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: 396KL

Calculation Name: 4KD6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4KD6

Chain ID: A

ChEMBL ID:

UniProt ID: B1GB42

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 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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2576799.487354
FMO2-HF: Nuclear repulsion 2491819.689721
FMO2-HF: Total energy -84979.797634
FMO2-MP2: Total energy -85222.978545


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:4:ASP)


Summations of interaction energy for fragment #1(A:4:ASP)
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.
-2.1174.8762.77-3.877-5.8861.7347234759768E-18
Interaction energy analysis for fragmet #1(A:4:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.930 / q_NPA : -0.969
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].
3A6LEU0-0.030-0.0133.1205.8567.8330.042-0.763-1.2560.003
4A7PHE00.0320.0015.505-4.311-4.3110.0000.0000.0000.000
5A8SER0-0.009-0.0079.064-0.036-0.0360.0000.0000.0000.000
6A9ASN0-0.025-0.01312.048-0.662-0.6620.0000.0000.0000.000
7A10HIS00.0140.00814.154-0.830-0.8300.0000.0000.0000.000
8A11GLY00.0320.00918.352-0.615-0.6150.0000.0000.0000.000
9A12ARG10.9200.96020.139-11.866-11.8660.0000.0000.0000.000
10A13VAL00.0050.03117.559-0.122-0.1220.0000.0000.0000.000
11A14ALA00.0530.04414.8810.5840.5840.0000.0000.0000.000
12A15VAL0-0.003-0.01711.269-0.686-0.6860.0000.0000.0000.000
13A16ILE0-0.018-0.0098.8881.9821.9820.0000.0000.0000.000
14A17THR00.0030.0037.179-2.585-2.5850.0000.0000.0000.000
15A18LEU0-0.019-0.0075.9025.1935.1930.0000.0000.0000.000
16A19ASN00.013-0.0102.328-12.991-11.3230.877-0.781-1.7650.006
17A20ARG10.8580.9142.369-32.085-29.6231.814-1.986-2.290-0.011
18A21PRO00.0680.0314.218-3.550-3.4130.000-0.027-0.1090.000
19A22GLU-1-0.933-0.9596.58831.21331.2130.0000.0000.0000.000
20A23ARG10.8320.9137.302-24.726-24.7260.0000.0000.0000.000
21A24LEU0-0.016-0.0139.074-0.670-0.6700.0000.0000.0000.000
22A25ASN0-0.023-0.0306.2501.2871.2870.0000.0000.0000.000
23A26ALA00.0100.0287.3150.0380.0380.0000.0000.0000.000
24A27TRP00.0420.0186.8993.6963.6960.0000.0000.0000.000
25A28THR00.013-0.0045.745-1.807-1.8070.0000.0000.0000.000
26A29THR00.0510.0078.3660.9460.9460.0000.0000.0000.000
27A30PRO00.0730.0386.405-0.371-0.3710.0000.0000.0000.000
28A31MET0-0.0570.0123.605-0.7000.0490.037-0.320-0.4660.002
29A32ARG10.8500.9216.059-22.382-22.3820.0000.0000.0000.000
30A33GLU-1-0.930-0.9599.53723.47623.4760.0000.0000.0000.000
31A34THR00.0320.0166.090-0.152-0.1520.0000.0000.0000.000
32A35ILE0-0.022-0.0147.465-1.337-1.3370.0000.0000.0000.000
33A36ILE0-0.0220.0089.606-2.107-2.1070.0000.0000.0000.000
34A37ASP-1-0.898-0.93511.46321.97321.9730.0000.0000.0000.000
35A38ALA0-0.039-0.02810.532-1.388-1.3880.0000.0000.0000.000
36A39LEU0-0.032-0.01512.511-1.569-1.5690.0000.0000.0000.000
37A40GLU-1-0.887-0.94815.08015.35215.3520.0000.0000.0000.000
38A41ARG10.9140.95813.635-22.758-22.7580.0000.0000.0000.000
39A42PHE00.0630.02112.448-0.800-0.8000.0000.0000.0000.000
40A43ASN00.0680.05517.857-1.139-1.1390.0000.0000.0000.000
41A44ARG10.8960.94620.762-12.890-12.8900.0000.0000.0000.000
42A45ASP-1-0.832-0.92318.65415.53515.5350.0000.0000.0000.000
43A46PRO0-0.038-0.01721.553-0.294-0.2940.0000.0000.0000.000
44A47GLU-1-0.895-0.95320.42613.07713.0770.0000.0000.0000.000
45A48VAL0-0.069-0.01518.2540.1000.1000.0000.0000.0000.000
46A49ALA0-0.057-0.04121.236-0.472-0.4720.0000.0000.0000.000
47A50ALA00.003-0.00121.177-0.484-0.4840.0000.0000.0000.000
48A51ILE0-0.0020.00515.4500.6640.6640.0000.0000.0000.000
49A52ILE00.0070.02114.845-0.715-0.7150.0000.0000.0000.000
50A53MET0-0.0100.00211.5931.2501.2500.0000.0000.0000.000
51A54THR0-0.028-0.03111.376-1.380-1.3800.0000.0000.0000.000
52A55GLY00.0310.0249.3122.1252.1250.0000.0000.0000.000
53A56ALA0-0.0020.0147.383-1.282-1.2820.0000.0000.0000.000
54A57GLY0-0.031-0.0239.455-0.582-0.5820.0000.0000.0000.000
55A58ASN00.0270.01512.2910.1770.1770.0000.0000.0000.000
56A59ARG10.9670.99013.719-17.563-17.5630.0000.0000.0000.000
57A60ALA0-0.016-0.02512.053-0.842-0.8420.0000.0000.0000.000
58A61PHE00.0070.04911.6971.2041.2040.0000.0000.0000.000
59A62SER0-0.016-0.0469.6701.1951.1950.0000.0000.0000.000
60A63ALA00.0110.00511.348-1.384-1.3840.0000.0000.0000.000
61A64GLY0-0.0020.02412.004-1.049-1.0490.0000.0000.0000.000
62A65GLN0-0.006-0.00611.3201.4521.4520.0000.0000.0000.000
63A66ASP-1-0.746-0.8649.33923.42023.4200.0000.0000.0000.000
64A67LEU0-0.018-0.02011.390-0.553-0.5530.0000.0000.0000.000
65A68SER0-0.046-0.00912.003-0.846-0.8460.0000.0000.0000.000
66A81TRP00.0240.00313.8460.0540.0540.0000.0000.0000.000
67A82VAL00.0930.02418.8460.6800.6800.0000.0000.0000.000
68A83LYS11.0311.02421.255-12.567-12.5670.0000.0000.0000.000
69A84GLU-1-0.881-0.94715.94018.16018.1600.0000.0000.0000.000
70A85TRP00.0330.00913.3920.8170.8170.0000.0000.0000.000
71A86GLN00.0780.04717.5470.2410.2410.0000.0000.0000.000
72A87ARG10.8520.92916.859-17.066-17.0660.0000.0000.0000.000
73A88TYR00.008-0.01011.5860.2230.2230.0000.0000.0000.000
74A89TYR00.006-0.01516.2920.1550.1550.0000.0000.0000.000
75A90THR0-0.028-0.02819.388-0.654-0.6540.0000.0000.0000.000
76A91ALA00.0030.00616.653-0.464-0.4640.0000.0000.0000.000
77A92LEU0-0.025-0.01315.425-0.044-0.0440.0000.0000.0000.000
78A93ARG10.7960.87218.839-11.869-11.8690.0000.0000.0000.000
79A94SER0-0.057-0.02721.223-0.797-0.7970.0000.0000.0000.000
80A95LEU0-0.074-0.01518.052-0.220-0.2200.0000.0000.0000.000
81A96SER0-0.081-0.05822.144-0.598-0.5980.0000.0000.0000.000
82A97LYS10.8180.90621.993-14.227-14.2270.0000.0000.0000.000
83A98PRO00.0210.00422.5510.3240.3240.0000.0000.0000.000
84A99LEU0-0.025-0.00416.4000.6000.6000.0000.0000.0000.000
85A100VAL0-0.001-0.00819.326-0.567-0.5670.0000.0000.0000.000
86A101MET0-0.035-0.00715.6621.3381.3380.0000.0000.0000.000
87A102ALA00.0310.01115.930-0.872-0.8720.0000.0000.0000.000
88A103LEU0-0.020-0.02315.6121.1181.1180.0000.0000.0000.000
89A104ASN00.0450.01312.268-0.866-0.8660.0000.0000.0000.000
90A105GLY00.0710.00916.041-0.299-0.2990.0000.0000.0000.000
91A106THR0-0.012-0.00616.655-0.198-0.1980.0000.0000.0000.000
92A107ALA00.0020.01115.0751.0801.0800.0000.0000.0000.000
93A108ALA00.0080.00715.862-0.949-0.9490.0000.0000.0000.000
94A109GLY00.0220.01616.0940.8580.8580.0000.0000.0000.000
95A110SER00.0450.00914.525-0.027-0.0270.0000.0000.0000.000
96A111ALA0-0.0010.00213.0600.1970.1970.0000.0000.0000.000
97A112PHE0-0.009-0.00514.825-0.152-0.1520.0000.0000.0000.000
98A113GLN00.0330.00018.447-0.010-0.0100.0000.0000.0000.000
99A114VAL0-0.015-0.00813.868-0.266-0.2660.0000.0000.0000.000
100A115ALA00.0220.00516.891-0.176-0.1760.0000.0000.0000.000
101A116LEU0-0.042-0.02617.943-0.438-0.4380.0000.0000.0000.000
102A117LEU0-0.025-0.00819.169-0.538-0.5380.0000.0000.0000.000
103A118GLY0-0.032-0.00520.0740.1130.1130.0000.0000.0000.000
104A119ASP-1-0.784-0.86920.66512.03212.0320.0000.0000.0000.000
105A120ILE0-0.049-0.03522.691-0.484-0.4840.0000.0000.0000.000
106A121ARG10.8320.90820.377-11.795-11.7950.0000.0000.0000.000
107A122VAL0-0.0110.00221.012-0.694-0.6940.0000.0000.0000.000
108A123GLY00.0300.01520.3570.7370.7370.0000.0000.0000.000
109A124HIS00.0690.04818.721-1.005-1.0050.0000.0000.0000.000
110A125PRO00.024-0.01823.1870.1490.1490.0000.0000.0000.000
111A126GLY00.0000.02022.498-0.283-0.2830.0000.0000.0000.000
112A127VAL0-0.105-0.03218.9750.3560.3560.0000.0000.0000.000
113A128ARG10.9500.97620.261-12.322-12.3220.0000.0000.0000.000
114A129MET0-0.014-0.01719.2780.5540.5540.0000.0000.0000.000
115A130GLY00.0240.01920.663-0.627-0.6270.0000.0000.0000.000
116A131GLN00.0610.01920.6780.9380.9380.0000.0000.0000.000
117A132PRO00.0290.02120.149-0.451-0.4510.0000.0000.0000.000
118A133GLU-1-0.835-0.93320.32113.06613.0660.0000.0000.0000.000
119A134ILE00.0310.02622.927-0.064-0.0640.0000.0000.0000.000
120A135ASN0-0.030-0.01324.712-0.538-0.5380.0000.0000.0000.000
121A136ALA0-0.069-0.02122.225-0.045-0.0450.0000.0000.0000.000
122A137GLY0-0.0080.00024.2750.0490.0490.0000.0000.0000.000
123A138ILE0-0.033-0.00821.6930.0070.0070.0000.0000.0000.000
124A139ALA00.0160.00825.095-0.190-0.1900.0000.0000.0000.000
125A140SER0-0.024-0.01625.2120.4940.4940.0000.0000.0000.000
126A141THR00.025-0.00325.386-0.244-0.2440.0000.0000.0000.000
127A142THR00.0560.01821.589-0.143-0.1430.0000.0000.0000.000
128A143GLY00.0380.02023.733-0.044-0.0440.0000.0000.0000.000
129A144PRO0-0.029-0.01524.441-0.163-0.1630.0000.0000.0000.000
130A145TRP00.0350.03224.278-0.061-0.0610.0000.0000.0000.000
131A146ILE00.0140.00222.465-0.225-0.2250.0000.0000.0000.000
132A147MET0-0.034-0.01425.408-0.155-0.1550.0000.0000.0000.000
133A148ASN00.0370.00227.701-0.404-0.4040.0000.0000.0000.000
134A149ALA0-0.0220.00029.251-0.294-0.2940.0000.0000.0000.000
135A150MET0-0.068-0.02425.049-0.056-0.0560.0000.0000.0000.000
136A151LEU0-0.019-0.00228.097-0.178-0.1780.0000.0000.0000.000
137A152GLY00.0080.02132.173-0.285-0.2850.0000.0000.0000.000
138A153MET00.028-0.00533.6120.2340.2340.0000.0000.0000.000
139A154SER0-0.039-0.01134.8920.1190.1190.0000.0000.0000.000
140A155ARG10.9990.99331.826-8.535-8.5350.0000.0000.0000.000
141A156THR00.0520.02529.5510.2510.2510.0000.0000.0000.000
142A157ILE0-0.0070.01630.5370.2390.2390.0000.0000.0000.000
143A158GLU-1-0.807-0.88332.0859.1279.1270.0000.0000.0000.000
144A159LEU00.0150.01427.1760.1500.1500.0000.0000.0000.000
145A160THR0-0.065-0.05327.6280.3630.3630.0000.0000.0000.000
146A161LEU0-0.039-0.03228.5290.1210.1210.0000.0000.0000.000
147A162THR0-0.043-0.03229.9900.0730.0730.0000.0000.0000.000
148A163GLY00.0000.01726.1080.1110.1110.0000.0000.0000.000
149A164ARG10.7320.82425.129-9.059-9.0590.0000.0000.0000.000
150A165LEU0-0.065-0.03820.9000.3040.3040.0000.0000.0000.000
151A166MET0-0.018-0.00224.373-0.444-0.4440.0000.0000.0000.000
152A167GLU-1-0.834-0.93724.56511.29411.2940.0000.0000.0000.000
153A168ALA00.0450.03124.435-0.204-0.2040.0000.0000.0000.000
154A169GLU-1-0.864-0.93825.6748.8428.8420.0000.0000.0000.000
155A170GLU-1-0.791-0.86628.9559.1779.1770.0000.0000.0000.000
156A171CYS0-0.047-0.03024.922-0.008-0.0080.0000.0000.0000.000
157A172HIS0-0.050-0.01127.251-0.249-0.2490.0000.0000.0000.000
158A173ARG10.9000.96128.792-8.820-8.8200.0000.0000.0000.000
159A174ILE0-0.129-0.07828.671-0.278-0.2780.0000.0000.0000.000
160A175GLY00.0390.03330.240-0.046-0.0460.0000.0000.0000.000
161A176LEU0-0.057-0.01924.9090.2170.2170.0000.0000.0000.000
162A177ILE0-0.018-0.01422.9500.4640.4640.0000.0000.0000.000
163A178HIS00.0590.04025.440-0.087-0.0870.0000.0000.0000.000
164A179HIS0-0.003-0.01425.671-0.466-0.4660.0000.0000.0000.000
165A180LEU00.0110.01625.0090.4950.4950.0000.0000.0000.000
166A181VAL0-0.061-0.03123.558-0.377-0.3770.0000.0000.0000.000
167A182ASP-1-0.871-0.93624.94810.79910.7990.0000.0000.0000.000
168A183GLU-1-0.894-0.97519.08614.64014.6400.0000.0000.0000.000
169A184ASP-1-0.950-0.98920.14812.85312.8530.0000.0000.0000.000
170A185LYS10.9430.97821.302-11.391-11.3910.0000.0000.0000.000
171A186VAL0-0.041-0.00718.3570.0000.0000.0000.0000.0000.000
172A187PHE00.0120.00414.7040.0820.0820.0000.0000.0000.000
173A188ASP-1-0.824-0.92318.34913.51813.5180.0000.0000.0000.000
174A189LYS10.8900.96121.424-11.074-11.0740.0000.0000.0000.000
175A190ALA00.0030.00418.836-0.265-0.2650.0000.0000.0000.000
176A191LEU00.0230.00218.770-0.086-0.0860.0000.0000.0000.000
177A192GLU-1-0.885-0.92720.97910.52510.5250.0000.0000.0000.000
178A193ILE00.0150.00523.685-0.317-0.3170.0000.0000.0000.000
179A194ALA0-0.011-0.01120.884-0.250-0.2500.0000.0000.0000.000
180A195THR0-0.052-0.04722.891-0.109-0.1090.0000.0000.0000.000
181A196GLU-1-0.946-0.96524.9119.8079.8070.0000.0000.0000.000
182A197LEU0-0.051-0.05124.912-0.371-0.3710.0000.0000.0000.000
183A198ALA0-0.029-0.01324.185-0.164-0.1640.0000.0000.0000.000
184A199ALA0-0.050-0.01326.187-0.203-0.2030.0000.0000.0000.000
185A200LYS10.9010.96529.547-9.941-9.9410.0000.0000.0000.000
186A201PRO00.010-0.01130.9560.1860.1860.0000.0000.0000.000
187A202PRO00.0720.02329.520-0.033-0.0330.0000.0000.0000.000
188A203VAL0-0.037-0.01330.5170.1780.1780.0000.0000.0000.000
189A204ALA00.0340.02233.0990.0010.0010.0000.0000.0000.000
190A205MET00.0550.04927.6740.0610.0610.0000.0000.0000.000
191A206ARG10.9700.98928.549-9.752-9.7520.0000.0000.0000.000
192A207LEU0-0.059-0.04129.5640.0240.0240.0000.0000.0000.000
193A208ASP-1-0.887-0.94231.4839.0619.0610.0000.0000.0000.000
194A209LYS10.8150.89722.747-12.788-12.7880.0000.0000.0000.000
195A210GLN0-0.070-0.03428.7120.2460.2460.0000.0000.0000.000
196A211ARG10.9070.95030.145-8.597-8.5970.0000.0000.0000.000
197A212PHE00.0440.01528.309-0.136-0.1360.0000.0000.0000.000
198A213ARG10.9490.99824.864-11.628-11.6280.0000.0000.0000.000
199A214GLU-1-0.840-0.92229.0308.8258.8250.0000.0000.0000.000
200A215MET0-0.069-0.03332.508-0.221-0.2210.0000.0000.0000.000
201A216THR0-0.006-0.01029.1990.0570.0570.0000.0000.0000.000
202A217GLU-1-0.849-0.90128.33010.93510.9350.0000.0000.0000.000
203A218PRO00.0050.00230.7260.1010.1010.0000.0000.0000.000
204A219GLY00.0180.00931.780-0.050-0.0500.0000.0000.0000.000
205A220PHE0-0.001-0.00622.9280.2960.2960.0000.0000.0000.000
206A221ILE0-0.024-0.02028.1370.2220.2220.0000.0000.0000.000
207A222ASP-1-0.912-0.94230.1549.0139.0130.0000.0000.0000.000
208A223CYS0-0.046-0.01427.0280.1920.1920.0000.0000.0000.000
209A224ILE00.0040.00325.0320.2720.2720.0000.0000.0000.000
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