Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: JM8G9

Calculation Name: 1Y0K-A-Xray316

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Y0K

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HVP2

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 182
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1995474.011563
FMO2-HF: Nuclear repulsion 1924332.922044
FMO2-HF: Total energy -71141.089519
FMO2-MP2: Total energy -71352.580786


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.
-8.436-3.486.541-2.567-8.931-0.011
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 : 0.006 / q_NPA : -0.003
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 -1-0.833-0.9392.488-4.769-2.3551.171-1.487-2.098-0.012
4A4ALA 0-0.028-0.0104.9840.7730.9640.000-0.010-0.1810.000
5A5ASP -1-0.810-0.9132.9690.0050.7810.213-0.203-0.7860.000
6A6TYR 00.0130.0092.519-0.6991.4204.555-2.369-4.3060.003
7A7LEU 00.0150.0033.5451.144-0.2960.0601.775-0.395-0.001
8A8ARG 10.8850.9406.468-0.580-0.5800.0000.0000.0000.000
9A9LEU 0-0.033-0.0022.601-1.438-0.5590.542-0.269-1.152-0.001
10A10LEU 00.004-0.0066.211-0.771-0.7540.000-0.004-0.0130.000
11A11THR 0-0.031-0.0258.672-0.351-0.3510.0000.0000.0000.000
12A12ARG 10.9790.9925.352-1.174-1.1740.0000.0000.0000.000
13A13GLN 00.0300.0299.721-0.145-0.1450.0000.0000.0000.000
14A14ALA 00.0160.00611.452-0.102-0.1020.0000.0000.0000.000
15A15GLU -1-0.897-0.97114.1740.2850.2850.0000.0000.0000.000
16A16GLN 00.0260.01611.701-0.013-0.0130.0000.0000.0000.000
17A17ALA 00.0060.01315.711-0.041-0.0410.0000.0000.0000.000
18A18ASN 00.020-0.00317.731-0.037-0.0370.0000.0000.0000.000
19A19ASP -1-0.901-0.94418.4390.1490.1490.0000.0000.0000.000
20A20PHE 0-0.038-0.02019.878-0.020-0.0200.0000.0000.0000.000
21A21LEU 0-0.035-0.02421.654-0.017-0.0170.0000.0000.0000.000
22A22SER 0-0.091-0.04123.526-0.014-0.0140.0000.0000.0000.000
23A23ASN 00.0080.00623.896-0.014-0.0140.0000.0000.0000.000
24A24ALA 0-0.0250.01825.775-0.008-0.0080.0000.0000.0000.000
25A25ARG 10.9610.96327.611-0.040-0.0400.0000.0000.0000.000
26A26LYS 10.8960.93830.271-0.031-0.0310.0000.0000.0000.000
27A27TRP 00.0380.01131.3740.0030.0030.0000.0000.0000.000
28A28ASP -1-0.866-0.92828.0800.0430.0430.0000.0000.0000.000
29A29ARG 10.9450.98526.103-0.059-0.0590.0000.0000.0000.000
30A30GLU -1-0.824-0.92226.9460.0400.0400.0000.0000.0000.000
31A31ARG 10.8310.90627.709-0.033-0.0330.0000.0000.0000.000
32A32TRP 0-0.003-0.00119.410-0.003-0.0030.0000.0000.0000.000
33A33VAL 00.0150.00824.0950.0020.0020.0000.0000.0000.000
34A34CYS 0-0.036-0.01324.934-0.003-0.0030.0000.0000.0000.000
35A35GLN 00.0230.01325.191-0.002-0.0020.0000.0000.0000.000
36A36ARG 10.8780.93919.627-0.058-0.0580.0000.0000.0000.000
37A37PHE 0-0.014-0.01021.951-0.004-0.0040.0000.0000.0000.000
38A38LEU 0-0.011-0.01324.143-0.007-0.0070.0000.0000.0000.000
39A39GLU -1-0.769-0.84621.3450.0220.0220.0000.0000.0000.000
40A40ALA 0-0.010-0.00420.571-0.007-0.0070.0000.0000.0000.000
41A41LEU 0-0.118-0.04721.526-0.012-0.0120.0000.0000.0000.000
42A42ASN 0-0.043-0.00824.018-0.004-0.0040.0000.0000.0000.000
43A43VAL 0-0.023-0.00625.325-0.004-0.0040.0000.0000.0000.000
44A44PRO 0-0.001-0.00728.2390.0040.0040.0000.0000.0000.000
45A45TYR 0-0.081-0.06624.8510.0020.0020.0000.0000.0000.000
46A46ARG 10.8650.90630.7940.0010.0010.0000.0000.0000.000
47A47GLN 0-0.014-0.01229.5840.0000.0000.0000.0000.0000.000
48A48GLU -1-0.830-0.91132.8240.0050.0050.0000.0000.0000.000
49A49ASP -1-0.869-0.92733.9410.0010.0010.0000.0000.0000.000
50A50PHE 0-0.083-0.03029.4500.0010.0010.0000.0000.0000.000
51A51ALA 00.0230.01134.8910.0000.0000.0000.0000.0000.000
52A52ALA 00.0030.00437.2210.0010.0010.0000.0000.0000.000
53A53PRO 0-0.0170.00238.637-0.002-0.0020.0000.0000.0000.000
54A54GLY 0-0.021-0.01341.6300.0010.0010.0000.0000.0000.000
55A55GLU -1-0.942-0.96844.3100.0130.0130.0000.0000.0000.000
56A56GLN 0-0.0370.01338.5940.0020.0020.0000.0000.0000.000
57A57PRO 0-0.049-0.01239.0930.0000.0000.0000.0000.0000.000
58A58PRO 00.004-0.00536.787-0.002-0.0020.0000.0000.0000.000
59A59ASP -1-0.825-0.92433.8590.0280.0280.0000.0000.0000.000
60A60VAL 0-0.056-0.03531.7900.0000.0000.0000.0000.0000.000
61A61LEU 0-0.0110.00034.913-0.001-0.0010.0000.0000.0000.000
62A62PHE 00.0330.00032.2760.0010.0010.0000.0000.0000.000
63A63LYS 10.9080.96634.4470.0020.0020.0000.0000.0000.000
64A64GLY 00.0160.01537.597-0.002-0.0020.0000.0000.0000.000
65A65ALA 0-0.021-0.01634.5910.0000.0000.0000.0000.0000.000
66A66GLY 00.0480.01436.5950.0010.0010.0000.0000.0000.000
67A67PHE 0-0.013-0.02130.9500.0000.0000.0000.0000.0000.000
68A68GLU -1-0.694-0.78033.9020.0240.0240.0000.0000.0000.000
69A69VAL 0-0.045-0.02928.3630.0010.0010.0000.0000.0000.000
70A70PHE 0-0.038-0.03529.0520.0010.0010.0000.0000.0000.000
71A71PHE 00.0300.00824.6510.0030.0030.0000.0000.0000.000
72A72VAL 0-0.041-0.01624.007-0.006-0.0060.0000.0000.0000.000
73A73LEU 00.0270.00921.8010.0120.0120.0000.0000.0000.000
74A74ASP -1-0.834-0.92819.9900.1440.1440.0000.0000.0000.000
75A75GLU -1-0.843-0.93319.6620.1790.1790.0000.0000.0000.000
76A76NME 0-0.0090.00721.408-0.004-0.0040.0000.0000.0000.000
77A104ACE 00.0220.00017.161-0.006-0.0060.0000.0000.0000.000
78A105ARG 10.8970.92210.037-0.034-0.0340.0000.0000.0000.000
79A106PRO 00.0060.04510.950-0.061-0.0610.0000.0000.0000.000
80A107GLN 00.0290.01912.978-0.031-0.0310.0000.0000.0000.000
81A108ARG 10.9060.9369.3970.0260.0260.0000.0000.0000.000
82A109ILE 0-0.049-0.01015.287-0.018-0.0180.0000.0000.0000.000
83A110ALA 00.0950.04118.772-0.002-0.0020.0000.0000.0000.000
84A111ALA 00.0280.01320.9720.0180.0180.0000.0000.0000.000
85A112ALA 00.003-0.00722.3670.0100.0100.0000.0000.0000.000
86A113GLU -1-0.873-0.95123.101-0.013-0.0130.0000.0000.0000.000
87A114LEU 0-0.037-0.01619.5700.0100.0100.0000.0000.0000.000
88A115GLN 00.018-0.00222.9630.0070.0070.0000.0000.0000.000
89A116ALA 00.0080.01926.0050.0020.0020.0000.0000.0000.000
90A117ARG 10.9160.96222.182-0.059-0.0590.0000.0000.0000.000
91A118LEU 00.0180.00625.4300.0050.0050.0000.0000.0000.000
92A119ALA 0-0.0040.01328.641-0.001-0.0010.0000.0000.0000.000
93A120PRO 0-0.025-0.01430.246-0.002-0.0020.0000.0000.0000.000
94A121THR 00.0260.00130.516-0.002-0.0020.0000.0000.0000.000
95A122LEU 00.0310.02531.200-0.002-0.0020.0000.0000.0000.000
96A123ARG 10.8250.88134.232-0.014-0.0140.0000.0000.0000.000
97A124LYS 10.9340.97335.543-0.027-0.0270.0000.0000.0000.000
98A125LYS 10.8680.93333.661-0.028-0.0280.0000.0000.0000.000
99A126ALA 00.0450.02838.193-0.001-0.0010.0000.0000.0000.000
100A127HIS 00.0080.00940.133-0.002-0.0020.0000.0000.0000.000
101A128ASN 00.011-0.01140.060-0.002-0.0020.0000.0000.0000.000
102A129TYR 0-0.082-0.11837.8010.0000.0000.0000.0000.0000.000
103A130SER 00.0070.00643.490-0.001-0.0010.0000.0000.0000.000
104A131GLU -1-0.972-0.98245.9380.0070.0070.0000.0000.0000.000
105A132ARG 10.8400.93042.630-0.015-0.0150.0000.0000.0000.000
106A133GLY 0-0.0040.01748.1640.0000.0000.0000.0000.0000.000
107A134ILE 0-0.062-0.03442.7480.0000.0000.0000.0000.0000.000
108A135ASP -1-0.847-0.92045.3050.0020.0020.0000.0000.0000.000
109A136HIS 0-0.037-0.03840.5630.0000.0000.0000.0000.0000.000
110A137GLY 00.0250.01540.3670.0010.0010.0000.0000.0000.000
111A138GLU -1-0.950-0.96741.8500.0000.0000.0000.0000.0000.000
112A139LEU 0-0.086-0.03237.5240.0020.0020.0000.0000.0000.000
113A140ASP -1-0.760-0.84533.8400.0030.0030.0000.0000.0000.000
114A141LEU 0-0.020-0.00931.9650.0040.0040.0000.0000.0000.000
115A142LEU 0-0.001-0.00226.140-0.002-0.0020.0000.0000.0000.000
116A143ALA 0-0.0150.00225.9190.0040.0040.0000.0000.0000.000
117A144PHE 00.0550.00818.9690.0040.0040.0000.0000.0000.000
118A145VAL 0-0.046-0.03720.3360.0000.0000.0000.0000.0000.000
119A146ASN 0-0.049-0.04716.6710.0480.0480.0000.0000.0000.000
120A147LEU 0-0.041-0.01017.527-0.018-0.0180.0000.0000.0000.000
121A148LYS 10.9250.98415.375-0.235-0.2350.0000.0000.0000.000
122A149ARG 10.7850.88215.266-0.120-0.1200.0000.0000.0000.000
123A150ALA 0-0.017-0.01016.006-0.029-0.0290.0000.0000.0000.000
124A151VAL 00.0190.01711.0450.0480.0480.0000.0000.0000.000
125A152PRO 00.0300.01914.335-0.052-0.0520.0000.0000.0000.000
126A153ASP -1-0.862-0.93014.668-0.148-0.1480.0000.0000.0000.000
127A154PHE 0-0.016-0.01413.2100.0040.0040.0000.0000.0000.000
128A155ASN 0-0.0050.01214.189-0.005-0.0050.0000.0000.0000.000
129A156THR 0-0.046-0.01617.8000.0120.0120.0000.0000.0000.000
130A157PRO 00.0250.01220.9980.0080.0080.0000.0000.0000.000
131A158PHE 00.020-0.01321.2100.0060.0060.0000.0000.0000.000
132A159PRO 0-0.0130.01525.694-0.003-0.0030.0000.0000.0000.000
133A160PRO 00.0700.01429.2010.0040.0040.0000.0000.0000.000
134A161PRO 00.0410.04230.8620.0020.0020.0000.0000.0000.000
135A162THR 0-0.002-0.02132.5550.0020.0020.0000.0000.0000.000
136A163GLU -1-0.858-0.89534.8690.0070.0070.0000.0000.0000.000
137A164TYR 0-0.024-0.04129.5390.0010.0010.0000.0000.0000.000
138A165LEU 00.0020.00635.2830.0000.0000.0000.0000.0000.000
139A166ARG 10.9240.95337.4360.0060.0060.0000.0000.0000.000
140A167GLN 0-0.0050.00435.9320.0010.0010.0000.0000.0000.000
141A168GLY 00.0300.02639.8400.0010.0010.0000.0000.0000.000
142A169TRP 0-0.037-0.01235.5910.0010.0010.0000.0000.0000.000
143A170ARG 10.8800.93238.014-0.004-0.0040.0000.0000.0000.000
144A171SER 0-0.072-0.06733.444-0.002-0.0020.0000.0000.0000.000
145A172LEU 0-0.0020.02129.6590.0030.0030.0000.0000.0000.000
146A173SER 0-0.0050.00127.130-0.006-0.0060.0000.0000.0000.000
147A174MET 0-0.046-0.01123.1500.0060.0060.0000.0000.0000.000
148A175VAL 00.0330.00920.642-0.007-0.0070.0000.0000.0000.000
149A176GLY 00.0440.03418.5010.0020.0020.0000.0000.0000.000
150A177PRO 00.006-0.00113.973-0.006-0.0060.0000.0000.0000.000
151A178THR 0-0.006-0.00911.7710.0020.0020.0000.0000.0000.000
152A179PHE 00.007-0.00114.110-0.041-0.0410.0000.0000.0000.000
153A180ALA 00.0690.04317.3900.0080.0080.0000.0000.0000.000
154A181ARG 10.8930.94621.1320.0100.0100.0000.0000.0000.000
155A182VAL 00.0390.03924.0310.0070.0070.0000.0000.0000.000
156A183LEU 0-0.094-0.05525.808-0.006-0.0060.0000.0000.0000.000
157A184PHE 0-0.022-0.02629.082-0.005-0.0050.0000.0000.0000.000
158A185ALA 00.0380.00132.6990.0030.0030.0000.0000.0000.000
159A186HIS 00.0090.01835.077-0.004-0.0040.0000.0000.0000.000
160A187SER 0-0.022-0.02138.7710.0010.0010.0000.0000.0000.000
161A188GLY 00.0290.01741.0340.0000.0000.0000.0000.0000.000
162A189ALA 0-0.0050.00836.2000.0010.0010.0000.0000.0000.000
163A190PRO 00.0460.01835.132-0.002-0.0020.0000.0000.0000.000
164A191GLU -1-0.930-0.97035.702-0.018-0.0180.0000.0000.0000.000
165A192PHE 00.0360.01530.418-0.002-0.0020.0000.0000.0000.000
166A193LEU 00.0020.01630.378-0.001-0.0010.0000.0000.0000.000
167A194ARG 10.9110.95231.5760.0110.0110.0000.0000.0000.000
168A195ALA 0-0.016-0.00332.047-0.003-0.0030.0000.0000.0000.000
169A196ASN 0-0.063-0.05127.240-0.008-0.0080.0000.0000.0000.000
170A197LEU 0-0.0100.01027.8430.0000.0000.0000.0000.0000.000
171A198GLY 0-0.025-0.01028.272-0.004-0.0040.0000.0000.0000.000
172A199ARG 10.9350.97023.9960.0300.0300.0000.0000.0000.000
173A200SER 0-0.022-0.02020.1660.0100.0100.0000.0000.0000.000
174A201ILE 0-0.0150.01518.752-0.018-0.0180.0000.0000.0000.000
175A202LEU 00.000-0.00913.6420.0220.0220.0000.0000.0000.000
176A203PHE 0-0.0280.00213.635-0.034-0.0340.0000.0000.0000.000
177A204ASP -1-0.883-0.9359.683-0.050-0.0500.0000.0000.0000.000
178A205ALA 0-0.051-0.0486.4190.0670.0670.0000.0000.0000.000
179A206GLY 0-0.032-0.0218.427-0.158-0.1580.0000.0000.0000.000
180A207VAL 0-0.028-0.00710.582-0.048-0.0480.0000.0000.0000.000
181A208GLY 0-0.017-0.00113.492-0.018-0.0180.0000.0000.0000.000
182A209LEU -1-0.959-0.97813.7330.0870.0870.0000.0000.0000.000