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: 85G5Y

Calculation Name: 5CS0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5CS0

Chain ID: A

ChEMBL ID:

UniProt ID: Q00955

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 OptHSide
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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2339838.806974
FMO2-HF: Nuclear repulsion 2255820.633976
FMO2-HF: Total energy -84018.172998
FMO2-MP2: Total energy -84267.601422


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:797:LYS)


Summations of interaction energy for fragment #1(A:797:LYS)
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.
62.24267.2330.932-2.215-3.710.007
Interaction energy analysis for fragmet #1(A:797:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 1.045 / q_NPA : 1.010
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].
3A799ALA00.0620.0273.3940.7453.1630.018-1.046-1.3910.004
4A800TYR00.0070.0032.4860.0131.7400.912-0.940-1.7000.002
5A801LYS10.9890.9883.79041.12941.7330.003-0.210-0.3970.001
6A802PHE00.0100.0205.6082.8762.8760.0000.0000.0000.000
7A803LYS11.0090.9947.74022.63822.6380.0000.0000.0000.000
8A804SER00.0010.0258.3191.0861.0860.0000.0000.0000.000
9A805LEU00.0250.0008.9531.1871.1870.0000.0000.0000.000
10A806VAL00.0170.01711.5271.5041.5040.0000.0000.0000.000
11A807SER0-0.012-0.01512.6731.4301.4300.0000.0000.0000.000
12A808THR0-0.019-0.00813.5721.0201.0200.0000.0000.0000.000
13A809LEU0-0.009-0.00415.5470.9600.9600.0000.0000.0000.000
14A810GLU-1-0.790-0.90417.421-12.659-12.6590.0000.0000.0000.000
15A811ASN0-0.044-0.03017.8701.1531.1530.0000.0000.0000.000
16A812ILE0-0.027-0.00520.0020.5250.5250.0000.0000.0000.000
17A813LEU0-0.052-0.01821.5380.6360.6360.0000.0000.0000.000
18A814LYS10.7840.87420.85413.39613.3960.0000.0000.0000.000
19A815GLY00.0140.02925.0690.3490.3490.0000.0000.0000.000
20A816TYR0-0.053-0.02021.5500.1570.1570.0000.0000.0000.000
21A817ASP-1-0.836-0.90925.754-10.540-10.5400.0000.0000.0000.000
22A818ASN00.001-0.03124.217-0.801-0.8010.0000.0000.0000.000
23A819GLN00.0300.01324.849-0.658-0.6580.0000.0000.0000.000
24A820VAL00.0450.04024.683-0.155-0.1550.0000.0000.0000.000
25A821ILE00.0520.02819.785-0.292-0.2920.0000.0000.0000.000
26A822MET0-0.0330.02821.175-0.638-0.6380.0000.0000.0000.000
27A823ASN0-0.004-0.03622.530-0.144-0.1440.0000.0000.0000.000
28A824ALA0-0.0090.01121.414-0.059-0.0590.0000.0000.0000.000
29A825SER00.001-0.02818.124-0.636-0.6360.0000.0000.0000.000
30A826LEU0-0.051-0.01419.084-0.521-0.5210.0000.0000.0000.000
31A827GLN00.002-0.01421.386-0.155-0.1550.0000.0000.0000.000
32A828GLN00.0150.00416.4420.1910.1910.0000.0000.0000.000
33A829LEU0-0.0210.00515.450-0.626-0.6260.0000.0000.0000.000
34A830ILE00.003-0.00218.252-0.191-0.1910.0000.0000.0000.000
35A831GLU-1-0.958-0.97118.987-14.430-14.4300.0000.0000.0000.000
36A832VAL0-0.043-0.03913.669-0.181-0.1810.0000.0000.0000.000
37A833LEU0-0.027-0.00616.337-0.423-0.4230.0000.0000.0000.000
38A834ARG10.8280.90018.73312.86312.8630.0000.0000.0000.000
39A835ASN0-0.0090.00816.7040.7810.7810.0000.0000.0000.000
40A836PRO00.0580.01318.101-0.857-0.8570.0000.0000.0000.000
41A837LYS10.9380.96015.24314.80714.8070.0000.0000.0000.000
42A838LEU0-0.0070.01912.656-1.306-1.3060.0000.0000.0000.000
43A839PRO00.0510.03213.531-1.647-1.6470.0000.0000.0000.000
44A840TYR0-0.036-0.03614.108-1.312-1.3120.0000.0000.0000.000
45A841SER0-0.056-0.0379.488-0.911-0.9110.0000.0000.0000.000
46A842GLU-1-0.816-0.9039.418-27.931-27.9310.0000.0000.0000.000
47A843TRP00.0650.0249.386-2.931-2.9310.0000.0000.0000.000
48A844LYS10.9380.9658.25521.87521.8750.0000.0000.0000.000
49A845LEU0-0.067-0.0304.074-2.125-1.883-0.001-0.019-0.2220.000
50A846HIS00.016-0.0026.173-7.162-7.1620.0000.0000.0000.000
51A847ILE00.0460.0237.5940.6820.6820.0000.0000.0000.000
52A848SER0-0.045-0.0316.6221.5501.5500.0000.0000.0000.000
53A849ALA0-0.070-0.0255.447-1.489-1.4890.0000.0000.0000.000
54A850LEU0-0.007-0.0067.6051.4911.4910.0000.0000.0000.000
55A851HIS00.0150.01010.4561.1551.1550.0000.0000.0000.000
56A852SER0-0.0280.01112.3231.1901.1900.0000.0000.0000.000
57A853ARG10.9120.94612.52222.77922.7790.0000.0000.0000.000
58A854LEU0-0.073-0.02214.2590.8150.8150.0000.0000.0000.000
59A855PRO00.011-0.00517.0880.4650.4650.0000.0000.0000.000
60A856ALA00.0740.04120.284-0.337-0.3370.0000.0000.0000.000
61A857LYS11.0071.02121.75511.37111.3710.0000.0000.0000.000
62A858LEU0-0.003-0.00118.573-0.003-0.0030.0000.0000.0000.000
63A859ASP-1-0.796-0.91516.132-19.590-19.5900.0000.0000.0000.000
64A860GLU-1-0.867-0.93118.848-13.282-13.2820.0000.0000.0000.000
65A861GLN0-0.126-0.07821.5240.2380.2380.0000.0000.0000.000
66A862MET0-0.060-0.03915.9470.2990.2990.0000.0000.0000.000
67A863GLU-1-0.903-0.92917.286-16.465-16.4650.0000.0000.0000.000
68A864GLU-1-0.777-0.91118.813-12.090-12.0900.0000.0000.0000.000
69A865LEU0-0.063-0.02221.9270.5930.5930.0000.0000.0000.000
70A866VAL00.0200.01816.1570.3740.3740.0000.0000.0000.000
71A867ALA00.0090.01519.6090.0960.0960.0000.0000.0000.000
72A868ARG10.8880.94220.42612.06212.0620.0000.0000.0000.000
73A869SER0-0.040-0.04321.4540.5230.5230.0000.0000.0000.000
74A870LEU00.0000.01016.3740.1900.1900.0000.0000.0000.000
75A871ARG10.8220.91920.67812.56312.5630.0000.0000.0000.000
76A872ARG10.9370.97423.36210.76810.7680.0000.0000.0000.000
77A873GLY00.0010.01023.7500.3540.3540.0000.0000.0000.000
78A874ALA0-0.043-0.01024.2170.1850.1850.0000.0000.0000.000
79A875VAL00.0260.00922.549-0.658-0.6580.0000.0000.0000.000
80A876PHE00.0410.02215.9730.1580.1580.0000.0000.0000.000
81A877PRO00.0120.02619.8190.3230.3230.0000.0000.0000.000
82A878ALA00.0230.00719.896-0.099-0.0990.0000.0000.0000.000
83A879ARG10.9490.95520.90311.86111.8610.0000.0000.0000.000
84A880GLN0-0.037-0.02423.884-0.100-0.1000.0000.0000.0000.000
85A881LEU00.0150.00917.3560.3190.3190.0000.0000.0000.000
86A882SER00.0570.02220.453-0.405-0.4050.0000.0000.0000.000
87A883LYS10.9010.97321.32912.44212.4420.0000.0000.0000.000
88A884LEU0-0.071-0.03821.6100.4030.4030.0000.0000.0000.000
89A885ILE00.0590.02816.5360.1740.1740.0000.0000.0000.000
90A886ASP-1-0.860-0.94520.681-14.046-14.0460.0000.0000.0000.000
91A887MET0-0.097-0.05523.2820.5090.5090.0000.0000.0000.000
92A888ALA0-0.0040.00221.7390.3350.3350.0000.0000.0000.000
93A889VAL00.0240.00720.2670.0050.0050.0000.0000.0000.000
94A890LYS10.8890.95723.19411.00911.0090.0000.0000.0000.000
95A891ASN00.010-0.01726.4630.8200.8200.0000.0000.0000.000
96A892PRO0-0.013-0.01627.097-0.360-0.3600.0000.0000.0000.000
97A893GLU-1-0.857-0.90428.002-11.092-11.0920.0000.0000.0000.000
98A894TYR0-0.066-0.03223.162-0.316-0.3160.0000.0000.0000.000
99A895ASN0-0.066-0.03622.395-1.126-1.1260.0000.0000.0000.000
100A896PRO00.0240.02024.1820.3760.3760.0000.0000.0000.000
101A897ASP-1-0.880-0.93624.015-12.028-12.0280.0000.0000.0000.000
102A898LYS10.8560.92323.75611.12311.1230.0000.0000.0000.000
103A899LEU00.0540.02719.267-0.388-0.3880.0000.0000.0000.000
104A900LEU00.0080.01217.500-1.093-1.0930.0000.0000.0000.000
105A901GLY0-0.006-0.00217.085-0.976-0.9760.0000.0000.0000.000
106A902ALA00.022-0.00116.206-0.764-0.7640.0000.0000.0000.000
107A903VAL0-0.023-0.00313.046-1.611-1.6110.0000.0000.0000.000
108A904VAL0-0.001-0.02212.284-1.925-1.9250.0000.0000.0000.000
109A905GLU-1-0.887-0.91612.729-21.613-21.6130.0000.0000.0000.000
110A906PRO00.0140.0018.586-0.149-0.1490.0000.0000.0000.000
111A907LEU0-0.030-0.02110.705-0.001-0.0010.0000.0000.0000.000
112A908ALA00.003-0.00612.6331.2981.2980.0000.0000.0000.000
113A909ASP-1-0.812-0.90612.715-22.462-22.4620.0000.0000.0000.000
114A910ILE0-0.056-0.0199.7731.0891.0890.0000.0000.0000.000
115A911ALA0-0.028-0.01614.3071.1401.1400.0000.0000.0000.000
116A912HIS00.0200.00717.5271.2491.2490.0000.0000.0000.000
117A913LYS10.8740.96212.17125.56725.5670.0000.0000.0000.000
118A914TYR0-0.023-0.03514.5431.4111.4110.0000.0000.0000.000
119A915SER0-0.069-0.04219.7451.0531.0530.0000.0000.0000.000
120A916ASN0-0.039-0.01322.7430.8210.8210.0000.0000.0000.000
121A917GLY00.0030.00223.3560.4710.4710.0000.0000.0000.000
122A918LEU0-0.002-0.01119.542-0.259-0.2590.0000.0000.0000.000
123A919GLU-1-0.777-0.86121.608-11.448-11.4480.0000.0000.0000.000
124A920ALA00.0150.00823.976-0.022-0.0220.0000.0000.0000.000
125A921HIS00.0590.03215.3040.4080.4080.0000.0000.0000.000
126A922GLU-1-0.792-0.86919.853-13.454-13.4540.0000.0000.0000.000
127A923HIS0-0.023-0.01921.057-0.336-0.3360.0000.0000.0000.000
128A924SER0-0.057-0.03519.845-0.024-0.0240.0000.0000.0000.000
129A925ILE00.0310.02216.009-0.348-0.3480.0000.0000.0000.000
130A926PHE00.006-0.01619.4110.0360.0360.0000.0000.0000.000
131A927VAL00.0030.00322.5070.3560.3560.0000.0000.0000.000
132A928HIS0-0.037-0.01518.1300.4430.4430.0000.0000.0000.000
133A929PHE0-0.010-0.01316.8710.1080.1080.0000.0000.0000.000
134A930LEU0-0.045-0.02521.7710.3700.3700.0000.0000.0000.000
135A931GLU-1-0.740-0.86523.910-10.953-10.9530.0000.0000.0000.000
136A932GLU-1-0.947-0.94918.744-16.312-16.3120.0000.0000.0000.000
137A933TYR0-0.075-0.06723.0770.3360.3360.0000.0000.0000.000
138A934TYR0-0.003-0.03425.6650.2740.2740.0000.0000.0000.000
139A935GLU-1-0.806-0.89525.059-10.931-10.9310.0000.0000.0000.000
140A936VAL0-0.057-0.02324.4610.1300.1300.0000.0000.0000.000
141A937GLU-1-0.735-0.86227.513-10.461-10.4610.0000.0000.0000.000
142A938LYS10.8320.92029.45411.05611.0560.0000.0000.0000.000
143A939LEU0-0.092-0.04029.0280.2730.2730.0000.0000.0000.000
144A940PHE0-0.070-0.02829.7190.3290.3290.0000.0000.0000.000
145A961ASP-1-0.889-0.96425.437-12.165-12.1650.0000.0000.0000.000
146A962LEU00.024-0.00827.958-0.186-0.1860.0000.0000.0000.000
147A963ASP-1-0.840-0.90423.458-12.812-12.8120.0000.0000.0000.000
148A964LYS10.9510.98123.78011.51211.5120.0000.0000.0000.000
149A965VAL0-0.023-0.00824.804-0.051-0.0510.0000.0000.0000.000
150A966ALA00.0220.01926.2250.1570.1570.0000.0000.0000.000
151A967LEU00.018-0.00220.4240.0270.0270.0000.0000.0000.000
152A968THR0-0.039-0.02024.210-0.111-0.1110.0000.0000.0000.000
153A969VAL00.0110.00526.1520.1230.1230.0000.0000.0000.000
154A970LEU00.0070.01122.5780.2310.2310.0000.0000.0000.000
155A971SER00.0440.03823.2920.2850.2850.0000.0000.0000.000
156A972HIS10.8890.92825.01410.19610.1960.0000.0000.0000.000
157A973SER0-0.099-0.05827.5550.2920.2920.0000.0000.0000.000
158A974LYS10.9050.95125.25412.07812.0780.0000.0000.0000.000
159A975VAL00.0340.02527.781-0.157-0.1570.0000.0000.0000.000
160A976SER0-0.044-0.01029.637-0.058-0.0580.0000.0000.0000.000
161A977ALA00.0490.01126.0450.0400.0400.0000.0000.0000.000
162A978LYS10.8440.91624.52812.01612.0160.0000.0000.0000.000
163A979ASN00.0160.00126.546-0.237-0.2370.0000.0000.0000.000
164A980ASN0-0.035-0.00228.0740.3200.3200.0000.0000.0000.000
165A981LEU00.0380.02421.4510.0960.0960.0000.0000.0000.000
166A982ILE00.0590.01424.909-0.019-0.0190.0000.0000.0000.000
167A983LEU0-0.056-0.02827.4700.2940.2940.0000.0000.0000.000
168A984ALA0-0.007-0.00326.6380.2100.2100.0000.0000.0000.000
169A985ILE0-0.013-0.00522.7660.0530.0530.0000.0000.0000.000
170A986LEU00.0210.00726.8170.1610.1610.0000.0000.0000.000
171A987LYS10.8730.92130.2919.1359.1350.0000.0000.0000.000
172A988HIS00.0200.01925.9160.2830.2830.0000.0000.0000.000
173A989TYR00.039-0.01624.9340.0440.0440.0000.0000.0000.000
174A990GLN00.0050.02730.3900.3350.3350.0000.0000.0000.000
175A991PRO0-0.035-0.02033.0430.2370.2370.0000.0000.0000.000
176A992LEU00.0090.00128.9240.1950.1950.0000.0000.0000.000
177A993CYS0-0.041-0.01732.081-0.010-0.0100.0000.0000.0000.000
178A994LYS10.9020.96334.3577.8247.8240.0000.0000.0000.000
179A995LEU0-0.028-0.00636.0070.1940.1940.0000.0000.0000.000
180A996SER00.0050.00733.3980.1230.1230.0000.0000.0000.000
181A997SER00.0850.02835.545-0.005-0.0050.0000.0000.0000.000
182A998LYS10.8350.90230.31210.38310.3830.0000.0000.0000.000
183A999VAL00.001-0.00129.592-0.208-0.2080.0000.0000.0000.000
184A1000SER00.0590.01031.436-0.210-0.2100.0000.0000.0000.000
185A1001ALA0-0.036-0.00333.631-0.028-0.0280.0000.0000.0000.000
186A1002ILE0-0.041-0.01326.940-0.108-0.1080.0000.0000.0000.000
187A1003PHE00.012-0.00625.656-0.269-0.2690.0000.0000.0000.000
188A1004SER0-0.0110.00830.4920.1060.1060.0000.0000.0000.000
189A1005THR00.0300.00530.6520.2030.2030.0000.0000.0000.000
190A1006PRO00.0210.00927.7830.1250.1250.0000.0000.0000.000
191A1007LEU0-0.0140.00229.9470.0220.0220.0000.0000.0000.000
192A1008GLN0-0.016-0.00332.7310.2310.2310.0000.0000.0000.000
193A1009HIS10.8360.89929.48310.53110.5310.0000.0000.0000.000
194A1010ILE0-0.035-0.02028.7000.1150.1150.0000.0000.0000.000
195A1011VAL0-0.044-0.02532.9050.1530.1530.0000.0000.0000.000
196A1012GLU-1-0.869-0.91535.175-8.953-8.9530.0000.0000.0000.000
197A1013LEU0-0.080-0.01031.460-0.010-0.0100.0000.0000.0000.000
198A1014GLU-1-0.917-0.95636.116-7.493-7.4930.0000.0000.0000.000
199A1015SER00.0370.01835.6220.0440.0440.0000.0000.0000.000
200A1016LYS10.9600.96738.5867.4857.4850.0000.0000.0000.000
201A1017ALA0-0.041-0.03334.363-0.007-0.0070.0000.0000.0000.000
202A1018THR00.0640.04132.527-0.154-0.1540.0000.0000.0000.000
203A1019ALA00.0290.04034.951-0.014-0.0140.0000.0000.0000.000
204A1020LYS10.9570.95936.3388.2638.2630.0000.0000.0000.000
205A1021VAL00.0340.01431.1050.0500.0500.0000.0000.0000.000
206A1022ALA00.0730.04634.321-0.061-0.0610.0000.0000.0000.000
207A1023LEU0-0.041-0.02136.3450.1090.1090.0000.0000.0000.000
208A1024GLN00.007-0.00234.6680.0230.0230.0000.0000.0000.000
209A1025ALA00.0370.02333.581-0.008-0.0080.0000.0000.0000.000
210A1026ARG10.9110.93835.1947.5837.5830.0000.0000.0000.000
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