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: 39YGL

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 OptH
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 -2281826.934087
FMO2-HF: Nuclear repulsion 2203604.702008
FMO2-HF: Total energy -78222.232078
FMO2-MP2: Total energy -78452.539146


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.
-1.1050.5340.016-0.626-1.0290.002
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 : -0.017 / q_NPA : -0.018
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].
3A4PRO00.0350.0173.5200.0911.7300.016-0.626-1.0290.002
4A5TYR0-0.040-0.0315.940-0.370-0.3700.0000.0000.0000.000
5A6VAL0-0.0010.0048.0580.1190.1190.0000.0000.0000.000
6A7ARG10.9560.98911.262-0.243-0.2430.0000.0000.0000.000
7A8LEU00.002-0.00213.7950.0210.0210.0000.0000.0000.000
8A9ASP-1-0.866-0.93017.5620.0950.0950.0000.0000.0000.000
9A10LYS10.9660.97619.501-0.051-0.0510.0000.0000.0000.000
10A11ASN0-0.056-0.03422.479-0.003-0.0030.0000.0000.0000.000
11A12ASP-1-0.835-0.92919.5720.0010.0010.0000.0000.0000.000
12A13ALA00.0080.01821.431-0.013-0.0130.0000.0000.0000.000
13A14ALA00.0360.01523.1590.0070.0070.0000.0000.0000.000
14A15VAL0-0.029-0.01225.127-0.009-0.0090.0000.0000.0000.000
15A16LEU0-0.011-0.01326.7830.0050.0050.0000.0000.0000.000
16A17LEU0-0.032-0.01928.875-0.005-0.0050.0000.0000.0000.000
17A18VAL0-0.008-0.02330.0380.0040.0040.0000.0000.0000.000
18A19ASP-1-0.666-0.81332.744-0.054-0.0540.0000.0000.0000.000
19A20HIS0-0.0010.03331.2690.0020.0020.0000.0000.0000.000
20A21GLN0-0.039-0.04636.4320.0010.0010.0000.0000.0000.000
21A22ALA0-0.016-0.01540.070-0.002-0.0020.0000.0000.0000.000
22A23GLY00.0250.02442.8840.0000.0000.0000.0000.0000.000
23A24LEU00.0060.00337.635-0.001-0.0010.0000.0000.0000.000
24A25LEU00.0090.00236.701-0.003-0.0030.0000.0000.0000.000
25A26SER0-0.093-0.03539.227-0.001-0.0010.0000.0000.0000.000
26A27LEU0-0.042-0.03038.3690.0000.0000.0000.0000.0000.000
27A28VAL0-0.072-0.00934.238-0.003-0.0030.0000.0000.0000.000
28A29ARG10.9120.94835.9550.0510.0510.0000.0000.0000.000
29A30ASP-1-0.820-0.90530.283-0.083-0.0830.0000.0000.0000.000
30A31ILE0-0.039-0.00429.294-0.003-0.0030.0000.0000.0000.000
31A32GLU-1-0.846-0.92033.492-0.044-0.0440.0000.0000.0000.000
32A33PRO00.0590.00436.202-0.001-0.0010.0000.0000.0000.000
33A34ASP-1-0.903-0.93338.174-0.037-0.0370.0000.0000.0000.000
34A35LYS10.8940.93731.0170.0610.0610.0000.0000.0000.000
35A36PHE00.003-0.00431.2520.0000.0000.0000.0000.0000.000
36A37LYS10.9971.00534.1150.0300.0300.0000.0000.0000.000
37A38ASN0-0.029-0.02233.0150.0050.0050.0000.0000.0000.000
38A39ASN0-0.008-0.01429.7910.0060.0060.0000.0000.0000.000
39A40VAL00.0180.01930.8600.0000.0000.0000.0000.0000.000
40A41LEU0-0.031-0.02932.7570.0020.0020.0000.0000.0000.000
41A42ALA0-0.0270.00430.4150.0030.0030.0000.0000.0000.000
42A43LEU00.0190.00226.6720.0030.0030.0000.0000.0000.000
43A44GLY00.0350.02029.6800.0030.0030.0000.0000.0000.000
44A45ASP-1-0.771-0.88232.612-0.018-0.0180.0000.0000.0000.000
45A46LEU0-0.044-0.01525.8330.0050.0050.0000.0000.0000.000
46A47ALA00.0030.01228.7190.0050.0050.0000.0000.0000.000
47A48LYS10.8520.92229.6930.0160.0160.0000.0000.0000.000
48A49TYR0-0.121-0.07228.5020.0040.0040.0000.0000.0000.000
49A50PHE0-0.042-0.03125.7230.0050.0050.0000.0000.0000.000
50A51ASN0-0.077-0.02928.6490.0020.0020.0000.0000.0000.000
51A52LEU00.0100.01425.2470.0020.0020.0000.0000.0000.000
52A53PRO0-0.0190.00227.904-0.003-0.0030.0000.0000.0000.000
53A54THR0-0.010-0.01629.324-0.005-0.0050.0000.0000.0000.000
54A55ILE0-0.0160.00430.2500.0030.0030.0000.0000.0000.000
55A56LEU0-0.0010.00932.653-0.004-0.0040.0000.0000.0000.000
56A57THR0-0.054-0.02533.6460.0000.0000.0000.0000.0000.000
57A58THR0-0.028-0.03936.479-0.002-0.0020.0000.0000.0000.000
58A59SER00.0080.01337.8950.0010.0010.0000.0000.0000.000
59A60ALA00.0310.00639.7960.0010.0010.0000.0000.0000.000
60A61GLU-1-0.810-0.88142.905-0.029-0.0290.0000.0000.0000.000
61A62THR0-0.064-0.01344.3790.0010.0010.0000.0000.0000.000
62A63GLY00.0340.00247.3680.0010.0010.0000.0000.0000.000
63A64PRO0-0.022-0.01945.9260.0000.0000.0000.0000.0000.000
64A65ASN00.0140.00741.0380.0000.0000.0000.0000.0000.000
65A66GLY00.0150.02242.978-0.001-0.0010.0000.0000.0000.000
66A67PRO00.0270.01643.496-0.001-0.0010.0000.0000.0000.000
67A68LEU00.0730.03337.352-0.001-0.0010.0000.0000.0000.000
68A69VAL0-0.005-0.00238.3630.0020.0020.0000.0000.0000.000
69A70PRO00.000-0.02740.8490.0000.0000.0000.0000.0000.000
70A71GLU-1-0.880-0.93539.358-0.027-0.0270.0000.0000.0000.000
71A72LEU00.0420.02134.9020.0020.0020.0000.0000.0000.000
72A73LYS10.8970.95538.3050.0270.0270.0000.0000.0000.000
73A74ALA0-0.031-0.01741.1390.0020.0020.0000.0000.0000.000
74A75GLN0-0.023-0.00835.8210.0000.0000.0000.0000.0000.000
75A76PHE0-0.065-0.03833.1430.0020.0020.0000.0000.0000.000
76A77PRO0-0.006-0.00238.275-0.001-0.0010.0000.0000.0000.000
77A78ASP-1-0.891-0.94339.805-0.009-0.0090.0000.0000.0000.000
78A79ALA0-0.083-0.02335.8100.0000.0000.0000.0000.0000.000
79A80PRO0-0.011-0.00735.0280.0000.0000.0000.0000.0000.000
80A81TYR0-0.011-0.02536.904-0.002-0.0020.0000.0000.0000.000
81A82ILE0-0.018-0.00535.9210.0010.0010.0000.0000.0000.000
82A83ALA00.0390.04138.726-0.003-0.0030.0000.0000.0000.000
83A84ARG10.7100.82135.7110.0510.0510.0000.0000.0000.000
84A85PRO00.001-0.01340.382-0.001-0.0010.0000.0000.0000.000
85A86GLY0-0.005-0.01341.4960.0010.0010.0000.0000.0000.000
86A87ASN0-0.0060.01036.444-0.002-0.0020.0000.0000.0000.000
87A88ILE00.0320.02834.3980.0000.0000.0000.0000.0000.000
88A89ASN00.0660.02729.287-0.002-0.0020.0000.0000.0000.000
89A90ALA00.026-0.00331.5040.0030.0030.0000.0000.0000.000
90A91TRP0-0.021-0.03626.4450.0030.0030.0000.0000.0000.000
91A92ASP-1-0.874-0.92631.091-0.060-0.0600.0000.0000.0000.000
92A93ASN0-0.113-0.05334.0990.0050.0050.0000.0000.0000.000
93A94GLU-1-0.869-0.95134.957-0.035-0.0350.0000.0000.0000.000
94A95ASP-1-0.926-0.95935.865-0.027-0.0270.0000.0000.0000.000
95A96PHE0-0.045-0.02929.7380.0010.0010.0000.0000.0000.000
96A97VAL00.0530.03529.8930.0010.0010.0000.0000.0000.000
97A98LYS10.9550.97231.4240.0240.0240.0000.0000.0000.000
98A99ALA0-0.0160.00332.9640.0030.0030.0000.0000.0000.000
99A100VAL00.0300.00027.3950.0030.0030.0000.0000.0000.000
100A101LYS10.8410.91427.4830.0550.0550.0000.0000.0000.000
101A102ALA0-0.049-0.01229.1440.0040.0040.0000.0000.0000.000
102A103THR0-0.069-0.03927.8760.0050.0050.0000.0000.0000.000
103A104GLY0-0.029-0.01727.0560.0060.0060.0000.0000.0000.000
104A105LYS10.7720.90923.8410.0020.0020.0000.0000.0000.000
105A106LYS10.9170.96717.0150.0830.0830.0000.0000.0000.000
106A107GLN00.0140.00316.295-0.017-0.0170.0000.0000.0000.000
107A108LEU00.0060.00620.4240.0120.0120.0000.0000.0000.000
108A109ILE00.0090.00621.664-0.014-0.0140.0000.0000.0000.000
109A110ILE0-0.008-0.00823.3330.0090.0090.0000.0000.0000.000
110A111ALA00.0050.00125.175-0.008-0.0080.0000.0000.0000.000
111A112GLY00.0580.00327.9340.0050.0050.0000.0000.0000.000
112A113VAL0-0.072-0.00930.991-0.004-0.0040.0000.0000.0000.000
113A114VAL00.0300.01032.5590.0030.0030.0000.0000.0000.000
114A115THR00.045-0.01926.4650.0000.0000.0000.0000.0000.000
115A116GLU-1-0.770-0.87927.788-0.087-0.0870.0000.0000.0000.000
116A117VAL0-0.051-0.01728.868-0.001-0.0010.0000.0000.0000.000
117A118CYS0-0.048-0.04030.130-0.002-0.0020.0000.0000.0000.000
118A119VAL0-0.0050.02525.2210.0010.0010.0000.0000.0000.000
119A120ALA00.023-0.01824.883-0.004-0.0040.0000.0000.0000.000
120A121PHE0-0.044-0.01425.289-0.005-0.0050.0000.0000.0000.000
121A122PRO00.0300.02126.751-0.003-0.0030.0000.0000.0000.000
122A123ALA00.0120.01122.160-0.002-0.0020.0000.0000.0000.000
123A124LEU0-0.022-0.02621.369-0.009-0.0090.0000.0000.0000.000
124A125SER00.0080.01122.885-0.001-0.0010.0000.0000.0000.000
125A126ALA00.0250.01523.1720.0010.0010.0000.0000.0000.000
126A127ILE0-0.023-0.01317.5870.0020.0020.0000.0000.0000.000
127A128GLU-1-0.991-0.98119.847-0.110-0.1100.0000.0000.0000.000
128A129GLU-1-0.848-0.91321.984-0.062-0.0620.0000.0000.0000.000
129A130GLY0-0.027-0.00119.3550.0100.0100.0000.0000.0000.000
130A131PHE0-0.077-0.04119.0080.0060.0060.0000.0000.0000.000
131A132ASP-1-0.907-0.94215.418-0.173-0.1730.0000.0000.0000.000
132A133VAL0-0.014-0.01817.6050.0240.0240.0000.0000.0000.000
133A134PHE0-0.008-0.01015.115-0.028-0.0280.0000.0000.0000.000
134A135VAL00.0200.00319.3330.0190.0190.0000.0000.0000.000
135A136VAL00.0060.00321.426-0.007-0.0070.0000.0000.0000.000
136A137THR0-0.044-0.03821.8870.0080.0080.0000.0000.0000.000
137A138ASP-1-0.823-0.91124.657-0.078-0.0780.0000.0000.0000.000
138A139ALA00.0110.00627.2110.0080.0080.0000.0000.0000.000
139A140SER0-0.008-0.01127.0110.0050.0050.0000.0000.0000.000
140A141GLY00.0050.01929.353-0.002-0.0020.0000.0000.0000.000
141A142THR0-0.056-0.05630.2020.0020.0020.0000.0000.0000.000
142A143PHE00.0480.02733.0080.0030.0030.0000.0000.0000.000
143A144ASN00.001-0.01133.337-0.001-0.0010.0000.0000.0000.000
144A145GLU-1-0.838-0.94429.668-0.094-0.0940.0000.0000.0000.000
145A146ILE0-0.0120.01728.788-0.008-0.0080.0000.0000.0000.000
146A147THR0-0.016-0.02728.976-0.006-0.0060.0000.0000.0000.000
147A148ARG10.8850.95326.2140.0970.0970.0000.0000.0000.000
148A149HIS0-0.001-0.01424.531-0.011-0.0110.0000.0000.0000.000
149A150SER0-0.0030.00823.861-0.012-0.0120.0000.0000.0000.000
150A151ALA00.0070.01024.280-0.008-0.0080.0000.0000.0000.000
151A152TRP0-0.006-0.01720.908-0.011-0.0110.0000.0000.0000.000
152A153ASP-1-0.945-0.95619.745-0.211-0.2110.0000.0000.0000.000
153A154ARG10.9770.98419.4220.1020.1020.0000.0000.0000.000
154A155MET0-0.022-0.00720.185-0.003-0.0030.0000.0000.0000.000
155A156SER0-0.0080.00315.431-0.025-0.0250.0000.0000.0000.000
156A157GLN0-0.051-0.01515.099-0.024-0.0240.0000.0000.0000.000
157A158ALA0-0.034-0.02115.899-0.017-0.0170.0000.0000.0000.000
158A159GLY0-0.0040.00313.697-0.005-0.0050.0000.0000.0000.000
159A160ALA0-0.029-0.00414.5640.0000.0000.0000.0000.0000.000
160A161GLN0-0.054-0.03212.586-0.052-0.0520.0000.0000.0000.000
161A162LEU0-0.036-0.01615.6680.0370.0370.0000.0000.0000.000
162A163MET00.0100.01217.021-0.010-0.0100.0000.0000.0000.000
163A164THR0-0.0050.00019.5040.0050.0050.0000.0000.0000.000
164A165TRP00.0460.00722.3840.0060.0060.0000.0000.0000.000
165A166PHE00.0100.01123.2200.0060.0060.0000.0000.0000.000
166A167GLY00.0360.01420.2150.0080.0080.0000.0000.0000.000
167A168VAL00.0150.00320.0080.0090.0090.0000.0000.0000.000
168A169ALA00.008-0.00121.4060.0130.0130.0000.0000.0000.000
169A170CYS0-0.031-0.01720.7230.0130.0130.0000.0000.0000.000
170A171GLU-1-0.829-0.89114.925-0.050-0.0500.0000.0000.0000.000
171A172LEU0-0.0090.00618.7330.0230.0230.0000.0000.0000.000
172A173HIS00.0090.00621.4090.0120.0120.0000.0000.0000.000
173A174ARG10.7870.90516.890-0.075-0.0750.0000.0000.0000.000
174A175ASP-1-0.828-0.92320.7830.0770.0770.0000.0000.0000.000
175A176TRP00.0580.02323.675-0.004-0.0040.0000.0000.0000.000
176A177ARG10.8200.87924.582-0.076-0.0760.0000.0000.0000.000
177A178ASN0-0.061-0.01424.1910.0040.0040.0000.0000.0000.000
178A179ASP-1-0.809-0.89728.4750.0120.0120.0000.0000.0000.000
179A180ILE0-0.0040.00830.420-0.004-0.0040.0000.0000.0000.000
180A181ALA00.0410.01631.720-0.004-0.0040.0000.0000.0000.000
181A182GLY00.0400.03632.983-0.004-0.0040.0000.0000.0000.000
182A183LEU00.0130.00925.914-0.005-0.0050.0000.0000.0000.000
183A184ALA00.005-0.00630.301-0.005-0.0050.0000.0000.0000.000
184A185THR0-0.018-0.00932.495-0.004-0.0040.0000.0000.0000.000
185A186LEU0-0.0160.00528.579-0.003-0.0030.0000.0000.0000.000
186A187PHE00.005-0.02425.641-0.005-0.0050.0000.0000.0000.000
187A188SER00.017-0.00131.458-0.004-0.0040.0000.0000.0000.000
188A189ASN0-0.064-0.04235.051-0.001-0.0010.0000.0000.0000.000
189A190HIS10.7760.88632.0210.0280.0280.0000.0000.0000.000
190A191ILE00.0230.03728.866-0.005-0.0050.0000.0000.0000.000
191A192PRO00.0310.01033.0420.0030.0030.0000.0000.0000.000
192A193ASP-1-0.874-0.93732.849-0.038-0.0380.0000.0000.0000.000
193A194TYR00.005-0.00830.1490.0020.0020.0000.0000.0000.000
194A195ARG10.9600.98333.4810.0220.0220.0000.0000.0000.000
195A196ASN0-0.010-0.00436.8040.0040.0040.0000.0000.0000.000
196A197LEU0-0.026-0.00932.5530.0020.0020.0000.0000.0000.000
197A198MET0-0.0070.00135.1650.0020.0020.0000.0000.0000.000
198A199THR0-0.0010.01637.5420.0020.0020.0000.0000.0000.000
199A200SER0-0.021-0.01639.7930.0010.0010.0000.0000.0000.000
200A201TYR0-0.020-0.01037.5360.0020.0020.0000.0000.0000.000
201A202ASP-1-0.878-0.94539.7660.0000.0000.0000.0000.0000.000
202A203THR0-0.150-0.06241.8650.0010.0010.0000.0000.0000.000
203A204LEU0-0.031-0.01842.0140.0010.0010.0000.0000.0000.000
204A205THR0-0.090-0.03140.3050.0020.0020.0000.0000.0000.000