003-0.01517.5420.9250.9250.0000.0000.0000.000
48A61ALA0-0.047-0.00717.3100.8610.8610.0000.0000.0000.000
49A62LYS10.8120.88617.73815.50815.5080.0000.0000.0000.000
50A63HIS0-0.038-0.02820.8351.0051.0050.0000.0000.0000.000
51A64GLY00.0310.01723.2850.4840.4840.0000.0000.0000.000
52A65TRP00.0040.00523.3230.5450.5450.0000.0000.0000.000
53A66PHE00.0560.01020.1140.2930.2930.0000.0000.0000.000
54A67LEU00.0090.01125.6960.4200.4200.0000.0000.0000.000
55A68ARG10.9020.95428.7209.7759.7750.0000.0000.0000.000
56A69HIS10.8250.90927.34910.55210.5520.0000.0000.0000.000
57A70GLY00.0370.04330.5460.1170.1170.0000.0000.0000.000
58A71LEU0-0.057-0.00925.6820.0330.0330.0000.0000.0000.000
59A72PHE00.0410.02024.173-0.131-0.1310.0000.0000.0000.000
60A73CYS0-0.051-0.03319.330-0.456-0.4560.0000.0000.0000.000
61A74ILE00.0070.02019.705-0.139-0.1390.0000.0000.0000.000
62A75VAL00.007-0.00515.917-0.828-0.8280.0000.0000.0000.000
63A76ASN0-0.0170.00716.0261.0971.0970.0000.0000.0000.000
64A77ILE0-0.018-0.01116.242-1.075-1.0750.0000.0000.0000.000
65A78ASP-1-0.739-0.87315.724-17.424-17.4240.0000.0000.0000.000
66A79ARG10.8540.88418.79811.77211.7720.0000.0000.0000.000
67A80GLY0-0.0130.00318.3150.3240.3240.0000.0000.0000.000
68A81MET00.0060.00313.1080.1880.1880.0000.0000.0000.000
69A82ALA00.0420.02818.1540.2900.2900.0000.0000.0000.000
70A83GLN0-0.007-0.00521.1520.3450.3450.0000.0000.0000.000
71A84LEU0-0.022-0.00815.8760.2720.2720.0000.0000.0000.000
72A85VAL00.0120.01820.2340.2970.2970.0000.0000.0000.000
73A86LEU0-0.014-0.00222.1850.5410.5410.0000.0000.0000.000
74A87GLN0-0.045-0.01723.2090.6700.6700.0000.0000.0000.000
75A88ASP-1-0.811-0.87718.971-16.028-16.0280.0000.0000.0000.000
76A89LYS10.9260.93821.49513.57513.5750.0000.0000.0000.000
77A90ASP-1-0.839-0.89018.600-15.164-15.1640.0000.0000.0000.000
78A91ILE0-0.014-0.01615.791-0.090-0.0900.0000.0000.0000.000
79A92ARG10.8510.91719.70411.93811.9380.0000.0000.0000.000
80A93ALA0-0.0240.00523.0360.3940.3940.0000.0000.0000.000
81A94LEU0-0.030-0.01517.9480.1780.1780.0000.0000.0000.000
82A95LEU00.0170.00420.8000.2140.2140.0000.0000.0000.000
83A96HIS0-0.025-0.02822.9170.5250.5250.0000.0000.0000.000
84A97ALA0-0.0180.00924.5460.4670.4670.0000.0000.0000.000
85A98MET0-0.077-0.02319.3960.1700.1700.0000.0000.0000.000
86A99LEU00.0190.00524.710-0.214-0.2140.0000.0000.0000.000
87A100PHE00.0280.02122.0120.1770.1770.0000.0000.0000.000
88A101VAL0-0.021-0.00920.406-0.229-0.2290.0000.0000.0000.000
89A102GLU-1-0.851-0.92022.785-10.440-10.4400.0000.0000.0000.000
90A103LEU0-0.014-0.00520.773-0.657-0.6570.0000.0000.0000.000
91A104GLN0-0.051-0.04920.3541.1161.1160.0000.0000.0000.000
92A105VAL0-0.021-0.00720.700-0.710-0.7100.0000.0000.0000.000
93A106ALA00.0470.02321.5960.2900.2900.0000.0000.0000.000
94A107GLU-1-0.733-0.90123.453-9.621-9.6210.0000.0000.0000.000
95A108HIS00.0070.00120.1840.4920.4920.0000.0000.0000.000
96A109PHE0-0.062-0.02321.876-0.271-0.2710.0000.0000.0000.000
97A110SER0-0.035-0.01824.3650.0040.0040.0000.0000.0000.000
98A111CYS0-0.090-0.04927.1530.0460.0460.0000.0000.0000.000
99A112GLN00.025-0.01427.868-0.509-0.5090.0000.0000.0000.000
100A113ASP-1-0.879-0.89030.440-8.977-8.9770.0000.0000.0000.000
101A114ASN0-0.077-0.03233.2350.2390.2390.0000.0000.0000.000
102A115VAL00.018-0.00735.6320.0950.0950.0000.0000.0000.000
103A116LEU0-0.029-0.01837.3420.0410.0410.0000.0000.0000.000
104A117VAL00.0390.02033.237-0.208-0.2080.0000.0000.0000.000
105A118ASP-1-0.709-0.84029.388-10.607-10.6070.0000.0000.0000.000
106A119PRO00.034-0.00331.844-0.077-0.0770.0000.0000.0000.000
107A120LEU0-0.0300.00024.387-0.025-0.0250.0000.0000.0000.000
108A121ILE00.0380.02426.921-0.199-0.1990.0000.0000.0000.000
109A122HIS00.0280.01329.4050.1560.1560.0000.0000.0000.000
110A123ALA0-0.024-0.01829.4640.1090.1090.0000.0000.0000.000
111A124LEU0-0.007-0.02324.380-0.076-0.0760.0000.0000.0000.000
112A125HIS00.0240.02028.379-0.233-0.2330.0000.0000.0000.000
113A126LYS10.8620.94931.1739.0059.0050.0000.0000.0000.000
114A127GLN0-0.066-0.01327.432-0.034-0.0340.0000.0000.0000.000
115A128PRO00.0300.01628.5960.0940.0940.0000.0000.0000.000
116A129ASN0-0.069-0.03524.9480.1670.1670.0000.0000.0000.000
117A130PRO00.0610.04027.4120.0230.0230.0000.0000.0000.000
118A131LEU00.0060.00425.954-0.536-0.5360.0000.0000.0000.000
119A132TRP0-0.029-0.03324.4630.4520.4520.0000.0000.0000.000
120A133LEU0-0.037-0.01425.415-0.301-0.3010.0000.0000.0000.000
121A134GLY00.018-0.01923.2150.2130.2130.0000.0000.0000.000
122A135ASP-1-0.821-0.90324.042-11.659-11.6590.0000.0000.0000.000
123A136LEU00.0140.00925.9460.2430.2430.0000.0000.0000.000
124A137GLY0-0.016-0.01829.6130.0970.0970.0000.0000.0000.000
125A138VAL0-0.046-0.02026.0210.1560.1560.0000.0000.0000.000
126A139GLY0-0.032-0.00629.2170.1090.1090.0000.0000.0000.000
127A140ASN0-0.056-0.03026.1500.1720.1720.0000.0000.0000.000
128A141ALA0-0.0070.00329.566-0.107-0.1070.0000.0000.0000.000
129A142THR00.0220.01631.5830.1870.1870.0000.0000.0000.000
130A143ALA00.0540.01833.516-0.200-0.2000.0000.0000.0000.000
131A144ALA00.0210.02135.5750.0630.0630.0000.0000.0000.000
132A145PRO00.036-0.00431.4060.1280.1280.0000.0000.0000.000
133A146LEU00.0230.01433.504-0.016-0.0160.0000.0000.0000.000
134A147VAL0-0.025-0.01834.7060.1210.1210.0000.0000.0000.000
135A148CYS0-0.099-0.04736.7690.2340.2340.0000.0000.0000.000
136A149GLY00.0140.01636.6270.0330.0330.0000.0000.0000.000
137A150CYS0-0.083-0.04131.757-0.073-0.0730.0000.0000.0000.000
138A151PHE0-0.008-0.00328.057-0.220-0.2200.0000.0000.0000.000
139A152SER00.0170.00530.0580.3320.3320.0000.0000.0000.000
140A153GLY00.0180.00229.2630.1850.1850.0000.0000.0000.000
141A154VAL0-0.020-0.01528.398-0.199-0.1990.0000.0000.0000.000
142A155LYS10.8300.92221.30212.61512.6150.0000.0000.0000.000
143A156LEU0-0.039-0.01327.626-0.010-0.0100.0000.0000.0000.000
144A157ASP-1-0.767-0.89526.466-10.638-10.6380.0000.0000.0000.000
145A158ARG10.9560.98520.33912.28412.2840.0000.0000.0000.000
146A159SER00.0250.01127.2100.2750.2750.0000.0000.0000.000
147A160PHE0-0.0030.00129.2960.4320.4320.0000.0000.0000.000
148A161PHE00.0160.00130.0930.3290.3290.0000.0000.0000.000
149A162VAL00.0140.00229.8290.2930.2930.0000.0000.0000.000
150A163SER0-0.070-0.02032.5790.3250.3250.0000.0000.0000.000
151A164GLN0-0.042-0.05235.1440.4860.4860.0000.0000.0000.000
152A165ILE0-0.0260.01234.4310.2340.2340.0000.0000.0000.000
153A166GLU-1-0.793-0.88536.976-7.429-7.4290.0000.0000.0000.000
154A167LYS10.8540.95039.3327.5917.5910.0000.0000.0000.000
155A168MET00.0490.01442.106-0.021-0.0210.0000.0000.0000.000
156A169THR0-0.018-0.01742.9130.0540.0540.0000.0000.0000.000
157A170PHE00.0480.03635.106-0.070-0.0700.0000.0000.0000.000
158A171PRO00.0650.00940.291-0.105-0.1050.0000.0000.0000.000
159A172LEU0-0.014-0.00342.258-0.009-0.0090.0000.0000.0000.000
160A173LEU0-0.0040.00836.660-0.012-0.0120.0000.0000.0000.000
161A174VAL00.0500.02636.761-0.120-0.1200.0000.0000.0000.000
162A175LYS10.8800.94438.8676.4716.4710.0000.0000.0000.000
163A176HIS0-0.015-0.01941.6140.1560.1560.0000.0000.0000.000
164A177ILE00.0200.01234.578-0.030-0.0300.0000.0000.0000.000
165A178ARG10.8340.91137.1817.5277.5270.0000.0000.0000.000
166A179HIS0-0.092-0.03038.6690.1670.1670.0000.0000.0000.000
167A180TYR0-0.045-0.02237.7910.1040.1040.0000.0000.0000.000
168A181CYS0-0.037-0.00833.079-0.216-0.2160.0000.0000.0000.000
169A182ASP-1-0.777-0.84735.707-7.815-7.8150.0000.0000.0000.000
170A183LYS10.8620.92432.2118.3948.3940.0000.0000.0000.000
171A184ILE00.0500.01631.548-0.195-0.1950.0000.0000.0000.000
172A185VAL0-0.006-0.00426.0810.1450.1450.0000.0000.0000.000
173A186VAL00.001-0.00228.926-0.034-0.0340.0000.0000.0000.000
174A187GLY00.0700.02324.752-0.090-0.0900.0000.0000.0000.000
175A188GLY0-0.056-0.03023.3600.2360.2360.0000.0000.0000.000
176A189GLN0-0.033-0.02424.3360.4830.4830.0000.0000.0000.000
177A190GLU-1-0.904-0.95124.096-10.866-10.8660.0000.0000.0000.000
178A191ASN0-0.019-0.02526.3990.2780.2780.0000.0000.0000.000
179A192ALA00.0630.01629.741-0.042-0.0420.0000.0000.0000.000
180A193ARG10.8740.95732.7128.1058.1050.0000.0000.0000.000
181A194TYR0-0.014-0.04332.3710.1460.1460.0000.0000.0000.000
182A195LEU00.0270.03331.2190.1220.1220.0000.0000.0000.000
183A196PRO00.0330.01335.2390.0740.0740.0000.0000.0000.000
184A197ALA00.0330.02338.2090.1260.1260.0000.0000.0000.000
185A198LEU0-0.028-0.02032.4580.0440.0440.0000.0000.0000.000
186A199LYS10.8960.91536.7427.3187.3180.0000.0000.0000.000
187A200THR0-0.087-0.04438.5130.1450.1450.0000.0000.0000.000
188A201ALA0-0.049-0.02438.6330.1120.1120.0000.0000.0000.000
189A202GLY0-0.017-0.00139.3570.0430.0430.0000.0000.0000.000
190A203ILE0-0.052-0.03032.776-0.114-0.1140.0000.0000.0000.000
191A204TRP00.0030.01129.5670.0600.0600.0000.0000.0000.000
192A205ALA00.0240.00029.3430.0190.0190.0000.0000.0000.000
193A206THR0-0.012-0.00928.4470.0090.0090.0000.0000.0000.000
194A207GLN0-0.003-0.02220.0340.2650.2650.0000.0000.0000.000
195A208GLY0-0.003-0.00922.3300.2210.2210.0000.0000.0000.000
196A209THR00.0600.03219.7730.0070.0070.0000.0000.0000.000
197A210LEU0-0.0340.00122.1260.1100.1100.0000.0000.0000.000
198A211PHE0-0.073-0.04023.9620.2720.2720.0000.0000.0000.000
199A212PRO00.0110.00120.189-0.377-0.3770.0000.0000.0000.000
200A213SER0-0.002-0.00316.0080.3380.3380.0000.0000.0000.000
201A214VAL0-0.0020.01416.5220.0200.0200.0000.0000.0000.000
202A215ALA00.0750.02412.919-0.542-0.5420.0000.0000.0000.000
203A216LEU0-0.019-0.00813.4620.9920.9920.0000.0000.0000.000
204A217GLU-1-0.873-0.96311.955-20.947-20.9470.0000.0000.0000.000
205A218GLU-1-0.956-0.97115.356-14.825-14.8250.0000.0000.0000.000
206A219ILE00.0050.01618.1650.7100.7100.0000.0000.0000.000
207A220GLU-1-0.853-0.92519.775-13.107-13.1070.0000.0000.0000.000
208A221THR0-0.067-0.03620.4410.6340.6340.0000.0000.0000.000
209A222LEU0-0.029-0.00420.9560.4250.4250.0000.0000.0000.000
210A223LEU00.0240.01123.8120.3270.3270.0000.0000.0000.000
211A224LEU00.0460.03927.177-0.015-0.0150.0000.0000.0000.000