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: 2NRMR

Calculation Name: 1JY5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JY5

Chain ID: A

ChEMBL ID:

UniProt ID: Q9M7C7

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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2367106.898642
FMO2-HF: Nuclear repulsion 2284203.139056
FMO2-HF: Total energy -82903.759586
FMO2-MP2: Total energy -83137.028007


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:HIS)


Summations of interaction energy for fragment #1(A:2:HIS)
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.
-31.059-24.42711.657-7.06-11.225-0.023
Interaction energy analysis for fragmet #1(A:2:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : -0.004
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].
3A4GLU-1-0.853-0.9211.858-22.216-21.9618.162-4.412-4.005-0.035
4A5PHE0-0.0030.0043.8621.0361.394-0.001-0.025-0.3320.000
5A6ASP-1-0.785-0.8625.447-3.005-3.0050.0000.0000.0000.000
6A7TYR0-0.040-0.0388.9710.3720.3720.0000.0000.0000.000
7A8PHE00.025-0.0019.400-0.292-0.2920.0000.0000.0000.000
8A9THR00.022-0.01612.2820.1620.1620.0000.0000.0000.000
9A10LEU0-0.030-0.00714.5670.0660.0660.0000.0000.0000.000
10A11ALA00.0190.01017.1260.0020.0020.0000.0000.0000.000
11A12LEU0-0.015-0.00718.9150.0610.0610.0000.0000.0000.000
12A13THR00.0340.01822.463-0.014-0.0140.0000.0000.0000.000
13A14TRP0-0.037-0.03724.946-0.003-0.0030.0000.0000.0000.000
14A15SER00.004-0.02828.6400.0160.0160.0000.0000.0000.000
15A16GLY00.0370.00830.1050.0150.0150.0000.0000.0000.000
16A17THR0-0.058-0.04830.2480.0130.0130.0000.0000.0000.000
17A18GLU-1-0.845-0.90726.2530.0080.0080.0000.0000.0000.000
18A19CYS0-0.107-0.02530.3700.0080.0080.0000.0000.0000.000
19A20LEU00.0540.02733.917-0.002-0.0020.0000.0000.0000.000
20A21SER0-0.028-0.01336.2370.0080.0080.0000.0000.0000.000
21A22VAL0-0.015-0.01133.6210.0060.0060.0000.0000.0000.000
22A23LYS10.9210.95933.918-0.073-0.0730.0000.0000.0000.000
23A24ASP-1-0.745-0.82731.5160.1330.1330.0000.0000.0000.000
24A25SER0-0.012-0.03335.036-0.014-0.0140.0000.0000.0000.000
25A26CYS0-0.071-0.02928.2370.0180.0180.0000.0000.0000.000
26A27PRO00.0430.01332.670-0.007-0.0070.0000.0000.0000.000
27A28THR00.0320.01126.901-0.012-0.0120.0000.0000.0000.000
28A29ASN00.0030.01428.891-0.015-0.0150.0000.0000.0000.000
29A30ALA00.0660.02229.710-0.008-0.0080.0000.0000.0000.000
30A32SER0-0.101-0.04933.937-0.008-0.0080.0000.0000.0000.000
31A33ARG10.8620.93829.337-0.096-0.0960.0000.0000.0000.000
32A34SER00.004-0.00736.050-0.008-0.0080.0000.0000.0000.000
33A35GLU-1-0.859-0.91935.4930.0190.0190.0000.0000.0000.000
34A36VAL0-0.0030.01732.064-0.006-0.0060.0000.0000.0000.000
35A37GLU-1-0.868-0.93135.133-0.058-0.0580.0000.0000.0000.000
36A38THR0-0.080-0.03433.6270.0100.0100.0000.0000.0000.000
37A39GLY00.0780.03831.565-0.008-0.0080.0000.0000.0000.000
38A40PHE00.0060.01026.0760.0100.0100.0000.0000.0000.000
39A41THR0-0.0340.01925.5110.0160.0160.0000.0000.0000.000
40A42ILE00.0200.00419.097-0.018-0.0180.0000.0000.0000.000
41A43LYS10.8200.90818.281-0.061-0.0610.0000.0000.0000.000
42A44GLY00.008-0.02016.1330.0920.0920.0000.0000.0000.000
43A45LEU00.0030.02612.310-0.071-0.0710.0000.0000.0000.000
44A46TRP0-0.068-0.04611.0280.1450.1450.0000.0000.0000.000
45A47PRO00.0090.0316.367-0.052-0.0520.0000.0000.0000.000
46A48ASP-1-0.767-0.8738.195-1.035-1.0350.0000.0000.0000.000
47A49TYR0-0.050-0.0652.530-0.6971.3930.433-1.008-1.515-0.007
48A50ASP-1-0.870-0.9499.017-1.513-1.5130.0000.0000.0000.000
49A51ASP-1-0.953-0.9489.863-1.682-1.6820.0000.0000.0000.000
50A52GLY00.0000.00312.5440.2320.2320.0000.0000.0000.000
51A53THR0-0.119-0.0768.8920.1550.1550.0000.0000.0000.000
52A54TRP0-0.009-0.0177.950-0.228-0.2280.0000.0000.0000.000
53A55PRO0-0.0370.0063.415-0.0340.9120.060-0.233-0.7720.001
54A56SER00.000-0.0415.293-0.0500.043-0.001-0.003-0.0880.000
55A57CYS0-0.127-0.0616.1480.3620.3620.0000.0000.0000.000
56A58CYS0-0.0720.0162.644-3.826-1.6253.006-1.267-3.9400.018
57A59GLU-1-0.881-0.9403.9781.5491.8530.001-0.048-0.2560.000
58A60GLY00.0200.0045.8810.3750.3750.0000.0000.0000.000
59A61ALA0-0.031-0.0038.666-0.266-0.2660.0000.0000.0000.000
60A62LYS10.9050.94211.939-0.665-0.6650.0000.0000.0000.000
61A63TYR00.0720.03314.276-0.092-0.0920.0000.0000.0000.000
62A64ASP-1-0.881-0.94315.9980.5010.5010.0000.0000.0000.000
63A65GLN00.0400.01519.084-0.057-0.0570.0000.0000.0000.000
64A66ASN0-0.043-0.03621.704-0.083-0.0830.0000.0000.0000.000
65A67GLU-1-0.871-0.91316.4950.5240.5240.0000.0000.0000.000
66A68ILE00.0180.00318.262-0.044-0.0440.0000.0000.0000.000
67A69SER0-0.0030.00321.278-0.044-0.0440.0000.0000.0000.000
68A70ILE0-0.031-0.01324.058-0.018-0.0180.0000.0000.0000.000
69A71LEU00.0050.01520.297-0.023-0.0230.0000.0000.0000.000
70A72SER0-0.034-0.02524.365-0.015-0.0150.0000.0000.0000.000
71A73ASN0-0.029-0.01625.8440.0040.0040.0000.0000.0000.000
72A74ASP-1-0.826-0.92525.3500.0040.0040.0000.0000.0000.000
73A75LEU0-0.010-0.00820.238-0.010-0.0100.0000.0000.0000.000
74A76SER0-0.032-0.00924.014-0.001-0.0010.0000.0000.0000.000
75A77LYS10.8110.88827.086-0.019-0.0190.0000.0000.0000.000
76A78TYR0-0.0060.00025.063-0.014-0.0140.0000.0000.0000.000
77A79TRP0-0.026-0.00615.436-0.033-0.0330.0000.0000.0000.000
78A80PRO0-0.0140.01122.9360.0360.0360.0000.0000.0000.000
79A81SER00.0050.00524.910-0.017-0.0170.0000.0000.0000.000
80A82TYR00.035-0.02825.780-0.012-0.0120.0000.0000.0000.000
81A83SER0-0.068-0.04927.503-0.004-0.0040.0000.0000.0000.000
82A85PRO0-0.050-0.00227.5550.0170.0170.0000.0000.0000.000
83A86SER0-0.031-0.03123.2320.0080.0080.0000.0000.0000.000
84A87SER0-0.017-0.02619.662-0.026-0.0260.0000.0000.0000.000
85A88SER0-0.003-0.01218.5630.0270.0270.0000.0000.0000.000
86A89ALA00.0130.00313.500-0.047-0.0470.0000.0000.0000.000
87A91GLY00.0290.03212.3430.1090.1090.0000.0000.0000.000
88A92SER0-0.053-0.01915.422-0.054-0.0540.0000.0000.0000.000
89A93PHE0-0.012-0.01717.930-0.002-0.0020.0000.0000.0000.000
90A94ASP-1-0.794-0.87417.3450.7210.7210.0000.0000.0000.000
91A95ALA0-0.025-0.01420.264-0.062-0.0620.0000.0000.0000.000
92A96SER0-0.018-0.01320.972-0.028-0.0280.0000.0000.0000.000
93A97ASP-1-0.750-0.88519.8080.2940.2940.0000.0000.0000.000
94A98LEU0-0.012-0.00618.0530.0280.0280.0000.0000.0000.000
95A99ALA0-0.027-0.01316.3950.0700.0700.0000.0000.0000.000
96A100TYR00.0000.02015.0650.1500.1500.0000.0000.0000.000
97A101GLU-1-0.784-0.89214.0160.2980.2980.0000.0000.0000.000
98A102TRP00.000-0.00110.5640.0310.0310.0000.0000.0000.000
99A103ALA0-0.0040.00410.5290.2580.2580.0000.0000.0000.000
100A104LYS10.9110.9309.415-0.061-0.0610.0000.0000.0000.000
101A105HIS10.8940.9398.4710.3180.3180.0000.0000.0000.000
102A106GLY00.0300.0298.006-0.262-0.2620.0000.0000.0000.000
103A107THR0-0.032-0.0026.599-0.563-0.5630.0000.0000.0000.000
104A109SER00.0130.0014.326-2.748-2.636-0.001-0.024-0.0870.000
105A110SER0-0.0240.0125.114-0.467-0.352-0.001-0.010-0.1040.000
106A111PRO0-0.041-0.0464.236-1.679-1.521-0.001-0.030-0.1260.000
107A112VAL0-0.029-0.0147.3830.3400.3400.0000.0000.0000.000
108A113LEU0-0.016-0.0048.8790.2300.2300.0000.0000.0000.000
109A114GLY00.0290.0119.1800.1180.1180.0000.0000.0000.000
110A115ASN0-0.088-0.05611.0910.2460.2460.0000.0000.0000.000
111A116GLN00.0380.01413.024-0.087-0.0870.0000.0000.0000.000
112A117TYR00.0360.02014.595-0.088-0.0880.0000.0000.0000.000
113A118GLU-1-0.822-0.87813.886-0.103-0.1030.0000.0000.0000.000
114A119TYR00.0150.01011.1480.0050.0050.0000.0000.0000.000
115A120PHE0-0.003-0.00613.565-0.073-0.0730.0000.0000.0000.000
116A121SER0-0.026-0.04016.906-0.062-0.0620.0000.0000.0000.000
117A122THR0-0.002-0.01114.847-0.049-0.0490.0000.0000.0000.000
118A123THR0-0.017-0.01915.469-0.061-0.0610.0000.0000.0000.000
119A124LEU0-0.016-0.01017.553-0.011-0.0110.0000.0000.0000.000
120A125MET0-0.0310.00018.9810.0000.0000.0000.0000.0000.000
121A126LEU0-0.034-0.02116.183-0.006-0.0060.0000.0000.0000.000
122A127TYR0-0.037-0.04120.6390.0040.0040.0000.0000.0000.000
123A128PHE0-0.034-0.02722.8160.0050.0050.0000.0000.0000.000
124A129LYS10.8720.95922.6960.4050.4050.0000.0000.0000.000
125A130TYR00.004-0.00521.760-0.023-0.0230.0000.0000.0000.000
126A131ASN00.0750.02825.628-0.003-0.0030.0000.0000.0000.000
127A132ILE00.0180.00124.9710.0070.0070.0000.0000.0000.000
128A133SER00.008-0.00428.2590.0090.0090.0000.0000.0000.000
129A134GLU-1-0.897-0.91331.112-0.141-0.1410.0000.0000.0000.000
130A135ILE00.0660.03928.6130.0030.0030.0000.0000.0000.000
131A136LEU0-0.025-0.00830.7090.0020.0020.0000.0000.0000.000
132A137SER0-0.061-0.04133.7920.0100.0100.0000.0000.0000.000
133A138GLU-1-0.945-0.97436.373-0.141-0.1410.0000.0000.0000.000
134A139SER0-0.079-0.04535.351-0.002-0.0020.0000.0000.0000.000
135A140GLY0-0.031-0.01037.8740.0010.0010.0000.0000.0000.000
136A141TYR0-0.068-0.03235.4060.0080.0080.0000.0000.0000.000
137A142LEU00.0360.02136.043-0.002-0.0020.0000.0000.0000.000
138A143PRO00.0350.02035.7400.0020.0020.0000.0000.0000.000
139A144SER0-0.014-0.01137.8050.0080.0080.0000.0000.0000.000
140A145ASN0-0.0050.00539.691-0.006-0.0060.0000.0000.0000.000
141A146THR0-0.047-0.03441.5370.0030.0030.0000.0000.0000.000
142A147ALA0-0.0160.01441.123-0.001-0.0010.0000.0000.0000.000
143A148GLU-1-0.919-0.95040.021-0.074-0.0740.0000.0000.0000.000
144A149TYR0-0.034-0.04737.028-0.003-0.0030.0000.0000.0000.000
145A150LYS10.8760.93037.4340.1400.1400.0000.0000.0000.000
146A151VAL00.0420.02931.194-0.006-0.0060.0000.0000.0000.000
147A152GLU-1-0.843-0.92733.040-0.176-0.1760.0000.0000.0000.000
148A153GLY00.0320.01734.219-0.013-0.0130.0000.0000.0000.000
149A154ILE00.0280.01830.740-0.006-0.0060.0000.0000.0000.000
150A155MET0-0.034-0.01526.642-0.010-0.0100.0000.0000.0000.000
151A156SER0-0.030-0.00830.400-0.024-0.0240.0000.0000.0000.000
152A157ALA00.0180.02433.084-0.008-0.0080.0000.0000.0000.000
153A158ILE00.0140.00526.532-0.005-0.0050.0000.0000.0000.000
154A159GLN0-0.024-0.00627.400-0.011-0.0110.0000.0000.0000.000
155A160SER0-0.071-0.05329.474-0.008-0.0080.0000.0000.0000.000
156A161ALA0-0.0200.00230.2740.0000.0000.0000.0000.0000.000
157A162LEU0-0.042-0.03324.287-0.006-0.0060.0000.0000.0000.000
158A163ARG10.8790.93726.4490.2900.2900.0000.0000.0000.000
159A164VAL0-0.0040.01822.552-0.027-0.0270.0000.0000.0000.000
160A165THR0-0.048-0.04924.6720.0590.0590.0000.0000.0000.000
161A166PRO0-0.0150.00623.224-0.040-0.0400.0000.0000.0000.000
162A167VAL00.007-0.00620.6090.0140.0140.0000.0000.0000.000
163A168VAL0-0.002-0.01723.0800.0160.0160.0000.0000.0000.000
164A169LYS10.9100.97320.4970.3410.3410.0000.0000.0000.000
165A170CYS0-0.0240.01825.9860.0230.0230.0000.0000.0000.000
166A171LYS10.8290.90928.7020.0140.0140.0000.0000.0000.000
167A172SER0-0.055-0.03130.7400.0110.0110.0000.0000.0000.000
168A173ASP-1-0.895-0.94133.280-0.080-0.0800.0000.0000.0000.000
169A174ALA00.0260.02633.537-0.012-0.0120.0000.0000.0000.000
170A175VAL00.0450.00028.930-0.004-0.0040.0000.0000.0000.000
171A176GLU-1-0.889-0.91426.003-0.036-0.0360.0000.0000.0000.000
172A177GLN00.007-0.00220.256-0.035-0.0350.0000.0000.0000.000
173A178VAL00.0000.00923.826-0.016-0.0160.0000.0000.0000.000
174A179GLN0-0.013-0.01218.553-0.020-0.0200.0000.0000.0000.000
175A180ILE00.0350.01119.6030.0010.0010.0000.0000.0000.000
176A181CYS0-0.0310.01416.747-0.118-0.1180.0000.0000.0000.000
177A182PHE00.0360.00215.5730.1030.1030.0000.0000.0000.000
178A183ASP-1-0.678-0.80414.290-1.181-1.1810.0000.0000.0000.000
179A184LYS10.7700.8818.4473.6423.6420.0000.0000.0000.000
180A185THR0-0.093-0.05412.5880.0680.0680.0000.0000.0000.000
181A186LEU0-0.063-0.02814.3730.1490.1490.0000.0000.0000.000
182A187GLN0-0.092-0.05217.1660.1930.1930.0000.0000.0000.000
183A188LEU0-0.036-0.01018.569-0.071-0.0710.0000.0000.0000.000
184A189GLN0-0.029-0.02815.422-0.094-0.0940.0000.0000.0000.000
185A190GLU-1-0.769-0.88120.114-0.490-0.4900.0000.0000.0000.000
186A192PRO00.0650.03514.7140.0620.0620.0000.0000.0000.000
187A193SER0-0.029-0.01117.7630.0830.0830.0000.0000.0000.000
188A194THR0-0.024-0.01519.9430.0030.0030.0000.0000.0000.000
189A195ALA0-0.034-0.01322.0910.0250.0250.0000.0000.0000.000
190A196SER00.010-0.00925.184-0.005-0.0050.0000.0000.0000.000
191A197THR0-0.005-0.01125.0880.0150.0150.0000.0000.0000.000
192A199PRO00.0330.01530.754-0.009-0.0090.0000.0000.0000.000
193A200SER0-0.028-0.02634.242-0.010-0.0100.0000.0000.0000.000
194A201LEU0-0.069-0.03036.485-0.006-0.0060.0000.0000.0000.000
195A202VAL00.0460.02332.6890.0000.0000.0000.0000.0000.000
196A203SER00.0310.00635.9200.0000.0000.0000.0000.0000.000
197A204LEU00.002-0.00332.289-0.008-0.0080.0000.0000.0000.000
198A205PRO00.0040.02334.1240.0040.0040.0000.0000.0000.000
199A206ILE00.0280.00135.494-0.004-0.0040.0000.0000.0000.000
200A207LYS10.8140.90432.9400.0020.0020.0000.0000.0000.000
201A208ASN0-0.080-0.04136.359-0.007-0.0070.0000.0000.0000.000