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: YY2K2

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 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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2470110.356789
FMO2-HF: Nuclear repulsion 2385643.148601
FMO2-HF: Total energy -84467.208188
FMO2-MP2: Total energy -84713.070287


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.
-25.749-11.85914.898-10.29-18.495-0.075
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 : -0.064 / q_NPA : -0.023
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-1-0.779-0.8673.564-3.316-0.8200.013-0.997-1.5120.002
4A4LEU0-0.011-0.0074.9380.3420.437-0.001-0.008-0.0860.000
5A5TYR0-0.033-0.0568.4540.1770.1770.0000.0000.0000.000
6A6LEU0-0.030-0.01711.0080.0370.0370.0000.0000.0000.000
7A7LEU00.0140.01013.6150.0080.0080.0000.0000.0000.000
8A8GLY00.0250.00716.1610.0310.0310.0000.0000.0000.000
9A9VAL0-0.0200.00919.277-0.012-0.0120.0000.0000.0000.000
10A10VAL00.009-0.00321.9820.0180.0180.0000.0000.0000.000
11A11PRO0-0.001-0.00124.2960.0000.0000.0000.0000.0000.000
12A12SER00.1340.06227.5630.0120.0120.0000.0000.0000.000
13A13ARG10.9860.99228.5990.0740.0740.0000.0000.0000.000
14A14ARG10.7880.88726.6270.0770.0770.0000.0000.0000.000
15A15PHE00.0430.02922.9160.0070.0070.0000.0000.0000.000
16A16GLU-1-0.869-0.93126.992-0.004-0.0040.0000.0000.0000.000
17A17ALA00.0220.00928.9850.0080.0080.0000.0000.0000.000
18A18VAL0-0.012-0.00323.5960.0060.0060.0000.0000.0000.000
19A19VAL00.0650.04323.3960.0080.0080.0000.0000.0000.000
20A20ASN0-0.012-0.00425.2280.0230.0230.0000.0000.0000.000
21A21SER0-0.064-0.04026.3650.0100.0100.0000.0000.0000.000
22A22LEU0-0.029-0.01220.1380.0070.0070.0000.0000.0000.000
23A23SER0-0.007-0.01323.2050.0220.0220.0000.0000.0000.000
24A24LYS10.9130.97825.058-0.027-0.0270.0000.0000.0000.000
25A25THR0-0.104-0.07324.2660.0030.0030.0000.0000.0000.000
26A26LEU0-0.067-0.01118.7510.0060.0060.0000.0000.0000.000
27A27ASP-1-0.843-0.90719.2890.2280.2280.0000.0000.0000.000
28A28GLY0-0.047-0.00819.3450.0100.0100.0000.0000.0000.000
29A29PRO0-0.025-0.02319.258-0.014-0.0140.0000.0000.0000.000
30A30LYS10.8530.92711.909-0.420-0.4200.0000.0000.0000.000
31A31THR0-0.015-0.04517.797-0.008-0.0080.0000.0000.0000.000
32A32ILE0-0.061-0.02613.2350.0350.0350.0000.0000.0000.000
33A33LEU00.0520.01416.578-0.034-0.0340.0000.0000.0000.000
34A34GLU-1-0.835-0.88611.548-0.139-0.1390.0000.0000.0000.000
35A35PHE00.0290.01015.659-0.032-0.0320.0000.0000.0000.000
36A36TRP0-0.023-0.0418.122-0.063-0.0630.0000.0000.0000.000
37A37VAL00.0030.00215.1700.0260.0260.0000.0000.0000.000
38A38VAL0-0.009-0.01214.336-0.065-0.0650.0000.0000.0000.000
39A39TYR0-0.047-0.04015.7950.0670.0670.0000.0000.0000.000
40A40ARG10.8350.90516.4170.2070.2070.0000.0000.0000.000
41A41PRO00.015-0.00317.2650.0380.0380.0000.0000.0000.000
42A42LYS10.8860.96119.8670.2270.2270.0000.0000.0000.000
43A43ASP-1-0.860-0.95023.593-0.204-0.2040.0000.0000.0000.000
44A44VAL0-0.047-0.02726.4330.0140.0140.0000.0000.0000.000
45A45PRO0-0.0340.00926.2980.0110.0110.0000.0000.0000.000
46A46PRO00.0820.04026.701-0.013-0.0130.0000.0000.0000.000
47A47ASN0-0.083-0.03427.460-0.005-0.0050.0000.0000.0000.000
48A48LEU0-0.008-0.00822.1950.0050.0050.0000.0000.0000.000
49A49PRO0-0.017-0.00822.494-0.005-0.0050.0000.0000.0000.000
50A50ARG10.9740.98920.3360.3790.3790.0000.0000.0000.000
51A51GLN00.0600.02216.093-0.003-0.0030.0000.0000.0000.000
52A52PRO00.0320.00715.672-0.036-0.0360.0000.0000.0000.000
53A53ASP-1-0.867-0.91110.965-0.880-0.8800.0000.0000.0000.000
54A54SER0-0.054-0.03110.767-0.135-0.1350.0000.0000.0000.000
55A55TRP0-0.055-0.03813.0090.0900.0900.0000.0000.0000.000
56A56LEU00.0180.01111.952-0.171-0.1710.0000.0000.0000.000
57A57ARG10.8320.90710.0961.2231.2230.0000.0000.0000.000
58A58LEU0-0.006-0.00310.478-0.084-0.0840.0000.0000.0000.000
59A59CYS0-0.0100.00510.0250.0600.0600.0000.0000.0000.000
60A60SER00.0250.02212.1270.0790.0790.0000.0000.0000.000
61A61ASN00.011-0.01013.906-0.028-0.0280.0000.0000.0000.000
62A62ILE00.000-0.01115.4260.0130.0130.0000.0000.0000.000
63A63GLU-1-0.838-0.88618.1590.0590.0590.0000.0000.0000.000
64A64SER0-0.100-0.04318.7330.0210.0210.0000.0000.0000.000
65A65HIS0-0.005-0.03319.9740.0040.0040.0000.0000.0000.000
66A66ASP-1-0.870-0.89823.2040.0370.0370.0000.0000.0000.000
67A67GLU-1-0.936-0.98326.588-0.025-0.0250.0000.0000.0000.000
68A68THR0-0.015-0.03227.472-0.007-0.0070.0000.0000.0000.000
69A69ASP-1-0.888-0.95426.160-0.003-0.0030.0000.0000.0000.000
70A70THR0-0.033-0.02327.763-0.007-0.0070.0000.0000.0000.000
71A71GLU-1-0.926-0.95326.878-0.055-0.0550.0000.0000.0000.000
72A72TRP00.0840.05318.833-0.001-0.0010.0000.0000.0000.000
73A73SER0-0.066-0.01820.8420.0130.0130.0000.0000.0000.000
74A74LYS10.8570.90520.8570.0450.0450.0000.0000.0000.000
75A75ASN0-0.052-0.00622.8060.0190.0190.0000.0000.0000.000
76A76THR00.0250.00216.9610.0120.0120.0000.0000.0000.000
77A77GLN0-0.0430.00113.1150.0680.0680.0000.0000.0000.000
78A78TRP0-0.015-0.00213.502-0.014-0.0140.0000.0000.0000.000
79A79SER0-0.045-0.0257.8170.1350.1350.0000.0000.0000.000
80A80MET0-0.021-0.0069.115-0.052-0.0520.0000.0000.0000.000
81A81TYR00.022-0.0133.404-0.2100.1000.008-0.042-0.2750.000
82A82LEU00.0230.0256.3600.3560.3560.0000.0000.0000.000
83A83GLU-1-0.849-0.9066.486-2.556-2.5560.0000.0000.0000.000
84A84GLY00.0420.0197.4850.5150.5150.0000.0000.0000.000
85A85ASN0-0.075-0.0439.130-0.005-0.0050.0000.0000.0000.000
86A86SER00.0360.01310.843-0.062-0.0620.0000.0000.0000.000
87A87GLU-1-0.855-0.9509.848-0.638-0.6380.0000.0000.0000.000
88A88PRO0-0.054-0.02913.5100.0320.0320.0000.0000.0000.000
89A89LYS10.9250.94217.2580.2620.2620.0000.0000.0000.000
90A90ARG10.8490.91713.6920.4970.4970.0000.0000.0000.000
91A91GLU-1-0.895-0.94217.779-0.339-0.3390.0000.0000.0000.000
92A92ASP-1-0.940-0.95820.269-0.173-0.1730.0000.0000.0000.000
93A93LYS10.8130.90616.2960.2420.2420.0000.0000.0000.000
94A94CYS0-0.0120.00312.0980.0010.0010.0000.0000.0000.000
95A95GLY00.0600.04012.8030.0050.0050.0000.0000.0000.000
96A96ILE0-0.036-0.0237.975-0.070-0.0700.0000.0000.0000.000
97A97ARG10.8030.8906.6532.3562.3560.0000.0000.0000.000
98A98PRO00.0310.0344.558-1.021-0.945-0.001-0.042-0.0330.000
99A99VAL0-0.024-0.0172.401-0.4811.2851.243-0.835-2.1740.000
100A100ASN0-0.0090.0052.286-10.445-8.3316.005-3.655-4.464-0.046
101A101ARG10.9460.9632.774-5.816-5.0273.011-0.860-2.9390.002
102A102ALA00.0180.0164.7720.4590.563-0.001-0.004-0.0990.000
103A103LYS10.8970.9568.268-0.724-0.7240.0000.0000.0000.000
104A104LEU0-0.016-0.00710.6230.0230.0230.0000.0000.0000.000
105A105THR00.033-0.00514.1720.0020.0020.0000.0000.0000.000
106A106ASN0-0.016-0.00417.5800.0020.0020.0000.0000.0000.000
107A107GLY00.0330.02121.340-0.018-0.0180.0000.0000.0000.000
108A108SER00.009-0.01321.902-0.003-0.0030.0000.0000.0000.000
109A109VAL00.0300.01115.545-0.013-0.0130.0000.0000.0000.000
110A110THR00.022-0.00719.011-0.028-0.0280.0000.0000.0000.000
111A111GLU-1-0.855-0.90920.142-0.110-0.1100.0000.0000.0000.000
112A112PHE0-0.031-0.01517.4160.0000.0000.0000.0000.0000.000
113A113VAL00.029-0.00315.790-0.013-0.0130.0000.0000.0000.000
114A114GLU-1-0.859-0.91018.853-0.205-0.2050.0000.0000.0000.000
115A115LYS10.8880.94022.1530.1220.1220.0000.0000.0000.000
116A116MET0-0.066-0.00915.6090.0050.0050.0000.0000.0000.000
117A117GLY00.0000.01520.580-0.012-0.0120.0000.0000.0000.000
118A118TYR0-0.026-0.00814.732-0.008-0.0080.0000.0000.0000.000
119A119GLU-1-0.823-0.91520.745-0.208-0.2080.0000.0000.0000.000
120A120PHE00.006-0.00520.266-0.038-0.0380.0000.0000.0000.000
121A121SER0-0.0490.00019.3300.0000.0000.0000.0000.0000.000
122A122HIS0-0.003-0.02517.774-0.005-0.0050.0000.0000.0000.000
123A123GLU-1-0.724-0.85218.635-0.218-0.2180.0000.0000.0000.000
124A124TYR0-0.040-0.00713.1910.0040.0040.0000.0000.0000.000
125A125ILE00.0240.02217.990-0.008-0.0080.0000.0000.0000.000
126A126ILE0-0.065-0.00313.896-0.016-0.0160.0000.0000.0000.000
127A127GLN00.0950.04917.1280.0250.0250.0000.0000.0000.000
128A128GLY00.015-0.01118.069-0.027-0.0270.0000.0000.0000.000
129A129LEU0-0.0190.01318.5140.0260.0260.0000.0000.0000.000
130A130GLU-1-0.799-0.90211.4790.2270.2270.0000.0000.0000.000
131A131TYR00.0440.01415.9060.0110.0110.0000.0000.0000.000
132A132PHE0-0.006-0.02212.3160.0370.0370.0000.0000.0000.000
133A133PHE00.0840.03815.685-0.042-0.0420.0000.0000.0000.000
134A134PHE0-0.027-0.01315.8140.0000.0000.0000.0000.0000.000
135A135ASP-1-0.911-0.95711.9360.5340.5340.0000.0000.0000.000
136A136THR0-0.089-0.04011.2290.0700.0700.0000.0000.0000.000
137A137THR00.0190.00610.2110.0660.0660.0000.0000.0000.000
138A138VAL0-0.012-0.00612.194-0.127-0.1270.0000.0000.0000.000
139A139ARG10.8100.88010.9100.1060.1060.0000.0000.0000.000
140A140ILE0-0.0110.00214.868-0.057-0.0570.0000.0000.0000.000
141A141TYR0-0.014-0.03113.5360.0260.0260.0000.0000.0000.000
142A142GLN00.0220.02418.399-0.020-0.0200.0000.0000.0000.000
143A143THR00.001-0.00617.366-0.004-0.0040.0000.0000.0000.000
144A144LEU0-0.012-0.01919.8150.0090.0090.0000.0000.0000.000
145A145ILE00.012-0.00321.563-0.027-0.0270.0000.0000.0000.000
146A146PRO00.0040.01022.5190.0180.0180.0000.0000.0000.000
147A147SER00.0000.01225.290-0.004-0.0040.0000.0000.0000.000
148A148GLN0-0.018-0.02027.766-0.001-0.0010.0000.0000.0000.000
149A149GLN0-0.009-0.00725.111-0.011-0.0110.0000.0000.0000.000
150A150ARG10.8010.88221.2610.2030.2030.0000.0000.0000.000
151A151SER0-0.0030.01624.0840.0200.0200.0000.0000.0000.000
152A152ILE00.0480.02121.873-0.013-0.0130.0000.0000.0000.000
153A153LYS10.9130.96324.5590.0620.0620.0000.0000.0000.000
154A154PRO0-0.0070.03327.276-0.011-0.0110.0000.0000.0000.000
155A155PRO0-0.018-0.01728.7700.0040.0040.0000.0000.0000.000
156A156PHE00.007-0.01223.691-0.010-0.0100.0000.0000.0000.000
157A157HIS00.004-0.00826.4860.0100.0100.0000.0000.0000.000
158A158PRO00.0340.02825.268-0.015-0.0150.0000.0000.0000.000
159A159MET0-0.033-0.02422.654-0.006-0.0060.0000.0000.0000.000
160A160ASN0-0.040-0.03326.4510.0080.0080.0000.0000.0000.000
161A161GLU-1-0.897-0.95328.600-0.090-0.0900.0000.0000.0000.000
162A162GLU-1-0.965-0.96630.559-0.082-0.0820.0000.0000.0000.000
163A163GLN0-0.062-0.02722.206-0.002-0.0020.0000.0000.0000.000
164A164PRO0-0.062-0.02823.5800.0110.0110.0000.0000.0000.000
165A165TRP00.0440.01621.127-0.014-0.0140.0000.0000.0000.000
166A166ILE0-0.022-0.01916.304-0.002-0.0020.0000.0000.0000.000
167A167LEU0-0.011-0.01417.2140.0240.0240.0000.0000.0000.000
168A168HIS0-0.026-0.0138.7080.1010.1010.0000.0000.0000.000
169A169VAL00.0220.00512.9740.0720.0720.0000.0000.0000.000
170A170TYR0-0.025-0.0166.630-0.162-0.1620.0000.0000.0000.000
171A171THR00.0190.0017.9910.3910.3910.0000.0000.0000.000
172A172HIS0-0.045-0.0362.649-0.9070.5503.519-1.388-3.588-0.009
173A173VAL0-0.004-0.0043.392-0.0980.6200.024-0.182-0.559-0.001
174A174ALA0-0.038-0.0212.873-4.180-1.8770.680-1.374-1.609-0.012
175A175ASP-1-0.803-0.9102.835-0.5941.0680.398-0.903-1.157-0.011
176A176ALA00.0190.0044.878-0.380-0.3800.0000.0000.0000.000
177A177SER0-0.015-0.0096.186-0.198-0.1980.0000.0000.0000.000
178A178ASN0-0.0040.0128.461-0.122-0.1220.0000.0000.0000.000
179A179GLN00.0610.01210.258-0.036-0.0360.0000.0000.0000.000
180A180VAL0-0.008-0.00212.649-0.041-0.0410.0000.0000.0000.000
181A181ALA0-0.006-0.0038.8740.0020.0020.0000.0000.0000.000
182A182MET00.0310.0187.582-0.090-0.0900.0000.0000.0000.000
183A183ALA00.0020.00410.323-0.046-0.0460.0000.0000.0000.000
184A184LYS10.9310.96412.277-0.203-0.2030.0000.0000.0000.000
185A185ALA00.0610.0349.0810.0320.0320.0000.0000.0000.000
186A186GLU-1-0.742-0.86111.117-0.311-0.3110.0000.0000.0000.000
187A187ALA0-0.0170.00413.5570.0110.0110.0000.0000.0000.000
188A188ASN00.0110.01313.130-0.048-0.0480.0000.0000.0000.000
189A189LEU00.0430.03010.7790.0030.0030.0000.0000.0000.000
190A190THR0-0.065-0.03914.972-0.011-0.0110.0000.0000.0000.000
191A191LYS10.8400.92117.264-0.102-0.1020.0000.0000.0000.000
192A192VAL00.0400.01715.931-0.001-0.0010.0000.0000.0000.000
193A193LYS10.9160.97018.6220.1410.1410.0000.0000.0000.000
194A194THR00.003-0.01420.037-0.002-0.0020.0000.0000.0000.000
195A195LEU0-0.044-0.00521.8330.0010.0010.0000.0000.0000.000
196A196LEU00.0210.01218.9430.0020.0020.0000.0000.0000.000
197A197SER0-0.070-0.02823.051-0.012-0.0120.0000.0000.0000.000
198A198ALA0-0.0160.00025.079-0.005-0.0050.0000.0000.0000.000
199A199PHE0-0.020-0.01623.343-0.002-0.0020.0000.0000.0000.000
200A200CYS00.0460.01221.757-0.010-0.0100.0000.0000.0000.000
201A201ASP-1-0.831-0.88023.330-0.167-0.1670.0000.0000.0000.000
202A202LEU0-0.044-0.01617.258-0.019-0.0190.0000.0000.0000.000
203A203LYS10.8750.90318.7870.2420.2420.0000.0000.0000.000
204A204ASN00.0060.01115.418-0.104-0.1040.0000.0000.0000.000
205A205VAL00.0330.02815.6840.0440.0440.0000.0000.0000.000
206A206ARG10.8660.93615.0530.5170.5170.0000.0000.0000.000
207A207LEU00.0620.04010.7210.0320.0320.0000.0000.0000.000