FMODB

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

Last updated: 2025-07-23

All entries: 44592

Number of unique PDB entries: 7794

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FMODB ID: VQ781

Calculation Name: 3ME0-A-Xray372

Preferred Name: Chaperone protein PapD

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

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:

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
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
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2429472.830033
FMO2-HF: Nuclear repulsion 2344737.065445
FMO2-HF: Total energy -84735.764589
FMO2-MP2: Total energy -84984.849825


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.
-18.404-16.24919.853-9.72-12.291-0.072
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 : -0.018 / q_NPA : -0.008
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].
3A3SER0-0.036-0.0053.873-0.2171.324-0.012-0.761-0.7690.003
4A4LEU0-0.009-0.0225.8830.2310.2310.0000.0000.0000.000
5A5ASP-1-0.764-0.8399.441-0.564-0.5640.0000.0000.0000.000
6A6ARG10.8040.88312.6720.6620.6620.0000.0000.0000.000
7A7THR00.0410.01113.213-0.063-0.0630.0000.0000.0000.000
8A8ARG10.8310.91414.9030.3250.3250.0000.0000.0000.000
9A9ALA00.0100.00317.850-0.023-0.0230.0000.0000.0000.000
10A10VAL00.0100.01219.6400.0210.0210.0000.0000.0000.000
11A11PHE0-0.005-0.01323.360-0.012-0.0120.0000.0000.0000.000
12A12ASP-1-0.741-0.83825.014-0.166-0.1660.0000.0000.0000.000
13A13GLY0-0.004-0.01328.286-0.006-0.0060.0000.0000.0000.000
14A14SER0-0.097-0.08330.9240.0140.0140.0000.0000.0000.000
15A15GLU-1-0.885-0.92428.313-0.206-0.2060.0000.0000.0000.000
16A16LYS10.9350.96429.0860.1970.1970.0000.0000.0000.000
17A17SER0-0.096-0.06424.641-0.017-0.0170.0000.0000.0000.000
18A18MET00.0220.04120.2440.0170.0170.0000.0000.0000.000
19A19THR00.000-0.01418.5170.0030.0030.0000.0000.0000.000
20A20LEU0-0.028-0.00614.7440.0380.0380.0000.0000.0000.000
21A21ASP-1-0.843-0.92813.724-0.644-0.6440.0000.0000.0000.000
22A22ILE0-0.047-0.0399.107-0.118-0.1180.0000.0000.0000.000
23A23SER0-0.024-0.0467.1330.5180.5180.0000.0000.0000.000
24A24ASN0-0.0040.0062.774-2.552-1.6150.419-0.530-0.825-0.007
25A25ASP-1-0.802-0.8823.729-0.5650.1290.008-0.307-0.3960.000
26A26ASN00.0270.0222.336-0.172-0.0382.651-1.143-1.6430.002
27A27LYS10.8730.9253.656-0.800-0.8120.0080.056-0.0520.000
28A28GLN0-0.002-0.0016.699-0.175-0.1750.0000.0000.0000.000
29A29LEU0-0.021-0.0075.940-0.105-0.1050.0000.0000.0000.000
30A30PRO00.0000.0205.765-0.058-0.0580.0000.0000.0000.000
31A31TYR00.025-0.0052.686-1.685-0.8884.431-1.703-3.526-0.010
32A32LEU0-0.021-0.0086.0560.0680.0680.0000.0000.0000.000
33A33ALA00.0320.0056.922-0.485-0.4850.0000.0000.0000.000
34A34GLN00.0330.0238.9360.2730.2730.0000.0000.0000.000
35A35ALA00.0280.00911.342-0.167-0.1670.0000.0000.0000.000
36A36TRP0-0.118-0.08112.9360.0810.0810.0000.0000.0000.000
37A37ILE00.0290.02217.015-0.039-0.0390.0000.0000.0000.000
38A38GLU-1-0.759-0.84418.200-0.378-0.3780.0000.0000.0000.000
39A39ASN00.026-0.01121.731-0.014-0.0140.0000.0000.0000.000
40A40GLU-1-0.810-0.90924.086-0.175-0.1750.0000.0000.0000.000
41A41ASN0-0.042-0.02725.6580.0070.0070.0000.0000.0000.000
42A42GLN0-0.039-0.02720.511-0.014-0.0140.0000.0000.0000.000
43A43GLU-1-0.814-0.86822.463-0.173-0.1730.0000.0000.0000.000
44A44LYS10.8770.94417.3180.4090.4090.0000.0000.0000.000
45A45ILE0-0.025-0.00822.4180.0230.0230.0000.0000.0000.000
46A46ILE0-0.032-0.02821.403-0.032-0.0320.0000.0000.0000.000
47A47THR00.0170.00524.274-0.006-0.0060.0000.0000.0000.000
48A48GLY00.0120.02026.8620.0100.0100.0000.0000.0000.000
49A49PRO00.0180.01927.718-0.002-0.0020.0000.0000.0000.000
50A50VAL00.0400.00523.2110.0010.0010.0000.0000.0000.000
51A51ILE0-0.036-0.00722.720-0.004-0.0040.0000.0000.0000.000
52A52ALA00.0270.00117.603-0.011-0.0110.0000.0000.0000.000
53A53THR0-0.075-0.01819.2280.0260.0260.0000.0000.0000.000
54A54PRO00.0480.00915.437-0.012-0.0120.0000.0000.0000.000
55A55PRO00.0380.00016.001-0.066-0.0660.0000.0000.0000.000
56A56VAL0-0.018-0.00912.595-0.063-0.0630.0000.0000.0000.000
57A57GLN0-0.0020.01711.1580.0850.0850.0000.0000.0000.000
58A58ARG10.8290.86410.1820.1930.1930.0000.0000.0000.000
59A59LEU0-0.0070.0136.6080.0320.0320.0000.0000.0000.000
60A60GLU-1-0.703-0.8287.766-0.279-0.2790.0000.0000.0000.000
61A61PRO0-0.011-0.0046.735-0.181-0.1810.0000.0000.0000.000
62A62GLY0-0.023-0.0066.1710.0410.0410.0000.0000.0000.000
63A63ALA0-0.048-0.0077.724-0.042-0.0420.0000.0000.0000.000
64A64LYS10.9030.9448.2330.4790.4790.0000.0000.0000.000
65A65SER0-0.002-0.01610.7950.1620.1620.0000.0000.0000.000
66A66MET0-0.0090.00412.743-0.016-0.0160.0000.0000.0000.000
67A67VAL0-0.0280.00413.298-0.003-0.0030.0000.0000.0000.000
68A68ARG10.9560.98215.9890.3770.3770.0000.0000.0000.000
69A69LEU0-0.0030.00917.9050.0010.0010.0000.0000.0000.000
70A70SER0-0.029-0.02421.3070.0310.0310.0000.0000.0000.000
71A71THR00.0290.01725.032-0.008-0.0080.0000.0000.0000.000
72A72THR0-0.0010.00927.9900.0070.0070.0000.0000.0000.000
73A73PRO00.0660.01530.7120.0010.0010.0000.0000.0000.000
74A74ASP-1-0.805-0.87932.830-0.137-0.1370.0000.0000.0000.000
75A75ILE0-0.012-0.00629.1070.0040.0040.0000.0000.0000.000
76A76SER0-0.034-0.02432.6430.0050.0050.0000.0000.0000.000
77A77LYS10.8050.88535.7660.1400.1400.0000.0000.0000.000
78A78LEU0-0.0200.00729.9930.0020.0020.0000.0000.0000.000
79A79PRO00.0110.00633.8010.0060.0060.0000.0000.0000.000
80A80GLN00.003-0.01734.591-0.008-0.0080.0000.0000.0000.000
81A81ASP-1-0.832-0.90136.653-0.105-0.1050.0000.0000.0000.000
82A82ARG10.8450.90931.4790.1430.1430.0000.0000.0000.000
83A83GLU-1-0.754-0.85927.900-0.196-0.1960.0000.0000.0000.000
84A84SER0-0.047-0.02129.1160.0150.0150.0000.0000.0000.000
85A85LEU0-0.049-0.00622.682-0.016-0.0160.0000.0000.0000.000
86A86PHE00.000-0.00122.6430.0120.0120.0000.0000.0000.000
87A87TYR0-0.038-0.02418.253-0.007-0.0070.0000.0000.0000.000
88A88PHE00.0350.01812.6110.0080.0080.0000.0000.0000.000
89A89ASN0-0.041-0.01313.644-0.018-0.0180.0000.0000.0000.000
90A90LEU00.0510.0228.1810.0570.0570.0000.0000.0000.000
91A91ARG10.8530.9197.9180.6100.6100.0000.0000.0000.000
92A92GLU-1-0.759-0.8581.914-13.865-15.4419.858-4.478-3.804-0.060
93A93ILE0-0.032-0.0306.2430.5360.5360.0000.0000.0000.000
94A94PRO0-0.0050.0145.183-0.114-0.1140.0000.0000.0000.000
95A95PRO00.000-0.0146.3390.0540.0540.0000.0000.0000.000
96A96ARG10.7840.8889.487-0.189-0.1890.0000.0000.0000.000
97A97SER00.0500.03011.523-0.043-0.0430.0000.0000.0000.000
98A98GLU-1-0.820-0.90712.8250.1690.1690.0000.0000.0000.000
99A99LYS10.9250.96814.392-0.533-0.5330.0000.0000.0000.000
100A100ALA00.0540.02417.078-0.001-0.0010.0000.0000.0000.000
101A101ASN0-0.030-0.02018.8020.0210.0210.0000.0000.0000.000
102A102VAL0-0.0060.00614.0490.0450.0450.0000.0000.0000.000
103A103LEU00.0230.01813.657-0.060-0.0600.0000.0000.0000.000
104A104GLN0-0.018-0.0118.5240.0740.0740.0000.0000.0000.000
105A105ILE0-0.002-0.0057.515-0.158-0.1580.0000.0000.0000.000
106A106ALA0-0.017-0.0105.4570.3270.3270.0000.0000.0000.000
107A107LEU0-0.0070.0022.0420.129-0.2312.490-0.854-1.2760.000
108A108GLN00.008-0.0125.435-0.373-0.3730.0000.0000.0000.000
109A109THR0-0.0090.0067.4390.2010.2010.0000.0000.0000.000
110A110LYS10.8120.8779.9150.4090.4090.0000.0000.0000.000
111A111ILE0-0.029-0.00113.1060.0550.0550.0000.0000.0000.000
112A112LYS10.8770.90215.7980.2240.2240.0000.0000.0000.000
113A113LEU0-0.0010.00219.272-0.029-0.0290.0000.0000.0000.000
114A114PHE00.0300.00321.0880.0190.0190.0000.0000.0000.000
115A115TYR00.0250.01824.675-0.005-0.0050.0000.0000.0000.000
116A116ARG10.7790.82626.4890.2070.2070.0000.0000.0000.000
117A117PRO00.0270.02629.604-0.003-0.0030.0000.0000.0000.000
118A118ALA00.0500.02932.8900.0040.0040.0000.0000.0000.000
119A119ALA0-0.040-0.01734.6440.0040.0040.0000.0000.0000.000
120A120ILE0-0.0300.00232.2720.0060.0060.0000.0000.0000.000
121A121LYS10.8670.93231.5250.1580.1580.0000.0000.0000.000
122A122THR00.0280.04329.8260.0040.0040.0000.0000.0000.000
123A123ARG10.8130.87431.6970.1000.1000.0000.0000.0000.000
124A124PRO00.016-0.01629.508-0.005-0.0050.0000.0000.0000.000
125A125ASN0-0.050-0.02527.5650.0000.0000.0000.0000.0000.000
126A126GLU-1-0.793-0.85129.798-0.105-0.1050.0000.0000.0000.000
127A127VAL0-0.052-0.02430.753-0.007-0.0070.0000.0000.0000.000
128A128TRP00.0430.00027.9150.0050.0050.0000.0000.0000.000
129A129GLN00.0300.01928.6050.0130.0130.0000.0000.0000.000
130A130ASP-1-0.869-0.94533.008-0.077-0.0770.0000.0000.0000.000
131A131GLN0-0.069-0.03336.1510.0050.0050.0000.0000.0000.000
132A132LEU0-0.030-0.00232.2400.0000.0000.0000.0000.0000.000
133A133ILE0-0.026-0.00636.8750.0060.0060.0000.0000.0000.000
134A134LEU0-0.012-0.00635.892-0.002-0.0020.0000.0000.0000.000
135A135ASN0-0.045-0.03139.8120.0070.0070.0000.0000.0000.000
136A136LYS10.8360.92341.5070.0280.0280.0000.0000.0000.000
137A137VAL0-0.0040.00340.9190.0010.0010.0000.0000.0000.000
138A138SER00.009-0.00143.1320.0020.0020.0000.0000.0000.000
139A139GLY00.0140.00640.938-0.002-0.0020.0000.0000.0000.000
140A140GLY00.0490.01938.3690.0000.0000.0000.0000.0000.000
141A141TYR0-0.021-0.01637.4560.0040.0040.0000.0000.0000.000
142A142ARG10.7640.85037.4170.0520.0520.0000.0000.0000.000
143A143ILE00.0040.00533.2380.0020.0020.0000.0000.0000.000
144A144GLU-1-0.797-0.89237.092-0.060-0.0600.0000.0000.0000.000
145A145ASN00.009-0.01132.7860.0030.0030.0000.0000.0000.000
146A146PRO00.0230.01736.179-0.003-0.0030.0000.0000.0000.000
147A147THR0-0.022-0.01434.102-0.004-0.0040.0000.0000.0000.000
148A148PRO00.0210.00734.858-0.001-0.0010.0000.0000.0000.000
149A149TYR00.018-0.02330.025-0.005-0.0050.0000.0000.0000.000
150A150TYR00.004-0.02327.1260.0080.0080.0000.0000.0000.000
151A151VAL0-0.025-0.01128.223-0.004-0.0040.0000.0000.0000.000
152A152THR0-0.037-0.01722.599-0.002-0.0020.0000.0000.0000.000
153A153VAL00.0230.01025.961-0.001-0.0010.0000.0000.0000.000
154A154ILE0-0.058-0.05422.557-0.005-0.0050.0000.0000.0000.000
155A155GLY00.0900.05825.8430.0080.0080.0000.0000.0000.000
156A156LEU0-0.036-0.01828.733-0.005-0.0050.0000.0000.0000.000
157A157GLY00.0310.01332.5600.0060.0060.0000.0000.0000.000
158A158GLY00.013-0.01134.866-0.003-0.0030.0000.0000.0000.000
159A159SER0-0.047-0.03136.1080.0020.0020.0000.0000.0000.000
160A160GLU-1-0.896-0.95932.822-0.035-0.0350.0000.0000.0000.000
161A161LYS10.9250.93430.438-0.019-0.0190.0000.0000.0000.000
162A162GLN0-0.0030.01130.5210.0000.0000.0000.0000.0000.000
163A163ALA0-0.032-0.01630.798-0.001-0.0010.0000.0000.0000.000
164A164GLU-1-0.968-0.98426.654-0.046-0.0460.0000.0000.0000.000
165A165GLU-1-0.868-0.91525.8190.0140.0140.0000.0000.0000.000
166A166GLY0-0.059-0.01527.6310.0090.0090.0000.0000.0000.000
167A167GLU-1-0.920-0.95826.088-0.012-0.0120.0000.0000.0000.000
168A168PHE0-0.059-0.03526.966-0.003-0.0030.0000.0000.0000.000
169A169GLU-1-0.805-0.87426.336-0.052-0.0520.0000.0000.0000.000
170A170THR0-0.043-0.02122.605-0.010-0.0100.0000.0000.0000.000
171A171VAL00.0010.01625.781-0.004-0.0040.0000.0000.0000.000
172A172MET0-0.0440.00924.533-0.018-0.0180.0000.0000.0000.000
173A173LEU00.0280.04327.7150.0000.0000.0000.0000.0000.000
174A174SER00.0520.01630.092-0.014-0.0140.0000.0000.0000.000
175A175PRO0-0.047-0.00130.7010.0090.0090.0000.0000.0000.000
176A176ARG10.7750.88033.7890.1030.1030.0000.0000.0000.000
177A177SER0-0.018-0.00634.3350.0030.0030.0000.0000.0000.000
178A178GLU-1-0.796-0.87936.844-0.059-0.0590.0000.0000.0000.000
179A179GLN00.007-0.00130.876-0.008-0.0080.0000.0000.0000.000
180A180THR0-0.026-0.01635.7480.0020.0020.0000.0000.0000.000
181A181VAL0-0.0070.01032.274-0.003-0.0030.0000.0000.0000.000
182A182LYS10.8350.89032.2370.0460.0460.0000.0000.0000.000
183A183SER0-0.025-0.03034.173-0.002-0.0020.0000.0000.0000.000
184A184ALA00.0240.02836.4800.0020.0020.0000.0000.0000.000
185A185ASN0-0.004-0.00939.006-0.006-0.0060.0000.0000.0000.000
186A186TYR00.0150.00235.1060.0050.0050.0000.0000.0000.000
187A187ASN0-0.019-0.01141.555-0.003-0.0030.0000.0000.0000.000
188A188THR00.0200.00041.254-0.001-0.0010.0000.0000.0000.000
189A189PRO0-0.0020.00238.0850.0010.0010.0000.0000.0000.000
190A190TYR0-0.0150.01434.400-0.002-0.0020.0000.0000.0000.000
191A191LEU00.0170.01931.3030.0020.0020.0000.0000.0000.000
192A192SER00.018-0.00127.430-0.003-0.0030.0000.0000.0000.000
193A193TYR00.031-0.00126.795-0.004-0.0040.0000.0000.0000.000
194A194ILE0-0.035-0.00820.159-0.003-0.0030.0000.0000.0000.000
195A195ASN00.0430.02023.399-0.020-0.0200.0000.0000.0000.000
196A196ASP-1-0.729-0.85622.565-0.219-0.2190.0000.0000.0000.000
197A197TYR0-0.043-0.01519.928-0.034-0.0340.0000.0000.0000.000
198A198GLY0-0.007-0.00518.628-0.035-0.0350.0000.0000.0000.000
199A199GLY0-0.016-0.00119.6620.0130.0130.0000.0000.0000.000
200A200ARG10.9720.97020.2390.0950.0950.0000.0000.0000.000
201A201PRO00.0190.02724.6130.0120.0120.0000.0000.0000.000
202A202VAL00.0360.02728.264-0.001-0.0010.0000.0000.0000.000
203A203LEU0-0.0110.00731.0510.0000.0000.0000.0000.0000.000
204A204SER00.0340.02834.4510.0040.0040.0000.0000.0000.000
205A205PHE0-0.002-0.01135.543-0.003-0.0030.0000.0000.0000.000
206A206ILE0-0.023-0.01640.1990.0040.0040.0000.0000.0000.000
207A207CYS0-0.024-0.00241.4230.0000.0000.0000.0000.0000.000
208A208ASN00.009-0.00445.7740.0030.0030.0000.0000.0000.000
209A209GLY00.0410.02749.052-0.002-0.0020.0000.0000.0000.000
210A210SER0-0.016-0.01047.5340.0000.0000.0000.0000.0000.000
211A211ARG10.9660.99444.6130.0390.0390.0000.0000.0000.000
212A213SER00.0490.02640.944-0.003-0.0030.0000.0000.0000.000
213A214VAL00.0290.02236.9400.0030.0030.0000.0000.0000.000
214A215LYS10.8840.94140.0380.0340.0340.0000.0000.0000.000
215A216LYS10.9840.99641.2290.0540.0540.0000.0000.0000.000