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: 5J4YZ

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 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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2519247.07275
FMO2-HF: Nuclear repulsion 2435568.717079
FMO2-HF: Total energy -83678.355671
FMO2-MP2: Total energy -83921.308608


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.
-22.459-17.8350.202-2.05-2.7750.002
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 : 0.993 / q_NPA : 0.984
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].
3A4PHE00.0240.0143.788-3.579-1.003-0.020-1.320-1.2360.003
4A5PHE00.021-0.0016.5310.5290.5290.0000.0000.0000.000
5A6MET00.0090.03510.3260.4230.4230.0000.0000.0000.000
6A7ALA00.001-0.00613.4300.0020.0020.0000.0000.0000.000
7A8GLU-1-0.834-0.88917.007-14.361-14.3610.0000.0000.0000.000
8A9PRO0-0.004-0.00219.5800.3080.3080.0000.0000.0000.000
9A10ILE0-0.022-0.01322.9630.2530.2530.0000.0000.0000.000
10A11ARG10.8430.90125.80610.50810.5080.0000.0000.0000.000
11A12ALA00.0490.01429.3620.0680.0680.0000.0000.0000.000
12A13MET0-0.054-0.01333.0270.0200.0200.0000.0000.0000.000
13A14GLU-1-0.846-0.90535.530-7.557-7.5570.0000.0000.0000.000
14A15GLY00.0040.01532.4860.0630.0630.0000.0000.0000.000
15A16ASP-1-0.854-0.89831.236-8.995-8.9950.0000.0000.0000.000
16A17LEU0-0.074-0.03624.698-0.106-0.1060.0000.0000.0000.000
17A18LEU0-0.029-0.01628.2350.2340.2340.0000.0000.0000.000
18A19GLY00.0300.00525.3130.0540.0540.0000.0000.0000.000
19A20VAL0-0.049-0.01219.5550.0050.0050.0000.0000.0000.000
20A21GLU-1-0.729-0.83918.150-13.960-13.9600.0000.0000.0000.000
21A22ILE0-0.015-0.00613.619-0.413-0.4130.0000.0000.0000.000
22A23ILE0-0.030-0.00612.577-0.096-0.0960.0000.0000.0000.000
23A24THR0-0.030-0.0197.474-0.965-0.9650.0000.0000.0000.000
24A25HIS00.0040.0148.0230.3920.3920.0000.0000.0000.000
25A26PHE0-0.027-0.0372.686-1.2170.8310.222-0.730-1.539-0.001
26A39VAL00.0610.0157.521-0.049-0.0490.0000.0000.0000.000
27A40ILE00.0430.0388.2820.2750.2750.0000.0000.0000.000
28A41SER00.0160.00710.565-0.034-0.0340.0000.0000.0000.000
29A42SER0-0.058-0.03312.3520.8920.8920.0000.0000.0000.000
30A43TRP00.0090.0135.908-0.744-0.7440.0000.0000.0000.000
31A44ASP-1-0.755-0.86111.417-22.863-22.8630.0000.0000.0000.000
32A45ASN00.040-0.01512.938-1.447-1.4470.0000.0000.0000.000
33A46SER00.0210.02612.676-0.389-0.3890.0000.0000.0000.000
34A47GLN0-0.085-0.0557.878-3.476-3.4760.0000.0000.0000.000
35A48LYS10.8220.9009.96018.57218.5720.0000.0000.0000.000
36A49ARG10.7830.85912.48117.56117.5610.0000.0000.0000.000
37A50ARG10.8710.9117.47429.75729.7570.0000.0000.0000.000
38A51PHE00.0420.0237.4200.2970.2970.0000.0000.0000.000
39A52LEU00.0440.0149.6810.7620.7620.0000.0000.0000.000
40A53LEU0-0.030-0.01613.1821.1111.1110.0000.0000.0000.000
41A54ASP-1-0.859-0.8977.928-29.477-29.4770.0000.0000.0000.000
42A55LEU00.0290.03811.1981.1731.1730.0000.0000.0000.000
43A56LEU00.007-0.00512.2631.2901.2900.0000.0000.0000.000
44A57ARG10.9250.95314.10319.74319.7430.0000.0000.0000.000
45A58THR00.0070.00111.8760.6310.6310.0000.0000.0000.000
46A59ILE0-0.001-0.00814.3930.8970.8970.0000.0000.0000.000
47A60ALA00.005-0.00517.3560.9320.9320.0000.0000.0000.000
48A61ALA0-0.050-0.01316.7260.8380.8380.0000.0000.0000.000
49A62LYS10.8000.88416.75415.59715.5970.0000.0000.0000.000
50A63HIS0-0.047-0.03220.2731.0481.0480.0000.0000.0000.000
51A64GLY00.0210.01723.0160.4680.4680.0000.0000.0000.000
52A65TRP0-0.002-0.00323.2000.5440.5440.0000.0000.0000.000
53A66PHE00.0490.01519.7660.2660.2660.0000.0000.0000.000
54A67LEU00.0410.02125.3550.4580.4580.0000.0000.0000.000
55A68ARG10.8980.95628.4409.8049.8040.0000.0000.0000.000
56A69HIS10.8130.89626.59810.61110.6110.0000.0000.0000.000
57A70GLY00.0320.03830.1060.1220.1220.0000.0000.0000.000
58A71LEU0-0.0560.00125.5410.0220.0220.0000.0000.0000.000
59A72PHE00.0440.02024.518-0.205-0.2050.0000.0000.0000.000
60A73CYS0-0.052-0.03319.658-0.477-0.4770.0000.0000.0000.000
61A74ILE00.0200.03020.206-0.278-0.2780.0000.0000.0000.000
62A75VAL00.007-0.00716.074-0.841-0.8410.0000.0000.0000.000
63A76ASN0-0.0250.00116.2981.0641.0640.0000.0000.0000.000
64A77ILE0-0.013-0.00816.532-1.048-1.0480.0000.0000.0000.000
65A78ASP-1-0.747-0.87216.269-17.474-17.4740.0000.0000.0000.000
66A79ARG10.8470.86819.26111.80111.8010.0000.0000.0000.000
67A80GLY0-0.0040.00818.9990.4130.4130.0000.0000.0000.000
68A81MET00.0020.00613.3150.0820.0820.0000.0000.0000.000
69A82ALA00.0390.02518.4640.2560.2560.0000.0000.0000.000
70A83GLN0-0.003-0.00421.4740.3460.3460.0000.0000.0000.000
71A84LEU0-0.035-0.01616.0670.2860.2860.0000.0000.0000.000
72A85VAL00.0200.01320.0720.2940.2940.0000.0000.0000.000
73A86LEU0-0.0310.00122.2100.5490.5490.0000.0000.0000.000
74A87GLN0-0.034-0.01423.5040.6040.6040.0000.0000.0000.000
75A88ASP-1-0.797-0.86919.368-15.716-15.7160.0000.0000.0000.000
76A89LYS10.9100.92521.55513.73713.7370.0000.0000.0000.000
77A90ASP-1-0.841-0.88118.770-14.792-14.7920.0000.0000.0000.000
78A91ILE0-0.011-0.01216.107-0.156-0.1560.0000.0000.0000.000
79A92ARG10.8580.91719.74311.90811.9080.0000.0000.0000.000
80A93ALA0-0.026-0.00122.9650.3620.3620.0000.0000.0000.000
81A94LEU0-0.038-0.01917.3690.1920.1920.0000.0000.0000.000
82A95LEU00.0230.01120.5830.1920.1920.0000.0000.0000.000
83A96HIS0-0.026-0.03122.2720.4420.4420.0000.0000.0000.000
84A97ALA0-0.0250.00324.3980.4670.4670.0000.0000.0000.000
85A98MET0-0.071-0.02119.0830.1590.1590.0000.0000.0000.000
86A99LEU00.0180.00724.384-0.224-0.2240.0000.0000.0000.000
87A100PHE00.0310.02621.9040.1940.1940.0000.0000.0000.000
88A101VAL0-0.022-0.01019.934-0.278-0.2780.0000.0000.0000.000
89A102GLU-1-0.872-0.93022.765-10.697-10.6970.0000.0000.0000.000
90A103LEU0-0.012-0.01421.136-0.655-0.6550.0000.0000.0000.000
91A104GLN0-0.050-0.04220.7271.0971.0970.0000.0000.0000.000
92A105VAL0-0.013-0.00921.087-0.723-0.7230.0000.0000.0000.000
93A106ALA00.0400.01821.9180.1550.1550.0000.0000.0000.000
94A107GLU-1-0.729-0.89823.801-9.831-9.8310.0000.0000.0000.000
95A108HIS00.0120.00020.6320.5550.5550.0000.0000.0000.000
96A109PHE0-0.042-0.01622.090-0.410-0.4100.0000.0000.0000.000
97A110SER0-0.054-0.02624.5700.0480.0480.0000.0000.0000.000
98A111CYS0-0.103-0.06427.880-0.126-0.1260.0000.0000.0000.000
99A112GLN0-0.002-0.01428.435-0.522-0.5220.0000.0000.0000.000
100A113ASP-1-0.865-0.90730.604-9.148-9.1480.0000.0000.0000.000
101A114ASN0-0.075-0.03332.6140.1300.1300.0000.0000.0000.000
102A115VAL00.035-0.00135.678-0.028-0.0280.0000.0000.0000.000
103A116LEU0-0.015-0.00237.6450.0650.0650.0000.0000.0000.000
104A117VAL00.0360.01433.660-0.236-0.2360.0000.0000.0000.000
105A118ASP-1-0.699-0.81629.742-10.690-10.6900.0000.0000.0000.000
106A119PRO00.033-0.00531.911-0.093-0.0930.0000.0000.0000.000
107A120LEU0-0.0330.00124.593-0.001-0.0010.0000.0000.0000.000
108A121ILE00.0400.02526.960-0.204-0.2040.0000.0000.0000.000
109A122HIS00.0380.01729.5460.1950.1950.0000.0000.0000.000
110A123ALA0-0.019-0.00729.6430.1790.1790.0000.0000.0000.000
111A124LEU00.011-0.00324.407-0.052-0.0520.0000.0000.0000.000
112A125HIS00.0270.02028.506-0.257-0.2570.0000.0000.0000.000
113A126LYS10.8330.92631.4559.2099.2090.0000.0000.0000.000
114A127GLN0-0.032-0.00527.250-0.034-0.0340.0000.0000.0000.000
115A128PRO00.0080.00628.4810.1030.1030.0000.0000.0000.000
116A129ASN0-0.037-0.02524.5680.2250.2250.0000.0000.0000.000
117A130PRO00.0490.03327.3220.0090.0090.0000.0000.0000.000
118A131LEU00.0040.01526.324-0.568-0.5680.0000.0000.0000.000
119A132TRP0-0.013-0.02524.8720.4190.4190.0000.0000.0000.000
120A133LEU0-0.031-0.00825.832-0.269-0.2690.0000.0000.0000.000
121A134GLY00.019-0.00723.3780.2090.2090.0000.0000.0000.000
122A135ASP-1-0.825-0.91024.183-11.841-11.8410.0000.0000.0000.000
123A136LEU00.003-0.00326.1170.2800.2800.0000.0000.0000.000
124A137GLY00.011-0.01929.8840.1570.1570.0000.0000.0000.000
125A138VAL0-0.070-0.02826.2250.1860.1860.0000.0000.0000.000
126A139GLY0-0.0120.00229.4620.1230.1230.0000.0000.0000.000
127A140ASN0-0.047-0.02526.0660.2250.2250.0000.0000.0000.000
128A141ALA0-0.0050.00529.717-0.103-0.1030.0000.0000.0000.000
129A142THR00.0050.00931.7540.2250.2250.0000.0000.0000.000
130A143ALA00.0390.00533.909-0.183-0.1830.0000.0000.0000.000
131A144ALA00.0200.02135.7200.0440.0440.0000.0000.0000.000
132A145PRO00.025-0.00431.5440.1400.1400.0000.0000.0000.000
133A146LEU00.0170.01533.7310.0160.0160.0000.0000.0000.000
134A147VAL0-0.010-0.01135.0020.1340.1340.0000.0000.0000.000
135A148CYS0-0.087-0.03436.8510.2450.2450.0000.0000.0000.000
136A149GLY00.0320.02036.635-0.005-0.0050.0000.0000.0000.000
137A150CYS0-0.125-0.06432.081-0.066-0.0660.0000.0000.0000.000
138A151PHE00.008-0.00128.192-0.319-0.3190.0000.0000.0000.000
139A152SER00.0210.01030.1530.2540.2540.0000.0000.0000.000
140A153GLY00.003-0.00730.0400.2460.2460.0000.0000.0000.000
141A154VAL0-0.019-0.02028.848-0.213-0.2130.0000.0000.0000.000
142A155LYS10.8140.91521.81813.04713.0470.0000.0000.0000.000
143A156LEU0-0.028-0.00327.984-0.010-0.0100.0000.0000.0000.000
144A157ASP-1-0.768-0.86326.247-11.026-11.0260.0000.0000.0000.000
145A158ARG10.8460.92121.48212.35312.3530.0000.0000.0000.000
146A159SER00.004-0.01727.1820.2690.2690.0000.0000.0000.000
147A160PHE0-0.0110.00529.2030.4410.4410.0000.0000.0000.000
148A161PHE00.0290.01930.1700.3580.3580.0000.0000.0000.000
149A162VAL00.0230.01030.1150.3200.3200.0000.0000.0000.000
150A163SER0-0.077-0.03532.7880.3500.3500.0000.0000.0000.000
151A164GLN0-0.048-0.05435.2650.5150.5150.0000.0000.0000.000
152A165ILE0-0.0200.00434.4800.2440.2440.0000.0000.0000.000
153A166GLU-1-0.798-0.87137.102-7.657-7.6570.0000.0000.0000.000
154A167LYS10.8630.95239.4177.7487.7480.0000.0000.0000.000
155A168MET00.0330.00642.193-0.034-0.0340.0000.0000.0000.000
156A169THR00.003-0.00542.6120.0540.0540.0000.0000.0000.000
157A170PHE00.0450.03235.114-0.055-0.0550.0000.0000.0000.000
158A171PRO00.0710.01540.355-0.112-0.1120.0000.0000.0000.000
159A172LEU0-0.022-0.00142.493-0.004-0.0040.0000.0000.0000.000
160A173LEU0-0.0050.00936.6770.0040.0040.0000.0000.0000.000
161A174VAL00.0450.02537.021-0.124-0.1240.0000.0000.0000.000
162A175LYS10.8950.94739.1956.5816.5810.0000.0000.0000.000
163A176HIS0-0.033-0.03141.9770.1890.1890.0000.0000.0000.000
164A177ILE00.0260.01934.883-0.028-0.0280.0000.0000.0000.000
165A178ARG10.7820.86937.5167.6717.6710.0000.0000.0000.000
166A179HIS0-0.069-0.02338.9930.1720.1720.0000.0000.0000.000
167A180TYR0-0.044-0.01938.2140.1310.1310.0000.0000.0000.000
168A181CYS0-0.039-0.00933.414-0.222-0.2220.0000.0000.0000.000
169A182ASP-1-0.786-0.85535.741-7.946-7.9460.0000.0000.0000.000
170A183LYS10.8590.92332.5378.4708.4700.0000.0000.0000.000
171A184ILE00.0470.02731.987-0.255-0.2550.0000.0000.0000.000
172A185VAL0-0.003-0.00126.5470.1600.1600.0000.0000.0000.000
173A186VAL00.001-0.01029.532-0.024-0.0240.0000.0000.0000.000
174A187GLY00.0750.02825.339-0.126-0.1260.0000.0000.0000.000
175A188GLY0-0.037-0.02323.9340.2710.2710.0000.0000.0000.000
176A189GLN0-0.033-0.03024.8840.5550.5550.0000.0000.0000.000
177A190GLU-1-0.814-0.90023.821-11.697-11.6970.0000.0000.0000.000
178A191ASN0-0.027-0.02626.9250.3180.3180.0000.0000.0000.000
179A192ALA00.0560.01730.417-0.004-0.0040.0000.0000.0000.000
180A193ARG10.8410.93033.4898.1968.1960.0000.0000.0000.000
181A194TYR00.011-0.02432.5360.1570.1570.0000.0000.0000.000
182A195LEU00.0270.03231.9630.1450.1450.0000.0000.0000.000
183A196PRO00.0470.01435.9350.0790.0790.0000.0000.0000.000
184A197ALA00.0220.02838.5610.1480.1480.0000.0000.0000.000
185A198LEU0-0.016-0.01132.8060.0640.0640.0000.0000.0000.000
186A199LYS10.8890.91337.1967.4467.4460.0000.0000.0000.000
187A200THR0-0.075-0.04739.2460.1500.1500.0000.0000.0000.000
188A201ALA0-0.048-0.02539.1170.1260.1260.0000.0000.0000.000
189A202GLY00.0020.01940.1290.0410.0410.0000.0000.0000.000
190A203ILE0-0.029-0.02533.395-0.085-0.0850.0000.0000.0000.000
191A204TRP0-0.0010.01130.1860.0720.0720.0000.0000.0000.000
192A205ALA00.016-0.00629.9230.0270.0270.0000.0000.0000.000
193A206THR0-0.020-0.01529.0270.0520.0520.0000.0000.0000.000
194A207GLN00.007-0.01620.4590.2710.2710.0000.0000.0000.000
195A208GLY0-0.005-0.00622.9620.1810.1810.0000.0000.0000.000
196A209THR00.0650.02520.7780.0740.0740.0000.0000.0000.000
197A210LEU0-0.0450.00023.1920.1270.1270.0000.0000.0000.000
198A211PHE0-0.062-0.03924.7970.3440.3440.0000.0000.0000.000
199A212PRO00.003-0.00521.381-0.403-0.4030.0000.0000.0000.000
200A213SER0-0.002-0.02417.3460.4150.4150.0000.0000.0000.000
201A214VAL0-0.0100.01416.904-0.158-0.1580.0000.0000.0000.000
202A215ALA00.0860.03012.520-0.611-0.6110.0000.0000.0000.000
203A216LEU0-0.033-0.01612.8791.1241.1240.0000.0000.0000.000
204A217GLU-1-0.858-0.96411.183-20.987-20.9870.0000.0000.0000.000
205A218GLU-1-0.951-0.96714.365-15.253-15.2530.0000.0000.0000.000
206A219ILE0-0.0050.01717.3190.7600.7600.0000.0000.0000.000
207A220GLU-1-0.824-0.91419.199-13.332-13.3320.0000.0000.0000.000
208A221THR0-0.060-0.03920.1020.6250.6250.0000.0000.0000.000
209A222LEU0-0.044-0.01020.9200.4430.4430.0000.0000.0000.000
210A223LEU00.0250.00824.0220.3020.3020.0000.0000.0000.000
211A224LEU0-0.004-0.00327.330-0.156-0.1560.0000.0000.0000.000