Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: Z693N

Calculation Name: 3TL4-X-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3TL4

Chain ID: X

ChEMBL ID:

UniProt ID: P13188

Base Structure: X-ray

Registration Date: 2023-06-26

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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1849106.513912
FMO2-HF: Nuclear repulsion 1775871.876112
FMO2-HF: Total energy -73234.6378
FMO2-MP2: Total energy -73451.584712


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(X:2:SER)


Summations of interaction energy for fragment #1(X:2:SER)
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.
-15.589-6.4012.777-5.688-6.277-0.04
Interaction energy analysis for fragmet #1(X:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : 0.021
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].
3X4VAL00.009-0.0173.832-4.288-1.654-0.014-1.595-1.0250.010
4X5GLU-1-0.815-0.8826.653-1.179-1.1790.0000.0000.0000.000
5X6GLU-1-0.815-0.8912.393-14.966-9.9912.649-3.643-3.981-0.050
6X7LEU0-0.057-0.0332.9530.5971.3540.093-0.212-0.6390.000
7X8THR0-0.040-0.0445.0850.7890.843-0.001-0.002-0.0510.000
8X9GLN00.0060.0047.9680.4060.4060.0000.0000.0000.000
9X10LEU00.0180.0306.9950.2570.2570.0000.0000.0000.000
10X11PHE0-0.005-0.0226.8250.2020.2020.0000.0000.0000.000
11X12SER00.024-0.00310.7190.1460.1460.0000.0000.0000.000
12X13GLN0-0.0240.00211.0990.0760.0760.0000.0000.0000.000
13X14VAL0-0.0280.00712.4410.0790.0790.0000.0000.0000.000
14X15GLY00.0310.00714.8400.0700.0700.0000.0000.0000.000
15X16PHE0-0.113-0.06013.0370.0550.0550.0000.0000.0000.000
16X17GLU-1-0.866-0.93616.057-0.256-0.2560.0000.0000.0000.000
17X18ASP-1-0.824-0.91316.211-0.379-0.3790.0000.0000.0000.000
18X19LYS10.8980.93816.4540.1260.1260.0000.0000.0000.000
19X20LYS10.7810.87816.0320.1400.1400.0000.0000.0000.000
20X21VAL00.0720.02810.9140.0200.0200.0000.0000.0000.000
21X22LYS10.9460.97712.2720.2250.2250.0000.0000.0000.000
22X23GLU-1-0.866-0.91614.151-0.089-0.0890.0000.0000.0000.000
23X24ILE00.0380.01410.1670.0470.0470.0000.0000.0000.000
24X25VAL00.0300.0288.1050.0750.0750.0000.0000.0000.000
25X26LYS10.8750.93610.2390.2320.2320.0000.0000.0000.000
26X27ASN0-0.039-0.01112.4030.1380.1380.0000.0000.0000.000
27X28LYS10.9810.9717.747-0.001-0.0010.0000.0000.0000.000
28X29LYS11.0341.0428.110-0.399-0.3990.0000.0000.0000.000
29X30VAL00.005-0.0109.8330.0510.0510.0000.0000.0000.000
30X31SER0-0.004-0.0046.653-0.052-0.0520.0000.0000.0000.000
31X32ASP-1-0.845-0.9214.9970.9560.971-0.001-0.004-0.0100.000
32X33SER0-0.015-0.0076.3900.2080.2080.0000.0000.0000.000
33X34LEU0-0.021-0.0058.9710.0000.0000.0000.0000.0000.000
34X35TYR0-0.025-0.0323.0990.1110.8640.051-0.232-0.5710.000
35X36LYS10.8670.9256.757-0.555-0.5550.0000.0000.0000.000
36X37LEU0-0.031-0.0198.467-0.125-0.1250.0000.0000.0000.000
37X38ILE0-0.026-0.0279.765-0.056-0.0560.0000.0000.0000.000
38X39LYS10.9040.9686.0550.4300.4300.0000.0000.0000.000
39X40GLU-1-0.831-0.88210.7520.4030.4030.0000.0000.0000.000
40X41THR0-0.076-0.04013.937-0.035-0.0350.0000.0000.0000.000
41X42PRO00.0330.00415.529-0.010-0.0100.0000.0000.0000.000
42X43SER00.005-0.00715.344-0.012-0.0120.0000.0000.0000.000
43X44ASP-1-0.920-0.95016.697-0.134-0.1340.0000.0000.0000.000
44X45TYR00.0140.00917.5280.0080.0080.0000.0000.0000.000
45X46GLN0-0.016-0.00418.633-0.023-0.0230.0000.0000.0000.000
46X47TRP00.0280.01214.6710.0230.0230.0000.0000.0000.000
47X48ASN00.0420.01419.2400.0000.0000.0000.0000.0000.000
48X49LYS10.9860.97820.4120.0830.0830.0000.0000.0000.000
49X50SER0-0.035-0.01021.4930.0060.0060.0000.0000.0000.000
50X51THR00.0830.02719.7620.0020.0020.0000.0000.0000.000
51X52ARG10.9230.98216.3110.2290.2290.0000.0000.0000.000
52X53ALA0-0.027-0.01516.8650.0050.0050.0000.0000.0000.000
53X54LEU0-0.0150.00619.0410.0150.0150.0000.0000.0000.000
54X55VAL00.0540.02714.0080.0260.0260.0000.0000.0000.000
55X56HIS0-0.015-0.00213.6880.0220.0220.0000.0000.0000.000
56X57ASN0-0.014-0.00415.5740.0280.0280.0000.0000.0000.000
57X58LEU00.0740.06216.1820.0200.0200.0000.0000.0000.000
58X59ALA00.0140.00812.0640.0420.0420.0000.0000.0000.000
59X60SER0-0.126-0.07614.0050.0440.0440.0000.0000.0000.000
60X61PHE0-0.018-0.01716.2260.0100.0100.0000.0000.0000.000
61X62VAL00.0140.00913.5460.0070.0070.0000.0000.0000.000
62X63LYS10.8790.93813.520-0.215-0.2150.0000.0000.0000.000
63X64GLY0-0.035-0.02210.675-0.001-0.0010.0000.0000.0000.000
64X65THR0-0.076-0.02011.6140.1150.1150.0000.0000.0000.000
65X66ASP-1-0.850-0.93712.8910.8060.8060.0000.0000.0000.000
66X67LEU0-0.087-0.03514.732-0.067-0.0670.0000.0000.0000.000
67X68PRO00.0230.00017.3840.0040.0040.0000.0000.0000.000
68X69LYS10.8820.94319.621-0.196-0.1960.0000.0000.0000.000
69X70SER00.0070.00915.527-0.005-0.0050.0000.0000.0000.000
70X71GLU-1-0.820-0.91817.1720.1950.1950.0000.0000.0000.000
71X72LEU0-0.0380.00018.269-0.041-0.0410.0000.0000.0000.000
72X73ILE00.017-0.00719.374-0.023-0.0230.0000.0000.0000.000
73X74VAL0-0.009-0.00215.311-0.029-0.0290.0000.0000.0000.000
74X75ASN0-0.006-0.02018.553-0.046-0.0460.0000.0000.0000.000
75X76GLY00.0470.03421.303-0.017-0.0170.0000.0000.0000.000
76X77ILE0-0.042-0.02518.929-0.015-0.0150.0000.0000.0000.000
77X78ILE0-0.073-0.03118.348-0.016-0.0160.0000.0000.0000.000
78X79ASN0-0.060-0.04221.550-0.003-0.0030.0000.0000.0000.000
79X80GLY0-0.053-0.01624.779-0.003-0.0030.0000.0000.0000.000
80X81ASP-1-0.747-0.85026.4520.0330.0330.0000.0000.0000.000
81X82LEU0-0.071-0.03623.1570.0020.0020.0000.0000.0000.000
82X83LYS10.9580.97724.8850.0120.0120.0000.0000.0000.000
83X84THR00.0280.00826.694-0.005-0.0050.0000.0000.0000.000
84X85SER00.037-0.01523.6180.0050.0050.0000.0000.0000.000
85X86LEU0-0.0190.00225.0040.0120.0120.0000.0000.0000.000
86X87GLN00.0220.01527.0420.0020.0020.0000.0000.0000.000
87X88VAL00.0250.01620.5000.0100.0100.0000.0000.0000.000
88X89ASP-1-0.829-0.89623.1690.1100.1100.0000.0000.0000.000
89X90ALA0-0.026-0.01124.5990.0130.0130.0000.0000.0000.000
90X91ALA00.0610.03423.9590.0080.0080.0000.0000.0000.000
91X92PHE0-0.015-0.02318.7790.0130.0130.0000.0000.0000.000
92X93LYS10.7680.85822.722-0.084-0.0840.0000.0000.0000.000
93X94TYR00.0360.03125.6460.0080.0080.0000.0000.0000.000
94X95VAL00.0530.02121.4280.0010.0010.0000.0000.0000.000
95X96LYS10.8990.95321.834-0.186-0.1860.0000.0000.0000.000
96X97ALA0-0.072-0.02823.7850.0070.0070.0000.0000.0000.000
97X98ASN0-0.039-0.02527.034-0.006-0.0060.0000.0000.0000.000
98X99GLY00.0400.03623.9270.0010.0010.0000.0000.0000.000
99X100GLU-1-0.837-0.92622.7250.2140.2140.0000.0000.0000.000
100X101ALA0-0.015-0.00225.217-0.011-0.0110.0000.0000.0000.000
101X102SER0-0.020-0.01825.085-0.018-0.0180.0000.0000.0000.000
102X103THR00.019-0.00126.8250.0000.0000.0000.0000.0000.000
103X104LYS10.9100.95026.581-0.046-0.0460.0000.0000.0000.000
104X105MET00.0100.00627.901-0.003-0.0030.0000.0000.0000.000
105X106GLY00.0880.06430.953-0.004-0.0040.0000.0000.0000.000
106X107MET00.0010.01124.5130.0030.0030.0000.0000.0000.000
107X108ASN0-0.050-0.05228.2570.0020.0020.0000.0000.0000.000
108X109GLU-1-0.938-0.95730.1990.0550.0550.0000.0000.0000.000
109X110ASN0-0.084-0.03930.860-0.003-0.0030.0000.0000.0000.000
110X111SER0-0.075-0.06427.9860.0060.0060.0000.0000.0000.000
111X112GLY00.013-0.00430.012-0.005-0.0050.0000.0000.0000.000
112X113VAL0-0.010-0.00428.939-0.006-0.0060.0000.0000.0000.000
113X114GLY0-0.019-0.00131.9380.0010.0010.0000.0000.0000.000
114X115ILE0-0.062-0.02334.815-0.002-0.0020.0000.0000.0000.000
115X116GLU-1-0.939-0.96835.836-0.001-0.0010.0000.0000.0000.000
116X117ILE0-0.073-0.02638.2680.0000.0000.0000.0000.0000.000
117X118THR00.0540.00640.665-0.002-0.0020.0000.0000.0000.000
118X119GLU-1-0.859-0.93943.171-0.002-0.0020.0000.0000.0000.000
119X120ASP-1-0.896-0.96344.9290.0060.0060.0000.0000.0000.000
120X121GLN00.0660.06143.7310.0000.0000.0000.0000.0000.000
121X122VAL0-0.012-0.00242.3190.0020.0020.0000.0000.0000.000
122X123ARG10.8020.88045.179-0.001-0.0010.0000.0000.0000.000
123X124ASN0-0.030-0.02048.8010.0010.0010.0000.0000.0000.000
124X125TYR00.0230.00444.6690.0010.0010.0000.0000.0000.000
125X126VAL00.000-0.00246.6520.0010.0010.0000.0000.0000.000
126X127MET0-0.031-0.01749.1010.0000.0000.0000.0000.0000.000
127X128GLN0-0.086-0.03950.6440.0000.0000.0000.0000.0000.000
128X129TYR0-0.005-0.04149.0410.0000.0000.0000.0000.0000.000
129X130ILE0-0.002-0.01751.3900.0000.0000.0000.0000.0000.000
130X131GLN00.0100.01354.051-0.001-0.0010.0000.0000.0000.000
131X132GLU-1-0.900-0.94351.8980.0210.0210.0000.0000.0000.000
132X133ASN0-0.031-0.00151.9710.0010.0010.0000.0000.0000.000
133X134LYS10.9250.97055.684-0.012-0.0120.0000.0000.0000.000
134X135GLU-1-0.887-0.95858.4700.0130.0130.0000.0000.0000.000
135X136ARG10.8790.95550.845-0.020-0.0200.0000.0000.0000.000
136X137ILE00.000-0.01953.467-0.001-0.0010.0000.0000.0000.000
137X138LEU0-0.039-0.02057.094-0.001-0.0010.0000.0000.0000.000
138X139THR0-0.053-0.02560.452-0.001-0.0010.0000.0000.0000.000
139X140GLU-1-0.934-0.96356.5070.0120.0120.0000.0000.0000.000
140X141ARG10.7990.87757.900-0.006-0.0060.0000.0000.0000.000
141X142TYR0-0.006-0.04754.1800.0000.0000.0000.0000.0000.000
142X143LYS10.9040.96953.338-0.007-0.0070.0000.0000.0000.000
143X144LEU00.0440.03251.6120.0010.0010.0000.0000.0000.000
144X145VAL00.0040.01048.9370.0010.0010.0000.0000.0000.000
145X146PRO0-0.031-0.02946.5160.0000.0000.0000.0000.0000.000
146X147GLY00.0090.00545.9510.0010.0010.0000.0000.0000.000
147X148ILE00.0380.02947.1900.0010.0010.0000.0000.0000.000
148X149PHE00.0380.00440.1570.0010.0010.0000.0000.0000.000
149X150ALA0-0.073-0.04942.2960.0010.0010.0000.0000.0000.000
150X151ASP-1-0.773-0.85542.5180.0250.0250.0000.0000.0000.000
151X152VAL00.001-0.00743.3230.0010.0010.0000.0000.0000.000
152X153LYS10.8210.92238.393-0.015-0.0150.0000.0000.0000.000
153X154ASN0-0.049-0.01739.3600.0040.0040.0000.0000.0000.000
154X155LEU00.0200.03940.7660.0030.0030.0000.0000.0000.000
155X156LYS10.8980.92039.693-0.036-0.0360.0000.0000.0000.000
156X157GLU-1-0.854-0.91039.7880.0320.0320.0000.0000.0000.000
157X158LEU0-0.028-0.01440.182-0.002-0.0020.0000.0000.0000.000
158X159LYS10.9080.97931.892-0.058-0.0580.0000.0000.0000.000
159X160TRP00.023-0.01630.4080.0030.0030.0000.0000.0000.000
160X161ALA00.0260.03235.323-0.003-0.0030.0000.0000.0000.000
161X162ASP-1-0.759-0.84735.591-0.005-0.0050.0000.0000.0000.000
162X163PRO00.0260.00534.762-0.001-0.0010.0000.0000.0000.000
163X164ARG10.7690.84834.6200.0130.0130.0000.0000.0000.000
164X165SER0-0.008-0.00238.862-0.001-0.0010.0000.0000.0000.000
165X166PHE00.0330.01138.8610.0000.0000.0000.0000.0000.000
166X167LYS10.8180.89742.831-0.002-0.0020.0000.0000.0000.000
167X168PRO00.0480.01543.8330.0000.0000.0000.0000.0000.000
168X169ILE00.0350.03144.8850.0000.0000.0000.0000.0000.000
169X170ILE00.0030.00245.6060.0010.0010.0000.0000.0000.000
170X171ASP-1-0.825-0.90048.6880.0010.0010.0000.0000.0000.000
171X172GLN0-0.0040.00250.1180.0010.0010.0000.0000.0000.000
172X173GLU-1-0.742-0.85351.3150.0040.0040.0000.0000.0000.000
173X174VAL0-0.0010.00152.3040.0010.0010.0000.0000.0000.000
174X175LEU0-0.0060.00854.8490.0000.0000.0000.0000.0000.000
175X176LYS10.7960.88054.683-0.003-0.0030.0000.0000.0000.000
176X177LEU0-0.035-0.00257.5270.0000.0000.0000.0000.0000.000
177X178LEU0-0.045-0.00656.8730.0000.0000.0000.0000.0000.000
178X179GLY00.0580.04760.4040.0000.0000.0000.0000.0000.000
179X180PRO00.000-0.01159.8820.0000.0000.0000.0000.0000.000
180X181LYS10.9070.95853.2940.0000.0000.0000.0000.0000.000
181X182ASP-1-0.741-0.83560.2320.0020.0020.0000.0000.0000.000
182X183GLU-1-0.866-0.93462.6920.0030.0030.0000.0000.0000.000
183X184ARG10.8210.87863.493-0.004-0.0040.0000.0000.0000.000
184X185ASP-1-0.879-0.94558.6340.0050.0050.0000.0000.0000.000
185X186LEU0-0.035-0.00758.8440.0000.0000.0000.0000.0000.000
186X187ILE0-0.038-0.01154.8520.0010.0010.0000.0000.0000.000