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: 94JQ2

Calculation Name: 1YAC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YAC

Chain ID: A

ChEMBL ID:

UniProt ID: P21367

Base Structure: X-ray

Registration Date: 2023-09-20

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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2286904.457661
FMO2-HF: Nuclear repulsion 2208681.366469
FMO2-HF: Total energy -78223.091192
FMO2-MP2: Total energy -78453.331595


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:2:THR)


Summations of interaction energy for fragment #1(A:2:THR)
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.
-1.525-0.2990.004-0.465-0.7660
Interaction energy analysis for fragmet #1(A:2:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / q_NPA : -0.014
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].
3A4PRO00.0280.0173.742-1.758-0.5320.004-0.465-0.7660.000
4A5TYR0-0.046-0.0416.0980.5520.5520.0000.0000.0000.000
5A6VAL0-0.0090.0048.0460.2060.2060.0000.0000.0000.000
6A7ARG10.9590.98911.1680.9830.9830.0000.0000.0000.000
7A8LEU00.0450.03213.6990.0360.0360.0000.0000.0000.000
8A9ASP-1-0.816-0.89517.460-0.489-0.4890.0000.0000.0000.000
9A10LYS10.8960.94819.5950.3270.3270.0000.0000.0000.000
10A11ASN0-0.015-0.00422.5400.0260.0260.0000.0000.0000.000
11A12ASP-1-0.872-0.94120.002-0.292-0.2920.0000.0000.0000.000
12A13ALA00.0210.03321.067-0.007-0.0070.0000.0000.0000.000
13A14ALA00.0280.01522.8160.0200.0200.0000.0000.0000.000
14A15VAL0-0.039-0.02324.919-0.015-0.0150.0000.0000.0000.000
15A16LEU0-0.005-0.00526.6450.0180.0180.0000.0000.0000.000
16A17LEU0-0.017-0.01028.755-0.004-0.0040.0000.0000.0000.000
17A18VAL00.001-0.01129.9660.0090.0090.0000.0000.0000.000
18A19ASP-1-0.716-0.83232.653-0.080-0.0800.0000.0000.0000.000
19A20HIS0-0.0010.01131.0470.0080.0080.0000.0000.0000.000
20A21GLN0-0.031-0.03336.177-0.002-0.0020.0000.0000.0000.000
21A22ALA0-0.029-0.01939.8610.0010.0010.0000.0000.0000.000
22A23GLY00.0200.02242.7420.0010.0010.0000.0000.0000.000
23A24LEU00.0020.01137.6010.0020.0020.0000.0000.0000.000
24A25LEU00.0160.00736.537-0.002-0.0020.0000.0000.0000.000
25A26SER0-0.075-0.02838.8840.0010.0010.0000.0000.0000.000
26A27LEU0-0.008-0.01737.7920.0040.0040.0000.0000.0000.000
27A28VAL0-0.059-0.00633.7100.0010.0010.0000.0000.0000.000
28A29ARG10.8160.89335.2480.0530.0530.0000.0000.0000.000
29A30ASP-1-0.790-0.87729.934-0.089-0.0890.0000.0000.0000.000
30A31ILE0-0.0200.00828.683-0.004-0.0040.0000.0000.0000.000
31A32GLU-1-0.812-0.89032.972-0.083-0.0830.0000.0000.0000.000
32A33PRO00.0600.01135.635-0.006-0.0060.0000.0000.0000.000
33A34ASP-1-0.888-0.93537.782-0.076-0.0760.0000.0000.0000.000
34A35LYS10.8490.90631.2720.0930.0930.0000.0000.0000.000
35A36PHE00.0270.01431.304-0.008-0.0080.0000.0000.0000.000
36A37LYS10.9100.94833.6970.0760.0760.0000.0000.0000.000
37A38ASN0-0.033-0.02032.430-0.002-0.0020.0000.0000.0000.000
38A39ASN0-0.001-0.00629.388-0.005-0.0050.0000.0000.0000.000
39A40VAL00.0040.00830.637-0.010-0.0100.0000.0000.0000.000
40A41LEU0-0.034-0.02332.587-0.003-0.0030.0000.0000.0000.000
41A42ALA0-0.0170.00430.272-0.003-0.0030.0000.0000.0000.000
42A43LEU00.013-0.00326.485-0.012-0.0120.0000.0000.0000.000
43A44GLY00.0340.02129.533-0.007-0.0070.0000.0000.0000.000
44A45ASP-1-0.809-0.89632.639-0.133-0.1330.0000.0000.0000.000
45A46LEU0-0.050-0.01925.604-0.005-0.0050.0000.0000.0000.000
46A47ALA0-0.0030.00428.659-0.010-0.0100.0000.0000.0000.000
47A48LYS10.8380.92029.6050.1280.1280.0000.0000.0000.000
48A49TYR0-0.088-0.06428.481-0.002-0.0020.0000.0000.0000.000
49A50PHE0-0.038-0.03525.742-0.004-0.0040.0000.0000.0000.000
50A51ASN0-0.067-0.03028.6650.0030.0030.0000.0000.0000.000
51A52LEU00.0180.03324.904-0.001-0.0010.0000.0000.0000.000
52A53PRO00.0010.00427.6780.0150.0150.0000.0000.0000.000
53A54THR0-0.018-0.01129.110-0.011-0.0110.0000.0000.0000.000
54A55ILE0-0.027-0.01230.6310.0100.0100.0000.0000.0000.000
55A56LEU0-0.0010.00832.626-0.004-0.0040.0000.0000.0000.000
56A57THR0-0.043-0.02733.4320.0060.0060.0000.0000.0000.000
57A58THR0-0.003-0.02136.239-0.002-0.0020.0000.0000.0000.000
58A59SER00.0360.03337.7160.0040.0040.0000.0000.0000.000
59A60ALA00.0190.00639.5420.0010.0010.0000.0000.0000.000
60A61GLU-1-0.725-0.81642.520-0.068-0.0680.0000.0000.0000.000
61A62THR0-0.071-0.01944.0280.0000.0000.0000.0000.0000.000
62A63GLY00.0360.00747.0250.0030.0030.0000.0000.0000.000
63A64PRO0-0.018-0.01845.989-0.002-0.0020.0000.0000.0000.000
64A65ASN00.0110.00041.3930.0010.0010.0000.0000.0000.000
65A66GLY00.0230.02442.627-0.003-0.0030.0000.0000.0000.000
66A67PRO00.0400.01043.220-0.002-0.0020.0000.0000.0000.000
67A68LEU00.0180.00636.7460.0000.0000.0000.0000.0000.000
68A69VAL0-0.027-0.01138.1280.0030.0030.0000.0000.0000.000
69A70PRO00.005-0.01040.845-0.003-0.0030.0000.0000.0000.000
70A71GLU-1-0.822-0.90239.407-0.086-0.0860.0000.0000.0000.000
71A72LEU00.0400.01534.455-0.002-0.0020.0000.0000.0000.000
72A73LYS10.8400.92338.0610.0700.0700.0000.0000.0000.000
73A74ALA0-0.014-0.00540.9220.0010.0010.0000.0000.0000.000
74A75GLN0-0.027-0.00835.694-0.002-0.0020.0000.0000.0000.000
75A76PHE0-0.035-0.03132.826-0.006-0.0060.0000.0000.0000.000
76A77PRO00.0140.02038.2700.0010.0010.0000.0000.0000.000
77A78ASP-1-0.915-0.96339.138-0.094-0.0940.0000.0000.0000.000
78A79ALA0-0.045-0.00635.787-0.003-0.0030.0000.0000.0000.000
79A80PRO0-0.014-0.01134.8670.0070.0070.0000.0000.0000.000
80A81TYR0-0.005-0.03536.529-0.005-0.0050.0000.0000.0000.000
81A82ILE0-0.028-0.01535.3920.0050.0050.0000.0000.0000.000
82A83ALA00.0150.02838.339-0.002-0.0020.0000.0000.0000.000
83A84ARG10.7330.82035.3980.0810.0810.0000.0000.0000.000
84A85PRO0-0.029-0.03540.2720.0010.0010.0000.0000.0000.000
85A86GLY00.0070.00141.2620.0030.0030.0000.0000.0000.000
86A87ASN0-0.076-0.03436.8620.0030.0030.0000.0000.0000.000
87A88ILE00.0540.04034.382-0.005-0.0050.0000.0000.0000.000
88A89ASN00.0310.00429.500-0.013-0.0130.0000.0000.0000.000
89A90ALA00.0320.01131.0340.0030.0030.0000.0000.0000.000
90A91TRP0-0.028-0.03626.019-0.005-0.0050.0000.0000.0000.000
91A92ASP-1-0.854-0.90930.983-0.055-0.0550.0000.0000.0000.000
92A93ASN0-0.042-0.01833.9930.0030.0030.0000.0000.0000.000
93A94GLU-1-0.866-0.93934.903-0.058-0.0580.0000.0000.0000.000
94A95ASP-1-0.844-0.90835.743-0.072-0.0720.0000.0000.0000.000
95A96PHE00.0110.00329.632-0.006-0.0060.0000.0000.0000.000
96A97VAL00.0360.01930.245-0.009-0.0090.0000.0000.0000.000
97A98LYS10.8220.89331.5110.0610.0610.0000.0000.0000.000
98A99ALA0-0.0020.00333.307-0.005-0.0050.0000.0000.0000.000
99A100VAL00.016-0.00127.369-0.008-0.0080.0000.0000.0000.000
100A101LYS10.8220.90027.9200.0870.0870.0000.0000.0000.000
101A102ALA0-0.039-0.01429.635-0.005-0.0050.0000.0000.0000.000
102A103THR0-0.059-0.03627.891-0.007-0.0070.0000.0000.0000.000
103A104GLY0-0.0080.00327.414-0.008-0.0080.0000.0000.0000.000
104A105LYS10.7330.86323.9040.2320.2320.0000.0000.0000.000
105A106LYS10.8450.91716.5190.3730.3730.0000.0000.0000.000
106A107GLN0-0.027-0.02615.9830.0220.0220.0000.0000.0000.000
107A108LEU00.0150.00120.4460.0290.0290.0000.0000.0000.000
108A109ILE00.0220.01521.755-0.011-0.0110.0000.0000.0000.000
109A110ILE0-0.019-0.00723.2500.0250.0250.0000.0000.0000.000
110A111ALA00.0050.00224.902-0.008-0.0080.0000.0000.0000.000
111A112GLY00.0620.01027.6870.0060.0060.0000.0000.0000.000
112A113VAL0-0.065-0.01530.438-0.001-0.0010.0000.0000.0000.000
113A114VAL00.0100.01432.5820.0030.0030.0000.0000.0000.000
114A115THR00.058-0.00826.093-0.001-0.0010.0000.0000.0000.000
115A116GLU-1-0.768-0.87827.530-0.075-0.0750.0000.0000.0000.000
116A117VAL0-0.051-0.03128.6610.0060.0060.0000.0000.0000.000
117A118CYS0-0.037-0.02529.631-0.002-0.0020.0000.0000.0000.000
118A119VAL0-0.0010.02224.817-0.007-0.0070.0000.0000.0000.000
119A120ALA00.033-0.01324.506-0.008-0.0080.0000.0000.0000.000
120A121PHE0-0.041-0.01324.9920.0010.0010.0000.0000.0000.000
121A122PRO00.0190.02026.6410.0000.0000.0000.0000.0000.000
122A123ALA00.0050.00321.866-0.010-0.0100.0000.0000.0000.000
123A124LEU0-0.018-0.01021.189-0.010-0.0100.0000.0000.0000.000
124A125SER00.0410.01422.8810.0000.0000.0000.0000.0000.000
125A126ALA00.0060.01123.0890.0010.0010.0000.0000.0000.000
126A127ILE0-0.025-0.01417.662-0.013-0.0130.0000.0000.0000.000
127A128GLU-1-1.007-0.98820.014-0.055-0.0550.0000.0000.0000.000
128A129GLU-1-0.834-0.89022.374-0.087-0.0870.0000.0000.0000.000
129A130GLY0-0.0130.00619.278-0.003-0.0030.0000.0000.0000.000
130A131PHE0-0.029-0.02319.063-0.033-0.0330.0000.0000.0000.000
131A132ASP-1-0.871-0.92415.745-0.476-0.4760.0000.0000.0000.000
132A133VAL0-0.006-0.00417.7090.0080.0080.0000.0000.0000.000
133A134PHE0-0.020-0.02214.949-0.029-0.0290.0000.0000.0000.000
134A135VAL00.0150.00619.3260.0310.0310.0000.0000.0000.000
135A136VAL00.0290.00921.220-0.013-0.0130.0000.0000.0000.000
136A137THR0-0.076-0.05921.1660.0280.0280.0000.0000.0000.000
137A138ASP-1-0.805-0.90724.077-0.173-0.1730.0000.0000.0000.000
138A139ALA00.0090.00927.0060.0100.0100.0000.0000.0000.000
139A140SER00.004-0.01226.6620.0050.0050.0000.0000.0000.000
140A141GLY00.0110.01428.965-0.001-0.0010.0000.0000.0000.000
141A142THR0-0.079-0.06829.8030.0050.0050.0000.0000.0000.000
142A143PHE00.0760.04132.7930.0010.0010.0000.0000.0000.000
143A144ASN0-0.010-0.01432.8600.0030.0030.0000.0000.0000.000
144A145GLU-1-0.771-0.88529.155-0.074-0.0740.0000.0000.0000.000
145A146ILE00.0000.01528.358-0.004-0.0040.0000.0000.0000.000
146A147THR0-0.017-0.01128.4380.0000.0000.0000.0000.0000.000
147A148ARG10.8140.87425.6600.0890.0890.0000.0000.0000.000
148A149HIS0-0.026-0.01024.133-0.018-0.0180.0000.0000.0000.000
149A150SER0-0.004-0.01223.4480.0020.0020.0000.0000.0000.000
150A151ALA0-0.024-0.00224.1570.0000.0000.0000.0000.0000.000
151A152TRP0-0.003-0.01820.618-0.012-0.0120.0000.0000.0000.000
152A153ASP-1-0.879-0.91819.342-0.054-0.0540.0000.0000.0000.000
153A154ARG10.9410.97019.2230.0490.0490.0000.0000.0000.000
154A155MET0-0.0220.00620.045-0.004-0.0040.0000.0000.0000.000
155A156SER00.0170.00514.470-0.028-0.0280.0000.0000.0000.000
156A157GLN0-0.139-0.06914.806-0.009-0.0090.0000.0000.0000.000
157A158ALA0-0.011-0.00215.9850.0180.0180.0000.0000.0000.000
158A159GLY0-0.016-0.00613.412-0.012-0.0120.0000.0000.0000.000
159A160ALA0-0.012-0.00214.236-0.066-0.0660.0000.0000.0000.000
160A161GLN0-0.060-0.03311.905-0.091-0.0910.0000.0000.0000.000
161A162LEU0-0.014-0.00515.4720.0270.0270.0000.0000.0000.000
162A163MET0-0.0130.01016.388-0.032-0.0320.0000.0000.0000.000
163A164THR00.0130.02319.4360.0260.0260.0000.0000.0000.000
164A165TRP00.024-0.00422.313-0.031-0.0310.0000.0000.0000.000
165A166PHE00.0150.01523.263-0.013-0.0130.0000.0000.0000.000
166A167GLY00.0320.02020.036-0.013-0.0130.0000.0000.0000.000
167A168VAL00.015-0.00119.945-0.036-0.0360.0000.0000.0000.000
168A169ALA00.0070.00021.266-0.015-0.0150.0000.0000.0000.000
169A170CYS0-0.052-0.02620.6320.0010.0010.0000.0000.0000.000
170A171GLU-1-0.834-0.89714.715-0.701-0.7010.0000.0000.0000.000
171A172LEU00.0030.01218.789-0.030-0.0300.0000.0000.0000.000
172A173HIS0-0.008-0.01621.475-0.007-0.0070.0000.0000.0000.000
173A174ARG10.7140.83817.2830.5270.5270.0000.0000.0000.000
174A175ASP-1-0.815-0.89220.621-0.309-0.3090.0000.0000.0000.000
175A176TRP00.0740.03323.4010.0180.0180.0000.0000.0000.000
176A177ARG10.8240.87624.2850.2870.2870.0000.0000.0000.000
177A178ASN0-0.065-0.02124.3480.0110.0110.0000.0000.0000.000
178A179ASP-1-0.767-0.86228.268-0.158-0.1580.0000.0000.0000.000
179A180ILE00.0080.01730.161-0.008-0.0080.0000.0000.0000.000
180A181ALA00.0310.02231.7560.0020.0020.0000.0000.0000.000
181A182GLY00.0410.02633.1290.0060.0060.0000.0000.0000.000
182A183LEU0-0.0030.00625.9170.0020.0020.0000.0000.0000.000
183A184ALA00.0110.00630.2920.0020.0020.0000.0000.0000.000
184A185THR0-0.023-0.02432.5230.0100.0100.0000.0000.0000.000
185A186LEU0-0.021-0.00228.5170.0070.0070.0000.0000.0000.000
186A187PHE00.008-0.01825.4700.0040.0040.0000.0000.0000.000
187A188SER00.0110.01131.3920.0100.0100.0000.0000.0000.000
188A189ASN0-0.022-0.01435.0590.0130.0130.0000.0000.0000.000
189A190HIS10.7750.87931.9970.1360.1360.0000.0000.0000.000
190A191ILE00.0250.02828.368-0.002-0.0020.0000.0000.0000.000
191A192PRO00.0420.01732.8870.0000.0000.0000.0000.0000.000
192A193ASP-1-0.875-0.93732.923-0.105-0.1050.0000.0000.0000.000
193A194TYR00.0180.00029.844-0.003-0.0030.0000.0000.0000.000
194A195ARG10.9130.94933.5460.1080.1080.0000.0000.0000.000
195A196ASN0-0.0090.00837.0810.0060.0060.0000.0000.0000.000
196A197LEU0-0.0160.00132.5370.0040.0040.0000.0000.0000.000
197A198MET0-0.0170.00434.986-0.001-0.0010.0000.0000.0000.000
198A199THR00.0190.00237.3530.0040.0040.0000.0000.0000.000
199A200SER0-0.037-0.01639.3100.0060.0060.0000.0000.0000.000
200A201TYR0-0.011-0.00237.5080.0020.0020.0000.0000.0000.000
201A202ASP-1-0.858-0.92639.632-0.104-0.1040.0000.0000.0000.000
202A203THR0-0.109-0.06441.7200.0050.0050.0000.0000.0000.000
203A204LEU0-0.052-0.01141.8620.0050.0050.0000.0000.0000.000
204A205THR0-0.136-0.08440.5210.0010.0010.0000.0000.0000.000