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

tag_button

FMODB ID: JQYQ9

Calculation Name: 4TR5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4TR5

Chain ID: A

ChEMBL ID:

UniProt ID: W2E3J5

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 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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2309994.774422
FMO2-HF: Nuclear repulsion 2229778.224978
FMO2-HF: Total energy -80216.549444
FMO2-MP2: Total energy -80454.765635


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:14:GLU)


Summations of interaction energy for fragment #1(A:14:GLU)
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.
-260.467-261.62523.766-13.312-9.2950.113
Interaction energy analysis for fragmet #1(A:14:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.890 / q_NPA : -0.928
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].
3A16LEU00.0460.0272.9911.8144.4960.146-1.422-1.4070.000
4A17TYR0-0.050-0.0641.628-38.339-42.87123.620-11.594-7.4940.111
5A18PHE00.0370.0096.688-2.573-2.5730.0000.0000.0000.000
6A19GLN0-0.008-0.01410.2790.4690.4690.0000.0000.0000.000
7A20GLY00.0350.0389.754-0.890-0.8900.0000.0000.0000.000
8A21SER0-0.058-0.0449.3413.6333.6330.0000.0000.0000.000
9A22HIS0-0.0180.02210.501-3.412-3.4120.0000.0000.0000.000
10A23MET0-0.008-0.01212.932-2.385-2.3850.0000.0000.0000.000
11A24VAL0-0.014-0.01412.4622.2012.2010.0000.0000.0000.000
12A25GLY00.0480.02111.348-1.747-1.7470.0000.0000.0000.000
13A26GLU-1-0.781-0.8878.63833.62233.6220.0000.0000.0000.000
14A27LYS10.8010.9035.047-42.522-42.392-0.001-0.003-0.1250.000
15A28GLU-1-0.886-0.9537.18037.35437.3540.0000.0000.0000.000
16A29TYR0-0.044-0.0409.497-1.472-1.4720.0000.0000.0000.000
17A30LYS10.9650.9883.767-73.526-72.9640.001-0.293-0.2690.002
18A31ALA0-0.019-0.0197.002-1.154-1.1540.0000.0000.0000.000
19A32TRP0-0.018-0.0208.556-2.411-2.4110.0000.0000.0000.000
20A33GLU-1-0.779-0.88412.11918.77518.7750.0000.0000.0000.000
21A34LYS10.8980.9567.440-36.165-36.1650.0000.0000.0000.000
22A35LYS10.9010.95511.049-28.500-28.5000.0000.0000.0000.000
23A36LEU0-0.0340.01413.923-1.919-1.9190.0000.0000.0000.000
24A37ARG10.8790.92217.001-14.322-14.3220.0000.0000.0000.000
25A38ALA00.0590.02019.7210.0880.0880.0000.0000.0000.000
26A39ASN00.0650.01421.3150.0700.0700.0000.0000.0000.000
27A40GLU-1-0.793-0.85920.08515.68915.6890.0000.0000.0000.000
28A41LYS10.8980.95015.633-20.303-20.3030.0000.0000.0000.000
29A42GLU-1-0.786-0.87620.53613.38413.3840.0000.0000.0000.000
30A43LEU0-0.0160.00024.002-0.463-0.4630.0000.0000.0000.000
31A44VAL00.0280.01520.121-0.424-0.4240.0000.0000.0000.000
32A45LYS10.8580.92821.904-14.196-14.1960.0000.0000.0000.000
33A46GLU-1-0.814-0.88924.29010.34710.3470.0000.0000.0000.000
34A47TYR0-0.010-0.01425.155-0.676-0.6760.0000.0000.0000.000
35A48THR0-0.066-0.05824.003-0.139-0.1390.0000.0000.0000.000
36A49ALA0-0.043-0.00226.453-0.268-0.2680.0000.0000.0000.000
37A50ASN0-0.013-0.01629.249-0.387-0.3870.0000.0000.0000.000
38A51ALA00.1000.05629.115-0.124-0.1240.0000.0000.0000.000
39A52LYS10.9360.95231.009-9.654-9.6540.0000.0000.0000.000
40A53PRO00.0010.00334.067-0.199-0.1990.0000.0000.0000.000
41A54PHE00.0280.02331.293-0.180-0.1800.0000.0000.0000.000
42A55ASN00.0540.01329.377-0.113-0.1130.0000.0000.0000.000
43A56THR0-0.022-0.00633.501-0.168-0.1680.0000.0000.0000.000
44A57TYR0-0.065-0.04535.729-0.345-0.3450.0000.0000.0000.000
45A58LEU00.0170.01231.475-0.165-0.1650.0000.0000.0000.000
46A59ARG10.8340.87933.947-9.484-9.4840.0000.0000.0000.000
47A60ALA0-0.034-0.00237.458-0.165-0.1650.0000.0000.0000.000
48A61ASN0-0.026-0.00939.458-0.371-0.3710.0000.0000.0000.000
49A62GLU-1-0.862-0.91037.9178.0058.0050.0000.0000.0000.000
50A63GLY0-0.062-0.04135.0020.0980.0980.0000.0000.0000.000
51A64LYS10.8740.94635.488-7.752-7.7520.0000.0000.0000.000
52A65LEU0-0.022-0.01633.4700.0280.0280.0000.0000.0000.000
53A66GLY00.0200.00637.984-0.170-0.1700.0000.0000.0000.000
54A67PHE0-0.0060.00340.793-0.178-0.1780.0000.0000.0000.000
55A68LYS10.9320.97039.412-8.228-8.2280.0000.0000.0000.000
56A69PRO00.1110.05838.5310.3070.3070.0000.0000.0000.000
57A70GLU-1-0.798-0.89237.0608.9328.9320.0000.0000.0000.000
58A71ILE0-0.033-0.01834.8300.3150.3150.0000.0000.0000.000
59A72ASP-1-0.735-0.85933.7819.1569.1560.0000.0000.0000.000
60A73LYS10.8190.89133.199-8.491-8.4910.0000.0000.0000.000
61A74LYS10.8060.88430.111-9.940-9.9400.0000.0000.0000.000
62A75ILE00.0350.02028.8730.4880.4880.0000.0000.0000.000
63A76LEU00.0240.02028.7780.3960.3960.0000.0000.0000.000
64A77LYS10.9230.95926.552-10.651-10.6510.0000.0000.0000.000
65A78LEU00.0070.00823.5300.6990.6990.0000.0000.0000.000
66A79ASP-1-0.767-0.85223.79412.34212.3420.0000.0000.0000.000
67A80GLU-1-0.867-0.91523.62513.44513.4450.0000.0000.0000.000
68A81ALA00.0060.00520.4020.8260.8260.0000.0000.0000.000
69A82LEU00.000-0.00418.9931.2211.2210.0000.0000.0000.000
70A83LYS10.8410.91519.228-12.451-12.4510.0000.0000.0000.000
71A84LYS10.7600.87215.829-17.021-17.0210.0000.0000.0000.000
72A85SER0-0.020-0.00613.0881.7761.7760.0000.0000.0000.000
73A86LYS10.9280.96713.756-18.795-18.7950.0000.0000.0000.000
74A87LEU00.0010.00912.8582.1342.1340.0000.0000.0000.000
75A88SER00.0470.0248.896-1.976-1.9760.0000.0000.0000.000
76A89GLU-1-0.912-0.95711.56124.74524.7450.0000.0000.0000.000
77A90THR0-0.023-0.02214.124-0.158-0.1580.0000.0000.0000.000
78A91VAL00.0380.03714.5180.3530.3530.0000.0000.0000.000
79A92GLN0-0.014-0.01417.543-1.416-1.4160.0000.0000.0000.000
80A93VAL0-0.0080.00619.1010.5260.5260.0000.0000.0000.000
81A94TYR0-0.039-0.05221.535-0.963-0.9630.0000.0000.0000.000
82A95ARG10.8300.87924.896-10.801-10.8010.0000.0000.0000.000
83A96GLY00.0220.03027.765-0.237-0.2370.0000.0000.0000.000
84A97ASP-1-0.838-0.90830.77810.35210.3520.0000.0000.0000.000
85A98ASP-1-0.775-0.88333.9338.6328.6320.0000.0000.0000.000
86A99THR0-0.002-0.01537.6730.1190.1190.0000.0000.0000.000
87A100SER0-0.002-0.01739.030-0.101-0.1010.0000.0000.0000.000
88A101ILE0-0.041-0.01533.598-0.066-0.0660.0000.0000.0000.000
89A102PHE00.0000.00337.6860.0550.0550.0000.0000.0000.000
90A103GLY00.0300.02540.657-0.152-0.1520.0000.0000.0000.000
91A104LYS10.9720.94543.099-7.070-7.0700.0000.0000.0000.000
92A105GLU-1-0.924-0.93846.7666.6996.6990.0000.0000.0000.000
93A106PHE00.0440.01344.082-0.079-0.0790.0000.0000.0000.000
94A107GLN0-0.055-0.00943.347-0.035-0.0350.0000.0000.0000.000
95A108ASN00.0250.00144.7380.1740.1740.0000.0000.0000.000
96A109SER00.0300.02447.790-0.056-0.0560.0000.0000.0000.000
97A110ILE0-0.044-0.02342.766-0.016-0.0160.0000.0000.0000.000
98A111TYR0-0.051-0.05839.9250.1220.1220.0000.0000.0000.000
99A112GLN00.0440.02645.999-0.129-0.1290.0000.0000.0000.000
100A113GLY00.0170.01148.645-0.013-0.0130.0000.0000.0000.000
101A114ASN0-0.053-0.03643.0280.1190.1190.0000.0000.0000.000
102A115LYS10.9190.95844.422-6.893-6.8930.0000.0000.0000.000
103A116VAL00.0140.01041.428-0.061-0.0610.0000.0000.0000.000
104A117ASN00.0230.00844.774-0.097-0.0970.0000.0000.0000.000
105A118ARG10.9120.93144.880-7.084-7.0840.0000.0000.0000.000
106A119GLU-1-0.889-0.95047.3996.1426.1420.0000.0000.0000.000
107A120LEU0-0.050-0.02546.9480.0150.0150.0000.0000.0000.000
108A121PHE00.0490.01039.5610.1000.1000.0000.0000.0000.000
109A122ARG10.8980.95744.019-6.434-6.4340.0000.0000.0000.000
110A123LYS11.0281.02045.765-6.260-6.2600.0000.0000.0000.000
111A124LEU0-0.0210.00640.6770.0680.0680.0000.0000.0000.000
112A125ARG10.7920.86840.267-7.237-7.2370.0000.0000.0000.000
113A126ASP-1-0.833-0.90241.6007.2057.2050.0000.0000.0000.000
114A127GLU-1-0.814-0.89042.8047.5577.5570.0000.0000.0000.000
115A128TYR0-0.019-0.02037.6290.2200.2200.0000.0000.0000.000
116A129GLN00.0340.00737.1290.3580.3580.0000.0000.0000.000
117A130GLY0-0.026-0.01336.662-0.189-0.1890.0000.0000.0000.000
118A131LYS10.8220.92637.289-7.472-7.4720.0000.0000.0000.000
119A132ILE0-0.009-0.01032.8760.3200.3200.0000.0000.0000.000
120A133ARG10.8680.93833.775-8.568-8.5680.0000.0000.0000.000
121A134THR00.036-0.00132.3580.3790.3790.0000.0000.0000.000
122A135GLU-1-0.804-0.84229.9999.6329.6320.0000.0000.0000.000
123A136TYR0-0.041-0.05430.9380.4430.4430.0000.0000.0000.000
124A137GLY0-0.004-0.00631.4090.0810.0810.0000.0000.0000.000
125A138TYR0-0.018-0.05425.6000.0590.0590.0000.0000.0000.000
126A139LEU0-0.025-0.00225.952-0.339-0.3390.0000.0000.0000.000
127A140SER0-0.018-0.02023.9550.5080.5080.0000.0000.0000.000
128A141THR0-0.048-0.03421.867-0.427-0.4270.0000.0000.0000.000
129A142SER00.0000.00221.4700.5090.5090.0000.0000.0000.000
130A143ILE00.0250.01215.228-0.392-0.3920.0000.0000.0000.000
131A144VAL0-0.023-0.00618.959-0.107-0.1070.0000.0000.0000.000
132A145SER00.0420.03316.8771.3201.3200.0000.0000.0000.000
133A146ASN00.0310.00118.4230.4550.4550.0000.0000.0000.000
134A147GLN00.0230.01821.358-1.276-1.2760.0000.0000.0000.000
135A148GLN00.0200.01323.4050.2020.2020.0000.0000.0000.000
136A149PHE0-0.039-0.03124.696-0.530-0.5300.0000.0000.0000.000
137A150ALA00.026-0.00128.5880.0360.0360.0000.0000.0000.000
138A151MET00.0040.00631.013-0.125-0.1250.0000.0000.0000.000
139A152ARG10.8320.93232.856-9.714-9.7140.0000.0000.0000.000
140A153PRO00.0540.02735.3090.0580.0580.0000.0000.0000.000
141A154VAL0-0.0040.01434.234-0.063-0.0630.0000.0000.0000.000
142A155LEU00.0250.02628.2760.2590.2590.0000.0000.0000.000
143A156THR00.0140.00328.847-0.223-0.2230.0000.0000.0000.000
144A157THR0-0.049-0.01424.9750.2880.2880.0000.0000.0000.000
145A158LEU00.0180.01023.889-0.339-0.3390.0000.0000.0000.000
146A159LYS10.9290.96622.248-11.740-11.7400.0000.0000.0000.000
147A160VAL00.018-0.00319.186-0.556-0.5560.0000.0000.0000.000
148A161PRO00.0040.01619.1400.8660.8660.0000.0000.0000.000
149A162LYS10.9460.96114.234-20.370-20.3700.0000.0000.0000.000
150A163GLY0-0.040-0.02416.341-0.865-0.8650.0000.0000.0000.000
151A164ALA0-0.015-0.00117.881-0.597-0.5970.0000.0000.0000.000
152A165HIS0-0.010-0.00417.4840.6430.6430.0000.0000.0000.000
153A166ALA0-0.004-0.00916.803-0.816-0.8160.0000.0000.0000.000
154A167GLY00.0340.03216.6621.0931.0930.0000.0000.0000.000
155A168TYR0-0.023-0.01113.474-0.129-0.1290.0000.0000.0000.000
156A169VAL00.012-0.00516.515-0.017-0.0170.0000.0000.0000.000
157A170ASP-1-0.782-0.88316.70019.45819.4580.0000.0000.0000.000
158A171LYS10.7990.88318.682-14.358-14.3580.0000.0000.0000.000
159A172ILE0-0.0470.00116.776-0.953-0.9530.0000.0000.0000.000
160A173SER0-0.036-0.03520.970-0.338-0.3380.0000.0000.0000.000
161A174GLN00.0260.00922.8450.0360.0360.0000.0000.0000.000
162A175TYR00.0120.00924.3810.0320.0320.0000.0000.0000.000
163A176LYS10.8560.91825.470-11.600-11.6000.0000.0000.0000.000
164A177GLY00.0450.05423.3050.1380.1380.0000.0000.0000.000
165A178GLN00.0260.02319.6100.1740.1740.0000.0000.0000.000
166A179TYR00.0460.01113.7990.3880.3880.0000.0000.0000.000
167A180GLU-1-0.856-0.90317.64313.07613.0760.0000.0000.0000.000
168A181LEU0-0.0020.00816.3161.0331.0330.0000.0000.0000.000
169A182LEU0-0.046-0.02818.900-1.066-1.0660.0000.0000.0000.000
170A183LEU00.007-0.00720.7850.4640.4640.0000.0000.0000.000
171A184PRO00.0420.01321.640-0.459-0.4590.0000.0000.0000.000
172A185ARG10.8310.92324.441-11.007-11.0070.0000.0000.0000.000
173A186ASN0-0.017-0.01228.0580.0410.0410.0000.0000.0000.000
174A187THR00.0170.01925.8440.1030.1030.0000.0000.0000.000
175A188LYS10.9020.93928.054-10.757-10.7570.0000.0000.0000.000
176A189TYR00.009-0.00428.2000.4170.4170.0000.0000.0000.000
177A190LYS10.9260.97529.831-9.761-9.7610.0000.0000.0000.000
178A191ILE00.0080.00331.0670.3540.3540.0000.0000.0000.000
179A192ASP-1-0.847-0.88529.73210.29010.2900.0000.0000.0000.000
180A193LYS10.9230.96333.061-9.188-9.1880.0000.0000.0000.000
181A194MET0-0.0110.00434.1040.2070.2070.0000.0000.0000.000
182A195TYR0-0.111-0.07831.814-0.383-0.3830.0000.0000.0000.000
183A196ILE00.0070.00637.2450.1300.1300.0000.0000.0000.000
184A197ILE00.0050.00732.930-0.040-0.0400.0000.0000.0000.000
185A198VAL0-0.001-0.00637.297-0.100-0.1000.0000.0000.0000.000
186A199ASN00.0180.02035.664-0.008-0.0080.0000.0000.0000.000
187A200LYS10.9960.99138.786-7.918-7.9180.0000.0000.0000.000
188A201GLY00.0020.00040.4360.0850.0850.0000.0000.0000.000
189A202SER00.0130.00438.676-0.037-0.0370.0000.0000.0000.000
190A203GLU-1-0.794-0.86040.0367.3107.3100.0000.0000.0000.000
191A204THR00.0200.03234.0290.0810.0810.0000.0000.0000.000
192A205ILE0-0.016-0.00537.087-0.057-0.0570.0000.0000.0000.000
193A206LYS10.8520.92029.096-10.476-10.4760.0000.0000.0000.000
194A207ILE00.016-0.00732.417-0.222-0.2220.0000.0000.0000.000
195A208GLU-1-0.833-0.90729.00910.82610.8260.0000.0000.0000.000
196A209ALA00.009-0.00128.629-0.334-0.3340.0000.0000.0000.000
197A210THR0-0.010-0.03425.6350.7380.7380.0000.0000.0000.000
198A211VAL0-0.014-0.00123.711-0.441-0.4410.0000.0000.0000.000
199A212GLN0-0.007-0.01025.2240.4930.4930.0000.0000.0000.000
200A213PRO0-0.0040.00823.361-0.138-0.1380.0000.0000.0000.000