FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 8961Y

Calculation Name: 2REM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2REM

Chain ID: A

ChEMBL ID:

UniProt ID: Q9PDE3

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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2034870.696156
FMO2-HF: Nuclear repulsion 1962388.19483
FMO2-HF: Total energy -72482.501325
FMO2-MP2: Total energy -72697.188341


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:4:HIS)


Summations of interaction energy for fragment #1(A:4: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.
-184.091-181.04822.054-11.506-13.59-0.111
Interaction energy analysis for fragmet #1(A:4:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.884 / q_NPA : 0.927
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].
3A6PRO0-0.0030.0022.754-12.284-7.9761.894-2.220-3.983-0.004
4A7VAL0-0.003-0.0092.25711.98313.5170.980-0.730-1.784-0.005
5A8VAL0-0.021-0.0074.5240.2060.251-0.001-0.008-0.0350.000
6A9GLY0-0.016-0.0217.5791.1171.1170.0000.0000.0000.000
7A10GLU-1-0.964-0.9683.447-61.016-60.2900.008-0.183-0.551-0.001
8A11ASP-1-0.742-0.8531.729-127.575-131.37319.176-8.339-7.039-0.101
9A12TYR00.0120.0094.7119.0289.138-0.001-0.018-0.0900.000
10A13VAL00.0060.0198.071-0.676-0.6760.0000.0000.0000.000
11A14GLU-1-0.809-0.90010.988-20.052-20.0520.0000.0000.0000.000
12A15ILE0-0.039-0.01013.8700.7280.7280.0000.0000.0000.000
13A16PRO00.0320.02117.3430.3890.3890.0000.0000.0000.000
14A17ASP-1-0.876-0.95720.147-12.413-12.4130.0000.0000.0000.000
15A18GLY0-0.0100.00220.0000.5050.5050.0000.0000.0000.000
16A19ARG10.9270.95521.03312.13312.1330.0000.0000.0000.000
17A20PRO0-0.0230.01222.451-0.205-0.2050.0000.0000.0000.000
18A21PHE0-0.036-0.02923.3760.6230.6230.0000.0000.0000.000
19A22ALA0-0.013-0.00125.5990.6180.6180.0000.0000.0000.000
20A23PRO00.0270.00526.633-0.468-0.4680.0000.0000.0000.000
21A24LEU00.0330.03822.6290.1860.1860.0000.0000.0000.000
22A25ALA0-0.037-0.01926.5830.0440.0440.0000.0000.0000.000
23A26GLY00.0270.01727.3420.2310.2310.0000.0000.0000.000
24A27LYS10.7510.87024.81811.96611.9660.0000.0000.0000.000
25A28ILE00.0320.02818.278-0.088-0.0880.0000.0000.0000.000
26A29GLU-1-0.783-0.86721.081-13.699-13.6990.0000.0000.0000.000
27A30VAL00.012-0.00116.589-0.946-0.9460.0000.0000.0000.000
28A31VAL0-0.0070.00319.1900.7490.7490.0000.0000.0000.000
29A32GLU-1-0.793-0.91017.880-16.706-16.7060.0000.0000.0000.000
30A33ILE0-0.029-0.01519.0311.0291.0290.0000.0000.0000.000
31A34PHE00.0370.00719.863-0.576-0.5760.0000.0000.0000.000
32A35GLY00.0700.00022.2290.5260.5260.0000.0000.0000.000
33A36TYR0-0.026-0.02724.860-0.072-0.0720.0000.0000.0000.000
34A37THR00.0420.02927.307-0.044-0.0440.0000.0000.0000.000
35A38CYS0-0.075-0.01520.790-0.036-0.0360.0000.0000.0000.000
36A39PRO00.0640.03322.907-0.163-0.1630.0000.0000.0000.000
37A40HIS00.0250.00017.884-0.201-0.2010.0000.0000.0000.000
38A41CYS0-0.066-0.00319.204-0.565-0.5650.0000.0000.0000.000
39A42ALA00.0280.02620.871-0.029-0.0290.0000.0000.0000.000
40A43HIS0-0.001-0.00519.985-0.092-0.0920.0000.0000.0000.000
41A44PHE0-0.045-0.00814.295-0.554-0.5540.0000.0000.0000.000
42A45ASP-1-0.757-0.86818.704-13.011-13.0110.0000.0000.0000.000
43A46SER0-0.006-0.00521.749-0.166-0.1660.0000.0000.0000.000
44A47LYS10.9000.95515.85717.47017.4700.0000.0000.0000.000
45A48LEU0-0.0060.01216.967-0.387-0.3870.0000.0000.0000.000
46A49GLN00.011-0.01719.0260.1410.1410.0000.0000.0000.000
47A50ALA0-0.022-0.00320.8190.2520.2520.0000.0000.0000.000
48A51TRP0-0.048-0.03114.7290.3570.3570.0000.0000.0000.000
49A52GLY00.0230.00519.059-0.002-0.0020.0000.0000.0000.000
50A53ALA0-0.051-0.02921.3160.3150.3150.0000.0000.0000.000
51A54ARG10.8660.92815.63818.11218.1120.0000.0000.0000.000
52A55GLN0-0.0050.00716.4780.1510.1510.0000.0000.0000.000
53A56ALA00.0240.02620.9930.8410.8410.0000.0000.0000.000
54A57LYS10.9640.95923.01910.72610.7260.0000.0000.0000.000
55A58ASP-1-0.740-0.82922.131-14.563-14.5630.0000.0000.0000.000
56A59VAL00.0460.03319.739-0.049-0.0490.0000.0000.0000.000
57A60ARG10.7470.83822.57013.32513.3250.0000.0000.0000.000
58A61PHE00.0460.02819.915-0.299-0.2990.0000.0000.0000.000
59A62THR0-0.066-0.03421.9661.0141.0140.0000.0000.0000.000
60A63LEU00.0190.03522.283-0.607-0.6070.0000.0000.0000.000
61A64VAL00.002-0.00423.5190.7120.7120.0000.0000.0000.000
62A65PRO0-0.0300.00724.019-0.421-0.4210.0000.0000.0000.000
63A66ALA00.0520.00123.3100.0400.0400.0000.0000.0000.000
64A67VAL0-0.095-0.03225.2000.3380.3380.0000.0000.0000.000
65A68PHE0-0.010-0.01721.446-0.134-0.1340.0000.0000.0000.000
66A69GLY00.0330.02827.6510.0650.0650.0000.0000.0000.000
67A70GLY0-0.021-0.02530.722-0.172-0.1720.0000.0000.0000.000
68A71VAL00.027-0.00130.1890.0930.0930.0000.0000.0000.000
69A72TRP00.0040.01222.753-0.073-0.0730.0000.0000.0000.000
70A73ASP-1-0.803-0.90629.797-10.176-10.1760.0000.0000.0000.000
71A74PRO00.0180.00432.2680.0550.0550.0000.0000.0000.000
72A75PHE00.0770.02530.3670.0540.0540.0000.0000.0000.000
73A76ALA0-0.029-0.01129.310-0.112-0.1120.0000.0000.0000.000
74A77ARG10.7890.87330.5368.6438.6430.0000.0000.0000.000
75A78ALA00.0080.01033.4260.1800.1800.0000.0000.0000.000
76A79TYR0-0.008-0.00227.7540.2100.2100.0000.0000.0000.000
77A80LEU0-0.016-0.00830.3710.1160.1160.0000.0000.0000.000
78A81ALA00.0130.00033.3430.1750.1750.0000.0000.0000.000
79A82ALA00.0470.02234.0450.1910.1910.0000.0000.0000.000
80A83ASP-1-0.899-0.93832.138-9.946-9.9460.0000.0000.0000.000
81A84VAL0-0.053-0.02734.3310.1520.1520.0000.0000.0000.000
82A85LEU0-0.054-0.02237.5060.2640.2640.0000.0000.0000.000
83A86GLY0-0.0070.01036.6960.1420.1420.0000.0000.0000.000
84A87VAL0-0.016-0.02136.6110.0020.0020.0000.0000.0000.000
85A88ALA00.0320.03331.306-0.119-0.1190.0000.0000.0000.000
86A89LYS10.9140.93129.24310.33010.3300.0000.0000.0000.000
87A90ARG10.8580.95431.3308.1958.1950.0000.0000.0000.000
88A91SER0-0.013-0.02232.9420.1170.1170.0000.0000.0000.000
89A92HIS00.0060.02724.4380.4810.4810.0000.0000.0000.000
90A93THR00.014-0.01926.7590.0400.0400.0000.0000.0000.000
91A94ALA00.0200.01128.594-0.025-0.0250.0000.0000.0000.000
92A95MET0-0.0020.02430.7880.2530.2530.0000.0000.0000.000
93A96PHE0-0.007-0.00724.0180.0120.0120.0000.0000.0000.000
94A97GLU-1-0.801-0.88228.777-9.242-9.2420.0000.0000.0000.000
95A98ALA0-0.012-0.01330.8050.1990.1990.0000.0000.0000.000
96A99ILE0-0.044-0.01430.1730.2010.2010.0000.0000.0000.000
97A100HIS0-0.079-0.05927.1070.1540.1540.0000.0000.0000.000
98A101GLU-1-0.945-0.96128.244-10.917-10.9170.0000.0000.0000.000
99A102LYS10.7400.85131.9519.2009.2000.0000.0000.0000.000
100A103GLY00.0080.02534.3240.2550.2550.0000.0000.0000.000
101A104SER0-0.040-0.02735.8280.1580.1580.0000.0000.0000.000
102A105VAL0-0.031-0.02135.2090.1830.1830.0000.0000.0000.000
103A106PRO00.0060.02935.160-0.299-0.2990.0000.0000.0000.000
104A107ILE00.0380.00329.626-0.116-0.1160.0000.0000.0000.000
105A108GLN0-0.024-0.03433.635-0.232-0.2320.0000.0000.0000.000
106A109ASN0-0.049-0.04036.242-0.016-0.0160.0000.0000.0000.000
107A110VAL00.0060.03935.3520.1850.1850.0000.0000.0000.000
108A111GLY00.0460.03138.499-0.029-0.0290.0000.0000.0000.000
109A112PRO0-0.051-0.04040.456-0.126-0.1260.0000.0000.0000.000
110A113ASP-1-0.871-0.94841.635-7.223-7.2230.0000.0000.0000.000
111A114GLU-1-0.784-0.90040.566-7.850-7.8500.0000.0000.0000.000
112A115LEU0-0.021-0.00935.789-0.103-0.1030.0000.0000.0000.000
113A116ALA0-0.032-0.01339.463-0.050-0.0500.0000.0000.0000.000
114A117VAL0-0.012-0.00442.4760.0600.0600.0000.0000.0000.000
115A118PHE00.0120.01034.4070.0130.0130.0000.0000.0000.000
116A119TYR0-0.002-0.02933.626-0.047-0.0470.0000.0000.0000.000
117A120ALA00.0070.01439.9930.0280.0280.0000.0000.0000.000
118A121GLY0-0.0180.00341.5250.1190.1190.0000.0000.0000.000
119A122TYR0-0.039-0.02936.186-0.129-0.1290.0000.0000.0000.000
120A123GLY0-0.031-0.01840.822-0.042-0.0420.0000.0000.0000.000
121A124VAL0-0.075-0.03040.5750.1220.1220.0000.0000.0000.000
122A125GLN00.0480.01643.8460.0800.0800.0000.0000.0000.000
123A126PRO00.0680.02545.434-0.102-0.1020.0000.0000.0000.000
124A127ASP-1-0.850-0.92045.832-6.528-6.5280.0000.0000.0000.000
125A128ARG10.9450.97243.1797.2207.2200.0000.0000.0000.000
126A129PHE00.0270.03437.759-0.169-0.1690.0000.0000.0000.000
127A130VAL00.0270.01542.327-0.164-0.1640.0000.0000.0000.000
128A131ALA0-0.003-0.00444.154-0.066-0.0660.0000.0000.0000.000
129A132THR0-0.081-0.05739.612-0.047-0.0470.0000.0000.0000.000
130A133PHE00.011-0.00536.751-0.145-0.1450.0000.0000.0000.000
131A134ASN0-0.056-0.03239.674-0.243-0.2430.0000.0000.0000.000
132A135GLY00.0650.05041.6240.1560.1560.0000.0000.0000.000
133A136PRO0-0.002-0.01440.707-0.229-0.2290.0000.0000.0000.000
134A137GLU-1-0.756-0.85037.189-8.863-8.8630.0000.0000.0000.000
135A138VAL00.0200.01535.865-0.300-0.3000.0000.0000.0000.000
136A139GLU-1-0.775-0.85435.808-8.854-8.8540.0000.0000.0000.000
137A140LYS10.8460.89935.7068.4188.4180.0000.0000.0000.000
138A141ARG10.8260.89832.5719.1029.1020.0000.0000.0000.000
139A142PHE00.0200.02231.450-0.409-0.4090.0000.0000.0000.000
140A143GLN00.014-0.00731.368-0.545-0.5450.0000.0000.0000.000
141A144ALA0-0.0130.00530.470-0.244-0.2440.0000.0000.0000.000
142A145ALA00.004-0.00327.318-0.408-0.4080.0000.0000.0000.000
143A146ARG10.9150.96026.5509.4039.4030.0000.0000.0000.000
144A147ALA0-0.021-0.00827.339-0.275-0.2750.0000.0000.0000.000
145A148TYR0-0.001-0.02520.848-0.524-0.5240.0000.0000.0000.000
146A149ALA00.0320.01622.659-0.635-0.6350.0000.0000.0000.000
147A150LEU0-0.049-0.03822.695-0.445-0.4450.0000.0000.0000.000
148A151LYS10.7740.89822.38313.22613.2260.0000.0000.0000.000
149A152VAL00.011-0.00817.552-0.389-0.3890.0000.0000.0000.000
150A153ARG10.8710.95018.20613.01513.0150.0000.0000.0000.000
151A154PRO00.0440.02017.404-0.758-0.7580.0000.0000.0000.000
152A155VAL0-0.022-0.01016.0610.9020.9020.0000.0000.0000.000
153A156GLY00.0220.02417.150-0.546-0.5460.0000.0000.0000.000
154A157THR0-0.029-0.01618.1130.0550.0550.0000.0000.0000.000
155A158PRO00.0340.00015.2390.4400.4400.0000.0000.0000.000
156A159THR0-0.004-0.01814.995-1.412-1.4120.0000.0000.0000.000
157A160ILE0-0.0030.00713.3581.2181.2180.0000.0000.0000.000
158A161VAL00.0020.00414.254-1.252-1.2520.0000.0000.0000.000
159A162VAL00.0040.00013.8060.9090.9090.0000.0000.0000.000
160A163ASN00.006-0.04116.3480.3790.3790.0000.0000.0000.000
161A164GLY00.0010.00519.1240.6280.6280.0000.0000.0000.000
162A165ARG10.7780.88316.20818.90218.9020.0000.0000.0000.000
163A166TYR0-0.033-0.04611.902-0.841-0.8410.0000.0000.0000.000
164A167MET0-0.0190.01012.7181.3781.3780.0000.0000.0000.000
165A168VAL0-0.030-0.0168.651-1.795-1.7950.0000.0000.0000.000
166A169THR0-0.070-0.0497.5753.3723.3720.0000.0000.0000.000
167A170GLY00.0360.0146.173-2.906-2.9060.0000.0000.0000.000
168A171HIS0-0.067-0.0386.2764.9844.9840.0000.0000.0000.000
169A172ASP-1-0.797-0.8937.961-26.829-26.8290.0000.0000.0000.000
170A173PHE00.0170.01310.213-1.206-1.2060.0000.0000.0000.000
171A174GLU-1-0.804-0.93110.983-21.129-21.1290.0000.0000.0000.000
172A175ASP-1-0.852-0.9135.048-53.960-53.887-0.001-0.002-0.0700.000
173A176THR00.006-0.0087.588-2.071-2.0710.0000.0000.0000.000
174A177LEU0-0.0280.0029.6900.3920.3920.0000.0000.0000.000
175A178ARG10.8590.9275.41340.88540.8850.0000.0000.0000.000
176A179ILE0-0.0110.0054.510-0.0020.043-0.001-0.006-0.0380.000
177A180THR0-0.012-0.0267.7992.1932.1930.0000.0000.0000.000
178A181ASP-1-0.837-0.91111.409-20.973-20.9730.0000.0000.0000.000
179A182TYR0-0.0190.0087.1973.1493.1490.0000.0000.0000.000
180A183LEU0-0.0030.0039.5791.9751.9750.0000.0000.0000.000
181A184VAL0-0.014-0.01211.9311.9791.9790.0000.0000.0000.000
182A185SER0-0.037-0.03813.1711.9841.9840.0000.0000.0000.000
183A186ARG10.8970.9579.74128.61228.6120.0000.0000.0000.000
184A187GLU-1-0.831-0.88314.662-17.330-17.3300.0000.0000.0000.000
185A188ARG10.8170.87717.42318.09618.0960.0000.0000.0000.000
186A189ALA0-0.030-0.00416.8150.9930.9930.0000.0000.0000.000
187A190ALA00.0240.00617.9840.8590.8590.0000.0000.0000.000
188A191SER0-0.111-0.05819.7520.9800.9800.0000.0000.0000.000
189A192HIS0-0.028-0.00721.7851.0921.0920.0000.0000.0000.000
190A193GLY0-0.056-0.01721.2950.1680.1680.0000.0000.0000.000