FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

tag_button

FMODB ID: 1N82Z

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:

Apendix: None


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 201
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2090575.491969
FMO2-HF: Nuclear repulsion 2015177.048508
FMO2-HF: Total energy -75398.443461
FMO2-MP2: Total energy -75618.127947


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.
-7.847-38.80560.885-8.125-21.8020.028
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 : 0.053 / q_NPA : 0.095
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].
3A437GLY0-0.035-0.0242.226-0.7662.1960.899-1.607-2.253-0.006
4A438ASP-1-0.845-0.9232.964-5.036-3.5120.225-0.357-1.393-0.005
5A439ARG10.8850.9504.0251.2331.3930.0000.001-0.1600.000
6A440ARG10.8380.8962.7720.5211.4200.434-0.334-0.999-0.002
7A441PRO00.0060.0098.6570.3090.3090.0000.0000.0000.000
8A442ILE0-0.0210.0027.8850.0300.0300.0000.0000.0000.000
9A443THR00.015-0.01511.068-0.096-0.0960.0000.0000.0000.000
10A444ILE0-0.054-0.02812.6160.0940.0940.0000.0000.0000.000
11A445LEU00.0410.02314.686-0.111-0.1110.0000.0000.0000.000
12A446THR0-0.020-0.01416.9040.1090.1090.0000.0000.0000.000
13A447SER00.027-0.00419.376-0.041-0.0410.0000.0000.0000.000
14A448ASP-1-0.803-0.89722.6290.3840.3840.0000.0000.0000.000
15A449LEU0-0.0090.00725.211-0.029-0.0290.0000.0000.0000.000
16A450ARG10.8050.88427.627-0.310-0.3100.0000.0000.0000.000
17A451GLY0-0.0080.00331.022-0.015-0.0150.0000.0000.0000.000
18A452PHE00.0480.01829.909-0.016-0.0160.0000.0000.0000.000
19A453THR00.0090.00029.453-0.002-0.0020.0000.0000.0000.000
20A454SER0-0.019-0.01631.596-0.003-0.0030.0000.0000.0000.000
21A455THR00.003-0.00735.241-0.004-0.0040.0000.0000.0000.000
22A456SER0-0.0080.01433.013-0.008-0.0080.0000.0000.0000.000
23A457GLU-1-0.935-0.97034.4940.2180.2180.0000.0000.0000.000
24A458GLY0-0.099-0.03836.984-0.009-0.0090.0000.0000.0000.000
25A459LEU0-0.048-0.00835.227-0.009-0.0090.0000.0000.0000.000
26A460ASN00.0160.01137.7610.0100.0100.0000.0000.0000.000
27A461PRO00.049-0.00734.1420.0060.0060.0000.0000.0000.000
28A462GLU-1-0.961-0.98133.1680.1730.1730.0000.0000.0000.000
29A463GLU-1-0.894-0.95633.9050.1620.1620.0000.0000.0000.000
30A464VAL00.0040.01230.3960.0070.0070.0000.0000.0000.000
31A465VAL00.0170.00428.3720.0140.0140.0000.0000.0000.000
32A466LYS10.9190.97129.228-0.154-0.1540.0000.0000.0000.000
33A467VAL00.0300.00930.9780.0010.0010.0000.0000.0000.000
34A468LEU00.0280.00926.2500.0050.0050.0000.0000.0000.000
35A469ASN0-0.019-0.00826.1060.0400.0400.0000.0000.0000.000
36A470ILE0-0.062-0.01426.8280.0020.0020.0000.0000.0000.000
37A471TYR00.0780.02824.162-0.007-0.0070.0000.0000.0000.000
38A472PHE0-0.009-0.01122.6030.0110.0110.0000.0000.0000.000
39A473GLY0-0.025-0.00623.0340.0190.0190.0000.0000.0000.000
40A474LYS10.9480.98624.480-0.191-0.1910.0000.0000.0000.000
41A475MET0-0.009-0.00722.255-0.004-0.0040.0000.0000.0000.000
42A476ALA0-0.009-0.00719.9510.0190.0190.0000.0000.0000.000
43A477ASP-1-0.925-0.95219.9270.2300.2300.0000.0000.0000.000
44A478VAL0-0.014-0.00921.557-0.012-0.0120.0000.0000.0000.000
45A479ILE00.010-0.01416.017-0.001-0.0010.0000.0000.0000.000
46A480THR0-0.053-0.02516.5380.0190.0190.0000.0000.0000.000
47A481HIS0-0.067-0.01417.338-0.052-0.0520.0000.0000.0000.000
48A482HIS0-0.042-0.03418.068-0.038-0.0380.0000.0000.0000.000
49A483GLY00.0080.01014.309-0.007-0.0070.0000.0000.0000.000
50A484GLY0-0.037-0.01112.5060.0250.0250.0000.0000.0000.000
51A485THR0-0.048-0.0488.482-0.133-0.1330.0000.0000.0000.000
52A486ILE00.0150.00311.6380.0810.0810.0000.0000.0000.000
53A487ASP-1-0.897-0.9539.4372.2852.2850.0000.0000.0000.000
54A488GLU-1-0.932-0.99511.7841.1491.1490.0000.0000.0000.000
55A489PHE00.0320.03514.809-0.063-0.0630.0000.0000.0000.000
56A490MET0-0.0550.01717.7060.0480.0480.0000.0000.0000.000
57A491GLY0-0.002-0.00220.247-0.031-0.0310.0000.0000.0000.000
58A492ASP-1-0.850-0.93623.8700.3490.3490.0000.0000.0000.000
59A493GLY00.0870.03622.017-0.020-0.0200.0000.0000.0000.000
60A494ILE0-0.089-0.03617.8330.0300.0300.0000.0000.0000.000
61A495LEU0-0.024-0.00712.644-0.019-0.0190.0000.0000.0000.000
62A496VAL00.008-0.01313.7400.0770.0770.0000.0000.0000.000
63A497LEU0-0.059-0.0327.9650.0700.0700.0000.0000.0000.000
64A498PHE00.0690.04011.059-0.039-0.0390.0000.0000.0000.000
65A499GLY00.1020.0408.434-0.019-0.0190.0000.0000.0000.000
66A500ALA0-0.0330.0064.739-0.254-0.126-0.001-0.028-0.1000.000
67A501PRO00.0320.0203.276-0.4420.1160.055-0.151-0.4620.000
68A502THR0-0.0330.0002.919-5.034-3.3630.193-0.961-0.903-0.011
69A503SER00.0040.0035.7850.2980.2980.0000.0000.0000.000
70A504GLN0-0.043-0.0158.312-0.121-0.1210.0000.0000.0000.000
71A505GLN0-0.022-0.02112.0680.0610.0610.0000.0000.0000.000
72A506ASP-1-0.836-0.91315.2500.0260.0260.0000.0000.0000.000
73A507ASP-1-0.778-0.89410.7570.1480.1480.0000.0000.0000.000
74A508ALA00.0300.00114.1360.0580.0580.0000.0000.0000.000
75A509LEU00.003-0.00617.0240.0170.0170.0000.0000.0000.000
76A510ARG10.7770.89312.142-0.162-0.1620.0000.0000.0000.000
77A511ALA0-0.0060.01216.1000.0230.0230.0000.0000.0000.000
78A512VAL00.003-0.00417.8820.0110.0110.0000.0000.0000.000
79A513ALA0-0.008-0.00221.2640.0000.0000.0000.0000.0000.000
80A514CYS00.0050.01619.0320.0100.0100.0000.0000.0000.000
81A515GLY00.0250.00621.0520.0050.0050.0000.0000.0000.000
82A516VAL0-0.012-0.00922.914-0.006-0.0060.0000.0000.0000.000
83A517GLU-1-0.837-0.90724.2090.1610.1610.0000.0000.0000.000
84A518MET0-0.025-0.02221.2940.0080.0080.0000.0000.0000.000
85A519GLN00.019-0.00825.181-0.017-0.0170.0000.0000.0000.000
86A520LEU0-0.083-0.03728.422-0.012-0.0120.0000.0000.0000.000
87A521ALA00.0070.00427.190-0.011-0.0110.0000.0000.0000.000
88A522LEU00.0360.00629.182-0.002-0.0020.0000.0000.0000.000
89A523ARG10.8810.93830.724-0.145-0.1450.0000.0000.0000.000
90A524GLU-1-0.895-0.94231.8460.1370.1370.0000.0000.0000.000
91A525VAL00.0090.01329.358-0.004-0.0040.0000.0000.0000.000
92A526ASN00.0130.01432.7850.0020.0020.0000.0000.0000.000
93A527GLN0-0.015-0.00335.563-0.011-0.0110.0000.0000.0000.000
94A528GLN0-0.035-0.02133.201-0.003-0.0030.0000.0000.0000.000
95A529VAL0-0.001-0.00233.559-0.003-0.0030.0000.0000.0000.000
96A530THR00.0030.00136.615-0.006-0.0060.0000.0000.0000.000
97A531GLY0-0.042-0.00840.097-0.007-0.0070.0000.0000.0000.000
98A532LEU0-0.089-0.05135.898-0.004-0.0040.0000.0000.0000.000
99A533GLY0-0.025-0.00340.2280.0000.0000.0000.0000.0000.000
100A534LEU0-0.0280.00137.5300.0000.0000.0000.0000.0000.000
101A535GLN0-0.027-0.02239.405-0.005-0.0050.0000.0000.0000.000
102A536PRO0-0.034-0.01636.6110.0080.0080.0000.0000.0000.000
103A537LEU00.007-0.00130.2800.0040.0040.0000.0000.0000.000
104A538GLU-1-0.892-0.95232.6040.1750.1750.0000.0000.0000.000
105A539MET0-0.033-0.01424.4660.0120.0120.0000.0000.0000.000
106A540GLY0-0.0120.00027.674-0.022-0.0220.0000.0000.0000.000
107A541ILE00.023-0.00122.0080.0340.0340.0000.0000.0000.000
108A542GLY0-0.032-0.00822.522-0.039-0.0390.0000.0000.0000.000
109A543ILE00.0170.00718.2920.0500.0500.0000.0000.0000.000
110A544ASN0-0.081-0.06717.546-0.116-0.1160.0000.0000.0000.000
111A545THR00.0780.05815.0140.0730.0730.0000.0000.0000.000
112A546GLY0-0.025-0.00414.403-0.072-0.0720.0000.0000.0000.000
113A547GLU-1-0.922-0.96310.9650.0260.0260.0000.0000.0000.000
114A548VAL0-0.065-0.0258.5790.0200.0200.0000.0000.0000.000
115A549VAL0-0.023-0.0156.125-0.202-0.2020.0000.0000.0000.000
116A550VAL00.0370.0193.091-0.2410.2251.170-0.352-1.284-0.002
117A551GLY00.017-0.0491.8421.383-6.50022.394-11.188-3.3230.014
118A552ASN0-0.064-0.0551.9053.895-21.02818.82011.850-5.7470.016
119A553ILE00.0200.0283.606-1.797-1.8750.0740.268-0.2630.004
120A554GLY00.0100.0007.361-0.413-0.4130.0000.0000.0000.000
121A555SER0-0.041-0.01710.228-0.084-0.0840.0000.0000.0000.000
122A556GLU-1-0.852-0.94210.8330.5260.5260.0000.0000.0000.000
123A557LYS10.8570.93212.091-0.300-0.3000.0000.0000.0000.000
124A558ARG10.9700.97612.444-0.868-0.8680.0000.0000.0000.000
125A559THR0-0.0030.0206.6610.3510.3510.0000.0000.0000.000
126A560LYS10.8820.9437.595-1.937-1.9370.0000.0000.0000.000
127A561TYR0-0.024-0.0202.122-2.392-8.83416.622-5.266-4.9150.020
128A562GLY00.0530.0285.668-0.709-0.7090.0000.0000.0000.000
129A563VAL00.0360.0076.2700.7110.7110.0000.0000.0000.000
130A564VAL0-0.025-0.0018.839-0.386-0.3860.0000.0000.0000.000
131A565GLY00.036-0.00310.754-0.096-0.0960.0000.0000.0000.000
132A566ALA0-0.004-0.00913.5910.0120.0120.0000.0000.0000.000
133A567GLN00.0550.03414.555-0.031-0.0310.0000.0000.0000.000
134A568VAL00.0780.04912.363-0.046-0.0460.0000.0000.0000.000
135A569ASN0-0.006-0.01015.4910.0000.0000.0000.0000.0000.000
136A570LEU0-0.032-0.01118.754-0.052-0.0520.0000.0000.0000.000
137A571THR0-0.0050.00016.674-0.054-0.0540.0000.0000.0000.000
138A572TYR00.082-0.00316.571-0.024-0.0240.0000.0000.0000.000
139A573ARG10.8970.94621.473-0.490-0.4900.0000.0000.0000.000
140A574ILE0-0.0290.03921.849-0.036-0.0360.0000.0000.0000.000
141A575GLU-1-0.862-0.94222.8770.3480.3480.0000.0000.0000.000
142A576SER0-0.097-0.08824.881-0.030-0.0300.0000.0000.0000.000
143A577TYR0-0.065-0.04427.636-0.029-0.0290.0000.0000.0000.000
144A578THR0-0.0250.04627.372-0.031-0.0310.0000.0000.0000.000
145A579THR0-0.022-0.00930.1120.0010.0010.0000.0000.0000.000
146A580GLY00.0560.01631.4130.0110.0110.0000.0000.0000.000
147A581GLY0-0.0170.00131.247-0.014-0.0140.0000.0000.0000.000
148A582GLN0-0.019-0.01530.142-0.001-0.0010.0000.0000.0000.000
149A583ILE00.0140.00224.3390.0240.0240.0000.0000.0000.000
150A584PHE0-0.0400.00026.154-0.025-0.0250.0000.0000.0000.000
151A585ILE00.0200.00722.6080.0380.0380.0000.0000.0000.000
152A586SER00.0250.00320.824-0.034-0.0340.0000.0000.0000.000
153A587SER00.0480.01323.570-0.013-0.0130.0000.0000.0000.000
154A588THR00.001-0.01619.106-0.011-0.0110.0000.0000.0000.000
155A589THR00.0240.02718.922-0.003-0.0030.0000.0000.0000.000
156A590LEU00.0160.01620.392-0.016-0.0160.0000.0000.0000.000
157A591GLU-1-0.981-0.98522.4150.0540.0540.0000.0000.0000.000
158A592ALA0-0.083-0.03217.754-0.023-0.0230.0000.0000.0000.000
159A593ALA0-0.016-0.00319.769-0.019-0.0190.0000.0000.0000.000
160A594GLY00.0110.00821.041-0.021-0.0210.0000.0000.0000.000
161A595ASP-1-0.937-0.98424.3880.0390.0390.0000.0000.0000.000
162A596ARG10.9180.98123.416-0.011-0.0110.0000.0000.0000.000
163A597VAL00.0080.01323.6030.0110.0110.0000.0000.0000.000
164A598HIS0-0.030-0.01126.687-0.010-0.0100.0000.0000.0000.000
165A599VAL00.011-0.00528.6100.0140.0140.0000.0000.0000.000
166A600ASN00.0040.00831.278-0.021-0.0210.0000.0000.0000.000
167A601GLY0-0.015-0.01332.949-0.009-0.0090.0000.0000.0000.000
168A602ASN0-0.048-0.01631.8410.0120.0120.0000.0000.0000.000
169A603ARG10.9820.99431.709-0.174-0.1740.0000.0000.0000.000
170A604THR0-0.024-0.00431.3700.0100.0100.0000.0000.0000.000
171A605VAL00.0040.01028.760-0.002-0.0020.0000.0000.0000.000
172A606GLN00.008-0.00929.536-0.009-0.0090.0000.0000.0000.000
173A607PRO0-0.0090.02326.233-0.004-0.0040.0000.0000.0000.000
174A608LYS10.9820.96428.541-0.237-0.2370.0000.0000.0000.000
175A609GLY00.0070.00827.0890.0210.0210.0000.0000.0000.000
176A610VAL0-0.039-0.00124.7160.0130.0130.0000.0000.0000.000
177A611LYS10.8720.95924.255-0.211-0.2110.0000.0000.0000.000
178A612ASP-1-0.836-0.92928.0080.1140.1140.0000.0000.0000.000
179A613PRO00.001-0.02028.5750.0190.0190.0000.0000.0000.000
180A614VAL0-0.045-0.02124.894-0.002-0.0020.0000.0000.0000.000
181A615VAL00.0210.01128.1780.0010.0010.0000.0000.0000.000
182A616ILE0-0.073-0.04125.9570.0130.0130.0000.0000.0000.000
183A617TRP0-0.020-0.03526.657-0.025-0.0250.0000.0000.0000.000
184A618ASP-1-0.818-0.91327.8800.1790.1790.0000.0000.0000.000
185A619VAL0-0.014-0.00525.414-0.016-0.0160.0000.0000.0000.000
186A620ALA0-0.0040.01028.8720.0040.0040.0000.0000.0000.000
187A621GLY00.038-0.01129.0260.0010.0010.0000.0000.0000.000
188A622VAL0-0.072-0.01924.2440.0020.0020.0000.0000.0000.000
189A623GLY00.0700.04327.531-0.003-0.0030.0000.0000.0000.000
190A624GLU-1-0.867-0.92927.8530.0290.0290.0000.0000.0000.000
191A625PRO0-0.073-0.05424.606-0.002-0.0020.0000.0000.0000.000
192A626TYR0-0.011-0.02620.3160.0000.0000.0000.0000.0000.000
193A627ASN0-0.045-0.02926.9120.0050.0050.0000.0000.0000.000
194A628LEU0-0.0150.01725.5170.0030.0030.0000.0000.0000.000
195A629SER00.029-0.01229.4850.0030.0030.0000.0000.0000.000
196A630LEU0-0.0020.00429.2930.0030.0030.0000.0000.0000.000
197A631ALA0-0.0090.00532.644-0.001-0.0010.0000.0000.0000.000
198A632VAL0-0.034-0.01935.819-0.002-0.0020.0000.0000.0000.000
199A633GLU-1-0.890-0.94536.2090.0590.0590.0000.0000.0000.000
200A634GLU-1-1.013-0.99939.1100.0650.0650.0000.0000.0000.000
201A635GLN0-0.048-0.01740.653-0.008-0.0080.0000.0000.0000.000