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: 662RZ

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 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 192
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2200801.609796
FMO2-HF: Nuclear repulsion 2122846.927722
FMO2-HF: Total energy -77954.682073
FMO2-MP2: Total energy -78176.531585


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.
-41.975-34.1931.967-3.917-5.8310.004
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 : -0.839 / q_NPA : -0.906
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].
3B56VAL00.0360.0123.813-3.887-0.8580.021-1.328-1.7220.012
4B57PRO0-0.0070.0196.015-6.969-6.942-0.001-0.006-0.0200.000
5B58VAL0-0.001-0.0129.355-0.547-0.5470.0000.0000.0000.000
6B59VAL0-0.004-0.00412.405-1.059-1.0590.0000.0000.0000.000
7B60PHE0-0.034-0.02415.421-0.496-0.4960.0000.0000.0000.000
8B61PRO0-0.051-0.03118.547-0.142-0.1420.0000.0000.0000.000
9B62GLY00.0600.02121.118-0.742-0.7420.0000.0000.0000.000
10B63PRO00.0180.00022.2290.8200.8200.0000.0000.0000.000
11B64VAL00.0580.01519.788-0.273-0.2730.0000.0000.0000.000
12B65SER0-0.025-0.01823.327-0.186-0.1860.0000.0000.0000.000
13B66GLN00.0530.02923.2540.6290.6290.0000.0000.0000.000
14B67GLU-1-0.871-0.93324.47210.79910.7990.0000.0000.0000.000
15B68GLY0-0.046-0.03222.7970.2590.2590.0000.0000.0000.000
16B69CYS0-0.011-0.00419.7250.7120.7120.0000.0000.0000.000
17B70CYS00.0320.05519.5840.6990.6990.0000.0000.0000.000
18B71GLN00.0890.02921.0530.4980.4980.0000.0000.0000.000
19B72PHE0-0.031-0.02716.0410.4130.4130.0000.0000.0000.000
20B73THR00.0090.00316.2461.1411.1410.0000.0000.0000.000
21B74CYS0-0.018-0.01817.0470.3760.3760.0000.0000.0000.000
22B75GLU-1-0.842-0.90217.84614.18314.1830.0000.0000.0000.000
23B76LEU00.0040.00810.5930.4980.4980.0000.0000.0000.000
24B77LEU0-0.012-0.00714.4380.4780.4780.0000.0000.0000.000
25B78LYS10.8400.90416.178-13.209-13.2090.0000.0000.0000.000
26B79HIS0-0.0040.00411.760-1.168-1.1680.0000.0000.0000.000
27B80ILE00.0220.01410.6470.1760.1760.0000.0000.0000.000
28B81MET0-0.080-0.02213.589-0.526-0.5260.0000.0000.0000.000
29B82TYR0-0.0040.00616.865-0.900-0.9000.0000.0000.0000.000
30B83GLN00.0320.02012.680-1.403-1.4030.0000.0000.0000.000
31B84ARG10.8050.85910.570-21.350-21.3500.0000.0000.0000.000
32B85GLN0-0.033-0.02714.599-1.335-1.3350.0000.0000.0000.000
33B86GLN0-0.0040.00116.855-1.329-1.3290.0000.0000.0000.000
34B87LEU00.0120.00019.560-0.784-0.7840.0000.0000.0000.000
35B88PRO00.0030.01421.2460.4360.4360.0000.0000.0000.000
36B89LEU00.0180.00223.206-0.049-0.0490.0000.0000.0000.000
37B90PRO00.0120.01220.5740.0660.0660.0000.0000.0000.000
38B91TYR00.0870.02421.529-0.629-0.6290.0000.0000.0000.000
39B92GLU-1-0.846-0.93623.48211.19011.1900.0000.0000.0000.000
40B93GLN0-0.064-0.04624.099-0.665-0.6650.0000.0000.0000.000
41B94LEU0-0.031-0.01125.050-0.448-0.4480.0000.0000.0000.000
42B95LYS10.9020.97827.568-10.824-10.8240.0000.0000.0000.000
43B96HIS10.9040.97929.679-10.269-10.2690.0000.0000.0000.000
44B124CYS0-0.012-0.01429.668-0.053-0.0530.0000.0000.0000.000
45B125GLN00.0630.01730.3040.0300.0300.0000.0000.0000.000
46B126GLN00.0130.01531.516-0.078-0.0780.0000.0000.0000.000
47B127ALA00.015-0.00226.0240.0730.0730.0000.0000.0000.000
48B128LEU00.0200.00926.3410.4280.4280.0000.0000.0000.000
49B129ALA00.0720.03727.7400.1670.1670.0000.0000.0000.000
50B130GLU-1-0.932-0.96525.39410.75010.7500.0000.0000.0000.000
51B131LEU0-0.013-0.01020.6810.2570.2570.0000.0000.0000.000
52B132GLU-1-0.944-0.98224.59410.04910.0490.0000.0000.0000.000
53B133SER0-0.0060.01927.252-0.039-0.0390.0000.0000.0000.000
54B134VAL00.005-0.00521.0180.0740.0740.0000.0000.0000.000
55B135LEU0-0.060-0.03921.0620.2350.2350.0000.0000.0000.000
56B136SER00.0700.04024.1990.0060.0060.0000.0000.0000.000
57B137HIS10.9250.95926.129-10.378-10.3780.0000.0000.0000.000
58B138LEU0-0.053-0.03119.7630.1890.1890.0000.0000.0000.000
59B139GLU-1-0.947-0.98623.96611.42611.4260.0000.0000.0000.000
60B140ASP-1-0.880-0.92826.5159.8419.8410.0000.0000.0000.000
61B141PHE0-0.028-0.02022.035-0.051-0.0510.0000.0000.0000.000
62B142PHE0-0.024-0.04919.2990.2120.2120.0000.0000.0000.000
63B143ALA0-0.0350.00225.504-0.089-0.0890.0000.0000.0000.000
64B144ARG10.8710.96028.511-9.702-9.7020.0000.0000.0000.000
65B145THR0-0.020-0.03025.035-0.257-0.2570.0000.0000.0000.000
66B146LEU0-0.0060.01024.0570.3660.3660.0000.0000.0000.000
67B147VAL00.0390.02918.770-0.073-0.0730.0000.0000.0000.000
68B148PRO0-0.0290.00218.7020.5370.5370.0000.0000.0000.000
69B149ARG10.8600.88211.910-19.780-19.7800.0000.0000.0000.000
70B150VAL00.0080.00814.205-1.257-1.2570.0000.0000.0000.000
71B151LEU0-0.030-0.01811.1861.4781.4780.0000.0000.0000.000
72B152ILE00.0230.01812.032-1.566-1.5660.0000.0000.0000.000
73B153LEU0-0.009-0.00911.6971.4581.4580.0000.0000.0000.000
74B154LEU00.0260.01312.153-1.187-1.1870.0000.0000.0000.000
75B155GLY00.0450.00614.6640.4500.4500.0000.0000.0000.000
76B156GLY0-0.034-0.01017.0860.3310.3310.0000.0000.0000.000
77B157ASN00.004-0.01418.544-0.145-0.1450.0000.0000.0000.000
78B158ALA00.1010.03617.3370.5860.5860.0000.0000.0000.000
79B159LEU0-0.0190.02416.6090.6990.6990.0000.0000.0000.000
80B160SER0-0.031-0.01416.2120.8620.8620.0000.0000.0000.000
81B161PRO00.0420.05712.602-0.697-0.6970.0000.0000.0000.000
82B162LYS10.8430.90914.023-15.366-15.3660.0000.0000.0000.000
83B163GLU-1-0.780-0.8019.25022.89022.8900.0000.0000.0000.000
84B164PHE0-0.023-0.0168.595-1.631-1.6310.0000.0000.0000.000
85B165TYR00.029-0.0257.2182.8142.8140.0000.0000.0000.000
86B166GLU-1-0.804-0.8697.61321.65321.6530.0000.0000.0000.000
87B167LEU0-0.026-0.0018.9102.2552.2550.0000.0000.0000.000
88B168ASP-1-0.858-0.92811.51920.54920.5490.0000.0000.0000.000
89B169LEU00.006-0.02113.0470.5720.5720.0000.0000.0000.000
90B170SER0-0.037-0.03415.770-1.238-1.2380.0000.0000.0000.000
91B171LEU0-0.033-0.01315.067-1.017-1.0170.0000.0000.0000.000
92B172LEU0-0.020-0.01017.900-0.458-0.4580.0000.0000.0000.000
93B173ALA0-0.066-0.03320.374-0.440-0.4400.0000.0000.0000.000
94B174PRO00.0340.01424.1820.0770.0770.0000.0000.0000.000
95B175TYR0-0.0010.00125.852-0.502-0.5020.0000.0000.0000.000
96B176SER0-0.054-0.03125.9020.0790.0790.0000.0000.0000.000
97B177VAL0-0.020-0.01628.125-0.100-0.1000.0000.0000.0000.000
98B178ASP-1-0.832-0.91829.98010.13710.1370.0000.0000.0000.000
99B179GLN0-0.083-0.01724.8290.6890.6890.0000.0000.0000.000
100B180SER00.0030.01127.833-0.225-0.2250.0000.0000.0000.000
101B181LEU0-0.018-0.01721.978-0.058-0.0580.0000.0000.0000.000
102B182SER00.0630.02525.7240.1810.1810.0000.0000.0000.000
103B183THR00.0850.03522.2080.5800.5800.0000.0000.0000.000
104B184ALA00.0350.02421.5280.6840.6840.0000.0000.0000.000
105B185ALA0-0.027-0.01721.3430.5870.5870.0000.0000.0000.000
106B186CYS0-0.030-0.01019.0910.8280.8280.0000.0000.0000.000
107B187LEU00.0570.02617.2641.3341.3340.0000.0000.0000.000
108B188ARG10.9670.98716.353-12.925-12.9250.0000.0000.0000.000
109B189ARG10.8880.96515.221-18.316-18.3160.0000.0000.0000.000
110B190LEU00.0170.00711.9881.5391.5390.0000.0000.0000.000
111B191PHE00.021-0.00811.4782.1932.1930.0000.0000.0000.000
112B192ARG10.9280.96412.196-19.370-19.3700.0000.0000.0000.000
113B193ALA0-0.014-0.0089.7470.7990.7990.0000.0000.0000.000
114B194ILE00.0260.0187.1263.7193.7190.0000.0000.0000.000
115B195PHE0-0.026-0.0087.5862.1892.1890.0000.0000.0000.000
116B196MET0-0.071-0.0449.595-0.713-0.7130.0000.0000.0000.000
117B197ALA0-0.0090.0104.200-0.639-0.2490.032-0.171-0.2520.002
118B198ASP-1-0.948-0.9675.07937.98338.0950.000-0.009-0.1030.000
119B199ALA00.0080.0145.3841.0601.0600.0000.0000.0000.000
120B200PHE0-0.092-0.0736.188-3.896-3.8960.0000.0000.0000.000
121B201SER00.0590.0557.440-3.248-3.2480.0000.0000.0000.000
122B202GLU-1-0.893-0.9488.43226.74626.7460.0000.0000.0000.000
123B203LEU00.0340.01611.754-1.189-1.1890.0000.0000.0000.000
124B204GLN0-0.072-0.02515.157-1.118-1.1180.0000.0000.0000.000
125B205ALA00.0430.02115.9750.7520.7520.0000.0000.0000.000
126B206PRO0-0.036-0.01015.013-0.317-0.3170.0000.0000.0000.000
127B207PRO0-0.0100.00517.421-0.553-0.5530.0000.0000.0000.000
128B208LEU00.0430.01618.9030.5070.5070.0000.0000.0000.000
129B209MET0-0.090-0.04114.242-0.259-0.2590.0000.0000.0000.000
130B210GLY0-0.0040.00219.619-0.653-0.6530.0000.0000.0000.000
131B211THR00.026-0.00915.9820.7700.7700.0000.0000.0000.000
132B212VAL0-0.007-0.00717.248-0.748-0.7480.0000.0000.0000.000
133B213VAL00.0490.02616.5800.9090.9090.0000.0000.0000.000
134B214MET0-0.046-0.02416.766-0.878-0.8780.0000.0000.0000.000
135B215ALA00.0450.02817.0920.9430.9430.0000.0000.0000.000
136B216GLN0-0.0010.00618.431-0.180-0.1800.0000.0000.0000.000
137B217GLY00.0790.02020.5160.1630.1630.0000.0000.0000.000
138B218HIS00.0170.01123.930-0.105-0.1050.0000.0000.0000.000
139B219ARG10.9460.96027.117-10.255-10.2550.0000.0000.0000.000
140B220ASN0-0.037-0.02329.001-0.240-0.2400.0000.0000.0000.000
141B221CYS0-0.071-0.01228.220-0.238-0.2380.0000.0000.0000.000
142B222GLY00.0270.01030.905-0.117-0.1170.0000.0000.0000.000
143B223GLU-1-0.813-0.89926.90410.47310.4730.0000.0000.0000.000
144B224ASP-1-0.920-0.95330.1949.1209.1200.0000.0000.0000.000
145B225TRP0-0.022-0.01124.718-0.012-0.0120.0000.0000.0000.000
146B226PHE0-0.072-0.06221.6340.1860.1860.0000.0000.0000.000
147B227ARG10.9470.96425.783-10.138-10.1380.0000.0000.0000.000
148B228PRO00.0560.03625.2430.5090.5090.0000.0000.0000.000
149B229LYS10.8620.92522.684-11.562-11.5620.0000.0000.0000.000
150B230LEU00.0470.01123.4630.4960.4960.0000.0000.0000.000
151B231ASN0-0.0040.00424.6310.1470.1470.0000.0000.0000.000
152B232TYR0-0.056-0.06215.9310.2070.2070.0000.0000.0000.000
153B233ARG10.9490.96818.210-13.700-13.7000.0000.0000.0000.000
154B234VAL00.0010.01011.844-0.175-0.1750.0000.0000.0000.000
155B235PRO0-0.0090.00312.202-0.046-0.0460.0000.0000.0000.000
156B236SER00.0120.00911.6791.2471.2470.0000.0000.0000.000
157B237ARG10.9170.94610.678-17.820-17.8200.0000.0000.0000.000
158B238GLY0-0.008-0.0109.589-0.669-0.6690.0000.0000.0000.000
159B239HIS0-0.0010.0032.923-2.610-1.3180.231-0.590-0.9330.004
160B240LYS10.8140.9084.184-26.467-26.194-0.001-0.056-0.2160.000
161B241LEU00.0380.0132.455-0.0062.2841.684-1.677-2.296-0.014
162B242THR00.0160.0243.692-5.589-5.2200.001-0.080-0.2890.000
163B243VAL0-0.0040.0176.0914.5224.5220.0000.0000.0000.000
164B244THR00.0250.0168.546-1.841-1.8410.0000.0000.0000.000
165B245LEU0-0.030-0.01310.9350.1510.1510.0000.0000.0000.000
166B246SER00.0170.00614.253-1.027-1.0270.0000.0000.0000.000
167B247CYS0-0.048-0.03416.9300.0240.0240.0000.0000.0000.000
168B248GLY00.0300.03219.002-0.769-0.7690.0000.0000.0000.000
169B249ARG10.9440.98620.751-14.110-14.1100.0000.0000.0000.000
170B250PRO00.0200.00821.5470.6470.6470.0000.0000.0000.000
171B251SER00.009-0.00222.5380.3860.3860.0000.0000.0000.000
172B252ILE0-0.013-0.00622.778-0.617-0.6170.0000.0000.0000.000
173B253ARG10.9630.97323.689-10.355-10.3550.0000.0000.0000.000
174B254THR00.0460.02222.8050.2570.2570.0000.0000.0000.000
175B255THR00.0110.00823.1470.4810.4810.0000.0000.0000.000
176B256ALA0-0.020-0.00122.794-0.317-0.3170.0000.0000.0000.000
177B257TRP0-0.022-0.02120.324-0.408-0.4080.0000.0000.0000.000
178B258GLU-1-0.885-0.94723.56111.00711.0070.0000.0000.0000.000
179B259ASP-1-0.948-0.95926.01310.26310.2630.0000.0000.0000.000
180B260TYR0-0.052-0.02222.714-0.195-0.1950.0000.0000.0000.000
181B261ILE0-0.033-0.00723.2240.1370.1370.0000.0000.0000.000
182B262TRP00.0170.00214.9220.0700.0700.0000.0000.0000.000
183B263PHE00.0290.01321.409-0.697-0.6970.0000.0000.0000.000
184B264GLN0-0.038-0.03720.5820.9480.9480.0000.0000.0000.000
185B265ALA00.0480.03221.643-0.578-0.5780.0000.0000.0000.000
186B266PRO0-0.099-0.03423.5230.1320.1320.0000.0000.0000.000
187B267VAL0-0.0080.00025.388-0.308-0.3080.0000.0000.0000.000
188B268THR0-0.038-0.00821.6670.6210.6210.0000.0000.0000.000
189B269PHE00.0530.02420.068-0.308-0.3080.0000.0000.0000.000
190B270LYS10.8710.91921.175-11.644-11.6440.0000.0000.0000.000
191B271GLY00.0430.03221.382-0.104-0.1040.0000.0000.0000.000
192B272PHE0-0.026-0.02322.002-0.459-0.4590.0000.0000.0000.000