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: LNY39

Calculation Name: 1JYK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JYK

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H2

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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3135874.228049
FMO2-HF: Nuclear repulsion 3043078.899833
FMO2-HF: Total energy -92795.328217
FMO2-MP2: Total energy -93071.971983


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:GLU)


Summations of interaction energy for fragment #1(A:3:GLU)
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.
91.332103.5289.935-9.542-12.5860.091
Interaction energy analysis for fragmet #1(A:3:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.840 / q_NPA : -0.931
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].
3A5ARG10.8460.9412.971-58.374-54.0440.045-1.946-2.4300.009
4A6VAL0-0.0070.0124.1657.3107.5900.000-0.039-0.2400.000
5A7LYS10.7830.8661.966-108.921-107.4438.810-5.352-4.9370.075
6A8ALA0-0.0080.0037.480-2.297-2.2970.0000.0000.0000.000
7A9ILE00.0110.0267.221-0.308-0.3080.0000.0000.0000.000
8A10ILE00.0040.00110.876-1.612-1.6120.0000.0000.0000.000
9A11LEU0-0.004-0.00814.279-0.101-0.1010.0000.0000.0000.000
10A12ALA0-0.014-0.01916.815-1.134-1.1340.0000.0000.0000.000
11A13ALA0-0.0170.00219.375-0.635-0.6350.0000.0000.0000.000
12A14GLY00.0040.00321.050-0.615-0.6150.0000.0000.0000.000
13A15LEU00.0700.02423.876-0.084-0.0840.0000.0000.0000.000
14A16GLY00.0030.00826.994-0.237-0.2370.0000.0000.0000.000
15A17THR00.0450.03028.261-0.198-0.1980.0000.0000.0000.000
16A18ARG10.8430.92926.498-11.747-11.7470.0000.0000.0000.000
17A19LEU0-0.051-0.00728.190-0.179-0.1790.0000.0000.0000.000
18A20ARG10.9271.00832.486-8.649-8.6490.0000.0000.0000.000
19A21PRO0-0.064-0.07335.321-0.170-0.1700.0000.0000.0000.000
20A22LEU00.0170.00632.366-0.018-0.0180.0000.0000.0000.000
21A23THR0-0.014-0.01929.2180.0050.0050.0000.0000.0000.000
22A24GLU-1-0.978-0.96631.8008.5348.5340.0000.0000.0000.000
23A25ASN0-0.001-0.01233.384-0.096-0.0960.0000.0000.0000.000
24A26THR00.0360.02029.0900.0340.0340.0000.0000.0000.000
25A27PRO00.0380.04924.980-0.073-0.0730.0000.0000.0000.000
26A28LYS10.9220.91223.318-13.382-13.3820.0000.0000.0000.000
27A29ALA0-0.0100.00921.699-0.079-0.0790.0000.0000.0000.000
28A30LEU0-0.029-0.02223.5790.1710.1710.0000.0000.0000.000
29A31VAL00.0120.02226.217-0.482-0.4820.0000.0000.0000.000
30A32GLN0-0.044-0.03028.3340.1610.1610.0000.0000.0000.000
31A33VAL00.0260.02428.890-0.320-0.3200.0000.0000.0000.000
32A34ASN0-0.001-0.01031.0100.0050.0050.0000.0000.0000.000
33A35GLN0-0.060-0.02832.9580.1740.1740.0000.0000.0000.000
34A36LYS10.8390.91025.621-12.322-12.3220.0000.0000.0000.000
35A37PRO0-0.033-0.00825.4810.0090.0090.0000.0000.0000.000
36A38LEU00.0560.02124.4640.2890.2890.0000.0000.0000.000
37A39ILE00.0340.01418.0250.2950.2950.0000.0000.0000.000
38A40GLU-1-0.794-0.88320.54913.23013.2300.0000.0000.0000.000
39A41TYR0-0.010-0.01722.1790.1780.1780.0000.0000.0000.000
40A42GLN0-0.024-0.01518.4420.8240.8240.0000.0000.0000.000
41A43ILE00.003-0.00216.9610.8280.8280.0000.0000.0000.000
42A44GLU-1-0.797-0.88317.97913.81313.8130.0000.0000.0000.000
43A45PHE00.0360.02419.5260.1440.1440.0000.0000.0000.000
44A46LEU0-0.012-0.00313.1460.3370.3370.0000.0000.0000.000
45A47LYS10.8680.92515.757-18.054-18.0540.0000.0000.0000.000
46A48GLU-1-0.960-0.96917.16113.78613.7860.0000.0000.0000.000
47A49LYS10.8450.93015.924-15.982-15.9820.0000.0000.0000.000
48A50GLY0-0.035-0.00814.7400.6510.6510.0000.0000.0000.000
49A51ILE0-0.048-0.00910.1251.8381.8380.0000.0000.0000.000
50A52ASN0-0.008-0.03611.885-1.373-1.3730.0000.0000.0000.000
51A53ASP-1-0.845-0.9156.27845.53945.5390.0000.0000.0000.000
52A54ILE00.0310.0089.0901.6871.6870.0000.0000.0000.000
53A55ILE00.0120.0117.062-1.887-1.8870.0000.0000.0000.000
54A56ILE0-0.003-0.00311.362-0.693-0.6930.0000.0000.0000.000
55A57ILE00.0190.01712.288-0.450-0.4500.0000.0000.0000.000
56A58VAL00.004-0.00815.887-1.179-1.1790.0000.0000.0000.000
57A59GLY00.066-0.00919.5010.3320.3320.0000.0000.0000.000
58A60TYR0-0.065-0.02622.489-0.444-0.4440.0000.0000.0000.000
59A61LEU0-0.016-0.00525.3370.2280.2280.0000.0000.0000.000
60A62LYS10.9440.97622.125-13.115-13.1150.0000.0000.0000.000
61A63GLU-1-0.875-0.93823.70312.02512.0250.0000.0000.0000.000
62A64GLN0-0.038-0.02626.025-0.006-0.0060.0000.0000.0000.000
63A65PHE00.027-0.00920.6860.0610.0610.0000.0000.0000.000
64A66ASP-1-0.908-0.94621.90714.42414.4240.0000.0000.0000.000
65A67TYR0-0.076-0.06022.2610.4780.4780.0000.0000.0000.000
66A68LEU00.0150.00519.8450.0770.0770.0000.0000.0000.000
67A69LYS10.9220.97217.822-15.169-15.1690.0000.0000.0000.000
68A70GLU-1-0.939-0.97319.07613.60713.6070.0000.0000.0000.000
69A71LYS10.8130.93921.750-12.749-12.7490.0000.0000.0000.000
70A72TYR0-0.054-0.05718.215-0.178-0.1780.0000.0000.0000.000
71A73GLY00.0080.01916.5130.8020.8020.0000.0000.0000.000
72A74VAL0-0.035-0.00114.1361.4431.4430.0000.0000.0000.000
73A75ARG10.8780.9366.203-41.041-41.0410.0000.0000.0000.000
74A76LEU0-0.025-0.00813.6170.2120.2120.0000.0000.0000.000
75A77VAL00.0170.00711.9110.0690.0690.0000.0000.0000.000
76A78PHE0-0.046-0.02515.280-0.757-0.7570.0000.0000.0000.000
77A79ASN00.0700.02817.9800.0050.0050.0000.0000.0000.000
78A80ASP-1-0.934-0.98919.50513.66813.6680.0000.0000.0000.000
79A81LYS10.9270.98321.901-13.530-13.5300.0000.0000.0000.000
80A82TYR0-0.062-0.02322.287-0.363-0.3630.0000.0000.0000.000
81A83ALA0-0.036-0.02123.285-0.186-0.1860.0000.0000.0000.000
82A84ASP-1-0.931-0.95825.93511.32511.3250.0000.0000.0000.000
83A85TYR0-0.043-0.03821.629-0.106-0.1060.0000.0000.0000.000
84A86ASN00.0110.00923.2170.3740.3740.0000.0000.0000.000
85A87ASN0-0.037-0.03318.7370.5980.5980.0000.0000.0000.000
86A88PHE00.0680.03617.4921.2691.2690.0000.0000.0000.000
87A89TYR00.011-0.01016.3461.3791.3790.0000.0000.0000.000
88A90SER0-0.036-0.02716.1040.4930.4930.0000.0000.0000.000
89A91LEU00.0280.02510.4121.1371.1370.0000.0000.0000.000
90A92TYR00.0020.00211.7142.3442.3440.0000.0000.0000.000
91A93LEU0-0.046-0.02412.5521.2561.2560.0000.0000.0000.000
92A94VAL0-0.035-0.0118.5780.6360.6360.0000.0000.0000.000
93A95LYS10.8280.9097.785-21.169-21.1690.0000.0000.0000.000
94A96GLU-1-0.883-0.9396.24735.74835.7480.0000.0000.0000.000
95A97GLU-1-0.929-0.9663.45573.51274.5910.024-0.373-0.7300.002
96A98LEU0-0.050-0.0194.2432.6162.8560.000-0.031-0.2080.000
97A99ALA00.0320.0052.690-6.841-5.3710.463-0.837-1.0950.006
98A100ASN0-0.051-0.0332.6923.6286.2250.536-0.675-2.457-0.003
99A101SER00.0410.0184.916-0.284-0.187-0.001-0.003-0.0920.000
100A102TYR0-0.008-0.0317.095-3.880-3.8800.0000.0000.0000.000
101A103VAL0-0.0220.00410.3361.7831.7830.0000.0000.0000.000
102A104ILE0-0.039-0.03912.569-1.336-1.3360.0000.0000.0000.000
103A105ASP-1-0.842-0.91115.79716.60416.6040.0000.0000.0000.000
104A106ALA0-0.030-0.03719.018-0.285-0.2850.0000.0000.0000.000
105A107ASP-1-0.858-0.90020.65012.90312.9030.0000.0000.0000.000
106A108ASN00.0890.04921.696-1.004-1.0040.0000.0000.0000.000
107A109TYR0-0.015-0.01123.7380.3510.3510.0000.0000.0000.000
108A110LEU0-0.026-0.01519.841-0.120-0.1200.0000.0000.0000.000
109A111PHE00.0250.01324.446-0.158-0.1580.0000.0000.0000.000
110A112LYS10.8300.90724.945-11.701-11.7010.0000.0000.0000.000
111A113ASN0-0.062-0.03319.3800.9350.9350.0000.0000.0000.000
112A114MET00.0050.01918.4070.0190.0190.0000.0000.0000.000
113A115PHE00.0000.01414.8680.5510.5510.0000.0000.0000.000
114A116ARG10.8410.88014.533-17.597-17.5970.0000.0000.0000.000
115A117ASN0-0.0170.00311.3200.6520.6520.0000.0000.0000.000
116A118ASP-1-0.790-0.86811.32619.39419.3940.0000.0000.0000.000
117A119LEU00.0120.01111.670-0.955-0.9550.0000.0000.0000.000
118A120THR0-0.046-0.02810.5581.6471.6470.0000.0000.0000.000
119A121ARG10.9510.99111.316-16.068-16.0680.0000.0000.0000.000
120A122SER00.0140.01011.7960.9160.9160.0000.0000.0000.000
121A123THR0-0.059-0.02612.767-2.005-2.0050.0000.0000.0000.000
122A124TYR00.0560.02415.2491.1251.1250.0000.0000.0000.000
123A125PHE00.004-0.01614.914-0.569-0.5690.0000.0000.0000.000
124A126SER0-0.012-0.01219.802-0.279-0.2790.0000.0000.0000.000
125A127VAL00.0240.02523.257-0.340-0.3400.0000.0000.0000.000
126A128TYR0-0.099-0.05826.6430.1200.1200.0000.0000.0000.000
127A129ARG10.8020.89228.891-10.963-10.9630.0000.0000.0000.000
128A130GLU-1-0.829-0.91732.0018.4498.4490.0000.0000.0000.000
129A131ASP-1-0.970-0.97935.2858.2858.2850.0000.0000.0000.000
130A132CYS0-0.061-0.01832.1080.1780.1780.0000.0000.0000.000
131A133THR0-0.047-0.04232.555-0.405-0.4050.0000.0000.0000.000
132A134ASN0-0.065-0.03130.1970.0970.0970.0000.0000.0000.000
133A135GLU-1-0.858-0.91127.65711.65911.6590.0000.0000.0000.000
134A136TRP0-0.043-0.02721.999-0.039-0.0390.0000.0000.0000.000
135A137PHE0-0.012-0.03126.2090.2080.2080.0000.0000.0000.000
136A138LEU0-0.009-0.00321.4360.2560.2560.0000.0000.0000.000
137A139VAL0-0.0140.00825.403-0.458-0.4580.0000.0000.0000.000
138A140TYR0-0.067-0.09224.7580.4940.4940.0000.0000.0000.000
139A141GLY00.0290.01626.783-0.440-0.4400.0000.0000.0000.000
140A142ASP-1-0.899-0.96127.60410.02310.0230.0000.0000.0000.000
141A143ASP-1-0.940-0.95823.76212.33312.3330.0000.0000.0000.000
142A144TYR0-0.067-0.03222.8010.6470.6470.0000.0000.0000.000
143A145LYS10.8940.95919.041-13.911-13.9110.0000.0000.0000.000
144A146VAL0-0.050-0.03820.269-0.622-0.6220.0000.0000.0000.000
145A147GLN0-0.045-0.02922.2770.2220.2220.0000.0000.0000.000
146A148ASP-1-0.889-0.95824.95311.60211.6020.0000.0000.0000.000
147A149ILE0-0.039-0.00620.6070.2050.2050.0000.0000.0000.000
148A150ILE0-0.009-0.00225.198-0.184-0.1840.0000.0000.0000.000
149A151VAL00.0340.00028.1220.2110.2110.0000.0000.0000.000
150A152ASP-1-0.999-0.98430.2998.6578.6570.0000.0000.0000.000
151A153SER00.0290.00432.689-0.286-0.2860.0000.0000.0000.000
152A154LYS10.9440.97333.887-8.120-8.1200.0000.0000.0000.000
153A155ALA00.0050.01233.968-0.050-0.0500.0000.0000.0000.000
154A156GLY00.0250.01831.277-0.028-0.0280.0000.0000.0000.000
155A157ARG10.8630.93426.171-11.308-11.3080.0000.0000.0000.000
156A158ILE00.0550.03825.8890.1630.1630.0000.0000.0000.000
157A159LEU0-0.0010.00820.5340.3490.3490.0000.0000.0000.000
158A160SER00.026-0.00721.950-0.322-0.3220.0000.0000.0000.000
159A161GLY00.0930.06319.551-0.284-0.2840.0000.0000.0000.000
160A162VAL0-0.045-0.02116.2860.7530.7530.0000.0000.0000.000
161A163SER00.0070.00914.713-0.400-0.4000.0000.0000.0000.000
162A164PHE0-0.020-0.0077.6201.4731.4730.0000.0000.0000.000
163A165TRP00.0370.0238.822-2.391-2.3910.0000.0000.0000.000
164A166ASP-1-0.727-0.8227.28331.00131.0010.0000.0000.0000.000
165A167ALA00.019-0.0163.4430.0980.6680.059-0.285-0.3440.002
166A168PRO00.004-0.0045.396-1.151-1.096-0.001-0.001-0.0530.000
167A169THR0-0.006-0.0378.407-2.292-2.2920.0000.0000.0000.000
168A170ALA00.0040.0016.622-1.396-1.3960.0000.0000.0000.000
169A171GLU-1-0.937-0.9587.50825.75325.7530.0000.0000.0000.000
170A172LYS10.8810.9449.028-20.091-20.0910.0000.0000.0000.000
171A173ILE00.0260.02411.582-1.272-1.2720.0000.0000.0000.000
172A174VAL00.0250.0178.569-1.584-1.5840.0000.0000.0000.000
173A175SER0-0.048-0.02211.927-2.056-2.0560.0000.0000.0000.000
174A176PHE0-0.033-0.03014.653-1.516-1.5160.0000.0000.0000.000
175A177ILE00.0280.00412.114-1.139-1.1390.0000.0000.0000.000
176A178ASP-1-0.869-0.92614.51321.49821.4980.0000.0000.0000.000
177A179LYS10.9370.95616.762-15.388-15.3880.0000.0000.0000.000
178A180ALA00.0700.04119.364-0.832-0.8320.0000.0000.0000.000
179A181TYR0-0.044-0.02818.374-0.637-0.6370.0000.0000.0000.000
180A182VAL0-0.079-0.03120.422-0.618-0.6180.0000.0000.0000.000
181A183SER0-0.036-0.02322.647-0.693-0.6930.0000.0000.0000.000
182A184GLY0-0.076-0.02925.085-0.483-0.4830.0000.0000.0000.000
183A185GLU-1-0.961-0.98124.75611.96711.9670.0000.0000.0000.000
184A186PHE00.016-0.01821.1300.4590.4590.0000.0000.0000.000
185A187VAL0-0.0220.00322.9190.2800.2800.0000.0000.0000.000
186A188ASP-1-0.838-0.92224.86411.35311.3530.0000.0000.0000.000
187A189LEU0-0.0680.00021.599-0.090-0.0900.0000.0000.0000.000
188A190TYR00.0310.01721.0140.1320.1320.0000.0000.0000.000
189A191TRP00.035-0.01613.9810.7080.7080.0000.0000.0000.000
190A192ASP-1-0.829-0.91017.12017.06017.0600.0000.0000.0000.000
191A193ASN0-0.011-0.03218.848-0.236-0.2360.0000.0000.0000.000
192A194MET0-0.0410.00516.449-0.125-0.1250.0000.0000.0000.000
193A195VAL0-0.0110.00715.7620.9260.9260.0000.0000.0000.000
194A196LYS10.9170.95418.310-12.693-12.6930.0000.0000.0000.000
195A197ASP-1-0.870-0.92921.79212.64812.6480.0000.0000.0000.000
196A198ASN0-0.069-0.05918.906-0.024-0.0240.0000.0000.0000.000
197A199ILE00.1100.05019.8500.3540.3540.0000.0000.0000.000
198A200LYS10.8350.94420.493-12.711-12.7110.0000.0000.0000.000
199A201GLU-1-0.987-0.97418.22514.00414.0040.0000.0000.0000.000
200A202LEU0-0.068-0.03014.2181.1021.1020.0000.0000.0000.000
201A203ASP-1-0.878-0.92415.06115.47715.4770.0000.0000.0000.000
202A204VAL0-0.007-0.01415.0501.3121.3120.0000.0000.0000.000
203A205TYR0-0.049-0.02516.395-0.986-0.9860.0000.0000.0000.000
204A206VAL0-0.0050.00118.4260.7020.7020.0000.0000.0000.000
205A207GLU-1-0.950-0.96219.28714.10214.1020.0000.0000.0000.000
206A208GLU-1-0.894-0.92521.21211.15011.1500.0000.0000.0000.000
207A209LEU00.003-0.00421.665-0.108-0.1080.0000.0000.0000.000
208A210GLU-1-0.868-0.93025.29310.38910.3890.0000.0000.0000.000
209A211GLY00.0330.00428.1490.2280.2280.0000.0000.0000.000
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