Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 9G692

Calculation Name: 5DAJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DAJ

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HY46

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 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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2317587.230812
FMO2-HF: Nuclear repulsion 2234740.246275
FMO2-HF: Total energy -82846.984537
FMO2-MP2: Total energy -83085.732432


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:LYS)


Summations of interaction energy for fragment #1(A:5:LYS)
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.
-47.515-44.4280.083-0.923-2.2460.004
Interaction energy analysis for fragmet #1(A:5:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.891 / q_NPA : 0.924
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].
3A7ASP-1-0.892-0.9353.216-32.152-29.9610.081-0.757-1.5140.004
4A8SER00.0370.0263.7201.6092.0180.001-0.101-0.3090.000
5A9GLU-1-0.804-0.8803.937-42.067-41.5800.001-0.065-0.4230.000
6A10LYS10.8510.9215.80943.29143.2910.0000.0000.0000.000
7A11THR0-0.028-0.0168.1544.5744.5740.0000.0000.0000.000
8A12ARG10.7880.8617.77834.46334.4630.0000.0000.0000.000
9A13THR0-0.017-0.0148.0742.5522.5520.0000.0000.0000.000
10A14ALA00.0010.00110.7712.2182.2180.0000.0000.0000.000
11A15ILE0-0.015-0.01212.6561.9211.9210.0000.0000.0000.000
12A16LEU00.0010.00112.0321.5051.5050.0000.0000.0000.000
13A17LEU0-0.0020.00313.8991.2231.2230.0000.0000.0000.000
14A18ALA00.0400.02416.8201.1481.1480.0000.0000.0000.000
15A19ALA0-0.011-0.01918.6170.9930.9930.0000.0000.0000.000
16A20GLU-1-0.802-0.88518.452-16.073-16.0730.0000.0000.0000.000
17A21GLU-1-0.938-0.97020.769-12.908-12.9080.0000.0000.0000.000
18A22LEU0-0.030-0.02423.0820.7560.7560.0000.0000.0000.000
19A23PHE0-0.002-0.02721.5340.5110.5110.0000.0000.0000.000
20A24LEU0-0.0190.00824.9090.4630.4630.0000.0000.0000.000
21A25GLU-1-0.856-0.92726.655-10.309-10.3090.0000.0000.0000.000
22A26LYS10.7850.89227.80911.51711.5170.0000.0000.0000.000
23A27GLY00.0540.04428.9410.3900.3900.0000.0000.0000.000
24A28VAL0-0.046-0.02425.405-0.163-0.1630.0000.0000.0000.000
25A29SER0-0.011-0.02627.607-0.263-0.2630.0000.0000.0000.000
26A30HIS0-0.0040.00530.366-0.090-0.0900.0000.0000.0000.000
27A31THR0-0.011-0.01525.089-0.074-0.0740.0000.0000.0000.000
28A32SER0-0.006-0.00625.839-0.185-0.1850.0000.0000.0000.000
29A33LEU00.0820.02020.134-0.227-0.2270.0000.0000.0000.000
30A34GLU-1-0.828-0.88520.949-11.704-11.7040.0000.0000.0000.000
31A35GLN00.0040.00922.915-0.249-0.2490.0000.0000.0000.000
32A36ILE00.0670.04118.941-0.074-0.0740.0000.0000.0000.000
33A37ALA0-0.021-0.00718.440-0.523-0.5230.0000.0000.0000.000
34A38ARG10.8300.89219.44911.21711.2170.0000.0000.0000.000
35A39ALA00.0030.00822.2520.1100.1100.0000.0000.0000.000
36A40ALA0-0.003-0.00416.622-0.224-0.2240.0000.0000.0000.000
37A41GLY0-0.0210.01617.214-0.759-0.7590.0000.0000.0000.000
38A42VAL0-0.035-0.01613.520-0.384-0.3840.0000.0000.0000.000
39A43THR00.026-0.00116.0740.6730.6730.0000.0000.0000.000
40A44ARG10.9330.93817.14711.12211.1220.0000.0000.0000.000
41A45GLY00.0040.00117.380-0.174-0.1740.0000.0000.0000.000
42A46ALA00.0440.02712.807-0.400-0.4000.0000.0000.0000.000
43A47VAL00.0360.02613.414-1.180-1.1800.0000.0000.0000.000
44A48TYR0-0.011-0.02015.885-0.093-0.0930.0000.0000.0000.000
45A49TRP0-0.038-0.0208.9530.7370.7370.0000.0000.0000.000
46A50HIS0-0.042-0.0258.476-2.508-2.5080.0000.0000.0000.000
47A51PHE00.0410.02012.040-0.960-0.9600.0000.0000.0000.000
48A52GLN00.0040.02014.4770.3160.3160.0000.0000.0000.000
49A53ASN0-0.080-0.05617.7930.9450.9450.0000.0000.0000.000
50A54LYS10.8060.89120.13410.84310.8430.0000.0000.0000.000
51A55ALA00.0250.02922.183-0.339-0.3390.0000.0000.0000.000
52A56HIS0-0.051-0.03715.971-1.317-1.3170.0000.0000.0000.000
53A57LEU0-0.0040.00317.046-0.720-0.7200.0000.0000.0000.000
54A58PHE00.0490.01118.019-0.693-0.6930.0000.0000.0000.000
55A59ASN0-0.011-0.00419.470-0.504-0.5040.0000.0000.0000.000
56A60GLU-1-0.749-0.86512.336-24.948-24.9480.0000.0000.0000.000
57A61MET0-0.065-0.01515.326-0.576-0.5760.0000.0000.0000.000
58A62LEU0-0.015-0.01017.086-0.174-0.1740.0000.0000.0000.000
59A63ASN00.000-0.01014.8451.3811.3810.0000.0000.0000.000
60A64GLN0-0.043-0.00611.5000.7140.7140.0000.0000.0000.000
61A65VAL0-0.040-0.02014.8600.0450.0450.0000.0000.0000.000
62A66ARG10.8050.90318.14816.30916.3090.0000.0000.0000.000
63A67LEU00.0480.03017.560-0.915-0.9150.0000.0000.0000.000
64A68PRO00.0080.01116.1830.4530.4530.0000.0000.0000.000
65A69PRO00.042-0.00218.5790.6110.6110.0000.0000.0000.000
66A70GLU-1-0.881-0.93018.627-15.652-15.6520.0000.0000.0000.000
67A71GLN00.0530.01816.7650.2360.2360.0000.0000.0000.000
68A72LEU0-0.037-0.00721.0670.6950.6950.0000.0000.0000.000
69A73THR0-0.030-0.04023.9890.5700.5700.0000.0000.0000.000
70A74GLU-1-0.949-0.95421.443-14.035-14.0350.0000.0000.0000.000
71A75ARG10.8190.87624.82012.30312.3030.0000.0000.0000.000
72A76LEU00.0200.01326.5380.4960.4960.0000.0000.0000.000
73A77SER0-0.047-0.04228.1840.4960.4960.0000.0000.0000.000
74A78GLY0-0.022-0.01130.3840.2970.2970.0000.0000.0000.000
75A79CYS0-0.0230.02331.070-0.050-0.0500.0000.0000.0000.000
76A80ASP-1-0.878-0.93328.425-11.121-11.1210.0000.0000.0000.000
77A81GLY0-0.034-0.04131.3180.2330.2330.0000.0000.0000.000
78A82SER0-0.075-0.04034.9200.2090.2090.0000.0000.0000.000
79A83ASP-1-0.779-0.87935.455-8.377-8.3770.0000.0000.0000.000
80A84PRO00.0380.02733.660-0.152-0.1520.0000.0000.0000.000
81A85LEU00.005-0.01433.939-0.196-0.1960.0000.0000.0000.000
82A86ARG10.8050.88035.1178.8388.8380.0000.0000.0000.000
83A87SER00.027-0.01130.368-0.061-0.0610.0000.0000.0000.000
84A88LEU0-0.024-0.00130.889-0.312-0.3120.0000.0000.0000.000
85A89TYR0-0.014-0.00332.267-0.191-0.1910.0000.0000.0000.000
86A90ASP-1-0.747-0.85230.936-9.568-9.5680.0000.0000.0000.000
87A91LEU0-0.0070.00525.307-0.291-0.2910.0000.0000.0000.000
88A92CYS0-0.069-0.04228.372-0.258-0.2580.0000.0000.0000.000
89A93LEU00.0340.02130.918-0.056-0.0560.0000.0000.0000.000
90A94GLU-1-0.783-0.85225.964-12.140-12.1400.0000.0000.0000.000
91A95ALA0-0.045-0.00326.338-0.407-0.4070.0000.0000.0000.000
92A96VAL0-0.009-0.01227.409-0.183-0.1830.0000.0000.0000.000
93A97GLN00.0530.02429.051-0.389-0.3890.0000.0000.0000.000
94A98SER0-0.060-0.04423.989-0.175-0.1750.0000.0000.0000.000
95A99LEU0-0.061-0.02525.297-0.527-0.5270.0000.0000.0000.000
96A100LEU00.0270.02627.661-0.119-0.1190.0000.0000.0000.000
97A101THR00.0100.00025.008-0.415-0.4150.0000.0000.0000.000
98A102GLN00.0120.00820.244-0.561-0.5610.0000.0000.0000.000
99A103GLU-1-0.820-0.89322.501-12.593-12.5930.0000.0000.0000.000
100A104LYS10.8570.92414.68019.99619.9960.0000.0000.0000.000
101A105LYS10.8990.95820.31912.94312.9430.0000.0000.0000.000
102A106ARG10.8190.89121.90712.31912.3190.0000.0000.0000.000
103A107ARG10.8730.93420.93914.86014.8600.0000.0000.0000.000
104A108ILE00.019-0.00118.0950.3840.3840.0000.0000.0000.000
105A109LEU0-0.006-0.00422.6350.2800.2800.0000.0000.0000.000
106A110THR00.028-0.00425.6230.5790.5790.0000.0000.0000.000
107A111ILE0-0.047-0.02522.7200.3480.3480.0000.0000.0000.000
108A112LEU0-0.055-0.03124.9650.3410.3410.0000.0000.0000.000
109A113MET0-0.055-0.00827.0360.4060.4060.0000.0000.0000.000
110A114GLN00.0010.00130.1600.1510.1510.0000.0000.0000.000
111A115ARG10.8190.92128.28410.76910.7690.0000.0000.0000.000
112A116CYS0-0.062-0.01927.643-0.281-0.2810.0000.0000.0000.000
113A117GLU-1-0.798-0.86729.780-9.097-9.0970.0000.0000.0000.000
114A118PHE0-0.021-0.00826.894-0.140-0.1400.0000.0000.0000.000
115A119THR00.0210.00131.7090.2230.2230.0000.0000.0000.000
116A120GLU-1-0.801-0.90431.193-9.877-9.8770.0000.0000.0000.000
117A121GLU-1-0.864-0.91228.220-11.463-11.4630.0000.0000.0000.000
118A122LEU0-0.009-0.02025.772-0.638-0.6380.0000.0000.0000.000
119A123ARG10.8170.89327.4339.6339.6330.0000.0000.0000.000
120A124GLU-1-0.741-0.84920.762-14.854-14.8540.0000.0000.0000.000
121A125ALA0-0.041-0.02223.359-0.402-0.4020.0000.0000.0000.000
122A126GLN00.0120.00824.372-0.086-0.0860.0000.0000.0000.000
123A127GLU-1-0.844-0.90827.089-10.638-10.6380.0000.0000.0000.000
124A128ARG10.8540.89720.03715.04215.0420.0000.0000.0000.000
125A129ASN00.0250.03424.307-0.725-0.7250.0000.0000.0000.000
126A130ASN0-0.004-0.00925.5280.1130.1130.0000.0000.0000.000
127A131ALA00.0020.00825.3050.2170.2170.0000.0000.0000.000
128A132PHE00.0000.00221.8650.0960.0960.0000.0000.0000.000
129A133VAL00.0030.00125.2040.1330.1330.0000.0000.0000.000
130A134GLN0-0.063-0.04628.6320.3360.3360.0000.0000.0000.000
131A135MET00.0370.01924.4690.0270.0270.0000.0000.0000.000
132A136PHE00.0340.01626.9530.1670.1670.0000.0000.0000.000
133A137ILE0-0.004-0.00428.5090.3330.3330.0000.0000.0000.000
134A138GLU-1-0.858-0.92330.659-9.867-9.8670.0000.0000.0000.000
135A139LEU0-0.015-0.00426.1100.2240.2240.0000.0000.0000.000
136A140CYS0-0.037-0.00730.6750.2640.2640.0000.0000.0000.000
137A141GLU-1-0.853-0.92333.325-8.197-8.1970.0000.0000.0000.000
138A142GLN00.021-0.00231.2810.3990.3990.0000.0000.0000.000
139A143LEU00.0050.00932.6650.2160.2160.0000.0000.0000.000
140A144PHE00.036-0.00735.1260.2440.2440.0000.0000.0000.000
141A145ALA0-0.053-0.03038.1100.2870.2870.0000.0000.0000.000
142A146ARG10.8760.95332.0939.6549.6540.0000.0000.0000.000
143A147ASP-1-0.883-0.94339.776-7.187-7.1870.0000.0000.0000.000
144A148GLU-1-0.899-0.97238.329-8.053-8.0530.0000.0000.0000.000
145A149CYS0-0.085-0.03137.7370.0580.0580.0000.0000.0000.000
146A150ARG10.9110.94841.3537.5277.5270.0000.0000.0000.000
147A151VAL0-0.043-0.02143.9830.1640.1640.0000.0000.0000.000
148A152ARG10.8030.86640.6267.7667.7660.0000.0000.0000.000
149A153LEU0-0.0060.02941.6230.0210.0210.0000.0000.0000.000
150A154HIS00.0010.01245.5270.3210.3210.0000.0000.0000.000
151A155PRO0-0.021-0.02848.545-0.041-0.0410.0000.0000.0000.000
152A156GLY0-0.0160.00350.2450.0130.0130.0000.0000.0000.000
153A157MET0-0.0050.00443.920-0.052-0.0520.0000.0000.0000.000
154A158THR0-0.007-0.00544.662-0.134-0.1340.0000.0000.0000.000
155A159PRO00.0600.02739.684-0.053-0.0530.0000.0000.0000.000
156A160ARG10.9651.01139.4907.2287.2280.0000.0000.0000.000
157A161ILE0-0.047-0.01740.106-0.116-0.1160.0000.0000.0000.000
158A162ALA00.0350.02040.395-0.099-0.0990.0000.0000.0000.000
159A163SER00.014-0.00835.532-0.114-0.1140.0000.0000.0000.000
160A164ARG10.8060.88735.8468.4918.4910.0000.0000.0000.000
161A165ALA0-0.0050.00237.602-0.065-0.0650.0000.0000.0000.000
162A166LEU00.0510.02434.279-0.023-0.0230.0000.0000.0000.000
163A167HIS00.003-0.00430.3380.1200.1200.0000.0000.0000.000
164A168ALA00.005-0.00134.110-0.163-0.1630.0000.0000.0000.000
165A169LEU00.0020.01736.7310.0070.0070.0000.0000.0000.000
166A170ILE00.0130.00830.288-0.056-0.0560.0000.0000.0000.000
167A171LEU0-0.026-0.01231.323-0.203-0.2030.0000.0000.0000.000
168A172GLY00.0100.00133.116-0.056-0.0560.0000.0000.0000.000
169A173LEU0-0.001-0.00634.3080.0140.0140.0000.0000.0000.000
170A174PHE0-0.002-0.01126.575-0.231-0.2310.0000.0000.0000.000
171A175ASN00.000-0.01731.9960.1920.1920.0000.0000.0000.000
172A176ASP-1-0.809-0.89533.719-8.154-8.1540.0000.0000.0000.000
173A177TRP0-0.0060.00430.263-0.150-0.1500.0000.0000.0000.000
174A178LEU0-0.058-0.03828.706-0.104-0.1040.0000.0000.0000.000
175A179ARG10.7750.88532.5138.1918.1910.0000.0000.0000.000
176A180ASP-1-0.830-0.89435.755-7.876-7.8760.0000.0000.0000.000
177A181PRO00.0460.02533.8500.1230.1230.0000.0000.0000.000
178A182ARG10.7440.82935.9627.8027.8020.0000.0000.0000.000
179A183LEU0-0.083-0.02438.6980.2120.2120.0000.0000.0000.000
180A184PHE00.000-0.00234.9130.1690.1690.0000.0000.0000.000
181A185ASP-1-0.749-0.85435.291-9.351-9.3510.0000.0000.0000.000
182A186PRO0-0.088-0.05631.7360.0420.0420.0000.0000.0000.000
183A187ASP-1-0.940-0.96932.243-10.019-10.0190.0000.0000.0000.000
184A188THR0-0.040-0.04833.6580.1330.1330.0000.0000.0000.000
185A189ASP-1-0.809-0.90337.323-7.842-7.8420.0000.0000.0000.000
186A190ALA0-0.035-0.02034.2270.1240.1240.0000.0000.0000.000
187A191GLU-1-0.862-0.93636.278-8.383-8.3830.0000.0000.0000.000
188A192HIS0-0.044-0.02737.8360.2740.2740.0000.0000.0000.000
189A193LEU0-0.028-0.01037.7660.1810.1810.0000.0000.0000.000
190A194LEU0-0.019-0.00133.7950.0440.0440.0000.0000.0000.000
191A195GLU-1-0.762-0.85038.416-7.391-7.3910.0000.0000.0000.000
192A196PRO0-0.033-0.01841.3940.1270.1270.0000.0000.0000.000
193A197MET0-0.0200.00638.8420.1660.1660.0000.0000.0000.000
194A198PHE00.0140.00235.0570.0730.0730.0000.0000.0000.000
195A199ARG10.8750.91641.1357.0557.0550.0000.0000.0000.000
196A200GLY0-0.0040.00844.4950.1820.1820.0000.0000.0000.000
197A201LEU0-0.065-0.02839.9210.0840.0840.0000.0000.0000.000
198A202VAL0-0.037-0.02641.3400.0680.0680.0000.0000.0000.000
199A203ARG10.8320.91244.6296.5866.5860.0000.0000.0000.000
200A204ASP-1-0.815-0.86644.866-7.071-7.0710.0000.0000.0000.000
201A205TRP0-0.106-0.07937.915-0.030-0.0300.0000.0000.0000.000