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: 5JM9Z

Calculation Name: 3ME0-A-Xray372

Preferred Name: Chaperone protein PapD

Target Type: SINGLE PROTEIN

Ligand Name:
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ligand 3-letter code:
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PDB ID: 3ME0

Chain ID: A

ChEMBL ID: CHEMBL3309037

UniProt ID: P15319

Base Structure: X-ray

Registration Date: 2023-09-24

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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2433072.66823
FMO2-HF: Nuclear repulsion 2348339.096606
FMO2-HF: Total energy -84733.571624
FMO2-MP2: Total energy -84982.667036


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:ALA)


Summations of interaction energy for fragment #1(A:1: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.
-21.831-18.1816.307-9.151-10.807-0.073
Interaction energy analysis for fragmet #1(A:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.013
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].
3A3SER0-0.055-0.0293.787-0.6211.184-0.021-0.902-0.8820.002
4A4LEU0-0.010-0.0185.4130.4040.4040.0000.0000.0000.000
5A5ASP-1-0.732-0.8448.964-0.652-0.6520.0000.0000.0000.000
6A6ARG10.8080.89512.0150.7200.7200.0000.0000.0000.000
7A7THR00.0270.01112.689-0.062-0.0620.0000.0000.0000.000
8A8ARG10.8790.94114.6120.3110.3110.0000.0000.0000.000
9A9ALA00.0220.00717.395-0.020-0.0200.0000.0000.0000.000
10A10VAL00.0020.01219.0350.0230.0230.0000.0000.0000.000
11A11PHE0-0.020-0.03022.751-0.016-0.0160.0000.0000.0000.000
12A12ASP-1-0.764-0.85424.402-0.175-0.1750.0000.0000.0000.000
13A13GLY00.002-0.01027.635-0.006-0.0060.0000.0000.0000.000
14A14SER0-0.097-0.08630.1380.0130.0130.0000.0000.0000.000
15A15GLU-1-0.956-0.95427.733-0.198-0.1980.0000.0000.0000.000
16A16LYS10.9620.97928.3770.2110.2110.0000.0000.0000.000
17A17SER0-0.083-0.07124.231-0.015-0.0150.0000.0000.0000.000
18A18MET00.0260.04419.6150.0190.0190.0000.0000.0000.000
19A19THR0-0.006-0.02218.3840.0020.0020.0000.0000.0000.000
20A20LEU0-0.056-0.01814.1890.0380.0380.0000.0000.0000.000
21A21ASP-1-0.852-0.92013.364-0.666-0.6660.0000.0000.0000.000
22A22ILE0-0.071-0.0478.757-0.124-0.1240.0000.0000.0000.000
23A23SER0-0.071-0.0717.0730.5060.5060.0000.0000.0000.000
24A24ASN00.0010.0033.073-2.262-1.4800.119-0.397-0.504-0.004
25A25ASP-1-0.813-0.8573.319-1.491-0.7450.022-0.362-0.4050.001
26A26ASN0-0.023-0.0112.426-0.776-0.0510.874-0.556-1.0420.002
27A27LYS10.9640.9674.132-0.724-0.6740.001-0.022-0.0290.000
28A28GLN00.0000.0016.854-0.287-0.2870.0000.0000.0000.000
29A29LEU0-0.047-0.0245.557-0.152-0.1520.0000.0000.0000.000
30A30PRO00.0030.0225.624-0.074-0.0740.0000.0000.0000.000
31A31TYR00.0290.0002.921-1.402-0.1303.109-1.253-3.129-0.007
32A32LEU0-0.022-0.0105.8940.0020.0020.0000.0000.0000.000
33A33ALA00.0400.0166.776-0.452-0.4520.0000.0000.0000.000
34A34GLN0-0.026-0.0128.5330.2700.2700.0000.0000.0000.000
35A35ALA00.0560.02811.223-0.144-0.1440.0000.0000.0000.000
36A36TRP0-0.129-0.06712.4460.0870.0870.0000.0000.0000.000
37A37ILE00.0140.00716.636-0.044-0.0440.0000.0000.0000.000
38A38GLU-1-0.823-0.91118.088-0.362-0.3620.0000.0000.0000.000
39A39ASN00.008-0.00721.169-0.015-0.0150.0000.0000.0000.000
40A40GLU-1-0.908-0.97323.708-0.173-0.1730.0000.0000.0000.000
41A41ASN0-0.028-0.00925.7310.0090.0090.0000.0000.0000.000
42A42GLN0-0.053-0.03720.753-0.006-0.0060.0000.0000.0000.000
43A43GLU-1-0.832-0.88622.468-0.176-0.1760.0000.0000.0000.000
44A44LYS10.9170.96018.0110.3750.3750.0000.0000.0000.000
45A45ILE0-0.013-0.00222.1630.0250.0250.0000.0000.0000.000
46A46ILE0-0.033-0.02821.486-0.031-0.0310.0000.0000.0000.000
47A47THR00.014-0.00324.138-0.006-0.0060.0000.0000.0000.000
48A48GLY00.0020.02126.1250.0130.0130.0000.0000.0000.000
49A49PRO00.0000.00527.3250.0020.0020.0000.0000.0000.000
50A50VAL00.0410.01022.372-0.001-0.0010.0000.0000.0000.000
51A51ILE0-0.032-0.00222.520-0.008-0.0080.0000.0000.0000.000
52A52ALA00.0260.00217.371-0.011-0.0110.0000.0000.0000.000
53A53THR0-0.077-0.00518.7320.0190.0190.0000.0000.0000.000
54A54PRO00.0490.00415.059-0.010-0.0100.0000.0000.0000.000
55A55PRO00.0450.00815.575-0.069-0.0690.0000.0000.0000.000
56A56VAL0-0.010-0.00811.900-0.080-0.0800.0000.0000.0000.000
57A57GLN00.0230.03611.0580.1360.1360.0000.0000.0000.000
58A58ARG10.8540.89910.0750.1080.1080.0000.0000.0000.000
59A59LEU0-0.0180.0066.6940.0650.0650.0000.0000.0000.000
60A60GLU-1-0.735-0.8647.597-0.237-0.2370.0000.0000.0000.000
61A61PRO00.0110.0046.784-0.179-0.1790.0000.0000.0000.000
62A62GLY0-0.061-0.0196.5060.0400.0400.0000.0000.0000.000
63A63ALA0-0.0180.0048.223-0.032-0.0320.0000.0000.0000.000
64A64LYS10.9580.9788.5550.4240.4240.0000.0000.0000.000
65A65SER00.008-0.01311.0700.1570.1570.0000.0000.0000.000
66A66MET00.0010.00112.788-0.003-0.0030.0000.0000.0000.000
67A67VAL0-0.043-0.00913.014-0.011-0.0110.0000.0000.0000.000
68A68ARG10.9470.98115.7500.4150.4150.0000.0000.0000.000
69A69LEU0-0.016-0.01017.725-0.002-0.0020.0000.0000.0000.000
70A70SER0-0.009-0.01721.1600.0310.0310.0000.0000.0000.000
71A71THR00.0360.02124.888-0.008-0.0080.0000.0000.0000.000
72A72THR00.0060.00827.7870.0050.0050.0000.0000.0000.000
73A73PRO00.0850.02730.3340.0010.0010.0000.0000.0000.000
74A74ASP-1-0.890-0.94932.629-0.146-0.1460.0000.0000.0000.000
75A75ILE0-0.052-0.02228.5160.0020.0020.0000.0000.0000.000
76A76SER0-0.056-0.02732.0810.0060.0060.0000.0000.0000.000
77A77LYS10.9330.96535.1190.1350.1350.0000.0000.0000.000
78A78LEU0-0.048-0.00529.4180.0030.0030.0000.0000.0000.000
79A79PRO00.0200.01133.3370.0060.0060.0000.0000.0000.000
80A80GLN00.003-0.01834.216-0.010-0.0100.0000.0000.0000.000
81A81ASP-1-0.859-0.92436.294-0.111-0.1110.0000.0000.0000.000
82A82ARG10.8720.92031.1850.1440.1440.0000.0000.0000.000
83A83GLU-1-0.752-0.86427.525-0.201-0.2010.0000.0000.0000.000
84A84SER0-0.043-0.02328.7320.0150.0150.0000.0000.0000.000
85A85LEU0-0.024-0.00122.710-0.014-0.0140.0000.0000.0000.000
86A86PHE00.0070.00122.2240.0100.0100.0000.0000.0000.000
87A87TYR0-0.016-0.01317.975-0.004-0.0040.0000.0000.0000.000
88A88PHE00.0210.01012.1150.0150.0150.0000.0000.0000.000
89A89ASN0-0.0020.00513.204-0.020-0.0200.0000.0000.0000.000
90A90LEU00.0500.0217.4460.0680.0680.0000.0000.0000.000
91A91ARG10.8880.9347.9680.5910.5910.0000.0000.0000.000
92A92GLU-1-0.772-0.8521.868-15.335-17.62711.605-5.281-4.032-0.067
93A93ILE0-0.029-0.0335.9590.5790.5790.0000.0000.0000.000
94A94PRO0-0.0010.0155.274-0.069-0.0690.0000.0000.0000.000
95A95PRO00.025-0.0056.3510.0180.0180.0000.0000.0000.000
96A96ARG10.8571.0899.460-0.358-0.3580.0000.0000.0000.000
97A97SER00.069-0.09311.185-0.034-0.0340.0000.0000.0000.000
98A98GLU-1-0.896-0.98612.6770.1410.1410.0000.0000.0000.000
99A99LYS10.9000.96714.278-0.508-0.5080.0000.0000.0000.000
100A100ALA00.0580.03016.698-0.007-0.0070.0000.0000.0000.000
101A101ASN0-0.049-0.02618.8150.0120.0120.0000.0000.0000.000
102A102VAL0-0.0010.00413.8430.0440.0440.0000.0000.0000.000
103A103LEU00.0340.02313.641-0.063-0.0630.0000.0000.0000.000
104A104GLN0-0.043-0.0298.3650.0790.0790.0000.0000.0000.000
105A105ILE00.011-0.0017.920-0.150-0.1500.0000.0000.0000.000
106A106ALA0-0.036-0.0035.9710.3170.3170.0000.0000.0000.000
107A107LEU00.0060.0032.617-0.2160.3470.598-0.378-0.7840.000
108A108GLN00.022-0.0125.604-0.578-0.5780.0000.0000.0000.000
109A109THR0-0.012-0.0047.3760.2650.2650.0000.0000.0000.000
110A110LYS10.8170.9129.8980.3950.3950.0000.0000.0000.000
111A111ILE0-0.0210.00612.6670.0700.0700.0000.0000.0000.000
112A112LYS10.8920.93715.3710.2340.2340.0000.0000.0000.000
113A113LEU00.0150.00818.690-0.033-0.0330.0000.0000.0000.000
114A114PHE00.015-0.00820.5280.0220.0220.0000.0000.0000.000
115A115TYR00.0090.01524.041-0.012-0.0120.0000.0000.0000.000
116A116ARG10.8080.86626.3890.2140.2140.0000.0000.0000.000
117A117PRO00.0020.01128.960-0.004-0.0040.0000.0000.0000.000
118A118ALA00.0650.03532.2030.0040.0040.0000.0000.0000.000
119A119ALA0-0.027-0.01633.9320.0040.0040.0000.0000.0000.000
120A120ILE0-0.0280.01031.8040.0060.0060.0000.0000.0000.000
121A121LYS10.9430.99830.6630.1660.1660.0000.0000.0000.000
122A122THR00.0110.02229.1380.0040.0040.0000.0000.0000.000
123A123ARG10.9060.94531.3470.0990.0990.0000.0000.0000.000
124A124PRO00.0400.00628.767-0.004-0.0040.0000.0000.0000.000
125A125ASN0-0.053-0.03727.6300.0030.0030.0000.0000.0000.000
126A126GLU-1-0.897-0.92529.539-0.110-0.1100.0000.0000.0000.000
127A127VAL0-0.033-0.01630.515-0.007-0.0070.0000.0000.0000.000
128A128TRP00.0370.01927.8760.0080.0080.0000.0000.0000.000
129A129GLN00.0330.00527.8080.0120.0120.0000.0000.0000.000
130A130ASP-1-0.920-0.96732.597-0.075-0.0750.0000.0000.0000.000
131A131GLN0-0.017-0.02035.7440.0060.0060.0000.0000.0000.000
132A132LEU0-0.055-0.01131.9400.0020.0020.0000.0000.0000.000
133A133ILE00.0090.01836.5370.0060.0060.0000.0000.0000.000
134A134LEU0-0.042-0.01535.863-0.002-0.0020.0000.0000.0000.000
135A135ASN0-0.103-0.07239.6490.0060.0060.0000.0000.0000.000
136A136LYS10.8410.90941.4720.0250.0250.0000.0000.0000.000
137A137VAL0-0.0060.01040.6480.0000.0000.0000.0000.0000.000
138A138SER00.0200.00142.8750.0020.0020.0000.0000.0000.000
139A139GLY00.0040.00241.114-0.001-0.0010.0000.0000.0000.000
140A140GLY0-0.0010.00038.3650.0000.0000.0000.0000.0000.000
141A141TYR00.0200.00137.1350.0030.0030.0000.0000.0000.000
142A142ARG10.9470.99037.4590.0480.0480.0000.0000.0000.000
143A143ILE00.000-0.00333.0480.0020.0020.0000.0000.0000.000
144A144GLU-1-0.809-0.88836.444-0.062-0.0620.0000.0000.0000.000
145A145ASN00.005-0.02332.2100.0040.0040.0000.0000.0000.000
146A146PRO00.0300.03135.659-0.003-0.0030.0000.0000.0000.000
147A147THR0-0.049-0.02033.442-0.005-0.0050.0000.0000.0000.000
148A148PRO00.0190.00134.2950.0000.0000.0000.0000.0000.000
149A149TYR0-0.013-0.05129.348-0.006-0.0060.0000.0000.0000.000
150A150TYR00.0460.00326.6460.0090.0090.0000.0000.0000.000
151A151VAL0-0.0130.00327.706-0.006-0.0060.0000.0000.0000.000
152A152THR0-0.071-0.04122.730-0.005-0.0050.0000.0000.0000.000
153A153VAL00.0240.00525.9990.0000.0000.0000.0000.0000.000
154A154ILE0-0.048-0.04622.320-0.004-0.0040.0000.0000.0000.000
155A155GLY00.0900.06025.7470.0100.0100.0000.0000.0000.000
156A156LEU0-0.020-0.01828.582-0.006-0.0060.0000.0000.0000.000
157A157GLY00.0250.01132.3180.0060.0060.0000.0000.0000.000
158A158GLY0-0.020-0.01834.507-0.004-0.0040.0000.0000.0000.000
159A159SER0-0.017-0.01935.5820.0010.0010.0000.0000.0000.000
160A160GLU-1-0.883-0.94532.162-0.028-0.0280.0000.0000.0000.000
161A161LYS11.0101.00130.892-0.030-0.0300.0000.0000.0000.000
162A162GLN0-0.015-0.00430.4840.0020.0020.0000.0000.0000.000
163A163ALA0-0.049-0.02330.756-0.001-0.0010.0000.0000.0000.000
164A164GLU-1-0.962-0.98126.806-0.032-0.0320.0000.0000.0000.000
165A165GLU-1-0.933-0.97425.9310.0270.0270.0000.0000.0000.000
166A166GLY0-0.077-0.02327.5140.0090.0090.0000.0000.0000.000
167A167GLU-1-0.953-0.96826.0580.0050.0050.0000.0000.0000.000
168A168PHE0-0.059-0.04727.155-0.004-0.0040.0000.0000.0000.000
169A169GLU-1-0.941-0.95426.373-0.048-0.0480.0000.0000.0000.000
170A170THR0-0.063-0.04322.857-0.012-0.0120.0000.0000.0000.000
171A171VAL00.0350.03125.675-0.002-0.0020.0000.0000.0000.000
172A172MET0-0.064-0.01323.965-0.014-0.0140.0000.0000.0000.000
173A173LEU00.0250.02927.2100.0000.0000.0000.0000.0000.000
174A174SER00.0440.01930.027-0.014-0.0140.0000.0000.0000.000
175A175PRO0-0.0490.02230.3110.0100.0100.0000.0000.0000.000
176A176ARG10.8530.94233.3540.1070.1070.0000.0000.0000.000
177A177SER0-0.047-0.05533.9050.0020.0020.0000.0000.0000.000
178A178GLU-1-0.868-0.94836.447-0.059-0.0590.0000.0000.0000.000
179A179GLN00.0200.00930.726-0.005-0.0050.0000.0000.0000.000
180A180THR0-0.024-0.02435.4760.0020.0020.0000.0000.0000.000
181A181VAL0-0.0080.01332.095-0.001-0.0010.0000.0000.0000.000
182A182LYS10.9640.98034.1010.0350.0350.0000.0000.0000.000
183A183SER00.000-0.02734.385-0.001-0.0010.0000.0000.0000.000
184A184ALA00.0310.03636.6340.0010.0010.0000.0000.0000.000
185A185ASN00.006-0.00239.056-0.007-0.0070.0000.0000.0000.000
186A186TYR00.0130.00935.9730.0030.0030.0000.0000.0000.000
187A187ASN0-0.021-0.02141.282-0.003-0.0030.0000.0000.0000.000
188A188THR00.010-0.00440.697-0.001-0.0010.0000.0000.0000.000
189A189PRO0-0.0190.00637.9870.0010.0010.0000.0000.0000.000
190A190TYR0-0.0100.01034.046-0.002-0.0020.0000.0000.0000.000
191A191LEU00.0170.01430.9010.0010.0010.0000.0000.0000.000
192A192SER00.0280.02626.971-0.003-0.0030.0000.0000.0000.000
193A193TYR00.0330.00026.839-0.005-0.0050.0000.0000.0000.000
194A194ILE0-0.059-0.01820.307-0.003-0.0030.0000.0000.0000.000
195A195ASN00.0470.01623.423-0.021-0.0210.0000.0000.0000.000
196A196ASP-1-0.750-0.88222.342-0.223-0.2230.0000.0000.0000.000
197A197TYR0-0.047-0.01919.581-0.036-0.0360.0000.0000.0000.000
198A198GLY0-0.015-0.00618.558-0.029-0.0290.0000.0000.0000.000
199A199GLY0-0.0050.00319.5490.0130.0130.0000.0000.0000.000
200A200ARG10.9330.94819.2230.1010.1010.0000.0000.0000.000
201A201PRO00.0230.03424.5670.0130.0130.0000.0000.0000.000
202A202VAL00.0440.01828.072-0.002-0.0020.0000.0000.0000.000
203A203LEU0-0.026-0.00430.8920.0000.0000.0000.0000.0000.000
204A204SER00.0050.00234.1310.0050.0050.0000.0000.0000.000
205A205PHE0-0.007-0.01235.014-0.002-0.0020.0000.0000.0000.000
206A206ILE0-0.017-0.01539.8020.0040.0040.0000.0000.0000.000
207A207CYS0-0.043-0.01640.9680.0000.0000.0000.0000.0000.000
208A208ASN00.0170.00445.4250.0030.0030.0000.0000.0000.000
209A209GLY00.0220.01648.789-0.002-0.0020.0000.0000.0000.000
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