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: MN97Z

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 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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2131507.426327
FMO2-HF: Nuclear repulsion 2056394.47702
FMO2-HF: Total energy -75112.949306
FMO2-MP2: Total energy -75328.282525


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.
-1.4540.158-0.019-0.764-0.8290.001
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 : -0.026 / 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].
3A7GLY00.0070.0133.877-0.5621.050-0.019-0.764-0.8290.001
4A8MET00.0250.0115.544-0.437-0.4370.0000.0000.0000.000
5A9PRO0-0.0180.0046.4790.1810.1810.0000.0000.0000.000
6A10ALA0-0.015-0.0068.970-0.029-0.0290.0000.0000.0000.000
7A11VAL0-0.020-0.01512.666-0.014-0.0140.0000.0000.0000.000
8A12GLU-1-0.901-0.97015.071-0.032-0.0320.0000.0000.0000.000
9A13SER0-0.007-0.03518.847-0.012-0.0120.0000.0000.0000.000
10A14ASN0-0.039-0.02620.5820.0020.0020.0000.0000.0000.000
11A15MET0-0.074-0.01723.0110.0070.0070.0000.0000.0000.000
12A16PHE00.0490.02926.4820.0080.0080.0000.0000.0000.000
13A17PRO0-0.009-0.00328.7200.0070.0070.0000.0000.0000.000
14A18LEU00.0520.03532.1460.0000.0000.0000.0000.0000.000
15A19GLY0-0.025-0.01134.927-0.001-0.0010.0000.0000.0000.000
16A20LYS10.8750.94532.0550.0800.0800.0000.0000.0000.000
17A21GLN0-0.037-0.03436.2320.0020.0020.0000.0000.0000.000
18A22ALA00.0420.02034.650-0.005-0.0050.0000.0000.0000.000
19A23PRO0-0.032-0.00631.3740.0020.0020.0000.0000.0000.000
20A24PRO00.0200.02034.5260.0010.0010.0000.0000.0000.000
21A25PHE00.0100.00133.194-0.007-0.0070.0000.0000.0000.000
22A26ALA0-0.019-0.02334.8030.0060.0060.0000.0000.0000.000
23A27LEU0-0.0140.00430.415-0.004-0.0040.0000.0000.0000.000
24A28THR0-0.001-0.00433.6840.0060.0060.0000.0000.0000.000
25A29ASN00.0480.01133.240-0.007-0.0070.0000.0000.0000.000
26A30VAL00.0010.00130.6160.0030.0030.0000.0000.0000.000
27A31ILE00.0050.01833.9890.0030.0030.0000.0000.0000.000
28A32ASP-1-0.863-0.92236.554-0.047-0.0470.0000.0000.0000.000
29A33GLY00.0090.01937.6260.0010.0010.0000.0000.0000.000
30A34ASN0-0.079-0.04738.625-0.002-0.0020.0000.0000.0000.000
31A35VAL0-0.029-0.02137.222-0.003-0.0030.0000.0000.0000.000
32A36VAL00.0110.01936.8650.0030.0030.0000.0000.0000.000
33A37ARG10.8980.94236.9100.0540.0540.0000.0000.0000.000
34A38LEU0-0.0160.00336.3220.0020.0020.0000.0000.0000.000
35A39GLU-1-0.915-0.98138.341-0.055-0.0550.0000.0000.0000.000
36A40ASP-1-0.852-0.92940.870-0.049-0.0490.0000.0000.0000.000
37A41VAL0-0.0140.00537.2350.0020.0020.0000.0000.0000.000
38A42LYS10.9050.97640.5640.0400.0400.0000.0000.0000.000
39A43SER00.0060.00941.9520.0030.0030.0000.0000.0000.000
40A44ASP-1-0.851-0.92543.710-0.028-0.0280.0000.0000.0000.000
41A45ALA0-0.029-0.02444.5860.0010.0010.0000.0000.0000.000
42A46ALA0-0.005-0.01539.421-0.001-0.0010.0000.0000.0000.000
43A47THR00.006-0.01336.6770.0020.0020.0000.0000.0000.000
44A48VAL0-0.010-0.00632.687-0.003-0.0030.0000.0000.0000.000
45A49ILE0-0.018-0.00730.009-0.001-0.0010.0000.0000.0000.000
46A50MET0-0.020-0.00728.1760.0020.0020.0000.0000.0000.000
47A51PHE00.0350.02723.844-0.002-0.0020.0000.0000.0000.000
48A52ILE0-0.017-0.02822.9780.0000.0000.0000.0000.0000.000
49A53CYS0-0.010-0.00419.510-0.011-0.0110.0000.0000.0000.000
50A54ASN00.0510.00922.1890.0210.0210.0000.0000.0000.000
51A55HIS0-0.047-0.02717.7040.0300.0300.0000.0000.0000.000
52A56CYS0-0.0060.03117.160-0.021-0.0210.0000.0000.0000.000
53A57PRO0-0.010-0.00515.6120.0150.0150.0000.0000.0000.000
54A58PHE00.0550.01115.0610.0140.0140.0000.0000.0000.000
55A59VAL00.0220.01220.1660.0050.0050.0000.0000.0000.000
56A60LYS10.8770.93621.5420.0580.0580.0000.0000.0000.000
57A61HIS0-0.061-0.03222.5290.0120.0120.0000.0000.0000.000
58A62VAL00.0170.00424.3390.0040.0040.0000.0000.0000.000
59A63GLN00.006-0.00725.4550.0040.0040.0000.0000.0000.000
60A64HIS00.0230.01728.287-0.002-0.0020.0000.0000.0000.000
61A65GLU-1-0.721-0.84330.504-0.007-0.0070.0000.0000.0000.000
62A66LEU0-0.015-0.01427.443-0.002-0.0020.0000.0000.0000.000
63A67VAL00.0350.02831.816-0.001-0.0010.0000.0000.0000.000
64A68ARG10.7960.89134.5930.0030.0030.0000.0000.0000.000
65A69LEU0-0.019-0.01333.1450.0000.0000.0000.0000.0000.000
66A70ALA00.0250.01535.6710.0000.0000.0000.0000.0000.000
67A71ASN00.005-0.00837.385-0.001-0.0010.0000.0000.0000.000
68A72ASP-1-0.827-0.89439.392-0.006-0.0060.0000.0000.0000.000
69A73TYR0-0.117-0.10739.1860.0010.0010.0000.0000.0000.000
70A74MET00.0030.02439.428-0.001-0.0010.0000.0000.0000.000
71A75PRO0-0.039-0.01942.2050.0000.0000.0000.0000.0000.000
72A76LYS10.8220.92342.6770.0140.0140.0000.0000.0000.000
73A77GLY00.0290.02345.2300.0000.0000.0000.0000.0000.000
74A78VAL0-0.0490.00038.872-0.002-0.0020.0000.0000.0000.000
75A79SER0-0.004-0.00839.4190.0010.0010.0000.0000.0000.000
76A80PHE00.020-0.01034.1970.0000.0000.0000.0000.0000.000
77A81VAL00.0050.00432.4400.0000.0000.0000.0000.0000.000
78A82ALA0-0.0160.00729.087-0.002-0.0020.0000.0000.0000.000
79A83ILE0-0.005-0.00627.1740.0000.0000.0000.0000.0000.000
80A84ASN0-0.017-0.02123.205-0.018-0.0180.0000.0000.0000.000
81A85SER00.033-0.02622.8240.0070.0070.0000.0000.0000.000
82A86ASN0-0.031-0.02818.500-0.029-0.0290.0000.0000.0000.000
83A87ASP-1-0.793-0.90118.220-0.265-0.2650.0000.0000.0000.000
84A88ALA0-0.009-0.00819.427-0.016-0.0160.0000.0000.0000.000
85A89GLU-1-0.938-0.96220.718-0.166-0.1660.0000.0000.0000.000
86A90GLN0-0.172-0.09614.492-0.068-0.0680.0000.0000.0000.000
87A91TYR0-0.023-0.00612.266-0.046-0.0460.0000.0000.0000.000
88A92PRO00.1050.05418.4980.0270.0270.0000.0000.0000.000
89A93GLU-1-0.887-0.93317.982-0.170-0.1700.0000.0000.0000.000
90A94ASP-1-0.759-0.84920.126-0.147-0.1470.0000.0000.0000.000
91A95SER00.0060.00023.2060.0070.0070.0000.0000.0000.000
92A96PRO00.040-0.00525.9040.0100.0100.0000.0000.0000.000
93A97GLU-1-0.878-0.91929.365-0.063-0.0630.0000.0000.0000.000
94A98ASN00.008-0.00625.2410.0190.0190.0000.0000.0000.000
95A99MET0-0.093-0.01926.6140.0030.0030.0000.0000.0000.000
96A100LYS10.8590.92528.5720.0570.0570.0000.0000.0000.000
97A101LYS10.8270.91129.5830.0690.0690.0000.0000.0000.000
98A102VAL00.0540.02826.1780.0050.0050.0000.0000.0000.000
99A103ALA0-0.022-0.01829.6200.0050.0050.0000.0000.0000.000
100A104GLU-1-0.995-0.98832.361-0.030-0.0300.0000.0000.0000.000
101A105GLU-1-0.961-0.99830.102-0.031-0.0310.0000.0000.0000.000
102A106LEU0-0.083-0.03828.3810.0060.0060.0000.0000.0000.000
103A107GLY0-0.0080.00233.0830.0010.0010.0000.0000.0000.000
104A108TYR0-0.017-0.00827.8030.0020.0020.0000.0000.0000.000
105A109PRO0-0.0150.00934.941-0.001-0.0010.0000.0000.0000.000
106A110PHE0-0.016-0.02031.2470.0000.0000.0000.0000.0000.000
107A111PRO0-0.001-0.00435.101-0.002-0.0020.0000.0000.0000.000
108A112TYR00.016-0.01625.911-0.005-0.0050.0000.0000.0000.000
109A113LEU00.0210.01031.3480.0000.0000.0000.0000.0000.000
110A114TYR00.0170.00427.877-0.006-0.0060.0000.0000.0000.000
111A115ASP-1-0.753-0.85926.468-0.132-0.1320.0000.0000.0000.000
112A116GLU-1-0.805-0.89126.029-0.175-0.1750.0000.0000.0000.000
113A117THR00.007-0.00525.745-0.015-0.0150.0000.0000.0000.000
114A118GLN0-0.018-0.01919.928-0.022-0.0220.0000.0000.0000.000
115A119GLU-1-0.896-0.93025.010-0.124-0.1240.0000.0000.0000.000
116A120VAL00.0170.00627.7580.0050.0050.0000.0000.0000.000
117A121ALA00.010-0.00223.4690.0040.0040.0000.0000.0000.000
118A122LYS10.8470.93122.3710.2000.2000.0000.0000.0000.000
119A123ALA0-0.032-0.00925.3860.0040.0040.0000.0000.0000.000
120A124TYR0-0.038-0.05327.7420.0100.0100.0000.0000.0000.000
121A125ASP-1-0.907-0.92723.964-0.131-0.1310.0000.0000.0000.000
122A126ALA0-0.0210.01323.5200.0020.0020.0000.0000.0000.000
123A127ALA00.016-0.00318.600-0.017-0.0170.0000.0000.0000.000
124A128CYS0-0.107-0.04117.747-0.024-0.0240.0000.0000.0000.000
125A129THR00.0290.02417.8750.0100.0100.0000.0000.0000.000
126A130PRO0-0.014-0.01119.1890.0010.0010.0000.0000.0000.000
127A131ASP-1-0.661-0.80622.110-0.109-0.1090.0000.0000.0000.000
128A132PHE0-0.042-0.02024.0300.0020.0020.0000.0000.0000.000
129A133TYR0-0.030-0.03526.1400.0000.0000.0000.0000.0000.000
130A134ILE0-0.010-0.00530.8180.0030.0030.0000.0000.0000.000
131A135PHE00.0100.00832.092-0.001-0.0010.0000.0000.0000.000
132A136ASP-1-0.737-0.87737.216-0.036-0.0360.0000.0000.0000.000
133A137ARG10.8630.94340.9280.0270.0270.0000.0000.0000.000
134A138ASP-1-0.918-0.95443.263-0.034-0.0340.0000.0000.0000.000
135A139LEU0-0.016-0.01438.836-0.002-0.0020.0000.0000.0000.000
136A140LYS10.8520.92538.4960.0330.0330.0000.0000.0000.000
137A141CYS0-0.046-0.00533.2060.0020.0020.0000.0000.0000.000
138A142VAL00.002-0.00235.8690.0020.0020.0000.0000.0000.000
139A143TYR0-0.019-0.03930.2800.0050.0050.0000.0000.0000.000
140A144ARG10.8380.90928.5340.0540.0540.0000.0000.0000.000
141A145GLY00.0230.02026.2630.0030.0030.0000.0000.0000.000
142A146GLN0-0.009-0.01226.020-0.001-0.0010.0000.0000.0000.000
143A147LEU00.0530.04326.9130.0010.0010.0000.0000.0000.000
144A148ASP-1-0.729-0.82828.2650.0040.0040.0000.0000.0000.000
145A149ASP-1-0.762-0.87127.6240.0050.0050.0000.0000.0000.000
146A150SER0-0.053-0.01626.5130.0070.0070.0000.0000.0000.000
147A151ARG10.8190.87521.101-0.003-0.0030.0000.0000.0000.000
148A152PRO00.0130.01118.9330.0110.0110.0000.0000.0000.000
149A153ASN0-0.029-0.01118.0570.0000.0000.0000.0000.0000.000
150A154ASN0-0.016-0.02620.1600.0110.0110.0000.0000.0000.000
151A155GLY00.0060.01323.6510.0000.0000.0000.0000.0000.000
152A156ILE0-0.034-0.00526.242-0.003-0.0030.0000.0000.0000.000
153A157PRO0-0.014-0.01928.178-0.002-0.0020.0000.0000.0000.000
154A158VAL00.0100.01727.698-0.002-0.0020.0000.0000.0000.000
155A159THR0-0.012-0.02230.3340.0000.0000.0000.0000.0000.000
156A160GLY00.0260.00432.068-0.002-0.0020.0000.0000.0000.000
157A161GLU-1-0.986-0.98733.2310.0020.0020.0000.0000.0000.000
158A162SER0-0.017-0.00931.4510.0000.0000.0000.0000.0000.000
159A163ILE00.0380.03030.036-0.002-0.0020.0000.0000.0000.000
160A164ARG10.7250.85234.0940.0080.0080.0000.0000.0000.000
161A165ALA00.0580.02937.202-0.001-0.0010.0000.0000.0000.000
162A166ALA0-0.029-0.01836.1740.0000.0000.0000.0000.0000.000
163A167LEU00.0130.00436.816-0.001-0.0010.0000.0000.0000.000
164A168ASP-1-0.833-0.89839.824-0.011-0.0110.0000.0000.0000.000
165A169ALA0-0.065-0.02941.1960.0000.0000.0000.0000.0000.000
166A170LEU00.002-0.01138.9890.0000.0000.0000.0000.0000.000
167A171LEU0-0.047-0.01743.2620.0000.0000.0000.0000.0000.000
168A172GLU-1-0.847-0.88845.810-0.009-0.0090.0000.0000.0000.000
169A173GLY0-0.0250.00446.7180.0010.0010.0000.0000.0000.000
170A174ARG10.7420.84642.7190.0120.0120.0000.0000.0000.000
171A175PRO0-0.003-0.01542.996-0.002-0.0020.0000.0000.0000.000
172A176VAL00.0040.01236.7330.0020.0020.0000.0000.0000.000
173A177PRO0-0.019-0.01636.4800.0000.0000.0000.0000.0000.000
174A178GLU-1-0.874-0.94436.143-0.021-0.0210.0000.0000.0000.000
175A179LYS10.8950.96331.171-0.005-0.0050.0000.0000.0000.000
176A180GLN00.004-0.00330.844-0.002-0.0020.0000.0000.0000.000
177A181LYS10.7970.89326.089-0.004-0.0040.0000.0000.0000.000
178A182PRO00.0740.02622.6030.0000.0000.0000.0000.0000.000
179A183SER0-0.064-0.04422.8690.0180.0180.0000.0000.0000.000
180A184ILE0-0.020-0.02016.371-0.003-0.0030.0000.0000.0000.000
181A185GLY00.0120.00216.8550.0190.0190.0000.0000.0000.000
182A186CYS0-0.009-0.02213.752-0.022-0.0220.0000.0000.0000.000
183A187SER00.0020.00213.1460.0170.0170.0000.0000.0000.000
184A188ILE0-0.0080.01114.898-0.012-0.0120.0000.0000.0000.000
185A189LYS10.8120.91912.1760.3880.3880.0000.0000.0000.000
186A190TRP00.0190.00215.8070.0310.0310.0000.0000.0000.000
187A191LYS10.8220.89616.8380.1490.1490.0000.0000.0000.000
188A192PRO0-0.042-0.02617.181-0.007-0.0070.0000.0000.0000.000
189A193SER0-0.0050.00018.2180.0260.0260.0000.0000.0000.000
190A194ALA0-0.0150.00620.1760.0060.0060.0000.0000.0000.000