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: YVL62

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 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 -2433822.64224
FMO2-HF: Nuclear repulsion 2349087.532037
FMO2-HF: Total energy -84735.110203
FMO2-MP2: Total energy -84984.100223


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.
-18.977-17.420.856-10.019-12.414-0.076
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 : -0.019 / q_NPA : -0.011
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].
3A3SER0-0.050-0.0223.787-0.5381.240-0.020-0.876-0.8820.002
4A4LEU0-0.006-0.0165.4360.3630.3630.0000.0000.0000.000
5A5ASP-1-0.739-0.8298.991-0.616-0.6160.0000.0000.0000.000
6A6ARG10.8080.88012.0330.7020.7020.0000.0000.0000.000
7A7THR00.0360.01512.709-0.054-0.0540.0000.0000.0000.000
8A8ARG10.8620.92914.6280.2990.2990.0000.0000.0000.000
9A9ALA00.0130.00317.356-0.021-0.0210.0000.0000.0000.000
10A10VAL00.0030.01519.0630.0230.0230.0000.0000.0000.000
11A11PHE0-0.012-0.02522.780-0.015-0.0150.0000.0000.0000.000
12A12ASP-1-0.727-0.83524.435-0.169-0.1690.0000.0000.0000.000
13A13GLY0-0.008-0.01627.668-0.006-0.0060.0000.0000.0000.000
14A14SER0-0.085-0.07130.1740.0130.0130.0000.0000.0000.000
15A15GLU-1-0.952-0.95327.831-0.198-0.1980.0000.0000.0000.000
16A16LYS10.9660.97928.5550.2060.2060.0000.0000.0000.000
17A17SER0-0.078-0.06224.259-0.016-0.0160.0000.0000.0000.000
18A18MET00.0240.04019.8560.0170.0170.0000.0000.0000.000
19A19THR0-0.002-0.01618.3720.0030.0030.0000.0000.0000.000
20A20LEU0-0.053-0.02314.3980.0390.0390.0000.0000.0000.000
21A21ASP-1-0.846-0.92113.435-0.672-0.6720.0000.0000.0000.000
22A22ILE0-0.064-0.0458.818-0.127-0.1270.0000.0000.0000.000
23A23SER0-0.037-0.0457.3280.5270.5270.0000.0000.0000.000
24A24ASN0-0.007-0.0033.075-2.421-1.7010.113-0.349-0.484-0.003
25A25ASP-1-0.824-0.8713.517-1.168-0.4430.011-0.352-0.3840.001
26A26ASN0-0.0020.0032.325-0.5440.0291.288-0.688-1.1730.002
27A27LYS10.9330.9484.081-0.681-0.6190.001-0.028-0.0350.000
28A28GLN00.0040.0046.811-0.229-0.2290.0000.0000.0000.000
29A29LEU0-0.035-0.0205.578-0.121-0.1210.0000.0000.0000.000
30A30PRO00.0000.0235.601-0.119-0.1190.0000.0000.0000.000
31A31TYR00.029-0.0032.667-1.066-0.9716.262-2.071-4.286-0.008
32A32LEU0-0.020-0.0105.8700.0210.0210.0000.0000.0000.000
33A33ALA00.0370.0146.803-0.445-0.4450.0000.0000.0000.000
34A34GLN0-0.011-0.0098.5760.3060.3060.0000.0000.0000.000
35A35ALA00.0540.02711.203-0.131-0.1310.0000.0000.0000.000
36A36TRP0-0.119-0.08112.6180.0860.0860.0000.0000.0000.000
37A37ILE00.0200.01316.617-0.040-0.0400.0000.0000.0000.000
38A38GLU-1-0.779-0.86017.819-0.353-0.3530.0000.0000.0000.000
39A39ASN00.014-0.01321.156-0.013-0.0130.0000.0000.0000.000
40A40GLU-1-0.863-0.94823.697-0.164-0.1640.0000.0000.0000.000
41A41ASN0-0.061-0.02925.7230.0110.0110.0000.0000.0000.000
42A42GLN0-0.057-0.04220.496-0.008-0.0080.0000.0000.0000.000
43A43GLU-1-0.797-0.86122.463-0.163-0.1630.0000.0000.0000.000
44A44LYS10.8890.94917.3500.3890.3890.0000.0000.0000.000
45A45ILE0-0.0110.00022.1520.0240.0240.0000.0000.0000.000
46A46ILE0-0.029-0.02921.332-0.030-0.0300.0000.0000.0000.000
47A47THR00.0160.00524.120-0.007-0.0070.0000.0000.0000.000
48A48GLY00.0030.01826.1010.0120.0120.0000.0000.0000.000
49A49PRO0-0.0110.00327.3020.0020.0020.0000.0000.0000.000
50A50VAL00.0430.01022.527-0.001-0.0010.0000.0000.0000.000
51A51ILE0-0.0280.00022.474-0.007-0.0070.0000.0000.0000.000
52A52ALA00.0240.00517.318-0.010-0.0100.0000.0000.0000.000
53A53THR0-0.069-0.00618.7910.0190.0190.0000.0000.0000.000
54A54PRO00.0420.00415.035-0.010-0.0100.0000.0000.0000.000
55A55PRO00.0490.00615.624-0.067-0.0670.0000.0000.0000.000
56A56VAL0-0.020-0.01111.936-0.076-0.0760.0000.0000.0000.000
57A57GLN00.0250.03111.0440.1030.1030.0000.0000.0000.000
58A58ARG10.8380.87710.0760.1560.1560.0000.0000.0000.000
59A59LEU0-0.0210.0066.6920.0590.0590.0000.0000.0000.000
60A60GLU-1-0.709-0.8387.639-0.314-0.3140.0000.0000.0000.000
61A61PRO00.0060.0046.775-0.202-0.2020.0000.0000.0000.000
62A62GLY0-0.042-0.0096.5140.0620.0620.0000.0000.0000.000
63A63ALA0-0.0340.0018.240-0.019-0.0190.0000.0000.0000.000
64A64LYS10.9250.9538.6250.5350.5350.0000.0000.0000.000
65A65SER00.005-0.01711.1470.1640.1640.0000.0000.0000.000
66A66MET00.0030.00412.881-0.001-0.0010.0000.0000.0000.000
67A67VAL0-0.047-0.00713.070-0.006-0.0060.0000.0000.0000.000
68A68ARG10.9500.98115.8080.4090.4090.0000.0000.0000.000
69A69LEU0-0.012-0.00517.731-0.001-0.0010.0000.0000.0000.000
70A70SER0-0.014-0.01821.2030.0300.0300.0000.0000.0000.000
71A71THR00.0400.02224.892-0.007-0.0070.0000.0000.0000.000
72A72THR0-0.0030.00527.7590.0060.0060.0000.0000.0000.000
73A73PRO00.0930.03030.3070.0020.0020.0000.0000.0000.000
74A74ASP-1-0.822-0.89532.839-0.136-0.1360.0000.0000.0000.000
75A75ILE0-0.041-0.01828.5620.0020.0020.0000.0000.0000.000
76A76SER0-0.055-0.03532.0720.0060.0060.0000.0000.0000.000
77A77LYS10.8360.90435.2170.1400.1400.0000.0000.0000.000
78A78LEU0-0.0430.00229.4740.0030.0030.0000.0000.0000.000
79A79PRO00.0240.01833.2990.0060.0060.0000.0000.0000.000
80A80GLN00.003-0.02434.154-0.009-0.0090.0000.0000.0000.000
81A81ASP-1-0.850-0.91036.329-0.104-0.1040.0000.0000.0000.000
82A82ARG10.8600.91331.1240.1380.1380.0000.0000.0000.000
83A83GLU-1-0.753-0.85927.559-0.192-0.1920.0000.0000.0000.000
84A84SER0-0.029-0.00928.7840.0160.0160.0000.0000.0000.000
85A85LEU0-0.030-0.00422.633-0.014-0.0140.0000.0000.0000.000
86A86PHE00.002-0.00422.2530.0090.0090.0000.0000.0000.000
87A87TYR0-0.019-0.01018.006-0.004-0.0040.0000.0000.0000.000
88A88PHE00.0180.00712.1050.0110.0110.0000.0000.0000.000
89A89ASN0-0.026-0.00613.190-0.014-0.0140.0000.0000.0000.000
90A90LEU00.0440.0177.5700.0430.0430.0000.0000.0000.000
91A91ARG10.8610.9277.9270.5590.5590.0000.0000.0000.000
92A92GLU-1-0.759-0.8561.873-13.636-16.36212.124-5.151-4.247-0.070
93A93ILE0-0.030-0.0316.0070.5790.5790.0000.0000.0000.000
94A94PRO0-0.0190.0085.143-0.101-0.1010.0000.0000.0000.000
95A95PRO00.021-0.0066.3290.0530.0530.0000.0000.0000.000
96A96ARG10.9020.9959.408-0.273-0.2730.0000.0000.0000.000
97A97SER00.0660.01811.185-0.045-0.0450.0000.0000.0000.000
98A98GLU-1-0.925-0.98412.6610.1300.1300.0000.0000.0000.000
99A99LYS10.9040.96414.193-0.513-0.5130.0000.0000.0000.000
100A100ALA00.0570.02516.665-0.005-0.0050.0000.0000.0000.000
101A101ASN0-0.045-0.02418.7720.0150.0150.0000.0000.0000.000
102A102VAL0-0.0040.00113.7870.0490.0490.0000.0000.0000.000
103A103LEU00.0280.02513.804-0.062-0.0620.0000.0000.0000.000
104A104GLN0-0.045-0.0388.1870.0980.0980.0000.0000.0000.000
105A105ILE00.0160.0047.816-0.149-0.1490.0000.0000.0000.000
106A106ALA0-0.030-0.0035.9950.3370.3370.0000.0000.0000.000
107A107LEU00.0150.0132.486-0.1480.2021.077-0.504-0.9230.000
108A108GLN00.027-0.0105.618-0.583-0.5830.0000.0000.0000.000
109A109THR0-0.028-0.0077.4660.2470.2470.0000.0000.0000.000
110A110LYS10.8110.8829.9280.3510.3510.0000.0000.0000.000
111A111ILE0-0.0200.01012.7280.0670.0670.0000.0000.0000.000
112A112LYS10.8520.88715.3990.2080.2080.0000.0000.0000.000
113A113LEU00.0100.00518.719-0.033-0.0330.0000.0000.0000.000
114A114PHE00.020-0.00720.5600.0220.0220.0000.0000.0000.000
115A115TYR00.0120.01524.072-0.007-0.0070.0000.0000.0000.000
116A116ARG10.7910.84026.2000.2060.2060.0000.0000.0000.000
117A117PRO00.0120.01928.991-0.004-0.0040.0000.0000.0000.000
118A118ALA00.0510.02532.2370.0040.0040.0000.0000.0000.000
119A119ALA0-0.031-0.01433.9650.0040.0040.0000.0000.0000.000
120A120ILE0-0.0230.00831.7550.0060.0060.0000.0000.0000.000
121A121LYS10.8940.95230.6070.1650.1650.0000.0000.0000.000
122A122THR00.0090.02229.2810.0050.0050.0000.0000.0000.000
123A123ARG10.7950.87731.3690.0980.0980.0000.0000.0000.000
124A124PRO00.0470.00428.712-0.004-0.0040.0000.0000.0000.000
125A125ASN0-0.053-0.03527.3920.0010.0010.0000.0000.0000.000
126A126GLU-1-0.799-0.86029.550-0.102-0.1020.0000.0000.0000.000
127A127VAL0-0.043-0.02230.527-0.007-0.0070.0000.0000.0000.000
128A128TRP00.0290.01027.7090.0070.0070.0000.0000.0000.000
129A129GLN00.0360.01128.0470.0120.0120.0000.0000.0000.000
130A130ASP-1-0.905-0.96332.608-0.071-0.0710.0000.0000.0000.000
131A131GLN0-0.031-0.02335.7510.0050.0050.0000.0000.0000.000
132A132LEU0-0.049-0.00731.9570.0020.0020.0000.0000.0000.000
133A133ILE0-0.0090.00836.5470.0050.0050.0000.0000.0000.000
134A134LEU0-0.030-0.01035.790-0.001-0.0010.0000.0000.0000.000
135A135ASN0-0.050-0.02739.6560.0050.0050.0000.0000.0000.000
136A136LYS10.8370.91641.4780.0200.0200.0000.0000.0000.000
137A137VAL00.0140.01140.8000.0000.0000.0000.0000.0000.000
138A138SER00.0050.00042.8770.0020.0020.0000.0000.0000.000
139A139GLY00.0280.01341.114-0.001-0.0010.0000.0000.0000.000
140A140GLY00.001-0.00138.3690.0010.0010.0000.0000.0000.000
141A141TYR00.006-0.00937.2320.0020.0020.0000.0000.0000.000
142A142ARG10.7900.88037.4650.0460.0460.0000.0000.0000.000
143A143ILE00.002-0.00333.1230.0010.0010.0000.0000.0000.000
144A144GLU-1-0.807-0.89836.457-0.056-0.0560.0000.0000.0000.000
145A145ASN0-0.005-0.02632.1770.0030.0030.0000.0000.0000.000
146A146PRO00.0290.02735.675-0.003-0.0030.0000.0000.0000.000
147A147THR0-0.037-0.02133.490-0.004-0.0040.0000.0000.0000.000
148A148PRO00.0300.00634.1880.0000.0000.0000.0000.0000.000
149A149TYR00.002-0.03329.377-0.005-0.0050.0000.0000.0000.000
150A150TYR00.0420.01026.6510.0090.0090.0000.0000.0000.000
151A151VAL0-0.0120.00427.726-0.006-0.0060.0000.0000.0000.000
152A152THR0-0.065-0.03622.744-0.003-0.0030.0000.0000.0000.000
153A153VAL00.0290.01026.011-0.001-0.0010.0000.0000.0000.000
154A154ILE0-0.058-0.06022.366-0.003-0.0030.0000.0000.0000.000
155A155GLY00.0860.06425.7480.0100.0100.0000.0000.0000.000
156A156LEU0-0.019-0.01528.578-0.006-0.0060.0000.0000.0000.000
157A157GLY00.0120.00332.3140.0060.0060.0000.0000.0000.000
158A158GLY00.002-0.01134.499-0.004-0.0040.0000.0000.0000.000
159A159SER0-0.026-0.02135.7520.0010.0010.0000.0000.0000.000
160A160GLU-1-0.888-0.94832.289-0.025-0.0250.0000.0000.0000.000
161A161LYS10.9160.92830.273-0.034-0.0340.0000.0000.0000.000
162A162GLN0-0.0040.00730.4680.0010.0010.0000.0000.0000.000
163A163ALA0-0.047-0.01930.744-0.001-0.0010.0000.0000.0000.000
164A164GLU-1-0.953-0.97626.830-0.027-0.0270.0000.0000.0000.000
165A165GLU-1-0.870-0.91525.9180.0330.0330.0000.0000.0000.000
166A166GLY0-0.065-0.02127.4970.0090.0090.0000.0000.0000.000
167A167GLU-1-0.947-0.96826.3270.0150.0150.0000.0000.0000.000
168A168PHE0-0.049-0.03927.162-0.005-0.0050.0000.0000.0000.000
169A169GLU-1-0.845-0.90326.370-0.033-0.0330.0000.0000.0000.000
170A170THR0-0.042-0.03222.712-0.011-0.0110.0000.0000.0000.000
171A171VAL00.0320.02925.680-0.002-0.0020.0000.0000.0000.000
172A172MET0-0.0120.04024.271-0.015-0.0150.0000.0000.0000.000
173A173LEU00.0180.02527.2390.0000.0000.0000.0000.0000.000
174A174SER00.0430.01930.047-0.013-0.0130.0000.0000.0000.000
175A175PRO0-0.053-0.00230.3540.0090.0090.0000.0000.0000.000
176A176ARG10.8180.90633.3790.1010.1010.0000.0000.0000.000
177A177SER0-0.040-0.03033.8970.0030.0030.0000.0000.0000.000
178A178GLU-1-0.795-0.88136.453-0.052-0.0520.0000.0000.0000.000
179A179GLN00.0090.00730.782-0.006-0.0060.0000.0000.0000.000
180A180THR0-0.013-0.01035.4900.0020.0020.0000.0000.0000.000
181A181VAL0-0.0130.00432.311-0.001-0.0010.0000.0000.0000.000
182A182LYS10.8580.92532.2500.0300.0300.0000.0000.0000.000
183A183SER0-0.025-0.03734.384-0.001-0.0010.0000.0000.0000.000
184A184ALA00.0380.03536.6320.0010.0010.0000.0000.0000.000
185A185ASN0-0.020-0.01139.052-0.006-0.0060.0000.0000.0000.000
186A186TYR00.0320.01434.9840.0050.0050.0000.0000.0000.000
187A187ASN0-0.025-0.01841.275-0.003-0.0030.0000.0000.0000.000
188A188THR00.0230.00140.753-0.001-0.0010.0000.0000.0000.000
189A189PRO0-0.0150.00337.9190.0010.0010.0000.0000.0000.000
190A190TYR0-0.0080.00734.078-0.003-0.0030.0000.0000.0000.000
191A191LEU00.0130.01330.9610.0020.0020.0000.0000.0000.000
192A192SER00.0180.01327.163-0.003-0.0030.0000.0000.0000.000
193A193TYR00.0400.00526.852-0.005-0.0050.0000.0000.0000.000
194A194ILE0-0.055-0.01620.312-0.004-0.0040.0000.0000.0000.000
195A195ASN00.0480.02023.411-0.019-0.0190.0000.0000.0000.000
196A196ASP-1-0.734-0.86122.354-0.213-0.2130.0000.0000.0000.000
197A197TYR0-0.046-0.02119.698-0.036-0.0360.0000.0000.0000.000
198A198GLY0-0.017-0.00518.566-0.028-0.0280.0000.0000.0000.000
199A199GLY0-0.0060.00219.5500.0140.0140.0000.0000.0000.000
200A200ARG10.9430.95219.5530.0760.0760.0000.0000.0000.000
201A201PRO00.0380.03924.5650.0120.0120.0000.0000.0000.000
202A202VAL00.0360.01528.070-0.001-0.0010.0000.0000.0000.000
203A203LEU0-0.0240.00230.888-0.001-0.0010.0000.0000.0000.000
204A204SER00.0230.01234.1300.0050.0050.0000.0000.0000.000
205A205PHE0-0.001-0.01035.107-0.003-0.0030.0000.0000.0000.000
206A206ILE0-0.019-0.01439.8010.0040.0040.0000.0000.0000.000
207A207CYS0-0.036-0.01341.0280.0000.0000.0000.0000.0000.000
208A208ASN00.0080.00245.4250.0030.0030.0000.0000.0000.000
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