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: MVK1Z

Calculation Name: 5JD6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5JD6

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-20

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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2736961.022957
FMO2-HF: Nuclear repulsion 2650026.719824
FMO2-HF: Total energy -86934.303133
FMO2-MP2: Total energy -87187.41783


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:3:ASP)


Summations of interaction energy for fragment #1(A:3:ASP)
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.
29.37545.2967.503-10.175-13.250.09
Interaction energy analysis for fragmet #1(A:3:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.791 / q_NPA : -0.917
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].
3A5LEU00.0030.0083.8202.9676.396-0.008-1.738-1.6830.006
4A6LYS10.8180.9075.923-37.864-37.8640.0000.0000.0000.000
5A7GLN0-0.018-0.0378.643-1.084-1.0840.0000.0000.0000.000
6A8GLU-1-0.793-0.84511.52025.08925.0890.0000.0000.0000.000
7A9GLY00.0030.00014.588-0.403-0.4030.0000.0000.0000.000
8A10LYS10.7470.85017.547-15.514-15.5140.0000.0000.0000.000
9A11PHE00.0060.01613.3850.1230.1230.0000.0000.0000.000
10A12THR00.0220.01110.628-0.082-0.0820.0000.0000.0000.000
11A13TYR0-0.032-0.0497.660-1.362-1.3620.0000.0000.0000.000
12A14LEU00.0500.0492.754-12.993-7.9041.154-2.966-3.2780.036
13A15GLU-1-0.791-0.8933.31319.92720.6340.031-0.339-0.3990.002
14A16LYS10.8000.9062.069-59.242-55.1755.610-3.757-5.9200.032
15A17GLY00.0380.0143.709-6.249-6.1300.011-0.060-0.0700.000
16A18GLU-1-0.990-1.0036.95924.44624.4460.0000.0000.0000.000
17A19GLY0-0.0110.01110.413-1.850-1.8500.0000.0000.0000.000
18A20THR00.002-0.00412.8680.6290.6290.0000.0000.0000.000
19A21PRO0-0.0140.00611.8341.7691.7690.0000.0000.0000.000
20A22ILE00.0100.01010.896-2.029-2.0290.0000.0000.0000.000
21A23VAL0-0.037-0.02210.3043.2643.2640.0000.0000.0000.000
22A24ILE00.000-0.0018.737-2.444-2.4440.0000.0000.0000.000
23A25LEU0-0.037-0.02511.7580.5230.5230.0000.0000.0000.000
24A26HIS00.017-0.00410.888-2.756-2.7560.0000.0000.0000.000
25A27GLY0-0.007-0.01714.107-1.457-1.4570.0000.0000.0000.000
26A28LEU0-0.030-0.03116.5250.5140.5140.0000.0000.0000.000
27A29MET0-0.0160.00417.138-0.502-0.5020.0000.0000.0000.000
28A30GLY00.0160.02214.0520.2820.2820.0000.0000.0000.000
29A31GLY00.0210.01311.9661.1801.1800.0000.0000.0000.000
30A32LEU0-0.018-0.0246.584-0.223-0.2230.0000.0000.0000.000
31A33SER0-0.005-0.0157.7241.1661.1660.0000.0000.0000.000
32A34ASN0-0.076-0.0659.071-1.968-1.9680.0000.0000.0000.000
33A35PHE00.051-0.0047.764-2.743-2.7430.0000.0000.0000.000
34A36ASP-1-0.796-0.8586.40240.94840.9480.0000.0000.0000.000
35A37GLY00.0180.0037.4701.3111.3110.0000.0000.0000.000
36A38VAL0-0.031-0.0069.177-1.319-1.3190.0000.0000.0000.000
37A39ILE0-0.005-0.0062.769-5.477-3.0910.706-1.309-1.7830.014
38A40ASP-1-0.821-0.9124.81748.43748.561-0.001-0.006-0.1170.000
39A41TYR0-0.088-0.0336.689-3.374-3.3740.0000.0000.0000.000
40A42PHE00.0510.0109.491-1.351-1.3510.0000.0000.0000.000
41A43PRO0-0.0180.0135.928-2.667-2.6670.0000.0000.0000.000
42A44GLU-1-0.808-0.9106.42435.96035.9600.0000.0000.0000.000
43A45LYS10.7180.85310.413-26.493-26.4930.0000.0000.0000.000
44A46GLY00.0140.02212.495-1.573-1.5730.0000.0000.0000.000
45A47TYR0-0.038-0.03011.490-0.964-0.9640.0000.0000.0000.000
46A48LYS10.8730.9317.991-28.220-28.2200.0000.0000.0000.000
47A49VAL00.0250.0255.798-3.066-3.0660.0000.0000.0000.000
48A50LEU0-0.029-0.0185.9555.3195.3190.0000.0000.0000.000
49A51ILE00.0160.0106.105-4.440-4.4400.0000.0000.0000.000
50A52PRO0-0.032-0.0058.2381.7011.7010.0000.0000.0000.000
51A53GLU-1-0.789-0.8889.66829.22329.2230.0000.0000.0000.000
52A54LEU00.0080.01312.928-2.088-2.0880.0000.0000.0000.000
53A55PRO00.0000.00716.437-0.321-0.3210.0000.0000.0000.000
54A56LEU0-0.012-0.01917.401-1.270-1.2700.0000.0000.0000.000
55A57TYR00.057-0.01020.481-0.790-0.7900.0000.0000.0000.000
56A58SER00.0270.01920.275-0.622-0.6220.0000.0000.0000.000
57A59MET0-0.0080.01622.779-0.331-0.3310.0000.0000.0000.000
58A60SER0-0.004-0.00625.047-0.647-0.6470.0000.0000.0000.000
59A61LEU00.0260.00727.9690.2680.2680.0000.0000.0000.000
60A62LEU00.010-0.01130.2000.1100.1100.0000.0000.0000.000
61A63LYS10.9700.99826.896-12.036-12.0360.0000.0000.0000.000
62A64THR00.0010.00625.2800.1550.1550.0000.0000.0000.000
63A65SER0-0.018-0.00725.854-0.468-0.4680.0000.0000.0000.000
64A66VAL00.0690.03224.3900.3870.3870.0000.0000.0000.000
65A67GLY00.0810.03724.3320.3750.3750.0000.0000.0000.000
66A68THR0-0.134-0.05923.812-0.035-0.0350.0000.0000.0000.000
67A69PHE00.0240.01720.2660.2100.2100.0000.0000.0000.000
68A70ALA00.0790.04220.2340.7320.7320.0000.0000.0000.000
69A71ARG10.8710.91721.654-11.656-11.6560.0000.0000.0000.000
70A72TYR0-0.013-0.02115.299-0.525-0.5250.0000.0000.0000.000
71A73LEU00.0310.01815.6360.6090.6090.0000.0000.0000.000
72A74LYS10.8170.90917.768-13.301-13.3010.0000.0000.0000.000
73A75GLU-1-0.810-0.88619.93615.00515.0050.0000.0000.0000.000
74A76PHE0-0.017-0.00810.2580.0240.0240.0000.0000.0000.000
75A77VAL00.011-0.00215.6900.8520.8520.0000.0000.0000.000
76A78ASP-1-0.798-0.88816.95314.38414.3840.0000.0000.0000.000
77A79PHE0-0.105-0.04813.258-0.382-0.3820.0000.0000.0000.000
78A80LYS10.7920.88110.512-27.637-27.6370.0000.0000.0000.000
79A81GLY0-0.0150.00815.7490.0950.0950.0000.0000.0000.000
80A82TYR0-0.021-0.01611.151-0.083-0.0830.0000.0000.0000.000
81A83GLU-1-0.917-0.96418.20013.20113.2010.0000.0000.0000.000
82A84ASN0-0.046-0.02219.831-0.237-0.2370.0000.0000.0000.000
83A85VAL0-0.0040.00015.4200.8630.8630.0000.0000.0000.000
84A86ILE00.0100.01915.338-1.127-1.1270.0000.0000.0000.000
85A87LEU0-0.040-0.01715.0801.4221.4220.0000.0000.0000.000
86A88LEU00.0360.01512.477-0.786-0.7860.0000.0000.0000.000
87A89GLY00.0050.00214.9611.1891.1890.0000.0000.0000.000
88A90ASN00.0130.00916.109-0.816-0.8160.0000.0000.0000.000
89A91SER0-0.030-0.03017.940-0.205-0.2050.0000.0000.0000.000
90A92LEU0-0.003-0.00920.017-0.442-0.4420.0000.0000.0000.000
91A93GLY00.0640.03817.198-0.527-0.5270.0000.0000.0000.000
92A94GLY00.0510.01818.2150.1030.1030.0000.0000.0000.000
93A95HIS0-0.068-0.03120.144-0.329-0.3290.0000.0000.0000.000
94A96ILE0-0.055-0.02819.461-0.618-0.6180.0000.0000.0000.000
95A97ALA00.0660.03518.360-0.326-0.3260.0000.0000.0000.000
96A98LEU00.0330.03120.287-0.545-0.5450.0000.0000.0000.000
97A99LEU0-0.042-0.02223.961-0.557-0.5570.0000.0000.0000.000
98A100ALA00.0140.00221.129-0.449-0.4490.0000.0000.0000.000
99A101THR00.0260.00022.357-0.289-0.2890.0000.0000.0000.000
100A102LYS10.7690.88324.589-11.266-11.2660.0000.0000.0000.000
101A103MET0-0.135-0.07126.220-0.454-0.4540.0000.0000.0000.000
102A104PHE0-0.008-0.00723.775-0.307-0.3070.0000.0000.0000.000
103A105PRO00.0270.01924.4050.4950.4950.0000.0000.0000.000
104A106GLU-1-0.892-0.96025.42612.54612.5460.0000.0000.0000.000
105A107ILE0-0.0100.00920.4680.1020.1020.0000.0000.0000.000
106A108VAL0-0.059-0.03420.1050.9730.9730.0000.0000.0000.000
107A109GLN00.0190.02519.436-0.433-0.4330.0000.0000.0000.000
108A110ALA00.0190.01219.937-0.587-0.5870.0000.0000.0000.000
109A111LEU0-0.040-0.01619.6310.9950.9950.0000.0000.0000.000
110A112VAL00.0100.01417.423-0.473-0.4730.0000.0000.0000.000
111A113ILE0-0.006-0.00618.8600.7490.7490.0000.0000.0000.000
112A114THR0-0.021-0.02017.132-0.191-0.1910.0000.0000.0000.000
113A115GLY00.0600.04719.7150.6500.6500.0000.0000.0000.000
114A116SER0-0.055-0.03321.4600.3690.3690.0000.0000.0000.000
115A117SER0-0.022-0.01322.682-0.595-0.5950.0000.0000.0000.000
116A118GLY00.0450.00624.9610.4020.4020.0000.0000.0000.000
117A119LEU0-0.0200.01527.648-0.502-0.5020.0000.0000.0000.000
118A153LYS10.9290.95520.106-13.965-13.9650.0000.0000.0000.000
119A154GLU-1-0.828-0.93520.00113.42913.4290.0000.0000.0000.000
120A155ILE0-0.0040.00217.892-0.106-0.1060.0000.0000.0000.000
121A156VAL00.001-0.00720.592-0.251-0.2510.0000.0000.0000.000
122A157ASP-1-0.886-0.94122.38312.47912.4790.0000.0000.0000.000
123A158GLU-1-0.877-0.94118.42516.08916.0890.0000.0000.0000.000
124A159VAL0-0.087-0.04321.813-0.177-0.1770.0000.0000.0000.000
125A160TYR00.0080.00624.635-0.767-0.7670.0000.0000.0000.000
126A161GLU-1-0.751-0.86222.38712.57712.5770.0000.0000.0000.000
127A162THR0-0.069-0.04123.790-0.240-0.2400.0000.0000.0000.000
128A163VAL0-0.067-0.03826.058-0.345-0.3450.0000.0000.0000.000
129A164SER0-0.029-0.00728.657-0.583-0.5830.0000.0000.0000.000
130A165ASP-1-0.731-0.81826.01711.80311.8030.0000.0000.0000.000
131A166ARG10.8500.91828.589-10.093-10.0930.0000.0000.0000.000
132A167ASN0-0.033-0.03928.602-0.455-0.4550.0000.0000.0000.000
133A168LYS10.7550.84122.001-13.711-13.7110.0000.0000.0000.000
134A169LEU00.0510.04726.9190.1550.1550.0000.0000.0000.000
135A170VAL00.013-0.00229.398-0.038-0.0380.0000.0000.0000.000
136A171LYS10.8360.92425.873-12.232-12.2320.0000.0000.0000.000
137A172THR00.0540.03125.6740.3660.3660.0000.0000.0000.000
138A173LEU00.0010.00926.952-0.039-0.0390.0000.0000.0000.000
139A174ALA0-0.035-0.01429.065-0.185-0.1850.0000.0000.0000.000
140A175ILE00.002-0.00322.847-0.116-0.1160.0000.0000.0000.000
141A176ALA00.0350.02027.003-0.029-0.0290.0000.0000.0000.000
142A177LYS10.9560.97728.965-9.284-9.2840.0000.0000.0000.000
143A178SER0-0.054-0.03428.331-0.138-0.1380.0000.0000.0000.000
144A179ALA00.0000.00126.753-0.015-0.0150.0000.0000.0000.000
145A180ILE00.0430.02528.562-0.080-0.0800.0000.0000.0000.000
146A181ARG10.9110.95631.922-9.406-9.4060.0000.0000.0000.000
147A182HIS0-0.022-0.01729.477-0.210-0.2100.0000.0000.0000.000
148A183ASN00.0160.01230.5340.4620.4620.0000.0000.0000.000
149A184MET00.0550.03626.693-0.350-0.3500.0000.0000.0000.000
150A185ALA00.0340.01831.280-0.088-0.0880.0000.0000.0000.000
151A186LYS10.8140.90834.279-9.594-9.5940.0000.0000.0000.000
152A187ASP-1-0.834-0.91331.6869.8309.8300.0000.0000.0000.000
153A188LEU00.0710.01428.541-0.023-0.0230.0000.0000.0000.000
154A189PRO00.0390.02331.9080.0700.0700.0000.0000.0000.000
155A190LYS10.8860.94934.027-9.154-9.1540.0000.0000.0000.000
156A191MET0-0.0210.00726.836-0.129-0.1290.0000.0000.0000.000
157A192LYS10.9160.94329.601-9.794-9.7940.0000.0000.0000.000
158A193THR00.0160.03524.656-0.134-0.1340.0000.0000.0000.000
159A194PRO00.0710.05324.589-0.013-0.0130.0000.0000.0000.000
160A195THR0-0.054-0.03723.5940.8020.8020.0000.0000.0000.000
161A196CYS0-0.0130.01821.331-0.476-0.4760.0000.0000.0000.000
162A197ILE0-0.023-0.01022.5730.5050.5050.0000.0000.0000.000
163A198ILE00.0580.02919.155-0.403-0.4030.0000.0000.0000.000
164A199TRP0-0.011-0.01221.6190.8020.8020.0000.0000.0000.000
165A200GLY00.0660.04823.658-0.085-0.0850.0000.0000.0000.000
166A201LYS10.8150.89324.688-10.688-10.6880.0000.0000.0000.000
167A202ASN00.0040.00327.093-0.487-0.4870.0000.0000.0000.000
168A203ASP-1-0.679-0.81124.66813.18813.1880.0000.0000.0000.000
169A204ASN0-0.066-0.04826.778-0.754-0.7540.0000.0000.0000.000
170A205VAL0-0.056-0.01424.469-0.274-0.2740.0000.0000.0000.000
171A206THR0-0.085-0.06324.9170.0600.0600.0000.0000.0000.000
172A207PRO00.0200.02827.2260.2920.2920.0000.0000.0000.000
173A208PRO00.0270.02528.7600.1320.1320.0000.0000.0000.000
174A209GLU-1-0.836-0.93029.7889.8439.8430.0000.0000.0000.000
175A210VAL0-0.032-0.02127.985-0.084-0.0840.0000.0000.0000.000
176A211ALA00.0090.01327.2600.1160.1160.0000.0000.0000.000
177A212GLU-1-0.832-0.92028.5529.7629.7620.0000.0000.0000.000
178A213ASP-1-0.859-0.90832.0609.1469.1460.0000.0000.0000.000
179A214PHE0-0.002-0.02226.501-0.075-0.0750.0000.0000.0000.000
180A215LYS10.8500.93630.137-10.405-10.4050.0000.0000.0000.000
181A216ARG10.7670.85731.418-9.246-9.2460.0000.0000.0000.000
182A217LEU0-0.069-0.02532.780-0.275-0.2750.0000.0000.0000.000
183A218LEU00.0270.01227.319-0.096-0.0960.0000.0000.0000.000
184A219PRO0-0.039-0.01031.493-0.093-0.0930.0000.0000.0000.000
185A220ASP-1-0.841-0.90429.15111.17711.1770.0000.0000.0000.000
186A221ALA00.009-0.00227.8190.4850.4850.0000.0000.0000.000
187A222ASP-1-0.753-0.83126.73211.25311.2530.0000.0000.0000.000
188A223LEU0-0.044-0.03226.6110.4170.4170.0000.0000.0000.000
189A224TYR0-0.021-0.00724.261-0.317-0.3170.0000.0000.0000.000
190A225TRP0-0.030-0.03825.4360.0330.0330.0000.0000.0000.000
191A226ILE00.0390.03420.4560.0770.0770.0000.0000.0000.000
192A227ASP-1-0.780-0.88024.70510.57210.5720.0000.0000.0000.000
193A228LYS10.8100.87525.657-10.129-10.1290.0000.0000.0000.000
194A229CYS0-0.052-0.00321.6570.6860.6860.0000.0000.0000.000
195A230GLY0-0.019-0.00923.157-0.530-0.5300.0000.0000.0000.000
196A231HIS10.7410.83420.828-14.567-14.5670.0000.0000.0000.000
197A232ALA00.0350.00916.3980.4210.4210.0000.0000.0000.000
198A233ALA00.0720.03017.1140.7100.7100.0000.0000.0000.000
199A234MET0-0.059-0.01312.9680.0810.0810.0000.0000.0000.000
200A235MET0-0.0090.01613.3501.5831.5830.0000.0000.0000.000
201A236GLU-1-0.786-0.88614.55414.58014.5800.0000.0000.0000.000
202A237HIS10.7990.88017.641-15.224-15.2240.0000.0000.0000.000
203A238PRO00.0430.02913.556-0.013-0.0130.0000.0000.0000.000
204A239GLU-1-0.884-0.94315.15417.65217.6520.0000.0000.0000.000
205A240GLU-1-0.823-0.91417.24113.91613.9160.0000.0000.0000.000
206A241PHE0-0.019-0.01214.284-0.166-0.1660.0000.0000.0000.000
207A242ASN00.003-0.02911.8500.9050.9050.0000.0000.0000.000
208A243GLN0-0.0020.01115.679-0.234-0.2340.0000.0000.0000.000
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210A245LEU00.0170.01615.269-0.420-0.4200.0000.0000.0000.000
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