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: R9M88

Calculation Name: 1WER-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WER

Chain ID: A

ChEMBL ID:

UniProt ID: P20936

Base Structure: X-ray

Registration Date: 2023-06-22

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 324
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4839026.054345
FMO2-HF: Nuclear repulsion 4707898.411205
FMO2-HF: Total energy -131127.64314
FMO2-MP2: Total energy -131504.615685


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(A:718:MET)


Summations of interaction energy for fragment #1(A:718:MET)
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.
-15.292-5.64816.836-7.468-19.015-0.009
Interaction energy analysis for fragmet #1(A:718:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.004
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].
3A720GLU-1-0.749-0.8813.688-2.993-1.2690.011-0.824-0.9110.003
4A721GLU-1-0.905-0.9596.073-1.327-1.3270.0000.0000.0000.000
5A722GLU-1-0.903-0.9322.2941.0612.3811.515-0.653-2.182-0.003
6A723TYR0-0.010-0.0132.160-10.404-7.0537.251-3.558-7.0430.003
7A724SER0-0.029-0.0305.1530.2820.335-0.001-0.001-0.0510.000
8A725GLU-1-0.840-0.9206.3790.0080.0080.0000.0000.0000.000
9A726PHE0-0.047-0.0407.0900.0920.0920.0000.0000.0000.000
10A727LYS10.8390.9078.9521.0851.0850.0000.0000.0000.000
11A728GLU-1-0.898-0.94610.796-0.314-0.3140.0000.0000.0000.000
12A729LEU0-0.078-0.03312.4460.0690.0690.0000.0000.0000.000
13A730ILE0-0.064-0.03810.9050.0370.0370.0000.0000.0000.000
14A731LEU0-0.0070.00214.7240.0200.0200.0000.0000.0000.000
15A732GLN0-0.032-0.00816.9860.0390.0390.0000.0000.0000.000
16A733LYS10.9360.94119.2920.1050.1050.0000.0000.0000.000
17A734GLU-1-0.871-0.92222.123-0.093-0.0930.0000.0000.0000.000
18A735LEU0-0.0110.00220.1120.0120.0120.0000.0000.0000.000
19A736HIS00.0400.01120.1540.0060.0060.0000.0000.0000.000
20A737VAL00.0370.01714.0890.0190.0190.0000.0000.0000.000
21A738VAL00.0380.01917.4500.0070.0070.0000.0000.0000.000
22A739TYR00.0380.00719.0550.0120.0120.0000.0000.0000.000
23A740ALA00.0120.01918.4230.0120.0120.0000.0000.0000.000
24A741LEU00.031-0.00114.1080.0160.0160.0000.0000.0000.000
25A742SER0-0.073-0.04818.2710.0070.0070.0000.0000.0000.000
26A743HIS0-0.0190.00221.566-0.001-0.0010.0000.0000.0000.000
27A744VAL0-0.009-0.01117.6490.0060.0060.0000.0000.0000.000
28A745CYS0-0.108-0.02718.1790.0080.0080.0000.0000.0000.000
29A746GLY00.0810.04220.786-0.009-0.0090.0000.0000.0000.000
30A747GLN0-0.006-0.02424.438-0.017-0.0170.0000.0000.0000.000
31A748ASP-1-0.937-0.95920.200-0.059-0.0590.0000.0000.0000.000
32A749ARG10.9210.96620.5820.0580.0580.0000.0000.0000.000
33A750THR00.0210.00421.959-0.019-0.0190.0000.0000.0000.000
34A751LEU00.0420.03215.556-0.032-0.0320.0000.0000.0000.000
35A752LEU00.0490.02616.461-0.046-0.0460.0000.0000.0000.000
36A753ALA00.010-0.00318.082-0.039-0.0390.0000.0000.0000.000
37A754SER0-0.045-0.03317.726-0.023-0.0230.0000.0000.0000.000
38A755ILE0-0.0100.00712.566-0.031-0.0310.0000.0000.0000.000
39A756LEU00.0030.00315.117-0.059-0.0590.0000.0000.0000.000
40A757LEU00.0140.00617.162-0.020-0.0200.0000.0000.0000.000
41A758ARG10.8390.88713.6120.5700.5700.0000.0000.0000.000
42A759ILE0-0.0050.00511.899-0.040-0.0400.0000.0000.0000.000
43A760PHE00.034-0.01014.846-0.010-0.0100.0000.0000.0000.000
44A761LEU0-0.038-0.00918.3640.0240.0240.0000.0000.0000.000
45A762HIS10.7710.88113.3140.9210.9210.0000.0000.0000.000
46A763GLU-1-0.773-0.86114.464-0.752-0.7520.0000.0000.0000.000
47A764LYS10.7780.88618.3060.3460.3460.0000.0000.0000.000
48A765LEU00.0360.02219.0550.0380.0380.0000.0000.0000.000
49A766GLU-1-0.794-0.88222.275-0.238-0.2380.0000.0000.0000.000
50A767SER00.020-0.01323.2760.0260.0260.0000.0000.0000.000
51A768LEU00.0000.01721.6180.0200.0200.0000.0000.0000.000
52A769LEU0-0.0070.01620.3890.0230.0230.0000.0000.0000.000
53A770LEU00.005-0.00523.5430.0220.0220.0000.0000.0000.000
54A771CYS0-0.017-0.01126.7540.0150.0150.0000.0000.0000.000
55A772THR0-0.024-0.01625.6680.0190.0190.0000.0000.0000.000
56A773LEU0-0.029-0.01823.1490.0150.0150.0000.0000.0000.000
57A774ASN00.012-0.02527.5530.0140.0140.0000.0000.0000.000
58A775ASP-1-0.850-0.89530.950-0.073-0.0730.0000.0000.0000.000
59A776ARG10.8790.95426.3450.0720.0720.0000.0000.0000.000
60A777GLU-1-0.822-0.90429.831-0.072-0.0720.0000.0000.0000.000
61A778ILE0-0.031-0.01532.7040.0070.0070.0000.0000.0000.000
62A779SER0-0.079-0.04833.6030.0080.0080.0000.0000.0000.000
63A780MET0-0.021-0.01030.4400.0080.0080.0000.0000.0000.000
64A781GLU-1-0.804-0.87735.700-0.044-0.0440.0000.0000.0000.000
65A782ASP-1-0.944-0.97138.384-0.029-0.0290.0000.0000.0000.000
66A783GLU-1-0.808-0.87741.587-0.035-0.0350.0000.0000.0000.000
67A784ALA00.0200.00942.340-0.003-0.0030.0000.0000.0000.000
68A785THR0-0.131-0.10143.060-0.004-0.0040.0000.0000.0000.000
69A786THR0-0.038-0.02440.516-0.001-0.0010.0000.0000.0000.000
70A787LEU00.0290.03236.914-0.003-0.0030.0000.0000.0000.000
71A788PHE0-0.001-0.01132.242-0.003-0.0030.0000.0000.0000.000
72A789ARG10.8470.92635.8800.0520.0520.0000.0000.0000.000
73A790ALA00.0010.01334.068-0.001-0.0010.0000.0000.0000.000
74A791THR00.002-0.00529.356-0.006-0.0060.0000.0000.0000.000
75A792THR0-0.019-0.03028.7630.0030.0030.0000.0000.0000.000
76A793LEU00.0330.01521.421-0.008-0.0080.0000.0000.0000.000
77A794ALA00.0640.04025.617-0.017-0.0170.0000.0000.0000.000
78A795SER00.0440.01827.766-0.008-0.0080.0000.0000.0000.000
79A796THR0-0.027-0.01624.791-0.005-0.0050.0000.0000.0000.000
80A797LEU0-0.035-0.01721.388-0.016-0.0160.0000.0000.0000.000
81A798MET00.0260.04225.256-0.018-0.0180.0000.0000.0000.000
82A799GLU-1-0.834-0.89828.467-0.127-0.1270.0000.0000.0000.000
83A800GLN0-0.051-0.03221.410-0.023-0.0230.0000.0000.0000.000
84A801TYR00.019-0.02724.405-0.010-0.0100.0000.0000.0000.000
85A802MET00.0000.02625.954-0.002-0.0020.0000.0000.0000.000
86A803LYS10.8530.93822.6900.2610.2610.0000.0000.0000.000
87A804ALA0-0.066-0.03924.070-0.002-0.0020.0000.0000.0000.000
88A805THR0-0.016-0.00525.962-0.002-0.0020.0000.0000.0000.000
89A806ALA00.0210.01028.4170.0080.0080.0000.0000.0000.000
90A807THR00.0250.00929.9710.0140.0140.0000.0000.0000.000
91A808GLN00.0180.00932.5350.0050.0050.0000.0000.0000.000
92A809PHE00.0530.04035.0150.0090.0090.0000.0000.0000.000
93A810VAL00.0300.01534.6210.0090.0090.0000.0000.0000.000
94A811HIS0-0.070-0.05834.7080.0100.0100.0000.0000.0000.000
95A812HIS0-0.025-0.02538.3340.0090.0090.0000.0000.0000.000
96A813ALA0-0.0100.01040.2350.0060.0060.0000.0000.0000.000
97A814LEU0-0.017-0.02039.1030.0060.0060.0000.0000.0000.000
98A815LYS10.9120.96938.0240.1290.1290.0000.0000.0000.000
99A816ASP-1-0.809-0.89141.971-0.092-0.0920.0000.0000.0000.000
100A817SER0-0.018-0.01945.6440.0030.0030.0000.0000.0000.000
101A818ILE0-0.001-0.00541.2820.0040.0040.0000.0000.0000.000
102A819LEU0-0.005-0.00342.4200.0020.0020.0000.0000.0000.000
103A820LYS10.9220.94945.8020.0740.0740.0000.0000.0000.000
104A821ILE0-0.043-0.02047.2060.0040.0040.0000.0000.0000.000
105A822MET0-0.082-0.04944.3040.0030.0030.0000.0000.0000.000
106A823GLU-1-0.934-0.95047.712-0.074-0.0740.0000.0000.0000.000
107A824SER0-0.059-0.00350.6690.0040.0040.0000.0000.0000.000
108A825LYS10.9290.94953.2600.0480.0480.0000.0000.0000.000
109A826GLN0-0.077-0.03556.0370.0030.0030.0000.0000.0000.000
110A827SER00.006-0.00555.547-0.003-0.0030.0000.0000.0000.000
111A828CYS0-0.0080.01653.6620.0000.0000.0000.0000.0000.000
112A829GLU-1-0.705-0.79155.347-0.044-0.0440.0000.0000.0000.000
113A830LEU00.0660.02956.0790.0010.0010.0000.0000.0000.000
114A831SER0-0.062-0.06556.6660.0020.0020.0000.0000.0000.000
115A832PRO00.0610.02559.1580.0000.0000.0000.0000.0000.000
116A833SER0-0.011-0.00560.5270.0000.0000.0000.0000.0000.000
117A834LYS10.8550.92254.0450.0410.0410.0000.0000.0000.000
118A835LEU0-0.033-0.00259.436-0.001-0.0010.0000.0000.0000.000
119A836GLU-1-0.912-0.96559.883-0.034-0.0340.0000.0000.0000.000
120A837LYS10.8530.94062.2300.0340.0340.0000.0000.0000.000
121A838ASN0-0.052-0.02565.094-0.001-0.0010.0000.0000.0000.000
122A839GLU-1-0.732-0.84059.984-0.043-0.0430.0000.0000.0000.000
123A840ASP-1-0.768-0.86464.422-0.035-0.0350.0000.0000.0000.000
124A841VAL00.0350.01761.835-0.001-0.0010.0000.0000.0000.000
125A842ASN0-0.040-0.02662.179-0.002-0.0020.0000.0000.0000.000
126A843THR0-0.009-0.02362.517-0.001-0.0010.0000.0000.0000.000
127A844ASN0-0.075-0.06058.838-0.002-0.0020.0000.0000.0000.000
128A845LEU0-0.044-0.01758.338-0.002-0.0020.0000.0000.0000.000
129A846THR0-0.017-0.01158.952-0.002-0.0020.0000.0000.0000.000
130A847HIS00.007-0.01254.697-0.003-0.0030.0000.0000.0000.000
131A848LEU00.0250.00852.246-0.002-0.0020.0000.0000.0000.000
132A849LEU00.005-0.00354.405-0.003-0.0030.0000.0000.0000.000
133A850ASN0-0.014-0.00255.899-0.002-0.0020.0000.0000.0000.000
134A851ILE0-0.002-0.00250.557-0.003-0.0030.0000.0000.0000.000
135A852LEU0-0.043-0.02250.081-0.003-0.0030.0000.0000.0000.000
136A853SER0-0.033-0.01751.320-0.002-0.0020.0000.0000.0000.000
137A854GLU-1-0.794-0.88050.145-0.076-0.0760.0000.0000.0000.000
138A855LEU00.003-0.00144.936-0.003-0.0030.0000.0000.0000.000
139A856VAL0-0.019-0.01647.290-0.004-0.0040.0000.0000.0000.000
140A857GLU-1-0.909-0.93848.187-0.070-0.0700.0000.0000.0000.000
141A858LYS10.8580.91145.7110.0820.0820.0000.0000.0000.000
142A859ILE0-0.017-0.00842.714-0.005-0.0050.0000.0000.0000.000
143A860PHE0-0.036-0.03543.794-0.003-0.0030.0000.0000.0000.000
144A861MET00.009-0.00345.477-0.003-0.0030.0000.0000.0000.000
145A862ALA00.0100.01741.057-0.003-0.0030.0000.0000.0000.000
146A863SER0-0.024-0.02140.701-0.009-0.0090.0000.0000.0000.000
147A864GLU-1-0.855-0.92340.016-0.114-0.1140.0000.0000.0000.000
148A865ILE0-0.073-0.02037.011-0.006-0.0060.0000.0000.0000.000
149A866LEU0-0.055-0.01334.926-0.011-0.0110.0000.0000.0000.000
150A867PRO00.0370.01731.2270.0020.0020.0000.0000.0000.000
151A868PRO00.0610.01532.9330.0030.0030.0000.0000.0000.000
152A869THR00.0400.01727.9620.0130.0130.0000.0000.0000.000
153A870LEU00.0100.01730.7690.0050.0050.0000.0000.0000.000
154A871ARG10.8430.90732.0550.1250.1250.0000.0000.0000.000
155A872TYR00.0270.02130.7140.0040.0040.0000.0000.0000.000
156A873ILE0-0.005-0.01228.2880.0090.0090.0000.0000.0000.000
157A874TYR0-0.025-0.04332.7010.0090.0090.0000.0000.0000.000
158A875GLY00.0980.05335.9780.0090.0090.0000.0000.0000.000
159A876CYS0-0.101-0.05033.6120.0080.0080.0000.0000.0000.000
160A877LEU0-0.0010.00633.8770.0080.0080.0000.0000.0000.000
161A878GLN0-0.065-0.03236.4880.0070.0070.0000.0000.0000.000
162A879LYS10.9180.95238.0260.0910.0910.0000.0000.0000.000
163A880SER00.014-0.01835.2110.0040.0040.0000.0000.0000.000
164A881VAL0-0.034-0.02538.0150.0060.0060.0000.0000.0000.000
165A882GLN0-0.013-0.00140.7470.0020.0020.0000.0000.0000.000
166A883HIS0-0.0140.00438.8440.0040.0040.0000.0000.0000.000
167A884LYS10.8100.91138.8940.0490.0490.0000.0000.0000.000
168A885TRP0-0.012-0.01940.0060.0030.0030.0000.0000.0000.000
169A886PRO00.0380.02345.253-0.001-0.0010.0000.0000.0000.000
170A887THR0-0.030-0.01347.4460.0000.0000.0000.0000.0000.000
171A888ASN0-0.011-0.00147.244-0.001-0.0010.0000.0000.0000.000
172A889THR00.0170.00147.859-0.003-0.0030.0000.0000.0000.000
173A890THR0-0.001-0.00648.012-0.003-0.0030.0000.0000.0000.000
174A891MET00.0140.03042.331-0.002-0.0020.0000.0000.0000.000
175A892ARG10.8420.92342.8720.0730.0730.0000.0000.0000.000
176A893THR00.0500.02942.965-0.004-0.0040.0000.0000.0000.000
177A894ARG10.9240.93043.2370.0500.0500.0000.0000.0000.000
178A895VAL0-0.0020.00037.802-0.002-0.0020.0000.0000.0000.000
179A896VAL00.0290.02538.458-0.005-0.0050.0000.0000.0000.000
180A897SER0-0.015-0.02738.890-0.006-0.0060.0000.0000.0000.000
181A898GLY0-0.022-0.01139.010-0.002-0.0020.0000.0000.0000.000
182A899PHE0-0.006-0.00732.201-0.004-0.0040.0000.0000.0000.000
183A900VAL00.0520.02135.911-0.003-0.0030.0000.0000.0000.000
184A901PHE00.022-0.00337.601-0.001-0.0010.0000.0000.0000.000
185A902LEU0-0.021-0.00838.123-0.001-0.0010.0000.0000.0000.000
186A903ARG10.7900.87033.0070.0980.0980.0000.0000.0000.000
187A904LEU00.0000.01032.783-0.010-0.0100.0000.0000.0000.000
188A905ILE00.0050.00435.5040.0010.0010.0000.0000.0000.000
189A906CYS0-0.060-0.03438.8520.0020.0020.0000.0000.0000.000
190A907PRO00.0140.00435.6470.0030.0030.0000.0000.0000.000
191A908ALA00.0040.01336.2960.0010.0010.0000.0000.0000.000
192A909ILE0-0.009-0.00337.6130.0010.0010.0000.0000.0000.000
193A910LEU0-0.021-0.01339.7960.0040.0040.0000.0000.0000.000
194A911ASN0-0.018-0.01835.0060.0040.0040.0000.0000.0000.000
195A912PRO00.0630.03436.753-0.007-0.0070.0000.0000.0000.000
196A913ARG10.8930.93735.0550.0950.0950.0000.0000.0000.000
197A914MET0-0.0220.00128.598-0.008-0.0080.0000.0000.0000.000
198A915PHE00.0090.01231.232-0.010-0.0100.0000.0000.0000.000
199A916ASN0-0.047-0.02930.6340.0000.0000.0000.0000.0000.000
200A917ILE0-0.043-0.00634.5110.0010.0010.0000.0000.0000.000
201A918ILE0-0.006-0.00837.8690.0040.0040.0000.0000.0000.000
202A919SER00.0470.02237.419-0.008-0.0080.0000.0000.0000.000
203A920ASP-1-0.922-0.95038.682-0.092-0.0920.0000.0000.0000.000
204A921SER0-0.048-0.03741.300-0.002-0.0020.0000.0000.0000.000
205A922PRO00.0500.02542.1310.0020.0020.0000.0000.0000.000
206A923SER00.0430.03445.3110.0030.0030.0000.0000.0000.000
207A924PRO00.0580.00948.631-0.001-0.0010.0000.0000.0000.000
208A925ILE00.0290.01750.5400.0000.0000.0000.0000.0000.000
209A926ALA00.0390.02847.7420.0000.0000.0000.0000.0000.000
210A927ALA00.0190.00646.340-0.002-0.0020.0000.0000.0000.000
211A928ARG10.7960.86747.3120.0470.0470.0000.0000.0000.000
212A929THR00.018-0.00249.8270.0010.0010.0000.0000.0000.000
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