Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 179JZ

Calculation Name: 4E16-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4E16

Chain ID: A

ChEMBL ID:

UniProt ID: Q180S3

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 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 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2679120.723766
FMO2-HF: Nuclear repulsion 2588728.514826
FMO2-HF: Total energy -90392.208941
FMO2-MP2: Total energy -90654.415438


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-23.211-17.00915.491-6.758-14.934-0.052
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.039 / q_NPA : -0.016
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].
3A3LYS10.8740.9582.458-12.923-8.6163.593-2.792-5.1070.001
4A4VAL00.0700.0403.2920.5880.4750.0140.405-0.3060.000
5A5HIS10.8150.8876.086-0.328-0.3280.0000.0000.0000.000
6A6PHE00.0250.0118.995-0.017-0.0170.0000.0000.0000.000
7A7VAL0-0.010-0.01312.0360.0710.0710.0000.0000.0000.000
8A8GLY00.0030.01514.971-0.026-0.0260.0000.0000.0000.000
9A9ALA0-0.015-0.01818.6220.0160.0160.0000.0000.0000.000
10A10GLY0-0.0030.01320.9690.0050.0050.0000.0000.0000.000
11A11PRO0-0.051-0.03624.024-0.008-0.0080.0000.0000.0000.000
12A12GLY00.009-0.00826.927-0.004-0.0040.0000.0000.0000.000
13A13ASP-1-0.863-0.93028.1970.0260.0260.0000.0000.0000.000
14A14LYS11.0071.01126.443-0.024-0.0240.0000.0000.0000.000
15A15GLU-1-0.963-0.99225.4240.0430.0430.0000.0000.0000.000
16A16LEU0-0.056-0.01426.5280.0050.0050.0000.0000.0000.000
17A17ILE0-0.0350.00718.6310.0030.0030.0000.0000.0000.000
18A18THR00.0270.00618.8790.0120.0120.0000.0000.0000.000
19A19LEU00.0470.02119.3530.0050.0050.0000.0000.0000.000
20A20LYS10.9450.95913.033-0.334-0.3340.0000.0000.0000.000
21A21GLY00.0670.02515.4280.0180.0180.0000.0000.0000.000
22A22TYR00.0710.04216.848-0.004-0.0040.0000.0000.0000.000
23A23LYS10.9230.97014.878-0.162-0.1620.0000.0000.0000.000
24A24LEU0-0.0100.01410.3200.0020.0020.0000.0000.0000.000
25A25LEU00.026-0.00613.911-0.017-0.0170.0000.0000.0000.000
26A26SER0-0.038-0.01616.276-0.006-0.0060.0000.0000.0000.000
27A27ASN0-0.101-0.07113.600-0.010-0.0100.0000.0000.0000.000
28A28ALA0-0.0150.01812.6840.0110.0110.0000.0000.0000.000
29A29ASP-1-0.787-0.86811.8830.1570.1570.0000.0000.0000.000
30A30VAL0-0.020-0.00811.299-0.005-0.0050.0000.0000.0000.000
31A31VAL00.0210.01012.597-0.020-0.0200.0000.0000.0000.000
32A32ILE00.0130.01512.2240.0010.0010.0000.0000.0000.000
33A33TYR00.0440.01915.932-0.005-0.0050.0000.0000.0000.000
34A34ALA00.0360.01719.033-0.006-0.0060.0000.0000.0000.000
35A35GLY00.015-0.00621.6470.0080.0080.0000.0000.0000.000
36A36SER0-0.060-0.03524.5500.0040.0040.0000.0000.0000.000
37A37LEU0-0.030-0.02324.4350.0040.0040.0000.0000.0000.000
38A38VAL0-0.0060.00921.2620.0030.0030.0000.0000.0000.000
39A39ASN0-0.023-0.02224.576-0.003-0.0030.0000.0000.0000.000
40A40PRO00.011-0.00625.2850.0020.0020.0000.0000.0000.000
41A41GLU-1-0.844-0.91725.7430.0180.0180.0000.0000.0000.000
42A42LEU0-0.022-0.00721.6680.0040.0040.0000.0000.0000.000
43A43LEU0-0.040-0.03320.6650.0050.0050.0000.0000.0000.000
44A44GLU-1-0.937-0.96422.7180.0240.0240.0000.0000.0000.000
45A45TYR0-0.077-0.05321.4910.0050.0050.0000.0000.0000.000
46A46CYS0-0.060-0.02119.3620.0070.0070.0000.0000.0000.000
47A47LYS10.8570.91814.948-0.103-0.1030.0000.0000.0000.000
48A48GLU-1-0.960-0.97720.5720.0360.0360.0000.0000.0000.000
49A49ASP-1-0.929-0.95420.5050.0470.0470.0000.0000.0000.000
50A50CYS0-0.115-0.05016.3430.0040.0040.0000.0000.0000.000
51A51GLN0-0.028-0.01715.949-0.013-0.0130.0000.0000.0000.000
52A52ILE00.0140.00216.507-0.013-0.0130.0000.0000.0000.000
53A53HIS00.0560.02515.628-0.008-0.0080.0000.0000.0000.000
54A54ASN00.0320.02018.794-0.010-0.0100.0000.0000.0000.000
55A55SER00.024-0.01618.2380.0000.0000.0000.0000.0000.000
56A56ALA0-0.054-0.03320.024-0.002-0.0020.0000.0000.0000.000
57A57HIS0-0.099-0.04923.0310.0020.0020.0000.0000.0000.000
58A58MET00.0090.04516.7870.0020.0020.0000.0000.0000.000
59A59ASP-1-0.890-0.94020.399-0.107-0.1070.0000.0000.0000.000
60A60LEU0-0.005-0.02015.435-0.006-0.0060.0000.0000.0000.000
61A61GLN0-0.021-0.02314.788-0.033-0.0330.0000.0000.0000.000
62A62GLU-1-0.843-0.92015.712-0.094-0.0940.0000.0000.0000.000
63A63ILE0-0.015-0.01413.147-0.004-0.0040.0000.0000.0000.000
64A64ILE0-0.006-0.00910.566-0.036-0.0360.0000.0000.0000.000
65A65ASP-1-0.877-0.93910.676-0.226-0.2260.0000.0000.0000.000
66A66VAL00.0080.01811.8550.0150.0150.0000.0000.0000.000
67A67MET0-0.080-0.0448.001-0.003-0.0030.0000.0000.0000.000
68A68ARG10.8940.9636.9550.1100.1100.0000.0000.0000.000
69A69GLU-1-0.882-0.9437.6450.1280.1280.0000.0000.0000.000
70A70GLY0-0.0300.0068.7820.1300.1300.0000.0000.0000.000
71A71ILE0-0.026-0.0262.433-0.724-0.0600.531-0.201-0.994-0.002
72A72GLU-1-0.914-0.9625.4280.8770.8770.0000.0000.0000.000
73A73ASN0-0.096-0.0537.8730.0290.0290.0000.0000.0000.000
74A74ASN0-0.116-0.0616.6860.5040.5040.0000.0000.0000.000
75A75LYS10.9530.9908.069-0.302-0.3020.0000.0000.0000.000
76A76SER0-0.053-0.0267.792-0.036-0.0360.0000.0000.0000.000
77A77VAL00.0310.0237.431-0.015-0.0150.0000.0000.0000.000
78A78VAL00.002-0.0088.965-0.024-0.0240.0000.0000.0000.000
79A79ARG10.8340.93711.7160.1370.1370.0000.0000.0000.000
80A80LEU00.013-0.00613.5520.0190.0190.0000.0000.0000.000
81A81GLN0-0.028-0.03216.627-0.031-0.0310.0000.0000.0000.000
82A82THR00.0170.00018.9480.0160.0160.0000.0000.0000.000
83A83GLY0-0.0090.00922.201-0.005-0.0050.0000.0000.0000.000
84A84ASP-1-0.861-0.94119.7280.0220.0220.0000.0000.0000.000
85A85PHE00.029-0.00615.818-0.014-0.0140.0000.0000.0000.000
86A86SER0-0.055-0.03720.067-0.017-0.0170.0000.0000.0000.000
87A87ILE0-0.031-0.01021.488-0.003-0.0030.0000.0000.0000.000
88A88TYR0-0.049-0.03024.8420.0020.0020.0000.0000.0000.000
89A89GLY00.0620.04220.7720.0020.0020.0000.0000.0000.000
90A90SER0-0.020-0.02719.778-0.006-0.0060.0000.0000.0000.000
91A91ILE00.0390.03014.232-0.012-0.0120.0000.0000.0000.000
92A92ARG10.9140.95915.2390.1040.1040.0000.0000.0000.000
93A93GLU-1-0.896-0.94115.659-0.175-0.1750.0000.0000.0000.000
94A94GLN00.0630.02512.644-0.028-0.0280.0000.0000.0000.000
95A95VAL0-0.0310.00011.063-0.078-0.0780.0000.0000.0000.000
96A96GLU-1-0.906-0.96011.102-0.317-0.3170.0000.0000.0000.000
97A97ASP-1-0.904-0.96912.495-0.337-0.3370.0000.0000.0000.000
98A98LEU00.000-0.0126.843-0.013-0.0130.0000.0000.0000.000
99A99ASN0-0.0170.0007.883-0.280-0.2800.0000.0000.0000.000
100A100LYS10.9230.9759.7110.2420.2420.0000.0000.0000.000
101A101LEU0-0.059-0.0248.5160.0670.0670.0000.0000.0000.000
102A102ASN0-0.069-0.0246.7490.0090.0090.0000.0000.0000.000
103A103ILE0-0.011-0.0012.825-1.070-0.3550.152-0.183-0.684-0.001
104A104ASP-1-0.864-0.9371.951-10.205-9.51111.164-4.511-7.347-0.048
105A105TYR0-0.022-0.0333.2310.1360.0710.0370.524-0.496-0.002
106A106ASP-1-0.868-0.9275.7051.3521.3520.0000.0000.0000.000
107A107CYS00.0030.0068.770-0.138-0.1380.0000.0000.0000.000
108A108THR0-0.042-0.01912.3120.0940.0940.0000.0000.0000.000
109A109PRO00.0320.01814.838-0.029-0.0290.0000.0000.0000.000
110A110GLY00.0290.00918.4830.0140.0140.0000.0000.0000.000
111A111VAL00.0120.00721.325-0.004-0.0040.0000.0000.0000.000
112A112SER00.0850.02925.138-0.008-0.0080.0000.0000.0000.000
113A113SER00.0740.02826.6180.0030.0030.0000.0000.0000.000
114A114PHE00.0100.00528.4100.0020.0020.0000.0000.0000.000
115A115LEU00.0050.01427.4790.0010.0010.0000.0000.0000.000
116A116GLY00.0400.02230.4320.0020.0020.0000.0000.0000.000
117A117ALA0-0.009-0.01931.7980.0000.0000.0000.0000.0000.000
118A118ALA0-0.014-0.00334.6180.0000.0000.0000.0000.0000.000
119A119SER00.007-0.00233.5070.0010.0010.0000.0000.0000.000
120A120SER0-0.068-0.03235.7040.0000.0000.0000.0000.0000.000
121A121LEU0-0.057-0.04737.337-0.001-0.0010.0000.0000.0000.000
122A122GLY0-0.0210.01339.1540.0000.0000.0000.0000.0000.000
123A123VAL0-0.074-0.03239.126-0.001-0.0010.0000.0000.0000.000
124A124GLU-1-0.906-0.96038.4550.0170.0170.0000.0000.0000.000
125A125TYR0-0.056-0.05934.416-0.003-0.0030.0000.0000.0000.000
126A126THR0-0.041-0.00737.342-0.001-0.0010.0000.0000.0000.000
127A127VAL00.0870.04439.9460.0020.0020.0000.0000.0000.000
128A128PRO00.034-0.00142.987-0.001-0.0010.0000.0000.0000.000
129A129GLU-1-0.954-0.97745.5400.0040.0040.0000.0000.0000.000
130A130ILE0-0.064-0.00545.691-0.001-0.0010.0000.0000.0000.000
131A131SER0-0.065-0.05542.006-0.001-0.0010.0000.0000.0000.000
132A132GLN00.0400.02040.7000.0010.0010.0000.0000.0000.000
133A133SER0-0.038-0.02337.8700.0000.0000.0000.0000.0000.000
134A134VAL00.0210.00634.8640.0000.0000.0000.0000.0000.000
135A135ILE0-0.0450.00035.550-0.001-0.0010.0000.0000.0000.000
136A136ILE00.0190.01130.7740.0010.0010.0000.0000.0000.000
137A137THR0-0.006-0.01133.095-0.003-0.0030.0000.0000.0000.000
138A138ARG10.9230.96427.8530.0440.0440.0000.0000.0000.000
139A139MET0-0.0300.01334.416-0.001-0.0010.0000.0000.0000.000
140A140GLU-1-0.856-0.94331.957-0.039-0.0390.0000.0000.0000.000
141A141GLY0-0.001-0.00536.4700.0020.0020.0000.0000.0000.000
142A142ARG10.7660.86939.0900.0210.0210.0000.0000.0000.000
143A143THR0-0.014-0.00937.004-0.002-0.0020.0000.0000.0000.000
144A144PRO00.0130.02138.2080.0010.0010.0000.0000.0000.000
145A145VAL00.0350.01436.577-0.002-0.0020.0000.0000.0000.000
146A146PRO00.0350.02936.6640.0020.0020.0000.0000.0000.000
147A147GLU-1-0.849-0.94339.722-0.020-0.0200.0000.0000.0000.000
148A148LYS10.8820.94138.8320.0270.0270.0000.0000.0000.000
149A149GLU-1-0.933-0.97433.881-0.034-0.0340.0000.0000.0000.000
150A150SER0-0.0590.00438.1320.0000.0000.0000.0000.0000.000
151A151ILE00.0520.00638.8570.0010.0010.0000.0000.0000.000
152A152GLN00.1070.05741.5390.0010.0010.0000.0000.0000.000
153A153SER0-0.075-0.02741.6840.0020.0020.0000.0000.0000.000
154A154TYR00.0390.00435.9880.0010.0010.0000.0000.0000.000
155A155ALA00.019-0.00141.7830.0010.0010.0000.0000.0000.000
156A156LYS10.9690.99444.6330.0130.0130.0000.0000.0000.000
157A157HIS0-0.048-0.01241.9900.0010.0010.0000.0000.0000.000
158A158GLN0-0.077-0.04545.1730.0020.0020.0000.0000.0000.000
159A159THR00.0650.05240.5060.0020.0020.0000.0000.0000.000
160A160SER0-0.046-0.01139.451-0.001-0.0010.0000.0000.0000.000
161A161MET0-0.052-0.01438.356-0.001-0.0010.0000.0000.0000.000
162A162VAL0-0.0030.00233.5660.0010.0010.0000.0000.0000.000
163A163ILE0-0.002-0.00635.543-0.002-0.0020.0000.0000.0000.000
164A164PHE00.0110.00729.8570.0010.0010.0000.0000.0000.000
165A165LEU0-0.0010.00634.330-0.002-0.0020.0000.0000.0000.000
166A166SER00.0750.00336.1140.0000.0000.0000.0000.0000.000
167A167VAL00.0240.03137.8140.0000.0000.0000.0000.0000.000
168A168GLN00.0400.02040.992-0.001-0.0010.0000.0000.0000.000
169A169GLU-1-0.883-0.96040.397-0.020-0.0200.0000.0000.0000.000
170A170ILE00.0260.00843.1200.0000.0000.0000.0000.0000.000
171A171GLU-1-0.911-0.95844.585-0.009-0.0090.0000.0000.0000.000
172A172LYS10.9530.97844.2700.0170.0170.0000.0000.0000.000
173A173VAL0-0.005-0.00341.8100.0000.0000.0000.0000.0000.000
174A174VAL00.0390.02444.2610.0000.0000.0000.0000.0000.000
175A175SER0-0.057-0.02747.1910.0000.0000.0000.0000.0000.000
176A176LYS10.9310.95042.7240.0190.0190.0000.0000.0000.000
177A177LEU0-0.0060.00043.0550.0000.0000.0000.0000.0000.000
178A178LEU0-0.023-0.00946.7650.0010.0010.0000.0000.0000.000
179A179GLU-1-0.950-0.96049.136-0.013-0.0130.0000.0000.0000.000
180A180GLY0-0.073-0.04147.6060.0000.0000.0000.0000.0000.000
181A181GLY0-0.020-0.01348.6830.0000.0000.0000.0000.0000.000
182A182TYR0-0.079-0.04243.6630.0000.0000.0000.0000.0000.000
183A183PRO00.1050.06549.9260.0000.0000.0000.0000.0000.000
184A184LYS10.9621.03151.9020.0060.0060.0000.0000.0000.000
185A185ASP-1-0.875-0.94253.081-0.002-0.0020.0000.0000.0000.000
186A186THR0-0.113-0.13147.6220.0010.0010.0000.0000.0000.000
187A187PRO0-0.017-0.00447.0540.0000.0000.0000.0000.0000.000
188A188ILE00.006-0.00743.6030.0000.0000.0000.0000.0000.000
189A189ALA0-0.048-0.01841.9920.0010.0010.0000.0000.0000.000
190A190VAL00.0140.02340.477-0.001-0.0010.0000.0000.0000.000
191A191ILE00.0300.01436.6930.0010.0010.0000.0000.0000.000
192A192TYR0-0.016-0.02236.609-0.002-0.0020.0000.0000.0000.000
193A193LYS10.9460.98131.5500.0080.0080.0000.0000.0000.000
194A194ALA00.0450.02232.6280.0020.0020.0000.0000.0000.000
195A195THR0-0.007-0.01030.9380.0010.0010.0000.0000.0000.000
196A196TRP0-0.0040.02728.1680.0010.0010.0000.0000.0000.000
197A197ALA00.0490.01633.1640.0000.0000.0000.0000.0000.000
198A198ASP-1-0.949-0.98235.4180.0000.0000.0000.0000.0000.000
199A199GLU-1-0.896-0.91336.2350.0070.0070.0000.0000.0000.000
200A200LYS10.9350.96437.5790.0000.0000.0000.0000.0000.000
201A201ILE00.0210.00840.154-0.001-0.0010.0000.0000.0000.000
202A202VAL0-0.035-0.01342.3250.0000.0000.0000.0000.0000.000
203A203LYS10.9940.98744.557-0.003-0.0030.0000.0000.0000.000
204A204GLY0-0.069-0.04346.7290.0000.0000.0000.0000.0000.000
205A205THR0-0.0170.00248.9470.0000.0000.0000.0000.0000.000
206A206LEU00.0690.01846.768-0.001-0.0010.0000.0000.0000.000
207A207SER0-0.076-0.07050.147-0.001-0.0010.0000.0000.0000.000
208A208ASP-1-0.869-0.90951.562-0.003-0.0030.0000.0000.0000.000
209A209ILE00.0470.03745.6640.0000.0000.0000.0000.0000.000
210A210ALA00.0380.01948.3000.0000.0000.0000.0000.0000.000
211A211VAL00.014-0.01149.3900.0000.0000.0000.0000.0000.000
212A212LYS10.9750.99849.2500.0010.0010.0000.0000.0000.000
213A213VAL00.0020.00444.5070.0000.0000.0000.0000.0000.000
214A214LYS10.9440.97446.8680.0070.0070.0000.0000.0000.000
215A215GLU-1-0.988-0.99849.001-0.003-0.0030.0000.0000.0000.000
216A216ASN00.0060.01145.8180.0010.0010.0000.0000.0000.000
217A217ASN0-0.081-0.01346.0570.0000.0000.0000.0000.0000.000
218A218ILE0-0.028-0.02240.697-0.001-0.0010.0000.0000.0000.000
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