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: LL599

Calculation Name: 1R8I-A-Xray315

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 189
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1878316.429401
FMO2-HF: Nuclear repulsion 1802105.982747
FMO2-HF: Total energy -76210.446654
FMO2-MP2: Total energy -76424.322049


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:31:ACE )


Summations of interaction energy for fragment #1(A:31:ACE )
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.
-0.341.4390.491-0.95-1.321-0.003
Interaction energy analysis for fragmet #1(A:31:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.010
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].
3A33GLU -1-0.826-0.9313.848-0.2770.944-0.006-0.554-0.661-0.002
4A34LEU 0-0.028-0.0032.646-0.0760.4160.497-0.384-0.605-0.001
5A35ILE 00.0270.0024.177-0.151-0.0850.000-0.012-0.0550.000
6A36LYS 10.8280.9306.0650.2150.2150.0000.0000.0000.000
7A37GLN 00.014-0.0077.9640.0210.0210.0000.0000.0000.000
8A38GLY 0-0.006-0.0029.6380.0000.0000.0000.0000.0000.000
9A39GLU -1-0.831-0.89510.783-0.199-0.1990.0000.0000.0000.000
10A40GLN 00.0300.00412.4190.0270.0270.0000.0000.0000.000
11A41LEU 0-0.008-0.00313.9630.0110.0110.0000.0000.0000.000
12A42GLU -1-0.854-0.93015.2200.0710.0710.0000.0000.0000.000
13A43GLN 0-0.028-0.02415.745-0.012-0.0120.0000.0000.0000.000
14A44MET 0-0.051-0.01117.0120.0020.0020.0000.0000.0000.000
15A45ALA 00.0530.02320.0300.0000.0000.0000.0000.0000.000
16A46GLN 0-0.042-0.00919.8580.0010.0010.0000.0000.0000.000
17A47GLN 00.0730.03622.053-0.004-0.0040.0000.0000.0000.000
18A48LEU 0-0.0170.01724.1790.0000.0000.0000.0000.0000.000
19A49GLU -1-0.898-0.95226.1660.0180.0180.0000.0000.0000.000
20A50GLN 0-0.029-0.01126.703-0.005-0.0050.0000.0000.0000.000
21A51LEU 0-0.034-0.02328.235-0.002-0.0020.0000.0000.0000.000
22A52LYS 10.8900.94230.209-0.020-0.0200.0000.0000.0000.000
23A53SER 00.0150.01331.9870.0000.0000.0000.0000.0000.000
24A54GLN 00.008-0.00231.513-0.001-0.0010.0000.0000.0000.000
25A55LEU 00.0210.02634.9620.0000.0000.0000.0000.0000.000
26A56GLU -1-0.849-0.91836.5040.0070.0070.0000.0000.0000.000
27A57THR 0-0.030-0.01038.0960.0000.0000.0000.0000.0000.000
28A58GLN 0-0.057-0.05637.5350.0020.0020.0000.0000.0000.000
29A59LYS 10.9200.98240.474-0.006-0.0060.0000.0000.0000.000
30A60ASN 00.0200.00542.4280.0000.0000.0000.0000.0000.000
31A61MET 0-0.038-0.03142.0530.0000.0000.0000.0000.0000.000
32A62TYR 0-0.008-0.04544.8710.0000.0000.0000.0000.0000.000
33A63GLU -1-0.866-0.96546.3860.0020.0020.0000.0000.0000.000
34A64SER 0-0.085-0.03548.2860.0000.0000.0000.0000.0000.000
35A65MET 00.0200.02447.3210.0000.0000.0000.0000.0000.000
36A66ALA 0-0.0190.00551.0270.0000.0000.0000.0000.0000.000
37A67LYS 10.8210.93249.9220.0000.0000.0000.0000.0000.000
38A68THR 0-0.059-0.04854.0400.0000.0000.0000.0000.0000.000
39A69THR 0-0.0040.02855.1080.0000.0000.0000.0000.0000.000
40A70ASN 0-0.0060.00457.2130.0000.0000.0000.0000.0000.000
41A71LEU 0-0.011-0.01257.3140.0000.0000.0000.0000.0000.000
42A72GLY 0-0.0040.00260.4370.0000.0000.0000.0000.0000.000
43A73ASP -1-1.008-0.99862.530-0.003-0.0030.0000.0000.0000.000
44A74LEU 0-0.058-0.05061.7220.0000.0000.0000.0000.0000.000
45A75LEU 00.0020.01261.0350.0000.0000.0000.0000.0000.000
46A76GLY 00.0100.01865.1770.0000.0000.0000.0000.0000.000
47A77THR 00.030-0.01168.9610.0000.0000.0000.0000.0000.000
48A78SER 0-0.058-0.04171.7340.0000.0000.0000.0000.0000.000
49A79THR 0-0.067-0.01467.6830.0000.0000.0000.0000.0000.000
50A80ASN 00.018-0.00568.1460.0000.0000.0000.0000.0000.000
51A81THR 0-0.0060.02168.3560.0000.0000.0000.0000.0000.000
52A82LEU 00.008-0.01368.8570.0000.0000.0000.0000.0000.000
53A83ALA 00.0640.03665.4000.0000.0000.0000.0000.0000.000
54A84ASN 0-0.035-0.02163.8720.0000.0000.0000.0000.0000.000
55A85ASN 00.068-0.00661.543-0.001-0.0010.0000.0000.0000.000
56A86LEU 0-0.059-0.02956.7880.0000.0000.0000.0000.0000.000
57A87PRO 0-0.0100.03555.7230.0000.0000.0000.0000.0000.000
58A88ASP -1-0.836-0.94353.068-0.017-0.0170.0000.0000.0000.000
59A89ASN 00.0650.00551.3610.0010.0010.0000.0000.0000.000
60A90TRP 00.0160.03446.558-0.001-0.0010.0000.0000.0000.000
61A91LYS 10.8850.97549.5470.0160.0160.0000.0000.0000.000
62A92GLU -1-0.870-0.94347.115-0.027-0.0270.0000.0000.0000.000
63A93VAL 0-0.0290.02346.171-0.001-0.0010.0000.0000.0000.000
64A94TYR 0-0.105-0.09646.5490.0000.0000.0000.0000.0000.000
65A95SER 0-0.031-0.04746.2590.0000.0000.0000.0000.0000.000
66A96ASP -1-0.865-0.94142.109-0.028-0.0280.0000.0000.0000.000
67A97ALA 0-0.050-0.05142.8110.0000.0000.0000.0000.0000.000
68A98MET 0-0.080-0.02144.2920.0010.0010.0000.0000.0000.000
69A99ASN 0-0.0030.00941.6320.0010.0010.0000.0000.0000.000
70A100SER 0-0.064-0.02539.472-0.001-0.0010.0000.0000.0000.000
71A101SER 00.0010.00935.5470.0020.0020.0000.0000.0000.000
72A102SER 0-0.058-0.03636.4080.0020.0020.0000.0000.0000.000
73A103SER 0-0.002-0.01438.482-0.001-0.0010.0000.0000.0000.000
74A104VAL 0-0.0300.00637.4410.0010.0010.0000.0000.0000.000
75A105THR 0-0.013-0.02539.9520.0010.0010.0000.0000.0000.000
76A106PRO 0-0.021-0.00443.586-0.002-0.0020.0000.0000.0000.000
77A107SER 00.0910.06143.4400.0000.0000.0000.0000.0000.000
78A108VAL 00.1040.03244.9110.0010.0010.0000.0000.0000.000
79A109ASN 00.0200.00545.1020.0000.0000.0000.0000.0000.000
80A110SER 0-0.055-0.01847.1090.0000.0000.0000.0000.0000.000
81A111MET 0-0.099-0.03348.8740.0010.0010.0000.0000.0000.000
82A112MET 0-0.009-0.01051.1730.0010.0010.0000.0000.0000.000
83A113GLY 0-0.059-0.02952.8380.0000.0000.0000.0000.0000.000
84A114GLN 0-0.005-0.02451.739-0.001-0.0010.0000.0000.0000.000
85A115PHE 00.0820.03148.5160.0000.0000.0000.0000.0000.000
86A116ASN 0-0.059-0.04750.524-0.001-0.0010.0000.0000.0000.000
87A117ALA 0-0.0140.00553.0360.0000.0000.0000.0000.0000.000
88A118GLU -1-0.831-0.93754.307-0.014-0.0140.0000.0000.0000.000
89A119VAL 0-0.087-0.03850.9040.0000.0000.0000.0000.0000.000
90A120ASP -1-0.842-0.89854.369-0.020-0.0200.0000.0000.0000.000
91A121ASP -1-0.977-0.98957.353-0.013-0.0130.0000.0000.0000.000
92A122MET 0-0.0380.02658.5170.0010.0010.0000.0000.0000.000
93A123THR 00.0600.04659.6600.0000.0000.0000.0000.0000.000
94A124PRO 00.0320.00459.1230.0000.0000.0000.0000.0000.000
95A125SER 0-0.043-0.03160.2210.0010.0010.0000.0000.0000.000
96A126GLU -1-0.932-0.97662.172-0.009-0.0090.0000.0000.0000.000
97A127ALA 00.004-0.00657.4690.0000.0000.0000.0000.0000.000
98A128ILE 0-0.0230.00156.8320.0000.0000.0000.0000.0000.000
99A129ALA 00.0530.03358.8540.0000.0000.0000.0000.0000.000
100A130TYR 0-0.0010.00555.9390.0010.0010.0000.0000.0000.000
101A131MET 0-0.032-0.04053.2080.0000.0000.0000.0000.0000.000
102A132ASN 00.0440.01555.7260.0000.0000.0000.0000.0000.000
103A133LYS 10.9540.99357.8300.0090.0090.0000.0000.0000.000
104A134LYS 10.9270.96855.1540.0110.0110.0000.0000.0000.000
105A135LEU 00.0220.00451.6940.0000.0000.0000.0000.0000.000
106A136ALA 0-0.025-0.01154.5050.0010.0010.0000.0000.0000.000
107A137GLU -1-0.987-0.99357.367-0.006-0.0060.0000.0000.0000.000
108A138LYS 10.8620.93452.9300.0090.0090.0000.0000.0000.000
109A139GLY 00.0370.01752.7220.0000.0000.0000.0000.0000.000
110A140ALA 00.0150.02850.6820.0000.0000.0000.0000.0000.000
111A141TYR 0-0.0040.00850.7810.0000.0000.0000.0000.0000.000
112A142ASP -1-0.867-0.91452.4360.0000.0000.0000.0000.0000.000
113A143ARG 10.9670.95349.984-0.002-0.0020.0000.0000.0000.000
114A144VAL 00.0040.04549.1160.0010.0010.0000.0000.0000.000
115A145MET 0-0.039-0.04748.6080.0010.0010.0000.0000.0000.000
116A146ALA 00.0030.02446.5670.0000.0000.0000.0000.0000.000
117A147GLU -1-0.887-0.96544.8020.0040.0040.0000.0000.0000.000
118A148LYS 10.8910.96543.902-0.003-0.0030.0000.0000.0000.000
119A149ALA 0-0.013-0.00342.3940.0010.0010.0000.0000.0000.000
120A150TYR 0-0.002-0.09040.0950.0000.0000.0000.0000.0000.000
121A151ASN 0-0.017-0.01739.2840.0010.0010.0000.0000.0000.000
122A152ASN 0-0.073-0.03538.4040.0010.0010.0000.0000.0000.000
123A153GLN 00.0790.03533.4210.0010.0010.0000.0000.0000.000
124A154MET 00.0110.00834.5240.0010.0010.0000.0000.0000.000
125A155GLN 0-0.060-0.03034.2320.0020.0020.0000.0000.0000.000
126A156GLU -1-0.832-0.91531.6640.0100.0100.0000.0000.0000.000
127A157LEU 0-0.019-0.01429.6160.0020.0020.0000.0000.0000.000
128A158SER 0-0.045-0.02729.1710.0040.0040.0000.0000.0000.000
129A159ASP -1-0.895-0.94229.3370.0290.0290.0000.0000.0000.000
130A160MET 0-0.065-0.03626.3540.0030.0030.0000.0000.0000.000
131A161GLN 0-0.0150.00025.0130.0030.0030.0000.0000.0000.000
132A162ALA 00.0580.03224.4140.0080.0080.0000.0000.0000.000
133A163LEU 0-0.053-0.02723.4340.0090.0090.0000.0000.0000.000
134A164THR 00.014-0.02619.5320.0070.0070.0000.0000.0000.000
135A165GLU -1-0.995-0.99019.7920.0870.0870.0000.0000.0000.000
136A166GLN 0-0.008-0.00520.0940.0130.0130.0000.0000.0000.000
137A167ILE 00.0120.00516.8860.0140.0140.0000.0000.0000.000
138A168LYS 10.9851.00315.565-0.071-0.0710.0000.0000.0000.000
139A169SER 0-0.084-0.05316.5680.0070.0070.0000.0000.0000.000
140A170THR 0-0.196-0.09316.8490.0030.0030.0000.0000.0000.000
141A171PRO 0-0.034-0.01212.815-0.022-0.0220.0000.0000.0000.000
142A172ASP -1-0.781-0.89215.0580.0620.0620.0000.0000.0000.000
143A173LEU 00.012-0.00811.872-0.012-0.0120.0000.0000.0000.000
144A174LYS 10.9580.99615.498-0.026-0.0260.0000.0000.0000.000
145A175SER 0-0.008-0.01618.749-0.006-0.0060.0000.0000.0000.000
146A176ILE 0-0.025-0.01014.074-0.003-0.0030.0000.0000.0000.000
147A177ALA 00.0220.02018.201-0.010-0.0100.0000.0000.0000.000
148A178ASP -1-0.904-0.95419.799-0.011-0.0110.0000.0000.0000.000
149A179LEU 0-0.038-0.01320.763-0.003-0.0030.0000.0000.0000.000
150A180GLN 00.0410.02819.823-0.001-0.0010.0000.0000.0000.000
151A181ALA 00.0420.01322.205-0.003-0.0030.0000.0000.0000.000
152A182ARG 10.8810.94025.253-0.008-0.0080.0000.0000.0000.000
153A183ILE 00.037-0.00122.7290.0000.0000.0000.0000.0000.000
154A184GLN 0-0.035-0.01625.490-0.005-0.0050.0000.0000.0000.000
155A185THR 0-0.031-0.01327.364-0.001-0.0010.0000.0000.0000.000
156A186SER 0-0.003-0.00829.9390.0010.0010.0000.0000.0000.000
157A187GLN 0-0.043-0.01025.9680.0050.0050.0000.0000.0000.000
158A188GLY 00.0190.00830.6180.0000.0000.0000.0000.0000.000
159A189ALA 0-0.0120.00733.3830.0010.0010.0000.0000.0000.000
160A190ILE 00.0440.02232.2130.0010.0010.0000.0000.0000.000
161A191GLN 00.0010.00331.2720.0000.0000.0000.0000.0000.000
162A192GLY 00.0260.00435.7530.0010.0010.0000.0000.0000.000
163A193GLU -1-0.732-0.79938.289-0.009-0.0090.0000.0000.0000.000
164A194GLN 00.003-0.01937.8770.0020.0020.0000.0000.0000.000
165A195ALA 00.0170.04540.4450.0010.0010.0000.0000.0000.000
166A196LYS 10.8470.90742.4890.0100.0100.0000.0000.0000.000
167A197LEU 0-0.0020.01541.5240.0010.0010.0000.0000.0000.000
168A198ASN 00.0460.02641.9180.0020.0020.0000.0000.0000.000
169A199LEU 00.0290.01945.9240.0010.0010.0000.0000.0000.000
170A200MET 0-0.010-0.01848.0320.0010.0010.0000.0000.0000.000
171A201ASN 0-0.049-0.03448.3070.0000.0000.0000.0000.0000.000
172A202MET 0-0.017-0.01349.9630.0000.0000.0000.0000.0000.000
173A203LEU 0-0.035-0.03451.6590.0000.0000.0000.0000.0000.000
174A204GLN 00.0920.03652.4650.0010.0010.0000.0000.0000.000
175A205GLN 00.0340.02153.2460.0010.0010.0000.0000.0000.000
176A206SER 0-0.043-0.04755.7550.0000.0000.0000.0000.0000.000
177A207GLN 00.0320.03256.1840.0010.0010.0000.0000.0000.000
178A208ASP -1-0.866-0.93457.981-0.006-0.0060.0000.0000.0000.000
179A209LYS 10.8040.91857.6610.0100.0100.0000.0000.0000.000
180A210LEU 00.0390.03062.0210.0000.0000.0000.0000.0000.000
181A211LEU 00.0320.03363.1550.0000.0000.0000.0000.0000.000
182A212ARG 10.8560.90361.3070.0060.0060.0000.0000.0000.000
183A213ALA 0-0.012-0.00666.3970.0000.0000.0000.0000.0000.000
184A214GLN 00.0620.05367.5190.0000.0000.0000.0000.0000.000
185A215LYS 10.8300.93567.0900.0040.0040.0000.0000.0000.000
186A216ASP -1-0.922-0.94971.550-0.006-0.0060.0000.0000.0000.000
187A217ARG 10.9540.95073.2430.0050.0050.0000.0000.0000.000
188A218ALA 0-0.065-0.02375.0320.0000.0000.0000.0000.0000.000
189A219NME 00.0070.01974.1020.0000.0000.0000.0000.0000.000