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: 5JRRZ

Calculation Name: 1TWD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TWD

Chain ID: A

ChEMBL ID:

UniProt ID: P67825

Base Structure: X-ray

Registration Date: 2023-09-22

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 234
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2761173.778112
FMO2-HF: Nuclear repulsion 2670454.523801
FMO2-HF: Total energy -90719.254311
FMO2-MP2: Total energy -90976.429182


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:2:ALA)


Summations of interaction energy for fragment #1(A:2:ALA)
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.
-5.4221.3057.966-5.688-9.008-0.025
Interaction energy analysis for fragmet #1(A:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.043 / q_NPA : 0.028
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].
3A4LEU00.017-0.0013.866-0.3731.423-0.006-0.906-0.8840.005
4A5GLU-1-0.782-0.8785.813-0.248-0.2480.0000.0000.0000.000
5A6ILE0-0.020-0.0288.6630.1240.1240.0000.0000.0000.000
6A7CYS0-0.052-0.02511.7660.0540.0540.0000.0000.0000.000
7A8CYS0-0.076-0.02114.7830.0140.0140.0000.0000.0000.000
8A9TYR00.0530.00818.0050.0240.0240.0000.0000.0000.000
9A10SER0-0.028-0.03521.6680.0170.0170.0000.0000.0000.000
10A11MET00.0160.02021.860-0.028-0.0280.0000.0000.0000.000
11A12GLU-1-0.824-0.90522.328-0.211-0.2110.0000.0000.0000.000
12A13CYS0-0.087-0.01419.312-0.012-0.0120.0000.0000.0000.000
13A14ALA00.0850.03517.698-0.035-0.0350.0000.0000.0000.000
14A15LEU0-0.035-0.01217.737-0.044-0.0440.0000.0000.0000.000
15A16THR0-0.003-0.01518.141-0.014-0.0140.0000.0000.0000.000
16A17ALA00.0340.01513.942-0.020-0.0200.0000.0000.0000.000
17A18GLN00.0600.03914.210-0.081-0.0810.0000.0000.0000.000
18A19GLN0-0.069-0.04815.379-0.027-0.0270.0000.0000.0000.000
19A20ASN0-0.071-0.03914.6760.0570.0570.0000.0000.0000.000
20A21GLY00.0520.03611.408-0.030-0.0300.0000.0000.0000.000
21A22ALA0-0.008-0.0029.715-0.269-0.2690.0000.0000.0000.000
22A23ASP-1-0.815-0.8926.502-2.763-2.7630.0000.0000.0000.000
23A24ARG10.6960.8128.2931.0431.0430.0000.0000.0000.000
24A25VAL0-0.022-0.00911.406-0.012-0.0120.0000.0000.0000.000
25A26GLU-1-0.774-0.87513.600-0.255-0.2550.0000.0000.0000.000
26A27LEU0-0.046-0.02915.0040.0140.0140.0000.0000.0000.000
27A28CYS00.0060.00518.0760.0250.0250.0000.0000.0000.000
28A29ALA00.0160.00320.9920.0000.0000.0000.0000.0000.000
29A30ALA00.022-0.00124.1330.0030.0030.0000.0000.0000.000
30A31PRO00.0550.02022.4290.0060.0060.0000.0000.0000.000
31A32LYS10.8190.91323.8010.0920.0920.0000.0000.0000.000
32A33GLU-1-0.810-0.89126.089-0.071-0.0710.0000.0000.0000.000
33A34GLY0-0.033-0.01022.0140.0040.0040.0000.0000.0000.000
34A35GLY00.0010.01421.040-0.009-0.0090.0000.0000.0000.000
35A36LEU0-0.043-0.00322.0680.0090.0090.0000.0000.0000.000
36A37THR00.048-0.00123.785-0.018-0.0180.0000.0000.0000.000
37A38PRO0-0.054-0.00922.5750.0100.0100.0000.0000.0000.000
38A39SER00.0490.02025.5580.0020.0020.0000.0000.0000.000
39A40LEU00.0800.02928.219-0.010-0.0100.0000.0000.0000.000
40A41GLY0-0.0100.00029.636-0.005-0.0050.0000.0000.0000.000
41A42VAL0-0.002-0.00524.537-0.006-0.0060.0000.0000.0000.000
42A43LEU00.0130.01723.814-0.017-0.0170.0000.0000.0000.000
43A44LYS10.9880.98625.4190.1170.1170.0000.0000.0000.000
44A45SER0-0.028-0.01327.205-0.009-0.0090.0000.0000.0000.000
45A46VAL00.0390.00520.696-0.006-0.0060.0000.0000.0000.000
46A47ARG10.8670.93722.7410.2140.2140.0000.0000.0000.000
47A48GLN0-0.050-0.01824.6270.0090.0090.0000.0000.0000.000
48A49ARG10.8750.93624.7580.2110.2110.0000.0000.0000.000
49A50VAL0-0.044-0.01718.362-0.010-0.0100.0000.0000.0000.000
50A51THR0-0.063-0.03319.1890.0200.0200.0000.0000.0000.000
51A52ILE00.0370.03313.5560.0100.0100.0000.0000.0000.000
52A53PRO00.010-0.00512.3910.0730.0730.0000.0000.0000.000
53A54VAL00.0130.00614.499-0.043-0.0430.0000.0000.0000.000
54A55HIS0-0.040-0.01413.683-0.001-0.0010.0000.0000.0000.000
55A56PRO0-0.002-0.00216.779-0.004-0.0040.0000.0000.0000.000
56A57ILE0-0.0070.01318.8850.0060.0060.0000.0000.0000.000
57A58ILE0-0.035-0.02020.1220.0090.0090.0000.0000.0000.000
58A59ARG10.8570.91722.7420.1100.1100.0000.0000.0000.000
59A60PRO00.0210.02025.049-0.004-0.0040.0000.0000.0000.000
60A61ARG10.7360.82327.9930.0600.0600.0000.0000.0000.000
61A62GLY00.0390.01826.689-0.005-0.0050.0000.0000.0000.000
62A63GLY0-0.048-0.02227.2720.0050.0050.0000.0000.0000.000
63A64ASP-1-0.785-0.86426.046-0.053-0.0530.0000.0000.0000.000
64A65PHE00.0170.00121.659-0.007-0.0070.0000.0000.0000.000
65A66CYS0-0.035-0.00726.4880.0000.0000.0000.0000.0000.000
66A67TYR0-0.019-0.01024.5540.0010.0010.0000.0000.0000.000
67A68SER00.016-0.02431.3550.0030.0030.0000.0000.0000.000
68A69ASP-1-0.825-0.93433.917-0.045-0.0450.0000.0000.0000.000
69A70GLY0-0.029-0.00435.633-0.002-0.0020.0000.0000.0000.000
70A71GLU-1-0.783-0.85831.672-0.061-0.0610.0000.0000.0000.000
71A72PHE00.0100.00328.483-0.006-0.0060.0000.0000.0000.000
72A73ALA00.003-0.00131.412-0.005-0.0050.0000.0000.0000.000
73A74ALA0-0.015-0.00332.236-0.003-0.0030.0000.0000.0000.000
74A75ILE00.0370.02326.287-0.007-0.0070.0000.0000.0000.000
75A76LEU00.001-0.00827.917-0.008-0.0080.0000.0000.0000.000
76A77GLU-1-0.822-0.86829.958-0.088-0.0880.0000.0000.0000.000
77A78ASP-1-0.870-0.91526.567-0.124-0.1240.0000.0000.0000.000
78A79VAL0-0.024-0.01524.322-0.013-0.0130.0000.0000.0000.000
79A80ARG10.8400.89226.2700.0760.0760.0000.0000.0000.000
80A81THR0-0.042-0.02728.490-0.004-0.0040.0000.0000.0000.000
81A82VAL0-0.035-0.03122.035-0.008-0.0080.0000.0000.0000.000
82A83ARG10.8340.91224.4920.0980.0980.0000.0000.0000.000
83A84GLU-1-0.847-0.91225.743-0.121-0.1210.0000.0000.0000.000
84A85LEU0-0.075-0.03226.2350.0000.0000.0000.0000.0000.000
85A86GLY00.0100.01124.632-0.011-0.0110.0000.0000.0000.000
86A87PHE0-0.062-0.03519.918-0.018-0.0180.0000.0000.0000.000
87A88PRO0-0.002-0.00116.5630.0130.0130.0000.0000.0000.000
88A89GLY00.0500.01017.002-0.002-0.0020.0000.0000.0000.000
89A90LEU0-0.040-0.01617.6460.0040.0040.0000.0000.0000.000
90A91VAL0-0.0060.00414.847-0.006-0.0060.0000.0000.0000.000
91A92THR0-0.018-0.03117.6010.0200.0200.0000.0000.0000.000
92A93GLY00.0410.01819.248-0.001-0.0010.0000.0000.0000.000
93A94VAL0-0.027-0.01621.784-0.001-0.0010.0000.0000.0000.000
94A95LEU0-0.036-0.01122.9800.0030.0030.0000.0000.0000.000
95A96ASP-1-0.754-0.85026.791-0.011-0.0110.0000.0000.0000.000
96A97VAL0-0.019-0.03129.563-0.002-0.0020.0000.0000.0000.000
97A98ASP-1-0.947-0.96431.1170.0010.0010.0000.0000.0000.000
98A99GLY0-0.0150.00527.0200.0050.0050.0000.0000.0000.000
99A100ASN0-0.080-0.06225.7410.0110.0110.0000.0000.0000.000
100A101VAL00.0440.01122.240-0.007-0.0070.0000.0000.0000.000
101A102ASP-1-0.772-0.86925.131-0.035-0.0350.0000.0000.0000.000
102A103MET00.0130.01125.392-0.009-0.0090.0000.0000.0000.000
103A104PRO00.0070.00428.082-0.005-0.0050.0000.0000.0000.000
104A105ARG10.7160.84729.8230.0420.0420.0000.0000.0000.000
105A106MET00.0360.01421.656-0.010-0.0100.0000.0000.0000.000
106A107GLU-1-0.850-0.92025.866-0.060-0.0600.0000.0000.0000.000
107A108LYS10.8470.91727.8440.0390.0390.0000.0000.0000.000
108A109ILE0-0.002-0.00123.594-0.005-0.0050.0000.0000.0000.000
109A110MET00.0070.01420.608-0.016-0.0160.0000.0000.0000.000
110A111ALA00.0080.00425.045-0.007-0.0070.0000.0000.0000.000
111A112ALA0-0.072-0.02527.886-0.002-0.0020.0000.0000.0000.000
112A113ALA00.032-0.00122.792-0.006-0.0060.0000.0000.0000.000
113A114GLY0-0.003-0.00424.334-0.011-0.0110.0000.0000.0000.000
114A115PRO0-0.038-0.02222.1810.0000.0000.0000.0000.0000.000
115A116LEU0-0.072-0.01120.099-0.023-0.0230.0000.0000.0000.000
116A117ALA00.015-0.00314.8520.0140.0140.0000.0000.0000.000
117A118VAL0-0.0100.00016.499-0.029-0.0290.0000.0000.0000.000
118A119THR00.010-0.00812.794-0.001-0.0010.0000.0000.0000.000
119A120PHE00.0370.01515.0650.0140.0140.0000.0000.0000.000
120A121HIS00.0560.01915.017-0.007-0.0070.0000.0000.0000.000
121A122ARG10.8890.91615.0200.0760.0760.0000.0000.0000.000
122A123ALA00.0250.02517.1680.0180.0180.0000.0000.0000.000
123A124PHE00.0700.02416.1140.0140.0140.0000.0000.0000.000
124A125ASP-1-0.811-0.87116.0300.0150.0150.0000.0000.0000.000
125A126MET0-0.052-0.01918.8530.0080.0080.0000.0000.0000.000
126A127CYS0-0.045-0.00221.238-0.003-0.0030.0000.0000.0000.000
127A128ALA00.0290.01623.0000.0100.0100.0000.0000.0000.000
128A129ASN0-0.007-0.00423.4810.0150.0150.0000.0000.0000.000
129A130PRO00.0420.04118.084-0.004-0.0040.0000.0000.0000.000
130A131LEU00.0600.03318.694-0.005-0.0050.0000.0000.0000.000
131A132TYR0-0.011-0.01820.634-0.003-0.0030.0000.0000.0000.000
132A133THR0-0.016-0.01219.579-0.014-0.0140.0000.0000.0000.000
133A134LEU0-0.006-0.00614.925-0.015-0.0150.0000.0000.0000.000
134A135ASN00.0280.01818.641-0.001-0.0010.0000.0000.0000.000
135A136ASN0-0.023-0.01821.842-0.011-0.0110.0000.0000.0000.000
136A137LEU0-0.008-0.01317.050-0.011-0.0110.0000.0000.0000.000
137A138ALA00.0100.00519.031-0.015-0.0150.0000.0000.0000.000
138A139GLU-1-0.960-0.96620.089-0.007-0.0070.0000.0000.0000.000
139A140LEU0-0.069-0.03621.949-0.007-0.0070.0000.0000.0000.000
140A141GLY00.0210.01520.339-0.012-0.0120.0000.0000.0000.000
141A142ILE0-0.088-0.04215.829-0.023-0.0230.0000.0000.0000.000
142A143ALA00.0110.00913.9090.0120.0120.0000.0000.0000.000
143A144ARG10.8180.8759.0380.5550.5550.0000.0000.0000.000
144A145VAL0-0.001-0.00511.3480.0060.0060.0000.0000.0000.000
145A146LEU0-0.0180.01710.3590.0140.0140.0000.0000.0000.000
146A147THR0-0.049-0.04511.1610.0420.0420.0000.0000.0000.000
147A148SER0-0.001-0.03711.4230.0060.0060.0000.0000.0000.000
148A149GLY00.0370.01813.7320.0310.0310.0000.0000.0000.000
149A150GLN0-0.079-0.05115.2770.0160.0160.0000.0000.0000.000
150A151LYS10.8450.93217.268-0.085-0.0850.0000.0000.0000.000
151A152SER00.0210.00718.249-0.014-0.0140.0000.0000.0000.000
152A153ASP-1-0.848-0.91115.5640.0410.0410.0000.0000.0000.000
153A154ALA00.0300.00410.7300.0200.0200.0000.0000.0000.000
154A155LEU0-0.0110.00712.2620.0480.0480.0000.0000.0000.000
155A156GLN0-0.057-0.05213.7480.0350.0350.0000.0000.0000.000
156A157GLY00.0000.00815.258-0.002-0.0020.0000.0000.0000.000
157A158LEU00.0120.0088.8390.0010.0010.0000.0000.0000.000
158A159SER0-0.007-0.00612.4700.0490.0490.0000.0000.0000.000
159A160LYS10.8730.91415.054-0.148-0.1480.0000.0000.0000.000
160A161ILE00.000-0.0038.996-0.008-0.0080.0000.0000.0000.000
161A162MET0-0.0180.00510.4720.0400.0400.0000.0000.0000.000
162A163GLU-1-0.865-0.91012.1910.1980.1980.0000.0000.0000.000
163A164LEU0-0.034-0.02613.298-0.019-0.0190.0000.0000.0000.000
164A165ILE00.0020.0058.025-0.034-0.0340.0000.0000.0000.000
165A166ALA0-0.035-0.00412.0190.0110.0110.0000.0000.0000.000
166A167HIS0-0.062-0.02915.149-0.017-0.0170.0000.0000.0000.000
167A168ARG10.8240.89116.056-0.126-0.1260.0000.0000.0000.000
168A169ASP-1-0.852-0.91517.1920.0850.0850.0000.0000.0000.000
169A170ALA00.0250.01915.051-0.018-0.0180.0000.0000.0000.000
170A171PRO0-0.0190.00713.9940.0000.0000.0000.0000.0000.000
171A172ILE00.001-0.0127.7380.0430.0430.0000.0000.0000.000
172A173ILE00.0040.0028.944-0.078-0.0780.0000.0000.0000.000
173A174MET0-0.058-0.0066.397-0.054-0.0540.0000.0000.0000.000
174A175ALA00.0320.0286.2950.0380.0380.0000.0000.0000.000
175A176GLY00.030-0.0027.580-0.130-0.1300.0000.0000.0000.000
176A177ALA00.0050.01010.3140.0410.0410.0000.0000.0000.000
177A178GLY0-0.009-0.00813.4070.0370.0370.0000.0000.0000.000
178A179VAL00.0320.0347.3640.0180.0180.0000.0000.0000.000
179A180ARG10.7990.88010.786-0.057-0.0570.0000.0000.0000.000
180A181ALA00.0660.02810.0610.0570.0570.0000.0000.0000.000
181A182GLU-1-0.829-0.90411.0840.0760.0760.0000.0000.0000.000
182A183ASN0-0.052-0.03411.0440.0390.0390.0000.0000.0000.000
183A184LEU00.0440.0264.0310.0020.093-0.001-0.013-0.0780.000
184A185HIS00.0340.0176.5680.1920.1920.0000.0000.0000.000
185A186HIS00.0430.0347.8500.2800.2800.0000.0000.0000.000
186A187PHE0-0.022-0.0215.6900.0110.0110.0000.0000.0000.000
187A188LEU0-0.0080.0082.626-0.576-0.3621.629-0.473-1.3700.001
188A189ASP-1-0.884-0.9374.7781.2391.252-0.001-0.004-0.0080.000
189A190ALA0-0.055-0.0337.850-0.083-0.0830.0000.0000.0000.000
190A191GLY0-0.0060.0015.646-0.190-0.1900.0000.0000.0000.000
191A192VAL0-0.061-0.0404.560-0.191-0.082-0.001-0.026-0.0820.000
192A193LEU00.0310.0152.658-1.0240.4431.286-1.092-1.661-0.011
193A194GLU-1-0.709-0.8082.578-4.532-2.4701.710-1.895-1.877-0.019
194A195VAL0-0.007-0.0062.744-0.1100.6440.446-0.186-1.0150.000
195A196HIS0-0.023-0.0244.651-0.226-0.262-0.001-0.0050.0420.000
196A197SER0-0.017-0.0338.3250.1460.1460.0000.0000.0000.000
197A198SER00.0310.00510.777-0.028-0.0280.0000.0000.0000.000
198A199ALA00.0020.02613.0100.0490.0490.0000.0000.0000.000
199A200GLY00.0800.03114.850-0.029-0.0290.0000.0000.0000.000
200A201ALA0-0.0090.00718.5380.0240.0240.0000.0000.0000.000
201A202TRP00.0170.00922.100-0.006-0.0060.0000.0000.0000.000
202A203GLN00.0490.05225.4660.0170.0170.0000.0000.0000.000
203A204ALA00.0460.00327.4120.0040.0040.0000.0000.0000.000
204A205SER0-0.011-0.00431.199-0.006-0.0060.0000.0000.0000.000
205A206PRO00.0010.00032.9580.0040.0040.0000.0000.0000.000
206A207MET0-0.012-0.00935.6450.0020.0020.0000.0000.0000.000
207A208ARG10.9410.97238.7710.0630.0630.0000.0000.0000.000
208A209TYR00.004-0.01141.4630.0030.0030.0000.0000.0000.000
209A210ARG10.9420.96838.6840.0490.0490.0000.0000.0000.000
210A211ASN00.0700.06343.8000.0030.0030.0000.0000.0000.000
211A225TYR00.039-0.00128.8330.0020.0020.0000.0000.0000.000
212A226SER0-0.090-0.04030.0660.0010.0010.0000.0000.0000.000
213A227ARG10.9470.95327.1920.1160.1160.0000.0000.0000.000
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215A229ILE0-0.036-0.03021.998-0.006-0.0060.0000.0000.0000.000
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