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: 52Y9Z

Calculation Name: 1TUE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TUE

Chain ID: A

ChEMBL ID:

UniProt ID: P06789

Base Structure: X-ray

Registration Date: 2023-06-22

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2526454.537032
FMO2-HF: Nuclear repulsion 2442407.393254
FMO2-HF: Total energy -84047.143778
FMO2-MP2: Total energy -84290.764672


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:425:SER)


Summations of interaction energy for fragment #1(A:425: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.
-69.053-63.81621.811-11.933-15.115-6.9388939039072E-18
Interaction energy analysis for fragmet #1(A:425:SER)
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 : 0.025
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].
3A427SER0-0.015-0.0032.181-7.040-3.9962.651-2.783-2.9120.023
4A428ASN00.0570.0174.4773.8163.930-0.001-0.029-0.0840.000
5A429MET00.0560.0255.9460.6250.6250.0000.0000.0000.000
6A430SER00.0180.0037.609-0.510-0.5100.0000.0000.0000.000
7A431GLN0-0.001-0.0046.7380.2860.2860.0000.0000.0000.000
8A432TRP00.0060.0072.196-8.657-7.8026.874-3.279-4.450-0.034
9A433ILE00.0460.0235.133-0.995-0.947-0.0010.000-0.0460.000
10A434ARG10.9610.9908.505-1.032-1.0320.0000.0000.0000.000
11A435PHE00.0010.0145.505-0.141-0.1410.0000.0000.0000.000
12A436ARG10.8060.8846.6990.4800.4800.0000.0000.0000.000
13A437CYS0-0.015-0.0169.218-0.005-0.0050.0000.0000.0000.000
14A438SER0-0.054-0.03411.512-0.013-0.0130.0000.0000.0000.000
15A439LYS10.8320.9219.8960.5900.5900.0000.0000.0000.000
16A440ILE0-0.0140.01112.462-0.062-0.0620.0000.0000.0000.000
17A441ASP-1-0.876-0.92915.460-0.159-0.1590.0000.0000.0000.000
18A442GLU-1-0.806-0.89919.0120.0290.0290.0000.0000.0000.000
19A443GLY0-0.0090.00921.207-0.016-0.0160.0000.0000.0000.000
20A444GLY00.0100.00921.950-0.020-0.0200.0000.0000.0000.000
21A445ASP-1-0.810-0.94322.9400.1060.1060.0000.0000.0000.000
22A446TRP0-0.027-0.00822.1770.0070.0070.0000.0000.0000.000
23A447ARG10.8870.95023.132-0.087-0.0870.0000.0000.0000.000
24A448PRO00.0580.02924.8150.0080.0080.0000.0000.0000.000
25A449ILE00.0210.02719.742-0.003-0.0030.0000.0000.0000.000
26A450VAL0-0.029-0.01623.8010.0090.0090.0000.0000.0000.000
27A451GLN0-0.024-0.01726.110-0.001-0.0010.0000.0000.0000.000
28A452PHE00.0270.02124.795-0.004-0.0040.0000.0000.0000.000
29A453LEU0-0.027-0.00822.7660.0010.0010.0000.0000.0000.000
30A454ARG10.8660.89827.093-0.146-0.1460.0000.0000.0000.000
31A455TYR0-0.058-0.03130.562-0.005-0.0050.0000.0000.0000.000
32A456GLN0-0.025-0.02128.189-0.006-0.0060.0000.0000.0000.000
33A457GLN0-0.046-0.02630.9980.0020.0020.0000.0000.0000.000
34A458ILE0-0.0290.00725.8290.0150.0150.0000.0000.0000.000
35A459GLU-1-0.764-0.86828.9000.1700.1700.0000.0000.0000.000
36A460PHE00.006-0.00123.0960.0240.0240.0000.0000.0000.000
37A461ILE00.004-0.00425.0290.0310.0310.0000.0000.0000.000
38A462THR00.0310.01125.3810.0340.0340.0000.0000.0000.000
39A463PHE00.0320.02019.4990.0360.0360.0000.0000.0000.000
40A464LEU0-0.008-0.00419.9980.0460.0460.0000.0000.0000.000
41A465GLY00.0280.01520.5730.0660.0660.0000.0000.0000.000
42A466ALA0-0.0030.00121.4580.0530.0530.0000.0000.0000.000
43A467LEU00.0170.01115.1210.0680.0680.0000.0000.0000.000
44A468LYS10.8290.90216.360-0.499-0.4990.0000.0000.0000.000
45A469SER0-0.057-0.02716.8960.1090.1090.0000.0000.0000.000
46A470PHE0-0.0090.00913.3670.1340.1340.0000.0000.0000.000
47A471LEU00.013-0.00311.0880.1730.1730.0000.0000.0000.000
48A472LYS10.8250.90911.622-0.735-0.7350.0000.0000.0000.000
49A473GLY0-0.0150.00512.5380.0840.0840.0000.0000.0000.000
50A474THR0-0.046-0.03713.423-0.082-0.0820.0000.0000.0000.000
51A475PRO00.0360.00417.035-0.058-0.0580.0000.0000.0000.000
52A476LYS10.8520.92119.116-0.350-0.3500.0000.0000.0000.000
53A477LYS10.9020.94319.283-0.447-0.4470.0000.0000.0000.000
54A478ASN0-0.0300.00513.1330.2190.2190.0000.0000.0000.000
55A479CYS0-0.035-0.01614.960-0.022-0.0220.0000.0000.0000.000
56A480LEU0-0.0160.00517.302-0.019-0.0190.0000.0000.0000.000
57A481VAL0-0.0060.00419.088-0.032-0.0320.0000.0000.0000.000
58A482PHE0-0.009-0.00519.9040.0130.0130.0000.0000.0000.000
59A483CYS00.0150.00023.663-0.026-0.0260.0000.0000.0000.000
60A484GLY00.0320.02127.1020.0060.0060.0000.0000.0000.000
61A485PRO00.0950.04829.196-0.009-0.0090.0000.0000.0000.000
62A486ALA00.0310.02628.6970.0040.0040.0000.0000.0000.000
63A487ASN00.0210.00429.2000.0010.0010.0000.0000.0000.000
64A488THR00.0050.00628.7720.0010.0010.0000.0000.0000.000
65A489GLY00.0120.01027.1450.0070.0070.0000.0000.0000.000
66A490LYS10.7570.87424.589-0.028-0.0280.0000.0000.0000.000
67A491SER00.016-0.01821.9710.0220.0220.0000.0000.0000.000
68A492TYR0-0.016-0.00320.931-0.006-0.0060.0000.0000.0000.000
69A493PHE00.0190.01220.556-0.005-0.0050.0000.0000.0000.000
70A494GLY00.0580.01918.4750.0190.0190.0000.0000.0000.000
71A495MET00.0380.01416.5470.0000.0000.0000.0000.0000.000
72A496SER0-0.039-0.02215.945-0.044-0.0440.0000.0000.0000.000
73A497PHE0-0.0110.00312.574-0.004-0.0040.0000.0000.0000.000
74A498ILE00.016-0.00111.5520.0510.0510.0000.0000.0000.000
75A499HIS0-0.036-0.02311.129-0.174-0.1740.0000.0000.0000.000
76A500PHE00.0250.02111.422-0.139-0.1390.0000.0000.0000.000
77A501ILE0-0.046-0.0347.578-0.042-0.0420.0000.0000.0000.000
78A502GLN0-0.050-0.0246.929-0.371-0.3710.0000.0000.0000.000
79A503GLY0-0.0030.0136.635-0.379-0.3790.0000.0000.0000.000
80A504ALA0-0.017-0.0068.422-0.277-0.2770.0000.0000.0000.000
81A505VAL0-0.019-0.02410.0670.2280.2280.0000.0000.0000.000
82A506ILE0-0.029-0.00112.613-0.076-0.0760.0000.0000.0000.000
83A507SER00.0450.00515.1490.0480.0480.0000.0000.0000.000
84A508PHE00.008-0.00618.916-0.004-0.0040.0000.0000.0000.000
85A509VAL00.0200.01721.270-0.010-0.0100.0000.0000.0000.000
86A510ASN00.0030.00323.4270.0210.0210.0000.0000.0000.000
87A511SER0-0.032-0.02323.627-0.011-0.0110.0000.0000.0000.000
88A512THR00.0190.00725.5690.0080.0080.0000.0000.0000.000
89A513SER00.0150.00421.7690.0010.0010.0000.0000.0000.000
90A514HIS10.8860.93816.827-0.033-0.0330.0000.0000.0000.000
91A515PHE00.0200.00216.918-0.022-0.0220.0000.0000.0000.000
92A516TRP00.0400.03117.100-0.048-0.0480.0000.0000.0000.000
93A517LEU0-0.017-0.01813.630-0.007-0.0070.0000.0000.0000.000
94A518GLU-1-0.892-0.94212.144-0.604-0.6040.0000.0000.0000.000
95A519PRO0-0.014-0.00610.595-0.162-0.1620.0000.0000.0000.000
96A520LEU0-0.028-0.0208.116-0.105-0.1050.0000.0000.0000.000
97A521THR0-0.039-0.0407.5920.3650.3650.0000.0000.0000.000
98A522ASP-1-0.909-0.9523.840-3.042-2.8510.001-0.086-0.1070.000
99A523THR0-0.0040.0122.220-9.167-7.0602.408-2.225-2.291-0.029
100A524LYS10.8360.9092.030-41.573-42.6929.880-3.530-5.2300.040
101A525VAL0-0.024-0.0195.0900.0050.002-0.001-0.0010.0050.000
102A526ALA00.0140.0258.684-0.433-0.4330.0000.0000.0000.000
103A527MET00.0020.01110.8290.1020.1020.0000.0000.0000.000
104A528LEU0-0.036-0.01514.472-0.080-0.0800.0000.0000.0000.000
105A529ASP-1-0.790-0.86117.7260.0000.0000.0000.0000.0000.000
106A530ASP-1-0.864-0.93020.607-0.010-0.0100.0000.0000.0000.000
107A531ALA00.0300.02621.822-0.011-0.0110.0000.0000.0000.000
108A532THR00.0430.03423.6560.0160.0160.0000.0000.0000.000
109A533THR00.0520.01326.6960.0120.0120.0000.0000.0000.000
110A534THR00.0000.01527.7990.0110.0110.0000.0000.0000.000
111A535CYS00.0100.02222.1660.0000.0000.0000.0000.0000.000
112A536TRP00.0450.00821.7230.0230.0230.0000.0000.0000.000
113A537THR00.0180.00525.6270.0160.0160.0000.0000.0000.000
114A538TYR0-0.047-0.03519.9050.0140.0140.0000.0000.0000.000
115A539PHE00.025-0.01217.2840.0090.0090.0000.0000.0000.000
116A540ASP-1-0.815-0.89122.7680.1600.1600.0000.0000.0000.000
117A541THR0-0.015-0.00325.6980.0120.0120.0000.0000.0000.000
118A542TYR0-0.002-0.01122.3200.0030.0030.0000.0000.0000.000
119A543MET0-0.0270.01415.686-0.012-0.0120.0000.0000.0000.000
120A544ARG10.8740.92919.659-0.093-0.0930.0000.0000.0000.000
121A545ASN00.0260.00518.1270.0140.0140.0000.0000.0000.000
122A546ALA00.0370.02315.5030.0620.0620.0000.0000.0000.000
123A547LEU00.0010.01116.4760.0910.0910.0000.0000.0000.000
124A548ASP-1-0.808-0.87619.2330.3840.3840.0000.0000.0000.000
125A549GLY0-0.005-0.00415.4700.0200.0200.0000.0000.0000.000
126A550ASN0-0.056-0.02615.0810.0850.0850.0000.0000.0000.000
127A551PRO0-0.014-0.00513.9120.0280.0280.0000.0000.0000.000
128A552ILE00.0060.00713.091-0.058-0.0580.0000.0000.0000.000
129A553SER00.0170.00014.925-0.004-0.0040.0000.0000.0000.000
130A554ILE00.0030.00412.6490.0200.0200.0000.0000.0000.000
131A555ASP-1-0.760-0.85016.455-0.125-0.1250.0000.0000.0000.000
132A556ARG10.9120.93918.8060.1810.1810.0000.0000.0000.000
133A557LYS11.0021.01919.7630.2970.2970.0000.0000.0000.000
134A558HIS00.011-0.01021.2190.0080.0080.0000.0000.0000.000
135A559LYS10.8160.87122.2500.0740.0740.0000.0000.0000.000
136A560PRO00.0350.03419.6670.0080.0080.0000.0000.0000.000
137A561LEU0-0.030-0.01119.455-0.023-0.0230.0000.0000.0000.000
138A562ILE00.0300.03213.1060.0370.0370.0000.0000.0000.000
139A563GLN0-0.011-0.02314.4910.0450.0450.0000.0000.0000.000
140A564LEU00.0280.0247.794-0.033-0.0330.0000.0000.0000.000
141A565LYS10.8650.9509.527-1.335-1.3350.0000.0000.0000.000
142A566CYS0-0.014-0.0039.1430.0450.0450.0000.0000.0000.000
143A567PRO00.0450.0327.0300.2480.2480.0000.0000.0000.000
144A568PRO00.0330.0189.075-0.308-0.3080.0000.0000.0000.000
145A569ILE00.001-0.00911.143-0.089-0.0890.0000.0000.0000.000
146A570LEU00.0020.00113.8210.0100.0100.0000.0000.0000.000
147A571LEU0-0.013-0.01016.055-0.079-0.0790.0000.0000.0000.000
148A572THR0-0.049-0.04318.9670.0220.0220.0000.0000.0000.000
149A573THR00.001-0.01422.231-0.011-0.0110.0000.0000.0000.000
150A574ASN00.0640.02425.6920.0120.0120.0000.0000.0000.000
151A575ILE0-0.026-0.01328.488-0.003-0.0030.0000.0000.0000.000
152A576HIS00.048-0.00128.2690.0050.0050.0000.0000.0000.000
153A577PRO0-0.032-0.00824.993-0.005-0.0050.0000.0000.0000.000
154A578ALA0-0.032-0.02128.1330.0100.0100.0000.0000.0000.000
155A579LYS10.8190.88730.225-0.121-0.1210.0000.0000.0000.000
156A580ASP-1-0.783-0.87333.7150.0780.0780.0000.0000.0000.000
157A581ASN0-0.047-0.03033.653-0.013-0.0130.0000.0000.0000.000
158A582ARG10.8210.90532.671-0.061-0.0610.0000.0000.0000.000
159A583TRP0-0.040-0.02228.366-0.007-0.0070.0000.0000.0000.000
160A584PRO00.0940.04229.2590.0180.0180.0000.0000.0000.000
161A585TYR0-0.087-0.05523.7440.0060.0060.0000.0000.0000.000
162A586LEU0-0.004-0.01923.0250.0280.0280.0000.0000.0000.000
163A587GLU-1-0.819-0.89625.3390.1660.1660.0000.0000.0000.000
164A588SER0-0.050-0.01527.7320.0190.0190.0000.0000.0000.000
165A589ARG10.7680.86022.729-0.240-0.2400.0000.0000.0000.000
166A590ILE00.0490.05220.9640.0400.0400.0000.0000.0000.000
167A591THR0-0.036-0.03321.9500.0130.0130.0000.0000.0000.000
168A592VAL00.0080.00722.5810.0100.0100.0000.0000.0000.000
169A593PHE0-0.0100.00522.4180.0090.0090.0000.0000.0000.000
170A594GLU-1-0.781-0.88826.2940.1170.1170.0000.0000.0000.000
171A595PHE0-0.043-0.01924.0890.0050.0050.0000.0000.0000.000
172A596PRO00.0000.00130.010-0.013-0.0130.0000.0000.0000.000
173A597ASN0-0.0070.00332.738-0.013-0.0130.0000.0000.0000.000
174A598ALA00.0320.01532.2010.0000.0000.0000.0000.0000.000
175A599PHE00.005-0.00226.3650.0080.0080.0000.0000.0000.000
176A600PRO0-0.0240.00930.390-0.006-0.0060.0000.0000.0000.000
177A601PHE00.013-0.00730.824-0.004-0.0040.0000.0000.0000.000
178A602ASP-1-0.770-0.90134.824-0.012-0.0120.0000.0000.0000.000
179A603LYS10.9000.95737.294-0.002-0.0020.0000.0000.0000.000
180A604ASN0-0.073-0.04138.431-0.003-0.0030.0000.0000.0000.000
181A605GLY00.0210.01936.889-0.006-0.0060.0000.0000.0000.000
182A606ASN0-0.052-0.01633.037-0.012-0.0120.0000.0000.0000.000
183A607PRO00.0090.00928.7150.0080.0080.0000.0000.0000.000
184A608VAL0-0.029-0.01731.1670.0010.0010.0000.0000.0000.000
185A609TYR0-0.032-0.01927.4140.0100.0100.0000.0000.0000.000
186A610GLU-1-0.841-0.91124.575-0.075-0.0750.0000.0000.0000.000
187A611ILE0-0.032-0.01819.7530.0210.0210.0000.0000.0000.000
188A612ASN00.0320.01219.107-0.019-0.0190.0000.0000.0000.000
189A613ASP-1-0.707-0.84313.857-0.305-0.3050.0000.0000.0000.000
190A614LYS10.9070.93216.2590.1270.1270.0000.0000.0000.000
191A615ASN00.0070.00418.6100.0350.0350.0000.0000.0000.000
192A616TRP0-0.018-0.02315.2500.0900.0900.0000.0000.0000.000
193A617LYS10.7810.89115.1150.0790.0790.0000.0000.0000.000
194A618CYS0-0.0060.01816.0640.0600.0600.0000.0000.0000.000
195A619PHE00.004-0.02317.7230.0280.0280.0000.0000.0000.000
196A620PHE00.0180.01713.2480.0630.0630.0000.0000.0000.000
197A621GLU-1-0.813-0.91416.2200.2410.2410.0000.0000.0000.000
198A622ARG10.8920.96718.224-0.184-0.1840.0000.0000.0000.000
199A623THR0-0.080-0.06518.7210.0140.0140.0000.0000.0000.000
200A624TRP00.0180.02111.2700.0250.0250.0000.0000.0000.000
201A625SER00.0170.00417.4460.0810.0810.0000.0000.0000.000
202A626ARG10.9060.94520.132-0.299-0.2990.0000.0000.0000.000
203A627LEU00.0250.00415.6290.0030.0030.0000.0000.0000.000
204A628ASP-1-0.821-0.88616.5000.9030.9030.0000.0000.0000.000
205A629LEU0-0.0170.00611.6060.1570.1570.0000.0000.0000.000