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: LJ249

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 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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2308014.1665
FMO2-HF: Nuclear repulsion 2225167.532349
FMO2-HF: Total energy -82846.63415
FMO2-MP2: Total energy -83085.343714


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.
-48.144-45.2440.057-0.982-1.9760.003
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 : 0.871 / q_NPA : 0.916
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-1-0.906-0.9533.345-30.412-28.1880.058-0.852-1.4310.003
4A8SER00.0250.0093.8720.9631.3020.000-0.098-0.2410.000
5A9GLU-1-0.790-0.8854.273-39.729-39.392-0.001-0.032-0.3040.000
6A10LYS10.8390.9176.23341.03141.0310.0000.0000.0000.000
7A11THR0-0.012-0.0078.6374.0914.0910.0000.0000.0000.000
8A12ARG10.8060.8838.01333.30233.3020.0000.0000.0000.000
9A13THR0-0.004-0.0018.7432.6162.6160.0000.0000.0000.000
10A14ALA0-0.0040.00611.4782.0572.0570.0000.0000.0000.000
11A15ILE0-0.003-0.00612.7131.8011.8010.0000.0000.0000.000
12A16LEU0-0.007-0.00312.5011.3931.3930.0000.0000.0000.000
13A17LEU00.0000.00014.5031.1161.1160.0000.0000.0000.000
14A18ALA00.0360.02717.3641.0751.0750.0000.0000.0000.000
15A19ALA00.003-0.01319.3250.9240.9240.0000.0000.0000.000
16A20GLU-1-0.821-0.88118.909-15.720-15.7200.0000.0000.0000.000
17A21GLU-1-0.929-0.97021.300-12.686-12.6860.0000.0000.0000.000
18A22LEU0-0.010-0.01623.5780.7260.7260.0000.0000.0000.000
19A23PHE0-0.027-0.02721.9860.5410.5410.0000.0000.0000.000
20A24LEU0-0.0020.01125.4520.5130.5130.0000.0000.0000.000
21A25GLU-1-0.920-0.95027.231-10.338-10.3380.0000.0000.0000.000
22A26LYS10.7850.88928.23511.25611.2560.0000.0000.0000.000
23A27GLY00.0290.03029.5330.4020.4020.0000.0000.0000.000
24A28VAL0-0.017-0.01525.986-0.176-0.1760.0000.0000.0000.000
25A29SER0-0.036-0.05028.364-0.300-0.3000.0000.0000.0000.000
26A30HIS0-0.0110.00230.688-0.070-0.0700.0000.0000.0000.000
27A31THR0-0.016-0.01125.082-0.035-0.0350.0000.0000.0000.000
28A32SER0-0.017-0.01026.070-0.286-0.2860.0000.0000.0000.000
29A33LEU00.0960.02220.011-0.279-0.2790.0000.0000.0000.000
30A34GLU-1-0.885-0.92421.352-11.454-11.4540.0000.0000.0000.000
31A35GLN00.0110.00023.114-0.326-0.3260.0000.0000.0000.000
32A36ILE00.0600.04319.059-0.066-0.0660.0000.0000.0000.000
33A37ALA0-0.020-0.00818.636-0.518-0.5180.0000.0000.0000.000
34A38ARG10.8700.91319.56010.97010.9700.0000.0000.0000.000
35A39ALA00.0040.00522.170-0.021-0.0210.0000.0000.0000.000
36A40ALA00.0190.01816.899-0.232-0.2320.0000.0000.0000.000
37A41GLY0-0.0460.00517.448-0.760-0.7600.0000.0000.0000.000
38A42VAL0-0.032-0.01613.704-0.652-0.6520.0000.0000.0000.000
39A43THR00.0320.01216.0250.7150.7150.0000.0000.0000.000
40A44ARG10.9430.94216.98510.97910.9790.0000.0000.0000.000
41A45GLY00.0190.00717.269-0.012-0.0120.0000.0000.0000.000
42A46ALA00.0540.03112.671-0.389-0.3890.0000.0000.0000.000
43A47VAL00.0280.02313.229-1.044-1.0440.0000.0000.0000.000
44A48TYR0-0.007-0.02215.422-0.232-0.2320.0000.0000.0000.000
45A49TRP0-0.057-0.0148.9040.7650.7650.0000.0000.0000.000
46A50HIS0-0.032-0.0238.381-2.407-2.4070.0000.0000.0000.000
47A51PHE00.0340.00912.023-0.681-0.6810.0000.0000.0000.000
48A52GLN00.0070.03114.5730.4100.4100.0000.0000.0000.000
49A53ASN0-0.053-0.03817.8030.9130.9130.0000.0000.0000.000
50A54LYS10.8500.90420.19510.74310.7430.0000.0000.0000.000
51A55ALA00.0230.02522.237-0.344-0.3440.0000.0000.0000.000
52A56HIS0-0.057-0.04016.007-1.201-1.2010.0000.0000.0000.000
53A57LEU0-0.0100.00217.400-0.738-0.7380.0000.0000.0000.000
54A58PHE00.025-0.00318.397-0.688-0.6880.0000.0000.0000.000
55A59ASN00.0100.00419.690-0.455-0.4550.0000.0000.0000.000
56A60GLU-1-0.765-0.87412.933-24.257-24.2570.0000.0000.0000.000
57A61MET0-0.063-0.01815.425-0.694-0.6940.0000.0000.0000.000
58A62LEU0-0.039-0.02417.345-0.168-0.1680.0000.0000.0000.000
59A63ASN00.0080.00315.4221.2721.2720.0000.0000.0000.000
60A64GLN0-0.028-0.00312.2590.8080.8080.0000.0000.0000.000
61A65VAL0-0.028-0.01415.166-0.182-0.1820.0000.0000.0000.000
62A66ARG10.8310.93118.14216.04516.0450.0000.0000.0000.000
63A67LEU00.0300.02017.970-0.811-0.8110.0000.0000.0000.000
64A68PRO00.0160.01616.0090.5190.5190.0000.0000.0000.000
65A69PRO00.035-0.00518.6820.5460.5460.0000.0000.0000.000
66A70GLU-1-0.880-0.94318.538-15.747-15.7470.0000.0000.0000.000
67A71GLN00.0400.01316.5380.3950.3950.0000.0000.0000.000
68A72LEU0-0.0170.00121.0230.6540.6540.0000.0000.0000.000
69A73THR0-0.019-0.03223.9980.4850.4850.0000.0000.0000.000
70A74GLU-1-0.955-0.95221.506-13.980-13.9800.0000.0000.0000.000
71A75ARG10.8050.87024.70512.21712.2170.0000.0000.0000.000
72A76LEU0-0.020-0.00826.3680.4930.4930.0000.0000.0000.000
73A77SER0-0.049-0.04128.2650.4710.4710.0000.0000.0000.000
74A78GLY0-0.011-0.00630.4700.2920.2920.0000.0000.0000.000
75A79CYS0-0.0320.03031.040-0.017-0.0170.0000.0000.0000.000
76A80ASP-1-0.872-0.92828.622-11.121-11.1210.0000.0000.0000.000
77A81GLY0-0.039-0.04431.3570.2740.2740.0000.0000.0000.000
78A82SER0-0.077-0.04834.8390.1830.1830.0000.0000.0000.000
79A83ASP-1-0.793-0.88435.490-8.345-8.3450.0000.0000.0000.000
80A84PRO00.0680.03834.061-0.164-0.1640.0000.0000.0000.000
81A85LEU0-0.037-0.02634.442-0.166-0.1660.0000.0000.0000.000
82A86ARG10.8180.88835.1468.8398.8390.0000.0000.0000.000
83A87SER00.042-0.01130.460-0.100-0.1000.0000.0000.0000.000
84A88LEU0-0.0210.00130.933-0.315-0.3150.0000.0000.0000.000
85A89TYR0-0.0020.00632.232-0.208-0.2080.0000.0000.0000.000
86A90ASP-1-0.760-0.86830.953-9.570-9.5700.0000.0000.0000.000
87A91LEU0-0.0070.00325.543-0.257-0.2570.0000.0000.0000.000
88A92CYS0-0.079-0.04828.604-0.253-0.2530.0000.0000.0000.000
89A93LEU00.0210.00931.076-0.076-0.0760.0000.0000.0000.000
90A94GLU-1-0.733-0.82526.328-11.969-11.9690.0000.0000.0000.000
91A95ALA0-0.051-0.01726.637-0.360-0.3600.0000.0000.0000.000
92A96VAL0-0.0060.00327.702-0.213-0.2130.0000.0000.0000.000
93A97GLN00.0470.01829.655-0.285-0.2850.0000.0000.0000.000
94A98SER0-0.095-0.06024.348-0.296-0.2960.0000.0000.0000.000
95A99LEU0-0.045-0.01425.794-0.468-0.4680.0000.0000.0000.000
96A100LEU00.0390.03028.102-0.141-0.1410.0000.0000.0000.000
97A101THR00.0110.00325.403-0.378-0.3780.0000.0000.0000.000
98A102GLN0-0.008-0.00120.987-0.740-0.7400.0000.0000.0000.000
99A103GLU-1-0.826-0.89922.820-12.557-12.5570.0000.0000.0000.000
100A104LYS10.8650.92715.03219.49819.4980.0000.0000.0000.000
101A105LYS10.9290.96420.64213.14713.1470.0000.0000.0000.000
102A106ARG10.8350.90822.16912.17712.1770.0000.0000.0000.000
103A107ARG10.8740.93021.68414.42614.4260.0000.0000.0000.000
104A108ILE00.0190.00118.3990.3680.3680.0000.0000.0000.000
105A109LEU0-0.011-0.00822.9320.2840.2840.0000.0000.0000.000
106A110THR00.018-0.00425.7650.5780.5780.0000.0000.0000.000
107A111ILE0-0.040-0.02323.2640.3650.3650.0000.0000.0000.000
108A112LEU0-0.047-0.02625.2760.3440.3440.0000.0000.0000.000
109A113MET0-0.037-0.01027.2360.4040.4040.0000.0000.0000.000
110A114GLN00.0010.00030.2790.2980.2980.0000.0000.0000.000
111A115ARG10.8540.94428.73610.57210.5720.0000.0000.0000.000
112A116CYS0-0.051-0.02228.311-0.303-0.3030.0000.0000.0000.000
113A117GLU-1-0.800-0.85230.441-8.990-8.9900.0000.0000.0000.000
114A118PHE0-0.018-0.02027.597-0.230-0.2300.0000.0000.0000.000
115A119THR00.0100.00432.1830.2090.2090.0000.0000.0000.000
116A120GLU-1-0.807-0.90631.832-9.607-9.6070.0000.0000.0000.000
117A121GLU-1-0.866-0.91028.229-11.300-11.3000.0000.0000.0000.000
118A122LEU0-0.013-0.01025.908-0.614-0.6140.0000.0000.0000.000
119A123ARG10.8730.92928.0289.4599.4590.0000.0000.0000.000
120A124GLU-1-0.740-0.86820.944-14.641-14.6410.0000.0000.0000.000
121A125ALA0-0.037-0.02124.217-0.311-0.3110.0000.0000.0000.000
122A126GLN00.0160.00725.227-0.065-0.0650.0000.0000.0000.000
123A127GLU-1-0.896-0.94027.348-10.678-10.6780.0000.0000.0000.000
124A128ARG10.8540.89720.42914.84114.8410.0000.0000.0000.000
125A129ASN0-0.0120.00524.791-0.669-0.6690.0000.0000.0000.000
126A130ASN00.000-0.01126.2940.0900.0900.0000.0000.0000.000
127A131ALA00.0000.01125.4150.1950.1950.0000.0000.0000.000
128A132PHE00.0010.00222.2860.0960.0960.0000.0000.0000.000
129A133VAL00.0090.00225.6080.1160.1160.0000.0000.0000.000
130A134GLN0-0.069-0.04928.9420.3260.3260.0000.0000.0000.000
131A135MET00.0310.01924.4800.0510.0510.0000.0000.0000.000
132A136PHE00.0270.01027.4940.1770.1770.0000.0000.0000.000
133A137ILE0-0.004-0.01028.8900.3300.3300.0000.0000.0000.000
134A138GLU-1-0.864-0.91931.141-9.713-9.7130.0000.0000.0000.000
135A139LEU0-0.017-0.00326.5900.2310.2310.0000.0000.0000.000
136A140CYS0-0.034-0.01031.1680.2630.2630.0000.0000.0000.000
137A141GLU-1-0.848-0.90433.699-8.135-8.1350.0000.0000.0000.000
138A142GLN00.016-0.00431.3880.3390.3390.0000.0000.0000.000
139A143LEU00.0100.00832.9870.2070.2070.0000.0000.0000.000
140A144PHE00.024-0.01735.5530.2260.2260.0000.0000.0000.000
141A145ALA0-0.065-0.04138.4840.2850.2850.0000.0000.0000.000
142A146ARG10.8930.96732.1229.5739.5730.0000.0000.0000.000
143A147ASP-1-0.897-0.94039.982-7.150-7.1500.0000.0000.0000.000
144A148GLU-1-0.890-0.96838.770-7.981-7.9810.0000.0000.0000.000
145A149CYS0-0.072-0.02237.8350.0810.0810.0000.0000.0000.000
146A150ARG10.9620.98441.4937.4467.4460.0000.0000.0000.000
147A151VAL0-0.044-0.02143.7810.1610.1610.0000.0000.0000.000
148A152ARG10.7910.87541.3567.6547.6540.0000.0000.0000.000
149A153LEU0-0.0120.02141.9880.0000.0000.0000.0000.0000.000
150A154HIS00.0060.01145.9550.3080.3080.0000.0000.0000.000
151A155PRO0-0.014-0.03048.925-0.055-0.0550.0000.0000.0000.000
152A156GLY0-0.0160.00050.5880.0300.0300.0000.0000.0000.000
153A157MET0-0.0150.01843.999-0.040-0.0400.0000.0000.0000.000
154A158THR0-0.017-0.01444.718-0.089-0.0890.0000.0000.0000.000
155A159PRO00.0640.02339.877-0.041-0.0410.0000.0000.0000.000
156A160ARG10.9751.01239.6777.2427.2420.0000.0000.0000.000
157A161ILE0-0.039-0.02440.002-0.151-0.1510.0000.0000.0000.000
158A162ALA00.0530.03640.542-0.072-0.0720.0000.0000.0000.000
159A163SER00.018-0.00135.663-0.110-0.1100.0000.0000.0000.000
160A164ARG10.7880.87336.2118.3708.3700.0000.0000.0000.000
161A165ALA0-0.0030.00538.185-0.063-0.0630.0000.0000.0000.000
162A166LEU00.0390.01534.650-0.039-0.0390.0000.0000.0000.000
163A167HIS00.0160.00230.5170.1190.1190.0000.0000.0000.000
164A168ALA00.0080.00634.462-0.169-0.1690.0000.0000.0000.000
165A169LEU00.0020.01436.946-0.024-0.0240.0000.0000.0000.000
166A170ILE00.0130.00430.844-0.054-0.0540.0000.0000.0000.000
167A171LEU0-0.029-0.01431.473-0.192-0.1920.0000.0000.0000.000
168A172GLY00.0230.00233.439-0.076-0.0760.0000.0000.0000.000
169A173LEU00.0060.01034.7740.0390.0390.0000.0000.0000.000
170A174PHE0-0.009-0.01326.955-0.216-0.2160.0000.0000.0000.000
171A175ASN0-0.032-0.02632.4620.1480.1480.0000.0000.0000.000
172A176ASP-1-0.815-0.90234.352-8.079-8.0790.0000.0000.0000.000
173A177TRP0-0.036-0.00930.384-0.209-0.2090.0000.0000.0000.000
174A178LEU0-0.051-0.03928.972-0.091-0.0910.0000.0000.0000.000
175A179ARG10.8100.91432.8868.1658.1650.0000.0000.0000.000
176A180ASP-1-0.851-0.90935.969-7.824-7.8240.0000.0000.0000.000
177A181PRO00.0520.02634.3460.1080.1080.0000.0000.0000.000
178A182ARG10.7570.83836.4487.7267.7260.0000.0000.0000.000
179A183LEU0-0.101-0.03039.1220.2010.2010.0000.0000.0000.000
180A184PHE0-0.001-0.01035.1300.1450.1450.0000.0000.0000.000
181A185ASP-1-0.733-0.84535.729-9.249-9.2490.0000.0000.0000.000
182A186PRO0-0.092-0.05632.1590.0350.0350.0000.0000.0000.000
183A187ASP-1-0.956-0.96933.079-9.751-9.7510.0000.0000.0000.000
184A188THR0-0.041-0.05334.1090.1350.1350.0000.0000.0000.000
185A189ASP-1-0.810-0.90437.644-7.806-7.8060.0000.0000.0000.000
186A190ALA0-0.048-0.02134.4070.1180.1180.0000.0000.0000.000
187A191GLU-1-0.887-0.95536.368-8.269-8.2690.0000.0000.0000.000
188A192HIS0-0.019-0.01838.2390.2760.2760.0000.0000.0000.000
189A193LEU0-0.033-0.00837.9110.1800.1800.0000.0000.0000.000
190A194LEU0-0.030-0.01234.2080.0590.0590.0000.0000.0000.000
191A195GLU-1-0.764-0.85038.888-7.345-7.3450.0000.0000.0000.000
192A196PRO0-0.008-0.00141.7710.1120.1120.0000.0000.0000.000
193A197MET0-0.0160.00639.3520.1530.1530.0000.0000.0000.000
194A198PHE00.016-0.00835.3940.0290.0290.0000.0000.0000.000
195A199ARG10.8390.90541.5036.9956.9950.0000.0000.0000.000
196A200GLY0-0.022-0.01244.9660.1580.1580.0000.0000.0000.000
197A201LEU0-0.058-0.02440.3530.0990.0990.0000.0000.0000.000
198A202VAL0-0.030-0.02941.4130.0790.0790.0000.0000.0000.000
199A203ARG10.8700.94244.7866.5216.5210.0000.0000.0000.000
200A204ASP-1-0.846-0.90746.253-6.797-6.7970.0000.0000.0000.000
201A205TRP0-0.091-0.04938.111-0.019-0.0190.0000.0000.0000.000