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: MN8LZ

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 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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2363141.652614
FMO2-HF: Nuclear repulsion 2280239.075232
FMO2-HF: Total energy -82902.577382
FMO2-MP2: Total energy -83135.920069


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.
-26.991-16.7815.531-5.588-10.151-0.009
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-1-0.886-0.9242.213-17.863-14.3912.345-2.673-3.144-0.012
4A5PHE0-0.026-0.0114.2020.2730.634-0.001-0.037-0.3230.000
5A6ASP-1-0.768-0.8815.326-2.705-2.667-0.001-0.001-0.0350.000
6A7TYR0-0.028-0.0138.9390.5370.5370.0000.0000.0000.000
7A8PHE00.0260.0099.314-0.391-0.3910.0000.0000.0000.000
8A9THR00.0240.01012.0080.2380.2380.0000.0000.0000.000
9A10LEU0-0.044-0.01614.2160.0260.0260.0000.0000.0000.000
10A11ALA00.0100.00516.7380.0410.0410.0000.0000.0000.000
11A12LEU0-0.005-0.00818.5210.0530.0530.0000.0000.0000.000
12A13THR00.021-0.01221.943-0.006-0.0060.0000.0000.0000.000
13A14TRP0-0.027-0.01624.3820.0090.0090.0000.0000.0000.000
14A15SER00.0880.01828.1220.0130.0130.0000.0000.0000.000
15A16GLY0-0.029-0.01829.6450.0160.0160.0000.0000.0000.000
16A17THR0-0.046-0.05029.6990.0170.0170.0000.0000.0000.000
17A18GLU-1-0.911-0.96026.619-0.142-0.1420.0000.0000.0000.000
18A19CYS0-0.151-0.05929.7670.0110.0110.0000.0000.0000.000
19A20LEU00.0450.03133.1190.0060.0060.0000.0000.0000.000
20A21SER0-0.053-0.03135.2620.0090.0090.0000.0000.0000.000
21A22VAL0-0.018-0.01233.1720.0090.0090.0000.0000.0000.000
22A23LYS10.9100.95833.7080.0120.0120.0000.0000.0000.000
23A24ASP-1-0.746-0.86931.7800.0170.0170.0000.0000.0000.000
24A25SER0-0.040-0.05035.158-0.010-0.0100.0000.0000.0000.000
25A26CYS0-0.083-0.01428.0490.0140.0140.0000.0000.0000.000
26A27PRO00.0410.01332.559-0.009-0.0090.0000.0000.0000.000
27A28THR00.0260.00626.699-0.008-0.0080.0000.0000.0000.000
28A29ASN0-0.009-0.00128.634-0.024-0.0240.0000.0000.0000.000
29A30ALA00.0360.01229.0890.0020.0020.0000.0000.0000.000
30A32SER0-0.081-0.03333.282-0.004-0.0040.0000.0000.0000.000
31A33ARG10.9210.97029.1440.0310.0310.0000.0000.0000.000
32A34SER00.005-0.00835.782-0.008-0.0080.0000.0000.0000.000
33A35GLU-1-0.991-0.98636.630-0.047-0.0470.0000.0000.0000.000
34A36VAL0-0.050-0.01331.860-0.005-0.0050.0000.0000.0000.000
35A37GLU-1-0.909-0.95235.171-0.130-0.1300.0000.0000.0000.000
36A38THR0-0.088-0.03633.1730.0000.0000.0000.0000.0000.000
37A39GLY00.0890.03731.005-0.002-0.0020.0000.0000.0000.000
38A40PHE0-0.014-0.01325.5440.0040.0040.0000.0000.0000.000
39A41THR00.0160.06024.4850.0120.0120.0000.0000.0000.000
40A42ILE0-0.002-0.01218.481-0.030-0.0300.0000.0000.0000.000
41A43LYS10.8640.95918.0260.2530.2530.0000.0000.0000.000
42A44GLY00.011-0.01415.4510.0640.0640.0000.0000.0000.000
43A45LEU00.0060.03011.894-0.044-0.0440.0000.0000.0000.000
44A46TRP0-0.063-0.06110.4120.0980.0980.0000.0000.0000.000
45A47PRO00.0030.0235.8470.0270.0270.0000.0000.0000.000
46A48ASP-1-0.773-0.9017.735-2.045-2.0450.0000.0000.0000.000
47A49TYR0-0.068-0.0622.247-1.6120.7290.536-1.179-1.698-0.008
48A50ASP-1-0.879-0.9718.502-1.534-1.5340.0000.0000.0000.000
49A51ASP-1-0.976-0.96710.301-1.748-1.7480.0000.0000.0000.000
50A52GLY0-0.0050.00112.1410.2490.2490.0000.0000.0000.000
51A53THR0-0.092-0.0508.6880.0800.0800.0000.0000.0000.000
52A54TRP0-0.048-0.0377.013-0.088-0.0880.0000.0000.0000.000
53A55PRO0-0.0480.0042.636-0.1391.1630.525-0.480-1.3470.003
54A56SER0-0.007-0.0414.7090.3090.448-0.001-0.012-0.1260.000
55A57CYS0-0.096-0.0426.7340.6040.6040.0000.0000.0000.000
56A58CYS0-0.0630.0033.257-1.4050.4312.128-0.972-2.9920.009
57A59GLU-1-0.907-0.9524.5111.7531.959-0.001-0.027-0.1780.000
58A60GLY00.0450.0096.306-0.015-0.0150.0000.0000.0000.000
59A61ALA0-0.060-0.0168.984-0.153-0.1530.0000.0000.0000.000
60A62LYS11.0000.99512.427-0.689-0.6890.0000.0000.0000.000
61A63TYR00.0360.00214.530-0.066-0.0660.0000.0000.0000.000
62A64ASP-1-0.863-0.94216.3540.3410.3410.0000.0000.0000.000
63A65GLN0-0.003-0.00419.250-0.059-0.0590.0000.0000.0000.000
64A66ASN0-0.074-0.04421.708-0.066-0.0660.0000.0000.0000.000
65A67GLU-1-0.938-0.96217.9850.2750.2750.0000.0000.0000.000
66A68ILE0-0.022-0.01018.181-0.043-0.0430.0000.0000.0000.000
67A69SER00.0230.02421.164-0.038-0.0380.0000.0000.0000.000
68A70ILE0-0.034-0.02224.134-0.014-0.0140.0000.0000.0000.000
69A71LEU0-0.0030.00720.074-0.019-0.0190.0000.0000.0000.000
70A72SER0-0.033-0.01124.149-0.018-0.0180.0000.0000.0000.000
71A73ASN00.002-0.01025.7400.0000.0000.0000.0000.0000.000
72A74ASP-1-0.859-0.93224.997-0.117-0.1170.0000.0000.0000.000
73A75LEU0-0.015-0.00919.935-0.019-0.0190.0000.0000.0000.000
74A76SER0-0.034-0.00623.654-0.004-0.0040.0000.0000.0000.000
75A77LYS10.9190.96226.6590.0990.0990.0000.0000.0000.000
76A78TYR00.009-0.01724.627-0.004-0.0040.0000.0000.0000.000
77A79TRP0-0.0070.01015.247-0.047-0.0470.0000.0000.0000.000
78A80PRO0-0.0200.00322.7550.0250.0250.0000.0000.0000.000
79A81SER00.0390.03824.023-0.020-0.0200.0000.0000.0000.000
80A82TYR00.027-0.04425.1190.0110.0110.0000.0000.0000.000
81A83SER00.002-0.01126.6590.0020.0020.0000.0000.0000.000
82A85PRO0-0.079-0.01127.5790.0200.0200.0000.0000.0000.000
83A86SER0-0.004-0.00923.868-0.001-0.0010.0000.0000.0000.000
84A87SER00.0440.02820.039-0.018-0.0180.0000.0000.0000.000
85A88SER0-0.047-0.02719.4560.0400.0400.0000.0000.0000.000
86A89ALA00.0330.00314.168-0.070-0.0700.0000.0000.0000.000
87A91GLY00.0130.01713.3430.0930.0930.0000.0000.0000.000
88A92SER0-0.031-0.01116.302-0.007-0.0070.0000.0000.0000.000
89A93PHE0-0.030-0.01818.648-0.016-0.0160.0000.0000.0000.000
90A94ASP-1-0.840-0.92717.4600.4310.4310.0000.0000.0000.000
91A95ALA0-0.038-0.02820.502-0.041-0.0410.0000.0000.0000.000
92A96SER0-0.015-0.02021.182-0.024-0.0240.0000.0000.0000.000
93A97ASP-1-0.781-0.89719.7890.0140.0140.0000.0000.0000.000
94A98LEU00.0100.00717.797-0.004-0.0040.0000.0000.0000.000
95A99ALA0-0.022-0.01016.1700.0220.0220.0000.0000.0000.000
96A100TYR0-0.0250.00215.3110.0500.0500.0000.0000.0000.000
97A101GLU-1-0.843-0.94713.663-0.240-0.2400.0000.0000.0000.000
98A102TRP0-0.0190.00710.363-0.110-0.1100.0000.0000.0000.000
99A103ALA00.0000.01110.3970.1220.1220.0000.0000.0000.000
100A104LYS10.9270.9509.7080.3790.3790.0000.0000.0000.000
101A105HIS10.9030.9458.0510.8320.8320.0000.0000.0000.000
102A106GLY00.0550.0217.381-0.342-0.3420.0000.0000.0000.000
103A107THR0-0.0290.0117.047-0.366-0.3660.0000.0000.0000.000
104A109SER0-0.006-0.0243.775-3.130-2.7220.002-0.199-0.211-0.001
105A110SER0-0.0300.0305.3420.1120.1120.0000.0000.0000.000
106A111PRO0-0.034-0.0464.488-1.080-0.973-0.001-0.008-0.0970.000
107A112VAL0-0.018-0.0067.6980.2380.2380.0000.0000.0000.000
108A113LEU0-0.012-0.0028.9130.2280.2280.0000.0000.0000.000
109A114GLY00.0410.0179.2950.0730.0730.0000.0000.0000.000
110A115ASN0-0.030-0.01211.3500.1960.1960.0000.0000.0000.000
111A116GLN00.1170.05312.780-0.178-0.1780.0000.0000.0000.000
112A117TYR00.0590.03614.118-0.096-0.0960.0000.0000.0000.000
113A118GLU-1-0.905-0.93613.765-0.252-0.2520.0000.0000.0000.000
114A119TYR0-0.0070.00510.7640.0080.0080.0000.0000.0000.000
115A120PHE00.006-0.01113.282-0.074-0.0740.0000.0000.0000.000
116A121SER0-0.019-0.03416.520-0.044-0.0440.0000.0000.0000.000
117A122THR00.009-0.00514.931-0.017-0.0170.0000.0000.0000.000
118A123THR0-0.020-0.01514.972-0.070-0.0700.0000.0000.0000.000
119A124LEU0-0.028-0.01817.1270.0030.0030.0000.0000.0000.000
120A125MET0-0.0230.01218.9430.0180.0180.0000.0000.0000.000
121A126LEU0-0.029-0.01516.2310.0140.0140.0000.0000.0000.000
122A127TYR0-0.051-0.05320.5710.0200.0200.0000.0000.0000.000
123A128PHE0-0.041-0.02722.3600.0190.0190.0000.0000.0000.000
124A129LYS10.8690.95923.2440.4580.4580.0000.0000.0000.000
125A130TYR0-0.006-0.01821.740-0.002-0.0020.0000.0000.0000.000
126A131ASN00.1050.06125.223-0.015-0.0150.0000.0000.0000.000
127A132ILE00.0520.00824.6950.0090.0090.0000.0000.0000.000
128A133SER00.000-0.01027.8420.0070.0070.0000.0000.0000.000
129A134GLU-1-0.925-0.95230.598-0.204-0.2040.0000.0000.0000.000
130A135ILE00.0520.03528.3230.0060.0060.0000.0000.0000.000
131A136LEU0-0.044-0.02130.2370.0080.0080.0000.0000.0000.000
132A137SER0-0.034-0.02033.4440.0140.0140.0000.0000.0000.000
133A138GLU-1-0.966-0.98535.548-0.195-0.1950.0000.0000.0000.000
134A139SER0-0.048-0.03235.7440.0010.0010.0000.0000.0000.000
135A140GLY0-0.060-0.02237.8000.0020.0020.0000.0000.0000.000
136A141TYR0-0.065-0.02335.1250.0090.0090.0000.0000.0000.000
137A142LEU00.0290.02035.772-0.006-0.0060.0000.0000.0000.000
138A143PRO00.0360.03235.0750.0010.0010.0000.0000.0000.000
139A144SER00.0140.00537.1950.0110.0110.0000.0000.0000.000
140A145ASN0-0.003-0.00139.123-0.009-0.0090.0000.0000.0000.000
141A146THR0-0.051-0.03641.1870.0030.0030.0000.0000.0000.000
142A147ALA0-0.038-0.00640.5590.0000.0000.0000.0000.0000.000
143A148GLU-1-0.897-0.94139.286-0.133-0.1330.0000.0000.0000.000
144A149TYR0-0.064-0.07536.4930.0020.0020.0000.0000.0000.000
145A150LYS10.9790.99236.9310.1690.1690.0000.0000.0000.000
146A151VAL00.0440.02530.476-0.007-0.0070.0000.0000.0000.000
147A152GLU-1-0.970-0.99332.389-0.243-0.2430.0000.0000.0000.000
148A153GLY00.0650.03933.822-0.010-0.0100.0000.0000.0000.000
149A154ILE00.0060.00230.273-0.005-0.0050.0000.0000.0000.000
150A155MET0-0.051-0.02626.456-0.015-0.0150.0000.0000.0000.000
151A156SER0-0.015-0.00230.067-0.023-0.0230.0000.0000.0000.000
152A157ALA00.0190.01532.659-0.005-0.0050.0000.0000.0000.000
153A158ILE00.010-0.00126.365-0.005-0.0050.0000.0000.0000.000
154A159GLN00.0580.02527.871-0.034-0.0340.0000.0000.0000.000
155A160SER0-0.124-0.05429.177-0.007-0.0070.0000.0000.0000.000
156A161ALA00.0010.01030.2200.0050.0050.0000.0000.0000.000
157A162LEU0-0.050-0.03224.213-0.006-0.0060.0000.0000.0000.000
158A163ARG10.8530.92126.4380.3470.3470.0000.0000.0000.000
159A164VAL00.0040.02822.405-0.022-0.0220.0000.0000.0000.000
160A165THR0-0.007-0.01524.1960.0580.0580.0000.0000.0000.000
161A166PRO0-0.030-0.00222.683-0.051-0.0510.0000.0000.0000.000
162A167VAL00.0270.01419.5670.0330.0330.0000.0000.0000.000
163A168VAL00.015-0.00922.5710.0110.0110.0000.0000.0000.000
164A169LYS10.9130.96420.5570.4950.4950.0000.0000.0000.000
165A170CYS0-0.0310.00425.0710.0300.0300.0000.0000.0000.000
166A171LYS10.9781.01127.9300.1190.1190.0000.0000.0000.000
167A172SER0-0.013-0.01729.9490.0160.0160.0000.0000.0000.000
168A173ASP-1-0.986-1.01133.123-0.154-0.1540.0000.0000.0000.000
169A174ALA00.0020.03132.846-0.004-0.0040.0000.0000.0000.000
170A175VAL00.0350.00428.265-0.012-0.0120.0000.0000.0000.000
171A176GLU-1-0.911-0.94125.246-0.183-0.1830.0000.0000.0000.000
172A177GLN00.0100.01119.806-0.066-0.0660.0000.0000.0000.000
173A178VAL0-0.0010.01123.343-0.004-0.0040.0000.0000.0000.000
174A179GLN0-0.068-0.04818.181-0.056-0.0560.0000.0000.0000.000
175A180ILE00.0450.02419.3180.0200.0200.0000.0000.0000.000
176A181CYS0-0.0340.00416.141-0.163-0.1630.0000.0000.0000.000
177A182PHE00.027-0.00415.2430.1370.1370.0000.0000.0000.000
178A183ASP-1-0.657-0.77014.107-1.239-1.2390.0000.0000.0000.000
179A184LYS10.8370.8948.7243.0463.0460.0000.0000.0000.000
180A185THR0-0.140-0.08112.7410.1080.1080.0000.0000.0000.000
181A186LEU0-0.043-0.03314.6400.1390.1390.0000.0000.0000.000
182A187GLN0-0.096-0.04916.9080.2080.2080.0000.0000.0000.000
183A188LEU0-0.042-0.00918.408-0.087-0.0870.0000.0000.0000.000
184A189GLN0-0.009-0.00914.853-0.039-0.0390.0000.0000.0000.000
185A190GLU-1-0.838-0.92519.758-0.584-0.5840.0000.0000.0000.000
186A192PRO00.0480.02814.3290.0860.0860.0000.0000.0000.000
187A193SER00.0080.00417.4970.0770.0770.0000.0000.0000.000
188A194THR0-0.033-0.03119.656-0.032-0.0320.0000.0000.0000.000
189A195ALA0-0.038-0.00521.6650.0330.0330.0000.0000.0000.000
190A196SER00.014-0.00324.670-0.019-0.0190.0000.0000.0000.000
191A197THR0-0.030-0.02424.8150.0140.0140.0000.0000.0000.000
192A199PRO00.0310.02430.107-0.004-0.0040.0000.0000.0000.000
193A200SER0-0.011-0.01933.653-0.012-0.0120.0000.0000.0000.000
194A201LEU0-0.050-0.02735.892-0.006-0.0060.0000.0000.0000.000
195A202VAL00.0770.04332.145-0.002-0.0020.0000.0000.0000.000
196A203SER00.0570.02934.9430.0050.0050.0000.0000.0000.000
197A204LEU00.0040.00031.944-0.012-0.0120.0000.0000.0000.000
198A205PRO00.0240.03033.7290.0090.0090.0000.0000.0000.000
199A206ILE00.0360.01534.922-0.008-0.0080.0000.0000.0000.000
200A207LYS10.8590.93232.3920.0930.0930.0000.0000.0000.000
201A208ASN0-0.0090.00136.1160.0010.0010.0000.0000.0000.000