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: G54M1

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 OptHSide
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 -2040102.524282
FMO2-HF: Nuclear repulsion 1967620.45213
FMO2-HF: Total energy -72482.072152
FMO2-MP2: Total energy -72696.943008


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.
-202.221-195.72819.221-11.854-13.859-0.113
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 : 0.869 / q_NPA : 0.928
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].
3A6PRO0-0.0030.0042.655-13.723-9.5752.448-2.472-4.124-0.003
4A7VAL0-0.009-0.0052.09110.53311.4052.221-0.990-2.103-0.008
5A8VAL0-0.0010.0024.4650.4050.454-0.001-0.009-0.0390.000
6A9GLY0-0.040-0.0357.197-0.430-0.4300.0000.0000.0000.000
7A10GLU-1-0.976-0.9723.517-62.926-61.9360.018-0.409-0.599-0.003
8A11ASP-1-0.748-0.8691.771-131.800-131.56614.538-7.957-6.816-0.099
9A12TYR00.0320.0204.9538.6598.740-0.001-0.007-0.0720.000
10A13VAL00.0050.0188.289-0.690-0.6900.0000.0000.0000.000
11A14GLU-1-0.824-0.90011.141-19.419-19.4190.0000.0000.0000.000
12A15ILE0-0.052-0.01814.0560.7140.7140.0000.0000.0000.000
13A16PRO00.0330.02217.4230.4060.4060.0000.0000.0000.000
14A17ASP-1-0.888-0.96220.099-12.448-12.4480.0000.0000.0000.000
15A18GLY0-0.0180.00020.2840.5640.5640.0000.0000.0000.000
16A19ARG10.9240.95321.32711.81811.8180.0000.0000.0000.000
17A20PRO0-0.0260.00222.443-0.240-0.2400.0000.0000.0000.000
18A21PHE0-0.030-0.03223.4240.6200.6200.0000.0000.0000.000
19A22ALA0-0.033-0.01325.3870.6490.6490.0000.0000.0000.000
20A23PRO00.0250.00426.533-0.440-0.4400.0000.0000.0000.000
21A24LEU00.0380.03922.4900.2050.2050.0000.0000.0000.000
22A25ALA0-0.030-0.01426.4430.0690.0690.0000.0000.0000.000
23A26GLY00.0160.00127.4500.2030.2030.0000.0000.0000.000
24A27LYS10.8090.91325.00211.54911.5490.0000.0000.0000.000
25A28ILE00.0180.00818.333-0.104-0.1040.0000.0000.0000.000
26A29GLU-1-0.770-0.86521.248-13.653-13.6530.0000.0000.0000.000
27A30VAL00.0110.01216.664-0.885-0.8850.0000.0000.0000.000
28A31VAL0-0.008-0.00819.0930.8700.8700.0000.0000.0000.000
29A32GLU-1-0.823-0.93118.109-16.656-16.6560.0000.0000.0000.000
30A33ILE0-0.028-0.01819.2061.0211.0210.0000.0000.0000.000
31A34PHE00.0580.00819.952-0.626-0.6260.0000.0000.0000.000
32A35GLY00.0750.00922.3510.5430.5430.0000.0000.0000.000
33A36TYR00.002-0.03024.904-0.099-0.0990.0000.0000.0000.000
34A37THR00.0320.02827.565-0.095-0.0950.0000.0000.0000.000
35A38CYS0-0.0800.01021.596-0.248-0.2480.0000.0000.0000.000
36A39PRO00.0800.03922.827-0.140-0.1400.0000.0000.0000.000
37A40HIS00.0370.00617.938-0.189-0.1890.0000.0000.0000.000
38A41CYS0-0.0430.00719.600-0.437-0.4370.0000.0000.0000.000
39A42ALA00.0320.02221.101-0.036-0.0360.0000.0000.0000.000
40A43HIS0-0.004-0.00320.129-0.020-0.0200.0000.0000.0000.000
41A44PHE0-0.051-0.01514.592-0.494-0.4940.0000.0000.0000.000
42A45ASP-1-0.783-0.88818.933-13.172-13.1720.0000.0000.0000.000
43A46SER00.0230.01321.737-0.198-0.1980.0000.0000.0000.000
44A47LYS10.9010.95315.90017.61117.6110.0000.0000.0000.000
45A48LEU0-0.0080.00816.949-0.464-0.4640.0000.0000.0000.000
46A49GLN0-0.014-0.02918.9230.1820.1820.0000.0000.0000.000
47A50ALA0-0.031-0.01020.6110.2470.2470.0000.0000.0000.000
48A51TRP0-0.070-0.06214.7920.6980.6980.0000.0000.0000.000
49A52GLY00.0260.00919.0010.0140.0140.0000.0000.0000.000
50A53ALA0-0.058-0.03221.4100.3390.3390.0000.0000.0000.000
51A54ARG10.9020.95915.50718.06218.0620.0000.0000.0000.000
52A55GLN0-0.0240.00916.2310.1060.1060.0000.0000.0000.000
53A56ALA00.0160.01820.7300.8200.8200.0000.0000.0000.000
54A57LYS10.9920.97122.74910.77910.7790.0000.0000.0000.000
55A58ASP-1-0.786-0.85522.230-14.416-14.4160.0000.0000.0000.000
56A59VAL00.0500.04519.706-0.228-0.2280.0000.0000.0000.000
57A60ARG10.7060.83222.74013.13513.1350.0000.0000.0000.000
58A61PHE00.0220.00919.961-0.431-0.4310.0000.0000.0000.000
59A62THR0-0.063-0.03722.3740.9580.9580.0000.0000.0000.000
60A63LEU00.0250.03222.653-0.596-0.5960.0000.0000.0000.000
61A64VAL0-0.035-0.02523.5330.6170.6170.0000.0000.0000.000
62A65PRO0-0.0250.01624.057-0.439-0.4390.0000.0000.0000.000
63A66ALA00.028-0.01123.5010.0190.0190.0000.0000.0000.000
64A67VAL0-0.068-0.02225.4020.3880.3880.0000.0000.0000.000
65A68PHE0-0.027-0.02521.415-0.138-0.1380.0000.0000.0000.000
66A69GLY00.0320.03327.6270.0640.0640.0000.0000.0000.000
67A70GLY0-0.005-0.02130.714-0.170-0.1700.0000.0000.0000.000
68A71VAL00.022-0.00529.9540.1160.1160.0000.0000.0000.000
69A72TRP0-0.0020.00722.884-0.037-0.0370.0000.0000.0000.000
70A73ASP-1-0.792-0.90029.791-10.209-10.2090.0000.0000.0000.000
71A74PRO00.0240.01032.3760.0410.0410.0000.0000.0000.000
72A75PHE00.0640.02030.4100.0500.0500.0000.0000.0000.000
73A76ALA0-0.0070.00429.530-0.125-0.1250.0000.0000.0000.000
74A77ARG10.7960.88330.7638.6938.6930.0000.0000.0000.000
75A78ALA0-0.0040.00133.4650.1740.1740.0000.0000.0000.000
76A79TYR00.0250.02228.8020.0730.0730.0000.0000.0000.000
77A80LEU0-0.010-0.00730.7200.1010.1010.0000.0000.0000.000
78A81ALA00.0180.00533.4480.1670.1670.0000.0000.0000.000
79A82ALA00.0240.01233.9200.1860.1860.0000.0000.0000.000
80A83ASP-1-0.927-0.98832.121-9.993-9.9930.0000.0000.0000.000
81A84VAL0-0.074-0.03834.2930.1410.1410.0000.0000.0000.000
82A85LEU0-0.067-0.03737.3950.2370.2370.0000.0000.0000.000
83A86GLY0-0.0070.01636.5480.1520.1520.0000.0000.0000.000
84A87VAL0-0.048-0.04036.557-0.001-0.0010.0000.0000.0000.000
85A88ALA00.0170.03731.242-0.085-0.0850.0000.0000.0000.000
86A89LYS10.9470.96329.44510.32310.3230.0000.0000.0000.000
87A90ARG10.9120.97231.2428.1678.1670.0000.0000.0000.000
88A91SER0-0.001-0.01233.4300.0490.0490.0000.0000.0000.000
89A92HIS00.0120.04724.6780.5230.5230.0000.0000.0000.000
90A93THR00.0510.00627.351-0.026-0.0260.0000.0000.0000.000
91A94ALA00.0350.02429.1660.0040.0040.0000.0000.0000.000
92A95MET0-0.0030.01530.9720.1930.1930.0000.0000.0000.000
93A96PHE00.0100.00524.1050.0240.0240.0000.0000.0000.000
94A97GLU-1-0.812-0.90528.983-9.334-9.3340.0000.0000.0000.000
95A98ALA0-0.035-0.01631.0320.1830.1830.0000.0000.0000.000
96A99ILE0-0.041-0.01830.1870.1870.1870.0000.0000.0000.000
97A100HIS0-0.087-0.06126.8620.1160.1160.0000.0000.0000.000
98A101GLU-1-0.972-0.97528.286-10.947-10.9470.0000.0000.0000.000
99A102LYS10.7670.87831.9509.1779.1770.0000.0000.0000.000
100A103GLY00.0300.03234.4870.2450.2450.0000.0000.0000.000
101A104SER0-0.049-0.03136.0170.1850.1850.0000.0000.0000.000
102A105VAL0-0.051-0.02535.2350.1960.1960.0000.0000.0000.000
103A106PRO00.0210.03035.267-0.282-0.2820.0000.0000.0000.000
104A107ILE00.0430.00429.889-0.105-0.1050.0000.0000.0000.000
105A108GLN0-0.026-0.03833.838-0.207-0.2070.0000.0000.0000.000
106A109ASN0-0.046-0.03036.4230.0060.0060.0000.0000.0000.000
107A110VAL00.0260.05135.5020.1880.1880.0000.0000.0000.000
108A111GLY00.0470.01438.565-0.050-0.0500.0000.0000.0000.000
109A112PRO0-0.045-0.04040.709-0.075-0.0750.0000.0000.0000.000
110A113ASP-1-0.891-0.94442.019-7.146-7.1460.0000.0000.0000.000
111A114GLU-1-0.779-0.89340.323-7.776-7.7760.0000.0000.0000.000
112A115LEU0-0.057-0.02736.014-0.112-0.1120.0000.0000.0000.000
113A116ALA0-0.020-0.01839.740-0.055-0.0550.0000.0000.0000.000
114A117VAL0-0.0180.00142.7260.0510.0510.0000.0000.0000.000
115A118PHE00.0250.01434.6090.0040.0040.0000.0000.0000.000
116A119TYR0-0.008-0.02633.881-0.038-0.0380.0000.0000.0000.000
117A120ALA00.0000.01940.2320.0400.0400.0000.0000.0000.000
118A121GLY0-0.0180.00241.6930.1310.1310.0000.0000.0000.000
119A122TYR0-0.060-0.04936.522-0.095-0.0950.0000.0000.0000.000
120A123GLY0-0.016-0.01140.958-0.039-0.0390.0000.0000.0000.000
121A124VAL0-0.061-0.02240.5800.0980.0980.0000.0000.0000.000
122A125GLN00.0370.01143.9120.0500.0500.0000.0000.0000.000
123A126PRO00.0900.03945.523-0.123-0.1230.0000.0000.0000.000
124A127ASP-1-0.849-0.91746.191-6.484-6.4840.0000.0000.0000.000
125A128ARG10.9380.96743.7877.1717.1710.0000.0000.0000.000
126A129PHE00.0240.02038.007-0.151-0.1510.0000.0000.0000.000
127A130VAL00.0340.01842.388-0.175-0.1750.0000.0000.0000.000
128A131ALA0-0.018-0.00944.119-0.078-0.0780.0000.0000.0000.000
129A132THR0-0.077-0.05539.706-0.067-0.0670.0000.0000.0000.000
130A133PHE0-0.005-0.01336.863-0.151-0.1510.0000.0000.0000.000
131A134ASN0-0.042-0.02440.038-0.249-0.2490.0000.0000.0000.000
132A135GLY00.0370.03741.9160.1300.1300.0000.0000.0000.000
133A136PRO00.022-0.00941.035-0.210-0.2100.0000.0000.0000.000
134A137GLU-1-0.773-0.85137.459-8.834-8.8340.0000.0000.0000.000
135A138VAL00.0470.02236.030-0.282-0.2820.0000.0000.0000.000
136A139GLU-1-0.762-0.83935.965-8.896-8.8960.0000.0000.0000.000
137A140LYS10.8610.90736.0988.3668.3660.0000.0000.0000.000
138A141ARG10.8540.91532.7649.0459.0450.0000.0000.0000.000
139A142PHE00.0120.01231.743-0.414-0.4140.0000.0000.0000.000
140A143GLN00.005-0.01331.667-0.570-0.5700.0000.0000.0000.000
141A144ALA0-0.036-0.00330.619-0.255-0.2550.0000.0000.0000.000
142A145ALA00.0160.00027.609-0.406-0.4060.0000.0000.0000.000
143A146ARG10.9130.95326.8529.3979.3970.0000.0000.0000.000
144A147ALA0-0.024-0.01527.462-0.322-0.3220.0000.0000.0000.000
145A148TYR00.0250.00820.975-0.518-0.5180.0000.0000.0000.000
146A149ALA00.0460.02222.894-0.642-0.6420.0000.0000.0000.000
147A150LEU0-0.062-0.03722.955-0.439-0.4390.0000.0000.0000.000
148A151LYS10.7990.90922.64313.13513.1350.0000.0000.0000.000
149A152VAL0-0.001-0.00717.939-0.411-0.4110.0000.0000.0000.000
150A153ARG10.8710.94518.53313.17913.1790.0000.0000.0000.000
151A154PRO00.0450.02317.406-0.792-0.7920.0000.0000.0000.000
152A155VAL0-0.013-0.00116.3920.9600.9600.0000.0000.0000.000
153A156GLY0-0.0080.00316.905-0.754-0.7540.0000.0000.0000.000
154A157THR0-0.033-0.01618.293-0.042-0.0420.0000.0000.0000.000
155A158PRO00.038-0.01315.5830.3350.3350.0000.0000.0000.000
156A159THR0-0.022-0.01715.161-1.384-1.3840.0000.0000.0000.000
157A160ILE00.0170.01613.4041.2791.2790.0000.0000.0000.000
158A161VAL0-0.017-0.00214.410-1.279-1.2790.0000.0000.0000.000
159A162VAL00.0140.00413.9951.1271.1270.0000.0000.0000.000
160A163ASN00.011-0.03516.4950.3660.3660.0000.0000.0000.000
161A164GLY0-0.011-0.00619.2730.5280.5280.0000.0000.0000.000
162A165ARG10.7930.89216.26518.37518.3750.0000.0000.0000.000
163A166TYR0-0.032-0.02111.960-0.888-0.8880.0000.0000.0000.000
164A167MET0-0.0160.02013.0151.0141.0140.0000.0000.0000.000
165A168VAL0-0.018-0.0228.741-1.778-1.7780.0000.0000.0000.000
166A169THR0-0.063-0.0387.6193.4183.4180.0000.0000.0000.000
167A170GLY00.0380.0206.770-4.164-4.1640.0000.0000.0000.000
168A171HIS0-0.080-0.0416.7714.5784.5780.0000.0000.0000.000
169A172ASP-1-0.798-0.8948.343-27.764-27.7640.0000.0000.0000.000
170A173PHE00.0260.01510.104-1.616-1.6160.0000.0000.0000.000
171A174GLU-1-0.825-0.93610.692-21.404-21.4040.0000.0000.0000.000
172A175ASP-1-0.837-0.9174.748-55.007-54.934-0.001-0.005-0.0670.000
173A176THR00.002-0.0117.498-2.017-2.0170.0000.0000.0000.000
174A177LEU0-0.0190.0039.5900.3030.3030.0000.0000.0000.000
175A178ARG10.8800.9485.61940.74140.7410.0000.0000.0000.000
176A179ILE0-0.0060.0024.7460.4170.463-0.001-0.005-0.0390.000
177A180THR0-0.011-0.0297.8822.3922.3920.0000.0000.0000.000
178A181ASP-1-0.852-0.91610.866-21.425-21.4250.0000.0000.0000.000
179A182TYR00.0110.0178.1662.0282.0280.0000.0000.0000.000
180A183LEU0-0.005-0.0039.7602.0432.0430.0000.0000.0000.000
181A184VAL0-0.008-0.00612.1022.0972.0970.0000.0000.0000.000
182A185SER0-0.057-0.04313.0111.9441.9440.0000.0000.0000.000
183A186ARG10.8870.95310.04028.51928.5190.0000.0000.0000.000
184A187GLU-1-0.823-0.90414.720-17.323-17.3230.0000.0000.0000.000
185A188ARG10.8500.89117.42017.77417.7740.0000.0000.0000.000
186A189ALA0-0.040-0.01016.5781.0031.0030.0000.0000.0000.000
187A190ALA00.0110.00217.9310.7830.7830.0000.0000.0000.000
188A191SER0-0.093-0.05019.6800.9600.9600.0000.0000.0000.000
189A192HIS0-0.068-0.02721.1361.0431.0430.0000.0000.0000.000
190A193GLY0-0.028-0.00321.3180.2920.2920.0000.0000.0000.000