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: 52GNZ

Calculation Name: 1T06-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1T06

Chain ID: A

ChEMBL ID:

UniProt ID: Q81BA8

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 235
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3004342.266971
FMO2-HF: Nuclear repulsion 2909920.552014
FMO2-HF: Total energy -94421.714957
FMO2-MP2: Total energy -94692.184451


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-21.872-9.2917.357-7.159-12.774-0.019
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.041 / q_NPA : -0.011
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].
3A3PHE00.1040.0323.808-0.6141.966-0.027-1.360-1.1920.006
4A4LYS10.9480.9796.5572.0982.0980.0000.0000.0000.000
5A5THR0-0.028-0.0302.497-2.854-0.5702.968-1.961-3.292-0.017
6A6VAL00.0440.0343.0890.6631.5060.072-0.163-0.751-0.001
7A7MET0-0.008-0.0045.4610.4190.4190.0000.0000.0000.000
8A8GLN0-0.037-0.0085.690-0.217-0.2170.0000.0000.0000.000
9A9GLU-1-0.925-0.9802.7240.5243.6590.785-1.780-2.140-0.023
10A10LEU0-0.027-0.0206.8780.0770.0770.0000.0000.0000.000
11A11GLU-1-0.977-0.9859.7560.1110.1110.0000.0000.0000.000
12A12ALA00.0300.0189.5470.0170.0170.0000.0000.0000.000
13A13LEU0-0.095-0.0479.1490.0160.0160.0000.0000.0000.000
14A14GLY0-0.0330.00712.475-0.030-0.0300.0000.0000.0000.000
15A15LYS10.9230.94515.534-0.488-0.4880.0000.0000.0000.000
16A16GLU-1-0.781-0.90018.9890.1000.1000.0000.0000.0000.000
17A17ARG10.9300.96222.338-0.280-0.2800.0000.0000.0000.000
18A18THR0-0.001-0.01119.254-0.022-0.0220.0000.0000.0000.000
19A19LYS10.9440.98320.304-0.072-0.0720.0000.0000.0000.000
20A20LYS10.8840.94321.918-0.134-0.1340.0000.0000.0000.000
21A21ILE0-0.039-0.00324.218-0.015-0.0150.0000.0000.0000.000
22A22TYR0-0.001-0.04718.006-0.023-0.0230.0000.0000.0000.000
23A23ILE00.0220.01723.884-0.016-0.0160.0000.0000.0000.000
24A24SER0-0.057-0.00425.951-0.010-0.0100.0000.0000.0000.000
25A25ASN0-0.099-0.07825.066-0.012-0.0120.0000.0000.0000.000
26A26GLY00.0410.02427.592-0.006-0.0060.0000.0000.0000.000
27A27ALA0-0.0300.00722.365-0.016-0.0160.0000.0000.0000.000
28A28HIS10.9250.94523.5380.0750.0750.0000.0000.0000.000
29A29GLU-1-0.852-0.90521.580-0.011-0.0110.0000.0000.0000.000
30A30PRO00.007-0.00418.418-0.009-0.0090.0000.0000.0000.000
31A31VAL0-0.007-0.01818.1390.0070.0070.0000.0000.0000.000
32A32PHE00.0270.00112.525-0.008-0.0080.0000.0000.0000.000
33A33GLY0-0.035-0.02417.0380.0180.0180.0000.0000.0000.000
34A34VAL0-0.0040.00612.2910.0340.0340.0000.0000.0000.000
35A35ALA0-0.0260.01615.634-0.045-0.0450.0000.0000.0000.000
36A36THR00.0970.03315.0530.1180.1180.0000.0000.0000.000
37A37GLY0-0.016-0.00814.3490.0940.0940.0000.0000.0000.000
38A38ALA0-0.040-0.02412.6770.1030.1030.0000.0000.0000.000
39A39MET00.0650.0409.7520.2600.2600.0000.0000.0000.000
40A40LYS10.9530.9859.110-0.704-0.7040.0000.0000.0000.000
41A41PRO0-0.060-0.0348.438-0.002-0.0020.0000.0000.0000.000
42A42ILE00.0830.0383.809-0.0800.4720.065-0.115-0.5010.000
43A43ALA00.0320.0134.617-0.114-0.037-0.001-0.008-0.0670.000
44A44LYS10.8780.9446.829-1.589-1.5890.0000.0000.0000.000
45A45LYS10.8800.9382.533-15.666-14.0612.434-1.204-2.8330.017
46A46ILE00.0040.0202.493-1.989-0.6691.063-0.552-1.831-0.001
47A47LYS10.9270.9744.7510.8500.957-0.001-0.009-0.0970.000
48A48LEU0-0.010-0.0137.505-0.296-0.2960.0000.0000.0000.000
49A49ASN0-0.004-0.0026.8230.1430.1430.0000.0000.0000.000
50A50GLN00.0910.0289.6510.0250.0250.0000.0000.0000.000
51A51GLU-1-0.876-0.93811.321-0.927-0.9270.0000.0000.0000.000
52A52LEU0-0.020-0.0034.671-0.121-0.043-0.001-0.007-0.0700.000
53A53ALA0-0.001-0.0069.1160.1790.1790.0000.0000.0000.000
54A54GLU-1-0.780-0.87611.075-0.335-0.3350.0000.0000.0000.000
55A55GLU-1-0.915-0.95910.481-1.601-1.6010.0000.0000.0000.000
56A56LEU0-0.048-0.0347.2260.1300.1300.0000.0000.0000.000
57A57TYR0-0.053-0.04011.6020.1380.1380.0000.0000.0000.000
58A58ALA00.001-0.00214.9240.0680.0680.0000.0000.0000.000
59A59THR0-0.063-0.04312.9980.0630.0630.0000.0000.0000.000
60A60GLY00.0200.01916.1580.0340.0340.0000.0000.0000.000
61A61ASN0-0.025-0.00815.0540.0970.0970.0000.0000.0000.000
62A62TYR00.0680.01715.806-0.001-0.0010.0000.0000.0000.000
63A63ASP-1-0.722-0.85913.9450.2490.2490.0000.0000.0000.000
64A64ALA00.0220.01011.4120.0910.0910.0000.0000.0000.000
65A65MET0-0.0240.00611.974-0.028-0.0280.0000.0000.0000.000
66A66TYR0-0.042-0.05913.969-0.010-0.0100.0000.0000.0000.000
67A67PHE0-0.047-0.0395.7290.1430.1430.0000.0000.0000.000
68A68ALA00.0200.01610.408-0.010-0.0100.0000.0000.0000.000
69A69GLY00.0370.01011.582-0.048-0.0480.0000.0000.0000.000
70A70ILE0-0.109-0.05810.6970.0220.0220.0000.0000.0000.000
71A71ILE0-0.052-0.0226.8970.0310.0310.0000.0000.0000.000
72A72ALA00.0370.03310.155-0.190-0.1900.0000.0000.0000.000
73A73ASP-1-0.851-0.94413.028-0.247-0.2470.0000.0000.0000.000
74A74PRO00.0340.01215.096-0.014-0.0140.0000.0000.0000.000
75A75LYS10.8320.91216.0580.2150.2150.0000.0000.0000.000
76A76ALA0-0.032-0.01017.5820.0080.0080.0000.0000.0000.000
77A77MET0-0.0680.00718.031-0.016-0.0160.0000.0000.0000.000
78A78SER0-0.012-0.01520.7970.0410.0410.0000.0000.0000.000
79A79GLU-1-0.821-0.93324.107-0.111-0.1110.0000.0000.0000.000
80A80SER00.0110.01025.8170.0030.0030.0000.0000.0000.000
81A81ASP-1-0.782-0.88820.593-0.319-0.3190.0000.0000.0000.000
82A82PHE00.000-0.01920.6900.0000.0000.0000.0000.0000.000
83A83ASP-1-0.852-0.93923.332-0.109-0.1090.0000.0000.0000.000
84A84ARG10.8530.93218.8660.3540.3540.0000.0000.0000.000
85A85TRP0-0.054-0.03414.5520.0390.0390.0000.0000.0000.000
86A86ILE0-0.060-0.00721.4620.0190.0190.0000.0000.0000.000
87A87ASP-1-0.892-0.93824.500-0.122-0.1220.0000.0000.0000.000
88A88GLY0-0.042-0.01122.2820.0000.0000.0000.0000.0000.000
89A89ALA0-0.063-0.04322.4690.0110.0110.0000.0000.0000.000
90A90TYR00.0100.00221.4550.0220.0220.0000.0000.0000.000
91A91PHE00.0180.00021.9500.0150.0150.0000.0000.0000.000
92A92TYR00.0620.01225.0360.0000.0000.0000.0000.0000.000
93A93MET0-0.091-0.00521.7790.0050.0050.0000.0000.0000.000
94A94LEU0-0.0040.01218.8690.0200.0200.0000.0000.0000.000
95A95SER00.0870.03321.737-0.006-0.0060.0000.0000.0000.000
96A96ASP-1-0.815-0.88324.4160.0350.0350.0000.0000.0000.000
97A97TYR0-0.029-0.03521.0930.0100.0100.0000.0000.0000.000
98A98VAL0-0.0340.00216.6420.0320.0320.0000.0000.0000.000
99A99VAL00.0230.00519.205-0.007-0.0070.0000.0000.0000.000
100A100ALA00.0440.03320.971-0.008-0.0080.0000.0000.0000.000
101A101VAL0-0.052-0.01918.8060.0020.0020.0000.0000.0000.000
102A102THR00.0390.05116.5740.0290.0290.0000.0000.0000.000
103A103LEU00.0120.03219.357-0.010-0.0100.0000.0000.0000.000
104A104SER0-0.072-0.07122.2710.0040.0040.0000.0000.0000.000
105A105GLU-1-0.994-1.01818.2590.1060.1060.0000.0000.0000.000
106A106SER0-0.0030.01821.609-0.016-0.0160.0000.0000.0000.000
107A107ASN0-0.066-0.05623.1080.0070.0070.0000.0000.0000.000
108A108ILE00.0610.02925.6010.0070.0070.0000.0000.0000.000
109A109ALA0-0.041-0.01026.2780.0030.0030.0000.0000.0000.000
110A110GLN00.0370.00227.6050.0010.0010.0000.0000.0000.000
111A111ASP-1-0.864-0.90231.223-0.055-0.0550.0000.0000.0000.000
112A112VAL00.015-0.00326.9700.0000.0000.0000.0000.0000.000
113A113ALA0-0.021-0.01629.3960.0030.0030.0000.0000.0000.000
114A114ASP-1-0.709-0.83030.545-0.018-0.0180.0000.0000.0000.000
115A115LYS10.8300.92630.8120.1010.1010.0000.0000.0000.000
116A116TRP0-0.035-0.03824.7440.0050.0050.0000.0000.0000.000
117A117ILE0-0.038-0.01032.4090.0030.0030.0000.0000.0000.000
118A118ALA0-0.002-0.00134.8490.0030.0030.0000.0000.0000.000
119A119SER0-0.062-0.02934.028-0.003-0.0030.0000.0000.0000.000
120A120GLY00.0350.01036.170-0.003-0.0030.0000.0000.0000.000
121A121ASP-1-0.891-0.94631.690-0.053-0.0530.0000.0000.0000.000
122A122GLU-1-0.823-0.90732.5870.0010.0010.0000.0000.0000.000
123A123LEU00.030-0.00227.9700.0100.0100.0000.0000.0000.000
124A124LYS10.9821.00529.1430.0940.0940.0000.0000.0000.000
125A125MET0-0.0400.00030.2190.0050.0050.0000.0000.0000.000
126A126SER0-0.073-0.06429.0410.0090.0090.0000.0000.0000.000
127A127ALA00.0120.01526.3800.0120.0120.0000.0000.0000.000
128A128GLY00.0380.02227.7840.0050.0050.0000.0000.0000.000
129A129TRP00.0520.00730.2380.0070.0070.0000.0000.0000.000
130A130SER0-0.030-0.03226.8300.0140.0140.0000.0000.0000.000
131A131CYS0-0.074-0.01926.4190.0130.0130.0000.0000.0000.000
132A132TYR0-0.016-0.05327.4380.0100.0100.0000.0000.0000.000
133A133CYS0-0.0710.00228.9230.0070.0070.0000.0000.0000.000
134A134TRP0-0.011-0.02024.3300.0250.0250.0000.0000.0000.000
135A135LEU0-0.004-0.00226.6740.0090.0090.0000.0000.0000.000
136A136LEU0-0.0140.00428.2770.0040.0040.0000.0000.0000.000
137A137GLY0-0.010-0.00227.7710.0060.0060.0000.0000.0000.000
138A138ASN0-0.063-0.04223.3920.0290.0290.0000.0000.0000.000
139A139ARG10.9110.96726.232-0.005-0.0050.0000.0000.0000.000
140A140LYS10.9760.98529.681-0.087-0.0870.0000.0000.0000.000
141A141ASP-1-0.722-0.87432.9940.0570.0570.0000.0000.0000.000
142A142ASN0-0.027-0.03136.0530.0000.0000.0000.0000.0000.000
143A143ALA0-0.054-0.00832.601-0.006-0.0060.0000.0000.0000.000
144A144PHE0-0.042-0.02230.996-0.006-0.0060.0000.0000.0000.000
145A145SER00.0160.01936.5490.0020.0020.0000.0000.0000.000
146A146GLU-1-0.859-0.94540.0550.0280.0280.0000.0000.0000.000
147A147SER00.015-0.00542.1050.0010.0010.0000.0000.0000.000
148A148LYS10.8590.92535.6140.0120.0120.0000.0000.0000.000
149A149ILE00.008-0.00636.1170.0000.0000.0000.0000.0000.000
150A150SER00.021-0.00139.7680.0030.0030.0000.0000.0000.000
151A151ASP-1-0.905-0.94743.1940.0050.0050.0000.0000.0000.000
152A152MET0-0.078-0.03335.157-0.001-0.0010.0000.0000.0000.000
153A153LEU0-0.048-0.02340.0000.0020.0020.0000.0000.0000.000
154A154GLU-1-0.801-0.91142.0120.0200.0200.0000.0000.0000.000
155A155MET00.0270.02339.629-0.002-0.0020.0000.0000.0000.000
156A156VAL0-0.032-0.02438.8070.0000.0000.0000.0000.0000.000
157A157LYS10.8810.94841.679-0.018-0.0180.0000.0000.0000.000
158A158ASP-1-0.911-0.94444.9860.0110.0110.0000.0000.0000.000
159A159THR0-0.072-0.05142.455-0.002-0.0020.0000.0000.0000.000
160A160ILE0-0.0100.00638.861-0.001-0.0010.0000.0000.0000.000
161A161HIS0-0.057-0.05541.418-0.001-0.0010.0000.0000.0000.000
162A162HIS0-0.051-0.02143.836-0.002-0.0020.0000.0000.0000.000
163A163SER0-0.036-0.01238.711-0.005-0.0050.0000.0000.0000.000
164A164PRO00.0320.01236.2650.0030.0030.0000.0000.0000.000
165A165GLU-1-0.762-0.89135.7910.0260.0260.0000.0000.0000.000
166A166ARG10.9190.93929.995-0.041-0.0410.0000.0000.0000.000
167A167THR00.0400.01032.7270.0040.0040.0000.0000.0000.000
168A168LYS10.8560.95034.526-0.019-0.0190.0000.0000.0000.000
169A169SER0-0.026-0.01731.6110.0080.0080.0000.0000.0000.000
170A170ALA0-0.0270.00931.0860.0080.0080.0000.0000.0000.000
171A171MET00.0160.02332.3310.0050.0050.0000.0000.0000.000
172A172ASN00.009-0.00135.7070.0090.0090.0000.0000.0000.000
173A173ASN0-0.022-0.01729.0230.0110.0110.0000.0000.0000.000
174A174PHE00.0520.01833.3470.0070.0070.0000.0000.0000.000
175A175LEU00.0120.00934.6700.0020.0020.0000.0000.0000.000
176A176ASN0-0.003-0.01234.6310.0040.0040.0000.0000.0000.000
177A177THR0-0.034-0.04131.1440.0070.0070.0000.0000.0000.000
178A178VAL00.0050.02934.0700.0030.0030.0000.0000.0000.000
179A179ALA00.0250.01136.9810.0010.0010.0000.0000.0000.000
180A180ILE0-0.056-0.00834.0850.0020.0020.0000.0000.0000.000
181A181SER0-0.072-0.06132.2550.0060.0060.0000.0000.0000.000
182A182TYR0-0.0160.00034.403-0.002-0.0020.0000.0000.0000.000
183A183VAL00.0400.00237.104-0.004-0.0040.0000.0000.0000.000
184A184PRO0-0.0260.00939.540-0.001-0.0010.0000.0000.0000.000
185A185LEU00.0220.02041.040-0.003-0.0030.0000.0000.0000.000
186A186HIS0-0.069-0.04240.7840.0000.0000.0000.0000.0000.000
187A187GLU-1-0.863-0.94742.5390.0510.0510.0000.0000.0000.000
188A188LYS10.9240.97744.977-0.025-0.0250.0000.0000.0000.000
189A189ALA0-0.0030.01040.827-0.001-0.0010.0000.0000.0000.000
190A190VAL0-0.040-0.01842.9250.0010.0010.0000.0000.0000.000
191A191GLU-1-0.955-0.98044.4660.0310.0310.0000.0000.0000.000
192A192ILE00.0610.01343.744-0.001-0.0010.0000.0000.0000.000
193A193ALA0-0.036-0.01242.201-0.001-0.0010.0000.0000.0000.000
194A194LYS10.8970.95143.905-0.041-0.0410.0000.0000.0000.000
195A195GLU-1-0.938-0.98247.2700.0260.0260.0000.0000.0000.000
196A196VAL0-0.058-0.00542.426-0.002-0.0020.0000.0000.0000.000
197A197GLY00.0030.01045.780-0.001-0.0010.0000.0000.0000.000
198A198ILE0-0.064-0.04542.4930.0030.0030.0000.0000.0000.000
199A199VAL00.0300.02339.041-0.004-0.0040.0000.0000.0000.000
200A200GLU-1-0.884-0.92539.9500.0410.0410.0000.0000.0000.000
201A201VAL0-0.018-0.00534.211-0.004-0.0040.0000.0000.0000.000
202A202LYS10.9300.94637.288-0.013-0.0130.0000.0000.0000.000
203A203ARG10.8420.91432.022-0.076-0.0760.0000.0000.0000.000
204A204ASP-1-0.833-0.91433.9340.0090.0090.0000.0000.0000.000
205A205ASN0-0.054-0.02034.7220.0050.0050.0000.0000.0000.000
206A206LYS10.8690.92730.705-0.076-0.0760.0000.0000.0000.000
207A207LYS10.9730.98836.772-0.066-0.0660.0000.0000.0000.000
208A208SER0-0.005-0.00736.9780.0060.0060.0000.0000.0000.000
209A209SER0-0.071-0.03934.5910.0090.0090.0000.0000.0000.000
210A210LEU00.0320.01937.018-0.005-0.0050.0000.0000.0000.000
211A211LEU0-0.0080.00134.6210.0070.0070.0000.0000.0000.000
212A212ASN00.0920.04838.605-0.008-0.0080.0000.0000.0000.000
213A213ALA00.0650.03238.8070.0060.0060.0000.0000.0000.000
214A214SER00.0620.03039.8490.0030.0030.0000.0000.0000.000
215A215GLU-1-0.929-0.96840.5030.0900.0900.0000.0000.0000.000
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