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: 1N3QZ

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 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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2038819.205047
FMO2-HF: Nuclear repulsion 1966337.834344
FMO2-HF: Total energy -72481.370703
FMO2-MP2: Total energy -72696.245202


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.
-205.088-202.19121.519-11.077-13.339-0.121
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 : 0.839 / q_NPA : 0.896
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].
3A6PRO0-0.001-0.0022.078-15.985-17.0799.660-3.016-5.551-0.023
4A7VAL0-0.0040.0032.08811.17612.1181.306-0.601-1.646-0.008
5A8VAL0-0.007-0.0024.6110.5190.561-0.001-0.006-0.0350.000
6A9GLY0-0.047-0.0437.723-0.414-0.4140.0000.0000.0000.000
7A10GLU-1-0.982-0.9763.519-65.903-65.2090.015-0.266-0.443-0.002
8A11ASP-1-0.733-0.8531.801-124.504-122.26410.540-7.178-5.603-0.088
9A12TYR00.0190.0084.9128.2888.361-0.001-0.010-0.0610.000
10A13VAL00.0030.0178.355-0.673-0.6730.0000.0000.0000.000
11A14GLU-1-0.871-0.94411.361-18.470-18.4700.0000.0000.0000.000
12A15ILE0-0.062-0.02214.3110.6690.6690.0000.0000.0000.000
13A16PRO00.0220.01417.6250.3750.3750.0000.0000.0000.000
14A17ASP-1-0.926-0.96920.386-12.148-12.1480.0000.0000.0000.000
15A18GLY0-0.018-0.00920.4350.5260.5260.0000.0000.0000.000
16A19ARG10.8910.93421.48511.63811.6380.0000.0000.0000.000
17A20PRO0-0.0230.00522.414-0.227-0.2270.0000.0000.0000.000
18A21PHE0-0.022-0.03023.4130.6000.6000.0000.0000.0000.000
19A22ALA0-0.035-0.01425.3110.6330.6330.0000.0000.0000.000
20A23PRO00.019-0.00426.471-0.415-0.4150.0000.0000.0000.000
21A24LEU00.0330.03022.5530.2020.2020.0000.0000.0000.000
22A25ALA0-0.031-0.01126.3880.0790.0790.0000.0000.0000.000
23A26GLY00.011-0.00227.2730.2000.2000.0000.0000.0000.000
24A27LYS10.8040.91124.89211.17311.1730.0000.0000.0000.000
25A28ILE00.0210.01218.130-0.099-0.0990.0000.0000.0000.000
26A29GLU-1-0.788-0.87721.155-13.255-13.2550.0000.0000.0000.000
27A30VAL00.0150.01816.713-0.867-0.8670.0000.0000.0000.000
28A31VAL0-0.006-0.00918.8900.7920.7920.0000.0000.0000.000
29A32GLU-1-0.816-0.93018.238-16.419-16.4190.0000.0000.0000.000
30A33ILE0-0.032-0.02019.3060.9830.9830.0000.0000.0000.000
31A34PHE00.0540.00820.242-0.643-0.6430.0000.0000.0000.000
32A35GLY00.0760.00422.7540.5240.5240.0000.0000.0000.000
33A36TYR0-0.005-0.05125.559-0.125-0.1250.0000.0000.0000.000
34A37THR00.0340.03428.245-0.120-0.1200.0000.0000.0000.000
35A38CYS0-0.0830.02922.138-0.247-0.2470.0000.0000.0000.000
36A39PRO00.0850.03723.325-0.133-0.1330.0000.0000.0000.000
37A40HIS00.0380.00818.439-0.427-0.4270.0000.0000.0000.000
38A41CYS0-0.0290.00520.199-0.421-0.4210.0000.0000.0000.000
39A42ALA00.0290.02421.797-0.012-0.0120.0000.0000.0000.000
40A43HIS0-0.010-0.00620.5190.1120.1120.0000.0000.0000.000
41A44PHE0-0.048-0.01815.515-0.482-0.4820.0000.0000.0000.000
42A45ASP-1-0.785-0.89419.624-13.116-13.1160.0000.0000.0000.000
43A46SER00.0260.01422.541-0.237-0.2370.0000.0000.0000.000
44A47LYS10.9130.95316.40517.51117.5110.0000.0000.0000.000
45A48LEU0-0.0100.01417.719-0.408-0.4080.0000.0000.0000.000
46A49GLN0-0.029-0.03019.8300.3030.3030.0000.0000.0000.000
47A50ALA0-0.032-0.00820.5590.2480.2480.0000.0000.0000.000
48A51TRP0-0.061-0.06514.6150.7730.7730.0000.0000.0000.000
49A52GLY00.0310.00918.9550.0180.0180.0000.0000.0000.000
50A53ALA0-0.055-0.03021.6590.3240.3240.0000.0000.0000.000
51A54ARG10.8990.96015.68517.22817.2280.0000.0000.0000.000
52A55GLN0-0.061-0.00216.834-0.397-0.3970.0000.0000.0000.000
53A56ALA00.0270.02020.6850.7610.7610.0000.0000.0000.000
54A57LYS10.9840.96522.69710.58710.5870.0000.0000.0000.000
55A58ASP-1-0.803-0.87222.418-13.802-13.8020.0000.0000.0000.000
56A59VAL00.0610.05019.608-0.199-0.1990.0000.0000.0000.000
57A60ARG10.7310.85822.65312.74612.7460.0000.0000.0000.000
58A61PHE00.0260.00820.273-0.386-0.3860.0000.0000.0000.000
59A62THR0-0.057-0.03222.4440.9110.9110.0000.0000.0000.000
60A63LEU00.0150.02822.756-0.587-0.5870.0000.0000.0000.000
61A64VAL0-0.037-0.02723.5000.5900.5900.0000.0000.0000.000
62A65PRO0-0.0180.01824.180-0.449-0.4490.0000.0000.0000.000
63A66ALA00.021-0.01323.5890.0190.0190.0000.0000.0000.000
64A67VAL0-0.059-0.01925.4960.3800.3800.0000.0000.0000.000
65A68PHE0-0.032-0.02721.582-0.144-0.1440.0000.0000.0000.000
66A69GLY00.0310.03027.6090.0500.0500.0000.0000.0000.000
67A70GLY0-0.003-0.02130.870-0.170-0.1700.0000.0000.0000.000
68A71VAL00.015-0.00730.4250.1240.1240.0000.0000.0000.000
69A72TRP00.0030.01323.488-0.031-0.0310.0000.0000.0000.000
70A73ASP-1-0.793-0.90330.101-10.105-10.1050.0000.0000.0000.000
71A74PRO00.0180.00832.5490.0510.0510.0000.0000.0000.000
72A75PHE00.0500.01431.0640.0550.0550.0000.0000.0000.000
73A76ALA0-0.0010.00929.816-0.122-0.1220.0000.0000.0000.000
74A77ARG10.8560.91631.0068.6848.6840.0000.0000.0000.000
75A78ALA0-0.0070.00233.8930.1770.1770.0000.0000.0000.000
76A79TYR00.0210.02328.8900.0890.0890.0000.0000.0000.000
77A80LEU0-0.006-0.00430.6330.1040.1040.0000.0000.0000.000
78A81ALA00.0240.00433.6440.1690.1690.0000.0000.0000.000
79A82ALA00.0110.00634.3450.1880.1880.0000.0000.0000.000
80A83ASP-1-0.951-0.99032.210-9.811-9.8110.0000.0000.0000.000
81A84VAL0-0.082-0.03534.5990.1440.1440.0000.0000.0000.000
82A85LEU0-0.087-0.04937.5820.2370.2370.0000.0000.0000.000
83A86GLY00.0010.02236.9270.1520.1520.0000.0000.0000.000
84A87VAL0-0.048-0.04237.127-0.001-0.0010.0000.0000.0000.000
85A88ALA00.0360.04431.722-0.083-0.0830.0000.0000.0000.000
86A89LYS10.9870.97529.60910.20210.2020.0000.0000.0000.000
87A90ARG10.8900.96432.0208.1048.1040.0000.0000.0000.000
88A91SER00.004-0.00834.1780.0360.0360.0000.0000.0000.000
89A92HIS00.0310.07525.5240.5180.5180.0000.0000.0000.000
90A93THR00.0520.00828.129-0.091-0.0910.0000.0000.0000.000
91A94ALA00.0480.03029.940-0.010-0.0100.0000.0000.0000.000
92A95MET0-0.0110.01231.7980.1780.1780.0000.0000.0000.000
93A96PHE00.0060.00225.0710.0090.0090.0000.0000.0000.000
94A97GLU-1-0.875-0.94829.653-9.474-9.4740.0000.0000.0000.000
95A98ALA0-0.050-0.02431.6200.1810.1810.0000.0000.0000.000
96A99ILE0-0.050-0.02130.6720.1820.1820.0000.0000.0000.000
97A100HIS0-0.098-0.07727.4610.1220.1220.0000.0000.0000.000
98A101GLU-1-0.962-0.96928.597-10.943-10.9430.0000.0000.0000.000
99A102LYS10.8520.92832.3668.9838.9830.0000.0000.0000.000
100A103GLY00.0340.03234.9610.2370.2370.0000.0000.0000.000
101A104SER0-0.052-0.03036.4650.1810.1810.0000.0000.0000.000
102A105VAL0-0.042-0.02035.8360.2030.2030.0000.0000.0000.000
103A106PRO00.0220.02835.819-0.267-0.2670.0000.0000.0000.000
104A107ILE00.0480.00730.455-0.094-0.0940.0000.0000.0000.000
105A108GLN0-0.022-0.03734.107-0.212-0.2120.0000.0000.0000.000
106A109ASN0-0.040-0.02536.9100.0570.0570.0000.0000.0000.000
107A110VAL00.0130.04436.1060.1960.1960.0000.0000.0000.000
108A111GLY00.0460.00939.143-0.054-0.0540.0000.0000.0000.000
109A112PRO0-0.037-0.03241.252-0.074-0.0740.0000.0000.0000.000
110A113ASP-1-0.906-0.95342.473-7.009-7.0090.0000.0000.0000.000
111A114GLU-1-0.775-0.88640.849-7.621-7.6210.0000.0000.0000.000
112A115LEU0-0.064-0.03136.610-0.109-0.1090.0000.0000.0000.000
113A116ALA0-0.013-0.01340.365-0.050-0.0500.0000.0000.0000.000
114A117VAL0-0.0170.00343.3300.0520.0520.0000.0000.0000.000
115A118PHE00.0200.00935.4420.0040.0040.0000.0000.0000.000
116A119TYR0-0.010-0.02734.479-0.041-0.0410.0000.0000.0000.000
117A120ALA0-0.0020.01940.9310.0430.0430.0000.0000.0000.000
118A121GLY0-0.023-0.00142.4920.1300.1300.0000.0000.0000.000
119A122TYR0-0.061-0.05037.120-0.090-0.0900.0000.0000.0000.000
120A123GLY0-0.021-0.01341.737-0.032-0.0320.0000.0000.0000.000
121A124VAL0-0.052-0.01841.1720.0980.0980.0000.0000.0000.000
122A125GLN00.0270.00644.4990.0440.0440.0000.0000.0000.000
123A126PRO00.1000.04346.078-0.124-0.1240.0000.0000.0000.000
124A127ASP-1-0.838-0.91246.649-6.413-6.4130.0000.0000.0000.000
125A128ARG10.9160.96144.3257.0397.0390.0000.0000.0000.000
126A129PHE00.0280.01738.413-0.143-0.1430.0000.0000.0000.000
127A130VAL00.0370.02042.717-0.172-0.1720.0000.0000.0000.000
128A131ALA0-0.017-0.00844.353-0.075-0.0750.0000.0000.0000.000
129A132THR0-0.076-0.05039.853-0.062-0.0620.0000.0000.0000.000
130A133PHE0-0.024-0.02137.159-0.163-0.1630.0000.0000.0000.000
131A134ASN0-0.021-0.01540.165-0.278-0.2780.0000.0000.0000.000
132A135GLY00.0250.02942.0200.1270.1270.0000.0000.0000.000
133A136PRO00.018-0.01140.978-0.208-0.2080.0000.0000.0000.000
134A137GLU-1-0.856-0.90337.275-8.669-8.6690.0000.0000.0000.000
135A138VAL00.0500.02236.133-0.284-0.2840.0000.0000.0000.000
136A139GLU-1-0.796-0.87635.884-8.767-8.7670.0000.0000.0000.000
137A140LYS10.9510.97535.7918.2978.2970.0000.0000.0000.000
138A141ARG10.8670.91332.7328.8908.8900.0000.0000.0000.000
139A142PHE00.0100.00931.593-0.407-0.4070.0000.0000.0000.000
140A143GLN0-0.003-0.01931.548-0.578-0.5780.0000.0000.0000.000
141A144ALA0-0.042-0.00630.473-0.250-0.2500.0000.0000.0000.000
142A145ALA00.0190.00227.484-0.396-0.3960.0000.0000.0000.000
143A146ARG10.9220.96826.7549.3449.3440.0000.0000.0000.000
144A147ALA0-0.032-0.01927.432-0.320-0.3200.0000.0000.0000.000
145A148TYR00.0290.00720.261-0.328-0.3280.0000.0000.0000.000
146A149ALA00.0540.02522.836-0.624-0.6240.0000.0000.0000.000
147A150LEU0-0.059-0.03722.961-0.437-0.4370.0000.0000.0000.000
148A151LYS10.8720.94823.16712.25812.2580.0000.0000.0000.000
149A152VAL00.003-0.00717.896-0.389-0.3890.0000.0000.0000.000
150A153ARG10.8750.94718.60613.18913.1890.0000.0000.0000.000
151A154PRO00.0430.02117.360-0.784-0.7840.0000.0000.0000.000
152A155VAL0-0.0110.00116.3090.9330.9330.0000.0000.0000.000
153A156GLY0-0.0080.00316.991-0.752-0.7520.0000.0000.0000.000
154A157THR0-0.036-0.02718.586-0.014-0.0140.0000.0000.0000.000
155A158PRO00.043-0.01516.3950.2620.2620.0000.0000.0000.000
156A159THR0-0.021-0.01615.028-1.348-1.3480.0000.0000.0000.000
157A160ILE00.0170.01913.4971.2911.2910.0000.0000.0000.000
158A161VAL0-0.026-0.00514.231-1.155-1.1550.0000.0000.0000.000
159A162VAL00.0170.00413.8651.1061.1060.0000.0000.0000.000
160A163ASN00.017-0.02416.3910.3840.3840.0000.0000.0000.000
161A164GLY0-0.014-0.00919.2560.4960.4960.0000.0000.0000.000
162A165ARG10.8490.94216.41217.49017.4900.0000.0000.0000.000
163A166TYR00.0170.00712.015-0.892-0.8920.0000.0000.0000.000
164A167MET0-0.0100.01813.0871.0621.0620.0000.0000.0000.000
165A168VAL0-0.021-0.0208.730-1.689-1.6890.0000.0000.0000.000
166A169THR0-0.071-0.0477.4983.1073.1070.0000.0000.0000.000
167A170GLY00.0440.0287.400-4.051-4.0510.0000.0000.0000.000
168A171HIS0-0.073-0.0306.7664.0774.0770.0000.0000.0000.000
169A172ASP-1-0.840-0.9268.588-27.380-27.3800.0000.0000.0000.000
170A173PHE00.0200.00110.721-1.270-1.2700.0000.0000.0000.000
171A174GLU-1-0.841-0.94410.713-20.804-20.8040.0000.0000.0000.000
172A175ASP-1-0.872-0.9395.427-52.178-52.1780.0000.0000.0000.000
173A176THR00.0200.0118.292-1.615-1.6150.0000.0000.0000.000
174A177LEU0-0.017-0.00110.4100.3670.3670.0000.0000.0000.000
175A178ARG10.9541.0006.29835.90935.9090.0000.0000.0000.000
176A179ILE0-0.0070.0055.2630.6120.6120.0000.0000.0000.000
177A180THR0-0.013-0.0338.0472.1802.1800.0000.0000.0000.000
178A181ASP-1-0.860-0.91010.563-21.133-21.1330.0000.0000.0000.000
179A182TYR0-0.007-0.0078.1141.4101.4100.0000.0000.0000.000
180A183LEU0-0.011-0.0089.7071.9611.9610.0000.0000.0000.000
181A184VAL00.0020.00111.9981.9591.9590.0000.0000.0000.000
182A185SER0-0.041-0.03012.9461.9031.9030.0000.0000.0000.000
183A186ARG10.8980.96910.41227.04727.0470.0000.0000.0000.000
184A187GLU-1-0.871-0.93414.091-17.162-17.1620.0000.0000.0000.000
185A188ARG10.8520.89317.14917.06317.0630.0000.0000.0000.000
186A189ALA0-0.045-0.02616.4590.9130.9130.0000.0000.0000.000
187A190ALA00.0090.00217.4780.7330.7330.0000.0000.0000.000
188A191SER0-0.092-0.03519.1710.9480.9480.0000.0000.0000.000
189A192HIS0-0.057-0.02020.6970.9530.9530.0000.0000.0000.000
190A193GLY0-0.031-0.00620.9400.2520.2520.0000.0000.0000.000