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

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FMODB ID: 8216Y

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 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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1889681.071628
FMO2-HF: Nuclear repulsion 1820900.80821
FMO2-HF: Total energy -68780.263418
FMO2-MP2: Total energy -68983.90989


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.
-24.175-10.9917.346-7.125-13.403-0.045
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 : -0.033 / q_NPA : -0.024
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-1-0.775-0.8883.815-4.205-2.743-0.009-0.668-0.7850.003
4A16VAL0-0.098-0.0505.7980.6510.6510.0000.0000.0000.000
5A17GLN0-0.076-0.0528.152-0.016-0.0160.0000.0000.0000.000
6A18ILE0-0.021-0.02011.6860.0740.0740.0000.0000.0000.000
7A19PHE0-0.007-0.01014.4070.0650.0650.0000.0000.0000.000
8A20LYS10.8870.93515.7220.0650.0650.0000.0000.0000.000
9A21ASP-1-0.821-0.90117.949-0.088-0.0880.0000.0000.0000.000
10A22SER0-0.036-0.02021.0080.0190.0190.0000.0000.0000.000
11A23PRO00.002-0.01721.809-0.019-0.0190.0000.0000.0000.000
12A24VAL00.0400.04018.7350.0080.0080.0000.0000.0000.000
13A25VAL0-0.0050.00920.8530.0090.0090.0000.0000.0000.000
14A26GLY00.0250.01320.952-0.026-0.0260.0000.0000.0000.000
15A27TRP0-0.036-0.02223.1510.0120.0120.0000.0000.0000.000
16A28SER00.0000.01825.714-0.024-0.0240.0000.0000.0000.000
17A29GLY00.0470.02727.8070.0120.0120.0000.0000.0000.000
18A30SER0-0.064-0.07831.120-0.010-0.0100.0000.0000.0000.000
19A31GLY0-0.0460.00033.9010.0060.0060.0000.0000.0000.000
20A32MET0-0.052-0.04237.1750.0070.0070.0000.0000.0000.000
21A33GLY00.0320.02836.5010.0050.0050.0000.0000.0000.000
22A34GLU-1-0.810-0.88935.708-0.101-0.1010.0000.0000.0000.000
23A35LEU0-0.043-0.00628.689-0.003-0.0030.0000.0000.0000.000
24A36GLU-1-0.809-0.87432.174-0.103-0.1030.0000.0000.0000.000
25A37THR0-0.051-0.03129.728-0.008-0.0080.0000.0000.0000.000
26A38ILE0-0.006-0.00630.2400.0100.0100.0000.0000.0000.000
27A39GLY0-0.027-0.01430.023-0.003-0.0030.0000.0000.0000.000
28A40ASP-1-0.871-0.92429.605-0.084-0.0840.0000.0000.0000.000
29A41THR0-0.005-0.01124.328-0.015-0.0150.0000.0000.0000.000
30A42LEU00.0290.00423.9060.0080.0080.0000.0000.0000.000
31A43PRO0-0.0200.00426.4850.0050.0050.0000.0000.0000.000
32A44VAL00.0030.00424.462-0.014-0.0140.0000.0000.0000.000
33A45ASP-1-0.801-0.87527.005-0.100-0.1000.0000.0000.0000.000
34A46THR00.016-0.00927.881-0.007-0.0070.0000.0000.0000.000
35A47THR0-0.090-0.04330.0070.0050.0050.0000.0000.0000.000
36A48VAL0-0.0180.00128.0720.0010.0010.0000.0000.0000.000
37A49THR0-0.044-0.00726.790-0.006-0.0060.0000.0000.0000.000
38A50TYR0-0.050-0.04920.2600.0160.0160.0000.0000.0000.000
39A51ASN0-0.006-0.00319.4690.0150.0150.0000.0000.0000.000
40A52GLY0-0.025-0.00422.3580.0090.0090.0000.0000.0000.000
41A53LEU0-0.028-0.00719.6470.0190.0190.0000.0000.0000.000
42A54PRO00.007-0.00823.779-0.007-0.0070.0000.0000.0000.000
43A55THR0-0.002-0.00723.325-0.018-0.0180.0000.0000.0000.000
44A56LEU0-0.0190.01020.9920.0180.0180.0000.0000.0000.000
45A57ARG10.8200.88224.2100.1000.1000.0000.0000.0000.000
46A58LEU00.0000.02124.9380.0070.0070.0000.0000.0000.000
47A59ASN00.011-0.01127.538-0.003-0.0030.0000.0000.0000.000
48A60VAL00.0020.03231.3300.0070.0070.0000.0000.0000.000
49A61GLN0-0.051-0.04033.5550.0050.0050.0000.0000.0000.000
50A62THR0-0.052-0.03937.0620.0050.0050.0000.0000.0000.000
51A63THR00.0240.01537.873-0.002-0.0020.0000.0000.0000.000
52A64VAL00.0390.03438.479-0.003-0.0030.0000.0000.0000.000
53A65GLN0-0.039-0.01939.396-0.006-0.0060.0000.0000.0000.000
54A66SER00.003-0.03640.5060.0030.0030.0000.0000.0000.000
55A67GLY00.0020.02737.592-0.004-0.0040.0000.0000.0000.000
56A68TRP00.0110.01631.621-0.007-0.0070.0000.0000.0000.000
57A69TRP00.0740.02326.6540.0060.0060.0000.0000.0000.000
58A70ILE0-0.013-0.01125.067-0.008-0.0080.0000.0000.0000.000
59A71SER0-0.014-0.01924.5060.0070.0070.0000.0000.0000.000
60A72LEU00.0030.00521.799-0.021-0.0210.0000.0000.0000.000
61A73LEU00.0150.00718.7440.0200.0200.0000.0000.0000.000
62A74THR0-0.039-0.03817.738-0.027-0.0270.0000.0000.0000.000
63A75LEU00.0350.02911.002-0.009-0.0090.0000.0000.0000.000
64A76ARG10.8990.9409.6600.2390.2390.0000.0000.0000.000
65A77GLY00.0350.02015.5110.0350.0350.0000.0000.0000.000
66A78TRP0-0.015-0.01218.5990.0110.0110.0000.0000.0000.000
67A79ASN0-0.081-0.02916.4830.0120.0120.0000.0000.0000.000
68A80THR0-0.0160.00014.792-0.025-0.0250.0000.0000.0000.000
69A81HIS0-0.010-0.0186.9530.1400.1400.0000.0000.0000.000
70A82ASP-1-0.822-0.8778.226-0.345-0.3450.0000.0000.0000.000
71A83LEU0-0.020-0.0196.146-0.082-0.0820.0000.0000.0000.000
72A84SER0-0.048-0.0556.564-0.177-0.1770.0000.0000.0000.000
73A85GLN0-0.040-0.0302.543-1.1900.1551.061-0.587-1.819-0.004
74A86TYR0-0.037-0.0353.013-4.022-0.1871.257-1.476-3.615-0.014
75A87VAL0-0.023-0.0074.198-0.0500.0010.001-0.008-0.0430.000
76A88GLU-1-0.935-0.9666.202-0.704-0.7040.0000.0000.0000.000
77A89ASN0-0.053-0.0446.0310.4490.4490.0000.0000.0000.000
78A90GLY00.0520.0446.000-0.126-0.1260.0000.0000.0000.000
79A91TYR0-0.030-0.0326.4570.5580.5580.0000.0000.0000.000
80A92LEU0-0.017-0.0079.301-0.128-0.1280.0000.0000.0000.000
81A93GLU-1-0.782-0.87410.134-1.165-1.1650.0000.0000.0000.000
82A94PHE0-0.003-0.01313.2010.0320.0320.0000.0000.0000.000
83A95ASP-1-0.813-0.88116.450-0.372-0.3720.0000.0000.0000.000
84A96ILE0-0.035-0.03919.7490.0150.0150.0000.0000.0000.000
85A97LYS10.8470.93722.9660.1690.1690.0000.0000.0000.000
86A98GLY00.0630.02526.7240.0010.0010.0000.0000.0000.000
87A99LYS10.7980.90129.7290.1260.1260.0000.0000.0000.000
88A100GLU-1-0.975-1.00733.153-0.112-0.1120.0000.0000.0000.000
89A101GLY0-0.024-0.00931.2720.0020.0020.0000.0000.0000.000
90A102GLY0-0.061-0.03430.7260.0070.0070.0000.0000.0000.000
91A103GLU-1-0.784-0.90428.914-0.171-0.1710.0000.0000.0000.000
92A104ASP-1-0.785-0.90527.286-0.240-0.2400.0000.0000.0000.000
93A105PHE0-0.067-0.04323.0670.0150.0150.0000.0000.0000.000
94A106VAL0-0.012-0.00123.586-0.018-0.0180.0000.0000.0000.000
95A107ILE00.014-0.00218.8040.0060.0060.0000.0000.0000.000
96A108GLY00.015-0.00217.685-0.009-0.0090.0000.0000.0000.000
97A109PHE0-0.0020.01012.789-0.019-0.0190.0000.0000.0000.000
98A110ARG10.8130.87916.7990.2120.2120.0000.0000.0000.000
99A111ASP-1-0.754-0.82016.219-0.242-0.2420.0000.0000.0000.000
100A112LYS10.8630.91217.4550.1380.1380.0000.0000.0000.000
101A113VAL00.0270.01918.2300.0050.0050.0000.0000.0000.000
102A114TYR0-0.005-0.01420.793-0.001-0.0010.0000.0000.0000.000
103A115GLU-1-0.910-0.95622.168-0.057-0.0570.0000.0000.0000.000
104A116ARG10.7380.83219.0260.1800.1800.0000.0000.0000.000
105A117VAL00.003-0.02124.824-0.005-0.0050.0000.0000.0000.000
106A118TYR0-0.048-0.02223.3980.0060.0060.0000.0000.0000.000
107A119GLY00.0470.01425.503-0.006-0.0060.0000.0000.0000.000
108A120LEU00.0040.02523.927-0.008-0.0080.0000.0000.0000.000
109A121GLU-1-0.852-0.91721.637-0.143-0.1430.0000.0000.0000.000
110A122ILE0-0.053-0.01620.5360.0070.0070.0000.0000.0000.000
111A123ASP-1-0.761-0.85319.682-0.238-0.2380.0000.0000.0000.000
112A124VAL0-0.063-0.02415.9020.0130.0130.0000.0000.0000.000
113A125THR0-0.026-0.02618.555-0.026-0.0260.0000.0000.0000.000
114A126THR00.0360.01919.5090.0180.0180.0000.0000.0000.000
115A127VAL0-0.0040.00722.0600.0100.0100.0000.0000.0000.000
116A128ILE00.0240.00621.675-0.022-0.0220.0000.0000.0000.000
117A129SER0-0.002-0.01923.384-0.018-0.0180.0000.0000.0000.000
118A130ASN0-0.090-0.04022.9170.0210.0210.0000.0000.0000.000
119A131TYR0-0.107-0.08517.5920.0010.0010.0000.0000.0000.000
120A132VAL0-0.0020.00221.384-0.015-0.0150.0000.0000.0000.000
121A133THR0-0.0170.00723.6520.0220.0220.0000.0000.0000.000
122A134VAL00.0100.01525.380-0.001-0.0010.0000.0000.0000.000
123A135THR00.0550.05727.5930.0140.0140.0000.0000.0000.000
124A136THR0-0.016-0.00829.043-0.006-0.0060.0000.0000.0000.000
125A137ASP-1-0.927-0.95728.817-0.148-0.1480.0000.0000.0000.000
126A138TRP0-0.006-0.01123.102-0.010-0.0100.0000.0000.0000.000
127A139GLN0-0.031-0.02322.847-0.012-0.0120.0000.0000.0000.000
128A140HIS0-0.011-0.00413.8270.0570.0570.0000.0000.0000.000
129A141VAL0-0.0070.00118.0240.0030.0030.0000.0000.0000.000
130A142LYS10.8160.89410.6811.1141.1140.0000.0000.0000.000
131A143ILE0-0.027-0.00614.2240.0560.0560.0000.0000.0000.000
132A144PRO00.0300.02711.460-0.119-0.1190.0000.0000.0000.000
133A145LEU00.0390.0147.4210.1330.1330.0000.0000.0000.000
134A146ARG10.7930.89210.3610.8880.8880.0000.0000.0000.000
135A147ASP-1-0.823-0.89012.547-0.482-0.4820.0000.0000.0000.000
136A148LEU0-0.030-0.01314.6270.0610.0610.0000.0000.0000.000
137A149MET0-0.058-0.02610.7940.0330.0330.0000.0000.0000.000
138A150LYS10.9480.97212.3730.5100.5100.0000.0000.0000.000
139A151ILE00.0170.02515.6170.0410.0410.0000.0000.0000.000
140A152ASN0-0.0230.00418.933-0.005-0.0050.0000.0000.0000.000
141A153ASN0-0.016-0.03120.2890.0370.0370.0000.0000.0000.000
142A154GLY0-0.015-0.00820.5240.0200.0200.0000.0000.0000.000
143A155PHE0-0.029-0.01013.1790.0090.0090.0000.0000.0000.000
144A156ASP-1-0.757-0.83914.139-0.241-0.2410.0000.0000.0000.000
145A157PRO0-0.028-0.02610.241-0.004-0.0040.0000.0000.0000.000
146A158SER0-0.071-0.05110.133-0.056-0.0560.0000.0000.0000.000
147A159SER0-0.022-0.03011.3790.0680.0680.0000.0000.0000.000
148A160VAL00.0240.00911.7210.0230.0230.0000.0000.0000.000
149A161THR0-0.016-0.00513.8360.0100.0100.0000.0000.0000.000
150A162CYS0-0.072-0.03516.4090.0150.0150.0000.0000.0000.000
151A163LEU00.0460.03715.488-0.034-0.0340.0000.0000.0000.000
152A164VAL0-0.026-0.02017.2620.0440.0440.0000.0000.0000.000
153A165PHE00.0320.01219.788-0.019-0.0190.0000.0000.0000.000
154A166SER00.002-0.01623.4420.0160.0160.0000.0000.0000.000
155A167LYS10.8670.95326.6760.1150.1150.0000.0000.0000.000
156A168ARG10.9491.00228.5420.1690.1690.0000.0000.0000.000
157A169TYR0-0.021-0.02330.4240.0120.0120.0000.0000.0000.000
158A170ALA0-0.047-0.04233.780-0.002-0.0020.0000.0000.0000.000
159A171ASP-1-0.903-0.94535.837-0.116-0.1160.0000.0000.0000.000
160A172PRO0-0.019-0.00734.933-0.007-0.0070.0000.0000.0000.000
161A173PHE00.0190.00628.348-0.003-0.0030.0000.0000.0000.000
162A174THR0-0.014-0.03731.0250.0070.0070.0000.0000.0000.000
163A175VAL0-0.0090.00825.745-0.001-0.0010.0000.0000.0000.000
164A176TRP0-0.062-0.04225.9740.0100.0100.0000.0000.0000.000
165A177PHE00.0200.00720.049-0.014-0.0140.0000.0000.0000.000
166A178SER00.033-0.00720.2320.0420.0420.0000.0000.0000.000
167A179ASP-1-0.818-0.87914.834-0.539-0.5390.0000.0000.0000.000
168A180ILE00.0060.01414.585-0.074-0.0740.0000.0000.0000.000
169A181LYS10.8540.92310.0730.7870.7870.0000.0000.0000.000
170A182ILE0-0.023-0.0066.9300.0300.0300.0000.0000.0000.000
171A183THR00.0250.0155.587-0.232-0.2320.0000.0000.0000.000
172A184SER00.050-0.0102.243-0.2790.4961.713-0.852-1.6350.002
173A185GLU-1-0.959-0.9522.981-6.461-4.8500.210-0.951-0.871-0.010
174A186ASP-1-0.846-0.8972.378-2.035-1.3700.669-0.304-1.0300.000
175A187ASN0-0.069-0.0442.377-6.565-3.1252.444-2.279-3.605-0.022