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: Q1GRY

Calculation Name: 1R8I-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1R8I

Chain ID: A

ChEMBL ID:

UniProt ID: Q9L6G5

Base Structure: X-ray

Registration Date: 2023-06-20

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 187
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1872359.683092
FMO2-HF: Nuclear repulsion 1796316.753955
FMO2-HF: Total energy -76042.929137
FMO2-MP2: Total energy -76255.702616


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:32:THR)


Summations of interaction energy for fragment #1(A:32:THR)
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.
-1.5031.8470.048-1.548-1.850.005
Interaction energy analysis for fragmet #1(A:32:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : -0.015
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].
3A34LEU0-0.037-0.0073.229-2.5420.6690.049-1.541-1.7200.005
4A35ILE00.0380.0114.510-0.574-0.435-0.001-0.007-0.1300.000
5A36LYS10.8220.9095.6151.9101.9100.0000.0000.0000.000
6A37GLN00.019-0.0096.3400.4260.4260.0000.0000.0000.000
7A38GLY00.0110.0189.2810.1470.1470.0000.0000.0000.000
8A39GLU-1-0.818-0.89010.253-1.163-1.1630.0000.0000.0000.000
9A40GLN0-0.011-0.00410.3600.2210.2210.0000.0000.0000.000
10A41LEU00.0160.01012.9790.0920.0920.0000.0000.0000.000
11A42GLU-1-0.804-0.89014.923-0.215-0.2150.0000.0000.0000.000
12A43GLN0-0.036-0.03813.1210.0850.0850.0000.0000.0000.000
13A44MET0-0.052-0.00315.1280.0560.0560.0000.0000.0000.000
14A45ALA00.0350.01919.4390.0350.0350.0000.0000.0000.000
15A46GLN0-0.047-0.02820.0240.0010.0010.0000.0000.0000.000
16A47GLN00.0150.00119.2340.0400.0400.0000.0000.0000.000
17A48LEU00.0120.01823.2650.0200.0200.0000.0000.0000.000
18A49GLU-1-0.790-0.86225.686-0.107-0.1070.0000.0000.0000.000
19A50GLN0-0.039-0.01525.3060.0040.0040.0000.0000.0000.000
20A51LEU0-0.013-0.01026.2020.0130.0130.0000.0000.0000.000
21A52LYS10.8540.90029.3780.1220.1220.0000.0000.0000.000
22A53SER00.0080.00631.3880.0090.0090.0000.0000.0000.000
23A54GLN0-0.034-0.01329.5060.0140.0140.0000.0000.0000.000
24A55LEU00.0320.02033.4220.0080.0080.0000.0000.0000.000
25A56GLU-1-0.769-0.85735.256-0.064-0.0640.0000.0000.0000.000
26A57THR0-0.058-0.03836.3860.0060.0060.0000.0000.0000.000
27A58GLN0-0.067-0.05035.4540.0040.0040.0000.0000.0000.000
28A59LYS10.8450.91939.2900.0700.0700.0000.0000.0000.000
29A60ASN0-0.035-0.04141.3110.0070.0070.0000.0000.0000.000
30A61MET0-0.0140.00140.0770.0040.0040.0000.0000.0000.000
31A62TYR00.016-0.03043.3070.0040.0040.0000.0000.0000.000
32A63GLU-1-0.759-0.84845.058-0.043-0.0430.0000.0000.0000.000
33A64SER0-0.037-0.00946.9510.0030.0030.0000.0000.0000.000
34A65MET0-0.0570.00744.8640.0030.0030.0000.0000.0000.000
35A66ALA00.0300.00949.1680.0020.0020.0000.0000.0000.000
36A67LYS10.7970.89649.5820.0470.0470.0000.0000.0000.000
37A68THR0-0.047-0.04552.0800.0010.0010.0000.0000.0000.000
38A69THR00.0000.00852.6090.0010.0010.0000.0000.0000.000
39A70ASN0-0.055-0.03554.8730.0020.0020.0000.0000.0000.000
40A71LEU00.0140.01654.6980.0010.0010.0000.0000.0000.000
41A72GLY0-0.007-0.00358.0990.0010.0010.0000.0000.0000.000
42A73ASP-1-0.935-0.96460.517-0.027-0.0270.0000.0000.0000.000
43A74LEU0-0.060-0.04559.1280.0000.0000.0000.0000.0000.000
44A75LEU0-0.034-0.00357.8320.0000.0000.0000.0000.0000.000
45A76GLY00.0350.03161.9370.0010.0010.0000.0000.0000.000
46A77THR00.030-0.00565.7790.0000.0000.0000.0000.0000.000
47A78SER0-0.051-0.03368.4510.0000.0000.0000.0000.0000.000
48A79THR0-0.0040.00764.3050.0000.0000.0000.0000.0000.000
49A80ASN0-0.065-0.02164.778-0.001-0.0010.0000.0000.0000.000
50A81THR00.0070.00365.6990.0000.0000.0000.0000.0000.000
51A82LEU0-0.009-0.00266.1130.0000.0000.0000.0000.0000.000
52A83ALA00.0280.03061.628-0.001-0.0010.0000.0000.0000.000
53A84ASN00.0240.00661.0530.0000.0000.0000.0000.0000.000
54A85ASN00.011-0.02057.825-0.001-0.0010.0000.0000.0000.000
55A86LEU0-0.0050.00053.4220.0000.0000.0000.0000.0000.000
56A87PRO0-0.0330.00951.887-0.001-0.0010.0000.0000.0000.000
57A88ASP-1-0.832-0.91649.085-0.044-0.0440.0000.0000.0000.000
58A89ASN00.0210.00547.0500.0010.0010.0000.0000.0000.000
59A90TRP0-0.008-0.00942.9080.0000.0000.0000.0000.0000.000
60A91LYS10.8750.94845.8500.0350.0350.0000.0000.0000.000
61A92GLU-1-0.910-0.95442.972-0.051-0.0510.0000.0000.0000.000
62A93VAL00.0210.01242.004-0.001-0.0010.0000.0000.0000.000
63A94TYR0-0.070-0.05742.729-0.002-0.0020.0000.0000.0000.000
64A95SER0-0.002-0.01042.099-0.001-0.0010.0000.0000.0000.000
65A96ASP-1-0.854-0.92338.033-0.068-0.0680.0000.0000.0000.000
66A97ALA0-0.047-0.02338.749-0.003-0.0030.0000.0000.0000.000
67A98MET0-0.075-0.02440.9330.0010.0010.0000.0000.0000.000
68A99ASN0-0.043-0.02537.0780.0030.0030.0000.0000.0000.000
69A100SER0-0.051-0.03035.598-0.005-0.0050.0000.0000.0000.000
70A101SER0-0.0010.01032.0070.0020.0020.0000.0000.0000.000
71A102SER0-0.086-0.04832.8680.0000.0000.0000.0000.0000.000
72A103SER0-0.026-0.01834.892-0.001-0.0010.0000.0000.0000.000
73A104VAL0-0.018-0.00234.775-0.001-0.0010.0000.0000.0000.000
74A105THR0-0.011-0.02237.2340.0050.0050.0000.0000.0000.000
75A106PRO00.000-0.00340.532-0.001-0.0010.0000.0000.0000.000
76A107SER00.0350.02839.9170.0000.0000.0000.0000.0000.000
77A108VAL00.0720.01241.6400.0030.0030.0000.0000.0000.000
78A109ASN00.0600.02240.9580.0040.0040.0000.0000.0000.000
79A110SER0-0.0130.01343.4900.0020.0020.0000.0000.0000.000
80A111MET0-0.063-0.01845.5170.0020.0020.0000.0000.0000.000
81A112MET00.0550.02747.2460.0030.0030.0000.0000.0000.000
82A113GLY0-0.046-0.03149.1950.0010.0010.0000.0000.0000.000
83A114GLN0-0.009-0.00446.5740.0000.0000.0000.0000.0000.000
84A115PHE00.0540.02443.723-0.001-0.0010.0000.0000.0000.000
85A116ASN0-0.014-0.03345.699-0.002-0.0020.0000.0000.0000.000
86A117ALA00.0160.02548.3160.0010.0010.0000.0000.0000.000
87A118GLU-1-0.745-0.86350.094-0.033-0.0330.0000.0000.0000.000
88A119VAL0-0.110-0.04946.528-0.001-0.0010.0000.0000.0000.000
89A120ASP-1-0.869-0.92949.912-0.032-0.0320.0000.0000.0000.000
90A121ASP-1-0.946-0.96752.497-0.024-0.0240.0000.0000.0000.000
91A122MET0-0.035-0.01254.6970.0000.0000.0000.0000.0000.000
92A123THR00.0500.03555.053-0.001-0.0010.0000.0000.0000.000
93A124PRO0-0.006-0.01655.331-0.001-0.0010.0000.0000.0000.000
94A125SER0-0.006-0.02056.6160.0010.0010.0000.0000.0000.000
95A126GLU-1-0.933-0.95758.351-0.025-0.0250.0000.0000.0000.000
96A127ALA00.010-0.00453.4440.0000.0000.0000.0000.0000.000
97A128ILE0-0.013-0.01152.642-0.001-0.0010.0000.0000.0000.000
98A129ALA00.0190.01255.415-0.001-0.0010.0000.0000.0000.000
99A130TYR0-0.011-0.03251.9010.0000.0000.0000.0000.0000.000
100A131MET0-0.028-0.01549.1950.0000.0000.0000.0000.0000.000
101A132ASN00.0340.02252.566-0.002-0.0020.0000.0000.0000.000
102A133LYS10.8310.90154.6890.0260.0260.0000.0000.0000.000
103A134LYS10.8420.93851.5710.0320.0320.0000.0000.0000.000
104A135LEU00.018-0.00348.447-0.001-0.0010.0000.0000.0000.000
105A136ALA0-0.033-0.00451.481-0.001-0.0010.0000.0000.0000.000
106A137GLU-1-0.841-0.91354.490-0.027-0.0270.0000.0000.0000.000
107A138LYS10.8090.91649.3250.0340.0340.0000.0000.0000.000
108A139GLY00.0340.02449.649-0.001-0.0010.0000.0000.0000.000
109A140ALA0-0.004-0.00247.895-0.002-0.0020.0000.0000.0000.000
110A141TYR00.0230.02048.043-0.002-0.0020.0000.0000.0000.000
111A142ASP-1-0.839-0.91749.671-0.036-0.0360.0000.0000.0000.000
112A143ARG10.7600.80847.9200.0410.0410.0000.0000.0000.000
113A144VAL00.0070.02847.411-0.002-0.0020.0000.0000.0000.000
114A145MET0-0.054-0.04046.538-0.001-0.0010.0000.0000.0000.000
115A146ALA00.0060.01643.896-0.002-0.0020.0000.0000.0000.000
116A147GLU-1-0.806-0.88842.717-0.047-0.0470.0000.0000.0000.000
117A148LYS10.9030.96542.4160.0360.0360.0000.0000.0000.000
118A149ALA00.0020.00639.966-0.001-0.0010.0000.0000.0000.000
119A150TYR00.001-0.04038.358-0.003-0.0030.0000.0000.0000.000
120A151ASN0-0.036-0.02937.555-0.006-0.0060.0000.0000.0000.000
121A152ASN0-0.035-0.00536.595-0.003-0.0030.0000.0000.0000.000
122A153GLN00.0600.03631.315-0.009-0.0090.0000.0000.0000.000
123A154MET00.0160.00832.847-0.009-0.0090.0000.0000.0000.000
124A155GLN0-0.098-0.03833.237-0.002-0.0020.0000.0000.0000.000
125A156GLU-1-0.762-0.84429.729-0.084-0.0840.0000.0000.0000.000
126A157LEU0-0.003-0.00728.038-0.007-0.0070.0000.0000.0000.000
127A158SER0-0.017-0.02628.121-0.010-0.0100.0000.0000.0000.000
128A159ASP-1-0.864-0.92528.994-0.071-0.0710.0000.0000.0000.000
129A160MET0-0.044-0.02024.886-0.005-0.0050.0000.0000.0000.000
130A161GLN0-0.0150.01324.226-0.003-0.0030.0000.0000.0000.000
131A162ALA00.0680.04124.023-0.007-0.0070.0000.0000.0000.000
132A163LEU0-0.024-0.01222.0760.0030.0030.0000.0000.0000.000
133A164THR0-0.009-0.03419.302-0.007-0.0070.0000.0000.0000.000
134A165GLU-1-0.958-0.99719.516-0.128-0.1280.0000.0000.0000.000
135A166GLN0-0.028-0.00520.2790.0020.0020.0000.0000.0000.000
136A167ILE00.0420.02116.2270.0140.0140.0000.0000.0000.000
137A168LYS10.7870.88415.7790.2350.2350.0000.0000.0000.000
138A169SER0-0.056-0.03916.7560.0030.0030.0000.0000.0000.000
139A170THR0-0.128-0.05517.7700.0270.0270.0000.0000.0000.000
140A171PRO00.0030.01113.182-0.007-0.0070.0000.0000.0000.000
141A172ASP-1-0.759-0.86214.4370.0560.0560.0000.0000.0000.000
142A173LEU0-0.003-0.0029.160-0.046-0.0460.0000.0000.0000.000
143A174LYS10.7790.87813.147-0.001-0.0010.0000.0000.0000.000
144A175SER00.006-0.03516.690-0.020-0.0200.0000.0000.0000.000
145A176ILE0-0.0020.00112.505-0.015-0.0150.0000.0000.0000.000
146A177ALA00.0070.01015.464-0.025-0.0250.0000.0000.0000.000
147A178ASP-1-0.814-0.88916.873-0.066-0.0660.0000.0000.0000.000
148A179LEU0-0.024-0.00718.7250.0020.0020.0000.0000.0000.000
149A180GLN0-0.006-0.00416.574-0.006-0.0060.0000.0000.0000.000
150A181ALA00.0220.00919.2660.0040.0040.0000.0000.0000.000
151A182ARG10.8010.86721.9880.1000.1000.0000.0000.0000.000
152A183ILE00.0510.01720.6940.0070.0070.0000.0000.0000.000
153A184GLN0-0.012-0.00221.553-0.008-0.0080.0000.0000.0000.000
154A185THR0-0.030-0.02024.1490.0110.0110.0000.0000.0000.000
155A186SER0-0.007-0.01927.3010.0060.0060.0000.0000.0000.000
156A187GLN0-0.058-0.02723.1240.0100.0100.0000.0000.0000.000
157A188GLY00.0340.02027.8320.0060.0060.0000.0000.0000.000
158A189ALA00.004-0.00129.7100.0070.0070.0000.0000.0000.000
159A190ILE00.0120.00630.6310.0070.0070.0000.0000.0000.000
160A191GLN0-0.004-0.00828.151-0.002-0.0020.0000.0000.0000.000
161A192GLY00.0460.02632.7410.0040.0040.0000.0000.0000.000
162A193GLU-1-0.752-0.83035.526-0.059-0.0590.0000.0000.0000.000
163A194GLN00.0210.01334.6200.0090.0090.0000.0000.0000.000
164A195ALA00.0010.02137.2360.0040.0040.0000.0000.0000.000
165A196LYS10.8650.90938.9540.0570.0570.0000.0000.0000.000
166A197LEU0-0.021-0.01539.4280.0040.0040.0000.0000.0000.000
167A198ASN00.0160.00538.9370.0040.0040.0000.0000.0000.000
168A199LEU00.0080.01342.7920.0030.0030.0000.0000.0000.000
169A200MET0-0.029-0.01645.1620.0020.0020.0000.0000.0000.000
170A201ASN0-0.009-0.01345.5420.0030.0030.0000.0000.0000.000
171A202MET00.0190.01346.9160.0020.0020.0000.0000.0000.000
172A203LEU0-0.001-0.00148.7040.0030.0030.0000.0000.0000.000
173A204GLN00.0400.02249.8530.0020.0020.0000.0000.0000.000
174A205GLN00.0320.02050.2030.0040.0040.0000.0000.0000.000
175A206SER00.0540.01652.8140.0020.0020.0000.0000.0000.000
176A207GLN0-0.027-0.02653.0160.0020.0020.0000.0000.0000.000
177A208ASP-1-0.771-0.85455.953-0.034-0.0340.0000.0000.0000.000
178A209LYS10.7340.85654.9400.0390.0390.0000.0000.0000.000
179A210LEU00.0690.03158.7040.0010.0010.0000.0000.0000.000
180A211LEU00.0050.00960.4050.0010.0010.0000.0000.0000.000
181A212ARG10.7930.86958.9670.0340.0340.0000.0000.0000.000
182A213ALA00.0230.02563.6190.0010.0010.0000.0000.0000.000
183A214GLN00.012-0.00964.3360.0020.0020.0000.0000.0000.000
184A215LYS10.8380.92465.0470.0270.0270.0000.0000.0000.000
185A216ASP-1-0.836-0.89069.013-0.021-0.0210.0000.0000.0000.000
186A217ARG10.8230.89070.7230.0210.0210.0000.0000.0000.000
187A218ALA0-0.057-0.01072.0440.0010.0010.0000.0000.0000.000