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: QNYJY

Calculation Name: 5F1S-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5F1S

Chain ID: A

ChEMBL ID:

UniProt ID: A0A060

Base Structure: X-ray

Registration Date: 2023-09-26

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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2115229.408188
FMO2-HF: Nuclear repulsion 2032715.206584
FMO2-HF: Total energy -82514.201604
FMO2-MP2: Total energy -82749.21617


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:ARG)


Summations of interaction energy for fragment #1(A:1:ARG)
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.
-103.366-101.16412.523-6.246-8.477-0.034
Interaction energy analysis for fragmet #1(A:1:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.956 / q_NPA : 0.964
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].
3A3THR0-0.063-0.0282.275-7.804-5.4101.466-1.079-2.7800.001
4A4THR0-0.004-0.0114.8834.2504.325-0.001-0.005-0.0680.000
5A5VAL0-0.025-0.0078.072-2.218-2.2180.0000.0000.0000.000
6A6GLY00.0150.00710.625-0.393-0.3930.0000.0000.0000.000
7A7ASP-1-0.864-0.93612.112-19.700-19.7000.0000.0000.0000.000
8A8LEU0-0.026-0.01015.4530.5350.5350.0000.0000.0000.000
9A9ALA0-0.008-0.00618.2030.4550.4550.0000.0000.0000.000
10A10VAL0-0.018-0.00521.9040.0320.0320.0000.0000.0000.000
11A11LEU0-0.044-0.00924.1850.2820.2820.0000.0000.0000.000
12A12GLU-1-0.802-0.90727.979-9.951-9.9510.0000.0000.0000.000
13A13GLY00.0280.01329.4770.3510.3510.0000.0000.0000.000
14A14ARG10.7820.89626.34610.61910.6190.0000.0000.0000.000
15A15SER00.0400.01524.1890.0040.0040.0000.0000.0000.000
16A16VAL0-0.040-0.01119.306-0.119-0.1190.0000.0000.0000.000
17A17MET00.0130.00117.3560.4580.4580.0000.0000.0000.000
18A18ILE0-0.0030.00112.842-0.480-0.4800.0000.0000.0000.000
19A19PRO0-0.0130.01010.9720.5060.5060.0000.0000.0000.000
20A20CYS0-0.0030.0178.748-0.084-0.0840.0000.0000.0000.000
21A21HIS00.0610.0246.1420.5470.5470.0000.0000.0000.000
22A22TYR0-0.019-0.0324.510-4.814-4.607-0.001-0.056-0.1500.000
23A23GLY00.0220.0223.5520.5181.0970.006-0.172-0.4130.000
24A24PRO00.0330.0084.2032.2352.3590.000-0.024-0.1000.000
25A25GLN00.005-0.0045.4141.1971.299-0.001-0.001-0.0990.000
26A26TYR0-0.009-0.0152.661-1.354-0.1730.477-0.632-1.0270.006
27A27ALA00.0300.0177.8600.6370.6370.0000.0000.0000.000
28A28SER0-0.010-0.01011.2070.4630.4630.0000.0000.0000.000
29A29TYR0-0.047-0.0039.8341.0171.0170.0000.0000.0000.000
30A30VAL00.0320.02512.120-0.438-0.4380.0000.0000.0000.000
31A31LYS10.8150.9079.11919.63119.6310.0000.0000.0000.000
32A32TYR0-0.026-0.02510.9831.4611.4610.0000.0000.0000.000
33A33TRP00.0440.01212.754-1.519-1.5190.0000.0000.0000.000
34A34CYS0-0.108-0.02314.4961.7731.7730.0000.0000.0000.000
35A35ARG10.9140.95716.40412.36812.3680.0000.0000.0000.000
36A36GLY00.0380.00718.6320.6320.6320.0000.0000.0000.000
37A37SER00.0110.00517.530-0.821-0.8210.0000.0000.0000.000
38A38VAL00.0130.01017.108-0.814-0.8140.0000.0000.0000.000
39A39LYS11.0091.02310.83920.44220.4420.0000.0000.0000.000
40A40ASP-1-0.934-0.98414.926-16.889-16.8890.0000.0000.0000.000
41A41LEU0-0.074-0.03816.9950.8090.8090.0000.0000.0000.000
42A43THR00.0160.00518.7400.5940.5940.0000.0000.0000.000
43A44SER0-0.011-0.01617.937-0.592-0.5920.0000.0000.0000.000
44A45LEU0-0.013-0.01018.6630.7290.7290.0000.0000.0000.000
45A46VAL0-0.043-0.03117.9250.6710.6710.0000.0000.0000.000
46A47ARG10.7790.84616.63913.44813.4480.0000.0000.0000.000
47A48SER00.0120.00615.5570.3630.3630.0000.0000.0000.000
48A49ASP-1-0.852-0.91617.428-13.198-13.1980.0000.0000.0000.000
49A50ALA0-0.0210.00619.7440.5780.5780.0000.0000.0000.000
50A51PRO0-0.0090.00022.5360.0590.0590.0000.0000.0000.000
51A52ARG10.9790.98521.88112.24312.2430.0000.0000.0000.000
52A61LYS11.0201.02224.94811.76411.7640.0000.0000.0000.000
53A62VAL0-0.058-0.03520.442-0.198-0.1980.0000.0000.0000.000
54A63VAL0-0.006-0.01021.5700.4750.4750.0000.0000.0000.000
55A64MET0-0.0040.01814.320-0.846-0.8460.0000.0000.0000.000
56A65PHE0-0.035-0.02017.3780.8090.8090.0000.0000.0000.000
57A66ASP-1-0.744-0.87613.041-20.669-20.6690.0000.0000.0000.000
58A67ASP-1-0.874-0.92914.337-15.744-15.7440.0000.0000.0000.000
59A68PRO00.022-0.01212.655-1.088-1.0880.0000.0000.0000.000
60A69VAL0-0.054-0.01712.662-0.819-0.8190.0000.0000.0000.000
61A70GLN0-0.032-0.00813.401-0.805-0.8050.0000.0000.0000.000
62A71GLN0-0.086-0.0247.9570.1550.1550.0000.0000.0000.000
63A72VAL00.016-0.0058.724-3.225-3.2250.0000.0000.0000.000
64A73PHE0-0.0250.0008.8821.9601.9600.0000.0000.0000.000
65A74THR0-0.009-0.00912.305-1.356-1.3560.0000.0000.0000.000
66A75VAL00.002-0.00914.5041.1211.1210.0000.0000.0000.000
67A76THR0-0.028-0.01116.825-0.178-0.1780.0000.0000.0000.000
68A77MET0-0.0020.01719.7440.1580.1580.0000.0000.0000.000
69A78THR00.007-0.01122.245-0.069-0.0690.0000.0000.0000.000
70A79GLU-1-0.961-0.97525.772-9.906-9.9060.0000.0000.0000.000
71A80LEU0-0.0150.01022.4750.0980.0980.0000.0000.0000.000
72A81GLN00.0440.00526.9330.5920.5920.0000.0000.0000.000
73A82LYS10.9790.99527.8079.6809.6800.0000.0000.0000.000
74A83GLU-1-0.896-0.95428.185-10.462-10.4620.0000.0000.0000.000
75A84ASP-1-0.860-0.91624.526-11.999-11.9990.0000.0000.0000.000
76A85SER0-0.035-0.00623.579-0.829-0.8290.0000.0000.0000.000
77A86GLY0-0.022-0.02121.9530.4040.4040.0000.0000.0000.000
78A87TRP0-0.0230.00714.250-0.377-0.3770.0000.0000.0000.000
79A88TYR0-0.030-0.04216.2220.9850.9850.0000.0000.0000.000
80A89TRP0-0.021-0.02410.413-1.798-1.7980.0000.0000.0000.000
81A91GLY00.0170.0048.770-1.666-1.6660.0000.0000.0000.000
82A92VAL00.0110.0015.9890.9800.9800.0000.0000.0000.000
83A93GLU-1-0.862-0.9018.569-15.320-15.3200.0000.0000.0000.000
84A94VAL0-0.011-0.0087.1360.6310.6310.0000.0000.0000.000
85A95GLY0-0.0150.00110.420-0.307-0.3070.0000.0000.0000.000
86A96GLY0-0.010-0.01411.347-0.278-0.2780.0000.0000.0000.000
87A97VAL00.0030.0065.407-0.241-0.2410.0000.0000.0000.000
88A98TRP00.0110.0136.8280.9980.9980.0000.0000.0000.000
89A99SER00.0390.0086.510-2.669-2.6690.0000.0000.0000.000
90A100ALA00.0180.0116.781-1.162-1.1620.0000.0000.0000.000
91A101ASP-1-0.889-0.9402.828-44.297-43.0930.203-0.505-0.9030.000
92A102VAL0-0.053-0.0321.869-11.852-15.61410.375-3.745-2.868-0.041
93A103THR0-0.053-0.0464.4364.7194.817-0.001-0.027-0.0690.000
94A104ALA00.0030.0095.838-3.705-3.7050.0000.0000.0000.000
95A105SER0-0.024-0.0067.9811.8241.8240.0000.0000.0000.000
96A106LEU00.0100.00811.498-1.387-1.3870.0000.0000.0000.000
97A107HIS0-0.024-0.00914.0341.7101.7100.0000.0000.0000.000
98A108ILE00.0070.00217.441-0.276-0.2760.0000.0000.0000.000
99A109ASN00.0210.00520.0940.8240.8240.0000.0000.0000.000
100A110VAL00.0090.00923.104-0.039-0.0390.0000.0000.0000.000
101A111ILE0-0.034-0.02025.9060.4420.4420.0000.0000.0000.000
102A112GLN0-0.052-0.05528.4860.1950.1950.0000.0000.0000.000
103A113GLY00.0270.00432.1470.0610.0610.0000.0000.0000.000
104A114LEU00.0050.00432.883-0.027-0.0270.0000.0000.0000.000
105A115SER0-0.035-0.01328.278-0.326-0.3260.0000.0000.0000.000
106A116VAL00.0190.00129.4450.3040.3040.0000.0000.0000.000
107A117VAL0-0.0170.00927.366-0.327-0.3270.0000.0000.0000.000
108A118ASN00.025-0.00227.427-0.560-0.5600.0000.0000.0000.000
109A119SER0-0.0050.00329.4010.2910.2910.0000.0000.0000.000
110A120MET00.0120.01731.1270.3580.3580.0000.0000.0000.000
111A121VAL0-0.0030.00132.285-0.213-0.2130.0000.0000.0000.000
112A122SER0-0.020-0.01534.9350.1760.1760.0000.0000.0000.000
113A123GLY00.0430.01837.090-0.115-0.1150.0000.0000.0000.000
114A124GLU-1-0.852-0.90939.869-7.101-7.1010.0000.0000.0000.000
115A125GLU-1-0.782-0.89243.035-6.351-6.3510.0000.0000.0000.000
116A126GLY0-0.037-0.01446.2890.0430.0430.0000.0000.0000.000
117A127THR0-0.078-0.04142.852-0.026-0.0260.0000.0000.0000.000
118A128SER0-0.023-0.05143.0660.0700.0700.0000.0000.0000.000
119A129VAL0-0.036-0.01238.160-0.183-0.1830.0000.0000.0000.000
120A130THR0-0.010-0.01036.1060.1320.1320.0000.0000.0000.000
121A131VAL0-0.0060.00835.067-0.282-0.2820.0000.0000.0000.000
122A132GLN0-0.001-0.00732.1050.1370.1370.0000.0000.0000.000
123A133CYS0-0.0270.01832.648-0.132-0.1320.0000.0000.0000.000
124A134LEU0-0.018-0.00828.4380.1040.1040.0000.0000.0000.000
125A135TYR0-0.015-0.03232.404-0.017-0.0170.0000.0000.0000.000
126A136SER00.0420.03431.561-0.083-0.0830.0000.0000.0000.000
127A137GLN00.014-0.01132.8840.2190.2190.0000.0000.0000.000
128A138GLY0-0.016-0.00935.0390.2590.2590.0000.0000.0000.000
129A139TYR0-0.037-0.01635.6470.3020.3020.0000.0000.0000.000
130A140ARG10.8780.92633.8239.1559.1550.0000.0000.0000.000
131A141GLN00.0180.00639.7810.1730.1730.0000.0000.0000.000
132A142HIS0-0.051-0.00841.6790.2020.2020.0000.0000.0000.000
133A143GLU-1-0.880-0.92143.357-6.742-6.7420.0000.0000.0000.000
134A144LYS10.7540.86039.1237.7167.7160.0000.0000.0000.000
135A145ARG10.9320.96042.0757.4707.4700.0000.0000.0000.000
136A146TRP00.0290.00738.223-0.342-0.3420.0000.0000.0000.000
137A147CYS0-0.112-0.03242.5610.0910.0910.0000.0000.0000.000
138A148ARG10.9420.96442.8626.7186.7180.0000.0000.0000.000
139A149SER0-0.048-0.03741.5870.1100.1100.0000.0000.0000.000
140A150GLY0-0.014-0.01143.6920.0860.0860.0000.0000.0000.000
141A151ASP-1-0.855-0.91846.638-6.095-6.0950.0000.0000.0000.000
142A152TRP00.009-0.00346.478-0.085-0.0850.0000.0000.0000.000
143A153SER0-0.110-0.05449.5180.0040.0040.0000.0000.0000.000
144A154SER00.0010.00347.770-0.006-0.0060.0000.0000.0000.000
145A156LEU00.0390.02846.6180.1290.1290.0000.0000.0000.000
146A157VAL00.004-0.01746.084-0.209-0.2090.0000.0000.0000.000
147A158THR0-0.045-0.00143.8760.0300.0300.0000.0000.0000.000
148A159ASP-1-0.776-0.89347.097-6.389-6.3890.0000.0000.0000.000
149A160GLY0-0.029-0.02348.168-0.133-0.1330.0000.0000.0000.000
150A161GLU-1-0.990-0.99248.411-6.298-6.2980.0000.0000.0000.000
151A162GLY0-0.036-0.01344.821-0.136-0.1360.0000.0000.0000.000
152A163ARG10.9090.94144.7206.5586.5580.0000.0000.0000.000
153A164TYR00.015-0.02746.9650.1090.1090.0000.0000.0000.000
154A165GLU-1-0.891-0.94547.652-6.556-6.5560.0000.0000.0000.000
155A166ASP-1-0.775-0.83950.018-6.148-6.1480.0000.0000.0000.000
156A167GLN0-0.047-0.05051.266-0.041-0.0410.0000.0000.0000.000
157A168ALA0-0.017-0.00149.169-0.033-0.0330.0000.0000.0000.000
158A169VAL0-0.008-0.00744.788-0.173-0.1730.0000.0000.0000.000
159A170GLU-1-0.921-0.95145.102-6.864-6.8640.0000.0000.0000.000
160A171ILE0-0.061-0.02941.906-0.238-0.2380.0000.0000.0000.000
161A172ARG10.9860.99741.6467.6227.6220.0000.0000.0000.000
162A173ASP-1-0.745-0.87439.932-8.225-8.2250.0000.0000.0000.000
163A174ASP-1-0.835-0.90335.946-8.671-8.6710.0000.0000.0000.000
164A175LEU0-0.004-0.00539.640-0.016-0.0160.0000.0000.0000.000
165A176THR0-0.079-0.03635.859-0.137-0.1370.0000.0000.0000.000
166A177LYS10.9020.94530.0619.8989.8980.0000.0000.0000.000
167A178ALA00.0270.00833.201-0.318-0.3180.0000.0000.0000.000
168A179PHE00.0100.02235.1150.1930.1930.0000.0000.0000.000
169A180THR0-0.065-0.03336.173-0.182-0.1820.0000.0000.0000.000
170A181VAL00.0540.01938.3650.1980.1980.0000.0000.0000.000
171A182THR00.008-0.00539.815-0.270-0.2700.0000.0000.0000.000
172A183LEU0-0.0070.00241.3120.1910.1910.0000.0000.0000.000
173A184LYS10.9030.93743.7436.3656.3650.0000.0000.0000.000
174A185GLY00.0280.04246.2390.0050.0050.0000.0000.0000.000
175A186LEU0-0.0650.00241.4560.0930.0930.0000.0000.0000.000
176A187ALA00.0590.02446.1110.1280.1280.0000.0000.0000.000
177A188ARG10.8880.91546.1476.3616.3610.0000.0000.0000.000
178A189ARG10.8980.95146.7186.0386.0380.0000.0000.0000.000
179A190ASP-1-0.833-0.91244.956-6.711-6.7110.0000.0000.0000.000
180A191THR00.0000.01841.485-0.238-0.2380.0000.0000.0000.000
181A192GLY0-0.021-0.01141.2670.1820.1820.0000.0000.0000.000
182A193TRP0-0.0090.00233.709-0.160-0.1600.0000.0000.0000.000
183A194TYR0-0.027-0.02239.0800.3100.3100.0000.0000.0000.000
184A195TRP0-0.004-0.01036.560-0.358-0.3580.0000.0000.0000.000
185A197ALA00.014-0.00537.867-0.165-0.1650.0000.0000.0000.000
186A198ALA00.0540.02139.0350.1020.1020.0000.0000.0000.000
187A199GLY00.0550.04440.188-0.130-0.1300.0000.0000.0000.000
188A200GLN0-0.055-0.03841.569-0.029-0.0290.0000.0000.0000.000
189A201GLN0-0.0050.01036.151-0.286-0.2860.0000.0000.0000.000
190A202GLN00.003-0.00736.6900.3030.3030.0000.0000.0000.000
191A203VAL0-0.028-0.00631.621-0.267-0.2670.0000.0000.0000.000
192A204ALA0-0.0080.00234.2460.2230.2230.0000.0000.0000.000
193A205VAL0-0.016-0.01733.741-0.341-0.3410.0000.0000.0000.000
194A206TYR00.001-0.00634.9600.3450.3450.0000.0000.0000.000
195A207ILE00.0160.01536.181-0.189-0.1890.0000.0000.0000.000
196A208LEU0-0.005-0.01937.2440.1530.1530.0000.0000.0000.000
197A209VAL00.0130.01539.494-0.082-0.0820.0000.0000.0000.000
198A210THR0-0.016-0.01639.4760.0370.0370.0000.0000.0000.000
199A211PRO0-0.039-0.03542.7350.1080.1080.0000.0000.0000.000
200A212PRO00.0110.02645.043-0.119-0.1190.0000.0000.0000.000
201A213SER0-0.049-0.01744.6800.1010.1010.0000.0000.0000.000
202A214HIS0-0.018-0.01046.8130.1200.1200.0000.0000.0000.000