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: VKGQ1

Calculation Name: 3ME0-B-Xray540

Preferred Name: Chaperone protein PapD

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3ME0

Chain ID: B

ChEMBL ID: CHEMBL3309037

UniProt ID: P15319

Base Structure: X-ray

Registration Date: 2025-07-09

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 236
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -956946.646343
FMO2-HF: Nuclear repulsion 908001.18037
FMO2-HF: Total energy -48945.465973
FMO2-MP2: Total energy -49086.413569


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(B:189:HIS)


Summations of interaction energy for fragment #1(B:189:HIS)
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.
-0.3022.4460.248-1.279-1.715-0.003
Interaction energy analysis for fragmet #1(B:189:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.182 / q_NPA : 0.040
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].
4B190HIS0-0.0910.0684.396-0.1590.080-0.001-0.088-0.1510.000
5B191HIS00.023-0.1133.880-0.1390.9660.001-0.519-0.5870.001
6B191HIS0-0.0740.0916.6080.0860.0860.0000.0000.0000.000
7B192HIS00.016-0.1173.3950.1050.4730.019-0.107-0.2790.000
8B192HIS0-0.0400.1013.184-0.6280.3490.230-0.557-0.649-0.004
9B193HIS00.138-0.0554.3410.2130.272-0.001-0.008-0.0490.000
10B193HIS0-0.0690.0945.2080.3040.3040.0000.0000.0000.000
11B194HIS00.037-0.1327.292-0.127-0.1270.0000.0000.0000.000
12B194HIS0-0.0470.1069.7450.0520.0520.0000.0000.0000.000
13B195GLY0-0.009-0.0848.2350.0020.0020.0000.0000.0000.000
14B196GLY0-0.023-0.03210.7000.0200.0200.0000.0000.0000.000
15B197CYS00.024-0.04813.007-0.039-0.0390.0000.0000.0000.000
16B197CYS0-0.1560.24715.465-0.001-0.0010.0000.0000.0000.000
17B198ARG00.083-0.11314.4580.0290.0290.0000.0000.0000.000
18B198ARG10.8911.0939.717-0.245-0.2450.0000.0000.0000.000
19B199PRO00.019-0.09915.712-0.025-0.0250.0000.0000.0000.000
20B200SER00.0430.03717.9950.0190.0190.0000.0000.0000.000
21B200SER0-0.0660.03420.412-0.009-0.0090.0000.0000.0000.000
22B201ALA00.083-0.07019.7170.0010.0010.0000.0000.0000.000
23B201ALA0-0.0810.10118.7100.0030.0030.0000.0000.0000.000
24B202GLN00.029-0.12020.7530.0070.0070.0000.0000.0000.000
25B202GLN0-0.0280.11123.0750.0060.0060.0000.0000.0000.000
26B203SER00.120-0.04524.4420.0050.0050.0000.0000.0000.000
27B203SER0-0.0520.07727.9900.0010.0010.0000.0000.0000.000
28B204LEU0-0.018-0.10127.409-0.010-0.0100.0000.0000.0000.000
29B204LEU0-0.0590.10825.340-0.001-0.0010.0000.0000.0000.000
30B205GLU00.154-0.11528.8590.0010.0010.0000.0000.0000.000
31B205GLU-1-0.923-0.78231.3160.0490.0490.0000.0000.0000.000
32B206ILE00.052-0.11632.322-0.002-0.0020.0000.0000.0000.000
33B206ILE0-0.1000.11733.2500.0000.0000.0000.0000.0000.000
34B207LYS00.118-0.11234.9610.0000.0000.0000.0000.0000.000
35B207LYS10.7401.02432.552-0.039-0.0390.0000.0000.0000.000
36B208HIS00.074-0.08237.382-0.003-0.0030.0000.0000.0000.000
37B208HIS10.7150.95439.612-0.020-0.0200.0000.0000.0000.000
38B209GLY00.013-0.09040.567-0.002-0.0020.0000.0000.0000.000
39B210ASP00.0890.00442.1950.0020.0020.0000.0000.0000.000
40B210ASP-1-0.963-0.84244.8760.0190.0190.0000.0000.0000.000
41B211LEU0-0.013-0.09545.815-0.002-0.0020.0000.0000.0000.000
42B211LEU0-0.0610.10145.3390.0000.0000.0000.0000.0000.000
43B212SER00.083-0.06047.9910.0000.0000.0000.0000.0000.000
44B212SER0-0.0270.05249.4780.0000.0000.0000.0000.0000.000
45B213ILE00.050-0.10750.4200.0000.0000.0000.0000.0000.000
46B213ILE0-0.0660.11048.4640.0000.0000.0000.0000.0000.000
47B214ASN00.087-0.08449.751-0.001-0.0010.0000.0000.0000.000
48B214ASN0-0.0940.04647.4190.0010.0010.0000.0000.0000.000
49B215SER00.029-0.08150.605-0.001-0.0010.0000.0000.0000.000
50B215SER0-0.0430.09652.7160.0000.0000.0000.0000.0000.000
51B216ALA00.157-0.08749.2160.0000.0000.0000.0000.0000.000
52B216ALA0-0.1210.09948.1970.0000.0000.0000.0000.0000.000
53B217ASN00.140-0.04948.6530.0010.0010.0000.0000.0000.000
54B217ASN0-0.1090.06050.3330.0010.0010.0000.0000.0000.000
55B218ASN00.136-0.03847.5130.0020.0020.0000.0000.0000.000
56B218ASN0-0.1470.03846.8080.0000.0000.0000.0000.0000.000
57B219HIS00.134-0.10045.513-0.002-0.0020.0000.0000.0000.000
58B219HIS0-0.0400.14442.4540.0010.0010.0000.0000.0000.000
59B220TYR00.065-0.09541.8000.0020.0020.0000.0000.0000.000
60B220TYR0-0.0790.09237.5810.0000.0000.0000.0000.0000.000
61B221ALA00.086-0.09738.731-0.002-0.0020.0000.0000.0000.000
62B221ALA0-0.0540.11037.9510.0010.0010.0000.0000.0000.000
63B222ALA00.066-0.12335.0190.0020.0020.0000.0000.0000.000
64B222ALA0-0.0660.10234.149-0.001-0.0010.0000.0000.0000.000
65B223GLN00.067-0.09730.793-0.001-0.0010.0000.0000.0000.000
66B223GLN0-0.1000.07627.914-0.005-0.0050.0000.0000.0000.000
67B224THR0-0.001-0.09528.6270.0010.0010.0000.0000.0000.000
68B224THR0-0.0540.06227.137-0.001-0.0010.0000.0000.0000.000
69B225LEU00.106-0.04724.504-0.003-0.0030.0000.0000.0000.000
70B225LEU0-0.0700.09222.7960.0020.0020.0000.0000.0000.000
71B226SER0-0.036-0.10521.778-0.006-0.0060.0000.0000.0000.000
72B226SER00.0160.08920.708-0.005-0.0050.0000.0000.0000.000
73B227VAL00.061-0.10819.2430.0150.0150.0000.0000.0000.000
74B227VAL0-0.0680.10318.7280.0010.0010.0000.0000.0000.000
75B228SER00.129-0.08415.329-0.020-0.0200.0000.0000.0000.000
76B228SER0-0.0080.09014.520-0.008-0.0080.0000.0000.0000.000
77B229CYS0-0.009-0.12314.3270.0390.0390.0000.0000.0000.000
78B230ASP00.121-0.09110.235-0.050-0.0500.0000.0000.0000.000
79B230ASP-1-0.902-0.8179.3550.1060.1060.0000.0000.0000.000
80B231VAL0-0.034-0.12811.337-0.074-0.0740.0000.0000.0000.000
81B231VAL0-0.0290.12311.7500.0000.0000.0000.0000.0000.000
82B232PRO0-0.016-0.11713.9170.0120.0120.0000.0000.0000.000
83B233ALA00.077-0.00717.4610.0100.0100.0000.0000.0000.000
84B233ALA0-0.0050.12317.8220.0030.0030.0000.0000.0000.000
85B234ASN00.060-0.08219.634-0.010-0.0100.0000.0000.0000.000
86B234ASN0-0.0830.07123.890-0.008-0.0080.0000.0000.0000.000
87B235ILE00.117-0.07722.5370.0080.0080.0000.0000.0000.000
88B235ILE0-0.0580.09919.5980.0010.0010.0000.0000.0000.000
89B236ARG00.115-0.07023.737-0.008-0.0080.0000.0000.0000.000
90B236ARG10.7200.96627.379-0.030-0.0300.0000.0000.0000.000
91B237PHE00.040-0.11426.3650.0100.0100.0000.0000.0000.000
92B237PHE0-0.0700.08323.1060.0000.0000.0000.0000.0000.000
93B238MET00.172-0.08028.068-0.007-0.0070.0000.0000.0000.000
94B238MET0-0.1080.10330.3340.0020.0020.0000.0000.0000.000
95B239LEU00.046-0.11030.4990.0070.0070.0000.0000.0000.000
96B239LEU0-0.0790.09931.3760.0000.0000.0000.0000.0000.000
97B240LEU00.069-0.11032.342-0.005-0.0050.0000.0000.0000.000
98B240LEU0-0.0710.12230.9920.0010.0010.0000.0000.0000.000
99B241ARG00.155-0.10034.0080.0010.0010.0000.0000.0000.000
100B241ARG10.7391.02638.534-0.033-0.0330.0000.0000.0000.000
101B242ASN00.090-0.06536.1590.0010.0010.0000.0000.0000.000
102B242ASN0-0.1210.07432.9300.0010.0010.0000.0000.0000.000
103B243THR00.083-0.06137.1430.0000.0000.0000.0000.0000.000
104B243THR0-0.0360.07139.4680.0010.0010.0000.0000.0000.000
105B244THR00.024-0.09340.538-0.002-0.0020.0000.0000.0000.000
106B244THR00.0020.08343.8310.0010.0010.0000.0000.0000.000
107B245PRO0-0.099-0.12942.8480.0000.0000.0000.0000.0000.000
108B246THR00.0550.00745.1780.0000.0000.0000.0000.0000.000
109B246THR0-0.0320.08347.5830.0000.0000.0000.0000.0000.000
110B247TYR00.005-0.12147.939-0.001-0.0010.0000.0000.0000.000
111B247TYR0-0.1350.06648.573-0.001-0.0010.0000.0000.0000.000
112B248SER00.076-0.08247.6020.0010.0010.0000.0000.0000.000
113B248SER0-0.0080.10250.0310.0000.0000.0000.0000.0000.000
114B249HIS0-0.081-0.11446.404-0.001-0.0010.0000.0000.0000.000
115B249HIS10.7370.99245.375-0.019-0.0190.0000.0000.0000.000
116B250GLY00.112-0.07946.736-0.001-0.0010.0000.0000.0000.000
117B251LYS00.1100.05743.8160.0020.0020.0000.0000.0000.000
118B251LYS10.8961.06443.564-0.007-0.0070.0000.0000.0000.000
119B252LYS00.025-0.12141.889-0.001-0.0010.0000.0000.0000.000
120B252LYS10.8151.00643.047-0.010-0.0100.0000.0000.0000.000
121B253PHE00.129-0.07438.5810.0000.0000.0000.0000.0000.000
122B253PHE0-0.0460.12936.3940.0000.0000.0000.0000.0000.000
123B254SER0-0.036-0.10340.098-0.002-0.0020.0000.0000.0000.000
124B254SER00.0220.07642.7890.0000.0000.0000.0000.0000.000
125B255VAL00.070-0.09039.1830.0010.0010.0000.0000.0000.000
126B255VAL0-0.1090.12437.3060.0000.0000.0000.0000.0000.000
127B256GLY00.036-0.08440.645-0.002-0.0020.0000.0000.0000.000
128B257LEU00.0750.00141.8170.0040.0040.0000.0000.0000.000
129B257LEU0-0.1270.09240.0120.0000.0000.0000.0000.0000.000
130B258GLY00.094-0.06843.4170.0000.0000.0000.0000.0000.000
131B259HIS00.1050.04146.346-0.001-0.0010.0000.0000.0000.000
132B259HIS0-0.1320.06747.304-0.001-0.0010.0000.0000.0000.000
133B260GLY00.059-0.10349.409-0.001-0.0010.0000.0000.0000.000
134B261TRP00.021-0.02647.415-0.002-0.0020.0000.0000.0000.000
135B261TRP0-0.0660.13246.6280.0000.0000.0000.0000.0000.000
136B262ASP00.098-0.07744.3840.0020.0020.0000.0000.0000.000
137B262ASP-1-0.770-0.75144.3690.0250.0250.0000.0000.0000.000
138B263SER00.100-0.05940.749-0.002-0.0020.0000.0000.0000.000
139B263SER0-0.0500.08040.0900.0000.0000.0000.0000.0000.000
140B264ILE00.061-0.08741.3170.0030.0030.0000.0000.0000.000
141B264ILE0-0.1310.08240.9350.0000.0000.0000.0000.0000.000
142B265VAL00.019-0.10036.950-0.001-0.0010.0000.0000.0000.000
143B265VAL0-0.0750.09035.0040.0010.0010.0000.0000.0000.000
144B266SER00.049-0.09236.2480.0010.0010.0000.0000.0000.000
145B266SER0-0.0670.04636.578-0.001-0.0010.0000.0000.0000.000
146B267VAL00.061-0.08231.9920.0010.0010.0000.0000.0000.000
147B267VAL0-0.0660.11830.9370.0000.0000.0000.0000.0000.000
148B268ASN00.105-0.07331.231-0.001-0.0010.0000.0000.0000.000
149B268ASN0-0.0860.07528.0910.0010.0010.0000.0000.0000.000
150B269GLY00.027-0.09932.406-0.003-0.0030.0000.0000.0000.000
151B270VAL00.056-0.03535.153-0.001-0.0010.0000.0000.0000.000
152B270VAL0-0.0630.14434.8370.0000.0000.0000.0000.0000.000
153B271ASP00.121-0.06736.4820.0030.0030.0000.0000.0000.000
154B271ASP-1-0.806-0.74940.6150.0110.0110.0000.0000.0000.000
155B272THR0-0.010-0.09538.6470.0020.0020.0000.0000.0000.000
156B272THR0-0.0930.06238.833-0.001-0.0010.0000.0000.0000.000
157B273GLY00.080-0.09235.9360.0010.0010.0000.0000.0000.000
158B274GLU00.070-0.00832.7940.0050.0050.0000.0000.0000.000
159B274GLU-1-0.894-0.74832.2680.0250.0250.0000.0000.0000.000
160B275THR00.031-0.05831.381-0.004-0.0040.0000.0000.0000.000
161B275THR0-0.0520.04729.464-0.001-0.0010.0000.0000.0000.000
162B276THR00.016-0.09728.0390.0070.0070.0000.0000.0000.000
163B276THR0-0.0130.07827.1940.0000.0000.0000.0000.0000.000
164B277MET00.052-0.09325.446-0.005-0.0050.0000.0000.0000.000
165B277MET0-0.0960.10323.884-0.001-0.0010.0000.0000.0000.000
166B278ARG00.120-0.08623.4460.0080.0080.0000.0000.0000.000
167B278ARG10.8181.05124.0650.0360.0360.0000.0000.0000.000
168B279TRP0-0.016-0.12919.511-0.005-0.0050.0000.0000.0000.000
169B279TRP0-0.0940.12718.2130.0070.0070.0000.0000.0000.000
170B280TYR00.135-0.08320.4560.0030.0030.0000.0000.0000.000
171B280TYR0-0.0640.10422.5390.0020.0020.0000.0000.0000.000
172B281LYS00.146-0.09317.544-0.007-0.0070.0000.0000.0000.000
173B281LYS10.8551.06616.4140.1900.1900.0000.0000.0000.000
174B282ALA00.082-0.10113.5280.0330.0330.0000.0000.0000.000
175B282ALA0-0.0520.14312.870-0.011-0.0110.0000.0000.0000.000
176B283GLY0-0.040-0.12214.936-0.024-0.0240.0000.0000.0000.000
177B284THR00.0170.02816.5230.0190.0190.0000.0000.0000.000
178B284THR0-0.0130.07317.3240.0050.0050.0000.0000.0000.000
179B285GLN00.055-0.11218.694-0.013-0.0130.0000.0000.0000.000
180B285GLN0-0.0870.07821.2390.0050.0050.0000.0000.0000.000
181B286ASN00.137-0.06122.3700.0110.0110.0000.0000.0000.000
182B286ASN0-0.0980.07324.390-0.002-0.0020.0000.0000.0000.000
183B287LEU00.121-0.10225.073-0.005-0.0050.0000.0000.0000.000
184B287LEU0-0.1370.10225.7500.0010.0010.0000.0000.0000.000
185B288THR00.070-0.08127.1000.0060.0060.0000.0000.0000.000
186B288THR0-0.0550.08030.815-0.001-0.0010.0000.0000.0000.000
187B289ILE00.079-0.08830.389-0.002-0.0020.0000.0000.0000.000
188B289ILE0-0.0810.11228.1820.0010.0010.0000.0000.0000.000
189B290GLY00.021-0.10031.950-0.001-0.0010.0000.0000.0000.000
190B291SER00.0700.02035.6940.0020.0020.0000.0000.0000.000
191B291SER0-0.0520.06436.9860.0010.0010.0000.0000.0000.000
192B292ARG00.136-0.08038.412-0.001-0.0010.0000.0000.0000.000
193B292ARG10.7060.97041.883-0.012-0.0120.0000.0000.0000.000
194B293LEU00.017-0.10842.1700.0010.0010.0000.0000.0000.000
195B293LEU0-0.0290.11142.4270.0000.0000.0000.0000.0000.000
196B294TYR00.125-0.08344.602-0.002-0.0020.0000.0000.0000.000
197B294TYR0-0.1590.03046.7880.0000.0000.0000.0000.0000.000
198B295GLY00.033-0.09447.6760.0020.0020.0000.0000.0000.000
199B296GLU00.0770.00850.864-0.002-0.0020.0000.0000.0000.000
200B296GLU-1-0.835-0.77253.2280.0160.0160.0000.0000.0000.000
201B297SER00.092-0.05854.3960.0000.0000.0000.0000.0000.000
202B297SER0-0.0590.05757.7670.0000.0000.0000.0000.0000.000
203B298SER00.061-0.09857.0410.0010.0010.0000.0000.0000.000
204B298SER0-0.0120.07158.3780.0000.0000.0000.0000.0000.000
205B299LYS0-0.019-0.08554.5790.0000.0000.0000.0000.0000.000
206B299LYS10.7851.00953.589-0.018-0.0180.0000.0000.0000.000
207B300ILE00.095-0.09353.2740.0020.0020.0000.0000.0000.000
208B300ILE0-0.1290.11452.2240.0000.0000.0000.0000.0000.000
209B301GLN00.076-0.11552.826-0.001-0.0010.0000.0000.0000.000
210B301GLN0-0.0720.12052.7540.0010.0010.0000.0000.0000.000
211B302PRO0-0.009-0.11652.1530.0000.0000.0000.0000.0000.000
212B303GLY00.0110.01050.4130.0000.0000.0000.0000.0000.000
213B304VAL00.108-0.01646.241-0.001-0.0010.0000.0000.0000.000
214B304VAL0-0.0710.12044.1410.0000.0000.0000.0000.0000.000
215B305LEU00.079-0.10344.5570.0020.0020.0000.0000.0000.000
216B305LEU0-0.0720.10943.9190.0000.0000.0000.0000.0000.000
217B306SER00.046-0.10840.6860.0000.0000.0000.0000.0000.000
218B306SER0-0.0430.08540.0310.0010.0010.0000.0000.0000.000
219B307GLY0-0.027-0.08939.178-0.001-0.0010.0000.0000.0000.000
220B308SER0-0.013-0.00235.2630.0000.0000.0000.0000.0000.000
221B308SER0-0.0050.09634.2000.0020.0020.0000.0000.0000.000
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