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: VR411

Calculation Name: 3C0T-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3C0T

Chain ID: A

ChEMBL ID:

UniProt ID: O14198

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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2471463.862706
FMO2-HF: Nuclear repulsion 2386996.105376
FMO2-HF: Total energy -84467.75733
FMO2-MP2: Total energy -84713.5915


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-25.055-15.7921.499-10.739-20.027-0.071
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.054 / q_NPA : -0.007
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].
3A3GLU-1-0.794-0.8772.908-5.124-2.2610.267-1.399-1.730-0.006
4A4LEU0-0.022-0.0135.0680.5390.622-0.001-0.008-0.0750.000
5A5TYR0-0.024-0.0468.4520.1830.1830.0000.0000.0000.000
6A6LEU0-0.019-0.00310.9950.0770.0770.0000.0000.0000.000
7A7LEU00.0110.00413.792-0.001-0.0010.0000.0000.0000.000
8A8GLY00.0270.00616.4180.0370.0370.0000.0000.0000.000
9A9VAL0-0.019-0.00119.429-0.019-0.0190.0000.0000.0000.000
10A10VAL00.0080.00422.1460.0220.0220.0000.0000.0000.000
11A11PRO00.0220.00824.4250.0020.0020.0000.0000.0000.000
12A12SER00.1410.06927.4210.0130.0130.0000.0000.0000.000
13A13ARG10.9820.99028.3490.0990.0990.0000.0000.0000.000
14A14ARG10.7790.87426.4470.1170.1170.0000.0000.0000.000
15A15PHE00.0320.02522.2860.0050.0050.0000.0000.0000.000
16A16GLU-1-0.863-0.92726.201-0.027-0.0270.0000.0000.0000.000
17A17ALA00.0210.01728.2770.0090.0090.0000.0000.0000.000
18A18VAL0-0.0060.00522.8780.0060.0060.0000.0000.0000.000
19A19VAL00.0580.03622.8590.0070.0070.0000.0000.0000.000
20A20ASN0-0.033-0.01124.5670.0250.0250.0000.0000.0000.000
21A21SER0-0.058-0.03925.8200.0120.0120.0000.0000.0000.000
22A22LEU0-0.029-0.00319.4060.0040.0040.0000.0000.0000.000
23A23SER00.024-0.01022.7130.0210.0210.0000.0000.0000.000
24A24LYS10.8930.97124.2750.0020.0020.0000.0000.0000.000
25A25THR0-0.100-0.08223.4620.0000.0000.0000.0000.0000.000
26A26LEU0-0.047-0.00318.105-0.001-0.0010.0000.0000.0000.000
27A27ASP-1-0.864-0.92118.3320.2120.2120.0000.0000.0000.000
28A28GLY0-0.023-0.00818.3560.0150.0150.0000.0000.0000.000
29A29PRO0-0.031-0.01519.227-0.012-0.0120.0000.0000.0000.000
30A30LYS10.8590.93211.957-0.326-0.3260.0000.0000.0000.000
31A31THR0-0.007-0.04618.221-0.021-0.0210.0000.0000.0000.000
32A32ILE0-0.076-0.03513.4420.0330.0330.0000.0000.0000.000
33A33LEU00.0610.02716.941-0.036-0.0360.0000.0000.0000.000
34A34GLU-1-0.823-0.87711.991-0.188-0.1880.0000.0000.0000.000
35A35PHE00.0260.00516.246-0.035-0.0350.0000.0000.0000.000
36A36TRP0-0.026-0.0388.745-0.037-0.0370.0000.0000.0000.000
37A37VAL0-0.014-0.01315.4830.0280.0280.0000.0000.0000.000
38A38VAL0-0.0050.00214.429-0.062-0.0620.0000.0000.0000.000
39A39TYR0-0.027-0.03615.8870.0700.0700.0000.0000.0000.000
40A40ARG10.8340.90616.5810.2110.2110.0000.0000.0000.000
41A41PRO00.018-0.00417.5860.0350.0350.0000.0000.0000.000
42A42LYS10.8710.95620.1700.2060.2060.0000.0000.0000.000
43A43ASP-1-0.830-0.93523.787-0.209-0.2090.0000.0000.0000.000
44A44VAL0-0.049-0.02926.5550.0160.0160.0000.0000.0000.000
45A45PRO0-0.0400.00626.3600.0110.0110.0000.0000.0000.000
46A46PRO00.0830.03827.179-0.014-0.0140.0000.0000.0000.000
47A47ASN0-0.083-0.03127.967-0.005-0.0050.0000.0000.0000.000
48A48LEU0-0.015-0.01122.5330.0030.0030.0000.0000.0000.000
49A49PRO0-0.0070.00022.881-0.006-0.0060.0000.0000.0000.000
50A50ARG10.9580.97120.6860.4190.4190.0000.0000.0000.000
51A51GLN00.0700.03616.3760.0080.0080.0000.0000.0000.000
52A52PRO00.0230.01916.065-0.024-0.0240.0000.0000.0000.000
53A53ASP-1-0.837-0.90311.370-0.940-0.9400.0000.0000.0000.000
54A54SER0-0.065-0.03711.255-0.111-0.1110.0000.0000.0000.000
55A55TRP0-0.026-0.02313.5780.0880.0880.0000.0000.0000.000
56A56LEU00.0360.02011.896-0.169-0.1690.0000.0000.0000.000
57A57ARG10.8190.8839.9371.3121.3120.0000.0000.0000.000
58A58LEU0-0.004-0.00210.453-0.075-0.0750.0000.0000.0000.000
59A59CYS0-0.013-0.00510.9160.0350.0350.0000.0000.0000.000
60A60SER00.0210.01812.9650.0900.0900.0000.0000.0000.000
61A61ASN00.005-0.01614.690-0.038-0.0380.0000.0000.0000.000
62A62ILE00.012-0.00216.2630.0190.0190.0000.0000.0000.000
63A63GLU-1-0.836-0.88518.6080.0520.0520.0000.0000.0000.000
64A64SER0-0.101-0.04019.2820.0270.0270.0000.0000.0000.000
65A65HIS0-0.025-0.02720.9300.0090.0090.0000.0000.0000.000
66A66ASP-1-0.863-0.89923.6870.0460.0460.0000.0000.0000.000
67A67GLU-1-0.921-0.98827.218-0.026-0.0260.0000.0000.0000.000
68A68THR0-0.020-0.02528.092-0.009-0.0090.0000.0000.0000.000
69A69ASP-1-0.828-0.90026.9460.0140.0140.0000.0000.0000.000
70A70THR0-0.018-0.02228.440-0.008-0.0080.0000.0000.0000.000
71A71GLU-1-0.903-0.94027.345-0.040-0.0400.0000.0000.0000.000
72A72TRP00.0450.02519.559-0.001-0.0010.0000.0000.0000.000
73A73SER0-0.046-0.00821.2660.0170.0170.0000.0000.0000.000
74A74LYS10.8390.90321.0900.0300.0300.0000.0000.0000.000
75A75ASN0-0.084-0.03522.8010.0220.0220.0000.0000.0000.000
76A76THR00.020-0.00718.2090.0090.0090.0000.0000.0000.000
77A77GLN0-0.0300.00414.0170.0650.0650.0000.0000.0000.000
78A78TRP0-0.030-0.00914.169-0.024-0.0240.0000.0000.0000.000
79A79SER0-0.034-0.0308.6690.1780.1780.0000.0000.0000.000
80A80MET0-0.014-0.0048.964-0.081-0.0810.0000.0000.0000.000
81A81TYR00.0280.0083.8750.0150.2610.001-0.032-0.2160.000
82A82LEU00.0100.0116.6580.3760.3760.0000.0000.0000.000
83A83GLU-1-0.844-0.8866.684-2.745-2.7450.0000.0000.0000.000
84A84GLY00.0210.0097.6850.5680.5680.0000.0000.0000.000
85A85ASN0-0.038-0.0299.334-0.069-0.0690.0000.0000.0000.000
86A86SER00.0220.01211.321-0.055-0.0550.0000.0000.0000.000
87A87GLU-1-0.848-0.9359.907-0.878-0.8780.0000.0000.0000.000
88A88PRO0-0.009-0.00313.7640.0530.0530.0000.0000.0000.000
89A89LYS10.9350.94417.4770.3170.3170.0000.0000.0000.000
90A90ARG10.7820.88913.6330.6660.6660.0000.0000.0000.000
91A91GLU-1-0.879-0.93617.714-0.463-0.4630.0000.0000.0000.000
92A92ASP-1-0.942-0.96420.389-0.235-0.2350.0000.0000.0000.000
93A93LYS10.7980.89916.2520.3650.3650.0000.0000.0000.000
94A94CYS0-0.027-0.01012.044-0.004-0.0040.0000.0000.0000.000
95A95GLY00.0670.05013.1100.0090.0090.0000.0000.0000.000
96A96ILE0-0.021-0.0157.986-0.071-0.0710.0000.0000.0000.000
97A97ARG10.7860.8636.7362.8372.8370.0000.0000.0000.000
98A98PRO00.0410.0384.883-1.141-1.1410.0000.0000.0000.000
99A99VAL0-0.032-0.0152.3360.3841.6831.073-0.608-1.7640.000
100A100ASN00.0260.0192.440-8.454-6.6384.783-2.749-3.850-0.036
101A101ARG10.8900.9222.486-6.580-8.0376.855-1.924-3.4750.006
102A102ALA00.0040.0154.6630.5840.691-0.001-0.005-0.1010.000
103A103LYS10.8860.9278.090-0.756-0.7560.0000.0000.0000.000
104A104LEU0-0.0180.00310.9750.0060.0060.0000.0000.0000.000
105A105THR00.025-0.00614.6230.0070.0070.0000.0000.0000.000
106A106ASN00.0150.01818.1860.0000.0000.0000.0000.0000.000
107A107GLY00.0380.02521.867-0.018-0.0180.0000.0000.0000.000
108A108SER00.004-0.03722.530-0.008-0.0080.0000.0000.0000.000
109A109VAL00.0290.01615.671-0.015-0.0150.0000.0000.0000.000
110A110THR00.015-0.01518.808-0.032-0.0320.0000.0000.0000.000
111A111GLU-1-0.809-0.87420.125-0.090-0.0900.0000.0000.0000.000
112A112PHE0-0.023-0.00917.379-0.004-0.0040.0000.0000.0000.000
113A113VAL00.0350.00415.684-0.013-0.0130.0000.0000.0000.000
114A114GLU-1-0.856-0.90318.805-0.188-0.1880.0000.0000.0000.000
115A115LYS10.8270.90122.2510.0980.0980.0000.0000.0000.000
116A116MET0-0.061-0.01315.8580.0080.0080.0000.0000.0000.000
117A117GLY00.0030.02020.390-0.015-0.0150.0000.0000.0000.000
118A118TYR0-0.027-0.00814.835-0.010-0.0100.0000.0000.0000.000
119A119GLU-1-0.853-0.93020.838-0.197-0.1970.0000.0000.0000.000
120A120PHE00.0190.00520.426-0.040-0.0400.0000.0000.0000.000
121A121SER0-0.051-0.01419.708-0.003-0.0030.0000.0000.0000.000
122A122HIS0-0.017-0.02617.876-0.024-0.0240.0000.0000.0000.000
123A123GLU-1-0.748-0.86019.087-0.208-0.2080.0000.0000.0000.000
124A124TYR0-0.035-0.00713.297-0.003-0.0030.0000.0000.0000.000
125A125ILE00.0130.01618.6040.0010.0010.0000.0000.0000.000
126A126ILE0-0.061-0.01713.994-0.029-0.0290.0000.0000.0000.000
127A127GLN00.0990.05117.1940.0290.0290.0000.0000.0000.000
128A128GLY00.003-0.02018.266-0.031-0.0310.0000.0000.0000.000
129A129LEU0-0.0170.01118.5170.0310.0310.0000.0000.0000.000
130A130GLU-1-0.800-0.88311.2580.0640.0640.0000.0000.0000.000
131A131TYR00.0230.00915.2110.0260.0260.0000.0000.0000.000
132A132PHE0-0.002-0.01111.6080.0100.0100.0000.0000.0000.000
133A133PHE00.0620.02814.855-0.037-0.0370.0000.0000.0000.000
134A134PHE0-0.0070.00015.176-0.011-0.0110.0000.0000.0000.000
135A135ASP-1-0.894-0.94212.0770.4030.4030.0000.0000.0000.000
136A136THR0-0.086-0.04110.6480.0500.0500.0000.0000.0000.000
137A137THR00.0210.0139.2930.1140.1140.0000.0000.0000.000
138A138VAL0-0.011-0.01111.315-0.157-0.1570.0000.0000.0000.000
139A139ARG10.8000.87510.8770.2160.2160.0000.0000.0000.000
140A140ILE0-0.001-0.00114.653-0.056-0.0560.0000.0000.0000.000
141A141TYR00.002-0.02113.2630.0360.0360.0000.0000.0000.000
142A142GLN00.0050.00718.323-0.023-0.0230.0000.0000.0000.000
143A143THR00.000-0.01017.4240.0040.0040.0000.0000.0000.000
144A144LEU00.0170.00019.8320.0170.0170.0000.0000.0000.000
145A145ILE00.001-0.00221.673-0.027-0.0270.0000.0000.0000.000
146A146PRO00.0190.00522.9230.0180.0180.0000.0000.0000.000
147A147SER0-0.0080.00625.800-0.004-0.0040.0000.0000.0000.000
148A148GLN0-0.016-0.01528.490-0.002-0.0020.0000.0000.0000.000
149A149GLN0-0.0070.00025.700-0.014-0.0140.0000.0000.0000.000
150A150ARG10.8010.88121.8140.1950.1950.0000.0000.0000.000
151A151SER0-0.0090.01424.8380.0220.0220.0000.0000.0000.000
152A152ILE00.0400.01622.594-0.013-0.0130.0000.0000.0000.000
153A153LYS10.9110.96425.2170.0550.0550.0000.0000.0000.000
154A154PRO00.0120.03028.045-0.013-0.0130.0000.0000.0000.000
155A155PRO0-0.025-0.01429.4320.0040.0040.0000.0000.0000.000
156A156PHE00.001-0.00924.575-0.008-0.0080.0000.0000.0000.000
157A157HIS0-0.003-0.00226.6280.0110.0110.0000.0000.0000.000
158A158PRO00.0330.02725.112-0.017-0.0170.0000.0000.0000.000
159A159MET0-0.034-0.01622.394-0.007-0.0070.0000.0000.0000.000
160A160ASN0-0.046-0.03126.1670.0070.0070.0000.0000.0000.000
161A161GLU-1-0.898-0.94928.616-0.107-0.1070.0000.0000.0000.000
162A162GLU-1-0.948-0.96630.618-0.105-0.1050.0000.0000.0000.000
163A163GLN0-0.050-0.01422.0250.0000.0000.0000.0000.0000.000
164A164PRO0-0.071-0.03523.9110.0120.0120.0000.0000.0000.000
165A165TRP00.0160.00921.036-0.020-0.0200.0000.0000.0000.000
166A166ILE0-0.006-0.00316.101-0.002-0.0020.0000.0000.0000.000
167A167LEU0-0.011-0.01216.8260.0290.0290.0000.0000.0000.000
168A168HIS0-0.027-0.0098.9200.1150.1150.0000.0000.0000.000
169A169VAL00.0260.00712.7010.0810.0810.0000.0000.0000.000
170A170TYR0-0.031-0.0386.182-0.175-0.1750.0000.0000.0000.000
171A171THR00.014-0.0087.2600.4710.4710.0000.0000.0000.000
172A172HIS0-0.016-0.0252.808-2.198-1.4824.725-1.589-3.853-0.009
173A173VAL00.0090.0033.1700.4751.3500.044-0.165-0.7530.000
174A174ALA0-0.023-0.0172.181-5.230-3.2413.264-2.390-2.864-0.015
175A175ASP-1-0.803-0.9102.8321.0361.7070.4900.137-1.298-0.011
176A176ALA00.0170.0004.582-0.649-0.592-0.001-0.007-0.0480.000
177A177SER0-0.025-0.0146.056-0.213-0.2130.0000.0000.0000.000
178A178ASN00.0000.0198.141-0.136-0.1360.0000.0000.0000.000
179A179GLN00.0610.0139.905-0.071-0.0710.0000.0000.0000.000
180A180VAL0-0.0010.00812.360-0.054-0.0540.0000.0000.0000.000
181A181ALA00.0070.0038.692-0.004-0.0040.0000.0000.0000.000
182A182MET00.0200.0237.450-0.146-0.1460.0000.0000.0000.000
183A183ALA00.0110.00310.266-0.050-0.0500.0000.0000.0000.000
184A184LYS10.9240.96312.176-0.171-0.1710.0000.0000.0000.000
185A185ALA00.0660.0329.3320.0250.0250.0000.0000.0000.000
186A186GLU-1-0.739-0.84911.315-0.440-0.4400.0000.0000.0000.000
187A187ALA0-0.0140.00713.6570.0210.0210.0000.0000.0000.000
188A188ASN0-0.0200.00613.727-0.020-0.0200.0000.0000.0000.000
189A189LEU00.0450.02110.6430.0130.0130.0000.0000.0000.000
190A190THR0-0.063-0.04114.931-0.002-0.0020.0000.0000.0000.000
191A191LYS10.8110.89817.965-0.031-0.0310.0000.0000.0000.000
192A192VAL00.0410.02815.9770.0060.0060.0000.0000.0000.000
193A193LYS10.8510.93418.5890.2180.2180.0000.0000.0000.000
194A194THR0-0.010-0.01619.9140.0040.0040.0000.0000.0000.000
195A195LEU0-0.0040.01721.6220.0020.0020.0000.0000.0000.000
196A196LEU00.0420.01718.5770.0040.0040.0000.0000.0000.000
197A197SER0-0.054-0.02422.694-0.007-0.0070.0000.0000.0000.000
198A198ALA0-0.016-0.00524.848-0.002-0.0020.0000.0000.0000.000
199A199PHE0-0.027-0.01422.9170.0020.0020.0000.0000.0000.000
200A200CYS0-0.014-0.01721.717-0.011-0.0110.0000.0000.0000.000
201A201ASP-1-0.765-0.86522.932-0.241-0.2410.0000.0000.0000.000
202A202LEU0-0.055-0.02117.346-0.018-0.0180.0000.0000.0000.000
203A203LYS10.8810.93018.7470.3350.3350.0000.0000.0000.000
204A204ASN00.0400.01115.419-0.134-0.1340.0000.0000.0000.000
205A205VAL00.0320.01415.8220.0720.0720.0000.0000.0000.000
206A206ARG10.8410.93115.2100.6180.6180.0000.0000.0000.000
207A207LEU00.0290.01711.1280.0140.0140.0000.0000.0000.000