Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: LNK59

Calculation Name: 1US7-B-Xray372

Preferred Name: Hsp90 co-chaperone Cdc37

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1US7

Chain ID: B

ChEMBL ID: CHEMBL1795123

UniProt ID: Q16543

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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1930823.352607
FMO2-HF: Nuclear repulsion 1848475.228002
FMO2-HF: Total energy -82348.124605
FMO2-MP2: Total energy -82581.135951


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:148:HIS)


Summations of interaction energy for fragment #1(B:148: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.
-12.108-7.8950.401-1.761-2.8540
Interaction energy analysis for fragmet #1(B:148:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / 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].
3B150THR00.0760.0393.875-3.131-1.037-0.001-0.987-1.1070.002
4B151PHE0-0.025-0.0163.461-3.180-2.2940.041-0.260-0.6670.001
5B152VAL00.0560.0204.218-1.922-1.725-0.001-0.024-0.1720.000
6B153GLU-1-0.894-0.9566.4563.3073.3070.0000.0000.0000.000
7B154LYS10.8650.9558.689-2.856-2.8560.0000.0000.0000.000
8B155TYR00.0360.0118.219-0.355-0.3550.0000.0000.0000.000
9B156GLU-1-0.753-0.84710.5850.6460.6460.0000.0000.0000.000
10B157LYS10.8800.92311.353-1.124-1.1240.0000.0000.0000.000
11B158GLN00.0500.03313.0800.0110.0110.0000.0000.0000.000
12B159ILE00.0010.0008.089-0.121-0.1210.0000.0000.0000.000
13B160LYS10.8900.94812.408-0.799-0.7990.0000.0000.0000.000
14B161HIS0-0.050-0.02014.996-0.102-0.1020.0000.0000.0000.000
15B162PHE00.0280.00414.657-0.045-0.0450.0000.0000.0000.000
16B163GLY00.023-0.00315.776-0.069-0.0690.0000.0000.0000.000
17B164MET0-0.028-0.01416.794-0.050-0.0500.0000.0000.0000.000
18B165LEU0-0.0570.00719.846-0.023-0.0230.0000.0000.0000.000
19B166ARG10.9570.96221.868-0.060-0.0600.0000.0000.0000.000
20B167ARG10.9480.98424.011-0.141-0.1410.0000.0000.0000.000
21B168TRP00.0740.03223.2330.0260.0260.0000.0000.0000.000
22B169ASP-1-0.848-0.90724.5790.1090.1090.0000.0000.0000.000
23B170ASP-1-0.874-0.94024.4690.1950.1950.0000.0000.0000.000
24B171SER0-0.013-0.00220.3950.0350.0350.0000.0000.0000.000
25B172GLN00.0140.00020.2280.0220.0220.0000.0000.0000.000
26B173LYS10.8460.91521.414-0.280-0.2800.0000.0000.0000.000
27B174TYR00.0660.02116.1930.0580.0580.0000.0000.0000.000
28B175LEU00.0390.01914.9940.0650.0650.0000.0000.0000.000
29B176SER0-0.076-0.04517.7410.0310.0310.0000.0000.0000.000
30B177ASP-1-0.875-0.91220.0730.3780.3780.0000.0000.0000.000
31B178ASN0-0.047-0.02815.2320.1530.1530.0000.0000.0000.000
32B179VAL00.0290.02514.9360.0430.0430.0000.0000.0000.000
33B180HIS0-0.044-0.02810.693-0.134-0.1340.0000.0000.0000.000
34B181LEU0-0.020-0.01910.1550.1800.1800.0000.0000.0000.000
35B182VAL0-0.0280.00910.729-0.115-0.1150.0000.0000.0000.000
36B183CYS0-0.057-0.0396.5070.0550.0550.0000.0000.0000.000
37B184GLU-1-0.770-0.8946.999-1.449-1.4490.0000.0000.0000.000
38B185GLU-1-0.894-0.9302.784-2.458-1.4290.363-0.487-0.905-0.003
39B186THR0-0.006-0.0235.0720.0920.099-0.001-0.003-0.0030.000
40B187ALA00.0140.0218.138-0.028-0.0280.0000.0000.0000.000
41B188ASN0-0.039-0.0396.2880.0450.0450.0000.0000.0000.000
42B189TYR00.0490.0236.7670.0950.0950.0000.0000.0000.000
43B190LEU0-0.024-0.0118.4140.0900.0900.0000.0000.0000.000
44B191VAL00.0260.02211.3840.0160.0160.0000.0000.0000.000
45B192ILE0-0.060-0.0288.9970.0110.0110.0000.0000.0000.000
46B193TRP00.0460.01212.1130.0850.0850.0000.0000.0000.000
47B194CYS0-0.049-0.02514.0410.0210.0210.0000.0000.0000.000
48B195ILE0-0.003-0.00513.994-0.009-0.0090.0000.0000.0000.000
49B196ASP-1-0.833-0.89514.2360.1950.1950.0000.0000.0000.000
50B197LEU0-0.026-0.01017.4180.0140.0140.0000.0000.0000.000
51B198GLU-1-0.760-0.88920.028-0.027-0.0270.0000.0000.0000.000
52B199VAL0-0.061-0.03919.672-0.005-0.0050.0000.0000.0000.000
53B200GLU-1-0.949-0.95819.7920.2620.2620.0000.0000.0000.000
54B201GLU-1-0.897-0.93623.2370.0580.0580.0000.0000.0000.000
55B202LYS10.7610.86822.441-0.226-0.2260.0000.0000.0000.000
56B203CYS00.0480.01223.4560.0030.0030.0000.0000.0000.000
57B204ALA0-0.017-0.00225.030-0.007-0.0070.0000.0000.0000.000
58B205LEU0-0.018-0.01720.9050.0020.0020.0000.0000.0000.000
59B206MET00.0070.02119.694-0.002-0.0020.0000.0000.0000.000
60B207GLU-1-0.797-0.89820.796-0.055-0.0550.0000.0000.0000.000
61B208GLN0-0.048-0.00821.933-0.036-0.0360.0000.0000.0000.000
62B209VAL0-0.011-0.01916.1520.0050.0050.0000.0000.0000.000
63B210ALA00.0600.03117.768-0.025-0.0250.0000.0000.0000.000
64B211HIS0-0.025-0.00919.008-0.045-0.0450.0000.0000.0000.000
65B212GLN0-0.014-0.00417.389-0.054-0.0540.0000.0000.0000.000
66B213THR0-0.071-0.05113.579-0.003-0.0030.0000.0000.0000.000
67B214ILE00.0720.04415.729-0.058-0.0580.0000.0000.0000.000
68B215VAL0-0.0050.01518.241-0.018-0.0180.0000.0000.0000.000
69B216MET0-0.045-0.00811.953-0.014-0.0140.0000.0000.0000.000
70B217GLN0-0.018-0.02712.964-0.005-0.0050.0000.0000.0000.000
71B218PHE00.0550.02015.419-0.027-0.0270.0000.0000.0000.000
72B219ILE0-0.066-0.02215.8900.0120.0120.0000.0000.0000.000
73B220LEU0-0.041-0.02111.064-0.016-0.0160.0000.0000.0000.000
74B221GLU-1-0.897-0.94415.191-0.507-0.5070.0000.0000.0000.000
75B222LEU00.0150.01417.973-0.001-0.0010.0000.0000.0000.000
76B223ALA0-0.053-0.04316.4300.0170.0170.0000.0000.0000.000
77B224LYS10.8970.93712.0311.0431.0430.0000.0000.0000.000
78B225SER0-0.038-0.00518.3440.0070.0070.0000.0000.0000.000
79B226LEU0-0.043-0.03221.8100.0080.0080.0000.0000.0000.000
80B227LYS10.8560.93720.5830.3420.3420.0000.0000.0000.000
81B228VAL0-0.0100.00119.502-0.018-0.0180.0000.0000.0000.000
82B229ASP-1-0.775-0.88713.760-0.033-0.0330.0000.0000.0000.000
83B230PRO00.0850.01712.8070.0500.0500.0000.0000.0000.000
84B231ARG10.8990.9489.010-0.384-0.3840.0000.0000.0000.000
85B232ALA0-0.039-0.02115.9480.0430.0430.0000.0000.0000.000
86B233CYS0-0.056-0.01018.940-0.013-0.0130.0000.0000.0000.000
87B234PHE00.0520.02117.676-0.009-0.0090.0000.0000.0000.000
88B235ARG10.9480.98219.742-0.210-0.2100.0000.0000.0000.000
89B236GLN00.0000.00123.084-0.013-0.0130.0000.0000.0000.000
90B237PHE00.0590.03521.391-0.010-0.0100.0000.0000.0000.000
91B238PHE00.0300.00819.775-0.001-0.0010.0000.0000.0000.000
92B239THR0-0.053-0.03624.8100.0030.0030.0000.0000.0000.000
93B240LYS10.9350.97126.5820.0910.0910.0000.0000.0000.000
94B241ILE0-0.0170.00025.040-0.002-0.0020.0000.0000.0000.000
95B242LYS10.8100.87927.568-0.066-0.0660.0000.0000.0000.000
96B243THR0-0.040-0.01630.1070.0070.0070.0000.0000.0000.000
97B244ALA0-0.0300.00629.586-0.008-0.0080.0000.0000.0000.000
98B245ASP-1-0.900-0.94531.725-0.073-0.0730.0000.0000.0000.000
99B246ARG10.8140.85833.0150.0700.0700.0000.0000.0000.000
100B247GLN00.0390.01733.7220.0030.0030.0000.0000.0000.000
101B248TYR00.0190.01724.762-0.004-0.0040.0000.0000.0000.000
102B249MET0-0.013-0.00727.225-0.005-0.0050.0000.0000.0000.000
103B250GLU-1-0.777-0.86029.718-0.085-0.0850.0000.0000.0000.000
104B251GLY00.0510.04628.982-0.005-0.0050.0000.0000.0000.000
105B252PHE00.004-0.01722.675-0.013-0.0130.0000.0000.0000.000
106B253ASN0-0.062-0.06025.3950.0000.0000.0000.0000.0000.000
107B254ASP-1-0.883-0.91527.238-0.148-0.1480.0000.0000.0000.000
108B255GLU-1-0.952-0.98322.676-0.307-0.3070.0000.0000.0000.000
109B256LEU0-0.053-0.02121.722-0.015-0.0150.0000.0000.0000.000
110B257GLU-1-0.804-0.90223.248-0.090-0.0900.0000.0000.0000.000
111B258ALA00.0240.01124.024-0.009-0.0090.0000.0000.0000.000
112B259PHE0-0.096-0.05615.764-0.027-0.0270.0000.0000.0000.000
113B260LYS10.8230.88820.5890.0560.0560.0000.0000.0000.000
114B261GLU-1-0.869-0.90622.595-0.129-0.1290.0000.0000.0000.000
115B262ARG10.9340.97218.6150.3800.3800.0000.0000.0000.000
116B263VAL0-0.057-0.01917.456-0.018-0.0180.0000.0000.0000.000
117B264ARG10.8740.91519.7150.0930.0930.0000.0000.0000.000
118B265GLY0-0.0160.00022.7390.0110.0110.0000.0000.0000.000
119B266ARG10.9140.93412.5600.5600.5600.0000.0000.0000.000
120B267ALA00.0330.02019.5340.0090.0090.0000.0000.0000.000
121B268LYS10.8620.90820.8170.1810.1810.0000.0000.0000.000
122B269LEU0-0.017-0.00319.8620.0040.0040.0000.0000.0000.000
123B270ARG10.7660.86915.269-0.003-0.0030.0000.0000.0000.000
124B271ILE00.0420.01521.0670.0180.0180.0000.0000.0000.000
125B272GLU-1-0.774-0.88024.554-0.136-0.1360.0000.0000.0000.000
126B273LYS10.7560.87320.5070.0350.0350.0000.0000.0000.000
127B274ALA00.0260.01224.2780.0080.0080.0000.0000.0000.000
128B275MET0-0.004-0.00325.7400.0080.0080.0000.0000.0000.000
129B276LYS10.9801.00426.9160.1270.1270.0000.0000.0000.000
130B277GLU-1-0.831-0.91124.014-0.017-0.0170.0000.0000.0000.000
131B278TYR0-0.059-0.03728.5710.0060.0060.0000.0000.0000.000
132B279GLU-1-0.912-0.96631.203-0.048-0.0480.0000.0000.0000.000
133B280GLU-1-0.938-0.97730.975-0.045-0.0450.0000.0000.0000.000
134B281GLU-1-0.828-0.90331.7460.0240.0240.0000.0000.0000.000
135B282GLU-1-0.841-0.88934.2360.0160.0160.0000.0000.0000.000
136B283ARG10.8030.90336.1790.0570.0570.0000.0000.0000.000
137B284LYS10.8010.87032.755-0.002-0.0020.0000.0000.0000.000
138B285LYS10.8020.88637.342-0.017-0.0170.0000.0000.0000.000
139B286ARG10.8360.90739.0190.0380.0380.0000.0000.0000.000
140B287LEU0-0.091-0.02638.849-0.004-0.0040.0000.0000.0000.000
141B288GLY00.0460.02343.0050.0050.0050.0000.0000.0000.000
142B289PRO0-0.068-0.03745.3620.0010.0010.0000.0000.0000.000
143B290GLY0-0.029-0.01247.0780.0020.0020.0000.0000.0000.000
144B291GLY0-0.042-0.01942.998-0.004-0.0040.0000.0000.0000.000
145B292LEU0-0.0230.00142.414-0.006-0.0060.0000.0000.0000.000
146B293ASP-1-0.701-0.83841.285-0.034-0.0340.0000.0000.0000.000
147B294PRO00.0250.01443.880-0.005-0.0050.0000.0000.0000.000
148B295VAL00.004-0.00543.721-0.001-0.0010.0000.0000.0000.000
149B296GLU-1-0.859-0.92240.450-0.066-0.0660.0000.0000.0000.000
150B297VAL0-0.038-0.02345.103-0.003-0.0030.0000.0000.0000.000
151B298TYR00.0090.01648.2660.0010.0010.0000.0000.0000.000
152B299GLU-1-0.910-0.95146.387-0.055-0.0550.0000.0000.0000.000
153B300SER0-0.144-0.06347.879-0.003-0.0030.0000.0000.0000.000
154B301LEU0-0.046-0.01849.7390.0000.0000.0000.0000.0000.000
155B302PRO0-0.003-0.00353.367-0.002-0.0020.0000.0000.0000.000
156B303GLU-1-0.931-0.95656.424-0.048-0.0480.0000.0000.0000.000
157B304GLU-1-0.849-0.94557.596-0.035-0.0350.0000.0000.0000.000
158B305LEU0-0.0260.00756.5560.0030.0030.0000.0000.0000.000
159B306GLN0-0.038-0.05857.086-0.001-0.0010.0000.0000.0000.000
160B307LYS10.9000.96655.6030.0370.0370.0000.0000.0000.000
161B308CYS0-0.079-0.02357.5260.0040.0040.0000.0000.0000.000
162B316MET00.026-0.00363.7190.0000.0000.0000.0000.0000.000
163B317LEU00.002-0.00864.658-0.001-0.0010.0000.0000.0000.000
164B318GLN0-0.008-0.00466.151-0.001-0.0010.0000.0000.0000.000
165B319ASP-1-0.819-0.91860.960-0.028-0.0280.0000.0000.0000.000
166B320ALA0-0.0170.00364.191-0.001-0.0010.0000.0000.0000.000
167B321ILE0-0.009-0.00766.261-0.001-0.0010.0000.0000.0000.000
168B322SER0-0.0130.01063.831-0.001-0.0010.0000.0000.0000.000
169B323LYS10.7630.88961.9730.0320.0320.0000.0000.0000.000
170B324MET0-0.014-0.01565.4400.0010.0010.0000.0000.0000.000
171B325ASP-1-0.773-0.89961.313-0.040-0.0400.0000.0000.0000.000
172B326PRO0-0.054-0.01761.8090.0010.0010.0000.0000.0000.000
173B327THR0-0.025-0.01460.1900.0020.0020.0000.0000.0000.000
174B328ASP-1-0.847-0.93757.327-0.054-0.0540.0000.0000.0000.000
175B329ALA00.0450.04457.5280.0000.0000.0000.0000.0000.000
176B330LYS10.9430.95655.4180.0420.0420.0000.0000.0000.000
177B331TYR0-0.047-0.02049.8010.0010.0010.0000.0000.0000.000
178B332HIS00.1040.04153.3780.0000.0000.0000.0000.0000.000
179B333MET00.0210.01854.1810.0030.0030.0000.0000.0000.000
180B334GLN0-0.086-0.05651.7800.0030.0030.0000.0000.0000.000
181B335ARG10.9540.97946.3660.0590.0590.0000.0000.0000.000
182B336CYS00.0040.02050.3850.0010.0010.0000.0000.0000.000
183B337ILE0-0.067-0.03552.5020.0040.0040.0000.0000.0000.000
184B338ASP-1-0.857-0.92348.120-0.028-0.0280.0000.0000.0000.000
185B339SER0-0.013-0.03647.3850.0020.0020.0000.0000.0000.000
186B340GLY0-0.015-0.01248.3790.0020.0020.0000.0000.0000.000
187B341LEU0-0.053-0.00550.4770.0020.0020.0000.0000.0000.000
188B342TRP00.0130.00352.7340.0010.0010.0000.0000.0000.000
189B343VAL00.0230.00754.5330.0000.0000.0000.0000.0000.000
190B344PRO0-0.038-0.02156.2850.0010.0010.0000.0000.0000.000
191B345ASN00.0100.01259.4150.0020.0020.0000.0000.0000.000
192B346SER0-0.037-0.02861.9570.0020.0020.0000.0000.0000.000
193B347LYS10.9661.00754.7560.0100.0100.0000.0000.0000.000