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

tag_button

FMODB ID: 16LNZ

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 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 236
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -958509.465242
FMO2-HF: Nuclear repulsion 909566.640391
FMO2-HF: Total energy -48942.824851
FMO2-MP2: Total energy -49083.915961


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.
-1.7762.4911.202-2.709-2.759-0.01
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 : 0.210 / q_NPA : 0.045
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].
4B190HIS0-0.0730.0554.519-0.1640.070-0.001-0.081-0.1520.000
5B191HIS00.042-0.1033.703-1.7380.3510.016-1.210-0.8950.000
6B191HIS0-0.1420.0584.8260.2370.398-0.001-0.037-0.1220.000
7B192HIS00.005-0.0983.0200.2370.6880.057-0.162-0.3470.000
8B192HIS0-0.0230.0972.826-0.5890.6721.131-1.200-1.192-0.010
9B193HIS00.099-0.0634.276-0.0120.0590.000-0.019-0.0510.000
10B193HIS0-0.0690.0945.3570.2850.2850.0000.0000.0000.000
11B194HIS00.055-0.1467.103-0.113-0.1130.0000.0000.0000.000
12B194HIS0-0.0490.1189.5860.0700.0700.0000.0000.0000.000
13B195GLY0-0.007-0.0778.661-0.013-0.0130.0000.0000.0000.000
14B196GLY00.019-0.00410.8850.0440.0440.0000.0000.0000.000
15B197CYS00.054-0.05312.411-0.049-0.0490.0000.0000.0000.000
16B197CYS0-0.1980.26215.4920.0000.0000.0000.0000.0000.000
17B198ARG00.048-0.11114.4760.0330.0330.0000.0000.0000.000
18B198ARG10.8921.0779.609-0.222-0.2220.0000.0000.0000.000
19B199PRO00.032-0.09015.569-0.028-0.0280.0000.0000.0000.000
20B200SER0-0.040-0.00918.0130.0160.0160.0000.0000.0000.000
21B200SER0-0.0760.05521.053-0.004-0.0040.0000.0000.0000.000
22B201ALA00.134-0.07919.5590.0070.0070.0000.0000.0000.000
23B201ALA0-0.0860.09418.4990.0010.0010.0000.0000.0000.000
24B202GLN00.010-0.10620.3950.0090.0090.0000.0000.0000.000
25B202GLN0-0.0370.11523.4100.0080.0080.0000.0000.0000.000
26B203SER00.149-0.04324.1270.0050.0050.0000.0000.0000.000
27B203SER0-0.0450.07927.3770.0010.0010.0000.0000.0000.000
28B204LEU00.000-0.12526.823-0.009-0.0090.0000.0000.0000.000
29B204LEU0-0.0590.11925.550-0.001-0.0010.0000.0000.0000.000
30B205GLU00.116-0.11828.6110.0020.0020.0000.0000.0000.000
31B205GLU-1-1.045-0.85231.2260.0390.0390.0000.0000.0000.000
32B206ILE00.142-0.11832.113-0.004-0.0040.0000.0000.0000.000
33B206ILE0-0.1100.13632.6640.0000.0000.0000.0000.0000.000
34B207LYS00.073-0.12034.6290.0020.0020.0000.0000.0000.000
35B207LYS10.8171.07432.133-0.025-0.0250.0000.0000.0000.000
36B208HIS00.049-0.09137.444-0.003-0.0030.0000.0000.0000.000
37B208HIS10.7290.96239.569-0.014-0.0140.0000.0000.0000.000
38B209GLY00.029-0.09140.589-0.002-0.0020.0000.0000.0000.000
39B210ASP00.1170.01042.3930.0020.0020.0000.0000.0000.000
40B210ASP-1-0.986-0.84945.1070.0120.0120.0000.0000.0000.000
41B211LEU00.046-0.11145.961-0.002-0.0020.0000.0000.0000.000
42B211LEU0-0.0910.11445.0590.0000.0000.0000.0000.0000.000
43B212SER00.055-0.07648.0210.0010.0010.0000.0000.0000.000
44B212SER0-0.0080.05549.8530.0000.0000.0000.0000.0000.000
45B213ILE00.028-0.07350.4700.0000.0000.0000.0000.0000.000
46B213ILE0-0.0310.08949.7750.0000.0000.0000.0000.0000.000
47B214ASN00.075-0.09949.811-0.001-0.0010.0000.0000.0000.000
48B214ASN0-0.0880.08247.4940.0010.0010.0000.0000.0000.000
49B215SER00.001-0.08650.1100.0000.0000.0000.0000.0000.000
50B215SER0-0.0490.08252.1580.0000.0000.0000.0000.0000.000
51B216ALA00.127-0.05748.9960.0000.0000.0000.0000.0000.000
52B216ALA0-0.1020.07548.1660.0000.0000.0000.0000.0000.000
53B217ASN00.129-0.08348.5200.0010.0010.0000.0000.0000.000
54B217ASN0-0.0690.07250.2620.0010.0010.0000.0000.0000.000
55B218ASN00.099-0.05347.4240.0010.0010.0000.0000.0000.000
56B218ASN0-0.1250.04748.1590.0010.0010.0000.0000.0000.000
57B219HIS00.148-0.08845.328-0.002-0.0020.0000.0000.0000.000
58B219HIS0-0.0060.15042.5090.0010.0010.0000.0000.0000.000
59B220TYR00.065-0.10441.5830.0020.0020.0000.0000.0000.000
60B220TYR0-0.0720.10136.5160.0000.0000.0000.0000.0000.000
61B221ALA00.133-0.13638.566-0.002-0.0020.0000.0000.0000.000
62B221ALA0-0.0990.15337.7260.0010.0010.0000.0000.0000.000
63B222ALA00.033-0.15634.8640.0020.0020.0000.0000.0000.000
64B222ALA0-0.0880.11734.073-0.001-0.0010.0000.0000.0000.000
65B223GLN00.066-0.09930.883-0.002-0.0020.0000.0000.0000.000
66B223GLN0-0.0970.09428.126-0.005-0.0050.0000.0000.0000.000
67B224THR00.026-0.07628.5540.0030.0030.0000.0000.0000.000
68B224THR0-0.0370.06826.685-0.002-0.0020.0000.0000.0000.000
69B225LEU00.062-0.07224.671-0.001-0.0010.0000.0000.0000.000
70B225LEU0-0.0460.11222.8760.0020.0020.0000.0000.0000.000
71B226SER00.059-0.07721.526-0.004-0.0040.0000.0000.0000.000
72B226SER00.0090.09520.4970.0030.0030.0000.0000.0000.000
73B227VAL00.062-0.12919.0530.0150.0150.0000.0000.0000.000
74B227VAL0-0.0720.12918.4990.0010.0010.0000.0000.0000.000
75B228SER00.051-0.09315.244-0.017-0.0170.0000.0000.0000.000
76B228SER0-0.0050.07614.598-0.012-0.0120.0000.0000.0000.000
77B229CYS00.080-0.11414.3260.0370.0370.0000.0000.0000.000
78B230ASP00.161-0.08910.297-0.047-0.0470.0000.0000.0000.000
79B230ASP-1-0.966-0.8508.8880.0390.0390.0000.0000.0000.000
80B231VAL0-0.077-0.11611.455-0.075-0.0750.0000.0000.0000.000
81B231VAL0-0.0270.10311.8520.0010.0010.0000.0000.0000.000
82B232PRO0-0.011-0.10213.9880.0110.0110.0000.0000.0000.000
83B233ALA00.0390.00417.3070.0130.0130.0000.0000.0000.000
84B233ALA00.0060.09217.6400.0030.0030.0000.0000.0000.000
85B234ASN00.122-0.07519.531-0.012-0.0120.0000.0000.0000.000
86B234ASN0-0.1100.07523.491-0.006-0.0060.0000.0000.0000.000
87B235ILE00.110-0.12022.0320.0100.0100.0000.0000.0000.000
88B235ILE0-0.0490.14019.5330.0010.0010.0000.0000.0000.000
89B236ARG00.119-0.11823.619-0.009-0.0090.0000.0000.0000.000
90B236ARG10.7091.04427.266-0.030-0.0300.0000.0000.0000.000
91B237PHE00.051-0.13326.5450.0100.0100.0000.0000.0000.000
92B237PHE0-0.0910.08923.1510.0000.0000.0000.0000.0000.000
93B238MET00.176-0.05927.957-0.007-0.0070.0000.0000.0000.000
94B238MET0-0.1170.08130.1660.0020.0020.0000.0000.0000.000
95B239LEU00.077-0.10030.3650.0070.0070.0000.0000.0000.000
96B239LEU0-0.0710.09931.6690.0000.0000.0000.0000.0000.000
97B240LEU0-0.001-0.14632.460-0.004-0.0040.0000.0000.0000.000
98B240LEU0-0.0830.13730.3750.0010.0010.0000.0000.0000.000
99B241ARG00.139-0.07433.8490.0010.0010.0000.0000.0000.000
100B241ARG10.7971.03138.422-0.031-0.0310.0000.0000.0000.000
101B242ASN00.135-0.05536.2200.0010.0010.0000.0000.0000.000
102B242ASN0-0.1590.04732.8690.0010.0010.0000.0000.0000.000
103B243THR00.084-0.06437.1780.0000.0000.0000.0000.0000.000
104B243THR0-0.0330.06739.0630.0010.0010.0000.0000.0000.000
105B244THR0-0.033-0.08740.389-0.002-0.0020.0000.0000.0000.000
106B244THR00.0170.07143.5310.0010.0010.0000.0000.0000.000
107B245PRO0-0.071-0.11342.7940.0000.0000.0000.0000.0000.000
108B246THR00.0910.00145.0940.0010.0010.0000.0000.0000.000
109B246THR0-0.0270.11248.0280.0000.0000.0000.0000.0000.000
110B247TYR00.034-0.10748.1430.0000.0000.0000.0000.0000.000
111B247TYR0-0.1520.04248.549-0.001-0.0010.0000.0000.0000.000
112B248SER00.026-0.09747.6720.0010.0010.0000.0000.0000.000
113B248SER0-0.0070.09349.2900.0000.0000.0000.0000.0000.000
114B249HIS00.035-0.10345.945-0.001-0.0010.0000.0000.0000.000
115B249HIS10.6800.98145.039-0.017-0.0170.0000.0000.0000.000
116B250GLY00.066-0.09646.276-0.001-0.0010.0000.0000.0000.000
117B251LYS00.1100.03543.8760.0020.0020.0000.0000.0000.000
118B251LYS10.9131.06743.409-0.006-0.0060.0000.0000.0000.000
119B252LYS00.004-0.09141.8510.0000.0000.0000.0000.0000.000
120B252LYS10.7580.94742.726-0.006-0.0060.0000.0000.0000.000
121B253PHE00.120-0.08938.4780.0010.0010.0000.0000.0000.000
122B253PHE0-0.0500.12536.1850.0000.0000.0000.0000.0000.000
123B254SER0-0.042-0.10039.991-0.002-0.0020.0000.0000.0000.000
124B254SER0-0.0200.05042.6020.0000.0000.0000.0000.0000.000
125B255VAL00.019-0.11439.1560.0020.0020.0000.0000.0000.000
126B255VAL0-0.0690.11537.1170.0000.0000.0000.0000.0000.000
127B256GLY00.022-0.07040.540-0.003-0.0030.0000.0000.0000.000
128B257LEU00.054-0.03841.6630.0030.0030.0000.0000.0000.000
129B257LEU0-0.1160.10739.9330.0000.0000.0000.0000.0000.000
130B258GLY00.095-0.05143.0960.0010.0010.0000.0000.0000.000
131B259HIS00.1520.05546.111-0.001-0.0010.0000.0000.0000.000
132B259HIS0-0.1910.06447.955-0.001-0.0010.0000.0000.0000.000
133B260GLY00.063-0.08749.7570.0000.0000.0000.0000.0000.000
134B261TRP00.0460.00947.138-0.001-0.0010.0000.0000.0000.000
135B261TRP0-0.0780.15546.4010.0000.0000.0000.0000.0000.000
136B262ASP00.158-0.08144.3520.0020.0020.0000.0000.0000.000
137B262ASP-1-0.785-0.73044.6340.0220.0220.0000.0000.0000.000
138B263SER00.071-0.05740.709-0.002-0.0020.0000.0000.0000.000
139B263SER0-0.0130.13239.5320.0000.0000.0000.0000.0000.000
140B264ILE00.072-0.11041.1550.0030.0030.0000.0000.0000.000
141B264ILE0-0.1290.09040.6990.0000.0000.0000.0000.0000.000
142B265VAL00.036-0.10836.679-0.003-0.0030.0000.0000.0000.000
143B265VAL0-0.0850.08834.6550.0010.0010.0000.0000.0000.000
144B266SER00.079-0.08236.2170.0020.0020.0000.0000.0000.000
145B266SER0-0.0570.07936.5860.0000.0000.0000.0000.0000.000
146B267VAL00.022-0.09531.9130.0010.0010.0000.0000.0000.000
147B267VAL0-0.0490.09630.9010.0000.0000.0000.0000.0000.000
148B268ASN00.071-0.09731.217-0.001-0.0010.0000.0000.0000.000
149B268ASN0-0.0900.08027.9390.0000.0000.0000.0000.0000.000
150B269GLY00.022-0.09532.213-0.003-0.0030.0000.0000.0000.000
151B270VAL00.068-0.00335.173-0.001-0.0010.0000.0000.0000.000
152B270VAL0-0.0450.12334.9670.0000.0000.0000.0000.0000.000
153B271ASP00.131-0.07036.4010.0030.0030.0000.0000.0000.000
154B271ASP-1-0.876-0.79939.8990.0050.0050.0000.0000.0000.000
155B272THR0-0.096-0.12238.2370.0030.0030.0000.0000.0000.000
156B272THR0-0.0530.08837.514-0.001-0.0010.0000.0000.0000.000
157B273GLY00.133-0.07135.7940.0010.0010.0000.0000.0000.000
158B274GLU00.083-0.02032.5870.0050.0050.0000.0000.0000.000
159B274GLU-1-0.898-0.77732.1860.0220.0220.0000.0000.0000.000
160B275THR0-0.024-0.06931.114-0.003-0.0030.0000.0000.0000.000
161B275THR0-0.0340.05129.105-0.001-0.0010.0000.0000.0000.000
162B276THR00.025-0.07527.8210.0060.0060.0000.0000.0000.000
163B276THR0-0.0160.07826.7860.0020.0020.0000.0000.0000.000
164B277MET00.093-0.12225.195-0.005-0.0050.0000.0000.0000.000
165B277MET0-0.0940.16423.874-0.002-0.0020.0000.0000.0000.000
166B278ARG00.126-0.08223.4860.0080.0080.0000.0000.0000.000
167B278ARG10.8511.07123.7480.0420.0420.0000.0000.0000.000
168B279TRP0-0.028-0.15519.568-0.005-0.0050.0000.0000.0000.000
169B279TRP0-0.0620.13318.2860.0080.0080.0000.0000.0000.000
170B280TYR00.133-0.12520.4940.0060.0060.0000.0000.0000.000
171B280TYR0-0.0740.13022.2010.0020.0020.0000.0000.0000.000
172B281LYS00.080-0.07317.580-0.003-0.0030.0000.0000.0000.000
173B281LYS10.8501.06416.2320.2000.2000.0000.0000.0000.000
174B282ALA00.110-0.10413.6730.0350.0350.0000.0000.0000.000
175B282ALA0-0.0330.13713.092-0.012-0.0120.0000.0000.0000.000
176B283GLY0-0.026-0.11515.100-0.021-0.0210.0000.0000.0000.000
177B284THR0-0.083-0.00916.8280.0190.0190.0000.0000.0000.000
178B284THR0-0.0100.07016.3790.0030.0030.0000.0000.0000.000
179B285GLN00.126-0.10218.774-0.011-0.0110.0000.0000.0000.000
180B285GLN0-0.0970.10521.2690.0060.0060.0000.0000.0000.000
181B286ASN00.136-0.10422.3240.0090.0090.0000.0000.0000.000
182B286ASN0-0.1140.08424.389-0.001-0.0010.0000.0000.0000.000
183B287LEU00.169-0.10624.956-0.004-0.0040.0000.0000.0000.000
184B287LEU0-0.1710.11025.3570.0010.0010.0000.0000.0000.000
185B288THR00.032-0.12926.8470.0040.0040.0000.0000.0000.000
186B288THR0-0.0400.10629.887-0.001-0.0010.0000.0000.0000.000
187B289ILE00.088-0.08430.191-0.002-0.0020.0000.0000.0000.000
188B289ILE0-0.0710.11728.3680.0010.0010.0000.0000.0000.000
189B290GLY00.006-0.08332.123-0.001-0.0010.0000.0000.0000.000
190B291SER00.0630.01835.7540.0020.0020.0000.0000.0000.000
191B291SER0-0.0610.02437.1030.0010.0010.0000.0000.0000.000
192B292ARG00.127-0.09938.439-0.002-0.0020.0000.0000.0000.000
193B292ARG10.8201.06741.656-0.006-0.0060.0000.0000.0000.000
194B293LEU00.025-0.11942.1670.0010.0010.0000.0000.0000.000
195B293LEU0-0.0570.11042.4040.0000.0000.0000.0000.0000.000
196B294TYR00.115-0.06944.659-0.002-0.0020.0000.0000.0000.000
197B294TYR0-0.1740.01946.6280.0000.0000.0000.0000.0000.000
198B295GLY00.020-0.12047.5350.0020.0020.0000.0000.0000.000
199B296GLU00.1100.03850.572-0.001-0.0010.0000.0000.0000.000
200B296GLU-1-1.002-0.86253.7800.0130.0130.0000.0000.0000.000
201B297SER00.119-0.10654.102-0.001-0.0010.0000.0000.0000.000
202B297SER0-0.0420.07257.2450.0000.0000.0000.0000.0000.000
203B298SER00.005-0.05156.7040.0000.0000.0000.0000.0000.000
204B298SER0-0.0430.04458.1390.0000.0000.0000.0000.0000.000
205B299LYS00.070-0.10754.3660.0000.0000.0000.0000.0000.000
206B299LYS10.8681.06553.589-0.017-0.0170.0000.0000.0000.000
207B300ILE00.025-0.08752.9790.0010.0010.0000.0000.0000.000
208B300ILE0-0.1050.13352.0510.0000.0000.0000.0000.0000.000
209B301GLN00.168-0.10653.0460.0000.0000.0000.0000.0000.000
210B301GLN0-0.0990.11352.7840.0010.0010.0000.0000.0000.000
211B302PRO0-0.023-0.11251.9800.0000.0000.0000.0000.0000.000
212B303GLY00.0110.00750.1990.0000.0000.0000.0000.0000.000
213B304VAL00.098-0.00545.841-0.001-0.0010.0000.0000.0000.000
214B304VAL0-0.0300.11743.9720.0000.0000.0000.0000.0000.000
215B305LEU00.084-0.10544.1240.0010.0010.0000.0000.0000.000
216B305LEU0-0.1060.12243.5360.0000.0000.0000.0000.0000.000
217B306SER00.054-0.12440.2460.0000.0000.0000.0000.0000.000
218B306SER0-0.0570.09839.6940.0010.0010.0000.0000.0000.000
219B307GLY00.001-0.08938.736-0.001-0.0010.0000.0000.0000.000
220B308SER0-0.037-0.02335.0040.0000.0000.0000.0000.0000.000
221B308SER00.0160.10934.1480.0020.0020.0000.0000.0000.000
222B309ALA00.058-0.06933.488-0.001-0.0010.0000.0000.0000.000
223B309ALA0-0.0400.06633.458-0.001-0.0010.0000.0000.0000.000
224B310THR00.029-0.06829.9660.0020.0020.0000.0000.0000.000
225B310THR0-0.0150.08728.3730.0020.0020.0000.0000.0000.000
226B311LEU00.152-0.08828.054-0.004-0.0040.0000.0000.0000.000
227B311LEU0-0.1050.11726.394-0.001-0.0010.0000.0000.0000.000
228B312LEU00.092-0.13526.4310.0080.0080.0000.0000.0000.000
229B312LEU0-0.1170.13025.6640.0000.0000.0000.0000.0000.000
230B313MET00.076-0.11123.040-0.011-0.0110.0000.0000.0000.000
231B313MET0-0.1040.10120.604-0.003-0.0030.0000.0000.0000.000
232B314ILE00.113-0.08823.4620.0150.0150.0000.0000.0000.000
233B314ILE0-0.1040.07525.840-0.001-0.0010.0000.0000.0000.000
234B315LEU00.032-0.16720.661-0.016-0.0160.0000.0000.0000.000
235B315LEU0-0.0500.15618.1470.0010.0010.0000.0000.0000.000
236B316PRO00.011-0.06720.5710.0080.0080.0000.0000.0000.000