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: Z6LVN

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 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 324
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4837076.111763
FMO2-HF: Nuclear repulsion 4705950.80533
FMO2-HF: Total energy -131125.306434
FMO2-MP2: Total energy -131502.38589


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.
-15.686-9.67118.165-7.318-16.864-0.003
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 : -0.007 / q_NPA : -0.010
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-1-0.819-0.9143.657-2.516-0.9520.019-0.714-0.8690.001
4A721GLU-1-0.932-0.9746.080-1.138-1.1380.0000.0000.0000.000
5A722GLU-1-0.930-0.9662.0431.5922.0114.069-1.191-3.298-0.006
6A723TYR00.006-0.0012.168-11.862-8.8326.114-3.319-5.8240.008
7A724SER0-0.039-0.0234.9370.3550.412-0.001-0.002-0.0550.000
8A725GLU-1-0.808-0.9145.864-0.330-0.3300.0000.0000.0000.000
9A726PHE0-0.050-0.0377.0530.1140.1140.0000.0000.0000.000
10A727LYS10.8590.9278.8700.7600.7600.0000.0000.0000.000
11A728GLU-1-0.905-0.94910.759-0.239-0.2390.0000.0000.0000.000
12A729LEU0-0.073-0.02212.2990.0590.0590.0000.0000.0000.000
13A730ILE0-0.078-0.04510.9840.0290.0290.0000.0000.0000.000
14A731LEU0-0.0210.00014.6680.0100.0100.0000.0000.0000.000
15A732GLN00.0000.01816.9920.0170.0170.0000.0000.0000.000
16A733LYS10.9940.98419.2890.0780.0780.0000.0000.0000.000
17A734GLU-1-0.953-0.98422.533-0.045-0.0450.0000.0000.0000.000
18A735LEU0-0.0130.00220.3480.0100.0100.0000.0000.0000.000
19A736HIS00.0370.00920.1530.0080.0080.0000.0000.0000.000
20A737VAL00.0390.01714.1340.0180.0180.0000.0000.0000.000
21A738VAL00.0390.02117.4900.0100.0100.0000.0000.0000.000
22A739TYR00.0430.00819.0990.0080.0080.0000.0000.0000.000
23A740ALA00.0120.01918.5030.0090.0090.0000.0000.0000.000
24A741LEU00.024-0.00514.3150.0140.0140.0000.0000.0000.000
25A742SER0-0.069-0.04418.5040.0020.0020.0000.0000.0000.000
26A743HIS0-0.0190.00321.782-0.004-0.0040.0000.0000.0000.000
27A744VAL00.004-0.00718.0320.0040.0040.0000.0000.0000.000
28A745CYS0-0.109-0.02818.4870.0090.0090.0000.0000.0000.000
29A746GLY00.0670.03521.143-0.011-0.0110.0000.0000.0000.000
30A747GLN0-0.028-0.02824.810-0.019-0.0190.0000.0000.0000.000
31A748ASP-1-0.921-0.95320.444-0.021-0.0210.0000.0000.0000.000
32A749ARG10.9430.97520.8610.0300.0300.0000.0000.0000.000
33A750THR00.006-0.00522.135-0.015-0.0150.0000.0000.0000.000
34A751LEU00.0510.02815.754-0.029-0.0290.0000.0000.0000.000
35A752LEU00.0500.02316.580-0.033-0.0330.0000.0000.0000.000
36A753ALA00.000-0.00718.154-0.030-0.0300.0000.0000.0000.000
37A754SER0-0.047-0.02517.972-0.024-0.0240.0000.0000.0000.000
38A755ILE0-0.0220.00012.845-0.033-0.0330.0000.0000.0000.000
39A756LEU0-0.007-0.00415.364-0.049-0.0490.0000.0000.0000.000
40A757LEU00.0150.00717.320-0.022-0.0220.0000.0000.0000.000
41A758ARG10.8620.91013.8420.4230.4230.0000.0000.0000.000
42A759ILE00.0010.01012.069-0.039-0.0390.0000.0000.0000.000
43A760PHE00.026-0.01315.102-0.015-0.0150.0000.0000.0000.000
44A761LEU0-0.029-0.01718.6400.0140.0140.0000.0000.0000.000
45A762HIS10.7590.88813.5010.7580.7580.0000.0000.0000.000
46A763GLU-1-0.844-0.93714.884-0.619-0.6190.0000.0000.0000.000
47A764LYS10.8290.93918.5320.2780.2780.0000.0000.0000.000
48A765LEU00.0220.01318.9400.0350.0350.0000.0000.0000.000
49A766GLU-1-0.874-0.95722.235-0.221-0.2210.0000.0000.0000.000
50A767SER00.0410.00723.5380.0230.0230.0000.0000.0000.000
51A768LEU00.0170.02621.4310.0170.0170.0000.0000.0000.000
52A769LEU0-0.0040.02720.5310.0210.0210.0000.0000.0000.000
53A770LEU0-0.005-0.01123.6520.0190.0190.0000.0000.0000.000
54A771CYS0-0.021-0.01126.7780.0120.0120.0000.0000.0000.000
55A772THR0-0.031-0.02625.7670.0150.0150.0000.0000.0000.000
56A773LEU0-0.016-0.01423.2990.0130.0130.0000.0000.0000.000
57A774ASN00.000-0.02127.5290.0110.0110.0000.0000.0000.000
58A775ASP-1-0.874-0.93330.999-0.046-0.0460.0000.0000.0000.000
59A776ARG10.9110.96726.1720.0320.0320.0000.0000.0000.000
60A777GLU-1-0.925-0.97630.156-0.035-0.0350.0000.0000.0000.000
61A778ILE0-0.028-0.01132.7460.0050.0050.0000.0000.0000.000
62A779SER0-0.095-0.05433.6430.0060.0060.0000.0000.0000.000
63A780MET0-0.030-0.02031.0120.0070.0070.0000.0000.0000.000
64A781GLU-1-0.820-0.88235.788-0.023-0.0230.0000.0000.0000.000
65A782ASP-1-0.961-0.98938.476-0.012-0.0120.0000.0000.0000.000
66A783GLU-1-0.871-0.94341.709-0.020-0.0200.0000.0000.0000.000
67A784ALA00.0120.00342.437-0.002-0.0020.0000.0000.0000.000
68A785THR0-0.101-0.05343.109-0.004-0.0040.0000.0000.0000.000
69A786THR0-0.024-0.01740.319-0.002-0.0020.0000.0000.0000.000
70A787LEU00.0320.03236.855-0.001-0.0010.0000.0000.0000.000
71A788PHE0-0.001-0.00832.246-0.003-0.0030.0000.0000.0000.000
72A789ARG10.8750.93835.9660.0340.0340.0000.0000.0000.000
73A790ALA00.0080.01634.257-0.001-0.0010.0000.0000.0000.000
74A791THR0-0.010-0.00229.556-0.007-0.0070.0000.0000.0000.000
75A792THR00.0620.02528.9590.0030.0030.0000.0000.0000.000
76A793LEU00.0320.00521.708-0.007-0.0070.0000.0000.0000.000
77A794ALA00.0700.04025.730-0.014-0.0140.0000.0000.0000.000
78A795SER00.0550.02727.796-0.008-0.0080.0000.0000.0000.000
79A796THR0-0.019-0.00924.861-0.005-0.0050.0000.0000.0000.000
80A797LEU0-0.014-0.00921.670-0.013-0.0130.0000.0000.0000.000
81A798MET00.0120.02825.502-0.017-0.0170.0000.0000.0000.000
82A799GLU-1-0.851-0.90528.692-0.095-0.0950.0000.0000.0000.000
83A800GLN0-0.041-0.04721.933-0.029-0.0290.0000.0000.0000.000
84A801TYR00.0710.01824.664-0.009-0.0090.0000.0000.0000.000
85A802MET00.0090.01926.129-0.005-0.0050.0000.0000.0000.000
86A803LYS10.8690.96522.3850.2070.2070.0000.0000.0000.000
87A804ALA0-0.075-0.03824.170-0.004-0.0040.0000.0000.0000.000
88A805THR0-0.028-0.00426.051-0.004-0.0040.0000.0000.0000.000
89A806ALA00.0230.01228.5190.0050.0050.0000.0000.0000.000
90A807THR00.0310.01229.9310.0110.0110.0000.0000.0000.000
91A808GLN00.0130.00432.5860.0040.0040.0000.0000.0000.000
92A809PHE00.0460.03235.0870.0070.0070.0000.0000.0000.000
93A810VAL00.0250.01134.4980.0080.0080.0000.0000.0000.000
94A811HIS0-0.083-0.05734.3960.0060.0060.0000.0000.0000.000
95A812HIS0-0.011-0.01238.3690.0070.0070.0000.0000.0000.000
96A813ALA0-0.0050.01340.3040.0050.0050.0000.0000.0000.000
97A814LEU0-0.021-0.02239.1020.0060.0060.0000.0000.0000.000
98A815LYS10.9400.97638.2690.1110.1110.0000.0000.0000.000
99A816ASP-1-0.871-0.94241.981-0.081-0.0810.0000.0000.0000.000
100A817SER0-0.025-0.01545.6450.0030.0030.0000.0000.0000.000
101A818ILE0-0.005-0.00941.2510.0030.0030.0000.0000.0000.000
102A819LEU0-0.006-0.00542.2630.0020.0020.0000.0000.0000.000
103A820LYS11.0071.00745.7790.0630.0630.0000.0000.0000.000
104A821ILE0-0.041-0.01947.2440.0030.0030.0000.0000.0000.000
105A822MET0-0.087-0.05144.3180.0020.0020.0000.0000.0000.000
106A823GLU-1-0.933-0.95247.686-0.065-0.0650.0000.0000.0000.000
107A824SER0-0.066-0.00550.6240.0040.0040.0000.0000.0000.000
108A825LYS10.9580.96553.2380.0410.0410.0000.0000.0000.000
109A826GLN0-0.079-0.03956.0130.0020.0020.0000.0000.0000.000
110A827SER00.0030.01255.564-0.002-0.0020.0000.0000.0000.000
111A828CYS00.0080.02953.8340.0000.0000.0000.0000.0000.000
112A829GLU-1-0.729-0.84755.627-0.035-0.0350.0000.0000.0000.000
113A830LEU00.0580.02055.7470.0010.0010.0000.0000.0000.000
114A831SER0-0.060-0.04656.7490.0010.0010.0000.0000.0000.000
115A832PRO00.0500.01559.2500.0000.0000.0000.0000.0000.000
116A833SER0-0.004-0.00360.6200.0000.0000.0000.0000.0000.000
117A834LYS10.9060.95053.5740.0320.0320.0000.0000.0000.000
118A835LEU0-0.0260.01059.483-0.001-0.0010.0000.0000.0000.000
119A836GLU-1-0.977-0.99259.335-0.028-0.0280.0000.0000.0000.000
120A837LYS10.9140.96463.2500.0280.0280.0000.0000.0000.000
121A838ASN0-0.059-0.02965.101-0.001-0.0010.0000.0000.0000.000
122A839GLU-1-0.770-0.89060.182-0.035-0.0350.0000.0000.0000.000
123A840ASP-1-0.821-0.91964.452-0.028-0.0280.0000.0000.0000.000
124A841VAL00.0260.01461.967-0.001-0.0010.0000.0000.0000.000
125A842ASN00.0250.01462.256-0.002-0.0020.0000.0000.0000.000
126A843THR0-0.024-0.01762.531-0.001-0.0010.0000.0000.0000.000
127A844ASN0-0.046-0.02858.929-0.002-0.0020.0000.0000.0000.000
128A845LEU0-0.042-0.01858.406-0.002-0.0020.0000.0000.0000.000
129A846THR0-0.012-0.00459.039-0.001-0.0010.0000.0000.0000.000
130A847HIS00.009-0.01254.584-0.003-0.0030.0000.0000.0000.000
131A848LEU00.0370.00852.408-0.002-0.0020.0000.0000.0000.000
132A849LEU0-0.002-0.00754.490-0.002-0.0020.0000.0000.0000.000
133A850ASN00.0040.01055.992-0.001-0.0010.0000.0000.0000.000
134A851ILE0-0.020-0.00750.716-0.002-0.0020.0000.0000.0000.000
135A852LEU0-0.044-0.02450.245-0.003-0.0030.0000.0000.0000.000
136A853SER0-0.041-0.02451.422-0.001-0.0010.0000.0000.0000.000
137A854GLU-1-0.829-0.91150.070-0.064-0.0640.0000.0000.0000.000
138A855LEU00.0070.00745.045-0.003-0.0030.0000.0000.0000.000
139A856VAL0-0.022-0.02047.383-0.003-0.0030.0000.0000.0000.000
140A857GLU-1-0.989-0.99148.307-0.060-0.0600.0000.0000.0000.000
141A858LYS10.9020.94645.7120.0690.0690.0000.0000.0000.000
142A859ILE0-0.015-0.00542.867-0.004-0.0040.0000.0000.0000.000
143A860PHE0-0.053-0.03843.916-0.002-0.0020.0000.0000.0000.000
144A861MET00.0170.00545.612-0.002-0.0020.0000.0000.0000.000
145A862ALA00.0050.01641.124-0.003-0.0030.0000.0000.0000.000
146A863SER0-0.030-0.02640.815-0.007-0.0070.0000.0000.0000.000
147A864GLU-1-0.876-0.94140.159-0.095-0.0950.0000.0000.0000.000
148A865ILE0-0.074-0.02037.114-0.005-0.0050.0000.0000.0000.000
149A866LEU0-0.049-0.01435.218-0.009-0.0090.0000.0000.0000.000
150A867PRO00.0360.01931.4220.0020.0020.0000.0000.0000.000
151A868PRO00.0660.01932.7610.0040.0040.0000.0000.0000.000
152A869THR00.0350.01728.0390.0100.0100.0000.0000.0000.000
153A870LEU00.0100.01830.9780.0050.0050.0000.0000.0000.000
154A871ARG10.8560.92032.2570.1040.1040.0000.0000.0000.000
155A872TYR00.0160.01830.8470.0040.0040.0000.0000.0000.000
156A873ILE0-0.007-0.01528.4410.0070.0070.0000.0000.0000.000
157A874TYR0-0.037-0.04532.9630.0080.0080.0000.0000.0000.000
158A875GLY00.1010.05336.2330.0070.0070.0000.0000.0000.000
159A876CYS0-0.091-0.04033.7260.0070.0070.0000.0000.0000.000
160A877LEU0-0.0110.00433.8260.0070.0070.0000.0000.0000.000
161A878GLN0-0.058-0.03036.5440.0060.0060.0000.0000.0000.000
162A879LYS10.9160.95138.1070.0670.0670.0000.0000.0000.000
163A880SER00.0210.00835.3700.0030.0030.0000.0000.0000.000
164A881VAL0-0.024-0.01638.1350.0050.0050.0000.0000.0000.000
165A882GLN0-0.0150.00340.7890.0020.0020.0000.0000.0000.000
166A883HIS0-0.0120.00539.5320.0020.0020.0000.0000.0000.000
167A884LYS10.8560.94539.1800.0270.0270.0000.0000.0000.000
168A885TRP0-0.019-0.01840.0720.0020.0020.0000.0000.0000.000
169A886PRO00.0340.01845.284-0.001-0.0010.0000.0000.0000.000
170A887THR0-0.025-0.00847.551-0.001-0.0010.0000.0000.0000.000
171A888ASN0-0.0080.00247.199-0.001-0.0010.0000.0000.0000.000
172A889THR00.017-0.00147.880-0.002-0.0020.0000.0000.0000.000
173A890THR00.001-0.00647.620-0.002-0.0020.0000.0000.0000.000
174A891MET00.0110.01242.209-0.002-0.0020.0000.0000.0000.000
175A892ARG10.8750.94642.8970.0550.0550.0000.0000.0000.000
176A893THR00.0440.03143.098-0.003-0.0030.0000.0000.0000.000
177A894ARG10.9260.94743.4860.0350.0350.0000.0000.0000.000
178A895VAL0-0.0010.00137.711-0.001-0.0010.0000.0000.0000.000
179A896VAL00.0400.02938.647-0.004-0.0040.0000.0000.0000.000
180A897SER0-0.024-0.02539.116-0.005-0.0050.0000.0000.0000.000
181A898GLY0-0.006-0.00639.257-0.002-0.0020.0000.0000.0000.000
182A899PHE0-0.013-0.01132.561-0.003-0.0030.0000.0000.0000.000
183A900VAL00.0600.02636.101-0.003-0.0030.0000.0000.0000.000
184A901PHE00.025-0.00737.786-0.001-0.0010.0000.0000.0000.000
185A902LEU0-0.009-0.00138.228-0.001-0.0010.0000.0000.0000.000
186A903ARG10.7860.87033.2300.0690.0690.0000.0000.0000.000
187A904LEU00.0090.01933.110-0.008-0.0080.0000.0000.0000.000
188A905ILE0-0.004-0.00335.6500.0000.0000.0000.0000.0000.000
189A906CYS0-0.059-0.02938.9770.0010.0010.0000.0000.0000.000
190A907PRO00.0140.00535.7780.0020.0020.0000.0000.0000.000
191A908ALA00.0130.01636.4160.0000.0000.0000.0000.0000.000
192A909ILE0-0.015-0.00337.6910.0000.0000.0000.0000.0000.000
193A910LEU0-0.021-0.01539.9330.0030.0030.0000.0000.0000.000
194A911ASN0-0.010-0.01334.7190.0030.0030.0000.0000.0000.000
195A912PRO00.0520.03236.793-0.006-0.0060.0000.0000.0000.000
196A913ARG10.9240.95734.9490.0810.0810.0000.0000.0000.000
197A914MET0-0.046-0.00828.276-0.009-0.0090.0000.0000.0000.000
198A915PHE00.0320.02131.239-0.008-0.0080.0000.0000.0000.000
199A916ASN0-0.049-0.03630.963-0.001-0.0010.0000.0000.0000.000
200A917ILE0-0.056-0.00334.4790.0000.0000.0000.0000.0000.000
201A918ILE0-0.006-0.01037.8400.0030.0030.0000.0000.0000.000
202A919SER00.0480.01037.367-0.007-0.0070.0000.0000.0000.000
203A920ASP-1-0.928-0.95338.601-0.081-0.0810.0000.0000.0000.000
204A921SER0-0.070-0.04841.223-0.002-0.0020.0000.0000.0000.000
205A922PRO00.0420.02442.0740.0020.0020.0000.0000.0000.000
206A923SER00.0530.03645.2850.0020.0020.0000.0000.0000.000
207A924PRO00.0530.00648.620-0.001-0.0010.0000.0000.0000.000
208A925ILE00.0400.02550.5330.0000.0000.0000.0000.0000.000
209A926ALA00.0340.02547.6620.0000.0000.0000.0000.0000.000
210A927ALA00.0140.00146.361-0.001-0.0010.0000.0000.0000.000
211A928ARG10.7840.88347.3450.0380.0380.0000.0000.0000.000
212A929THR00.017-0.00149.8430.0010.0010.0000.0000.0000.000
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