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: 858LY

Calculation Name: 4R9P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4R9P

Chain ID: A

ChEMBL ID:

UniProt ID: A1Z8R1

Base Structure: X-ray

Registration Date: 2023-06-21

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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2654624.314055
FMO2-HF: Nuclear repulsion 2568824.553724
FMO2-HF: Total energy -85799.760331
FMO2-MP2: Total energy -86047.118682


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:27:GLU)


Summations of interaction energy for fragment #1(A:27:GLU)
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.
-79.279-74.9370.154-2.083-2.4120.006
Interaction energy analysis for fragmet #1(A:27:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -1.005 / q_NPA : -0.998
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].
3A29ASP-1-0.895-0.9313.30227.46030.655-0.010-1.654-1.5320.003
4A30ILE0-0.024-0.0223.307-4.024-2.9780.166-0.397-0.8150.003
5A31TRP0-0.035-0.0155.740-1.448-1.486-0.001-0.0030.0430.000
6A32PHE00.0460.0045.708-1.382-1.3820.0000.0000.0000.000
7A33GLN0-0.005-0.00910.356-2.210-2.2100.0000.0000.0000.000
8A34LYS11.0071.00412.876-14.010-14.0100.0000.0000.0000.000
9A35ASP-1-0.816-0.91115.21214.76514.7650.0000.0000.0000.000
10A36LYS10.9000.9449.864-22.906-22.9060.0000.0000.0000.000
11A37LEU00.0520.05511.5390.0600.0600.0000.0000.0000.000
12A38TYR00.0130.00312.813-0.247-0.2470.0000.0000.0000.000
13A39LYS10.9700.98715.099-16.972-16.9720.0000.0000.0000.000
14A40GLU-1-0.838-0.9109.28125.55925.5590.0000.0000.0000.000
15A41HIS00.021-0.00311.4270.1840.1840.0000.0000.0000.000
16A42ILE0-0.005-0.00115.247-0.631-0.6310.0000.0000.0000.000
17A43GLN0-0.006-0.02115.7480.1450.1450.0000.0000.0000.000
18A44GLU-1-0.848-0.91611.84721.47721.4770.0000.0000.0000.000
19A45VAL0-0.013-0.01716.317-0.385-0.3850.0000.0000.0000.000
20A46LEU0-0.052-0.03619.735-0.655-0.6550.0000.0000.0000.000
21A47ASP-1-0.927-0.96117.22514.97814.9780.0000.0000.0000.000
22A48LYS10.8900.95614.805-17.468-17.4680.0000.0000.0000.000
23A49TRP0-0.025-0.00620.902-0.196-0.1960.0000.0000.0000.000
24A50THR0-0.014-0.02124.118-0.050-0.0500.0000.0000.0000.000
25A51GLN0-0.019-0.00321.7250.1050.1050.0000.0000.0000.000
26A52ILE0-0.097-0.03721.4460.2880.2880.0000.0000.0000.000
27A53ASP-1-0.845-0.92824.7549.9759.9750.0000.0000.0000.000
28A54ASP-1-0.856-0.93427.8489.6029.6020.0000.0000.0000.000
29A55GLU-1-0.871-0.91330.1349.5449.5440.0000.0000.0000.000
30A56ILE0-0.143-0.07624.0630.2330.2330.0000.0000.0000.000
31A57TRP00.011-0.02027.5470.1450.1450.0000.0000.0000.000
32A58ALA0-0.021-0.02724.1620.0750.0750.0000.0000.0000.000
33A59LYS10.9180.99015.489-17.377-17.3770.0000.0000.0000.000
34A60VAL0-0.019-0.01819.450-0.020-0.0200.0000.0000.0000.000
35A61ILE0-0.046-0.02113.2880.5040.5040.0000.0000.0000.000
36A62VAL0-0.0030.00615.043-0.788-0.7880.0000.0000.0000.000
37A63PHE00.020-0.00310.8981.7361.7360.0000.0000.0000.000
38A64GLU-1-0.725-0.83312.18019.72619.7260.0000.0000.0000.000
39A65ARG10.7910.88611.755-16.797-16.7970.0000.0000.0000.000
40A66ASN00.007-0.0079.040-0.752-0.7520.0000.0000.0000.000
41A67ARG10.9550.9794.268-48.126-47.987-0.001-0.029-0.1080.000
42A68ARG10.7690.8808.063-31.157-31.1570.0000.0000.0000.000
43A69VAL00.003-0.0038.7691.9331.9330.0000.0000.0000.000
44A70ALA00.0160.01411.254-0.753-0.7530.0000.0000.0000.000
45A71LYS10.8530.92912.018-21.877-21.8770.0000.0000.0000.000
46A72ALA00.0180.02015.792-0.282-0.2820.0000.0000.0000.000
47A73TYR00.0050.00218.3590.2550.2550.0000.0000.0000.000
48A74ALA0-0.009-0.00622.344-0.229-0.2290.0000.0000.0000.000
49A75ARG10.9170.95825.649-11.094-11.0940.0000.0000.0000.000
50A76ALA00.0430.02328.950-0.325-0.3250.0000.0000.0000.000
51A77PRO00.0500.04030.2720.2170.2170.0000.0000.0000.000
52A78VAL0-0.056-0.04031.8170.0460.0460.0000.0000.0000.000
53A79LEU00.0270.03024.0720.0700.0700.0000.0000.0000.000
54A80THR0-0.057-0.02928.305-0.292-0.2920.0000.0000.0000.000
55A81ILE00.0180.01822.7190.3380.3380.0000.0000.0000.000
56A82ASN00.019-0.00224.8860.0220.0220.0000.0000.0000.000
57A83GLY00.0410.01124.0070.5520.5520.0000.0000.0000.000
58A84SER0-0.0280.00425.0960.1330.1330.0000.0000.0000.000
59A85ASP-1-0.897-0.96522.75612.91512.9150.0000.0000.0000.000
60A86ASP-1-0.863-0.93723.02211.98011.9800.0000.0000.0000.000
61A87GLY0-0.0060.02120.7070.2230.2230.0000.0000.0000.000
62A88PHE0-0.059-0.03721.037-0.433-0.4330.0000.0000.0000.000
63A89ASP-1-0.788-0.89522.73611.20011.2000.0000.0000.0000.000
64A90GLY00.0030.00825.453-0.419-0.4190.0000.0000.0000.000
65A91MET0-0.040-0.03427.012-0.239-0.2390.0000.0000.0000.000
66A92ARG10.8890.93925.657-11.832-11.8320.0000.0000.0000.000
67A93ILE0-0.009-0.00320.5140.2840.2840.0000.0000.0000.000
68A94GLY0-0.021-0.01622.844-0.347-0.3470.0000.0000.0000.000
69A95LEU0-0.019-0.02819.0550.6640.6640.0000.0000.0000.000
70A96CYS0-0.066-0.03218.7841.1921.1920.0000.0000.0000.000
71A97GLY00.0580.05120.1160.0450.0450.0000.0000.0000.000
72A98PHE0-0.086-0.03114.7060.0970.0970.0000.0000.0000.000
73A99ASP-1-0.847-0.91413.06520.59620.5960.0000.0000.0000.000
74A100ASN0-0.051-0.06910.0613.7643.7640.0000.0000.0000.000
75A101PRO00.0130.0238.339-1.769-1.7690.0000.0000.0000.000
76A102MET0-0.030-0.0256.941-0.094-0.0940.0000.0000.0000.000
77A103ARG10.8080.89510.293-21.318-21.3180.0000.0000.0000.000
78A104ASP-1-0.761-0.85013.50219.21819.2180.0000.0000.0000.000
79A105GLN00.037-0.01815.739-0.047-0.0470.0000.0000.0000.000
80A106LYS10.9640.97619.305-14.030-14.0300.0000.0000.0000.000
81A107THR0-0.027-0.03415.750-0.766-0.7660.0000.0000.0000.000
82A108ASP-1-0.864-0.91718.58114.96714.9670.0000.0000.0000.000
83A109GLU-1-0.886-0.93620.07812.67112.6710.0000.0000.0000.000
84A110MET0-0.078-0.04721.377-0.803-0.8030.0000.0000.0000.000
85A111LYS10.8540.89916.739-18.370-18.3700.0000.0000.0000.000
86A112ARG10.8770.94022.224-14.300-14.3000.0000.0000.0000.000
87A113VAL0-0.026-0.00425.367-0.591-0.5910.0000.0000.0000.000
88A114ILE0-0.0050.02421.629-0.370-0.3700.0000.0000.0000.000
89A115GLY00.0080.00526.211-0.395-0.3950.0000.0000.0000.000
90A116GLN00.026-0.01728.4370.1950.1950.0000.0000.0000.000
91A117GLY00.0080.01627.4670.0110.0110.0000.0000.0000.000
92A118VAL00.0220.00026.653-0.411-0.4110.0000.0000.0000.000
93A119LYS10.9020.96528.855-9.475-9.4750.0000.0000.0000.000
94A120ILE00.005-0.00325.810-0.158-0.1580.0000.0000.0000.000
95A121LYS10.9700.97830.023-8.435-8.4350.0000.0000.0000.000
96A122MET0-0.0130.03929.739-0.018-0.0180.0000.0000.0000.000
97A123ASP-1-0.860-0.91532.8048.2638.2630.0000.0000.0000.000
98A124ASP-1-0.837-0.93336.0157.9037.9030.0000.0000.0000.000
99A125ALA0-0.093-0.04038.311-0.043-0.0430.0000.0000.0000.000
100A126GLY00.0580.02634.0180.0560.0560.0000.0000.0000.000
101A127ASN0-0.114-0.07832.8430.3280.3280.0000.0000.0000.000
102A128ILE00.0220.02227.5140.0590.0590.0000.0000.0000.000
103A129LEU0-0.038-0.03631.558-0.072-0.0720.0000.0000.0000.000
104A130ILE00.002-0.00627.8660.2970.2970.0000.0000.0000.000
105A131ARG10.9270.97731.795-8.566-8.5660.0000.0000.0000.000
106A132ARG10.8520.93531.239-9.293-9.2930.0000.0000.0000.000
107A133TYR00.0520.00731.859-0.267-0.2670.0000.0000.0000.000
108A134ALA0-0.0540.00329.583-0.160-0.1600.0000.0000.0000.000
109A135LYS11.0180.99931.687-9.246-9.2460.0000.0000.0000.000
110A136SER0-0.044-0.02328.490-0.190-0.1900.0000.0000.0000.000
111A137ASN00.008-0.00529.224-0.336-0.3360.0000.0000.0000.000
112A138VAL00.0280.01026.1680.3950.3950.0000.0000.0000.000
113A139TYR0-0.028-0.01325.320-0.396-0.3960.0000.0000.0000.000
114A140VAL00.0260.02625.3060.4780.4780.0000.0000.0000.000
115A141LYS10.9070.95622.024-12.857-12.8570.0000.0000.0000.000
116A142SER00.004-0.00624.4000.0350.0350.0000.0000.0000.000
117A143THR0-0.002-0.01020.9640.2700.2700.0000.0000.0000.000
118A144ALA0-0.0250.00822.0010.2720.2720.0000.0000.0000.000
119A145SER0-0.031-0.02420.2670.3740.3740.0000.0000.0000.000
120A146SER0-0.125-0.14222.071-0.030-0.0300.0000.0000.0000.000
121A147PRO00.005-0.01525.062-0.137-0.1370.0000.0000.0000.000
122A148ASN0-0.043-0.02227.6610.0320.0320.0000.0000.0000.000
123A149GLU-1-0.770-0.78624.94111.65711.6570.0000.0000.0000.000
124A150GLU-1-0.818-0.93229.2878.5948.5940.0000.0000.0000.000
125A151THR00.0070.02328.7240.2540.2540.0000.0000.0000.000
126A152SER00.016-0.02828.373-0.330-0.3300.0000.0000.0000.000
127A153ILE00.0620.06127.350-0.125-0.1250.0000.0000.0000.000
128A154GLY00.0480.03331.167-0.296-0.2960.0000.0000.0000.000
129A155ALA0-0.006-0.02734.5340.0860.0860.0000.0000.0000.000
130A156GLU-1-0.920-0.97237.1777.9087.9080.0000.0000.0000.000
131A157ILE00.0080.01130.5880.0170.0170.0000.0000.0000.000
132A158LEU0-0.041-0.02331.6790.0460.0460.0000.0000.0000.000
133A159LYS10.9130.96034.291-7.584-7.5840.0000.0000.0000.000
134A160LEU0-0.0230.01333.913-0.146-0.1460.0000.0000.0000.000
135A161PRO00.0470.00134.1580.2190.2190.0000.0000.0000.000
136A162ASN0-0.0260.00128.3790.2470.2470.0000.0000.0000.000
137A163GLN0-0.037-0.01928.3660.1490.1490.0000.0000.0000.000
138A164ALA00.0030.00229.7630.3430.3430.0000.0000.0000.000
139A165LEU00.0100.00829.573-0.342-0.3420.0000.0000.0000.000
140A166GLU-1-0.837-0.92732.6487.9997.9990.0000.0000.0000.000
141A167SER0-0.019-0.02335.6270.1820.1820.0000.0000.0000.000
142A168GLU-1-0.970-0.99035.9847.9767.9760.0000.0000.0000.000
143A169LYS10.9080.96937.100-7.915-7.9150.0000.0000.0000.000
144A170ILE0-0.045-0.02336.0910.2650.2650.0000.0000.0000.000
145A171VAL00.0380.03033.296-0.160-0.1600.0000.0000.0000.000
146A172LYS10.9120.94834.078-8.037-8.0370.0000.0000.0000.000
147A173LEU00.0140.00626.1230.0010.0010.0000.0000.0000.000
148A174PHE00.002-0.00228.6300.1600.1600.0000.0000.0000.000
149A175ASP-1-0.876-0.95730.7998.1348.1340.0000.0000.0000.000
150A176MET00.0760.04232.1430.0830.0830.0000.0000.0000.000
151A177LYS10.9580.98634.916-7.492-7.4920.0000.0000.0000.000
152A178LYS10.8040.90234.324-9.005-9.0050.0000.0000.0000.000
153A179PHE00.0450.02928.931-0.072-0.0720.0000.0000.0000.000
154A180GLN00.0290.00733.5020.0190.0190.0000.0000.0000.000
155A181SER0-0.077-0.03636.192-0.197-0.1970.0000.0000.0000.000
156A182ASN0-0.003-0.00332.386-0.387-0.3870.0000.0000.0000.000
157A183VAL00.0230.02332.1910.0140.0140.0000.0000.0000.000
158A184ASN0-0.045-0.02934.524-0.036-0.0360.0000.0000.0000.000
159A185ARG10.8560.89736.865-8.246-8.2460.0000.0000.0000.000
160A186GLU-1-0.792-0.90031.7939.2079.2070.0000.0000.0000.000
161A187LEU0-0.039-0.01135.140-0.056-0.0560.0000.0000.0000.000
162A188ARG10.9070.95336.638-7.505-7.5050.0000.0000.0000.000
163A189ARG10.8110.92834.445-8.788-8.7880.0000.0000.0000.000
164A190ALA00.0190.00537.9510.0140.0140.0000.0000.0000.000
165A191TYR0-0.032-0.01933.356-0.015-0.0150.0000.0000.0000.000
166A192PRO0-0.0180.01233.1040.2390.2390.0000.0000.0000.000
167A193ASP-1-0.794-0.86526.84111.15311.1530.0000.0000.0000.000
168A194ARG10.9100.94325.002-11.000-11.0000.0000.0000.0000.000
169A195ARG10.8600.88622.292-11.669-11.6690.0000.0000.0000.000
170A196ARG10.9831.00224.449-10.226-10.2260.0000.0000.0000.000
171A197LEU0-0.035-0.01126.715-0.050-0.0500.0000.0000.0000.000
172A198GLU-1-0.821-0.93222.74212.50812.5080.0000.0000.0000.000
173A199THR00.0130.01521.2520.1450.1450.0000.0000.0000.000
174A200GLN00.0240.02923.339-0.119-0.1190.0000.0000.0000.000
175A201CYS0-0.047-0.00324.228-0.381-0.3810.0000.0000.0000.000
176A202LEU0-0.0350.00119.0860.3170.3170.0000.0000.0000.000
177A203SER0-0.016-0.00922.797-0.591-0.5910.0000.0000.0000.000
178A204ALA00.0380.02620.5500.6120.6120.0000.0000.0000.000
179A205VAL0-0.023-0.00721.527-0.686-0.6860.0000.0000.0000.000
180A206ALA00.0220.00921.3410.7040.7040.0000.0000.0000.000
181A207PHE00.012-0.00621.618-0.910-0.9100.0000.0000.0000.000
182A208VAL0-0.0090.02323.0690.3730.3730.0000.0000.0000.000
183A209LYS10.8370.88122.759-13.375-13.3750.0000.0000.0000.000
184A210SER0-0.022-0.00522.8130.4410.4410.0000.0000.0000.000
185A211GLU-1-0.862-0.92420.20413.58213.5820.0000.0000.0000.000
186A212ASN0-0.047-0.03622.744-0.167-0.1670.0000.0000.0000.000
187A213ASP-1-0.804-0.89517.84516.68516.6850.0000.0000.0000.000
188A214ILE00.004-0.01216.5020.1430.1430.0000.0000.0000.000
189A215LEU0-0.027-0.01612.3170.5770.5770.0000.0000.0000.000
190A216GLU-1-0.891-0.93714.14817.56717.5670.0000.0000.0000.000
191A217CYS0-0.103-0.01916.765-0.942-0.9420.0000.0000.0000.000
192A218PRO00.0130.00916.4860.9870.9870.0000.0000.0000.000
193A219ILE00.0150.00416.6020.8370.8370.0000.0000.0000.000
194A220TRP0-0.052-0.03214.126-1.895-1.8950.0000.0000.0000.000
195A221VAL0-0.0010.01317.2050.8090.8090.0000.0000.0000.000
196A222LEU0-0.004-0.00216.210-0.620-0.6200.0000.0000.0000.000
197A223ILE0-0.016-0.01818.7840.1320.1320.0000.0000.0000.000
198A224VAL00.0110.00619.117-0.217-0.2170.0000.0000.0000.000
199A225ASN00.0400.01422.121-0.203-0.2030.0000.0000.0000.000
200A226VAL00.0610.01123.973-0.017-0.0170.0000.0000.0000.000
201A227VAL00.0870.04326.288-0.209-0.2090.0000.0000.0000.000
202A228ALA0-0.036-0.01627.862-0.241-0.2410.0000.0000.0000.000
203A229MET0-0.033-0.03322.030-0.032-0.0320.0000.0000.0000.000
204A230ASP-1-0.852-0.93127.2779.5259.5250.0000.0000.0000.000
205A231MET0-0.044-0.03029.934-0.288-0.2880.0000.0000.0000.000
206A232LEU0-0.0050.00727.130-0.224-0.2240.0000.0000.0000.000
207A233LYS10.8650.94826.145-11.008-11.0080.0000.0000.0000.000
208A234SER00.0090.01530.411-0.214-0.2140.0000.0000.0000.000
209A235LYS10.8270.91433.209-8.492-8.4920.0000.0000.0000.000
210A236LEU00.0190.02731.9770.0760.0760.0000.0000.0000.000