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

tag_button

FMODB ID: RY8Q8

Calculation Name: 1YQ1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YQ1

Chain ID: A

ChEMBL ID:

UniProt ID: Q93698

Base Structure: X-ray

Registration Date: 2023-09-27

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2410533.672959
FMO2-HF: Nuclear repulsion 2329582.040566
FMO2-HF: Total energy -80951.632393
FMO2-MP2: Total energy -81193.0599


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.
-3.679-2.253-0.011-0.653-0.7610.003
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 : 0.010 / 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].
3A3SER00.0240.0113.8800.4331.899-0.010-0.630-0.8250.003
4A4TYR0-0.002-0.0046.4530.6900.6900.0000.0000.0000.000
5A5LYS10.8280.9159.3101.0611.0610.0000.0000.0000.000
6A6LEU0-0.016-0.00412.5720.1270.1270.0000.0000.0000.000
7A7THR00.0110.02016.241-0.024-0.0240.0000.0000.0000.000
8A8TYR00.023-0.00919.1710.0550.0550.0000.0000.0000.000
9A9PHE00.0380.03122.696-0.015-0.0150.0000.0000.0000.000
10A10PHE00.0280.00325.060-0.005-0.0050.0000.0000.0000.000
11A11PHE0-0.0020.02126.5180.0070.0070.0000.0000.0000.000
12A12ARG10.8680.90226.7460.1050.1050.0000.0000.0000.000
13A13GLY0-0.025-0.02626.791-0.008-0.0080.0000.0000.0000.000
14A14LEU0-0.008-0.00226.9480.0140.0140.0000.0000.0000.000
15A15GLY00.0630.03223.030-0.001-0.0010.0000.0000.0000.000
16A16GLU-1-0.755-0.82822.253-0.197-0.1970.0000.0000.0000.000
17A17PRO00.011-0.00223.276-0.001-0.0010.0000.0000.0000.000
18A18ILE00.0110.01117.9440.0140.0140.0000.0000.0000.000
19A19ARG10.7480.84618.8150.2570.2570.0000.0000.0000.000
20A20LEU0-0.024-0.00419.3810.0000.0000.0000.0000.0000.000
21A21LEU00.0280.00918.2220.0120.0120.0000.0000.0000.000
22A22PHE00.0170.00211.9730.0140.0140.0000.0000.0000.000
23A23HIS0-0.055-0.03515.833-0.001-0.0010.0000.0000.0000.000
24A24LEU0-0.075-0.02018.0800.0210.0210.0000.0000.0000.000
25A25ALA00.0000.00015.7300.0250.0250.0000.0000.0000.000
26A26GLY0-0.0130.01015.4170.0440.0440.0000.0000.0000.000
27A27VAL0-0.036-0.0139.7000.0100.0100.0000.0000.0000.000
28A28GLN0-0.028-0.0268.447-0.263-0.2630.0000.0000.0000.000
29A29PHE0-0.017-0.0129.435-0.089-0.0890.0000.0000.0000.000
30A30GLU-1-0.822-0.89510.732-1.044-1.0440.0000.0000.0000.000
31A31GLU-1-0.760-0.88413.178-0.299-0.2990.0000.0000.0000.000
32A32VAL00.0090.01015.7100.0380.0380.0000.0000.0000.000
33A33ARG10.8420.91018.3330.4180.4180.0000.0000.0000.000
34A34MET00.0290.02120.8400.0110.0110.0000.0000.0000.000
35A35ASN00.035-0.00324.0290.0250.0250.0000.0000.0000.000
36A36PRO0-0.028-0.00327.616-0.001-0.0010.0000.0000.0000.000
37A37ASP-1-0.900-0.95330.080-0.150-0.1500.0000.0000.0000.000
38A38GLN0-0.021-0.00229.2450.0110.0110.0000.0000.0000.000
39A39THR0-0.061-0.04327.193-0.019-0.0190.0000.0000.0000.000
40A40TRP00.0100.00328.2050.0170.0170.0000.0000.0000.000
41A41LEU00.0170.01128.693-0.011-0.0110.0000.0000.0000.000
42A42ASP-1-0.830-0.92328.437-0.178-0.1780.0000.0000.0000.000
43A43ILE0-0.0100.01623.228-0.010-0.0100.0000.0000.0000.000
44A44LYS10.8670.93324.7790.1560.1560.0000.0000.0000.000
45A45ASP-1-0.868-0.93226.861-0.154-0.1540.0000.0000.0000.000
46A46SER0-0.004-0.01923.213-0.001-0.0010.0000.0000.0000.000
47A47THR0-0.030-0.00422.111-0.029-0.0290.0000.0000.0000.000
48A48PRO00.0320.01519.4000.0370.0370.0000.0000.0000.000
49A49MET0-0.045-0.02322.5310.0270.0270.0000.0000.0000.000
50A50LYS10.8020.89425.7210.1710.1710.0000.0000.0000.000
51A51GLN0-0.014-0.00325.8890.0100.0100.0000.0000.0000.000
52A52LEU00.0330.04922.710-0.018-0.0180.0000.0000.0000.000
53A53PRO0-0.090-0.05321.1430.0270.0270.0000.0000.0000.000
54A54VAL0-0.003-0.01217.6450.0310.0310.0000.0000.0000.000
55A55LEU0-0.0220.01413.148-0.032-0.0320.0000.0000.0000.000
56A56ASN0-0.012-0.04312.435-0.007-0.0070.0000.0000.0000.000
57A57ILE0-0.033-0.0197.898-0.011-0.0110.0000.0000.0000.000
58A58ASP-1-0.821-0.9084.386-5.265-5.305-0.001-0.0230.0640.000
59A59GLY0-0.0040.0067.9450.2700.2700.0000.0000.0000.000
60A60PHE0-0.0280.00410.8810.2220.2220.0000.0000.0000.000
61A61GLU-1-0.849-0.94212.872-0.604-0.6040.0000.0000.0000.000
62A62LEU0-0.031-0.01015.8580.0780.0780.0000.0000.0000.000
63A63PRO00.002-0.00218.507-0.020-0.0200.0000.0000.0000.000
64A64GLN00.0660.01521.6260.0250.0250.0000.0000.0000.000
65A65SER00.0270.02522.8400.0080.0080.0000.0000.0000.000
66A66GLY00.0590.02523.1100.0030.0030.0000.0000.0000.000
67A67ALA0-0.016-0.00522.4680.0160.0160.0000.0000.0000.000
68A68ILE0-0.009-0.00917.6410.0180.0180.0000.0000.0000.000
69A69LEU0-0.006-0.00118.9640.0120.0120.0000.0000.0000.000
70A70ARG10.8720.91420.6400.0340.0340.0000.0000.0000.000
71A71TYR00.0100.00613.2370.0440.0440.0000.0000.0000.000
72A72LEU0-0.016-0.01513.9830.0410.0410.0000.0000.0000.000
73A73ALA00.0240.01616.7780.0400.0400.0000.0000.0000.000
74A74ARG10.8000.85719.578-0.055-0.0550.0000.0000.0000.000
75A75LYS10.8260.91411.128-0.135-0.1350.0000.0000.0000.000
76A76PHE0-0.039-0.02011.8880.0500.0500.0000.0000.0000.000
77A77GLY00.0320.03816.3650.0080.0080.0000.0000.0000.000
78A78PHE0-0.014-0.01618.639-0.015-0.0150.0000.0000.0000.000
79A79ALA0-0.014-0.02022.202-0.023-0.0230.0000.0000.0000.000
80A80GLY00.0310.00623.756-0.013-0.0130.0000.0000.0000.000
81A81LYS10.7840.88125.360-0.051-0.0510.0000.0000.0000.000
82A82THR0-0.026-0.03127.4070.0100.0100.0000.0000.0000.000
83A83PRO00.0480.02128.716-0.007-0.0070.0000.0000.0000.000
84A84GLU-1-0.850-0.91129.7970.0630.0630.0000.0000.0000.000
85A85GLU-1-0.842-0.91729.1120.0490.0490.0000.0000.0000.000
86A86GLU-1-0.763-0.85624.5180.0820.0820.0000.0000.0000.000
87A87ALA0-0.0020.00528.652-0.011-0.0110.0000.0000.0000.000
88A88TRP0-0.016-0.01131.564-0.012-0.0120.0000.0000.0000.000
89A89VAL0-0.0030.00426.757-0.009-0.0090.0000.0000.0000.000
90A90ASP-1-0.800-0.88527.682-0.010-0.0100.0000.0000.0000.000
91A91ALA0-0.0070.00730.144-0.009-0.0090.0000.0000.0000.000
92A92VAL0-0.011-0.01031.775-0.006-0.0060.0000.0000.0000.000
93A93HIS00.0080.01027.252-0.013-0.0130.0000.0000.0000.000
94A94ASP-1-0.841-0.92530.962-0.045-0.0450.0000.0000.0000.000
95A95LEU00.0440.03633.117-0.005-0.0050.0000.0000.0000.000
96A96PHE0-0.029-0.02429.715-0.006-0.0060.0000.0000.0000.000
97A97LYS10.7600.86829.6400.0520.0520.0000.0000.0000.000
98A98ASP-1-0.858-0.92133.825-0.043-0.0430.0000.0000.0000.000
99A99PHE0-0.021-0.01537.027-0.002-0.0020.0000.0000.0000.000
100A100LEU0-0.062-0.03032.045-0.005-0.0050.0000.0000.0000.000
101A101ALA00.0090.00736.248-0.005-0.0050.0000.0000.0000.000
102A102GLU-1-0.748-0.86838.235-0.048-0.0480.0000.0000.0000.000
103A103PHE0-0.041-0.01036.102-0.001-0.0010.0000.0000.0000.000
104A104LYS10.9120.95833.1650.0940.0940.0000.0000.0000.000
105A105LYS10.8220.89339.2650.0480.0480.0000.0000.0000.000
106A106PHE00.0230.03742.3830.0030.0030.0000.0000.0000.000
107A107ALA0-0.021-0.02240.1620.0000.0000.0000.0000.0000.000
108A108ALA0-0.016-0.01042.037-0.002-0.0020.0000.0000.0000.000
109A109GLU-1-0.794-0.91943.444-0.048-0.0480.0000.0000.0000.000
110A110ARG10.8440.92144.4620.0620.0620.0000.0000.0000.000
111A111ARG10.8770.93740.0520.0830.0830.0000.0000.0000.000
112A112SER0-0.0310.00247.236-0.002-0.0020.0000.0000.0000.000
113A113GLY00.0320.03448.7090.0020.0020.0000.0000.0000.000
114A114LYS10.7750.85651.7690.0490.0490.0000.0000.0000.000
115A115SER0-0.015-0.03954.227-0.001-0.0010.0000.0000.0000.000
116A116ALA0-0.009-0.00257.291-0.001-0.0010.0000.0000.0000.000
117A117GLU-1-0.857-0.90359.936-0.037-0.0370.0000.0000.0000.000
118A118GLU-1-0.836-0.87253.948-0.048-0.0480.0000.0000.0000.000
119A119VAL0-0.009-0.01055.283-0.003-0.0030.0000.0000.0000.000
120A120GLU-1-0.838-0.91252.976-0.037-0.0370.0000.0000.0000.000
121A121LYS10.7770.85152.0430.0340.0340.0000.0000.0000.000
122A122PHE00.0390.02253.3200.0000.0000.0000.0000.0000.000
123A123ARG10.8760.93945.2960.0480.0480.0000.0000.0000.000
124A124SER00.002-0.01249.033-0.002-0.0020.0000.0000.0000.000
125A125GLU-1-0.840-0.91849.774-0.032-0.0320.0000.0000.0000.000
126A126PHE0-0.0140.00647.5140.0020.0020.0000.0000.0000.000
127A127PHE0-0.021-0.02441.8010.0000.0000.0000.0000.0000.000
128A128LEU0-0.0030.00046.0610.0000.0000.0000.0000.0000.000
129A129PRO00.0150.02247.5430.0010.0010.0000.0000.0000.000
130A130ALA00.0300.03243.8720.0020.0020.0000.0000.0000.000
131A131ARG10.7310.82342.6820.0370.0370.0000.0000.0000.000
132A132ASN00.0370.00743.3090.0000.0000.0000.0000.0000.000
133A133THR0-0.021-0.01244.4780.0030.0030.0000.0000.0000.000
134A134TYR00.000-0.01535.6310.0040.0040.0000.0000.0000.000
135A135PHE00.017-0.00439.0710.0020.0020.0000.0000.0000.000
136A136ASN00.0010.02042.0240.0020.0020.0000.0000.0000.000
137A137ILE0-0.0090.00539.4440.0030.0030.0000.0000.0000.000
138A138LEU00.0090.00435.4400.0030.0030.0000.0000.0000.000
139A139ASN0-0.057-0.05139.0740.0030.0030.0000.0000.0000.000
140A140GLY00.0590.03341.7220.0030.0030.0000.0000.0000.000
141A141LEU0-0.092-0.04936.2230.0040.0040.0000.0000.0000.000
142A142LEU00.0130.00836.2800.0030.0030.0000.0000.0000.000
143A143GLU-1-0.835-0.91538.746-0.003-0.0030.0000.0000.0000.000
144A144LYS10.8760.94739.953-0.010-0.0100.0000.0000.0000.000
145A145SER0-0.037-0.01435.3690.0060.0060.0000.0000.0000.000
146A146ASN0-0.022-0.01835.8520.0000.0000.0000.0000.0000.000
147A147SER00.026-0.00832.406-0.001-0.0010.0000.0000.0000.000
148A148GLY0-0.0150.00234.567-0.003-0.0030.0000.0000.0000.000
149A149PHE00.0040.00129.568-0.005-0.0050.0000.0000.0000.000
150A150LEU00.0000.00031.6090.0030.0030.0000.0000.0000.000
151A151ILE0-0.021-0.02130.9830.0010.0010.0000.0000.0000.000
152A152GLY00.0670.04431.1290.0010.0010.0000.0000.0000.000
153A153SER0-0.003-0.00530.214-0.003-0.0030.0000.0000.0000.000
154A154ASP-1-0.819-0.88926.0610.0490.0490.0000.0000.0000.000
155A155ILE0-0.0540.01424.6680.0000.0000.0000.0000.0000.000
156A156THR00.028-0.00625.3730.0090.0090.0000.0000.0000.000
157A157PHE00.032-0.01022.835-0.016-0.0160.0000.0000.0000.000
158A158ALA00.0170.01624.697-0.016-0.0160.0000.0000.0000.000
159A159ASP-1-0.746-0.85828.046-0.012-0.0120.0000.0000.0000.000
160A160LEU0-0.0040.00322.650-0.008-0.0080.0000.0000.0000.000
161A161VAL0-0.051-0.02226.890-0.013-0.0130.0000.0000.0000.000
162A162VAL00.0110.01828.394-0.005-0.0050.0000.0000.0000.000
163A163VAL00.0120.00829.407-0.003-0.0030.0000.0000.0000.000
164A164ASP-1-0.731-0.83528.571-0.119-0.1190.0000.0000.0000.000
165A165ASN00.0130.00330.7070.0020.0020.0000.0000.0000.000
166A166LEU00.0330.01233.300-0.001-0.0010.0000.0000.0000.000
167A167LEU0-0.0310.00431.4020.0010.0010.0000.0000.0000.000
168A168THR0-0.039-0.02333.684-0.003-0.0030.0000.0000.0000.000
169A169LEU0-0.011-0.00135.4790.0010.0010.0000.0000.0000.000
170A170LYS10.7940.90038.2310.0520.0520.0000.0000.0000.000
171A171ASN0-0.033-0.02235.546-0.002-0.0020.0000.0000.0000.000
172A172TYR00.0090.00737.8240.0000.0000.0000.0000.0000.000
173A173GLY0-0.0130.00441.6550.0030.0030.0000.0000.0000.000
174A174LEU0-0.036-0.02041.4810.0030.0030.0000.0000.0000.000
175A175PHE00.003-0.00139.1420.0030.0030.0000.0000.0000.000
176A176ASP-1-0.769-0.88242.678-0.042-0.0420.0000.0000.0000.000
177A177GLU-1-0.775-0.87639.004-0.045-0.0450.0000.0000.0000.000
178A178SER0-0.028-0.02942.5870.0030.0030.0000.0000.0000.000
179A179GLU-1-0.843-0.88545.884-0.031-0.0310.0000.0000.0000.000
180A180PHE0-0.014-0.01442.7430.0020.0020.0000.0000.0000.000
181A181THR00.0490.02242.3420.0000.0000.0000.0000.0000.000
182A182LYS10.8230.91541.7910.0090.0090.0000.0000.0000.000
183A183LEU00.0290.00738.3020.0000.0000.0000.0000.0000.000
184A184ALA0-0.0070.00337.501-0.003-0.0030.0000.0000.0000.000
185A185ALA0-0.0010.00937.487-0.002-0.0020.0000.0000.0000.000
186A186LEU00.0020.01232.5680.0000.0000.0000.0000.0000.000
187A187ARG10.8880.91533.3070.0560.0560.0000.0000.0000.000
188A188GLU-1-0.870-0.91732.752-0.045-0.0450.0000.0000.0000.000
189A189LYS10.8510.93131.971-0.010-0.0100.0000.0000.0000.000
190A190VAL00.0080.00727.3250.0040.0040.0000.0000.0000.000
191A191ASN0-0.082-0.05827.953-0.013-0.0130.0000.0000.0000.000
192A192SER0-0.067-0.06428.937-0.006-0.0060.0000.0000.0000.000
193A193TYR0-0.004-0.01123.7310.0060.0060.0000.0000.0000.000
194A194PRO00.0080.00323.487-0.013-0.0130.0000.0000.0000.000
195A195GLY00.0410.02620.8160.0060.0060.0000.0000.0000.000
196A196ILE0-0.035-0.02621.508-0.028-0.0280.0000.0000.0000.000
197A197LYS10.9220.98823.6830.0340.0340.0000.0000.0000.000
198A198GLU-1-0.852-0.94522.643-0.071-0.0710.0000.0000.0000.000
199A199TYR0-0.073-0.05921.010-0.024-0.0240.0000.0000.0000.000
200A200ILE0-0.017-0.02322.962-0.012-0.0120.0000.0000.0000.000
201A201ALA0-0.044-0.01526.548-0.001-0.0010.0000.0000.0000.000
202A202LYS10.9040.95020.7210.2080.2080.0000.0000.0000.000
203A203ARG10.7960.91124.9270.1140.1140.0000.0000.0000.000
204A204PRO00.0050.00826.1030.0130.0130.0000.0000.0000.000
205A205VAL0-0.038-0.02329.0500.0120.0120.0000.0000.0000.000