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: YY8Z2

Calculation Name: 1Y0K-A-Xray372

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: 2023-06-20

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 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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1987607.234397
FMO2-HF: Nuclear repulsion 1916635.877043
FMO2-HF: Total energy -70971.357353
FMO2-MP2: Total energy -71182.304857


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.
-8.528-2.7986.804-3.007-9.527-0.007
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 : 0.031 / q_NPA : 0.026
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-1-0.828-0.9342.495-5.153-1.8641.167-2.047-2.409-0.007
4A4ALA0-0.019-0.0074.9640.9861.173-0.001-0.009-0.1770.000
5A5ASP-1-0.789-0.8822.924-0.1260.6480.196-0.197-0.7730.000
6A6TYR00.0170.0132.404-0.6111.7814.499-2.527-4.3640.002
7A7LEU00.0100.0033.4931.498-0.2400.0562.105-0.423-0.001
8A8ARG10.8640.9196.453-0.501-0.5010.0000.0000.0000.000
9A9LEU0-0.032-0.0072.467-1.655-0.8470.888-0.329-1.368-0.001
10A10LEU00.0110.0006.142-0.814-0.796-0.001-0.003-0.0130.000
11A11THR0-0.032-0.0288.624-0.416-0.4160.0000.0000.0000.000
12A12ARG10.9760.9975.037-1.754-1.7540.0000.0000.0000.000
13A13GLN00.0190.0209.618-0.147-0.1470.0000.0000.0000.000
14A14ALA00.0180.00811.385-0.132-0.1320.0000.0000.0000.000
15A15GLU-1-0.838-0.92813.7650.4590.4590.0000.0000.0000.000
16A16GLN00.0180.01111.2480.0150.0150.0000.0000.0000.000
17A17ALA00.0020.01115.613-0.056-0.0560.0000.0000.0000.000
18A18ASN00.0270.00017.679-0.054-0.0540.0000.0000.0000.000
19A19ASP-1-0.886-0.92318.3210.2970.2970.0000.0000.0000.000
20A20PHE0-0.032-0.01019.791-0.032-0.0320.0000.0000.0000.000
21A21LEU0-0.020-0.01521.581-0.031-0.0310.0000.0000.0000.000
22A22SER0-0.066-0.03523.166-0.026-0.0260.0000.0000.0000.000
23A23ASN0-0.032-0.02323.816-0.031-0.0310.0000.0000.0000.000
24A24ALA0-0.0230.02525.693-0.012-0.0120.0000.0000.0000.000
25A25ARG10.9710.96527.553-0.139-0.1390.0000.0000.0000.000
26A26LYS10.8240.90530.242-0.103-0.1030.0000.0000.0000.000
27A27TRP00.0290.00431.3630.0080.0080.0000.0000.0000.000
28A28ASP-1-0.863-0.91928.3030.1700.1700.0000.0000.0000.000
29A29ARG10.9190.96226.178-0.156-0.1560.0000.0000.0000.000
30A30GLU-1-0.796-0.90126.9590.1370.1370.0000.0000.0000.000
31A31ARG10.8380.90428.350-0.152-0.1520.0000.0000.0000.000
32A32TRP00.0010.00219.4260.0050.0050.0000.0000.0000.000
33A33VAL00.0040.00224.1440.0150.0150.0000.0000.0000.000
34A34CYS0-0.040-0.01525.0100.0020.0020.0000.0000.0000.000
35A35GLN0-0.002-0.00225.381-0.006-0.0060.0000.0000.0000.000
36A36ARG10.8590.91619.650-0.262-0.2620.0000.0000.0000.000
37A37PHE0-0.013-0.01022.0700.0080.0080.0000.0000.0000.000
38A38LEU00.002-0.00624.258-0.004-0.0040.0000.0000.0000.000
39A39GLU-1-0.775-0.83421.4190.2370.2370.0000.0000.0000.000
40A40ALA0-0.024-0.00820.7180.0050.0050.0000.0000.0000.000
41A41LEU0-0.097-0.03921.686-0.010-0.0100.0000.0000.0000.000
42A42ASN0-0.049-0.01224.146-0.009-0.0090.0000.0000.0000.000
43A43VAL0-0.018-0.00525.513-0.017-0.0170.0000.0000.0000.000
44A44PRO00.0020.00028.3960.0070.0070.0000.0000.0000.000
45A45TYR0-0.059-0.06625.249-0.012-0.0120.0000.0000.0000.000
46A46ARG10.8290.89830.927-0.096-0.0960.0000.0000.0000.000
47A47GLN00.000-0.00629.7580.0070.0070.0000.0000.0000.000
48A48GLU-1-0.771-0.89232.9130.1020.1020.0000.0000.0000.000
49A49ASP-1-0.817-0.90033.9970.0990.0990.0000.0000.0000.000
50A50PHE0-0.075-0.02629.492-0.001-0.0010.0000.0000.0000.000
51A51ALA00.0200.01134.972-0.002-0.0020.0000.0000.0000.000
52A52ALA00.0140.01137.2820.0030.0030.0000.0000.0000.000
53A53PRO0-0.0150.00038.658-0.004-0.0040.0000.0000.0000.000
54A54GLY0-0.018-0.01241.6800.0010.0010.0000.0000.0000.000
55A55GLU-1-0.938-0.96444.3580.0590.0590.0000.0000.0000.000
56A56GLN0-0.0240.01938.3760.0060.0060.0000.0000.0000.000
57A57PRO0-0.050-0.00839.146-0.003-0.0030.0000.0000.0000.000
58A58PRO00.0150.00136.855-0.003-0.0030.0000.0000.0000.000
59A59ASP-1-0.826-0.94033.8940.1060.1060.0000.0000.0000.000
60A60VAL0-0.053-0.02931.7860.0010.0010.0000.0000.0000.000
61A61LEU0-0.0070.00734.973-0.001-0.0010.0000.0000.0000.000
62A62PHE00.021-0.00932.2310.0050.0050.0000.0000.0000.000
63A63LYS10.8260.92933.772-0.104-0.1040.0000.0000.0000.000
64A64GLY00.0220.01737.726-0.001-0.0010.0000.0000.0000.000
65A65ALA0-0.008-0.00634.667-0.004-0.0040.0000.0000.0000.000
66A66GLY00.0430.01536.7080.0000.0000.0000.0000.0000.000
67A67PHE0-0.011-0.02030.9840.0000.0000.0000.0000.0000.000
68A68GLU-1-0.696-0.80733.9400.0900.0900.0000.0000.0000.000
69A69VAL0-0.036-0.02328.4050.0040.0040.0000.0000.0000.000
70A70PHE0-0.035-0.03329.148-0.005-0.0050.0000.0000.0000.000
71A71PHE00.0280.00724.5940.0110.0110.0000.0000.0000.000
72A72VAL0-0.029-0.01224.029-0.016-0.0160.0000.0000.0000.000
73A73LEU00.0200.00721.6240.0230.0230.0000.0000.0000.000
74A74ASP-1-0.815-0.91319.8680.2410.2410.0000.0000.0000.000
75A75GLU-1-0.810-0.87620.3380.2490.2490.0000.0000.0000.000
76A105ARG10.9680.97110.3510.0950.0950.0000.0000.0000.000
77A106PRO0-0.035-0.00310.949-0.082-0.0820.0000.0000.0000.000
78A107GLN00.0180.01512.942-0.048-0.0480.0000.0000.0000.000
79A108ARG10.9250.9429.501-0.024-0.0240.0000.0000.0000.000
80A109ILE0-0.044-0.01215.229-0.038-0.0380.0000.0000.0000.000
81A110ALA00.0730.03618.7040.0130.0130.0000.0000.0000.000
82A111ALA00.0380.01220.9050.0240.0240.0000.0000.0000.000
83A112ALA00.002-0.00722.2950.0140.0140.0000.0000.0000.000
84A113GLU-1-0.856-0.94223.0740.0160.0160.0000.0000.0000.000
85A114LEU0-0.039-0.01819.4700.0130.0130.0000.0000.0000.000
86A115GLN00.011-0.00922.9370.0170.0170.0000.0000.0000.000
87A116ALA00.0190.03125.9940.0020.0020.0000.0000.0000.000
88A117ARG10.9190.96521.857-0.127-0.1270.0000.0000.0000.000
89A118LEU00.0070.00425.2910.0060.0060.0000.0000.0000.000
90A119ALA00.0000.01428.616-0.002-0.0020.0000.0000.0000.000
91A120PRO0-0.017-0.01130.226-0.004-0.0040.0000.0000.0000.000
92A121THR00.015-0.00530.385-0.006-0.0060.0000.0000.0000.000
93A122LEU00.0110.01831.201-0.003-0.0030.0000.0000.0000.000
94A123ARG10.8270.87534.296-0.050-0.0500.0000.0000.0000.000
95A124LYS10.9460.97735.442-0.069-0.0690.0000.0000.0000.000
96A125LYS10.8650.92533.430-0.098-0.0980.0000.0000.0000.000
97A126ALA00.0510.03138.162-0.003-0.0030.0000.0000.0000.000
98A127HIS00.0040.02640.108-0.003-0.0030.0000.0000.0000.000
99A128ASN00.016-0.01140.487-0.004-0.0040.0000.0000.0000.000
100A129TYR0-0.062-0.08137.858-0.002-0.0020.0000.0000.0000.000
101A130SER00.006-0.00943.462-0.002-0.0020.0000.0000.0000.000
102A131GLU-1-0.974-0.98145.9130.0360.0360.0000.0000.0000.000
103A132ARG10.8290.92242.814-0.061-0.0610.0000.0000.0000.000
104A133GLY0-0.0050.01448.128-0.001-0.0010.0000.0000.0000.000
105A134ILE0-0.072-0.03742.6610.0010.0010.0000.0000.0000.000
106A135ASP-1-0.851-0.91945.3020.0450.0450.0000.0000.0000.000
107A136HIS0-0.025-0.03640.5460.0030.0030.0000.0000.0000.000
108A137GLY00.0260.01540.3550.0040.0040.0000.0000.0000.000
109A138GLU-1-0.884-0.93841.7830.0560.0560.0000.0000.0000.000
110A139LEU0-0.092-0.03137.5710.0060.0060.0000.0000.0000.000
111A140ASP-1-0.751-0.84133.7830.0780.0780.0000.0000.0000.000
112A141LEU0-0.032-0.01431.9720.0080.0080.0000.0000.0000.000
113A142LEU00.001-0.00326.2030.0030.0030.0000.0000.0000.000
114A143ALA0-0.0140.00325.9970.0020.0020.0000.0000.0000.000
115A144PHE00.0560.00718.9090.0150.0150.0000.0000.0000.000
116A145VAL0-0.034-0.03320.426-0.011-0.0110.0000.0000.0000.000
117A146ASN0-0.073-0.06016.6880.0870.0870.0000.0000.0000.000
118A147LEU0-0.044-0.01117.499-0.035-0.0350.0000.0000.0000.000
119A148LYS10.8720.93215.593-0.341-0.3410.0000.0000.0000.000
120A149ARG10.7510.84615.210-0.179-0.1790.0000.0000.0000.000
121A150ALA0-0.028-0.01715.975-0.050-0.0500.0000.0000.0000.000
122A151VAL00.0230.01610.9980.0760.0760.0000.0000.0000.000
123A152PRO00.0270.02114.271-0.079-0.0790.0000.0000.0000.000
124A153ASP-1-0.841-0.91014.595-0.113-0.1130.0000.0000.0000.000
125A154PHE0-0.009-0.01212.995-0.002-0.0020.0000.0000.0000.000
126A155ASN0-0.050-0.01814.009-0.020-0.0200.0000.0000.0000.000
127A156THR0-0.033-0.00817.902-0.005-0.0050.0000.0000.0000.000
128A157PRO00.0200.01321.0990.0210.0210.0000.0000.0000.000
129A158PHE00.027-0.01321.0340.0040.0040.0000.0000.0000.000
130A159PRO0-0.0010.02125.769-0.005-0.0050.0000.0000.0000.000
131A160PRO00.0680.01429.2820.0100.0100.0000.0000.0000.000
132A161PRO00.0380.03830.776-0.003-0.0030.0000.0000.0000.000
133A162THR0-0.007-0.02032.5570.0020.0020.0000.0000.0000.000
134A163GLU-1-0.815-0.87134.9010.0440.0440.0000.0000.0000.000
135A164TYR0-0.029-0.05029.429-0.001-0.0010.0000.0000.0000.000
136A165LEU0-0.0010.00535.2740.0010.0010.0000.0000.0000.000
137A166ARG10.9080.94837.434-0.025-0.0250.0000.0000.0000.000
138A167GLN0-0.0140.00135.6110.0030.0030.0000.0000.0000.000
139A168GLY00.0320.02739.8210.0010.0010.0000.0000.0000.000
140A169TRP0-0.058-0.02035.6170.0010.0010.0000.0000.0000.000
141A170ARG10.8150.89537.893-0.071-0.0710.0000.0000.0000.000
142A171SER0-0.057-0.06633.4040.0000.0000.0000.0000.0000.000
143A172LEU0-0.0160.01429.7120.0020.0020.0000.0000.0000.000
144A173SER00.0000.00527.143-0.005-0.0050.0000.0000.0000.000
145A174MET0-0.037-0.00723.1930.0010.0010.0000.0000.0000.000
146A175VAL00.0270.00820.7880.0010.0010.0000.0000.0000.000
147A176GLY00.0520.03818.481-0.016-0.0160.0000.0000.0000.000
148A177PRO0-0.012-0.01013.7770.0060.0060.0000.0000.0000.000
149A178THR0-0.006-0.01511.5900.0310.0310.0000.0000.0000.000
150A179PHE0-0.0010.00214.103-0.033-0.0330.0000.0000.0000.000
151A180ALA00.0590.03917.3930.0000.0000.0000.0000.0000.000
152A181ARG10.8890.94921.136-0.091-0.0910.0000.0000.0000.000
153A182VAL00.0440.03724.0400.0040.0040.0000.0000.0000.000
154A183LEU0-0.098-0.05725.694-0.009-0.0090.0000.0000.0000.000
155A184PHE0-0.009-0.02329.088-0.011-0.0110.0000.0000.0000.000
156A185ALA00.027-0.00232.7070.0070.0070.0000.0000.0000.000
157A186HIS00.0140.02435.086-0.006-0.0060.0000.0000.0000.000
158A187SER0-0.002-0.01338.7820.0040.0040.0000.0000.0000.000
159A188GLY00.0190.01141.0480.0000.0000.0000.0000.0000.000
160A189ALA0-0.0010.01436.2020.0030.0030.0000.0000.0000.000
161A190PRO00.0410.01535.273-0.003-0.0030.0000.0000.0000.000
162A191GLU-1-0.825-0.90435.7140.0580.0580.0000.0000.0000.000
163A192PHE00.014-0.00230.604-0.001-0.0010.0000.0000.0000.000
164A193LEU00.0090.01730.6200.0060.0060.0000.0000.0000.000
165A194ARG10.8400.90531.592-0.056-0.0560.0000.0000.0000.000
166A195ALA0-0.024-0.00932.109-0.004-0.0040.0000.0000.0000.000
167A196ASN0-0.021-0.01827.0880.0050.0050.0000.0000.0000.000
168A197LEU0-0.0010.01927.8560.0040.0040.0000.0000.0000.000
169A198GLY0-0.017-0.00728.310-0.004-0.0040.0000.0000.0000.000
170A199ARG10.8820.93623.935-0.112-0.1120.0000.0000.0000.000
171A200SER0-0.029-0.02020.3580.0010.0010.0000.0000.0000.000
172A201ILE0-0.0060.01718.640-0.014-0.0140.0000.0000.0000.000
173A202LEU00.002-0.00513.7850.0160.0160.0000.0000.0000.000
174A203PHE0-0.0360.00513.710-0.017-0.0170.0000.0000.0000.000
175A204ASP-1-0.868-0.9289.9600.7550.7550.0000.0000.0000.000
176A205ALA0-0.054-0.0476.547-0.008-0.0080.0000.0000.0000.000
177A206GLY0-0.008-0.0108.564-0.101-0.1010.0000.0000.0000.000
178A207VAL0-0.021-0.00610.675-0.112-0.1120.0000.0000.0000.000
179A208GLY00.0020.00713.621-0.067-0.0670.0000.0000.0000.000
180A209LEU0-0.057-0.03013.701-0.097-0.0970.0000.0000.0000.000