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: 17GGZ

Calculation Name: 3WOH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WOH

Chain ID: A

ChEMBL ID:

UniProt ID: K9M8L2

Base Structure: X-ray

Registration Date: 2023-09-20

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 235
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2639594.23291
FMO2-HF: Nuclear repulsion 2552914.326692
FMO2-HF: Total energy -86679.906217
FMO2-MP2: Total energy -86929.325265


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:GLY)


Summations of interaction energy for fragment #1(A:5:GLY)
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.
-1.712.3930.554-2.187-2.470
Interaction energy analysis for fragmet #1(A:5:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / q_NPA : -0.016
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].
3A7LEU0-0.064-0.0223.491-1.1900.664-0.012-0.941-0.900-0.001
4A8SER0-0.063-0.0413.582-0.286-0.0990.002-0.049-0.1400.000
5A9GLY00.0120.0164.741-0.167-0.114-0.001-0.003-0.0490.000
6A10LYS10.8430.9316.729-0.263-0.2630.0000.0000.0000.000
7A11VAL00.0150.0069.3230.1830.1830.0000.0000.0000.000
8A12ALA0-0.004-0.00411.667-0.072-0.0720.0000.0000.0000.000
9A13LEU0-0.011-0.00613.313-0.002-0.0020.0000.0000.0000.000
10A14VAL00.0180.00715.267-0.023-0.0230.0000.0000.0000.000
11A15THR00.0320.01718.172-0.013-0.0130.0000.0000.0000.000
12A16GLY00.0280.00621.6150.0010.0010.0000.0000.0000.000
13A17GLY00.0290.01819.0640.0010.0010.0000.0000.0000.000
14A18SER0-0.039-0.03119.3420.0180.0180.0000.0000.0000.000
15A19ARG10.9130.92321.567-0.142-0.1420.0000.0000.0000.000
16A20GLY00.0440.03321.9920.0050.0050.0000.0000.0000.000
17A21LEU00.0460.00920.0280.0250.0250.0000.0000.0000.000
18A22GLY00.0870.04018.4850.0330.0330.0000.0000.0000.000
19A23ARG10.8870.95517.255-0.177-0.1770.0000.0000.0000.000
20A24ALA00.0050.00015.5930.0550.0550.0000.0000.0000.000
21A25MET0-0.026-0.01113.9280.0720.0720.0000.0000.0000.000
22A26ALA00.0190.01812.7350.1180.1180.0000.0000.0000.000
23A27LEU00.014-0.00111.4630.1520.1520.0000.0000.0000.000
24A28ARG10.7700.8527.773-0.581-0.5810.0000.0000.0000.000
25A29LEU00.015-0.0058.0580.3630.3630.0000.0000.0000.000
26A30ALA00.0500.0237.4070.5320.5320.0000.0000.0000.000
27A31ARG10.8950.9575.5170.0240.0240.0000.0000.0000.000
28A32ASP-1-0.779-0.8333.5851.3812.2370.082-0.354-0.5840.001
29A33GLY00.0460.0302.718-0.0381.0110.474-0.841-0.6820.000
30A34ALA0-0.021-0.0033.728-1.797-1.6930.0090.001-0.1150.000
31A35ALA00.0200.0097.199-0.065-0.0650.0000.0000.0000.000
32A36VAL0-0.014-0.00310.271-0.102-0.1020.0000.0000.0000.000
33A37ALA0-0.0060.00312.874-0.060-0.0600.0000.0000.0000.000
34A38ILE0-0.040-0.03915.905-0.012-0.0120.0000.0000.0000.000
35A39VAL00.0410.02018.739-0.032-0.0320.0000.0000.0000.000
36A40TYR0-0.139-0.10622.1780.0040.0040.0000.0000.0000.000
37A41VAL00.0620.03724.887-0.006-0.0060.0000.0000.0000.000
38A42SER00.028-0.00726.304-0.001-0.0010.0000.0000.0000.000
39A43ASP-1-0.799-0.86027.4750.1350.1350.0000.0000.0000.000
40A44ASP-1-0.742-0.85925.7590.1590.1590.0000.0000.0000.000
41A45SER0-0.045-0.03524.5790.0130.0130.0000.0000.0000.000
42A46SER00.0240.01423.2660.0050.0050.0000.0000.0000.000
43A47ALA00.0170.02920.9900.0220.0220.0000.0000.0000.000
44A48LYS10.9020.93719.677-0.199-0.1990.0000.0000.0000.000
45A49GLU-1-0.876-0.91720.0090.2090.2090.0000.0000.0000.000
46A50THR0-0.001-0.01316.0510.0170.0170.0000.0000.0000.000
47A51GLN0-0.044-0.02915.4790.0300.0300.0000.0000.0000.000
48A52GLY00.0500.02615.1310.0310.0310.0000.0000.0000.000
49A53GLU-1-0.883-0.90714.1600.2430.2430.0000.0000.0000.000
50A54ILE0-0.017-0.0189.9880.0260.0260.0000.0000.0000.000
51A55GLU-1-0.829-0.88810.6780.3870.3870.0000.0000.0000.000
52A56ARG10.8310.91212.538-0.231-0.2310.0000.0000.0000.000
53A57LEU0-0.097-0.0488.192-0.043-0.0430.0000.0000.0000.000
54A58GLY0-0.004-0.0068.3790.0290.0290.0000.0000.0000.000
55A59GLY0-0.0040.0027.7260.1440.1440.0000.0000.0000.000
56A60THR0-0.005-0.0158.627-0.212-0.2120.0000.0000.0000.000
57A61ALA00.0380.00610.9890.0870.0870.0000.0000.0000.000
58A62ARG10.8580.93513.819-0.384-0.3840.0000.0000.0000.000
59A63SER0-0.0170.00217.5240.0150.0150.0000.0000.0000.000
60A64TYR0-0.061-0.08518.462-0.004-0.0040.0000.0000.0000.000
61A65ARG10.8760.94023.328-0.123-0.1230.0000.0000.0000.000
62A66CYS0-0.033-0.01326.247-0.008-0.0080.0000.0000.0000.000
63A67ASP-1-0.828-0.90427.9090.1070.1070.0000.0000.0000.000
64A68VAL0-0.055-0.04426.500-0.001-0.0010.0000.0000.0000.000
65A69SER00.0330.01529.186-0.004-0.0040.0000.0000.0000.000
66A70ASP-1-0.887-0.94532.6180.0830.0830.0000.0000.0000.000
67A71ALA00.0130.00732.2740.0040.0040.0000.0000.0000.000
68A72GLU-1-0.866-0.92031.0270.0930.0930.0000.0000.0000.000
69A73GLN00.0460.04130.4000.0050.0050.0000.0000.0000.000
70A74VAL00.0530.01726.3160.0090.0090.0000.0000.0000.000
71A75THR0-0.006-0.04426.5680.0130.0130.0000.0000.0000.000
72A76ARG10.8800.94626.841-0.088-0.0880.0000.0000.0000.000
73A77CYS00.0260.02223.5520.0090.0090.0000.0000.0000.000
74A78VAL00.0590.03121.9200.0160.0160.0000.0000.0000.000
75A79LYS10.9240.95821.992-0.094-0.0940.0000.0000.0000.000
76A80ALA00.0020.01623.565-0.002-0.0020.0000.0000.0000.000
77A81VAL00.0180.01317.4920.0100.0100.0000.0000.0000.000
78A82THR0-0.074-0.05018.4980.0150.0150.0000.0000.0000.000
79A83ALA0-0.072-0.03119.513-0.001-0.0010.0000.0000.0000.000
80A84ASP-1-0.855-0.89218.4870.2230.2230.0000.0000.0000.000
81A85LEU0-0.071-0.03413.6990.0240.0240.0000.0000.0000.000
82A86GLY00.0470.03814.4590.0170.0170.0000.0000.0000.000
83A87PRO0-0.059-0.04316.1950.0030.0030.0000.0000.0000.000
84A88VAL00.0570.03015.3810.0250.0250.0000.0000.0000.000
85A89ASP-1-0.833-0.88612.6650.2310.2310.0000.0000.0000.000
86A90ILE00.0030.00310.654-0.032-0.0320.0000.0000.0000.000
87A91LEU0-0.0300.00014.8110.0230.0230.0000.0000.0000.000
88A92VAL00.0150.01115.751-0.019-0.0190.0000.0000.0000.000
89A93ASN0-0.031-0.02418.7950.0070.0070.0000.0000.0000.000
90A94ASN0-0.003-0.02921.049-0.021-0.0210.0000.0000.0000.000
91A95ALA0-0.052-0.00822.985-0.009-0.0090.0000.0000.0000.000
92A96GLY00.0420.01225.880-0.007-0.0070.0000.0000.0000.000
93A97ILE0-0.051-0.00828.9160.0020.0020.0000.0000.0000.000
94A98ILE00.0260.00630.204-0.003-0.0030.0000.0000.0000.000
95A99ARG10.8790.91433.971-0.072-0.0720.0000.0000.0000.000
96A100ASP-1-0.871-0.90537.0130.0650.0650.0000.0000.0000.000
97A101GLY00.0390.01739.473-0.001-0.0010.0000.0000.0000.000
98A102LEU00.004-0.01143.0930.0000.0000.0000.0000.0000.000
99A103ALA00.027-0.00145.0140.0010.0010.0000.0000.0000.000
100A104ALA00.0040.01045.9050.0000.0000.0000.0000.0000.000
101A105SER0-0.072-0.03946.213-0.001-0.0010.0000.0000.0000.000
102A106ILE0-0.073-0.02141.7370.0020.0020.0000.0000.0000.000
103A107LYS10.9570.96344.154-0.048-0.0480.0000.0000.0000.000
104A108ASP-1-0.856-0.91943.5980.0490.0490.0000.0000.0000.000
105A109GLU-1-0.859-0.91942.6090.0540.0540.0000.0000.0000.000
106A110ASP-1-0.839-0.92940.0380.0620.0620.0000.0000.0000.000
107A111TYR0-0.017-0.01538.9380.0050.0050.0000.0000.0000.000
108A112ASP-1-0.820-0.92338.7130.0650.0650.0000.0000.0000.000
109A113ALA0-0.0310.00736.6310.0050.0050.0000.0000.0000.000
110A114VAL0-0.0450.00434.3520.0080.0080.0000.0000.0000.000
111A115MET00.0530.04133.7300.0080.0080.0000.0000.0000.000
112A116ASN0-0.053-0.06234.1200.0050.0050.0000.0000.0000.000
113A117THR0-0.034-0.04630.6330.0070.0070.0000.0000.0000.000
114A118ASN0-0.058-0.04129.3750.0160.0160.0000.0000.0000.000
115A119LEU0-0.0290.00229.4260.0040.0040.0000.0000.0000.000
116A120LYS10.8600.93530.571-0.078-0.0780.0000.0000.0000.000
117A121GLY00.0790.04328.6710.0020.0020.0000.0000.0000.000
118A122ALA00.0070.00426.0500.0080.0080.0000.0000.0000.000
119A123PHE00.007-0.00126.8680.0020.0020.0000.0000.0000.000
120A124LEU0-0.045-0.00429.046-0.002-0.0020.0000.0000.0000.000
121A125PHE00.034-0.00122.8430.0040.0040.0000.0000.0000.000
122A126ILE00.0030.00924.0070.0070.0070.0000.0000.0000.000
123A127LYS10.8820.93325.430-0.088-0.0880.0000.0000.0000.000
124A128ALA0-0.064-0.02425.133-0.004-0.0040.0000.0000.0000.000
125A129CYS0-0.050-0.02721.1080.0070.0070.0000.0000.0000.000
126A130TYR0-0.059-0.04122.747-0.001-0.0010.0000.0000.0000.000
127A131PHE00.044-0.00225.050-0.006-0.0060.0000.0000.0000.000
128A132GLY0-0.033-0.00621.919-0.007-0.0070.0000.0000.0000.000
129A133PHE00.0560.01017.590-0.008-0.0080.0000.0000.0000.000
130A134ILE00.0400.03821.239-0.013-0.0130.0000.0000.0000.000
131A135ARG10.8810.93423.430-0.081-0.0810.0000.0000.0000.000
132A136LYS10.7890.85715.349-0.195-0.1950.0000.0000.0000.000
133A137ARG10.8460.94819.586-0.040-0.0400.0000.0000.0000.000
134A138SER00.0530.03615.488-0.007-0.0070.0000.0000.0000.000
135A139GLY00.0540.01116.6880.0150.0150.0000.0000.0000.000
136A140SER0-0.072-0.04015.329-0.033-0.0330.0000.0000.0000.000
137A141ILE00.010-0.00116.9860.0440.0440.0000.0000.0000.000
138A142ILE00.004-0.00815.868-0.019-0.0190.0000.0000.0000.000
139A143ASN00.019-0.00219.8740.0270.0270.0000.0000.0000.000
140A144ILE00.0110.00419.842-0.009-0.0090.0000.0000.0000.000
141A145SER0-0.029-0.03623.759-0.010-0.0100.0000.0000.0000.000
142A146SER00.0640.08426.607-0.002-0.0020.0000.0000.0000.000
143A147VAL00.0840.03728.132-0.005-0.0050.0000.0000.0000.000
144A148SER0-0.018-0.01130.254-0.005-0.0050.0000.0000.0000.000
145A149GLY0-0.031-0.02631.707-0.003-0.0030.0000.0000.0000.000
146A150VAL0-0.068-0.03429.784-0.003-0.0030.0000.0000.0000.000
147A151PHE0-0.026-0.01232.977-0.004-0.0040.0000.0000.0000.000
148A152GLY00.0130.02535.839-0.003-0.0030.0000.0000.0000.000
149A153SER00.009-0.04036.2920.0000.0000.0000.0000.0000.000
150A154ALA00.0040.00338.4700.0010.0010.0000.0000.0000.000
151A155GLY0-0.005-0.00340.6770.0010.0010.0000.0000.0000.000
152A156GLN00.0360.02534.6490.0010.0010.0000.0000.0000.000
153A157ALA00.0310.02337.8140.0030.0030.0000.0000.0000.000
154A158ASN00.0210.02538.7050.0020.0020.0000.0000.0000.000
155A159TYR00.0590.02929.4260.0060.0060.0000.0000.0000.000
156A160ALA00.0180.00233.9520.0040.0040.0000.0000.0000.000
157A161SER0-0.009-0.02534.9140.0000.0000.0000.0000.0000.000
158A162ALA00.0270.01633.3450.0010.0010.0000.0000.0000.000
159A163LYS10.8660.94726.932-0.118-0.1180.0000.0000.0000.000
160A164ALA00.0250.02630.8470.0030.0030.0000.0000.0000.000
161A165GLY0-0.001-0.00333.027-0.002-0.0020.0000.0000.0000.000
162A166LEU0-0.0060.00426.2810.0000.0000.0000.0000.0000.000
163A167ILE00.0060.01528.7640.0030.0030.0000.0000.0000.000
164A168GLY0-0.013-0.01129.966-0.003-0.0030.0000.0000.0000.000
165A169LEU00.0010.01328.372-0.003-0.0030.0000.0000.0000.000
166A170THR0-0.004-0.02124.8320.0040.0040.0000.0000.0000.000
167A171LYS10.8980.96427.302-0.049-0.0490.0000.0000.0000.000
168A172SER0-0.030-0.02529.663-0.006-0.0060.0000.0000.0000.000
169A173ILE00.0430.01925.379-0.002-0.0020.0000.0000.0000.000
170A174ALA0-0.0110.00525.692-0.002-0.0020.0000.0000.0000.000
171A175LYS10.9160.93726.665-0.035-0.0350.0000.0000.0000.000
172A176GLU-1-0.877-0.89129.2860.0550.0550.0000.0000.0000.000
173A177LEU0-0.013-0.00824.269-0.001-0.0010.0000.0000.0000.000
174A178ALA00.0230.02425.310-0.003-0.0030.0000.0000.0000.000
175A179GLU-1-0.926-0.96125.5190.0070.0070.0000.0000.0000.000
176A180ARG10.8080.90425.126-0.036-0.0360.0000.0000.0000.000
177A181ASN0-0.043-0.03618.8810.0030.0030.0000.0000.0000.000
178A182VAL0-0.0420.00120.1610.0070.0070.0000.0000.0000.000
179A183ARG10.8560.93414.896-0.070-0.0700.0000.0000.0000.000
180A184CYS0-0.0310.00520.5980.0250.0250.0000.0000.0000.000
181A185ASN0-0.001-0.01319.987-0.030-0.0300.0000.0000.0000.000
182A186ALA00.0080.00322.5170.0160.0160.0000.0000.0000.000
183A187VAL00.002-0.00219.327-0.008-0.0080.0000.0000.0000.000
184A188ALA00.1150.01322.7810.0040.0040.0000.0000.0000.000
185A189PRO0-0.076-0.03022.709-0.009-0.0090.0000.0000.0000.000
186A190GLY00.0350.01325.013-0.007-0.0070.0000.0000.0000.000
187A191LEU0-0.034-0.01327.8670.0060.0060.0000.0000.0000.000
188A192ILE0-0.041-0.01622.9810.0000.0000.0000.0000.0000.000
189A193ALA00.0080.04626.104-0.001-0.0010.0000.0000.0000.000
190A194THR0-0.060-0.07923.5430.0100.0100.0000.0000.0000.000
191A195ASP-1-0.886-0.92425.8060.1300.1300.0000.0000.0000.000
192A206ARG10.8720.90135.565-0.030-0.0300.0000.0000.0000.000
193A207LEU0-0.036-0.03831.3160.0010.0010.0000.0000.0000.000
194A208ASP-1-0.799-0.85834.8020.0260.0260.0000.0000.0000.000
195A209PRO0-0.0100.00435.355-0.002-0.0020.0000.0000.0000.000
196A210VAL00.000-0.00130.1280.0010.0010.0000.0000.0000.000
197A211PRO00.0460.03231.776-0.002-0.0020.0000.0000.0000.000
198A212MET0-0.038-0.01125.2800.0000.0000.0000.0000.0000.000
199A213ARG10.9190.96230.585-0.019-0.0190.0000.0000.0000.000
200A214ARG10.7610.84822.494-0.053-0.0530.0000.0000.0000.000
201A215PHE00.0380.01627.5300.0010.0010.0000.0000.0000.000
202A216GLY00.0060.00224.156-0.005-0.0050.0000.0000.0000.000
203A217ARG10.8480.88017.490-0.100-0.1000.0000.0000.0000.000
204A218PRO00.0240.00519.0900.0060.0060.0000.0000.0000.000
205A219ASP-1-0.806-0.89014.7930.1820.1820.0000.0000.0000.000
206A220GLU-1-0.748-0.83215.2880.0880.0880.0000.0000.0000.000
207A221VAL00.0080.00017.426-0.005-0.0050.0000.0000.0000.000
208A222ALA0-0.020-0.00513.8680.0110.0110.0000.0000.0000.000
209A223GLY00.0070.00512.6690.0600.0600.0000.0000.0000.000
210A224LEU00.0000.01313.4620.0020.0020.0000.0000.0000.000
211A225VAL00.009-0.01214.275-0.011-0.0110.0000.0000.0000.000
212A226ALA00.0080.0059.7300.0140.0140.0000.0000.0000.000
213A227PHE00.0080.00611.479-0.016-0.0160.0000.0000.0000.000
214A228LEU0-0.029-0.00913.106-0.046-0.0460.0000.0000.0000.000
215A229ALA0-0.0080.02111.860-0.026-0.0260.0000.0000.0000.000
216A230GLY00.0170.02210.5790.0140.0140.0000.0000.0000.000
217A231ASP-1-0.853-0.92410.624-0.100-0.1000.0000.0000.0000.000
218A232GLU-1-0.914-0.95011.449-0.376-0.3760.0000.0000.0000.000
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228A242CYS00.0100.01123.6400.0150.0150.0000.0000.0000.000
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230A244ASP-1-0.749-0.89323.6330.0580.0580.0000.0000.0000.000
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