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: LN729

Calculation Name: 2YWI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YWI

Chain ID: A

ChEMBL ID:

UniProt ID: Q5KZG6

Base Structure: X-ray

Registration Date: 2023-09-22

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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2126331.711463
FMO2-HF: Nuclear repulsion 2051219.590881
FMO2-HF: Total energy -75112.120582
FMO2-MP2: Total energy -75327.4007


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:5:VAL)


Summations of interaction energy for fragment #1(A:5:VAL)
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.
-2.438-0.581-0.032-0.815-1.010.002
Interaction energy analysis for fragmet #1(A:5:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.030 / q_NPA : -0.025
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].
3A7GLY00.0080.0103.796-1.0790.763-0.031-0.811-1.0000.002
4A8MET00.0200.0125.067-0.724-0.709-0.001-0.004-0.0100.000
5A9PRO0-0.029-0.0066.2650.2350.2350.0000.0000.0000.000
6A10ALA0-0.013-0.0018.903-0.017-0.0170.0000.0000.0000.000
7A11VAL0-0.011-0.00812.672-0.024-0.0240.0000.0000.0000.000
8A12GLU-1-0.929-0.98415.011-0.103-0.1030.0000.0000.0000.000
9A13SER0-0.024-0.04218.661-0.012-0.0120.0000.0000.0000.000
10A14ASN00.0010.01720.397-0.001-0.0010.0000.0000.0000.000
11A15MET0-0.106-0.03823.0250.0090.0090.0000.0000.0000.000
12A16PHE00.0680.04126.4670.0080.0080.0000.0000.0000.000
13A17PRO00.002-0.01228.8320.0090.0090.0000.0000.0000.000
14A18LEU00.0250.02232.0530.0010.0010.0000.0000.0000.000
15A19GLY0-0.024-0.02134.7810.0010.0010.0000.0000.0000.000
16A20LYS10.8660.94932.4730.1100.1100.0000.0000.0000.000
17A21GLN0-0.020-0.02836.1550.0030.0030.0000.0000.0000.000
18A22ALA00.0320.02034.545-0.006-0.0060.0000.0000.0000.000
19A23PRO0-0.038-0.01231.4670.0040.0040.0000.0000.0000.000
20A24PRO00.0300.02934.4430.0020.0020.0000.0000.0000.000
21A25PHE00.0280.00232.939-0.008-0.0080.0000.0000.0000.000
22A26ALA0-0.010-0.00534.4490.0080.0080.0000.0000.0000.000
23A27LEU0-0.021-0.00730.282-0.006-0.0060.0000.0000.0000.000
24A28THR00.0160.01833.3870.0070.0070.0000.0000.0000.000
25A29ASN00.0520.02732.960-0.010-0.0100.0000.0000.0000.000
26A30VAL0-0.024-0.01830.3740.0040.0040.0000.0000.0000.000
27A31ILE0-0.042-0.01833.7400.0030.0030.0000.0000.0000.000
28A32ASP-1-0.888-0.95236.298-0.062-0.0620.0000.0000.0000.000
29A33GLY0-0.028-0.00237.0630.0020.0020.0000.0000.0000.000
30A34ASN0-0.027-0.01138.097-0.001-0.0010.0000.0000.0000.000
31A35VAL0-0.052-0.02337.297-0.005-0.0050.0000.0000.0000.000
32A36VAL00.003-0.00436.6260.0050.0050.0000.0000.0000.000
33A37ARG10.9360.94736.8650.0740.0740.0000.0000.0000.000
34A38LEU0-0.0060.02036.3840.0030.0030.0000.0000.0000.000
35A39GLU-1-0.928-0.99538.438-0.075-0.0750.0000.0000.0000.000
36A40ASP-1-0.890-0.93440.740-0.065-0.0650.0000.0000.0000.000
37A41VAL0-0.039-0.01337.2370.0020.0020.0000.0000.0000.000
38A42LYS10.9360.97940.5720.0580.0580.0000.0000.0000.000
39A43SER00.0250.00742.0540.0030.0030.0000.0000.0000.000
40A44ASP-1-0.940-0.97343.729-0.043-0.0430.0000.0000.0000.000
41A45ALA0-0.073-0.03644.2190.0020.0020.0000.0000.0000.000
42A46ALA0-0.008-0.01639.120-0.001-0.0010.0000.0000.0000.000
43A47THR00.0010.00436.3350.0020.0020.0000.0000.0000.000
44A48VAL0-0.014-0.01732.558-0.003-0.0030.0000.0000.0000.000
45A49ILE0-0.0070.00429.9560.0000.0000.0000.0000.0000.000
46A50MET0-0.041-0.02128.2820.0000.0000.0000.0000.0000.000
47A51PHE00.0400.03523.867-0.001-0.0010.0000.0000.0000.000
48A52ILE0-0.003-0.02923.122-0.003-0.0030.0000.0000.0000.000
49A53CYS0-0.049-0.01819.081-0.014-0.0140.0000.0000.0000.000
50A54ASN00.0330.00422.0930.0260.0260.0000.0000.0000.000
51A55HIS0-0.047-0.01117.1920.0370.0370.0000.0000.0000.000
52A56CYS0-0.0220.03517.107-0.035-0.0350.0000.0000.0000.000
53A57PRO0-0.013-0.01015.5430.0230.0230.0000.0000.0000.000
54A58PHE00.0670.01714.7260.0210.0210.0000.0000.0000.000
55A59VAL00.0420.01219.9140.0120.0120.0000.0000.0000.000
56A60LYS10.8860.94121.7060.0810.0810.0000.0000.0000.000
57A61HIS0-0.053-0.02222.4440.0160.0160.0000.0000.0000.000
58A62VAL00.0300.00624.2450.0070.0070.0000.0000.0000.000
59A63GLN00.0150.00925.6790.0100.0100.0000.0000.0000.000
60A64HIS00.0330.01828.216-0.001-0.0010.0000.0000.0000.000
61A65GLU-1-0.739-0.85730.426-0.026-0.0260.0000.0000.0000.000
62A66LEU0-0.019-0.00727.624-0.001-0.0010.0000.0000.0000.000
63A67VAL00.0450.03131.861-0.001-0.0010.0000.0000.0000.000
64A68ARG10.8130.89834.7540.0210.0210.0000.0000.0000.000
65A69LEU0-0.020-0.01533.3630.0010.0010.0000.0000.0000.000
66A70ALA00.0200.01035.8050.0010.0010.0000.0000.0000.000
67A71ASN00.005-0.01137.473-0.001-0.0010.0000.0000.0000.000
68A72ASP-1-0.866-0.91839.686-0.022-0.0220.0000.0000.0000.000
69A73TYR0-0.113-0.10139.2310.0010.0010.0000.0000.0000.000
70A74MET0-0.0100.01539.381-0.001-0.0010.0000.0000.0000.000
71A75PRO0-0.049-0.02342.0790.0000.0000.0000.0000.0000.000
72A76LYS10.8660.94143.7050.0280.0280.0000.0000.0000.000
73A77GLY00.0310.02745.1340.0000.0000.0000.0000.0000.000
74A78VAL0-0.0480.00338.841-0.002-0.0020.0000.0000.0000.000
75A79SER00.0180.00839.4000.0020.0020.0000.0000.0000.000
76A80PHE00.014-0.00334.199-0.002-0.0020.0000.0000.0000.000
77A81VAL00.0190.00332.6890.0010.0010.0000.0000.0000.000
78A82ALA0-0.0080.01829.194-0.004-0.0040.0000.0000.0000.000
79A83ILE0-0.003-0.00626.9600.0020.0020.0000.0000.0000.000
80A84ASN0-0.033-0.02123.158-0.025-0.0250.0000.0000.0000.000
81A85SER00.029-0.02722.6970.0080.0080.0000.0000.0000.000
82A86ASN0-0.034-0.01118.569-0.032-0.0320.0000.0000.0000.000
83A87ASP-1-0.779-0.88717.949-0.305-0.3050.0000.0000.0000.000
84A88ALA00.002-0.00318.949-0.021-0.0210.0000.0000.0000.000
85A89GLU-1-0.940-0.96620.065-0.205-0.2050.0000.0000.0000.000
86A90GLN0-0.199-0.10214.057-0.097-0.0970.0000.0000.0000.000
87A91TYR0-0.028-0.01611.742-0.055-0.0550.0000.0000.0000.000
88A92PRO00.0850.04917.8740.0320.0320.0000.0000.0000.000
89A93GLU-1-0.866-0.94417.813-0.223-0.2230.0000.0000.0000.000
90A94ASP-1-0.771-0.88419.845-0.204-0.2040.0000.0000.0000.000
91A95SER00.0140.01822.8330.0070.0070.0000.0000.0000.000
92A96PRO00.0670.00425.3500.0090.0090.0000.0000.0000.000
93A97GLU-1-0.952-0.97128.850-0.078-0.0780.0000.0000.0000.000
94A98ASN0-0.029-0.03124.4250.0250.0250.0000.0000.0000.000
95A99MET0-0.070-0.01726.2450.0040.0040.0000.0000.0000.000
96A100LYS10.9410.98328.3750.0730.0730.0000.0000.0000.000
97A101LYS10.9520.97629.9140.0770.0770.0000.0000.0000.000
98A102VAL00.0460.03426.4370.0060.0060.0000.0000.0000.000
99A103ALA0-0.023-0.01429.8780.0060.0060.0000.0000.0000.000
100A104GLU-1-0.994-0.99132.464-0.039-0.0390.0000.0000.0000.000
101A105GLU-1-0.986-0.99530.085-0.042-0.0420.0000.0000.0000.000
102A106LEU0-0.084-0.04528.3160.0060.0060.0000.0000.0000.000
103A107GLY00.0020.01433.0020.0030.0030.0000.0000.0000.000
104A108TYR0-0.054-0.03827.6710.0020.0020.0000.0000.0000.000
105A109PRO00.0000.01034.762-0.001-0.0010.0000.0000.0000.000
106A110PHE0-0.026-0.01331.6220.0010.0010.0000.0000.0000.000
107A111PRO0-0.003-0.00835.395-0.002-0.0020.0000.0000.0000.000
108A112TYR00.016-0.01525.969-0.008-0.0080.0000.0000.0000.000
109A113LEU00.0290.00431.2040.0010.0010.0000.0000.0000.000
110A114TYR00.0110.00827.478-0.005-0.0050.0000.0000.0000.000
111A115ASP-1-0.792-0.89526.190-0.176-0.1760.0000.0000.0000.000
112A116GLU-1-0.858-0.94725.160-0.215-0.2150.0000.0000.0000.000
113A117THR00.0130.00824.846-0.017-0.0170.0000.0000.0000.000
114A118GLN0-0.026-0.01419.396-0.029-0.0290.0000.0000.0000.000
115A119GLU-1-0.972-0.98324.704-0.153-0.1530.0000.0000.0000.000
116A120VAL00.0180.01027.4890.0060.0060.0000.0000.0000.000
117A121ALA00.0140.00523.2920.0050.0050.0000.0000.0000.000
118A122LYS10.9300.96422.0260.2570.2570.0000.0000.0000.000
119A123ALA0-0.0300.00125.2280.0050.0050.0000.0000.0000.000
120A124TYR0-0.058-0.05627.6910.0120.0120.0000.0000.0000.000
121A125ASP-1-0.919-0.95523.689-0.197-0.1970.0000.0000.0000.000
122A126ALA0-0.0320.01023.507-0.002-0.0020.0000.0000.0000.000
123A127ALA00.016-0.01118.945-0.022-0.0220.0000.0000.0000.000
124A128CYS0-0.094-0.04217.773-0.039-0.0390.0000.0000.0000.000
125A129THR0-0.0120.02818.4620.0200.0200.0000.0000.0000.000
126A130PRO00.004-0.03019.350-0.006-0.0060.0000.0000.0000.000
127A131ASP-1-0.716-0.82722.465-0.171-0.1710.0000.0000.0000.000
128A132PHE0-0.027-0.01324.2190.0050.0050.0000.0000.0000.000
129A133TYR0-0.026-0.02726.149-0.001-0.0010.0000.0000.0000.000
130A134ILE00.0150.01230.8360.0040.0040.0000.0000.0000.000
131A135PHE0-0.011-0.01232.311-0.002-0.0020.0000.0000.0000.000
132A136ASP-1-0.765-0.88937.244-0.056-0.0560.0000.0000.0000.000
133A137ARG11.0161.01640.9380.0400.0400.0000.0000.0000.000
134A138ASP-1-1.025-1.00943.307-0.051-0.0510.0000.0000.0000.000
135A139LEU0-0.032-0.03538.632-0.003-0.0030.0000.0000.0000.000
136A140LYS10.9440.98838.5100.0520.0520.0000.0000.0000.000
137A141CYS0-0.066-0.00133.1150.0020.0020.0000.0000.0000.000
138A142VAL00.0360.01335.7800.0020.0020.0000.0000.0000.000
139A143TYR0-0.030-0.05729.7210.0060.0060.0000.0000.0000.000
140A144ARG10.8720.93428.5590.0860.0860.0000.0000.0000.000
141A145GLY00.0210.01826.0780.0030.0030.0000.0000.0000.000
142A146GLN0-0.029-0.02025.461-0.006-0.0060.0000.0000.0000.000
143A147LEU00.0410.04526.5550.0030.0030.0000.0000.0000.000
144A148ASP-1-0.728-0.84327.782-0.025-0.0250.0000.0000.0000.000
145A149ASP-1-0.809-0.90927.207-0.028-0.0280.0000.0000.0000.000
146A150SER0-0.080-0.04126.1890.0050.0050.0000.0000.0000.000
147A151ARG10.8350.89320.8560.0390.0390.0000.0000.0000.000
148A152PRO00.0150.00919.1640.0140.0140.0000.0000.0000.000
149A153ASN0-0.027-0.01918.3930.0000.0000.0000.0000.0000.000
150A154ASN00.001-0.00920.5320.0150.0150.0000.0000.0000.000
151A155GLY00.0060.01623.9510.0030.0030.0000.0000.0000.000
152A156ILE0-0.041-0.00626.7660.0000.0000.0000.0000.0000.000
153A157PRO0-0.014-0.01728.507-0.004-0.0040.0000.0000.0000.000
154A158VAL00.0170.01727.847-0.003-0.0030.0000.0000.0000.000
155A159THR0-0.010-0.01530.4770.0000.0000.0000.0000.0000.000
156A160GLY00.012-0.00631.698-0.001-0.0010.0000.0000.0000.000
157A161GLU-1-0.975-0.98832.739-0.019-0.0190.0000.0000.0000.000
158A162SER0-0.007-0.00731.182-0.001-0.0010.0000.0000.0000.000
159A163ILE00.0360.02430.131-0.001-0.0010.0000.0000.0000.000
160A164ARG10.7700.89334.1110.0280.0280.0000.0000.0000.000
161A165ALA00.0400.02736.8480.0010.0010.0000.0000.0000.000
162A166ALA0-0.030-0.02035.9180.0010.0010.0000.0000.0000.000
163A167LEU00.0150.00136.9250.0000.0000.0000.0000.0000.000
164A168ASP-1-0.824-0.89639.736-0.027-0.0270.0000.0000.0000.000
165A169ALA0-0.080-0.04041.1760.0010.0010.0000.0000.0000.000
166A170LEU0-0.003-0.00838.8690.0000.0000.0000.0000.0000.000
167A171LEU0-0.050-0.02143.1270.0010.0010.0000.0000.0000.000
168A172GLU-1-0.914-0.95745.652-0.022-0.0220.0000.0000.0000.000
169A173GLY0-0.0360.00346.6050.0010.0010.0000.0000.0000.000
170A174ARG10.7960.90443.4500.0280.0280.0000.0000.0000.000
171A175PRO00.001-0.01242.914-0.002-0.0020.0000.0000.0000.000
172A176VAL00.0110.01836.4810.0020.0020.0000.0000.0000.000
173A177PRO0-0.017-0.01036.6940.0000.0000.0000.0000.0000.000
174A178GLU-1-0.881-0.95736.481-0.043-0.0430.0000.0000.0000.000
175A179LYS10.8760.94931.0630.0220.0220.0000.0000.0000.000
176A180GLN00.0320.02530.695-0.005-0.0050.0000.0000.0000.000
177A181LYS10.8860.94726.4290.0300.0300.0000.0000.0000.000
178A182PRO00.1040.03522.4670.0020.0020.0000.0000.0000.000
179A183SER0-0.075-0.04122.7000.0190.0190.0000.0000.0000.000
180A184ILE00.010-0.00715.777-0.007-0.0070.0000.0000.0000.000
181A185GLY00.017-0.00817.1420.0270.0270.0000.0000.0000.000
182A186CYS0-0.048-0.03814.032-0.040-0.0400.0000.0000.0000.000
183A187SER00.0190.00513.1300.0180.0180.0000.0000.0000.000
184A188ILE00.0060.01614.953-0.015-0.0150.0000.0000.0000.000
185A189LYS10.7980.91112.1650.5080.5080.0000.0000.0000.000
186A190TRP00.0290.01315.5270.0470.0470.0000.0000.0000.000
187A191LYS10.8990.96216.1740.1970.1970.0000.0000.0000.000
188A192PRO0-0.020-0.01716.567-0.012-0.0120.0000.0000.0000.000
189A193SER0-0.024-0.01317.8810.0320.0320.0000.0000.0000.000
190A194ALA0-0.0040.01019.9020.0100.0100.0000.0000.0000.000