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: R94R8

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 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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1852798.487809
FMO2-HF: Nuclear repulsion 1779563.565986
FMO2-HF: Total energy -73234.921823
FMO2-MP2: Total energy -73451.926786


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.
-17.792-13.45410.619-6.867-8.089-0.049
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 : 0.002 / q_NPA : 0.009
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].
3X4VAL00.009-0.0193.886-2.630-0.576-0.010-1.259-0.7860.007
4X5GLU-1-0.811-0.8866.666-1.979-1.9790.0000.0000.0000.000
5X6GLU-1-0.775-0.8472.079-17.486-17.3369.801-4.632-5.319-0.057
6X7LEU0-0.038-0.0133.2960.9491.4220.010-0.091-0.3910.000
7X8THR0-0.031-0.0405.2450.7460.798-0.001-0.001-0.0500.000
8X9GLN0-0.0060.0167.7680.5010.5010.0000.0000.0000.000
9X10LEU00.0270.0306.4650.3000.3000.0000.0000.0000.000
10X11PHE0-0.016-0.0257.0350.2120.2120.0000.0000.0000.000
11X12SER00.018-0.01210.5250.1350.1350.0000.0000.0000.000
12X13GLN0-0.035-0.01010.5570.0720.0720.0000.0000.0000.000
13X14VAL0-0.030-0.00211.9500.0810.0810.0000.0000.0000.000
14X15GLY00.0360.00914.3800.0690.0690.0000.0000.0000.000
15X16PHE0-0.092-0.05812.8620.0510.0510.0000.0000.0000.000
16X17GLU-1-0.808-0.90515.679-0.225-0.2250.0000.0000.0000.000
17X18ASP-1-0.840-0.91516.005-0.362-0.3620.0000.0000.0000.000
18X19LYS10.9070.94416.2520.0990.0990.0000.0000.0000.000
19X20LYS10.7890.88815.8410.0490.0490.0000.0000.0000.000
20X21VAL00.0550.03710.8840.0300.0300.0000.0000.0000.000
21X22LYS10.9540.97212.5300.2800.2800.0000.0000.0000.000
22X23GLU-1-0.834-0.89614.8450.0070.0070.0000.0000.0000.000
23X24ILE00.0420.01710.3470.0410.0410.0000.0000.0000.000
24X25VAL00.0200.0208.4950.1040.1040.0000.0000.0000.000
25X26LYS10.8250.91710.6560.2160.2160.0000.0000.0000.000
26X27ASN0-0.0050.00212.8540.1580.1580.0000.0000.0000.000
27X28LYS10.9540.9687.752-0.044-0.0440.0000.0000.0000.000
28X29LYS11.0491.0418.259-0.598-0.5980.0000.0000.0000.000
29X30VAL0-0.0200.00110.2490.0830.0830.0000.0000.0000.000
30X31SER0-0.009-0.0086.957-0.102-0.1020.0000.0000.0000.000
31X32ASP-1-0.839-0.9365.1761.7961.808-0.001-0.003-0.0070.000
32X33SER0-0.040-0.0256.6270.2120.2120.0000.0000.0000.000
33X34LEU0-0.018-0.0109.122-0.014-0.0140.0000.0000.0000.000
34X35TYR0-0.030-0.0492.708-0.7720.8250.820-0.881-1.5360.001
35X36LYS10.8380.9076.526-0.870-0.8700.0000.0000.0000.000
36X37LEU0-0.017-0.0198.675-0.207-0.2070.0000.0000.0000.000
37X38ILE0-0.025-0.0119.490-0.112-0.1120.0000.0000.0000.000
38X39LYS10.9080.9675.4190.0140.0140.0000.0000.0000.000
39X40GLU-1-0.810-0.85410.2940.6200.6200.0000.0000.0000.000
40X41THR0-0.073-0.05413.552-0.078-0.0780.0000.0000.0000.000
41X42PRO00.0260.00715.249-0.008-0.0080.0000.0000.0000.000
42X43SER0-0.013-0.01414.866-0.013-0.0130.0000.0000.0000.000
43X44ASP-1-0.892-0.94016.424-0.081-0.0810.0000.0000.0000.000
44X45TYR00.0230.01217.349-0.009-0.0090.0000.0000.0000.000
45X46GLN0-0.030-0.00818.262-0.021-0.0210.0000.0000.0000.000
46X47TRP00.0340.01114.4100.0220.0220.0000.0000.0000.000
47X48ASN00.0480.02218.692-0.016-0.0160.0000.0000.0000.000
48X49LYS10.9830.97820.4570.0470.0470.0000.0000.0000.000
49X50SER0-0.0360.00422.0730.0130.0130.0000.0000.0000.000
50X51THR00.0650.01419.4810.0050.0050.0000.0000.0000.000
51X52ARG10.8780.94416.3590.1840.1840.0000.0000.0000.000
52X53ALA0-0.020-0.00917.0060.0170.0170.0000.0000.0000.000
53X54LEU0-0.0160.00219.0750.0230.0230.0000.0000.0000.000
54X55VAL00.0540.03113.8740.0330.0330.0000.0000.0000.000
55X56HIS0-0.0010.00613.8110.0290.0290.0000.0000.0000.000
56X57ASN0-0.033-0.00615.6960.0260.0260.0000.0000.0000.000
57X58LEU00.0850.06316.3080.0220.0220.0000.0000.0000.000
58X59ALA00.0070.00312.2190.0540.0540.0000.0000.0000.000
59X60SER0-0.087-0.06314.0840.0560.0560.0000.0000.0000.000
60X61PHE0-0.029-0.02116.5210.0030.0030.0000.0000.0000.000
61X62VAL00.0190.01313.348-0.003-0.0030.0000.0000.0000.000
62X63LYS10.8890.95113.335-0.378-0.3780.0000.0000.0000.000
63X64GLY0-0.016-0.01310.605-0.027-0.0270.0000.0000.0000.000
64X65THR0-0.092-0.03711.6440.0840.0840.0000.0000.0000.000
65X66ASP-1-0.838-0.92213.0371.0761.0760.0000.0000.0000.000
66X67LEU0-0.098-0.05914.257-0.106-0.1060.0000.0000.0000.000
67X68PRO00.0190.00617.2880.0080.0080.0000.0000.0000.000
68X69LYS10.8550.93019.575-0.291-0.2910.0000.0000.0000.000
69X70SER0-0.018-0.02315.571-0.011-0.0110.0000.0000.0000.000
70X71GLU-1-0.795-0.90517.2730.3240.3240.0000.0000.0000.000
71X72LEU0-0.0330.00618.353-0.054-0.0540.0000.0000.0000.000
72X73ILE00.012-0.00419.436-0.031-0.0310.0000.0000.0000.000
73X74VAL0-0.020-0.00615.312-0.038-0.0380.0000.0000.0000.000
74X75ASN0-0.011-0.02818.515-0.061-0.0610.0000.0000.0000.000
75X76GLY00.0430.02521.282-0.026-0.0260.0000.0000.0000.000
76X77ILE0-0.055-0.03218.931-0.022-0.0220.0000.0000.0000.000
77X78ILE0-0.077-0.03518.090-0.025-0.0250.0000.0000.0000.000
78X79ASN0-0.049-0.04021.409-0.006-0.0060.0000.0000.0000.000
79X80GLY0-0.032-0.00724.785-0.011-0.0110.0000.0000.0000.000
80X81ASP-1-0.748-0.84026.5950.0920.0920.0000.0000.0000.000
81X82LEU0-0.050-0.01723.0920.0010.0010.0000.0000.0000.000
82X83LYS10.9200.94624.862-0.052-0.0520.0000.0000.0000.000
83X84THR00.0210.00526.792-0.005-0.0050.0000.0000.0000.000
84X85SER00.034-0.01723.7300.0060.0060.0000.0000.0000.000
85X86LEU0-0.0070.00725.1220.0170.0170.0000.0000.0000.000
86X87GLN00.0350.02526.9370.0020.0020.0000.0000.0000.000
87X88VAL00.0060.00820.4790.0130.0130.0000.0000.0000.000
88X89ASP-1-0.836-0.89623.1580.1980.1980.0000.0000.0000.000
89X90ALA0-0.014-0.00124.8630.0150.0150.0000.0000.0000.000
90X91ALA00.0460.03023.8090.0090.0090.0000.0000.0000.000
91X92PHE0-0.005-0.01718.8420.0150.0150.0000.0000.0000.000
92X93LYS10.7710.86022.688-0.158-0.1580.0000.0000.0000.000
93X94TYR00.0490.03225.8400.0080.0080.0000.0000.0000.000
94X95VAL00.0480.02121.457-0.001-0.0010.0000.0000.0000.000
95X96LYS10.9040.95421.375-0.303-0.3030.0000.0000.0000.000
96X97ALA0-0.061-0.02423.5780.0050.0050.0000.0000.0000.000
97X98ASN0-0.049-0.02526.804-0.020-0.0200.0000.0000.0000.000
98X99GLY00.0320.02523.653-0.001-0.0010.0000.0000.0000.000
99X100GLU-1-0.831-0.92522.5830.3190.3190.0000.0000.0000.000
100X101ALA0-0.0100.00124.826-0.014-0.0140.0000.0000.0000.000
101X102SER0-0.021-0.01824.943-0.024-0.0240.0000.0000.0000.000
102X103THR00.0290.00226.6670.0010.0010.0000.0000.0000.000
103X104LYS10.8920.93726.100-0.118-0.1180.0000.0000.0000.000
104X105MET00.0080.00827.736-0.004-0.0040.0000.0000.0000.000
105X106GLY00.1040.06931.205-0.006-0.0060.0000.0000.0000.000
106X107MET0-0.0150.00724.5380.0070.0070.0000.0000.0000.000
107X108ASN0-0.040-0.04628.1810.0060.0060.0000.0000.0000.000
108X109GLU-1-0.916-0.94530.0370.1040.1040.0000.0000.0000.000
109X110ASN0-0.065-0.04330.717-0.006-0.0060.0000.0000.0000.000
110X111SER0-0.079-0.06427.9100.0060.0060.0000.0000.0000.000
111X112GLY00.0170.00630.013-0.005-0.0050.0000.0000.0000.000
112X113VAL0-0.035-0.02028.955-0.008-0.0080.0000.0000.0000.000
113X114GLY0-0.015-0.00232.0330.0000.0000.0000.0000.0000.000
114X115ILE0-0.059-0.01735.060-0.005-0.0050.0000.0000.0000.000
115X116GLU-1-0.924-0.96135.9370.0340.0340.0000.0000.0000.000
116X117ILE0-0.072-0.03638.4550.0000.0000.0000.0000.0000.000
117X118THR00.039-0.00440.965-0.003-0.0030.0000.0000.0000.000
118X119GLU-1-0.847-0.92643.1860.0200.0200.0000.0000.0000.000
119X120ASP-1-0.871-0.94545.2240.0270.0270.0000.0000.0000.000
120X121GLN00.0460.06043.111-0.001-0.0010.0000.0000.0000.000
121X122VAL0-0.0020.00342.4190.0020.0020.0000.0000.0000.000
122X123ARG10.7810.85945.360-0.021-0.0210.0000.0000.0000.000
123X124ASN0-0.034-0.02349.0070.0000.0000.0000.0000.0000.000
124X125TYR00.0240.00744.4130.0010.0010.0000.0000.0000.000
125X126VAL0-0.015-0.00546.8040.0010.0010.0000.0000.0000.000
126X127MET0-0.020-0.01749.316-0.001-0.0010.0000.0000.0000.000
127X128GLN0-0.083-0.03850.547-0.001-0.0010.0000.0000.0000.000
128X129TYR0-0.003-0.03649.511-0.001-0.0010.0000.0000.0000.000
129X130ILE0-0.002-0.01851.6470.0000.0000.0000.0000.0000.000
130X131GLN00.0150.01854.310-0.003-0.0030.0000.0000.0000.000
131X132GLU-1-0.903-0.95151.9700.0420.0420.0000.0000.0000.000
132X133ASN0-0.022-0.00152.2510.0010.0010.0000.0000.0000.000
133X134LYS10.9190.96655.903-0.027-0.0270.0000.0000.0000.000
134X135GLU-1-0.885-0.95558.7820.0270.0270.0000.0000.0000.000
135X136ARG10.8330.91750.796-0.040-0.0400.0000.0000.0000.000
136X137ILE0-0.014-0.01953.741-0.001-0.0010.0000.0000.0000.000
137X138LEU0-0.029-0.02357.173-0.001-0.0010.0000.0000.0000.000
138X139THR0-0.061-0.02260.398-0.001-0.0010.0000.0000.0000.000
139X140GLU-1-0.928-0.96656.4000.0260.0260.0000.0000.0000.000
140X141ARG10.8300.89958.049-0.018-0.0180.0000.0000.0000.000
141X142TYR0-0.056-0.07654.2980.0010.0010.0000.0000.0000.000
142X143LYS10.7860.90453.648-0.018-0.0180.0000.0000.0000.000
143X144LEU00.0480.03651.9560.0010.0010.0000.0000.0000.000
144X145VAL00.0010.01049.0870.0020.0020.0000.0000.0000.000
145X146PRO0-0.027-0.02846.6990.0010.0010.0000.0000.0000.000
146X147GLY00.0180.01445.9900.0030.0030.0000.0000.0000.000
147X148ILE00.0350.03147.2550.0020.0020.0000.0000.0000.000
148X149PHE00.040-0.00240.2990.0020.0020.0000.0000.0000.000
149X150ALA0-0.061-0.03642.6510.0030.0030.0000.0000.0000.000
150X151ASP-1-0.751-0.84842.9770.0490.0490.0000.0000.0000.000
151X152VAL00.001-0.00743.5920.0030.0030.0000.0000.0000.000
152X153LYS10.8200.91638.692-0.043-0.0430.0000.0000.0000.000
153X154ASN0-0.045-0.00439.4680.0080.0080.0000.0000.0000.000
154X155LEU00.0130.02441.3880.0030.0030.0000.0000.0000.000
155X156LYS10.8790.91639.558-0.067-0.0670.0000.0000.0000.000
156X157GLU-1-0.834-0.90139.5870.0660.0660.0000.0000.0000.000
157X158LEU0-0.013-0.00640.128-0.002-0.0020.0000.0000.0000.000
158X159LYS10.8650.95732.035-0.112-0.1120.0000.0000.0000.000
159X160TRP00.021-0.00830.6590.0080.0080.0000.0000.0000.000
160X161ALA00.0410.03835.403-0.004-0.0040.0000.0000.0000.000
161X162ASP-1-0.775-0.86335.9240.0320.0320.0000.0000.0000.000
162X163PRO00.0300.01435.088-0.003-0.0030.0000.0000.0000.000
163X164ARG10.7720.85234.640-0.023-0.0230.0000.0000.0000.000
164X165SER0-0.004-0.01039.132-0.003-0.0030.0000.0000.0000.000
165X166PHE00.0410.01638.848-0.002-0.0020.0000.0000.0000.000
166X167LYS10.8120.89643.057-0.023-0.0230.0000.0000.0000.000
167X168PRO00.0380.00744.024-0.001-0.0010.0000.0000.0000.000
168X169ILE00.0350.03744.983-0.001-0.0010.0000.0000.0000.000
169X170ILE00.0060.00145.7160.0000.0000.0000.0000.0000.000
170X171ASP-1-0.819-0.88948.8710.0200.0200.0000.0000.0000.000
171X172GLN00.0040.00350.1700.0000.0000.0000.0000.0000.000
172X173GLU-1-0.743-0.84451.5430.0210.0210.0000.0000.0000.000
173X174VAL00.004-0.00552.4790.0000.0000.0000.0000.0000.000
174X175LEU0-0.030-0.00354.979-0.001-0.0010.0000.0000.0000.000
175X176LYS10.7860.87354.861-0.021-0.0210.0000.0000.0000.000
176X177LEU0-0.050-0.00657.5280.0000.0000.0000.0000.0000.000
177X178LEU0-0.029-0.00257.0860.0000.0000.0000.0000.0000.000
178X179GLY00.0640.06060.633-0.001-0.0010.0000.0000.0000.000
179X180PRO00.0130.00459.9400.0010.0010.0000.0000.0000.000
180X181LYS10.9180.96353.591-0.014-0.0140.0000.0000.0000.000
181X182ASP-1-0.760-0.84660.3260.0140.0140.0000.0000.0000.000
182X183GLU-1-0.868-0.95062.7470.0130.0130.0000.0000.0000.000
183X184ARG10.8350.88963.506-0.015-0.0150.0000.0000.0000.000
184X185ASP-1-0.784-0.89758.5890.0180.0180.0000.0000.0000.000
185X186LEU0-0.040-0.00358.6890.0000.0000.0000.0000.0000.000
186X187ILE0-0.0050.00854.8380.0010.0010.0000.0000.0000.000