FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: R52K8

Calculation Name: 2QYF-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2QYF

Chain ID: B

ChEMBL ID:

UniProt ID: Q15013

Base Structure: X-ray

Registration Date: 2023-06-20

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 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 192
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2201822.88198
FMO2-HF: Nuclear repulsion 2123866.674089
FMO2-HF: Total energy -77956.207891
FMO2-MP2: Total energy -78177.862979


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:54:CYM)


Summations of interaction energy for fragment #1(B:54:CYM)
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.
-53.046-46.5414.871-4.235-7.1420.024
Interaction energy analysis for fragmet #1(B:54:CYM)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.771 / 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].
3B56VAL00.0410.0183.846-5.950-3.384-0.027-0.870-1.6690.018
4B57PRO0-0.0100.0095.690-6.690-6.6900.0000.0000.0000.000
5B58VAL0-0.013-0.0269.198-1.025-1.0250.0000.0000.0000.000
6B59VAL00.0300.02912.220-1.419-1.4190.0000.0000.0000.000
7B60PHE00.008-0.00315.331-0.408-0.4080.0000.0000.0000.000
8B61PRO0-0.047-0.03018.353-0.079-0.0790.0000.0000.0000.000
9B62GLY00.0560.02221.320-0.779-0.7790.0000.0000.0000.000
10B63PRO0-0.0060.00822.1640.8140.8140.0000.0000.0000.000
11B64VAL00.024-0.01319.741-0.254-0.2540.0000.0000.0000.000
12B65SER00.0420.02823.1980.0010.0010.0000.0000.0000.000
13B66GLN00.0900.04823.0230.7790.7790.0000.0000.0000.000
14B67GLU-1-0.903-0.95123.79111.06311.0630.0000.0000.0000.000
15B68GLY0-0.031-0.02422.3970.1870.1870.0000.0000.0000.000
16B69CYS0-0.042-0.03019.3320.7450.7450.0000.0000.0000.000
17B70CYS00.0370.05519.1570.6110.6110.0000.0000.0000.000
18B71GLN00.0430.01520.4520.5130.5130.0000.0000.0000.000
19B72PHE0-0.039-0.03716.0200.3260.3260.0000.0000.0000.000
20B73THR00.0180.00115.8921.1761.1760.0000.0000.0000.000
21B74CYS0-0.039-0.01316.7230.1740.1740.0000.0000.0000.000
22B75GLU-1-0.819-0.91318.15913.87413.8740.0000.0000.0000.000
23B76LEU00.0040.00610.4550.3740.3740.0000.0000.0000.000
24B77LEU00.0180.01313.9250.5990.5990.0000.0000.0000.000
25B78LYS10.7640.85915.818-13.113-13.1130.0000.0000.0000.000
26B79HIS0-0.0110.00012.361-1.034-1.0340.0000.0000.0000.000
27B80ILE00.0230.00910.3110.0360.0360.0000.0000.0000.000
28B81MET0-0.0580.00013.010-0.468-0.4680.0000.0000.0000.000
29B82TYR00.0070.01316.355-0.472-0.4720.0000.0000.0000.000
30B83GLN00.0170.01512.376-1.135-1.1350.0000.0000.0000.000
31B84ARG10.8230.89510.057-21.371-21.3710.0000.0000.0000.000
32B85GLN0-0.023-0.02914.028-1.146-1.1460.0000.0000.0000.000
33B86GLN0-0.030-0.02116.462-1.293-1.2930.0000.0000.0000.000
34B87LEU00.0200.01219.168-0.745-0.7450.0000.0000.0000.000
35B88PRO0-0.0120.00220.6710.4100.4100.0000.0000.0000.000
36B89LEU0-0.001-0.00722.776-0.041-0.0410.0000.0000.0000.000
37B90PRO00.0220.01120.4850.1410.1410.0000.0000.0000.000
38B91TYR00.0610.03321.232-0.546-0.5460.0000.0000.0000.000
39B92GLU-1-0.763-0.89723.13511.37311.3730.0000.0000.0000.000
40B93GLN0-0.073-0.04924.731-0.593-0.5930.0000.0000.0000.000
41B94LEU0-0.0010.00724.181-0.440-0.4400.0000.0000.0000.000
42B95LYS10.8240.92927.190-10.755-10.7550.0000.0000.0000.000
43B96HIS10.8780.96129.237-10.265-10.2650.0000.0000.0000.000
44B124CYS00.007-0.01129.082-0.093-0.0930.0000.0000.0000.000
45B125GLN00.0180.00729.3440.0490.0490.0000.0000.0000.000
46B126GLN00.0450.02430.4340.0030.0030.0000.0000.0000.000
47B127ALA00.0190.00725.6060.0950.0950.0000.0000.0000.000
48B128LEU00.0090.00925.8660.3900.3900.0000.0000.0000.000
49B129ALA00.0480.02026.8540.1940.1940.0000.0000.0000.000
50B130GLU-1-0.866-0.92625.32510.55810.5580.0000.0000.0000.000
51B131LEU0-0.035-0.01820.2370.3020.3020.0000.0000.0000.000
52B132GLU-1-0.853-0.93024.01510.43910.4390.0000.0000.0000.000
53B133SER0-0.067-0.02526.686-0.008-0.0080.0000.0000.0000.000
54B134VAL0-0.021-0.03120.7260.1100.1100.0000.0000.0000.000
55B135LEU0-0.047-0.02320.3820.2990.2990.0000.0000.0000.000
56B136SER00.0200.00723.4350.0360.0360.0000.0000.0000.000
57B137HIS10.8420.90526.011-10.359-10.3590.0000.0000.0000.000
58B138LEU0-0.033-0.01519.5760.2370.2370.0000.0000.0000.000
59B139GLU-1-0.864-0.93923.46911.28911.2890.0000.0000.0000.000
60B140ASP-1-0.836-0.89426.0729.9119.9110.0000.0000.0000.000
61B141PHE0-0.031-0.01921.851-0.014-0.0140.0000.0000.0000.000
62B142PHE0-0.001-0.04019.0880.1600.1600.0000.0000.0000.000
63B143ALA0-0.0370.00425.134-0.080-0.0800.0000.0000.0000.000
64B144ARG10.7890.92428.322-10.010-10.0100.0000.0000.0000.000
65B145THR0-0.043-0.04224.807-0.269-0.2690.0000.0000.0000.000
66B146LEU0-0.0150.01023.9520.3620.3620.0000.0000.0000.000
67B147VAL00.0400.02818.760-0.099-0.0990.0000.0000.0000.000
68B148PRO0-0.039-0.00218.5910.6550.6550.0000.0000.0000.000
69B149ARG10.8550.89012.137-20.561-20.5610.0000.0000.0000.000
70B150VAL00.0090.00814.130-1.359-1.3590.0000.0000.0000.000
71B151LEU0-0.031-0.00710.9571.6561.6560.0000.0000.0000.000
72B152ILE00.0200.00711.776-1.682-1.6820.0000.0000.0000.000
73B153LEU0-0.006-0.00611.5321.4521.4520.0000.0000.0000.000
74B154LEU00.0270.01911.565-1.231-1.2310.0000.0000.0000.000
75B155GLY00.0720.01514.7880.3930.3930.0000.0000.0000.000
76B156GLY0-0.038-0.01317.1860.4180.4180.0000.0000.0000.000
77B157ASN00.017-0.00518.397-0.394-0.3940.0000.0000.0000.000
78B158ALA00.0860.02717.2020.6610.6610.0000.0000.0000.000
79B159LEU00.0170.02416.6760.7140.7140.0000.0000.0000.000
80B160SER0-0.045-0.02116.0240.7740.7740.0000.0000.0000.000
81B161PRO00.0280.05512.659-0.859-0.8590.0000.0000.0000.000
82B162LYS10.8930.93814.535-15.582-15.5820.0000.0000.0000.000
83B163GLU-1-0.795-0.8639.39323.36823.3680.0000.0000.0000.000
84B164PHE0-0.025-0.0158.826-1.637-1.6370.0000.0000.0000.000
85B165TYR00.0570.0126.4013.0873.0870.0000.0000.0000.000
86B166GLU-1-0.836-0.9057.38322.54522.5450.0000.0000.0000.000
87B167LEU0-0.0110.0028.6142.3912.3910.0000.0000.0000.000
88B168ASP-1-0.798-0.86911.12521.80121.8010.0000.0000.0000.000
89B169LEU00.0260.00312.9090.4470.4470.0000.0000.0000.000
90B170SER0-0.053-0.04715.190-1.352-1.3520.0000.0000.0000.000
91B171LEU0-0.0100.00114.730-0.921-0.9210.0000.0000.0000.000
92B172LEU0-0.027-0.01217.328-0.348-0.3480.0000.0000.0000.000
93B173ALA0-0.030-0.02720.148-0.414-0.4140.0000.0000.0000.000
94B174PRO00.001-0.00723.984-0.038-0.0380.0000.0000.0000.000
95B175TYR00.0270.02725.780-0.417-0.4170.0000.0000.0000.000
96B176SER0-0.069-0.04225.2500.0910.0910.0000.0000.0000.000
97B177VAL00.004-0.00627.811-0.192-0.1920.0000.0000.0000.000
98B178ASP-1-0.846-0.91529.50610.43510.4350.0000.0000.0000.000
99B179GLN0-0.082-0.03325.1780.7060.7060.0000.0000.0000.000
100B180SER00.0320.01527.806-0.403-0.4030.0000.0000.0000.000
101B181LEU0-0.057-0.01822.139-0.072-0.0720.0000.0000.0000.000
102B182SER00.0720.02425.3300.1400.1400.0000.0000.0000.000
103B183THR00.1090.04921.8020.5540.5540.0000.0000.0000.000
104B184ALA00.0420.02621.1970.6740.6740.0000.0000.0000.000
105B185ALA0-0.045-0.01521.4610.4140.4140.0000.0000.0000.000
106B186CYS0-0.029-0.01118.7210.7530.7530.0000.0000.0000.000
107B187LEU00.0660.02916.8971.2281.2280.0000.0000.0000.000
108B188ARG10.9130.96216.078-12.746-12.7460.0000.0000.0000.000
109B189ARG10.8430.92315.186-17.784-17.7840.0000.0000.0000.000
110B190LEU00.0290.01912.1951.4391.4390.0000.0000.0000.000
111B191PHE00.0280.00011.3072.0122.0120.0000.0000.0000.000
112B192ARG10.9500.97911.789-19.065-19.0650.0000.0000.0000.000
113B193ALA0-0.011-0.0059.5000.7940.7940.0000.0000.0000.000
114B194ILE00.0170.0037.0453.1203.1200.0000.0000.0000.000
115B195PHE0-0.035-0.0147.4121.9631.9630.0000.0000.0000.000
116B196MET0-0.078-0.0529.609-1.052-1.0520.0000.0000.0000.000
117B197ALA0-0.0110.0083.8840.5910.7740.001-0.038-0.1460.000
118B198ASP-1-0.885-0.9254.87833.75633.826-0.001-0.001-0.0680.000
119B199ALA00.0070.0125.817-0.262-0.2620.0000.0000.0000.000
120B200PHE0-0.074-0.0606.691-3.312-3.3120.0000.0000.0000.000
121B201SER0-0.0090.0138.538-2.475-2.4750.0000.0000.0000.000
122B202GLU-1-0.857-0.9258.49624.91424.9140.0000.0000.0000.000
123B203LEU00.0220.00111.881-1.277-1.2770.0000.0000.0000.000
124B204GLN0-0.096-0.03214.965-1.244-1.2440.0000.0000.0000.000
125B205ALA00.0600.03015.4640.7150.7150.0000.0000.0000.000
126B206PRO0-0.0370.00014.752-0.359-0.3590.0000.0000.0000.000
127B207PRO00.0110.00216.933-0.626-0.6260.0000.0000.0000.000
128B208LEU00.0230.01318.7940.4880.4880.0000.0000.0000.000
129B209MET0-0.044-0.00814.240-0.445-0.4450.0000.0000.0000.000
130B210GLY00.0190.01619.642-0.613-0.6130.0000.0000.0000.000
131B211THR0-0.001-0.03015.5780.6710.6710.0000.0000.0000.000
132B212VAL0-0.027-0.00417.318-0.732-0.7320.0000.0000.0000.000
133B213VAL00.0400.01916.4820.9140.9140.0000.0000.0000.000
134B214MET0-0.049-0.02216.679-0.953-0.9530.0000.0000.0000.000
135B215ALA00.0450.03116.8371.0101.0100.0000.0000.0000.000
136B216GLN0-0.017-0.01617.7340.2930.2930.0000.0000.0000.000
137B217GLY00.0690.01420.4010.1330.1330.0000.0000.0000.000
138B218HIS0-0.021-0.00923.920-0.123-0.1230.0000.0000.0000.000
139B219ARG10.8730.91627.245-10.662-10.6620.0000.0000.0000.000
140B220ASN0-0.014-0.01229.153-0.181-0.1810.0000.0000.0000.000
141B221CYS0-0.084-0.02628.230-0.238-0.2380.0000.0000.0000.000
142B222GLY00.0290.00930.937-0.083-0.0830.0000.0000.0000.000
143B223GLU-1-0.813-0.90726.81210.49510.4950.0000.0000.0000.000
144B224ASP-1-0.885-0.93430.2119.1839.1830.0000.0000.0000.000
145B225TRP0-0.014-0.00224.668-0.019-0.0190.0000.0000.0000.000
146B226PHE0-0.022-0.04320.9960.2290.2290.0000.0000.0000.000
147B227ARG10.9750.98526.034-10.170-10.1700.0000.0000.0000.000
148B228PRO00.0350.01925.3560.5190.5190.0000.0000.0000.000
149B229LYS10.8190.89422.859-12.066-12.0660.0000.0000.0000.000
150B230LEU00.0480.01923.6560.5280.5280.0000.0000.0000.000
151B231ASN00.0040.00724.9130.1990.1990.0000.0000.0000.000
152B232TYR0-0.022-0.03115.9580.2200.2200.0000.0000.0000.000
153B233ARG10.9270.95818.158-14.026-14.0260.0000.0000.0000.000
154B234VAL00.0450.02911.695-0.391-0.3910.0000.0000.0000.000
155B235PRO0-0.0250.00112.479-0.145-0.1450.0000.0000.0000.000
156B236SER0-0.0020.00211.6801.5461.5460.0000.0000.0000.000
157B237ARG10.8440.90410.630-18.011-18.0110.0000.0000.0000.000
158B238GLY0-0.005-0.0099.872-1.021-1.0210.0000.0000.0000.000
159B239HIS0-0.025-0.0152.785-4.980-3.6670.762-0.781-1.2940.010
160B240LYS10.7800.8814.211-26.950-26.6880.000-0.071-0.1910.000
161B241LEU00.0320.0172.240-0.4751.3974.123-2.558-3.437-0.005
162B242THR0-0.0130.0073.265-7.011-6.7120.0140.096-0.4090.001
163B243VAL0-0.0140.0005.7534.6964.636-0.001-0.0120.0720.000
164B244THR00.005-0.0048.405-2.263-2.2630.0000.0000.0000.000
165B245LEU0-0.043-0.01910.7730.0030.0030.0000.0000.0000.000
166B246SER00.017-0.00213.850-0.959-0.9590.0000.0000.0000.000
167B247CYS0-0.046-0.03016.543-0.113-0.1130.0000.0000.0000.000
168B248GLY00.0260.02218.831-0.830-0.8300.0000.0000.0000.000
169B249ARG10.9250.97420.528-14.121-14.1210.0000.0000.0000.000
170B250PRO00.0210.02121.3070.6430.6430.0000.0000.0000.000
171B251SER00.001-0.00622.5020.2630.2630.0000.0000.0000.000
172B252ILE0-0.005-0.00622.252-0.567-0.5670.0000.0000.0000.000
173B253ARG10.9780.98723.831-10.614-10.6140.0000.0000.0000.000
174B254THR00.0400.00822.3380.4820.4820.0000.0000.0000.000
175B255THR0-0.034-0.02422.8040.3780.3780.0000.0000.0000.000
176B256ALA0-0.040-0.02322.930-0.267-0.2670.0000.0000.0000.000
177B257TRP00.0030.00220.115-0.312-0.3120.0000.0000.0000.000
178B258GLU-1-0.853-0.91123.48211.41211.4120.0000.0000.0000.000
179B259ASP-1-0.827-0.90325.81210.32410.3240.0000.0000.0000.000
180B260TYR0-0.054-0.01422.624-0.228-0.2280.0000.0000.0000.000
181B261ILE00.0100.02622.5600.6210.6210.0000.0000.0000.000
182B262TRP00.0300.01014.8270.1550.1550.0000.0000.0000.000
183B263PHE00.0100.00321.521-0.709-0.7090.0000.0000.0000.000
184B264GLN0-0.028-0.02120.6030.7880.7880.0000.0000.0000.000
185B265ALA00.0600.04221.463-0.572-0.5720.0000.0000.0000.000
186B266PRO0-0.088-0.02823.3030.0960.0960.0000.0000.0000.000
187B267VAL0-0.0010.00525.254-0.321-0.3210.0000.0000.0000.000
188B268THR0-0.042-0.02620.9590.6030.6030.0000.0000.0000.000
189B269PHE00.0510.02819.474-0.359-0.3590.0000.0000.0000.000
190B270LYS10.8280.89421.119-11.518-11.5180.0000.0000.0000.000
191B271GLY00.0270.03420.857-0.224-0.2240.0000.0000.0000.000
192B272PHE00.015-0.01421.765-0.340-0.3400.0000.0000.0000.000