Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

tag_button

FMODB ID: N1R7Q

Calculation Name: 2C24-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2C24

Chain ID: A

ChEMBL ID:

UniProt ID: P71140

Base Structure: X-ray

Registration Date: 2023-06-21

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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1893747.865786
FMO2-HF: Nuclear repulsion 1824967.314804
FMO2-HF: Total energy -68780.550983
FMO2-MP2: Total energy -68984.243273


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:13:LEU)


Summations of interaction energy for fragment #1(A:13:LEU)
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.
-22.544-12.44212.643-7.375-15.371-0.055
Interaction energy analysis for fragmet #1(A:13:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.036 / q_NPA : -0.025
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].
3A15ASP-1-0.775-0.8893.878-3.602-2.321-0.008-0.587-0.6870.003
4A16VAL0-0.097-0.0515.5740.5810.5810.0000.0000.0000.000
5A17GLN0-0.067-0.0528.0290.0370.0370.0000.0000.0000.000
6A18ILE0-0.023-0.01611.5220.0540.0540.0000.0000.0000.000
7A19PHE0-0.002-0.01214.3790.0500.0500.0000.0000.0000.000
8A20LYS10.8640.93215.9460.0240.0240.0000.0000.0000.000
9A21ASP-1-0.808-0.88918.198-0.054-0.0540.0000.0000.0000.000
10A22SER0-0.028-0.02321.0460.0130.0130.0000.0000.0000.000
11A23PRO00.002-0.01921.723-0.016-0.0160.0000.0000.0000.000
12A24VAL00.0370.04118.4860.0090.0090.0000.0000.0000.000
13A25VAL0-0.0020.01020.4000.0090.0090.0000.0000.0000.000
14A26GLY00.0270.01620.540-0.021-0.0210.0000.0000.0000.000
15A27TRP0-0.042-0.02222.8050.0100.0100.0000.0000.0000.000
16A28SER0-0.0130.00325.223-0.021-0.0210.0000.0000.0000.000
17A29GLY00.0550.03627.6380.0100.0100.0000.0000.0000.000
18A30SER0-0.060-0.07130.839-0.009-0.0090.0000.0000.0000.000
19A31GLY0-0.037-0.00133.6370.0050.0050.0000.0000.0000.000
20A32MET0-0.066-0.04936.8030.0050.0050.0000.0000.0000.000
21A33GLY00.0270.02336.5660.0040.0040.0000.0000.0000.000
22A34GLU-1-0.802-0.87835.286-0.084-0.0840.0000.0000.0000.000
23A35LEU0-0.057-0.01828.521-0.002-0.0020.0000.0000.0000.000
24A36GLU-1-0.794-0.86531.918-0.082-0.0820.0000.0000.0000.000
25A37THR0-0.044-0.03329.482-0.006-0.0060.0000.0000.0000.000
26A38ILE0-0.005-0.00829.9830.0080.0080.0000.0000.0000.000
27A39GLY0-0.027-0.01029.846-0.002-0.0020.0000.0000.0000.000
28A40ASP-1-0.871-0.92329.528-0.066-0.0660.0000.0000.0000.000
29A41THR0-0.015-0.02024.105-0.013-0.0130.0000.0000.0000.000
30A42LEU00.0210.00823.4650.0060.0060.0000.0000.0000.000
31A43PRO0-0.0030.00226.0260.0030.0030.0000.0000.0000.000
32A44VAL00.0040.00924.371-0.010-0.0100.0000.0000.0000.000
33A45ASP-1-0.772-0.84426.784-0.076-0.0760.0000.0000.0000.000
34A46THR00.005-0.01327.677-0.005-0.0050.0000.0000.0000.000
35A47THR0-0.100-0.05729.9840.0060.0060.0000.0000.0000.000
36A48VAL0-0.019-0.00127.8920.0010.0010.0000.0000.0000.000
37A49THR0-0.038-0.00826.717-0.003-0.0030.0000.0000.0000.000
38A50TYR0-0.043-0.05420.1370.0110.0110.0000.0000.0000.000
39A51ASN00.0000.00418.9740.0190.0190.0000.0000.0000.000
40A52GLY0-0.018-0.00122.2800.0110.0110.0000.0000.0000.000
41A53LEU0-0.049-0.01819.7070.0180.0180.0000.0000.0000.000
42A54PRO0-0.002-0.01223.856-0.006-0.0060.0000.0000.0000.000
43A55THR0-0.045-0.02123.324-0.015-0.0150.0000.0000.0000.000
44A56LEU0-0.010-0.00120.7950.0130.0130.0000.0000.0000.000
45A57ARG10.7910.87124.0940.0750.0750.0000.0000.0000.000
46A58LEU0-0.0070.00824.6840.0030.0030.0000.0000.0000.000
47A59ASN00.001-0.01127.419-0.003-0.0030.0000.0000.0000.000
48A60VAL0-0.0100.01431.1950.0040.0040.0000.0000.0000.000
49A61GLN0-0.028-0.02333.4740.0040.0040.0000.0000.0000.000
50A62THR0-0.035-0.03437.0210.0030.0030.0000.0000.0000.000
51A63THR00.0270.01837.734-0.002-0.0020.0000.0000.0000.000
52A64VAL00.0270.02038.269-0.003-0.0030.0000.0000.0000.000
53A65GLN0-0.033-0.00339.156-0.005-0.0050.0000.0000.0000.000
54A66SER0-0.002-0.01940.3790.0030.0030.0000.0000.0000.000
55A67GLY00.0330.01637.404-0.003-0.0030.0000.0000.0000.000
56A68TRP00.0050.00431.421-0.005-0.0050.0000.0000.0000.000
57A69TRP00.0780.02726.4490.0060.0060.0000.0000.0000.000
58A70ILE0-0.010-0.00724.712-0.008-0.0080.0000.0000.0000.000
59A71SER0-0.020-0.01924.1430.0070.0070.0000.0000.0000.000
60A72LEU00.0170.01021.464-0.017-0.0170.0000.0000.0000.000
61A73LEU00.0250.01018.6550.0200.0200.0000.0000.0000.000
62A74THR0-0.034-0.04217.344-0.025-0.0250.0000.0000.0000.000
63A75LEU00.0180.02110.678-0.002-0.0020.0000.0000.0000.000
64A76ARG10.8630.9279.4370.2190.2190.0000.0000.0000.000
65A77GLY00.0300.02815.3240.0340.0340.0000.0000.0000.000
66A78TRP0-0.023-0.03018.9790.0110.0110.0000.0000.0000.000
67A79ASN0-0.072-0.03216.7420.0040.0040.0000.0000.0000.000
68A80THR00.0000.00614.290-0.020-0.0200.0000.0000.0000.000
69A81HIS0-0.013-0.0146.6860.1520.1520.0000.0000.0000.000
70A82ASP-1-0.795-0.8617.049-0.361-0.3610.0000.0000.0000.000
71A83LEU00.002-0.0095.602-0.093-0.0930.0000.0000.0000.000
72A84SER0-0.070-0.0575.701-0.159-0.1590.0000.0000.0000.000
73A85GLN0-0.063-0.0482.612-1.1090.2490.663-0.517-1.504-0.001
74A86TYR0-0.024-0.0272.705-4.432-0.9864.619-2.097-5.969-0.021
75A87VAL0-0.032-0.0193.6060.023-0.0950.0260.210-0.1180.000
76A88GLU-1-0.860-0.9136.426-0.550-0.5500.0000.0000.0000.000
77A89ASN0-0.064-0.0605.8110.4120.4120.0000.0000.0000.000
78A90GLY00.0840.0545.263-0.184-0.1840.0000.0000.0000.000
79A91TYR0-0.041-0.0275.9540.5070.5070.0000.0000.0000.000
80A92LEU0-0.0070.0138.966-0.105-0.1050.0000.0000.0000.000
81A93GLU-1-0.782-0.8669.872-1.021-1.0210.0000.0000.0000.000
82A94PHE0-0.002-0.01812.8610.0320.0320.0000.0000.0000.000
83A95ASP-1-0.786-0.85716.166-0.290-0.2900.0000.0000.0000.000
84A96ILE0-0.039-0.03719.4280.0130.0130.0000.0000.0000.000
85A97LYS10.8360.92722.5910.1330.1330.0000.0000.0000.000
86A98GLY00.0660.02526.410-0.001-0.0010.0000.0000.0000.000
87A99LYS10.7310.84029.4720.1060.1060.0000.0000.0000.000
88A100GLU-1-0.892-0.93933.165-0.095-0.0950.0000.0000.0000.000
89A101GLY0-0.032-0.01031.3640.0020.0020.0000.0000.0000.000
90A102GLY0-0.043-0.02630.5090.0050.0050.0000.0000.0000.000
91A103GLU-1-0.777-0.88628.792-0.140-0.1400.0000.0000.0000.000
92A104ASP-1-0.755-0.88526.620-0.204-0.2040.0000.0000.0000.000
93A105PHE0-0.060-0.04422.9760.0130.0130.0000.0000.0000.000
94A106VAL0-0.0130.00523.375-0.016-0.0160.0000.0000.0000.000
95A107ILE00.0130.00318.5560.0050.0050.0000.0000.0000.000
96A108GLY00.017-0.00417.380-0.005-0.0050.0000.0000.0000.000
97A109PHE00.0030.00212.738-0.016-0.0160.0000.0000.0000.000
98A110ARG10.8030.86516.4200.1820.1820.0000.0000.0000.000
99A111ASP-1-0.728-0.80915.749-0.216-0.2160.0000.0000.0000.000
100A112LYS10.8530.90616.9680.1220.1220.0000.0000.0000.000
101A113VAL00.0380.02617.8340.0050.0050.0000.0000.0000.000
102A114TYR00.006-0.00420.4460.0000.0000.0000.0000.0000.000
103A115GLU-1-0.891-0.95221.838-0.058-0.0580.0000.0000.0000.000
104A116ARG10.7220.83518.5630.1630.1630.0000.0000.0000.000
105A117VAL0-0.006-0.02824.377-0.005-0.0050.0000.0000.0000.000
106A118TYR0-0.034-0.01423.1180.0060.0060.0000.0000.0000.000
107A119GLY00.0350.00625.055-0.003-0.0030.0000.0000.0000.000
108A120LEU0-0.0070.01823.420-0.008-0.0080.0000.0000.0000.000
109A121GLU-1-0.836-0.90121.247-0.121-0.1210.0000.0000.0000.000
110A122ILE0-0.060-0.02220.0370.0080.0080.0000.0000.0000.000
111A123ASP-1-0.775-0.85519.281-0.202-0.2020.0000.0000.0000.000
112A124VAL0-0.041-0.02315.3850.0090.0090.0000.0000.0000.000
113A125THR0-0.024-0.01617.986-0.024-0.0240.0000.0000.0000.000
114A126THR00.0470.02818.9470.0130.0130.0000.0000.0000.000
115A127VAL0-0.019-0.00821.6860.0130.0130.0000.0000.0000.000
116A128ILE00.0210.01621.288-0.017-0.0170.0000.0000.0000.000
117A129SER00.010-0.01322.855-0.016-0.0160.0000.0000.0000.000
118A130ASN0-0.111-0.05122.0800.0160.0160.0000.0000.0000.000
119A131TYR0-0.100-0.08317.010-0.003-0.0030.0000.0000.0000.000
120A132VAL00.003-0.00120.906-0.009-0.0090.0000.0000.0000.000
121A133THR0-0.0280.00023.2810.0170.0170.0000.0000.0000.000
122A134VAL00.0250.02224.9150.0010.0010.0000.0000.0000.000
123A135THR00.0100.01027.0950.0100.0100.0000.0000.0000.000
124A136THR00.016-0.01028.997-0.003-0.0030.0000.0000.0000.000
125A137ASP-1-0.918-0.93129.080-0.115-0.1150.0000.0000.0000.000
126A138TRP0-0.005-0.00322.838-0.008-0.0080.0000.0000.0000.000
127A139GLN0-0.040-0.03022.462-0.009-0.0090.0000.0000.0000.000
128A140HIS00.0010.01013.5140.0530.0530.0000.0000.0000.000
129A141VAL0-0.023-0.00817.3680.0080.0080.0000.0000.0000.000
130A142LYS10.8350.9049.8981.0391.0390.0000.0000.0000.000
131A143ILE0-0.0230.00113.5310.0480.0480.0000.0000.0000.000
132A144PRO00.0080.00710.741-0.090-0.0900.0000.0000.0000.000
133A145LEU00.0130.0026.5950.1140.1140.0000.0000.0000.000
134A146ARG10.7940.88510.0540.8250.8250.0000.0000.0000.000
135A147ASP-1-0.822-0.88411.869-0.429-0.4290.0000.0000.0000.000
136A148LEU0-0.038-0.02213.8920.0550.0550.0000.0000.0000.000
137A149MET0-0.049-0.01910.3100.0240.0240.0000.0000.0000.000
138A150LYS10.8940.94411.5590.5000.5000.0000.0000.0000.000
139A151ILE00.0040.02814.9690.0370.0370.0000.0000.0000.000
140A152ASN0-0.017-0.00918.339-0.006-0.0060.0000.0000.0000.000
141A153ASN0-0.045-0.03720.0430.0320.0320.0000.0000.0000.000
142A154GLY0-0.025-0.01020.3430.0140.0140.0000.0000.0000.000
143A155PHE00.0230.01312.8120.0110.0110.0000.0000.0000.000
144A156ASP-1-0.783-0.84713.722-0.218-0.2180.0000.0000.0000.000
145A157PRO0-0.019-0.0169.890-0.004-0.0040.0000.0000.0000.000
146A158SER0-0.066-0.0529.559-0.047-0.0470.0000.0000.0000.000
147A159SER0-0.022-0.03410.9200.0490.0490.0000.0000.0000.000
148A160VAL00.004-0.00211.0430.0240.0240.0000.0000.0000.000
149A161THR0-0.019-0.01213.2910.0130.0130.0000.0000.0000.000
150A162CYS0-0.075-0.03615.9420.0210.0210.0000.0000.0000.000
151A163LEU00.0460.04415.374-0.029-0.0290.0000.0000.0000.000
152A164VAL0-0.038-0.01816.8590.0390.0390.0000.0000.0000.000
153A165PHE00.0320.00819.657-0.017-0.0170.0000.0000.0000.000
154A166SER00.007-0.01423.2280.0130.0130.0000.0000.0000.000
155A167LYS10.8230.94226.6100.0930.0930.0000.0000.0000.000
156A168ARG10.9370.99128.1440.1470.1470.0000.0000.0000.000
157A169TYR0-0.038-0.02630.0380.0090.0090.0000.0000.0000.000
158A170ALA0-0.045-0.04033.675-0.001-0.0010.0000.0000.0000.000
159A171ASP-1-0.892-0.94435.280-0.098-0.0980.0000.0000.0000.000
160A172PRO0-0.035-0.00634.797-0.005-0.0050.0000.0000.0000.000
161A173PHE00.0130.00328.327-0.001-0.0010.0000.0000.0000.000
162A174THR0-0.017-0.03531.2500.0040.0040.0000.0000.0000.000
163A175VAL0-0.0030.00925.766-0.001-0.0010.0000.0000.0000.000
164A176TRP0-0.054-0.04025.9080.0070.0070.0000.0000.0000.000
165A177PHE00.0230.01219.799-0.010-0.0100.0000.0000.0000.000
166A178SER00.005-0.02020.1560.0250.0250.0000.0000.0000.000
167A179ASP-1-0.805-0.88314.823-0.393-0.3930.0000.0000.0000.000
168A180ILE00.0090.02514.680-0.067-0.0670.0000.0000.0000.000
169A181LYS10.8530.91510.0540.6320.6320.0000.0000.0000.000
170A182ILE0-0.023-0.0036.9340.0430.0430.0000.0000.0000.000
171A183THR00.021-0.0035.473-0.142-0.1420.0000.0000.0000.000
172A184SER00.019-0.0352.407-0.4000.3851.170-0.582-1.3730.000
173A185GLU-1-0.897-0.9303.182-4.947-3.9070.063-0.609-0.494-0.005
174A186ASP-1-0.850-0.8862.334-2.404-1.6141.021-0.428-1.3820.000
175A187ASN0-0.080-0.0442.141-6.598-5.0785.089-2.765-3.844-0.031