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: 6N59Z

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 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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1847266.56975
FMO2-HF: Nuclear repulsion 1774032.854337
FMO2-HF: Total energy -73233.715413
FMO2-MP2: Total energy -73450.664585


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.
-23.646-17.7956.798-6.085-6.564-0.059
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 : -0.024 / q_NPA : -0.008
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].
3X4VAL00.000-0.0253.832-2.392-0.3950.008-1.122-0.8820.007
4X5GLU-1-0.874-0.9296.8080.0150.0150.0000.0000.0000.000
5X6GLU-1-0.847-0.9262.166-19.757-17.1376.760-4.603-4.777-0.068
6X7LEU0-0.031-0.0233.730-0.928-0.1650.024-0.271-0.5170.002
7X8THR0-0.046-0.0335.603-0.371-0.3710.0000.0000.0000.000
8X9GLN0-0.021-0.0167.988-0.117-0.1170.0000.0000.0000.000
9X10LEU00.0270.0307.2670.0190.0190.0000.0000.0000.000
10X11PHE0-0.016-0.0218.018-0.004-0.0040.0000.0000.0000.000
11X12SER00.0240.00211.238-0.071-0.0710.0000.0000.0000.000
12X13GLN00.0000.01411.099-0.040-0.0400.0000.0000.0000.000
13X14VAL0-0.0360.00312.296-0.016-0.0160.0000.0000.0000.000
14X15GLY00.0350.01515.1130.0100.0100.0000.0000.0000.000
15X16PHE0-0.125-0.05813.6890.0100.0100.0000.0000.0000.000
16X17GLU-1-0.858-0.93716.6770.1040.1040.0000.0000.0000.000
17X18ASP-1-0.815-0.90616.6930.1870.1870.0000.0000.0000.000
18X19LYS10.9080.94217.100-0.146-0.1460.0000.0000.0000.000
19X20LYS10.8700.94516.938-0.350-0.3500.0000.0000.0000.000
20X21VAL00.0700.02911.7450.0760.0760.0000.0000.0000.000
21X22LYS10.9570.98213.174-0.232-0.2320.0000.0000.0000.000
22X23GLU-1-0.930-0.97315.0170.4520.4520.0000.0000.0000.000
23X24ILE00.0290.01011.0970.0340.0340.0000.0000.0000.000
24X25VAL00.0020.0118.8600.1050.1050.0000.0000.0000.000
25X26LYS10.8260.91811.102-0.454-0.4540.0000.0000.0000.000
26X27ASN0-0.039-0.00512.8600.0880.0880.0000.0000.0000.000
27X28LYS11.0360.9907.906-1.674-1.6740.0000.0000.0000.000
28X29LYS11.0181.0328.155-0.544-0.5440.0000.0000.0000.000
29X30VAL00.007-0.01110.1340.0330.0330.0000.0000.0000.000
30X31SER00.000-0.0047.568-0.135-0.1350.0000.0000.0000.000
31X32ASP-1-0.838-0.9124.7803.7253.777-0.001-0.005-0.0460.000
32X33SER0-0.035-0.0187.017-0.350-0.3500.0000.0000.0000.000
33X34LEU0-0.0060.0019.930-0.187-0.1870.0000.0000.0000.000
34X35TYR00.0300.0094.204-0.1750.2440.007-0.084-0.3420.000
35X36LYS10.9530.9747.257-0.808-0.8080.0000.0000.0000.000
36X37LEU0-0.044-0.0188.267-0.178-0.1780.0000.0000.0000.000
37X38ILE0-0.026-0.02510.130-0.101-0.1010.0000.0000.0000.000
38X39LYS10.9130.9736.8480.7860.7860.0000.0000.0000.000
39X40GLU-1-0.876-0.91610.4400.0180.0180.0000.0000.0000.000
40X41THR0-0.080-0.04813.4780.0310.0310.0000.0000.0000.000
41X42PRO00.019-0.00615.208-0.043-0.0430.0000.0000.0000.000
42X43SER00.015-0.00515.7170.0150.0150.0000.0000.0000.000
43X44ASP-1-0.933-0.95216.751-0.138-0.1380.0000.0000.0000.000
44X45TYR00.0210.01918.0840.0380.0380.0000.0000.0000.000
45X46GLN0-0.022-0.00718.7010.0080.0080.0000.0000.0000.000
46X47TRP00.0350.01714.8240.0510.0510.0000.0000.0000.000
47X48ASN00.0490.02019.6940.0050.0050.0000.0000.0000.000
48X49LYS10.9650.96421.162-0.099-0.0990.0000.0000.0000.000
49X50SER0-0.046-0.01322.3690.0190.0190.0000.0000.0000.000
50X51THR00.1080.03620.3280.0240.0240.0000.0000.0000.000
51X52ARG10.9150.96617.190-0.109-0.1090.0000.0000.0000.000
52X53ALA0-0.027-0.01617.7630.0540.0540.0000.0000.0000.000
53X54LEU0-0.0090.01019.9720.0300.0300.0000.0000.0000.000
54X55VAL00.0430.02514.4590.0200.0200.0000.0000.0000.000
55X56HIS0-0.0040.00114.3800.0110.0110.0000.0000.0000.000
56X57ASN0-0.010-0.00316.5150.0090.0090.0000.0000.0000.000
57X58LEU00.0640.04916.4430.0170.0170.0000.0000.0000.000
58X59ALA00.0140.00512.8760.0150.0150.0000.0000.0000.000
59X60SER0-0.111-0.06414.6920.0490.0490.0000.0000.0000.000
60X61PHE0-0.026-0.01317.099-0.008-0.0080.0000.0000.0000.000
61X62VAL0-0.011-0.00413.799-0.017-0.0170.0000.0000.0000.000
62X63LYS10.8850.94113.925-0.418-0.4180.0000.0000.0000.000
63X64GLY0-0.041-0.03010.700-0.002-0.0020.0000.0000.0000.000
64X65THR0-0.069-0.01111.634-0.007-0.0070.0000.0000.0000.000
65X66ASP-1-0.855-0.92912.2520.3990.3990.0000.0000.0000.000
66X67LEU0-0.093-0.05114.625-0.023-0.0230.0000.0000.0000.000
67X68PRO00.0320.00816.981-0.013-0.0130.0000.0000.0000.000
68X69LYS10.9130.96519.085-0.027-0.0270.0000.0000.0000.000
69X70SER0-0.002-0.00115.3140.0110.0110.0000.0000.0000.000
70X71GLU-1-0.838-0.92316.7860.0640.0640.0000.0000.0000.000
71X72LEU0-0.078-0.03017.937-0.016-0.0160.0000.0000.0000.000
72X73ILE00.020-0.00519.399-0.003-0.0030.0000.0000.0000.000
73X74VAL00.0060.00615.2460.0050.0050.0000.0000.0000.000
74X75ASN00.008-0.00418.612-0.016-0.0160.0000.0000.0000.000
75X76GLY00.0240.02221.215-0.009-0.0090.0000.0000.0000.000
76X77ILE0-0.022-0.01219.3010.0010.0010.0000.0000.0000.000
77X78ILE0-0.068-0.03418.560-0.009-0.0090.0000.0000.0000.000
78X79ASN0-0.077-0.03921.778-0.005-0.0050.0000.0000.0000.000
79X80GLY0-0.060-0.02025.049-0.006-0.0060.0000.0000.0000.000
80X81ASP-1-0.817-0.90426.7120.0440.0440.0000.0000.0000.000
81X82LEU0-0.090-0.04623.3060.0060.0060.0000.0000.0000.000
82X83LYS10.9600.97725.351-0.064-0.0640.0000.0000.0000.000
83X84THR00.0280.00927.3870.0100.0100.0000.0000.0000.000
84X85SER00.027-0.01824.4190.0000.0000.0000.0000.0000.000
85X86LEU0-0.0240.00025.7710.0120.0120.0000.0000.0000.000
86X87GLN00.0140.00227.5410.0030.0030.0000.0000.0000.000
87X88VAL00.0200.01521.0720.0000.0000.0000.0000.0000.000
88X89ASP-1-0.851-0.91123.5760.2130.2130.0000.0000.0000.000
89X90ALA0-0.028-0.01025.1190.0020.0020.0000.0000.0000.000
90X91ALA00.0620.03224.229-0.003-0.0030.0000.0000.0000.000
91X92PHE0-0.012-0.02119.0400.0010.0010.0000.0000.0000.000
92X93LYS10.8070.88022.938-0.183-0.1830.0000.0000.0000.000
93X94TYR00.0240.02425.848-0.005-0.0050.0000.0000.0000.000
94X95VAL00.0380.00821.336-0.008-0.0080.0000.0000.0000.000
95X96LYS10.8990.95721.977-0.248-0.2480.0000.0000.0000.000
96X97ALA0-0.071-0.02923.702-0.003-0.0030.0000.0000.0000.000
97X98ASN0-0.033-0.01626.866-0.013-0.0130.0000.0000.0000.000
98X99GLY00.0350.03423.522-0.010-0.0100.0000.0000.0000.000
99X100GLU-1-0.849-0.94721.9280.0400.0400.0000.0000.0000.000
100X101ALA0-0.0180.00224.583-0.014-0.0140.0000.0000.0000.000
101X102SER0-0.020-0.00924.672-0.003-0.0030.0000.0000.0000.000
102X103THR00.016-0.00626.317-0.009-0.0090.0000.0000.0000.000
103X104LYS11.0111.00126.727-0.009-0.0090.0000.0000.0000.000
104X105MET00.0070.00327.6080.0050.0050.0000.0000.0000.000
105X106GLY00.0940.06630.6530.0030.0030.0000.0000.0000.000
106X107MET0-0.0040.00924.4930.0110.0110.0000.0000.0000.000
107X108ASN0-0.002-0.02228.3410.0130.0130.0000.0000.0000.000
108X109GLU-1-0.937-0.95630.2090.0520.0520.0000.0000.0000.000
109X110ASN0-0.086-0.04130.9060.0030.0030.0000.0000.0000.000
110X111SER0-0.065-0.05528.2130.0150.0150.0000.0000.0000.000
111X112GLY00.0170.00630.2570.0030.0030.0000.0000.0000.000
112X113VAL0-0.0020.00029.061-0.002-0.0020.0000.0000.0000.000
113X114GLY0-0.024-0.00532.154-0.004-0.0040.0000.0000.0000.000
114X115ILE0-0.065-0.02135.101-0.004-0.0040.0000.0000.0000.000
115X116GLU-1-0.942-0.97236.2550.0480.0480.0000.0000.0000.000
116X117ILE0-0.071-0.02438.712-0.003-0.0030.0000.0000.0000.000
117X118THR00.0540.02041.2670.0020.0020.0000.0000.0000.000
118X119GLU-1-0.879-0.95943.7530.0430.0430.0000.0000.0000.000
119X120ASP-1-0.935-0.97845.6240.0350.0350.0000.0000.0000.000
120X121GLN00.0550.03243.9920.0010.0010.0000.0000.0000.000
121X122VAL0-0.0100.00243.1060.0010.0010.0000.0000.0000.000
122X123ARG10.8260.89845.860-0.041-0.0410.0000.0000.0000.000
123X124ASN00.0250.01549.514-0.001-0.0010.0000.0000.0000.000
124X125TYR00.0140.00145.4410.0000.0000.0000.0000.0000.000
125X126VAL0-0.005-0.00247.4800.0010.0010.0000.0000.0000.000
126X127MET0-0.034-0.01749.8470.0000.0000.0000.0000.0000.000
127X128GLN0-0.035-0.00750.740-0.002-0.0020.0000.0000.0000.000
128X129TYR0-0.002-0.04149.670-0.001-0.0010.0000.0000.0000.000
129X130ILE0-0.006-0.01252.1030.0000.0000.0000.0000.0000.000
130X131GLN0-0.022-0.01554.833-0.001-0.0010.0000.0000.0000.000
131X132GLU-1-0.946-0.97652.5220.0480.0480.0000.0000.0000.000
132X133ASN0-0.029-0.01052.7880.0010.0010.0000.0000.0000.000
133X134LYS10.9360.99156.459-0.036-0.0360.0000.0000.0000.000
134X135GLU-1-0.897-0.96559.2770.0370.0370.0000.0000.0000.000
135X136ARG10.9080.96252.319-0.056-0.0560.0000.0000.0000.000
136X137ILE00.005-0.02054.2990.0010.0010.0000.0000.0000.000
137X138LEU0-0.039-0.02058.0140.0000.0000.0000.0000.0000.000
138X139THR0-0.054-0.01661.438-0.001-0.0010.0000.0000.0000.000
139X140GLU-1-0.940-0.96857.5240.0500.0500.0000.0000.0000.000
140X141ARG10.8100.89458.883-0.039-0.0390.0000.0000.0000.000
141X142TYR0-0.012-0.07155.2760.0030.0030.0000.0000.0000.000
142X143LYS10.9310.97454.329-0.046-0.0460.0000.0000.0000.000
143X144LEU00.0390.03252.3830.0030.0030.0000.0000.0000.000
144X145VAL00.0110.01049.8870.0020.0020.0000.0000.0000.000
145X146PRO0-0.035-0.03447.5430.0020.0020.0000.0000.0000.000
146X147GLY00.0150.00946.9260.0040.0040.0000.0000.0000.000
147X148ILE00.0340.02548.1230.0010.0010.0000.0000.0000.000
148X149PHE0-0.012-0.01341.1760.0020.0020.0000.0000.0000.000
149X150ALA0-0.061-0.03943.2470.0030.0030.0000.0000.0000.000
150X151ASP-1-0.793-0.85943.3910.0740.0740.0000.0000.0000.000
151X152VAL0-0.002-0.00844.0680.0000.0000.0000.0000.0000.000
152X153LYS10.8730.93739.079-0.095-0.0950.0000.0000.0000.000
153X154ASN0-0.042-0.01640.1180.0080.0080.0000.0000.0000.000
154X155LEU00.0160.04141.5130.0000.0000.0000.0000.0000.000
155X156LYS10.9710.97640.244-0.061-0.0610.0000.0000.0000.000
156X157GLU-1-0.925-0.96640.2790.0630.0630.0000.0000.0000.000
157X158LEU0-0.028-0.01240.798-0.002-0.0020.0000.0000.0000.000
158X159LYS10.9330.98532.849-0.104-0.1040.0000.0000.0000.000
159X160TRP00.002-0.02430.8280.0100.0100.0000.0000.0000.000
160X161ALA00.0260.03435.885-0.002-0.0020.0000.0000.0000.000
161X162ASP-1-0.771-0.88336.3780.0860.0860.0000.0000.0000.000
162X163PRO00.0180.00935.642-0.005-0.0050.0000.0000.0000.000
163X164ARG10.7830.87635.452-0.081-0.0810.0000.0000.0000.000
164X165SER00.0060.00739.804-0.004-0.0040.0000.0000.0000.000
165X166PHE00.0310.00739.919-0.002-0.0020.0000.0000.0000.000
166X167LYS10.8840.94943.778-0.065-0.0650.0000.0000.0000.000
167X168PRO00.0480.01744.738-0.002-0.0020.0000.0000.0000.000
168X169ILE00.0520.03345.689-0.003-0.0030.0000.0000.0000.000
169X170ILE00.0000.00246.588-0.002-0.0020.0000.0000.0000.000
170X171ASP-1-0.883-0.94349.9110.0540.0540.0000.0000.0000.000
171X172GLN0-0.015-0.01250.6320.0000.0000.0000.0000.0000.000
172X173GLU-1-0.775-0.86652.4520.0380.0380.0000.0000.0000.000
173X174VAL00.0040.00753.239-0.001-0.0010.0000.0000.0000.000
174X175LEU0-0.0030.01155.789-0.001-0.0010.0000.0000.0000.000
175X176LYS10.8150.88855.527-0.038-0.0380.0000.0000.0000.000
176X177LEU0-0.0300.00258.318-0.001-0.0010.0000.0000.0000.000
177X178LEU0-0.055-0.01457.960-0.001-0.0010.0000.0000.0000.000
178X179GLY00.0620.04261.345-0.001-0.0010.0000.0000.0000.000
179X180PRO0-0.0030.00660.8570.0020.0020.0000.0000.0000.000
180X181LYS10.9030.95254.370-0.048-0.0480.0000.0000.0000.000
181X182ASP-1-0.743-0.85661.2230.0350.0350.0000.0000.0000.000
182X183GLU-1-0.881-0.94063.6940.0350.0350.0000.0000.0000.000
183X184ARG10.8190.89064.317-0.034-0.0340.0000.0000.0000.000
184X185ASP-1-0.869-0.92259.6140.0440.0440.0000.0000.0000.000
185X186LEU0-0.022-0.00159.8500.0020.0020.0000.0000.0000.000
186X187ILE0-0.057-0.02155.8420.0010.0010.0000.0000.0000.000