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: 98ZV2

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 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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3136389.719996
FMO2-HF: Nuclear repulsion 3043592.989317
FMO2-HF: Total energy -92796.730678
FMO2-MP2: Total energy -93073.313651


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.
53.36359.43823.531-14.277-15.3280.119
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 : -0.829 / q_NPA : -0.916
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].
3A5ARG10.8080.8942.520-71.789-65.2031.328-3.592-4.3230.029
4A6VAL00.0000.0084.2628.1318.4120.001-0.059-0.2230.000
5A7LYS10.7850.8931.861-125.394-132.48221.088-7.972-6.0280.091
6A8ALA00.002-0.0046.804-3.460-3.4600.0000.0000.0000.000
7A9ILE00.0100.0227.223-0.065-0.0650.0000.0000.0000.000
8A10ILE0-0.004-0.00310.986-1.792-1.7920.0000.0000.0000.000
9A11LEU00.0050.00014.264-0.136-0.1360.0000.0000.0000.000
10A12ALA0-0.021-0.02416.892-1.181-1.1810.0000.0000.0000.000
11A13ALA0-0.0090.00419.303-0.650-0.6500.0000.0000.0000.000
12A14GLY00.0140.00621.088-0.637-0.6370.0000.0000.0000.000
13A15LEU00.0600.01923.918-0.072-0.0720.0000.0000.0000.000
14A16GLY00.0240.01627.044-0.236-0.2360.0000.0000.0000.000
15A17THR00.0350.02228.329-0.185-0.1850.0000.0000.0000.000
16A18ARG10.7710.86426.502-11.943-11.9430.0000.0000.0000.000
17A19LEU0-0.0300.00128.134-0.210-0.2100.0000.0000.0000.000
18A20ARG10.8010.89732.577-8.663-8.6630.0000.0000.0000.000
19A21PRO0-0.062-0.06235.401-0.170-0.1700.0000.0000.0000.000
20A22LEU00.0250.00532.494-0.023-0.0230.0000.0000.0000.000
21A23THR00.000-0.01229.3140.0170.0170.0000.0000.0000.000
22A24GLU-1-0.846-0.85631.8758.5438.5430.0000.0000.0000.000
23A25ASN0-0.036-0.03533.228-0.202-0.2020.0000.0000.0000.000
24A26THR00.0230.02228.889-0.025-0.0250.0000.0000.0000.000
25A27PRO00.0500.05424.878-0.098-0.0980.0000.0000.0000.000
26A28LYS10.9300.93022.641-13.885-13.8850.0000.0000.0000.000
27A29ALA0-0.0160.00521.539-0.065-0.0650.0000.0000.0000.000
28A30LEU0-0.032-0.02422.9340.2010.2010.0000.0000.0000.000
29A31VAL00.0100.02025.843-0.475-0.4750.0000.0000.0000.000
30A32GLN0-0.046-0.03027.9960.1930.1930.0000.0000.0000.000
31A33VAL00.0300.02128.389-0.319-0.3190.0000.0000.0000.000
32A34ASN0-0.023-0.02630.4730.1260.1260.0000.0000.0000.000
33A35GLN0-0.060-0.02732.2530.0730.0730.0000.0000.0000.000
34A36LYS10.8550.91524.454-12.744-12.7440.0000.0000.0000.000
35A37PRO0-0.034-0.00524.7820.0070.0070.0000.0000.0000.000
36A38LEU00.0540.01924.3410.3390.3390.0000.0000.0000.000
37A39ILE00.0310.01017.6880.3350.3350.0000.0000.0000.000
38A40GLU-1-0.760-0.84919.93913.65013.6500.0000.0000.0000.000
39A41TYR0-0.006-0.01121.3400.2580.2580.0000.0000.0000.000
40A42GLN0-0.045-0.02418.1571.0171.0170.0000.0000.0000.000
41A43ILE00.011-0.00216.1190.9050.9050.0000.0000.0000.000
42A44GLU-1-0.791-0.85716.96314.34214.3420.0000.0000.0000.000
43A45PHE00.0110.00919.1820.1810.1810.0000.0000.0000.000
44A46LEU00.0110.00612.6820.3880.3880.0000.0000.0000.000
45A47LYS10.8790.92514.465-18.968-18.9680.0000.0000.0000.000
46A48GLU-1-0.938-0.95615.88914.41914.4190.0000.0000.0000.000
47A49LYS10.7860.89515.626-17.066-17.0660.0000.0000.0000.000
48A50GLY0-0.032-0.00714.0840.7110.7110.0000.0000.0000.000
49A51ILE0-0.044-0.0119.3352.2382.2380.0000.0000.0000.000
50A52ASN0-0.015-0.03710.696-2.096-2.0960.0000.0000.0000.000
51A53ASP-1-0.816-0.8585.84946.83146.8310.0000.0000.0000.000
52A54ILE00.0300.0088.0352.0202.0200.0000.0000.0000.000
53A55ILE00.0070.0166.439-2.177-2.1770.0000.0000.0000.000
54A56ILE0-0.006-0.00510.840-0.851-0.8510.0000.0000.0000.000
55A57ILE00.0160.01612.136-0.546-0.5460.0000.0000.0000.000
56A58VAL00.000-0.01015.923-1.182-1.1820.0000.0000.0000.000
57A59GLY00.0740.00419.5060.2750.2750.0000.0000.0000.000
58A60TYR0-0.060-0.03022.500-0.476-0.4760.0000.0000.0000.000
59A61LEU0-0.023-0.01125.3160.2340.2340.0000.0000.0000.000
60A62LYS10.9130.95622.100-12.606-12.6060.0000.0000.0000.000
61A63GLU-1-0.831-0.91423.22912.26912.2690.0000.0000.0000.000
62A64GLN0-0.049-0.03225.6100.0020.0020.0000.0000.0000.000
63A65PHE00.035-0.00420.0580.0690.0690.0000.0000.0000.000
64A66ASP-1-0.851-0.91021.08514.91714.9170.0000.0000.0000.000
65A67TYR0-0.047-0.05121.5050.4990.4990.0000.0000.0000.000
66A68LEU00.0120.00718.8260.0910.0910.0000.0000.0000.000
67A69LYS10.8470.92417.178-14.923-14.9230.0000.0000.0000.000
68A70GLU-1-0.947-0.97418.06314.01314.0130.0000.0000.0000.000
69A71LYS10.7740.90620.745-13.194-13.1940.0000.0000.0000.000
70A72TYR0-0.048-0.07516.976-0.165-0.1650.0000.0000.0000.000
71A73GLY0-0.0020.02015.2650.9580.9580.0000.0000.0000.000
72A74VAL0-0.045-0.00812.9551.5831.5830.0000.0000.0000.000
73A75ARG10.7380.8135.718-44.820-44.8200.0000.0000.0000.000
74A76LEU0-0.023-0.00912.9720.2160.2160.0000.0000.0000.000
75A77VAL00.0170.00511.9520.0120.0120.0000.0000.0000.000
76A78PHE0-0.052-0.02615.274-0.679-0.6790.0000.0000.0000.000
77A79ASN00.0610.02217.885-0.075-0.0750.0000.0000.0000.000
78A80ASP-1-0.906-0.96919.47813.58413.5840.0000.0000.0000.000
79A81LYS10.8410.92521.862-13.181-13.1810.0000.0000.0000.000
80A82TYR0-0.041-0.01322.298-0.353-0.3530.0000.0000.0000.000
81A83ALA0-0.044-0.02323.279-0.184-0.1840.0000.0000.0000.000
82A84ASP-1-0.898-0.92425.90311.03111.0310.0000.0000.0000.000
83A85TYR0-0.038-0.04121.730-0.401-0.4010.0000.0000.0000.000
84A86ASN00.0250.02423.2150.4410.4410.0000.0000.0000.000
85A87ASN0-0.030-0.03218.8440.5410.5410.0000.0000.0000.000
86A88PHE00.0540.03217.1611.2221.2220.0000.0000.0000.000
87A89TYR00.015-0.00816.3201.1711.1710.0000.0000.0000.000
88A90SER0-0.031-0.02316.1840.4460.4460.0000.0000.0000.000
89A91LEU00.0230.02010.1861.1841.1840.0000.0000.0000.000
90A92TYR00.0000.00211.6792.1722.1720.0000.0000.0000.000
91A93LEU0-0.033-0.01812.4681.1921.1920.0000.0000.0000.000
92A94VAL0-0.029-0.0108.5970.7090.7090.0000.0000.0000.000
93A95LYS10.8300.9237.743-19.532-19.5320.0000.0000.0000.000
94A96GLU-1-0.860-0.9246.41433.38033.3800.0000.0000.0000.000
95A97GLU-1-0.829-0.8883.36865.78766.8500.036-0.423-0.6760.003
96A98LEU0-0.038-0.0114.3145.0965.3020.000-0.033-0.1720.000
97A99ALA00.011-0.0082.767-6.268-4.8310.425-0.759-1.1030.005
98A100ASN0-0.051-0.0532.6714.5747.5070.442-1.218-2.158-0.008
99A101SER00.0440.0284.9972.2562.372-0.001-0.005-0.1090.000
100A102TYR0-0.016-0.0307.263-4.610-4.6100.0000.0000.0000.000
101A103VAL0-0.0120.00410.4801.9701.9700.0000.0000.0000.000
102A104ILE0-0.029-0.03112.695-1.420-1.4200.0000.0000.0000.000
103A105ASP-1-0.852-0.91715.93216.47616.4760.0000.0000.0000.000
104A106ALA0-0.019-0.02519.134-0.276-0.2760.0000.0000.0000.000
105A107ASP-1-0.836-0.90520.76712.89612.8960.0000.0000.0000.000
106A108ASN00.0530.03221.705-1.072-1.0720.0000.0000.0000.000
107A109TYR0-0.001-0.00623.7340.3890.3890.0000.0000.0000.000
108A110LEU0-0.020-0.01119.712-0.152-0.1520.0000.0000.0000.000
109A111PHE00.0260.01224.338-0.142-0.1420.0000.0000.0000.000
110A112LYS10.7850.87125.225-11.846-11.8460.0000.0000.0000.000
111A113ASN0-0.067-0.02319.3611.0321.0320.0000.0000.0000.000
112A114MET00.0230.01418.5090.0790.0790.0000.0000.0000.000
113A115PHE0-0.0070.01415.0590.4790.4790.0000.0000.0000.000
114A116ARG10.8440.87814.780-18.021-18.0210.0000.0000.0000.000
115A117ASN00.0240.01211.5460.4090.4090.0000.0000.0000.000
116A118ASP-1-0.791-0.85711.45619.81119.8110.0000.0000.0000.000
117A119LEU00.0030.01411.507-1.042-1.0420.0000.0000.0000.000
118A120THR0-0.037-0.0239.9821.6411.6410.0000.0000.0000.000
119A121ARG10.9320.98410.625-16.005-16.0050.0000.0000.0000.000
120A122SER00.0390.01310.7930.8220.8220.0000.0000.0000.000
121A123THR0-0.084-0.03912.256-1.933-1.9330.0000.0000.0000.000
122A124TYR00.0700.03115.2781.0301.0300.0000.0000.0000.000
123A125PHE00.000-0.01814.782-0.589-0.5890.0000.0000.0000.000
124A126SER0-0.009-0.01719.894-0.264-0.2640.0000.0000.0000.000
125A127VAL00.0070.01523.326-0.315-0.3150.0000.0000.0000.000
126A128TYR0-0.103-0.07026.7370.1310.1310.0000.0000.0000.000
127A129ARG10.7700.85429.191-11.050-11.0500.0000.0000.0000.000
128A130GLU-1-0.821-0.90732.0658.5098.5090.0000.0000.0000.000
129A131ASP-1-0.973-0.97935.4128.2398.2390.0000.0000.0000.000
130A132CYS0-0.075-0.01832.2260.1690.1690.0000.0000.0000.000
131A133THR0-0.051-0.04932.653-0.418-0.4180.0000.0000.0000.000
132A134ASN0-0.067-0.03330.4250.0530.0530.0000.0000.0000.000
133A135GLU-1-0.850-0.89827.86111.59311.5930.0000.0000.0000.000
134A136TRP0-0.048-0.03222.038-0.033-0.0330.0000.0000.0000.000
135A137PHE0-0.010-0.02626.2520.2360.2360.0000.0000.0000.000
136A138LEU0-0.005-0.00321.5060.2420.2420.0000.0000.0000.000
137A139VAL0-0.0170.00225.325-0.442-0.4420.0000.0000.0000.000
138A140TYR0-0.051-0.06524.1160.5040.5040.0000.0000.0000.000
139A141GLY00.0370.02125.884-0.427-0.4270.0000.0000.0000.000
140A142ASP-1-0.907-0.96626.73010.04510.0450.0000.0000.0000.000
141A143ASP-1-0.907-0.94423.05612.35312.3530.0000.0000.0000.000
142A144TYR0-0.082-0.04122.1110.6150.6150.0000.0000.0000.000
143A145LYS10.8830.94618.435-13.700-13.7000.0000.0000.0000.000
144A146VAL0-0.048-0.04019.903-0.625-0.6250.0000.0000.0000.000
145A147GLN0-0.054-0.03121.4040.1290.1290.0000.0000.0000.000
146A148ASP-1-0.888-0.97324.17211.45811.4580.0000.0000.0000.000
147A149ILE0-0.0120.00720.3970.1620.1620.0000.0000.0000.000
148A150ILE0-0.0070.00025.050-0.185-0.1850.0000.0000.0000.000
149A151VAL00.0340.00028.1540.2110.2110.0000.0000.0000.000
150A152ASP-1-0.992-0.98030.3658.6128.6120.0000.0000.0000.000
151A153SER00.0320.00632.663-0.283-0.2830.0000.0000.0000.000
152A154LYS10.9500.97533.979-8.102-8.1020.0000.0000.0000.000
153A155ALA0-0.0010.00833.982-0.038-0.0380.0000.0000.0000.000
154A156GLY00.0300.02031.264-0.039-0.0390.0000.0000.0000.000
155A157ARG10.7940.88226.230-11.382-11.3820.0000.0000.0000.000
156A158ILE00.0460.03626.0980.1380.1380.0000.0000.0000.000
157A159LEU0-0.0100.01520.4720.4030.4030.0000.0000.0000.000
158A160SER00.0390.00322.025-0.253-0.2530.0000.0000.0000.000
159A161GLY00.0700.05019.669-0.261-0.2610.0000.0000.0000.000
160A162VAL0-0.040-0.02316.4110.8190.8190.0000.0000.0000.000
161A163SER00.0010.01214.870-0.513-0.5130.0000.0000.0000.000
162A164PHE0-0.020-0.0097.7641.5521.5520.0000.0000.0000.000
163A165TRP00.0400.0238.757-2.536-2.5360.0000.0000.0000.000
164A166ASP-1-0.736-0.8296.64828.95628.9560.0000.0000.0000.000
165A167ALA00.006-0.0192.5800.1510.5990.213-0.205-0.455-0.001
166A168PRO00.0110.0004.657-0.519-0.426-0.001-0.011-0.0810.000
167A169THR0-0.005-0.0267.951-1.832-1.8320.0000.0000.0000.000
168A170ALA00.0070.0036.547-1.144-1.1440.0000.0000.0000.000
169A171GLU-1-0.947-0.9627.58524.63524.6350.0000.0000.0000.000
170A172LYS10.8810.9379.079-19.383-19.3830.0000.0000.0000.000
171A173ILE00.0280.02211.645-1.086-1.0860.0000.0000.0000.000
172A174VAL00.0160.0138.456-1.409-1.4090.0000.0000.0000.000
173A175SER0-0.046-0.01811.844-1.911-1.9110.0000.0000.0000.000
174A176PHE0-0.040-0.03514.754-1.345-1.3450.0000.0000.0000.000
175A177ILE00.0270.00412.227-1.050-1.0500.0000.0000.0000.000
176A178ASP-1-0.871-0.93513.92520.48120.4810.0000.0000.0000.000
177A179LYS10.9390.96216.647-15.065-15.0650.0000.0000.0000.000
178A180ALA00.0670.04419.279-0.794-0.7940.0000.0000.0000.000
179A181TYR0-0.042-0.02718.291-0.562-0.5620.0000.0000.0000.000
180A182VAL0-0.073-0.03519.958-0.574-0.5740.0000.0000.0000.000
181A183SER0-0.036-0.02522.527-0.666-0.6660.0000.0000.0000.000
182A184GLY0-0.078-0.03224.982-0.456-0.4560.0000.0000.0000.000
183A185GLU-1-0.963-0.97624.17211.86411.8640.0000.0000.0000.000
184A186PHE00.020-0.01621.0970.4660.4660.0000.0000.0000.000
185A187VAL0-0.0190.00322.8800.2940.2940.0000.0000.0000.000
186A188ASP-1-0.849-0.92224.81811.25611.2560.0000.0000.0000.000
187A189LEU0-0.077-0.01421.768-0.072-0.0720.0000.0000.0000.000
188A190TYR00.0230.01321.0500.1580.1580.0000.0000.0000.000
189A191TRP00.020-0.02114.0280.7270.7270.0000.0000.0000.000
190A192ASP-1-0.823-0.91217.14016.90216.9020.0000.0000.0000.000
191A193ASN00.007-0.02018.892-0.212-0.2120.0000.0000.0000.000
192A194MET0-0.053-0.00716.461-0.158-0.1580.0000.0000.0000.000
193A195VAL00.0120.01215.5890.9530.9530.0000.0000.0000.000
194A196LYS10.8710.92318.232-12.680-12.6800.0000.0000.0000.000
195A197ASP-1-0.861-0.91421.78212.27512.2750.0000.0000.0000.000
196A198ASN0-0.044-0.03418.6750.1380.1380.0000.0000.0000.000
197A199ILE00.0170.03219.0340.3150.3150.0000.0000.0000.000
198A200LYS10.8850.95519.853-11.946-11.9460.0000.0000.0000.000
199A201GLU-1-0.945-0.96017.87313.59413.5940.0000.0000.0000.000
200A202LEU0-0.065-0.02513.6391.0651.0650.0000.0000.0000.000
201A203ASP-1-0.901-0.93814.31015.10215.1020.0000.0000.0000.000
202A204VAL00.005-0.00214.1201.2321.2320.0000.0000.0000.000
203A205TYR0-0.032-0.01915.261-1.358-1.3580.0000.0000.0000.000
204A206VAL0-0.014-0.00118.1370.6910.6910.0000.0000.0000.000
205A207GLU-1-0.933-0.95819.25814.52214.5220.0000.0000.0000.000
206A208GLU-1-0.837-0.90421.23411.09411.0940.0000.0000.0000.000
207A209LEU00.0020.00421.683-0.066-0.0660.0000.0000.0000.000
208A210GLU-1-0.810-0.88025.42210.75010.7500.0000.0000.0000.000
209A211GLY00.0460.01928.3070.2590.2590.0000.0000.0000.000
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