FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: 92N72

Calculation Name: 2J2Z-A-Xray549

Preferred Name: Chaperone protein PapD

Target Type: SINGLE PROTEIN

Ligand Name: cobalt (ii) ion

Ligand 3-letter code: CO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2J2Z

Chain ID: A

ChEMBL ID: CHEMBL3309037

UniProt ID: P15319

Base Structure: X-ray

Registration Date: 2025-10-12

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
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. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2423279.247052
FMO2-HF: Nuclear repulsion 2338544.2042
FMO2-HF: Total energy -84735.042852
FMO2-MP2: Total energy -84984.033026


3D Structure Molmil
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.
-104.177-105.70628.783-14.173-13.08-0.137
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 : 1 / q_Mulliken : 0.737 / q_NPA : 0.845
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].
3A3SER0-0.067-0.0463.256-7.196-5.2060.014-1.105-0.900-0.004
24A24ASN0-0.008-0.0113.066-18.804-18.0550.104-0.352-0.501-0.003
25A25ASP-1-0.756-0.8313.877-36.911-36.5290.001-0.135-0.2480.000
26A26ASN0-0.022-0.0052.1967.8168.0141.849-0.795-1.2520.000
27A27LYS0-0.0090.0033.7503.9703.9950.005-0.005-0.0250.000
31A31TYR0-0.003-0.0122.673-8.287-7.6554.875-1.697-3.810-0.012
92A92GLU-1-0.747-0.8321.727-134.485-140.51021.916-9.911-5.979-0.117
107A107LEU0-0.0080.0023.3966.3646.8910.020-0.173-0.374-0.001
108A108GLN0-0.010-0.0285.2100.2820.275-0.0010.0000.0090.000
4A4LEU0-0.008-0.0215.7073.2933.2930.0000.0000.0000.000
5A5ASP-1-0.742-0.8299.323-20.916-20.9160.0000.0000.0000.000
6A6ARG10.8070.89012.51719.91319.9130.0000.0000.0000.000
7A7THR00.0440.00713.196-0.597-0.5970.0000.0000.0000.000
8A8ARG10.8310.91314.71616.54316.5430.0000.0000.0000.000
9A9ALA00.0190.00817.635-0.178-0.1780.0000.0000.0000.000
10A10VAL00.0160.02119.3470.3040.3040.0000.0000.0000.000
11A11PHE0-0.023-0.02722.834-0.269-0.2690.0000.0000.0000.000
12A12ASP-1-0.725-0.83024.528-10.236-10.2360.0000.0000.0000.000
13A13GLY0-0.029-0.02827.882-0.047-0.0470.0000.0000.0000.000
14A14SER0-0.108-0.07830.3710.3570.3570.0000.0000.0000.000
15A15GLU-1-0.880-0.92728.098-10.240-10.2400.0000.0000.0000.000
16A16LYS10.8400.90929.18410.35010.3500.0000.0000.0000.000
17A17SER0-0.071-0.05824.513-0.242-0.2420.0000.0000.0000.000
18A18MET00.0050.03320.0490.3160.3160.0000.0000.0000.000
19A19THR00.001-0.01418.6380.0560.0560.0000.0000.0000.000
20A20LEU0-0.046-0.01614.5410.4770.4770.0000.0000.0000.000
21A21ASP-1-0.843-0.92513.908-20.125-20.1250.0000.0000.0000.000
22A22ILE0-0.055-0.0429.152-1.712-1.7120.0000.0000.0000.000
23A23SER0-0.027-0.0407.7914.5314.5310.0000.0000.0000.000
28A28GLN0-0.025-0.0156.5881.7491.7490.0000.0000.0000.000
29A29LEU0-0.013-0.0106.0882.3642.3640.0000.0000.0000.000
30A30PRO00.0060.0165.724-3.598-3.5980.0000.0000.0000.000
32A32LEU0-0.022-0.0055.5263.8923.8920.0000.0000.0000.000
33A33ALA00.0430.0206.716-5.528-5.5280.0000.0000.0000.000
34A34GLN00.0210.0178.7023.8733.8730.0000.0000.0000.000
35A35ALA00.0240.00410.709-1.997-1.9970.0000.0000.0000.000
36A36TRP0-0.128-0.06712.2261.1341.1340.0000.0000.0000.000
37A37ILE00.0130.01016.240-0.784-0.7840.0000.0000.0000.000
38A38GLU-1-0.765-0.85517.556-18.101-18.1010.0000.0000.0000.000
39A39ASN00.023-0.00820.839-0.343-0.3430.0000.0000.0000.000
40A40GLU-1-0.901-0.96223.074-11.512-11.5120.0000.0000.0000.000
41A41ASN0-0.035-0.02024.713-0.088-0.0880.0000.0000.0000.000
42A42GLN0-0.022-0.00718.863-1.173-1.1730.0000.0000.0000.000
43A43GLU-1-0.814-0.87621.080-12.170-12.1700.0000.0000.0000.000
44A44LYS10.8810.93716.83917.82117.8210.0000.0000.0000.000
45A45ILE0-0.0120.00121.5990.6510.6510.0000.0000.0000.000
46A46ILE0-0.020-0.02120.770-0.699-0.6990.0000.0000.0000.000
47A47THR00.0170.00223.421-0.133-0.1330.0000.0000.0000.000
48A48GLY00.0390.03326.2230.3110.3110.0000.0000.0000.000
49A49PRO0-0.0040.00726.896-0.154-0.1540.0000.0000.0000.000
50A50VAL00.010-0.00522.7910.1560.1560.0000.0000.0000.000
51A51ILE0-0.0110.00422.300-0.216-0.2160.0000.0000.0000.000
52A52ALA00.0370.00517.122-0.124-0.1240.0000.0000.0000.000
53A53THR0-0.068-0.01118.8920.3560.3560.0000.0000.0000.000
54A54PRO00.0350.01015.230-0.028-0.0280.0000.0000.0000.000
55A55PRO00.0480.01015.745-1.050-1.0500.0000.0000.0000.000
56A56VAL0-0.006-0.01412.452-1.433-1.4330.0000.0000.0000.000
57A57GLN00.0050.02211.1531.6321.6320.0000.0000.0000.000
58A58ARG10.8580.90110.11720.40020.4000.0000.0000.0000.000
59A59LEU0-0.0090.0096.7841.3221.3220.0000.0000.0000.000
60A60GLU-1-0.739-0.8647.927-24.884-24.8840.0000.0000.0000.000
61A61PRO0-0.003-0.0026.686-2.877-2.8770.0000.0000.0000.000
62A62GLY00.023-0.0016.5972.7862.7860.0000.0000.0000.000
63A63ALA0-0.080-0.0198.3691.6321.6320.0000.0000.0000.000
64A64LYS10.9210.9578.78724.46024.4600.0000.0000.0000.000
65A65SER0-0.005-0.01711.4142.3432.3430.0000.0000.0000.000
66A66MET00.0020.00413.4040.0390.0390.0000.0000.0000.000
67A67VAL0-0.0310.00013.052-0.077-0.0770.0000.0000.0000.000
68A68ARG10.9640.98215.82115.03615.0360.0000.0000.0000.000
69A69LEU00.0120.01417.4680.0380.0380.0000.0000.0000.000
70A70SER00.007-0.01120.9980.7020.7020.0000.0000.0000.000
71A71THR00.0390.03524.726-0.002-0.0020.0000.0000.0000.000
72A72THR0-0.006-0.02127.6070.1810.1810.0000.0000.0000.000
73A73PRO00.038-0.00230.3090.0270.0270.0000.0000.0000.000
74A74ASP-1-0.836-0.88931.739-9.584-9.5840.0000.0000.0000.000
75A75ILE0-0.019-0.00228.2370.0670.0670.0000.0000.0000.000
76A76SER0-0.029-0.02131.7870.1500.1500.0000.0000.0000.000
77A77LYS10.8770.93534.6208.8338.8330.0000.0000.0000.000
78A78LEU0-0.0120.01328.864-0.003-0.0030.0000.0000.0000.000
79A79PRO00.0150.00333.3100.1810.1810.0000.0000.0000.000
80A80GLN00.008-0.01833.536-0.221-0.2210.0000.0000.0000.000
81A81ASP-1-0.811-0.89136.140-8.468-8.4680.0000.0000.0000.000
82A82ARG10.8630.91330.9179.9559.9550.0000.0000.0000.000
83A83GLU-1-0.743-0.85127.743-11.665-11.6650.0000.0000.0000.000
84A84SER0-0.047-0.02228.6730.3560.3560.0000.0000.0000.000
85A85LEU0-0.0310.00022.206-0.319-0.3190.0000.0000.0000.000
86A86PHE00.0110.00321.8850.3340.3340.0000.0000.0000.000
87A87TYR0-0.020-0.01117.365-0.474-0.4740.0000.0000.0000.000
88A88PHE00.0190.00812.3660.3880.3880.0000.0000.0000.000
89A89ASN0-0.012-0.01112.798-1.855-1.8550.0000.0000.0000.000
90A90LEU00.0280.0157.3381.0301.0300.0000.0000.0000.000
91A91ARG10.8520.9227.41023.86823.8680.0000.0000.0000.000
93A93ILE0-0.033-0.0305.8064.0124.0120.0000.0000.0000.000
94A94PRO0-0.0020.0085.104-1.556-1.5560.0000.0000.0000.000
95A95PRO00.0000.0115.4444.7254.7250.0000.0000.0000.000
96A96ARG10.8910.9298.31918.52518.5250.0000.0000.0000.000
97A97SER0-0.0060.00511.1311.7171.7170.0000.0000.0000.000
98A98GLU-1-0.845-0.92312.814-15.813-15.8130.0000.0000.0000.000
99A99LYS10.9220.97414.24919.65519.6550.0000.0000.0000.000
100A100ALA00.0560.02817.184-0.258-0.2580.0000.0000.0000.000
101A101ASN0-0.033-0.02918.867-0.378-0.3780.0000.0000.0000.000
102A102VAL0-0.019-0.00213.967-0.147-0.1470.0000.0000.0000.000
103A103LEU00.0320.02811.9860.3580.3580.0000.0000.0000.000
104A104GLN0-0.048-0.0387.7910.8820.8820.0000.0000.0000.000
105A105ILE00.004-0.0035.9481.5001.5000.0000.0000.0000.000
106A106ALA0-0.020-0.0104.934-4.879-4.8790.0000.0000.0000.000
109A109THR00.0090.0126.5361.4831.4830.0000.0000.0000.000
110A110LYS10.7990.8808.98220.01320.0130.0000.0000.0000.000
111A111ILE0-0.026-0.00112.4730.2420.2420.0000.0000.0000.000
112A112LYS10.8650.90015.04315.10115.1010.0000.0000.0000.000
113A113LEU0-0.015-0.00618.788-0.412-0.4120.0000.0000.0000.000
114A114PHE00.0300.00520.4870.4040.4040.0000.0000.0000.000
115A115TYR00.0180.01324.0540.0370.0370.0000.0000.0000.000
116A116ARG10.7910.83526.45311.87511.8750.0000.0000.0000.000
117A117PRO00.0040.02229.125-0.025-0.0250.0000.0000.0000.000
118A118ALA00.0430.01532.2620.0950.0950.0000.0000.0000.000
119A119ALA0-0.036-0.01434.3700.1020.1020.0000.0000.0000.000
120A120ILE0-0.0310.00132.0010.1740.1740.0000.0000.0000.000
121A121LYS10.8610.93931.2359.9169.9160.0000.0000.0000.000
122A122THR00.0200.03529.7590.1440.1440.0000.0000.0000.000
123A123ARG10.8710.92431.4048.6878.6870.0000.0000.0000.000
124A124PRO0-0.002-0.02229.421-0.199-0.1990.0000.0000.0000.000
125A125ASN0-0.042-0.03028.5350.0060.0060.0000.0000.0000.000
126A126GLU-1-0.854-0.90030.353-8.893-8.8930.0000.0000.0000.000
127A127VAL0-0.047-0.02130.970-0.348-0.3480.0000.0000.0000.000
128A128TRP00.0330.00828.0520.3070.3070.0000.0000.0000.000
129A129GLN00.0230.01028.2930.4390.4390.0000.0000.0000.000
130A130ASP-1-0.864-0.94732.826-8.719-8.7190.0000.0000.0000.000
131A131GLN0-0.025-0.01636.0130.3340.3340.0000.0000.0000.000
132A132LEU0-0.039-0.00931.9770.0830.0830.0000.0000.0000.000
133A133ILE0-0.039-0.01836.5780.2140.2140.0000.0000.0000.000
134A134LEU0-0.0250.00435.926-0.192-0.1920.0000.0000.0000.000
135A135ASN0-0.031-0.03239.7230.4270.4270.0000.0000.0000.000
136A136LYS10.8170.91841.0937.5697.5690.0000.0000.0000.000
137A137VAL00.0020.00640.8990.1850.1850.0000.0000.0000.000
138A138SER00.0400.00642.894-0.059-0.0590.0000.0000.0000.000
139A139GLY0-0.004-0.00240.883-0.158-0.1580.0000.0000.0000.000
140A140GLY0-0.0050.00238.494-0.242-0.2420.0000.0000.0000.000
141A141TYR00.0450.02937.3660.2680.2680.0000.0000.0000.000
142A142ARG10.8390.92737.3097.3167.3160.0000.0000.0000.000
143A143ILE00.0180.00432.7710.1640.1640.0000.0000.0000.000
144A144GLU-1-0.803-0.89636.678-7.652-7.6520.0000.0000.0000.000
145A145ASN00.0070.00532.4350.0970.0970.0000.0000.0000.000
146A146PRO00.0200.01135.825-0.007-0.0070.0000.0000.0000.000
147A147THR0-0.017-0.01333.7890.0160.0160.0000.0000.0000.000
148A148PRO00.006-0.00634.736-0.059-0.0590.0000.0000.0000.000
149A149TYR00.024-0.01129.868-0.089-0.0890.0000.0000.0000.000
150A150TYR00.024-0.00226.7620.2100.2100.0000.0000.0000.000
151A151VAL0-0.0040.00027.883-0.120-0.1200.0000.0000.0000.000
152A152THR0-0.049-0.02122.285-0.262-0.2620.0000.0000.0000.000
153A153VAL00.011-0.00125.638-0.100-0.1000.0000.0000.0000.000
154A154ILE0-0.008-0.02222.604-0.321-0.3210.0000.0000.0000.000
155A155GLY00.0750.05025.748-0.151-0.1510.0000.0000.0000.000
156A156LEU0-0.059-0.03128.8320.2290.2290.0000.0000.0000.000
157A157GLY00.0520.02832.651-0.072-0.0720.0000.0000.0000.000
158A158GLY0-0.026-0.02735.0890.1520.1520.0000.0000.0000.000
159A159SER0-0.038-0.03036.3260.1300.1300.0000.0000.0000.000
160A160GLU-1-0.897-0.95332.653-9.450-9.4500.0000.0000.0000.000
161A161LYS10.9520.96631.0229.9309.9300.0000.0000.0000.000
162A162GLN0-0.049-0.01530.933-0.171-0.1710.0000.0000.0000.000
163A163ALA0-0.022-0.00930.949-0.126-0.1260.0000.0000.0000.000
164A164GLU-1-0.930-0.97427.387-11.137-11.1370.0000.0000.0000.000
165A165GLU-1-0.910-0.95126.133-11.243-11.2430.0000.0000.0000.000
166A166GLY0-0.038-0.00427.8180.0260.0260.0000.0000.0000.000
167A167GLU-1-0.983-0.98627.268-11.419-11.4190.0000.0000.0000.000
168A168PHE0-0.043-0.03327.1250.6010.6010.0000.0000.0000.000
169A169GLU-1-0.898-0.93524.671-13.146-13.1460.0000.0000.0000.000
170A170THR0-0.060-0.02622.0200.0700.0700.0000.0000.0000.000
171A171VAL00.0120.01224.933-0.088-0.0880.0000.0000.0000.000
172A172MET0-0.0120.02023.898-0.508-0.5080.0000.0000.0000.000
173A173LEU0-0.0130.01227.1310.2170.2170.0000.0000.0000.000
174A174SER00.0440.00729.449-0.439-0.4390.0000.0000.0000.000
175A175PRO0-0.0270.00630.2370.2720.2720.0000.0000.0000.000
176A176ARG10.7650.88333.3708.5758.5750.0000.0000.0000.000
177A177SER0-0.028-0.01333.6790.0140.0140.0000.0000.0000.000
178A178GLU-1-0.834-0.93736.163-7.855-7.8550.0000.0000.0000.000
179A179GLN0-0.014-0.01530.230-0.202-0.2020.0000.0000.0000.000
180A180THR0-0.047-0.02035.2910.1830.1830.0000.0000.0000.000
181A181VAL00.0350.03431.872-0.147-0.1470.0000.0000.0000.000
182A182LYS10.8760.92934.2268.4978.4970.0000.0000.0000.000
183A183SER00.0480.00434.469-0.316-0.3160.0000.0000.0000.000
184A184ALA00.0250.02036.7640.2910.2910.0000.0000.0000.000
185A185ASN0-0.004-0.01239.352-0.063-0.0630.0000.0000.0000.000
186A186TYR00.0390.01936.1980.0230.0230.0000.0000.0000.000
187A187ASN0-0.006-0.00641.3150.1470.1470.0000.0000.0000.000
188A188THR00.003-0.00141.5590.1740.1740.0000.0000.0000.000
189A189PRO0-0.012-0.00238.118-0.142-0.1420.0000.0000.0000.000
190A190TYR0-0.0030.01334.4910.1480.1480.0000.0000.0000.000
191A191LEU00.0130.00931.114-0.097-0.0970.0000.0000.0000.000
192A192SER00.0040.00427.364-0.117-0.1170.0000.0000.0000.000
193A193TYR00.0360.00026.712-0.171-0.1710.0000.0000.0000.000
194A194ILE0-0.031-0.01020.063-0.262-0.2620.0000.0000.0000.000
195A195ASN00.0400.01723.641-0.290-0.2900.0000.0000.0000.000
196A196ASP-1-0.727-0.85522.460-12.890-12.8900.0000.0000.0000.000
197A197TYR0-0.010-0.00620.931-0.472-0.4720.0000.0000.0000.000
198A198GLY0-0.032-0.00318.709-0.788-0.7880.0000.0000.0000.000
199A199GLY0-0.0010.00819.725-0.184-0.1840.0000.0000.0000.000
200A200ARG10.9380.95720.54614.46714.4670.0000.0000.0000.000
201A201PRO00.0160.02324.6200.2200.2200.0000.0000.0000.000
202A202VAL00.0400.02528.415-0.131-0.1310.0000.0000.0000.000
203A203LEU0-0.0200.00731.2610.2010.2010.0000.0000.0000.000
204A204SER00.0080.01034.5860.0610.0610.0000.0000.0000.000
205A205PHE00.010-0.00735.4850.1040.1040.0000.0000.0000.000
206A206ILE0-0.022-0.01540.3220.1100.1100.0000.0000.0000.000
207A207CYS0-0.062-0.02741.3370.0140.0140.0000.0000.0000.000
208A208ASN0-0.001-0.00345.5980.1880.1880.0000.0000.0000.000
209A209GLY00.0480.02548.822-0.008-0.0080.0000.0000.0000.000
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