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: ZY8GN

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 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 192
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2201023.381901
FMO2-HF: Nuclear repulsion 2123067.83951
FMO2-HF: Total energy -77955.542391
FMO2-MP2: Total energy -78177.327181


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.
-43.587-35.8042.111-3.943-5.9540.009
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 : -0.818 / q_NPA : -0.881
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].
3B56VAL00.0260.0063.857-4.778-1.5720.004-1.386-1.8240.017
4B57PRO0-0.0030.0186.060-6.947-6.919-0.001-0.005-0.0220.000
5B58VAL0-0.003-0.0109.357-0.700-0.7000.0000.0000.0000.000
6B59VAL00.0160.01012.478-1.067-1.0670.0000.0000.0000.000
7B60PHE0-0.001-0.00215.454-0.515-0.5150.0000.0000.0000.000
8B61PRO0-0.048-0.02818.616-0.104-0.1040.0000.0000.0000.000
9B62GLY00.0640.02521.186-0.734-0.7340.0000.0000.0000.000
10B63PRO00.0110.00322.2710.8170.8170.0000.0000.0000.000
11B64VAL00.0620.01320.059-0.275-0.2750.0000.0000.0000.000
12B65SER00.0250.01423.394-0.086-0.0860.0000.0000.0000.000
13B66GLN00.0310.01223.1990.7380.7380.0000.0000.0000.000
14B67GLU-1-0.878-0.93724.59410.86510.8650.0000.0000.0000.000
15B68GLY0-0.038-0.03022.9140.2550.2550.0000.0000.0000.000
16B69CYS0-0.025-0.01419.8360.7180.7180.0000.0000.0000.000
17B70CYS00.0480.05619.7160.6930.6930.0000.0000.0000.000
18B71GLN00.0580.02321.1520.4680.4680.0000.0000.0000.000
19B72PHE0-0.032-0.02616.1990.4090.4090.0000.0000.0000.000
20B73THR00.0120.00116.3651.1261.1260.0000.0000.0000.000
21B74CYS0-0.030-0.01517.0900.3400.3400.0000.0000.0000.000
22B75GLU-1-0.834-0.90618.05113.99313.9930.0000.0000.0000.000
23B76LEU00.0040.00710.7430.4730.4730.0000.0000.0000.000
24B77LEU0-0.005-0.00614.5370.4810.4810.0000.0000.0000.000
25B78LYS10.7960.88016.205-13.126-13.1260.0000.0000.0000.000
26B79HIS0-0.014-0.00112.027-1.140-1.1400.0000.0000.0000.000
27B80ILE00.0230.01210.9250.1600.1600.0000.0000.0000.000
28B81MET0-0.069-0.01513.583-0.519-0.5190.0000.0000.0000.000
29B82TYR00.0020.00616.854-0.567-0.5670.0000.0000.0000.000
30B83GLN00.0250.02112.613-1.160-1.1600.0000.0000.0000.000
31B84ARG10.8060.88210.483-21.306-21.3060.0000.0000.0000.000
32B85GLN0-0.044-0.03114.560-1.214-1.2140.0000.0000.0000.000
33B86GLN0-0.012-0.00916.790-1.283-1.2830.0000.0000.0000.000
34B87LEU00.0220.01119.539-0.770-0.7700.0000.0000.0000.000
35B88PRO0-0.0040.00521.2140.4230.4230.0000.0000.0000.000
36B89LEU00.002-0.00523.298-0.042-0.0420.0000.0000.0000.000
37B90PRO00.0170.01420.6000.0610.0610.0000.0000.0000.000
38B91TYR00.0720.02521.651-0.567-0.5670.0000.0000.0000.000
39B92GLU-1-0.778-0.90023.60911.40311.4030.0000.0000.0000.000
40B93GLN0-0.070-0.05024.505-0.604-0.6040.0000.0000.0000.000
41B94LEU0-0.022-0.00524.824-0.437-0.4370.0000.0000.0000.000
42B95LYS10.8340.92827.790-10.728-10.7280.0000.0000.0000.000
43B96HIS10.8930.97529.475-10.261-10.2610.0000.0000.0000.000
44B124CYS00.009-0.01029.683-0.083-0.0830.0000.0000.0000.000
45B125GLN00.0330.00930.2920.0250.0250.0000.0000.0000.000
46B126GLN00.0170.01431.590-0.083-0.0830.0000.0000.0000.000
47B127ALA00.010-0.00326.0600.0760.0760.0000.0000.0000.000
48B128LEU00.0150.00726.3510.4130.4130.0000.0000.0000.000
49B129ALA00.0570.02927.7460.1580.1580.0000.0000.0000.000
50B130GLU-1-0.905-0.95325.58910.55310.5530.0000.0000.0000.000
51B131LEU0-0.028-0.01420.8220.2620.2620.0000.0000.0000.000
52B132GLU-1-0.852-0.92724.61710.20510.2050.0000.0000.0000.000
53B133SER0-0.0220.01427.280-0.033-0.0330.0000.0000.0000.000
54B134VAL00.002-0.01021.0930.0920.0920.0000.0000.0000.000
55B135LEU0-0.067-0.03621.2240.2380.2380.0000.0000.0000.000
56B136SER00.0570.03424.2410.0030.0030.0000.0000.0000.000
57B137HIS10.8620.91926.391-10.281-10.2810.0000.0000.0000.000
58B138LEU0-0.058-0.03419.9470.1880.1880.0000.0000.0000.000
59B139GLU-1-0.915-0.97724.02811.35611.3560.0000.0000.0000.000
60B140ASP-1-0.837-0.90326.5759.8809.8800.0000.0000.0000.000
61B141PHE0-0.018-0.02021.998-0.044-0.0440.0000.0000.0000.000
62B142PHE0-0.001-0.03219.4850.2030.2030.0000.0000.0000.000
63B143ALA0-0.051-0.00925.580-0.097-0.0970.0000.0000.0000.000
64B144ARG10.8140.93928.569-9.810-9.8100.0000.0000.0000.000
65B145THR0-0.033-0.03525.083-0.243-0.2430.0000.0000.0000.000
66B146LEU0-0.0080.01324.1340.3550.3550.0000.0000.0000.000
67B147VAL00.0330.02418.886-0.054-0.0540.0000.0000.0000.000
68B148PRO0-0.0250.00318.7580.5500.5500.0000.0000.0000.000
69B149ARG10.8570.88912.064-20.094-20.0940.0000.0000.0000.000
70B150VAL00.0070.00714.293-1.289-1.2890.0000.0000.0000.000
71B151LEU0-0.041-0.01911.2501.4791.4790.0000.0000.0000.000
72B152ILE00.0260.01712.096-1.603-1.6030.0000.0000.0000.000
73B153LEU0-0.012-0.00911.7431.4531.4530.0000.0000.0000.000
74B154LEU00.0240.01611.955-1.238-1.2380.0000.0000.0000.000
75B155GLY00.0540.00414.6780.4570.4570.0000.0000.0000.000
76B156GLY0-0.034-0.01017.1080.3450.3450.0000.0000.0000.000
77B157ASN0-0.008-0.01918.597-0.258-0.2580.0000.0000.0000.000
78B158ALA00.1010.03317.4050.6070.6070.0000.0000.0000.000
79B159LEU00.0010.01716.6720.7190.7190.0000.0000.0000.000
80B160SER0-0.034-0.01616.2490.8700.8700.0000.0000.0000.000
81B161PRO00.0470.06012.619-0.705-0.7050.0000.0000.0000.000
82B162LYS10.8910.94114.045-15.433-15.4330.0000.0000.0000.000
83B163GLU-1-0.801-0.8689.28023.23323.2330.0000.0000.0000.000
84B164PHE0-0.019-0.0108.619-1.621-1.6210.0000.0000.0000.000
85B165TYR00.0480.0087.2643.0263.0260.0000.0000.0000.000
86B166GLU-1-0.811-0.8837.68821.93721.9370.0000.0000.0000.000
87B167LEU0-0.0160.0058.9892.2432.2430.0000.0000.0000.000
88B168ASP-1-0.827-0.91211.50420.98920.9890.0000.0000.0000.000
89B169LEU0-0.003-0.02213.1400.5440.5440.0000.0000.0000.000
90B170SER0-0.039-0.03915.640-1.245-1.2450.0000.0000.0000.000
91B171LEU0-0.031-0.01215.128-1.033-1.0330.0000.0000.0000.000
92B172LEU0-0.027-0.00617.719-0.491-0.4910.0000.0000.0000.000
93B173ALA0-0.057-0.03320.374-0.430-0.4300.0000.0000.0000.000
94B174PRO00.0250.00824.1820.0430.0430.0000.0000.0000.000
95B175TYR00.0100.01025.852-0.462-0.4620.0000.0000.0000.000
96B176SER0-0.060-0.03125.7860.0790.0790.0000.0000.0000.000
97B177VAL0-0.005-0.01728.251-0.132-0.1320.0000.0000.0000.000
98B178ASP-1-0.844-0.91029.97010.28310.2830.0000.0000.0000.000
99B179GLN0-0.085-0.02225.2960.6450.6450.0000.0000.0000.000
100B180SER0-0.0020.00927.871-0.267-0.2670.0000.0000.0000.000
101B181LEU0-0.032-0.02622.049-0.097-0.0970.0000.0000.0000.000
102B182SER00.0690.02625.7820.1870.1870.0000.0000.0000.000
103B183THR00.1100.04922.4120.5520.5520.0000.0000.0000.000
104B184ALA00.0200.01821.6040.6890.6890.0000.0000.0000.000
105B185ALA0-0.032-0.01221.4010.5790.5790.0000.0000.0000.000
106B186CYS0-0.024-0.00919.2070.8130.8130.0000.0000.0000.000
107B187LEU00.0540.02117.3221.3091.3090.0000.0000.0000.000
108B188ARG10.9520.97816.418-12.821-12.8210.0000.0000.0000.000
109B189ARG10.8360.93015.405-17.838-17.8380.0000.0000.0000.000
110B190LEU00.0250.00712.3081.4851.4850.0000.0000.0000.000
111B191PHE00.029-0.00111.5332.0512.0510.0000.0000.0000.000
112B192ARG10.9230.95912.232-19.332-19.3320.0000.0000.0000.000
113B193ALA0-0.010-0.0069.8520.7370.7370.0000.0000.0000.000
114B194ILE00.0310.0177.1663.5193.5190.0000.0000.0000.000
115B195PHE0-0.030-0.0097.6041.9641.9640.0000.0000.0000.000
116B196MET0-0.064-0.0389.563-0.741-0.7410.0000.0000.0000.000
117B197ALA0-0.0130.0084.204-0.0820.1620.006-0.081-0.1700.001
118B198ASP-1-0.946-0.9675.00336.48536.572-0.001-0.002-0.0840.000
119B199ALA00.0180.0155.4450.8970.8970.0000.0000.0000.000
120B200PHE0-0.094-0.0726.237-3.588-3.5880.0000.0000.0000.000
121B201SER00.0620.0567.393-2.789-2.7890.0000.0000.0000.000
122B202GLU-1-0.883-0.9308.54825.76025.7600.0000.0000.0000.000
123B203LEU00.0320.01711.837-1.158-1.1580.0000.0000.0000.000
124B204GLN0-0.080-0.03615.226-1.136-1.1360.0000.0000.0000.000
125B205ALA00.0570.02915.9010.7270.7270.0000.0000.0000.000
126B206PRO0-0.036-0.00315.143-0.321-0.3210.0000.0000.0000.000
127B207PRO0-0.0130.00017.371-0.547-0.5470.0000.0000.0000.000
128B208LEU00.0480.01618.8730.4970.4970.0000.0000.0000.000
129B209MET0-0.070-0.03414.267-0.176-0.1760.0000.0000.0000.000
130B210GLY00.0010.00219.618-0.658-0.6580.0000.0000.0000.000
131B211THR00.020-0.01515.8540.7210.7210.0000.0000.0000.000
132B212VAL0-0.009-0.00717.291-0.755-0.7550.0000.0000.0000.000
133B213VAL00.0490.02916.6320.9090.9090.0000.0000.0000.000
134B214MET0-0.047-0.02416.862-0.925-0.9250.0000.0000.0000.000
135B215ALA00.0440.03217.1460.9620.9620.0000.0000.0000.000
136B216GLN0-0.0180.00018.338-0.057-0.0570.0000.0000.0000.000
137B217GLY00.0830.02420.6110.1560.1560.0000.0000.0000.000
138B218HIS00.0070.00424.025-0.117-0.1170.0000.0000.0000.000
139B219ARG10.8770.91827.215-10.423-10.4230.0000.0000.0000.000
140B220ASN0-0.036-0.02329.100-0.190-0.1900.0000.0000.0000.000
141B221CYS0-0.078-0.01828.324-0.238-0.2380.0000.0000.0000.000
142B222GLY00.0360.01230.997-0.121-0.1210.0000.0000.0000.000
143B223GLU-1-0.819-0.91426.91410.45210.4520.0000.0000.0000.000
144B224ASP-1-0.862-0.92530.2779.0719.0710.0000.0000.0000.000
145B225TRP0-0.028-0.00624.815-0.005-0.0050.0000.0000.0000.000
146B226PHE0-0.057-0.05421.5180.1760.1760.0000.0000.0000.000
147B227ARG10.9540.97025.846-10.097-10.0970.0000.0000.0000.000
148B228PRO00.0550.03425.3230.5060.5060.0000.0000.0000.000
149B229LYS10.8510.92522.757-11.726-11.7260.0000.0000.0000.000
150B230LEU00.0430.01323.5540.5170.5170.0000.0000.0000.000
151B231ASN0-0.0040.00224.7210.1150.1150.0000.0000.0000.000
152B232TYR0-0.041-0.03815.9590.2000.2000.0000.0000.0000.000
153B233ARG10.9410.96718.374-13.713-13.7130.0000.0000.0000.000
154B234VAL00.0230.01611.925-0.228-0.2280.0000.0000.0000.000
155B235PRO0-0.021-0.00112.294-0.042-0.0420.0000.0000.0000.000
156B236SER00.0170.01111.7541.2721.2720.0000.0000.0000.000
157B237ARG10.8430.90310.668-17.968-17.9680.0000.0000.0000.000
158B238GLY0-0.011-0.0139.608-0.686-0.6860.0000.0000.0000.000
159B239HIS0-0.0110.0032.968-3.125-1.7750.257-0.630-0.9760.005
160B240LYS10.7940.8964.234-25.880-25.615-0.001-0.056-0.2090.000
161B241LEU00.0440.0112.436-0.0362.1981.847-1.696-2.387-0.014
162B242THR00.0100.0183.744-5.888-5.5190.000-0.087-0.2820.000
163B243VAL0-0.0080.0156.1574.4484.4480.0000.0000.0000.000
164B244THR00.0190.0158.656-1.874-1.8740.0000.0000.0000.000
165B245LEU0-0.040-0.01510.9350.0830.0830.0000.0000.0000.000
166B246SER00.0230.00414.320-1.178-1.1780.0000.0000.0000.000
167B247CYS0-0.045-0.04016.892-0.008-0.0080.0000.0000.0000.000
168B248GLY00.0350.03418.963-0.782-0.7820.0000.0000.0000.000
169B249ARG10.9300.97820.699-14.104-14.1040.0000.0000.0000.000
170B250PRO00.0180.01021.4300.6610.6610.0000.0000.0000.000
171B251SER00.007-0.00222.5280.4180.4180.0000.0000.0000.000
172B252ILE0-0.013-0.00622.595-0.639-0.6390.0000.0000.0000.000
173B253ARG10.9800.98123.661-10.387-10.3870.0000.0000.0000.000
174B254THR00.0530.01522.7650.4000.4000.0000.0000.0000.000
175B255THR0-0.063-0.03423.1000.4630.4630.0000.0000.0000.000
176B256ALA0-0.0110.00722.766-0.324-0.3240.0000.0000.0000.000
177B257TRP0-0.020-0.02120.462-0.423-0.4230.0000.0000.0000.000
178B258GLU-1-0.842-0.91423.63511.15011.1500.0000.0000.0000.000
179B259ASP-1-0.868-0.91526.12010.18610.1860.0000.0000.0000.000
180B260TYR0-0.037-0.01422.918-0.192-0.1920.0000.0000.0000.000
181B261ILE0-0.027-0.00223.3120.1520.1520.0000.0000.0000.000
182B262TRP00.020-0.00114.8940.1180.1180.0000.0000.0000.000
183B263PHE00.0290.01021.504-0.691-0.6910.0000.0000.0000.000
184B264GLN0-0.031-0.02720.7270.7420.7420.0000.0000.0000.000
185B265ALA00.0470.03321.711-0.584-0.5840.0000.0000.0000.000
186B266PRO0-0.085-0.03223.5850.1260.1260.0000.0000.0000.000
187B267VAL00.0020.00325.456-0.284-0.2840.0000.0000.0000.000
188B268THR0-0.051-0.01121.3890.5860.5860.0000.0000.0000.000
189B269PHE00.0510.02219.770-0.325-0.3250.0000.0000.0000.000
190B270LYS10.8660.92221.190-11.557-11.5570.0000.0000.0000.000
191B271GLY00.0330.02921.343-0.111-0.1110.0000.0000.0000.000
192B272PHE0-0.009-0.01921.992-0.434-0.4340.0000.0000.0000.000