Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 8948Y

Calculation Name: 2W01-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2W01

Chain ID: A

ChEMBL ID:

UniProt ID: P72951

Base Structure: X-ray

Registration Date: 2023-09-23

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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2091424.688137
FMO2-HF: Nuclear repulsion 2016023.954129
FMO2-HF: Total energy -75400.734007
FMO2-MP2: Total energy -75620.35852


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:435:MET)


Summations of interaction energy for fragment #1(A:435: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.
-26.078-33.44841.06-13.805-19.8860.002
Interaction energy analysis for fragmet #1(A:435:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : 0.037
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].
3A437GLY0-0.024-0.0193.2650.5742.8730.014-1.080-1.2330.000
4A438ASP-1-0.840-0.9002.630-9.738-7.1171.113-1.391-2.343-0.015
5A439ARG10.8660.9284.5551.5451.697-0.001-0.014-0.1370.000
6A440ARG10.8530.9252.4102.0752.1631.801-0.517-1.373-0.005
7A441PRO0-0.0050.0038.2190.3430.3430.0000.0000.0000.000
8A442ILE0-0.0140.0017.091-0.056-0.0560.0000.0000.0000.000
9A443THR00.011-0.01510.326-0.051-0.0510.0000.0000.0000.000
10A444ILE0-0.056-0.02712.0840.1390.1390.0000.0000.0000.000
11A445LEU00.0350.03614.365-0.100-0.1000.0000.0000.0000.000
12A446THR0-0.035-0.02616.8890.0970.0970.0000.0000.0000.000
13A447SER00.0550.01619.387-0.051-0.0510.0000.0000.0000.000
14A448ASP-1-0.830-0.89222.7370.3680.3680.0000.0000.0000.000
15A449LEU00.0200.01525.664-0.023-0.0230.0000.0000.0000.000
16A450ARG10.7170.82627.558-0.313-0.3130.0000.0000.0000.000
17A451GLY00.0450.03431.163-0.017-0.0170.0000.0000.0000.000
18A452PHE00.0190.01130.240-0.013-0.0130.0000.0000.0000.000
19A453THR00.011-0.01229.042-0.008-0.0080.0000.0000.0000.000
20A454SER0-0.072-0.03831.550-0.007-0.0070.0000.0000.0000.000
21A455THR0-0.052-0.03334.946-0.013-0.0130.0000.0000.0000.000
22A456SER0-0.060-0.03232.831-0.007-0.0070.0000.0000.0000.000
23A457GLU-1-0.915-0.96434.7810.2120.2120.0000.0000.0000.000
24A458GLY0-0.076-0.02936.891-0.010-0.0100.0000.0000.0000.000
25A459LEU0-0.057-0.01735.497-0.008-0.0080.0000.0000.0000.000
26A460ASN0-0.020-0.02737.9470.0080.0080.0000.0000.0000.000
27A461PRO00.029-0.00833.7190.0070.0070.0000.0000.0000.000
28A462GLU-1-0.896-0.94733.1910.1720.1720.0000.0000.0000.000
29A463GLU-1-0.845-0.90333.8830.1640.1640.0000.0000.0000.000
30A464VAL00.0210.02130.5360.0080.0080.0000.0000.0000.000
31A465VAL00.0150.00228.2370.0150.0150.0000.0000.0000.000
32A466LYS10.8380.91929.235-0.158-0.1580.0000.0000.0000.000
33A467VAL00.0310.01331.0200.0020.0020.0000.0000.0000.000
34A468LEU00.0030.00726.4990.0080.0080.0000.0000.0000.000
35A469ASN0-0.048-0.02525.5790.0370.0370.0000.0000.0000.000
36A470ILE0-0.028-0.00126.7490.0060.0060.0000.0000.0000.000
37A471TYR00.006-0.01424.7780.0020.0020.0000.0000.0000.000
38A472PHE00.006-0.01222.3140.0110.0110.0000.0000.0000.000
39A473GLY0-0.0090.00122.7960.0240.0240.0000.0000.0000.000
40A474LYS10.8320.91324.266-0.208-0.2080.0000.0000.0000.000
41A475MET0-0.016-0.00622.369-0.004-0.0040.0000.0000.0000.000
42A476ALA00.0100.00119.9670.0260.0260.0000.0000.0000.000
43A477ASP-1-0.866-0.89620.3220.2530.2530.0000.0000.0000.000
44A478VAL0-0.0060.00121.721-0.004-0.0040.0000.0000.0000.000
45A479ILE00.018-0.00616.2460.0020.0020.0000.0000.0000.000
46A480THR0-0.066-0.04317.0410.0350.0350.0000.0000.0000.000
47A481HIS0-0.145-0.07817.981-0.042-0.0420.0000.0000.0000.000
48A482HIS0-0.029-0.02118.123-0.027-0.0270.0000.0000.0000.000
49A483GLY00.0130.01314.890-0.005-0.0050.0000.0000.0000.000
50A484GLY0-0.0070.00512.663-0.002-0.0020.0000.0000.0000.000
51A485THR0-0.064-0.0618.447-0.082-0.0820.0000.0000.0000.000
52A486ILE00.0240.00711.5590.0870.0870.0000.0000.0000.000
53A487ASP-1-0.823-0.9079.2752.4692.4690.0000.0000.0000.000
54A488GLU-1-0.909-0.94811.7121.2011.2010.0000.0000.0000.000
55A489PHE00.0270.01914.820-0.051-0.0510.0000.0000.0000.000
56A490MET0-0.0630.00518.2630.0410.0410.0000.0000.0000.000
57A491GLY00.0190.01220.600-0.036-0.0360.0000.0000.0000.000
58A492ASP-1-0.768-0.88324.0440.3290.3290.0000.0000.0000.000
59A493GLY00.0420.03122.639-0.021-0.0210.0000.0000.0000.000
60A494ILE0-0.060-0.03018.0870.0370.0370.0000.0000.0000.000
61A495LEU0-0.022-0.00413.407-0.021-0.0210.0000.0000.0000.000
62A496VAL00.021-0.00113.6950.0900.0900.0000.0000.0000.000
63A497LEU0-0.055-0.0198.087-0.014-0.0140.0000.0000.0000.000
64A498PHE00.0510.02810.937-0.005-0.0050.0000.0000.0000.000
65A499GLY00.0760.0408.206-0.058-0.0580.0000.0000.0000.000
66A500ALA0-0.0150.0024.558-0.608-0.483-0.001-0.027-0.0980.000
67A501PRO00.0390.0283.371-0.6450.0790.167-0.218-0.6740.001
68A502THR0-0.036-0.0113.278-3.705-2.9160.049-0.435-0.402-0.004
69A503SER0-0.014-0.0056.0510.1630.1630.0000.0000.0000.000
70A504GLN0-0.091-0.0588.397-0.119-0.1190.0000.0000.0000.000
71A505GLN0-0.030-0.02912.1350.0380.0380.0000.0000.0000.000
72A506ASP-1-0.752-0.85815.1100.0540.0540.0000.0000.0000.000
73A507ASP-1-0.751-0.86810.5660.1710.1710.0000.0000.0000.000
74A508ALA00.0210.00713.9610.0650.0650.0000.0000.0000.000
75A509LEU0-0.005-0.00516.6140.0190.0190.0000.0000.0000.000
76A510ARG10.7430.85812.121-0.219-0.2190.0000.0000.0000.000
77A511ALA0-0.0100.00715.7280.0240.0240.0000.0000.0000.000
78A512VAL00.000-0.01517.6070.0110.0110.0000.0000.0000.000
79A513ALA0-0.0040.00821.201-0.001-0.0010.0000.0000.0000.000
80A514CYS00.0160.02119.2040.0110.0110.0000.0000.0000.000
81A515GLY00.0420.01021.2050.0070.0070.0000.0000.0000.000
82A516VAL0-0.024-0.01522.853-0.008-0.0080.0000.0000.0000.000
83A517GLU-1-0.776-0.87323.9320.1930.1930.0000.0000.0000.000
84A518MET0-0.014-0.00821.1700.0040.0040.0000.0000.0000.000
85A519GLN00.023-0.00825.327-0.013-0.0130.0000.0000.0000.000
86A520LEU0-0.061-0.02128.326-0.019-0.0190.0000.0000.0000.000
87A521ALA00.0300.00827.139-0.010-0.0100.0000.0000.0000.000
88A522LEU0-0.009-0.01129.042-0.003-0.0030.0000.0000.0000.000
89A523ARG10.8070.89130.492-0.162-0.1620.0000.0000.0000.000
90A524GLU-1-0.900-0.94731.2720.1620.1620.0000.0000.0000.000
91A525VAL00.0300.01129.614-0.007-0.0070.0000.0000.0000.000
92A526ASN00.0110.00432.9340.0010.0010.0000.0000.0000.000
93A527GLN0-0.0270.00935.641-0.013-0.0130.0000.0000.0000.000
94A528GLN0-0.010-0.00633.0830.0030.0030.0000.0000.0000.000
95A529VAL00.000-0.00633.718-0.004-0.0040.0000.0000.0000.000
96A530THR0-0.002-0.01436.761-0.005-0.0050.0000.0000.0000.000
97A531GLY0-0.044-0.01740.053-0.007-0.0070.0000.0000.0000.000
98A532LEU0-0.081-0.04436.039-0.005-0.0050.0000.0000.0000.000
99A533GLY0-0.023-0.00240.376-0.001-0.0010.0000.0000.0000.000
100A534LEU0-0.050-0.01437.382-0.001-0.0010.0000.0000.0000.000
101A535GLN0-0.015-0.01739.480-0.007-0.0070.0000.0000.0000.000
102A536PRO0-0.029-0.00936.9140.0090.0090.0000.0000.0000.000
103A537LEU00.0200.01130.2920.0030.0030.0000.0000.0000.000
104A538GLU-1-0.877-0.93733.0500.1860.1860.0000.0000.0000.000
105A539MET00.005-0.00124.5350.0070.0070.0000.0000.0000.000
106A540GLY00.0310.03627.842-0.022-0.0220.0000.0000.0000.000
107A541ILE00.025-0.00622.1210.0340.0340.0000.0000.0000.000
108A542GLY0-0.023-0.00322.588-0.037-0.0370.0000.0000.0000.000
109A543ILE0-0.0020.00217.8020.0510.0510.0000.0000.0000.000
110A544ASN0-0.018-0.01917.488-0.092-0.0920.0000.0000.0000.000
111A545THR00.0000.01514.2780.0370.0370.0000.0000.0000.000
112A546GLY00.0260.02413.822-0.068-0.0680.0000.0000.0000.000
113A547GLU-1-0.883-0.94611.235-0.043-0.0430.0000.0000.0000.000
114A548VAL0-0.068-0.0308.7550.0680.0680.0000.0000.0000.000
115A549VAL0-0.018-0.0126.702-0.277-0.2770.0000.0000.0000.000
116A550VAL00.0130.0033.220-0.357-0.0541.077-0.299-1.080-0.001
117A551GLY00.024-0.0072.168-1.273-1.7155.738-3.462-1.8350.005
118A552ASN0-0.038-0.0282.077-11.034-18.41213.568-0.735-5.455-0.001
119A553ILE00.0180.0153.700-0.531-0.4640.0160.046-0.1280.002
120A554GLY00.002-0.0057.426-0.355-0.3550.0000.0000.0000.000
121A555SER0-0.034-0.01110.291-0.126-0.1260.0000.0000.0000.000
122A556GLU-1-0.806-0.91210.7420.4670.4670.0000.0000.0000.000
123A557LYS10.8370.90411.950-0.344-0.3440.0000.0000.0000.000
124A558ARG10.9580.97912.244-0.838-0.8380.0000.0000.0000.000
125A559THR0-0.0200.0146.7340.1350.1350.0000.0000.0000.000
126A560LYS10.7810.8477.659-2.074-2.0740.0000.0000.0000.000
127A561TYR00.003-0.0192.109-3.363-10.08117.519-5.673-5.1280.020
128A562GLY00.0400.0225.850-0.720-0.7200.0000.0000.0000.000
129A563VAL00.0230.0146.5011.0011.0010.0000.0000.0000.000
130A564VAL0-0.021-0.0079.000-0.404-0.4040.0000.0000.0000.000
131A565GLY00.0560.01310.996-0.113-0.1130.0000.0000.0000.000
132A566ALA0-0.015-0.01313.9170.0110.0110.0000.0000.0000.000
133A567GLN00.0700.04314.808-0.017-0.0170.0000.0000.0000.000
134A568VAL00.0710.04712.625-0.047-0.0470.0000.0000.0000.000
135A569ASN0-0.018-0.01815.850-0.021-0.0210.0000.0000.0000.000
136A570LEU0-0.010-0.00219.036-0.047-0.0470.0000.0000.0000.000
137A571THR00.0110.00616.847-0.059-0.0590.0000.0000.0000.000
138A572TYR00.053-0.01717.022-0.017-0.0170.0000.0000.0000.000
139A573ARG10.8410.92621.502-0.484-0.4840.0000.0000.0000.000
140A574ILE0-0.043-0.01121.535-0.034-0.0340.0000.0000.0000.000
141A575GLU-1-0.770-0.88023.0990.3130.3130.0000.0000.0000.000
142A576SER0-0.056-0.03225.130-0.028-0.0280.0000.0000.0000.000
143A577TYR0-0.059-0.04327.839-0.026-0.0260.0000.0000.0000.000
144A578THR0-0.0390.01127.560-0.028-0.0280.0000.0000.0000.000
145A579THR0-0.027-0.02230.3470.0040.0040.0000.0000.0000.000
146A580GLY00.0750.02931.6890.0070.0070.0000.0000.0000.000
147A581GLY0-0.053-0.01831.208-0.015-0.0150.0000.0000.0000.000
148A582GLN0-0.029-0.00430.286-0.001-0.0010.0000.0000.0000.000
149A583ILE00.0290.01224.1720.0240.0240.0000.0000.0000.000
150A584PHE0-0.025-0.00125.994-0.025-0.0250.0000.0000.0000.000
151A585ILE00.0090.00222.1080.0340.0340.0000.0000.0000.000
152A586SER00.0390.00020.138-0.022-0.0220.0000.0000.0000.000
153A587SER00.0370.00922.916-0.005-0.0050.0000.0000.0000.000
154A588THR00.0230.01318.674-0.004-0.0040.0000.0000.0000.000
155A589THR0-0.022-0.02218.006-0.004-0.0040.0000.0000.0000.000
156A590LEU00.0350.02319.680-0.014-0.0140.0000.0000.0000.000
157A591GLU-1-0.955-0.98822.0840.0430.0430.0000.0000.0000.000
158A592ALA0-0.063-0.02316.944-0.023-0.0230.0000.0000.0000.000
159A593ALA0-0.0060.01218.731-0.016-0.0160.0000.0000.0000.000
160A594GLY00.013-0.00220.601-0.020-0.0200.0000.0000.0000.000
161A595ASP-1-0.862-0.93324.0560.0310.0310.0000.0000.0000.000
162A596ARG10.8340.91623.679-0.021-0.0210.0000.0000.0000.000
163A597VAL0-0.0020.01322.9810.0120.0120.0000.0000.0000.000
164A598HIS0-0.039-0.01926.142-0.015-0.0150.0000.0000.0000.000
165A599VAL0-0.022-0.01828.2540.0140.0140.0000.0000.0000.000
166A600ASN0-0.002-0.00430.850-0.019-0.0190.0000.0000.0000.000
167A601GLY0-0.006-0.00432.577-0.009-0.0090.0000.0000.0000.000
168A602ASN0-0.080-0.03230.9010.0110.0110.0000.0000.0000.000
169A603ARG10.9640.99531.198-0.170-0.1700.0000.0000.0000.000
170A604THR00.0150.01530.8530.0100.0100.0000.0000.0000.000
171A605VAL0-0.012-0.01128.4980.0010.0010.0000.0000.0000.000
172A606GLN00.004-0.00629.938-0.009-0.0090.0000.0000.0000.000
173A607PRO00.0010.01826.496-0.002-0.0020.0000.0000.0000.000
174A608LYS10.9780.97328.921-0.222-0.2220.0000.0000.0000.000
175A609GLY00.0190.01727.3710.0220.0220.0000.0000.0000.000
176A610VAL0-0.042-0.01425.0750.0060.0060.0000.0000.0000.000
177A611LYS10.7710.87925.244-0.177-0.1770.0000.0000.0000.000
178A612ASP-1-0.782-0.87728.6100.1130.1130.0000.0000.0000.000
179A613PRO0-0.006-0.01528.8550.0160.0160.0000.0000.0000.000
180A614VAL0-0.020-0.00324.900-0.003-0.0030.0000.0000.0000.000
181A615VAL0-0.009-0.00527.6190.0000.0000.0000.0000.0000.000
182A616ILE0-0.058-0.01825.3820.0080.0080.0000.0000.0000.000
183A617TRP00.006-0.02825.986-0.023-0.0230.0000.0000.0000.000
184A618ASP-1-0.823-0.89127.2690.1800.1800.0000.0000.0000.000
185A619VAL00.005-0.01124.956-0.016-0.0160.0000.0000.0000.000
186A620ALA00.0190.01528.3990.0060.0060.0000.0000.0000.000
187A621GLY00.032-0.00528.7310.0030.0030.0000.0000.0000.000
188A622VAL0-0.081-0.02923.8440.0030.0030.0000.0000.0000.000
189A623GLY00.0920.06127.152-0.001-0.0010.0000.0000.0000.000
190A624GLU-1-0.858-0.91127.4940.0410.0410.0000.0000.0000.000
191A625PRO0-0.085-0.05024.347-0.002-0.0020.0000.0000.0000.000
192A626TYR0-0.008-0.02620.0390.0010.0010.0000.0000.0000.000
193A627ASN0-0.075-0.05826.7660.0050.0050.0000.0000.0000.000
194A628LEU00.0080.03225.2160.0020.0020.0000.0000.0000.000
195A629SER00.013-0.03029.2660.0020.0020.0000.0000.0000.000
196A630LEU0-0.0010.01229.0860.0010.0010.0000.0000.0000.000
197A631ALA0-0.005-0.00332.4090.0000.0000.0000.0000.0000.000
198A632VAL0-0.0020.00635.639-0.002-0.0020.0000.0000.0000.000
199A633GLU-1-0.902-0.94735.6960.0640.0640.0000.0000.0000.000
200A634GLU-1-0.962-0.98239.0830.0670.0670.0000.0000.0000.000
201A635GLN0-0.102-0.04340.047-0.010-0.0100.0000.0000.0000.000