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: 3JZJL

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 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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2311843.336509
FMO2-HF: Nuclear repulsion 2231626.335366
FMO2-HF: Total energy -80217.001143
FMO2-MP2: Total energy -80455.264166


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.
-318.998-326.31339.291-18.56-13.4160.181
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 : -0.784 / q_NPA : -0.869
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].
3A16LEU00.0430.0202.905-1.1701.4280.225-1.396-1.427-0.006
4A17TYR0-0.013-0.0391.574-25.088-35.60226.284-9.733-6.0370.081
5A18PHE00.0390.0156.496-3.366-3.3660.0000.0000.0000.000
6A19GLN0-0.009-0.01510.1640.9350.9350.0000.0000.0000.000
7A20GLY00.0290.0359.463-1.173-1.1730.0000.0000.0000.000
8A21SER0-0.031-0.0298.8326.4876.4870.0000.0000.0000.000
9A22HIS0-0.0300.01210.703-3.646-3.6460.0000.0000.0000.000
10A23MET0-0.014-0.01812.286-2.527-2.5270.0000.0000.0000.000
11A24VAL0-0.005-0.00511.9062.5032.5030.0000.0000.0000.000
12A25GLY00.0300.00811.210-1.938-1.9380.0000.0000.0000.000
13A26GLU-1-0.749-0.8647.87336.02236.0220.0000.0000.0000.000
14A27LYS10.7750.8784.945-41.454-41.318-0.001-0.004-0.1310.000
15A28GLU-1-0.879-0.9496.43038.15138.1510.0000.0000.0000.000
16A29TYR0-0.039-0.0398.968-1.437-1.4370.0000.0000.0000.000
17A30LYS10.8430.9171.911-141.874-141.40912.783-7.427-5.8210.106
18A31ALA0-0.026-0.0196.469-0.764-0.7640.0000.0000.0000.000
19A32TRP0-0.025-0.0238.014-3.073-3.0730.0000.0000.0000.000
20A33GLU-1-0.757-0.87711.43220.09820.0980.0000.0000.0000.000
21A34LYS10.9080.9586.688-41.060-41.0600.0000.0000.0000.000
22A35LYS10.8850.94910.515-28.754-28.7540.0000.0000.0000.000
23A36LEU0-0.0350.00814.021-2.079-2.0790.0000.0000.0000.000
24A37ARG10.8960.92016.862-14.498-14.4980.0000.0000.0000.000
25A38ALA00.0590.02619.629-0.054-0.0540.0000.0000.0000.000
26A39ASN00.0680.02721.3970.0350.0350.0000.0000.0000.000
27A40GLU-1-0.813-0.86419.86216.00616.0060.0000.0000.0000.000
28A41LYS10.8800.94015.391-21.389-21.3890.0000.0000.0000.000
29A42GLU-1-0.776-0.86820.07814.05714.0570.0000.0000.0000.000
30A43LEU0-0.024-0.00223.581-0.499-0.4990.0000.0000.0000.000
31A44VAL00.0220.00619.085-0.443-0.4430.0000.0000.0000.000
32A45LYS10.8420.91721.399-14.866-14.8660.0000.0000.0000.000
33A46GLU-1-0.800-0.87823.69410.58210.5820.0000.0000.0000.000
34A47TYR0-0.023-0.02324.077-0.662-0.6620.0000.0000.0000.000
35A48THR0-0.053-0.05522.647-0.145-0.1450.0000.0000.0000.000
36A49ALA0-0.0260.00525.208-0.240-0.2400.0000.0000.0000.000
37A50ASN0-0.020-0.02728.196-0.450-0.4500.0000.0000.0000.000
38A51ALA00.0850.05128.015-0.227-0.2270.0000.0000.0000.000
39A52LYS10.9260.96829.875-9.979-9.9790.0000.0000.0000.000
40A53PRO00.0130.00533.151-0.207-0.2070.0000.0000.0000.000
41A54PHE00.0300.02030.427-0.197-0.1970.0000.0000.0000.000
42A55ASN00.0460.01428.688-0.114-0.1140.0000.0000.0000.000
43A56THR0-0.028-0.00732.645-0.205-0.2050.0000.0000.0000.000
44A57TYR0-0.086-0.06335.183-0.316-0.3160.0000.0000.0000.000
45A58LEU00.0270.02030.659-0.155-0.1550.0000.0000.0000.000
46A59ARG10.8370.87133.715-9.571-9.5710.0000.0000.0000.000
47A60ALA0-0.028-0.00536.672-0.155-0.1550.0000.0000.0000.000
48A61ASN0-0.017-0.00438.547-0.365-0.3650.0000.0000.0000.000
49A62GLU-1-0.822-0.89937.2547.9667.9660.0000.0000.0000.000
50A63GLY0-0.058-0.03734.1190.1770.1770.0000.0000.0000.000
51A64LYS10.8140.90434.676-7.797-7.7970.0000.0000.0000.000
52A65LEU0-0.012-0.01332.625-0.048-0.0480.0000.0000.0000.000
53A66GLY00.0080.00337.054-0.171-0.1710.0000.0000.0000.000
54A67PHE00.0010.01239.892-0.174-0.1740.0000.0000.0000.000
55A68LYS10.9040.96238.350-8.357-8.3570.0000.0000.0000.000
56A69PRO00.1080.05737.7010.3290.3290.0000.0000.0000.000
57A70GLU-1-0.789-0.88436.2679.0199.0190.0000.0000.0000.000
58A71ILE0-0.023-0.01033.7360.3450.3450.0000.0000.0000.000
59A72ASP-1-0.723-0.84432.8589.2679.2670.0000.0000.0000.000
60A73LYS10.8300.88732.498-8.517-8.5170.0000.0000.0000.000
61A74LYS10.8040.89029.592-10.212-10.2120.0000.0000.0000.000
62A75ILE00.0410.01428.2270.5000.5000.0000.0000.0000.000
63A76LEU00.0450.02627.7700.4460.4460.0000.0000.0000.000
64A77LYS10.8670.93225.918-10.695-10.6950.0000.0000.0000.000
65A78LEU00.0240.01922.4090.7400.7400.0000.0000.0000.000
66A79ASP-1-0.777-0.85122.95012.47012.4700.0000.0000.0000.000
67A80GLU-1-0.842-0.91122.86313.41713.4170.0000.0000.0000.000
68A81ALA0-0.003-0.00119.9330.8020.8020.0000.0000.0000.000
69A82LEU00.0060.00018.3621.2401.2400.0000.0000.0000.000
70A83LYS10.8120.89518.466-12.277-12.2770.0000.0000.0000.000
71A84LYS10.7880.88315.470-17.420-17.4200.0000.0000.0000.000
72A85SER0-0.038-0.03512.7782.1252.1250.0000.0000.0000.000
73A86LYS10.9390.97113.567-18.394-18.3940.0000.0000.0000.000
74A87LEU0-0.0050.01113.0841.8991.8990.0000.0000.0000.000
75A88SER00.0690.0309.076-1.775-1.7750.0000.0000.0000.000
76A89GLU-1-0.940-0.96212.18623.22623.2260.0000.0000.0000.000
77A90THR00.001-0.01114.802-0.057-0.0570.0000.0000.0000.000
78A91VAL00.0360.03414.6090.2200.2200.0000.0000.0000.000
79A92GLN0-0.016-0.01817.856-1.436-1.4360.0000.0000.0000.000
80A93VAL00.0000.01318.9710.6060.6060.0000.0000.0000.000
81A94TYR0-0.045-0.05721.484-1.011-1.0110.0000.0000.0000.000
82A95ARG10.8350.89324.653-10.904-10.9040.0000.0000.0000.000
83A96GLY00.0470.03327.454-0.179-0.1790.0000.0000.0000.000
84A97ASP-1-0.846-0.91530.49410.58110.5810.0000.0000.0000.000
85A98ASP-1-0.771-0.88933.4058.7358.7350.0000.0000.0000.000
86A99THR0-0.003-0.02837.2150.1180.1180.0000.0000.0000.000
87A100SER0-0.030-0.02138.286-0.092-0.0920.0000.0000.0000.000
88A101ILE0-0.030-0.00933.185-0.083-0.0830.0000.0000.0000.000
89A102PHE00.0170.01137.3440.0420.0420.0000.0000.0000.000
90A103GLY00.0500.03740.399-0.161-0.1610.0000.0000.0000.000
91A104LYS10.9100.92342.883-7.232-7.2320.0000.0000.0000.000
92A105GLU-1-0.911-0.93746.5006.7246.7240.0000.0000.0000.000
93A106PHE00.0320.00743.804-0.059-0.0590.0000.0000.0000.000
94A107GLN0-0.0040.00043.039-0.050-0.0500.0000.0000.0000.000
95A108ASN00.0140.00844.4820.2300.2300.0000.0000.0000.000
96A109SER00.0310.02547.025-0.100-0.1000.0000.0000.0000.000
97A110ILE0-0.032-0.00342.521-0.040-0.0400.0000.0000.0000.000
98A111TYR0-0.032-0.05539.6720.1390.1390.0000.0000.0000.000
99A112GLN00.0350.02445.591-0.115-0.1150.0000.0000.0000.000
100A113GLY00.0220.01348.1260.0280.0280.0000.0000.0000.000
101A114ASN0-0.042-0.02942.6600.1390.1390.0000.0000.0000.000
102A115LYS10.8970.94544.193-6.922-6.9220.0000.0000.0000.000
103A116VAL00.0320.01741.304-0.052-0.0520.0000.0000.0000.000
104A117ASN00.0230.00944.600-0.109-0.1090.0000.0000.0000.000
105A118ARG10.8710.90444.880-7.133-7.1330.0000.0000.0000.000
106A119GLU-1-0.868-0.92347.3296.1296.1290.0000.0000.0000.000
107A120LEU00.010-0.00646.9960.0080.0080.0000.0000.0000.000
108A121PHE00.0590.01439.6860.0880.0880.0000.0000.0000.000
109A122ARG10.8810.96044.004-6.397-6.3970.0000.0000.0000.000
110A123LYS10.9570.96545.548-6.175-6.1750.0000.0000.0000.000
111A124LEU0-0.0150.01640.5530.0470.0470.0000.0000.0000.000
112A125ARG10.8010.87140.319-7.223-7.2230.0000.0000.0000.000
113A126ASP-1-0.812-0.88841.6297.1987.1980.0000.0000.0000.000
114A127GLU-1-0.802-0.88543.0577.4737.4730.0000.0000.0000.000
115A128TYR0-0.039-0.03437.3560.2470.2470.0000.0000.0000.000
116A129GLN00.0350.00737.1380.3370.3370.0000.0000.0000.000
117A130GLY0-0.031-0.00336.925-0.207-0.2070.0000.0000.0000.000
118A131LYS10.8310.92137.192-7.405-7.4050.0000.0000.0000.000
119A132ILE00.0020.00333.0320.3140.3140.0000.0000.0000.000
120A133ARG10.8520.92333.849-8.541-8.5410.0000.0000.0000.000
121A134THR00.0500.01132.1880.3450.3450.0000.0000.0000.000
122A135GLU-1-0.810-0.85029.7019.7279.7270.0000.0000.0000.000
123A136TYR0-0.026-0.01830.7780.3550.3550.0000.0000.0000.000
124A137GLY0-0.004-0.00830.7940.0560.0560.0000.0000.0000.000
125A138TYR0-0.007-0.05024.8760.0440.0440.0000.0000.0000.000
126A139LEU0-0.0100.00025.358-0.303-0.3030.0000.0000.0000.000
127A140SER0-0.007-0.02023.0710.4870.4870.0000.0000.0000.000
128A141THR0-0.067-0.03321.773-0.612-0.6120.0000.0000.0000.000
129A142SER0-0.006-0.00421.0890.6670.6670.0000.0000.0000.000
130A143ILE00.0170.00614.983-0.408-0.4080.0000.0000.0000.000
131A144VAL0-0.020-0.00618.687-0.123-0.1230.0000.0000.0000.000
132A145SER00.0320.02016.3541.4411.4410.0000.0000.0000.000
133A146ASN00.003-0.00618.0890.5470.5470.0000.0000.0000.000
134A147GLN00.0490.03520.962-1.284-1.2840.0000.0000.0000.000
135A148GLN00.0280.01123.0610.2920.2920.0000.0000.0000.000
136A149PHE0-0.024-0.02824.056-0.543-0.5430.0000.0000.0000.000
137A150ALA00.016-0.00628.164-0.121-0.1210.0000.0000.0000.000
138A151MET0-0.0270.00630.397-0.124-0.1240.0000.0000.0000.000
139A152ARG10.8460.93732.197-9.813-9.8130.0000.0000.0000.000
140A153PRO00.0270.01035.0220.0480.0480.0000.0000.0000.000
141A154VAL0-0.0170.00833.773-0.129-0.1290.0000.0000.0000.000
142A155LEU00.0300.02128.3450.2720.2720.0000.0000.0000.000
143A156THR00.0130.01528.991-0.179-0.1790.0000.0000.0000.000
144A157THR0-0.028-0.01025.0420.2510.2510.0000.0000.0000.000
145A158LEU00.0060.00424.277-0.399-0.3990.0000.0000.0000.000
146A159LYS10.9340.97222.708-11.353-11.3530.0000.0000.0000.000
147A160VAL00.008-0.00719.349-0.574-0.5740.0000.0000.0000.000
148A161PRO00.0150.01619.4790.7660.7660.0000.0000.0000.000
149A162LYS10.9340.95314.660-19.311-19.3110.0000.0000.0000.000
150A163GLY0-0.023-0.00916.669-0.865-0.8650.0000.0000.0000.000
151A164ALA0-0.018-0.01118.094-0.435-0.4350.0000.0000.0000.000
152A165HIS0-0.020-0.00717.6230.6300.6300.0000.0000.0000.000
153A166ALA0-0.008-0.00516.745-0.883-0.8830.0000.0000.0000.000
154A167GLY00.0280.04515.9601.2461.2460.0000.0000.0000.000
155A168TYR0-0.029-0.02013.403-0.241-0.2410.0000.0000.0000.000
156A169VAL00.021-0.00315.5250.2800.2800.0000.0000.0000.000
157A170ASP-1-0.785-0.87915.71820.33520.3350.0000.0000.0000.000
158A171LYS10.7870.88017.516-15.310-15.3100.0000.0000.0000.000
159A172ILE0-0.032-0.00415.995-1.009-1.0090.0000.0000.0000.000
160A173SER0-0.015-0.02320.150-0.444-0.4440.0000.0000.0000.000
161A174GLN00.0170.00622.336-0.035-0.0350.0000.0000.0000.000
162A175TYR00.0190.01123.677-0.064-0.0640.0000.0000.0000.000
163A176LYS10.8470.91224.784-11.991-11.9910.0000.0000.0000.000
164A177GLY00.0490.05022.2480.0070.0070.0000.0000.0000.000
165A178GLN0-0.0020.02318.934-0.027-0.0270.0000.0000.0000.000
166A179TYR00.0460.01113.0870.6910.6910.0000.0000.0000.000
167A180GLU-1-0.851-0.89816.88513.26513.2650.0000.0000.0000.000
168A181LEU00.0290.01616.0630.8670.8670.0000.0000.0000.000
169A182LEU0-0.020-0.00418.500-1.155-1.1550.0000.0000.0000.000
170A183LEU00.0240.00620.1540.4900.4900.0000.0000.0000.000
171A184PRO00.0270.00621.188-0.469-0.4690.0000.0000.0000.000
172A185ARG10.8410.93323.994-11.165-11.1650.0000.0000.0000.000
173A186ASN0-0.012-0.00527.7250.0610.0610.0000.0000.0000.000
174A187THR00.0080.00625.6530.0080.0080.0000.0000.0000.000
175A188LYS10.8850.93127.914-10.736-10.7360.0000.0000.0000.000
176A189TYR0-0.001-0.01428.2930.4230.4230.0000.0000.0000.000
177A190LYS10.9210.97930.011-9.633-9.6330.0000.0000.0000.000
178A191ILE00.0110.00831.1160.3800.3800.0000.0000.0000.000
179A192ASP-1-0.826-0.89530.13910.12110.1210.0000.0000.0000.000
180A193LYS10.9140.95933.289-9.170-9.1700.0000.0000.0000.000
181A194MET0-0.0080.00334.2220.1870.1870.0000.0000.0000.000
182A195TYR0-0.114-0.08032.271-0.324-0.3240.0000.0000.0000.000
183A196ILE00.0000.00737.7600.0930.0930.0000.0000.0000.000
184A197ILE0-0.0020.00833.091-0.062-0.0620.0000.0000.0000.000
185A198VAL00.0190.00537.543-0.123-0.1230.0000.0000.0000.000
186A199ASN00.0090.01136.1350.0310.0310.0000.0000.0000.000
187A200LYS10.9800.98238.741-7.949-7.9490.0000.0000.0000.000
188A201GLY00.0120.00240.5770.0550.0550.0000.0000.0000.000
189A202SER0-0.009-0.00438.767-0.038-0.0380.0000.0000.0000.000
190A203GLU-1-0.766-0.84940.1117.2457.2450.0000.0000.0000.000
191A204THR00.0330.04134.0950.1000.1000.0000.0000.0000.000
192A205ILE00.0030.01337.083-0.035-0.0350.0000.0000.0000.000
193A206LYS10.8020.89929.094-10.405-10.4050.0000.0000.0000.000
194A207ILE00.020-0.00132.321-0.255-0.2550.0000.0000.0000.000
195A208GLU-1-0.833-0.91129.47810.61410.6140.0000.0000.0000.000
196A209ALA0-0.0040.00128.656-0.361-0.3610.0000.0000.0000.000
197A210THR0-0.045-0.04025.8290.6620.6620.0000.0000.0000.000
198A211VAL00.0030.00023.445-0.408-0.4080.0000.0000.0000.000
199A212GLN0-0.015-0.01825.4790.3620.3620.0000.0000.0000.000
200A213PRO0-0.0080.00723.687-0.168-0.1680.0000.0000.0000.000