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: 3J12L

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 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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1927646.620181
FMO2-HF: Nuclear repulsion 1845301.191653
FMO2-HF: Total energy -82345.428529
FMO2-MP2: Total energy -82578.542002


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.
-12.552-8.4430.957-2.008-3.056-0.004
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 : 0.043 / q_NPA : 0.012
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].
3B150THR00.0630.0253.875-3.026-1.023-0.008-0.947-1.0470.001
4B151PHE0-0.005-0.0053.582-2.943-2.1170.028-0.233-0.6210.001
5B152VAL00.0540.0144.415-1.887-1.704-0.001-0.020-0.1620.000
6B153GLU-1-0.906-0.9566.4743.0763.0760.0000.0000.0000.000
7B154LYS10.8880.9738.687-3.124-3.1240.0000.0000.0000.000
8B155TYR0-0.001-0.0138.214-0.343-0.3430.0000.0000.0000.000
9B156GLU-1-0.854-0.91310.5780.6520.6520.0000.0000.0000.000
10B157LYS10.9490.96011.369-1.028-1.0280.0000.0000.0000.000
11B158GLN00.0640.04013.081-0.005-0.0050.0000.0000.0000.000
12B159ILE00.0210.0107.976-0.118-0.1180.0000.0000.0000.000
13B160LYS10.9280.97312.421-0.661-0.6610.0000.0000.0000.000
14B161HIS0-0.057-0.02015.003-0.094-0.0940.0000.0000.0000.000
15B162PHE00.0270.00714.594-0.037-0.0370.0000.0000.0000.000
16B163GLY00.0260.00415.782-0.070-0.0700.0000.0000.0000.000
17B164MET0-0.011-0.01116.796-0.050-0.0500.0000.0000.0000.000
18B165LEU0-0.0510.01819.821-0.018-0.0180.0000.0000.0000.000
19B166ARG10.9880.98921.871-0.033-0.0330.0000.0000.0000.000
20B167ARG10.9380.97424.015-0.118-0.1180.0000.0000.0000.000
21B168TRP00.0820.03123.1380.0260.0260.0000.0000.0000.000
22B169ASP-1-0.893-0.95124.5930.1020.1020.0000.0000.0000.000
23B170ASP-1-0.897-0.95924.6080.1840.1840.0000.0000.0000.000
24B171SER00.0130.02420.4540.0360.0360.0000.0000.0000.000
25B172GLN00.013-0.00420.2460.0140.0140.0000.0000.0000.000
26B173LYS10.9150.96521.436-0.266-0.2660.0000.0000.0000.000
27B174TYR00.0540.02216.0540.0540.0540.0000.0000.0000.000
28B175LEU00.0380.02315.2040.0680.0680.0000.0000.0000.000
29B176SER0-0.069-0.04417.6540.0400.0400.0000.0000.0000.000
30B177ASP-1-0.919-0.95319.8840.3950.3950.0000.0000.0000.000
31B178ASN0-0.085-0.05615.2990.1640.1640.0000.0000.0000.000
32B179VAL0-0.0030.01814.8630.0400.0400.0000.0000.0000.000
33B180HIS0-0.030-0.02210.473-0.130-0.1300.0000.0000.0000.000
34B181LEU0-0.016-0.0159.9650.1590.1590.0000.0000.0000.000
35B182VAL0-0.0260.02510.748-0.135-0.1350.0000.0000.0000.000
36B183CYS0-0.052-0.0366.3420.1030.1030.0000.0000.0000.000
37B184GLU-1-0.839-0.9246.967-2.403-2.4030.0000.0000.0000.000
38B185GLU-1-0.893-0.9402.583-2.475-1.3960.939-0.805-1.212-0.006
39B186THR0-0.044-0.0565.0710.0560.074-0.001-0.003-0.0140.000
40B187ALA00.0300.0298.142-0.028-0.0280.0000.0000.0000.000
41B188ASN0-0.013-0.0285.2620.5010.5010.0000.0000.0000.000
42B189TYR00.0370.0156.7550.0910.0910.0000.0000.0000.000
43B190LEU0-0.030-0.0158.3970.1130.1130.0000.0000.0000.000
44B191VAL00.0180.01211.3690.0250.0250.0000.0000.0000.000
45B192ILE0-0.062-0.0289.1790.0160.0160.0000.0000.0000.000
46B193TRP00.0420.01512.1490.1090.1090.0000.0000.0000.000
47B194CYS0-0.037-0.01114.0230.0380.0380.0000.0000.0000.000
48B195ILE00.000-0.00414.167-0.003-0.0030.0000.0000.0000.000
49B196ASP-1-0.846-0.92014.4970.0490.0490.0000.0000.0000.000
50B197LEU0-0.036-0.01817.5520.0260.0260.0000.0000.0000.000
51B198GLU-1-0.848-0.93720.075-0.087-0.0870.0000.0000.0000.000
52B199VAL0-0.061-0.04019.485-0.002-0.0020.0000.0000.0000.000
53B200GLU-1-1.028-1.01919.6990.1800.1800.0000.0000.0000.000
54B201GLU-1-0.888-0.93023.3550.0190.0190.0000.0000.0000.000
55B202LYS10.8470.92522.337-0.152-0.1520.0000.0000.0000.000
56B203CYS00.0600.03423.4390.0030.0030.0000.0000.0000.000
57B204ALA00.0180.01125.012-0.008-0.0080.0000.0000.0000.000
58B205LEU0-0.030-0.02520.9650.0030.0030.0000.0000.0000.000
59B206MET00.0270.03019.654-0.005-0.0050.0000.0000.0000.000
60B207GLU-1-0.844-0.92020.781-0.094-0.0940.0000.0000.0000.000
61B208GLN0-0.086-0.04221.870-0.034-0.0340.0000.0000.0000.000
62B209VAL0-0.007-0.01815.9610.0060.0060.0000.0000.0000.000
63B210ALA00.0520.01517.758-0.029-0.0290.0000.0000.0000.000
64B211HIS0-0.050-0.01518.995-0.042-0.0420.0000.0000.0000.000
65B212GLN0-0.039-0.02717.327-0.050-0.0500.0000.0000.0000.000
66B213THR0-0.061-0.04113.744-0.009-0.0090.0000.0000.0000.000
67B214ILE00.0700.04415.718-0.056-0.0560.0000.0000.0000.000
68B215VAL00.0030.01618.142-0.013-0.0130.0000.0000.0000.000
69B216MET0-0.039-0.00711.916-0.007-0.0070.0000.0000.0000.000
70B217GLN0-0.022-0.02913.3440.0080.0080.0000.0000.0000.000
71B218PHE00.0560.02215.409-0.014-0.0140.0000.0000.0000.000
72B219ILE0-0.071-0.02316.1230.0220.0220.0000.0000.0000.000
73B220LEU0-0.045-0.02411.107-0.015-0.0150.0000.0000.0000.000
74B221GLU-1-0.900-0.95415.190-0.522-0.5220.0000.0000.0000.000
75B222LEU00.0100.01118.0350.0040.0040.0000.0000.0000.000
76B223ALA0-0.042-0.03116.4030.0200.0200.0000.0000.0000.000
77B224LYS10.9650.97512.6841.0681.0680.0000.0000.0000.000
78B225SER0-0.048-0.00618.4570.0050.0050.0000.0000.0000.000
79B226LEU0-0.054-0.03521.7990.0100.0100.0000.0000.0000.000
80B227LYS10.8900.95220.6290.3150.3150.0000.0000.0000.000
81B228VAL0-0.0140.00319.373-0.014-0.0140.0000.0000.0000.000
82B229ASP-1-0.814-0.91713.7140.0570.0570.0000.0000.0000.000
83B230PRO00.0770.01812.6150.0420.0420.0000.0000.0000.000
84B231ARG10.9270.9728.414-0.701-0.7010.0000.0000.0000.000
85B232ALA0-0.032-0.01515.8300.0410.0410.0000.0000.0000.000
86B233CYS0-0.023-0.01618.838-0.024-0.0240.0000.0000.0000.000
87B234PHE00.0340.02217.576-0.016-0.0160.0000.0000.0000.000
88B235ARG10.9450.97519.685-0.213-0.2130.0000.0000.0000.000
89B236GLN0-0.029-0.02523.023-0.026-0.0260.0000.0000.0000.000
90B237PHE00.0540.04121.418-0.010-0.0100.0000.0000.0000.000
91B238PHE00.0260.00519.849-0.002-0.0020.0000.0000.0000.000
92B239THR0-0.056-0.01824.8200.0020.0020.0000.0000.0000.000
93B240LYS10.9640.97626.7070.1010.1010.0000.0000.0000.000
94B241ILE0-0.0010.00624.680-0.002-0.0020.0000.0000.0000.000
95B242LYS10.8760.93927.571-0.058-0.0580.0000.0000.0000.000
96B243THR0-0.079-0.03430.1130.0040.0040.0000.0000.0000.000
97B244ALA0-0.0010.01929.620-0.007-0.0070.0000.0000.0000.000
98B245ASP-1-0.899-0.94431.725-0.085-0.0850.0000.0000.0000.000
99B246ARG10.9430.95333.0100.0780.0780.0000.0000.0000.000
100B247GLN00.0510.02533.7130.0000.0000.0000.0000.0000.000
101B248TYR00.0170.01424.916-0.006-0.0060.0000.0000.0000.000
102B249MET0-0.022-0.00827.792-0.010-0.0100.0000.0000.0000.000
103B250GLU-1-0.915-0.96429.707-0.110-0.1100.0000.0000.0000.000
104B251GLY00.0470.04428.962-0.008-0.0080.0000.0000.0000.000
105B252PHE0-0.006-0.02122.722-0.017-0.0170.0000.0000.0000.000
106B253ASN0-0.040-0.04525.379-0.008-0.0080.0000.0000.0000.000
107B254ASP-1-0.889-0.91727.219-0.182-0.1820.0000.0000.0000.000
108B255GLU-1-0.936-0.97822.621-0.354-0.3540.0000.0000.0000.000
109B256LEU0-0.060-0.02221.853-0.021-0.0210.0000.0000.0000.000
110B257GLU-1-0.870-0.95423.226-0.145-0.1450.0000.0000.0000.000
111B258ALA00.0240.01123.905-0.012-0.0120.0000.0000.0000.000
112B259PHE0-0.085-0.05115.590-0.037-0.0370.0000.0000.0000.000
113B260LYS10.8720.91720.4640.0940.0940.0000.0000.0000.000
114B261GLU-1-0.875-0.90322.531-0.193-0.1930.0000.0000.0000.000
115B262ARG10.9380.96818.2150.4730.4730.0000.0000.0000.000
116B263VAL0-0.053-0.01217.513-0.027-0.0270.0000.0000.0000.000
117B264ARG10.9350.95219.7780.1520.1520.0000.0000.0000.000
118B265GLY0-0.0050.00622.8530.0120.0120.0000.0000.0000.000
119B266ARG10.9170.93612.6520.7430.7430.0000.0000.0000.000
120B267ALA00.0380.03019.6870.0010.0010.0000.0000.0000.000
121B268LYS10.9390.95420.9590.2340.2340.0000.0000.0000.000
122B269LEU0-0.022-0.00119.9880.0050.0050.0000.0000.0000.000
123B270ARG10.7760.89215.3750.1410.1410.0000.0000.0000.000
124B271ILE00.0430.01821.1530.0200.0200.0000.0000.0000.000
125B272GLU-1-0.846-0.93024.643-0.199-0.1990.0000.0000.0000.000
126B273LYS10.9130.96318.5170.2000.2000.0000.0000.0000.000
127B274ALA00.0400.02424.3460.0120.0120.0000.0000.0000.000
128B275MET00.003-0.00425.7790.0110.0110.0000.0000.0000.000
129B276LYS10.9530.99126.9330.1950.1950.0000.0000.0000.000
130B277GLU-1-0.956-0.98923.903-0.085-0.0850.0000.0000.0000.000
131B278TYR0-0.009-0.00528.5750.0090.0090.0000.0000.0000.000
132B279GLU-1-0.927-0.97431.217-0.083-0.0830.0000.0000.0000.000
133B280GLU-1-0.951-0.97130.644-0.083-0.0830.0000.0000.0000.000
134B281GLU-1-0.906-0.96831.5800.0000.0000.0000.0000.0000.000
135B282GLU-1-0.909-0.95634.217-0.015-0.0150.0000.0000.0000.000
136B283ARG10.8700.95435.9510.0890.0890.0000.0000.0000.000
137B284LYS10.8560.92033.3770.0300.0300.0000.0000.0000.000
138B285LYS10.8700.93737.6010.0110.0110.0000.0000.0000.000
139B286ARG10.8230.89339.3770.0680.0680.0000.0000.0000.000
140B287LEU0-0.091-0.02338.957-0.004-0.0040.0000.0000.0000.000
141B288GLY00.0380.01742.9660.0060.0060.0000.0000.0000.000
142B289PRO0-0.068-0.04145.3030.0010.0010.0000.0000.0000.000
143B290GLY0-0.016-0.00147.0010.0020.0020.0000.0000.0000.000
144B291GLY0-0.058-0.02642.936-0.005-0.0050.0000.0000.0000.000
145B292LEU0-0.0280.00042.361-0.007-0.0070.0000.0000.0000.000
146B293ASP-1-0.720-0.82641.411-0.061-0.0610.0000.0000.0000.000
147B294PRO00.0240.00843.857-0.004-0.0040.0000.0000.0000.000
148B295VAL00.018-0.00143.6340.0000.0000.0000.0000.0000.000
149B296GLU-1-0.886-0.96940.395-0.097-0.0970.0000.0000.0000.000
150B297VAL0-0.064-0.02745.101-0.002-0.0020.0000.0000.0000.000
151B298TYR00.0210.01848.2530.0020.0020.0000.0000.0000.000
152B299GLU-1-0.924-0.96146.258-0.075-0.0750.0000.0000.0000.000
153B300SER0-0.143-0.05947.917-0.003-0.0030.0000.0000.0000.000
154B301LEU0-0.056-0.02749.7390.0000.0000.0000.0000.0000.000
155B302PRO0-0.0030.00053.364-0.002-0.0020.0000.0000.0000.000
156B303GLU-1-0.920-0.95856.429-0.063-0.0630.0000.0000.0000.000
157B304GLU-1-0.925-0.97357.616-0.050-0.0500.0000.0000.0000.000
158B305LEU0-0.031-0.01056.6410.0030.0030.0000.0000.0000.000
159B306GLN00.005-0.02657.101-0.002-0.0020.0000.0000.0000.000
160B307LYS10.9230.98255.6040.0510.0510.0000.0000.0000.000
161B308CYS0-0.059-0.00957.5480.0040.0040.0000.0000.0000.000
162B316MET00.0440.01363.2840.0000.0000.0000.0000.0000.000
163B317LEU00.010-0.00864.6470.0000.0000.0000.0000.0000.000
164B318GLN0-0.011-0.00566.076-0.001-0.0010.0000.0000.0000.000
165B319ASP-1-0.867-0.96061.401-0.041-0.0410.0000.0000.0000.000
166B320ALA0-0.0410.00364.181-0.001-0.0010.0000.0000.0000.000
167B321ILE00.004-0.00566.237-0.001-0.0010.0000.0000.0000.000
168B322SER00.0210.01863.803-0.001-0.0010.0000.0000.0000.000
169B323LYS10.8250.93262.5120.0400.0400.0000.0000.0000.000
170B324MET0-0.006-0.01865.3950.0010.0010.0000.0000.0000.000
171B325ASP-1-0.826-0.92561.257-0.053-0.0530.0000.0000.0000.000
172B326PRO0-0.041-0.00461.4310.0020.0020.0000.0000.0000.000
173B327THR0-0.039-0.02159.9990.0020.0020.0000.0000.0000.000
174B328ASP-1-0.850-0.94056.951-0.069-0.0690.0000.0000.0000.000
175B329ALA00.0450.04057.4910.0000.0000.0000.0000.0000.000
176B330LYS10.9380.95854.7120.0580.0580.0000.0000.0000.000
177B331TYR0-0.061-0.02949.8140.0000.0000.0000.0000.0000.000
178B332HIS00.1150.05053.2030.0000.0000.0000.0000.0000.000
179B333MET00.0090.00854.1460.0020.0020.0000.0000.0000.000
180B334GLN0-0.086-0.05951.9330.0030.0030.0000.0000.0000.000
181B335ARG10.9360.96246.3000.0780.0780.0000.0000.0000.000
182B336CYS00.0190.02050.3460.0000.0000.0000.0000.0000.000
183B337ILE0-0.066-0.03552.4630.0040.0040.0000.0000.0000.000
184B338ASP-1-0.839-0.91348.034-0.043-0.0430.0000.0000.0000.000
185B339SER0-0.019-0.02147.3550.0010.0010.0000.0000.0000.000
186B340GLY0-0.007-0.00948.3460.0020.0020.0000.0000.0000.000
187B341LEU0-0.054-0.00450.2370.0030.0030.0000.0000.0000.000
188B342TRP00.002-0.00152.7110.0020.0020.0000.0000.0000.000
189B343VAL00.0150.00454.4220.0000.0000.0000.0000.0000.000
190B344PRO0-0.033-0.01556.0660.0010.0010.0000.0000.0000.000
191B345ASN00.0270.01159.3580.0020.0020.0000.0000.0000.000
192B346SER0-0.038-0.02361.9020.0030.0030.0000.0000.0000.000
193B347LYS10.9651.00354.8820.0220.0220.0000.0000.0000.000