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: PK2V3

Calculation Name: 1WPA-A-Xray31

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WPA

Chain ID: A

ChEMBL ID:

UniProt ID: Q16625

Base Structure: X-ray

Registration Date: 2018-09-06

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 177
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -939570.328117
FMO2-HF: Nuclear repulsion 888880.71558
FMO2-HF: Total energy -50689.612536
FMO2-MP2: Total energy -50835.7947


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:415:ACE)


Summations of interaction energy for fragment #1(A:415:ACE)
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.
0.2652.1860.505-1.223-1.201-0.005
Interaction energy analysis for fragmet #1(A:415:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.015
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].
3A417ILE00.0240.0073.8370.4141.523-0.004-0.514-0.5900.000
4A418ARG10.9450.9723.998-0.167-0.0310.000-0.022-0.1130.000
5A419GLU-1-0.929-0.9516.091-1.622-1.6220.0000.0000.0000.000
6A420TYR0-0.045-0.0477.5040.2120.2120.0000.0000.0000.000
7A421PRO00.0280.0319.1960.0050.0050.0000.0000.0000.000
8A422PRO00.0670.03310.345-0.022-0.0220.0000.0000.0000.000
9A423ILE0-0.066-0.00913.1720.0080.0080.0000.0000.0000.000
10A424THR00.0090.00816.2310.0320.0320.0000.0000.0000.000
11A425SER00.0530.02219.3840.0110.0110.0000.0000.0000.000
12A426ASP-1-0.791-0.90220.812-0.122-0.1220.0000.0000.0000.000
13A427GLN00.022-0.00222.419-0.018-0.0180.0000.0000.0000.000
14A428GLN00.0750.05614.5370.0210.0210.0000.0000.0000.000
15A429ARG10.8960.95517.8390.1020.1020.0000.0000.0000.000
16A430GLN0-0.028-0.02318.890-0.021-0.0210.0000.0000.0000.000
17A431LEU0-0.0080.01116.107-0.005-0.0050.0000.0000.0000.000
18A432TYR00.005-0.03012.291-0.052-0.0520.0000.0000.0000.000
19A433LYS10.8890.96815.9600.1610.1610.0000.0000.0000.000
20A434ARG10.9690.98518.5380.2020.2020.0000.0000.0000.000
21A435ASN00.0140.02114.395-0.055-0.0550.0000.0000.0000.000
22A436PHE0-0.033-0.01014.219-0.028-0.0280.0000.0000.0000.000
23A437ASP-1-0.796-0.91715.908-0.230-0.2300.0000.0000.0000.000
24A438THR0-0.0060.00117.7590.0150.0150.0000.0000.0000.000
25A439GLY00.0360.01515.0070.0050.0050.0000.0000.0000.000
26A440LEU0-0.016-0.01216.0070.0170.0170.0000.0000.0000.000
27A441GLN00.0060.02418.0860.0210.0210.0000.0000.0000.000
28A442GLU-1-0.823-0.90415.866-0.357-0.3570.0000.0000.0000.000
29A443TYR0-0.018-0.01615.4510.0240.0240.0000.0000.0000.000
30A444LYS10.9620.97817.7910.1940.1940.0000.0000.0000.000
31A445SER00.0260.02521.3560.0260.0260.0000.0000.0000.000
32A446LEU00.0390.02117.2620.0130.0130.0000.0000.0000.000
33A447GLN0-0.090-0.05019.333-0.003-0.0030.0000.0000.0000.000
34A448SER0-0.025-0.02121.4450.0180.0180.0000.0000.0000.000
35A449GLU-1-0.866-0.91823.797-0.118-0.1180.0000.0000.0000.000
36A450LEU0-0.063-0.03919.5050.0100.0100.0000.0000.0000.000
37A451ASP-1-0.895-0.96924.077-0.094-0.0940.0000.0000.0000.000
38A452GLU-1-0.884-0.92026.301-0.078-0.0780.0000.0000.0000.000
39A453ILE00.0850.04727.5910.0060.0060.0000.0000.0000.000
40A454ASN0-0.029-0.01324.8950.0130.0130.0000.0000.0000.000
41A455LYS10.8770.94329.1360.0770.0770.0000.0000.0000.000
42A456GLU-1-0.841-0.92631.840-0.052-0.0520.0000.0000.0000.000
43A457LEU00.002-0.00229.8550.0040.0040.0000.0000.0000.000
44A458SER0-0.064-0.01532.8980.0030.0030.0000.0000.0000.000
45A459ARG10.9180.93934.5750.0500.0500.0000.0000.0000.000
46A460LEU00.0260.02536.1000.0020.0020.0000.0000.0000.000
47A461ASP-1-0.859-0.94135.249-0.022-0.0220.0000.0000.0000.000
48A462LYS10.8450.90836.6390.0330.0330.0000.0000.0000.000
49A463GLU-1-0.847-0.91440.896-0.027-0.0270.0000.0000.0000.000
50A464LEU0-0.058-0.02039.3590.0010.0010.0000.0000.0000.000
51A465ASP-1-0.925-0.93941.714-0.015-0.0150.0000.0000.0000.000
52A466ASP-1-0.920-0.93844.397-0.019-0.0190.0000.0000.0000.000
53A467TYR0-0.087-0.03445.4920.0010.0010.0000.0000.0000.000
54A468ARG10.9740.98048.4000.0130.0130.0000.0000.0000.000
55A469GLU-1-0.735-0.84947.498-0.011-0.0110.0000.0000.0000.000
56A470GLU-1-0.942-0.95249.540-0.010-0.0100.0000.0000.0000.000
57A471SER0-0.117-0.06350.233-0.001-0.0010.0000.0000.0000.000
58A472GLU-1-0.901-0.96050.062-0.015-0.0150.0000.0000.0000.000
59A473GLU-1-0.859-0.91848.222-0.018-0.0180.0000.0000.0000.000
60A474TYR0-0.028-0.00644.205-0.002-0.0020.0000.0000.0000.000
61A475MET00.0050.00744.854-0.001-0.0010.0000.0000.0000.000
62A476ALA0-0.0100.00944.388-0.001-0.0010.0000.0000.0000.000
63A477ALA00.0640.03041.866-0.002-0.0020.0000.0000.0000.000
64A478ALA00.0360.02040.269-0.002-0.0020.0000.0000.0000.000
65A479ASP-1-0.855-0.90539.629-0.020-0.0200.0000.0000.0000.000
66A480GLU-1-0.851-0.92837.007-0.039-0.0390.0000.0000.0000.000
67A481TYR0-0.0090.00134.033-0.002-0.0020.0000.0000.0000.000
68A482ASN00.018-0.00234.699-0.002-0.0020.0000.0000.0000.000
69A483ARG10.8890.93534.4170.0280.0280.0000.0000.0000.000
70A484LEU00.0770.03331.970-0.004-0.0040.0000.0000.0000.000
71A485LYS10.8610.93930.3520.0150.0150.0000.0000.0000.000
72A486GLN0-0.0370.00329.5070.0010.0010.0000.0000.0000.000
73A487VAL00.0410.03527.869-0.001-0.0010.0000.0000.0000.000
74A488LYS10.8860.95925.0840.0430.0430.0000.0000.0000.000
75A489GLY0-0.038-0.03524.702-0.003-0.0030.0000.0000.0000.000
76A490SER0-0.022-0.01925.3430.0020.0020.0000.0000.0000.000
77A491ALA00.025-0.01122.398-0.005-0.0050.0000.0000.0000.000
78A492ASP-1-0.822-0.89821.281-0.121-0.1210.0000.0000.0000.000
79A493TYR00.0760.05521.409-0.015-0.0150.0000.0000.0000.000
80A494LYS10.9020.95219.6500.0150.0150.0000.0000.0000.000
81A495SER0-0.012-0.00317.046-0.015-0.0150.0000.0000.0000.000
82A496LYS10.9570.99116.3650.1020.1020.0000.0000.0000.000
83A497LYS10.9790.99317.0070.0380.0380.0000.0000.0000.000
84A498ASN0-0.066-0.03711.333-0.064-0.0640.0000.0000.0000.000
85A499HIS00.011-0.01412.346-0.087-0.0870.0000.0000.0000.000
86A500CYS00.0320.02312.787-0.072-0.0720.0000.0000.0000.000
87A501LYS10.8740.94511.6150.0820.0820.0000.0000.0000.000
88A502GLN00.0290.0306.2200.0530.0530.0000.0000.0000.000
89A503LEU00.0120.0138.800-0.249-0.2490.0000.0000.0000.000
90A504LYS10.9690.99711.3770.1680.1680.0000.0000.0000.000
91A505SER00.011-0.0016.7880.1010.1010.0000.0000.0000.000
92A506LYS10.9601.0127.3370.8790.8790.0000.0000.0000.000
93A507LEU0-0.024-0.0098.2820.0900.0900.0000.0000.0000.000
94A508SER0-0.045-0.0239.9300.0870.0870.0000.0000.0000.000
95A509HIS00.005-0.0016.7160.0960.0960.0000.0000.0000.000
96A510ILE00.0160.0138.7720.1230.1230.0000.0000.0000.000
97A511LYS10.9800.99811.3320.2830.2830.0000.0000.0000.000
98A512LYS10.8820.94510.5980.1340.1340.0000.0000.0000.000
99A513MET0-0.0220.0039.7640.0820.0820.0000.0000.0000.000
100A514VAL00.0250.00813.0620.0480.0480.0000.0000.0000.000
101A515GLY00.0120.00616.1800.0310.0310.0000.0000.0000.000
102A516ASP-1-0.769-0.87714.172-0.068-0.0680.0000.0000.0000.000
103A517TYR0-0.027-0.00117.2790.0190.0190.0000.0000.0000.000
104A518ASP-1-0.817-0.92918.994-0.126-0.1260.0000.0000.0000.000
105A519ARG10.8330.90317.7330.0830.0830.0000.0000.0000.000
106A520GLN00.0340.07418.869-0.002-0.0020.0000.0000.0000.000
107A521LYS10.8770.97323.3470.0970.0970.0000.0000.0000.000
108A522THR-1-0.835-0.84725.477-0.049-0.0490.0000.0000.0000.000
109A1HOH00.0110.0143.6220.5550.6790.004-0.065-0.0620.000
110A2HOH0-0.047-0.02528.678-0.001-0.0010.0000.0000.0000.000
111A3HOH0-0.082-0.08829.9750.0010.0010.0000.0000.0000.000
112A4HOH00.0090.0028.7110.0290.0290.0000.0000.0000.000
113A5HOH0-0.029-0.02621.418-0.005-0.0050.0000.0000.0000.000
114A6HOH0-0.037-0.03522.2500.0050.0050.0000.0000.0000.000
115A8HOH00.0020.00636.0970.0010.0010.0000.0000.0000.000
116A9HOH0-0.022-0.01640.871-0.001-0.0010.0000.0000.0000.000
117A10HOH00.0230.01654.0150.0000.0000.0000.0000.0000.000
118A12HOH0-0.013-0.00244.8120.0000.0000.0000.0000.0000.000
119A13HOH0-0.057-0.07219.5770.0030.0030.0000.0000.0000.000
120A14HOH0-0.047-0.02548.4180.0000.0000.0000.0000.0000.000
121A15HOH00.004-0.00914.801-0.010-0.0100.0000.0000.0000.000
122A16HOH0-0.005-0.00922.181-0.002-0.0020.0000.0000.0000.000
123A17HOH0-0.059-0.03913.6810.0120.0120.0000.0000.0000.000
124A18HOH0-0.043-0.02739.2020.0000.0000.0000.0000.0000.000
125A19HOH00.0110.00514.809-0.007-0.0070.0000.0000.0000.000
126A20HOH0-0.023-0.01734.3260.0000.0000.0000.0000.0000.000
127A21HOH0-0.046-0.03746.2920.0000.0000.0000.0000.0000.000
128A22HOH0-0.038-0.02633.5680.0010.0010.0000.0000.0000.000
129A23HOH0-0.030-0.01642.818-0.001-0.0010.0000.0000.0000.000
130A24HOH00.0100.00918.8980.0010.0010.0000.0000.0000.000
131A26HOH0-0.049-0.03448.3390.0000.0000.0000.0000.0000.000
132A28HOH0-0.034-0.02625.4060.0030.0030.0000.0000.0000.000
133A29HOH0-0.047-0.02744.8640.0000.0000.0000.0000.0000.000
134A30HOH0-0.053-0.04250.658-0.001-0.0010.0000.0000.0000.000
135A31HOH00.0350.02151.9780.0000.0000.0000.0000.0000.000
136A32HOH0-0.043-0.02515.2430.0010.0010.0000.0000.0000.000
137A35HOH0-0.006-0.01117.076-0.008-0.0080.0000.0000.0000.000
138A36HOH0-0.061-0.06049.1630.0000.0000.0000.0000.0000.000
139A37HOH00.0200.01633.1880.0000.0000.0000.0000.0000.000
140A38HOH0-0.040-0.0337.3740.0620.0620.0000.0000.0000.000
141A39HOH0-0.0080.00034.0830.0000.0000.0000.0000.0000.000
142A40HOH0-0.033-0.01723.534-0.001-0.0010.0000.0000.0000.000
143A42HOH0-0.021-0.01120.7640.0060.0060.0000.0000.0000.000
144A43HOH0-0.020-0.01745.688-0.001-0.0010.0000.0000.0000.000
145A45HOH0-0.028-0.0266.9740.0490.0490.0000.0000.0000.000
146A47HOH00.0200.02336.753-0.001-0.0010.0000.0000.0000.000
147A49HOH0-0.022-0.01923.3030.0020.0020.0000.0000.0000.000
148A51HOH0-0.033-0.01742.8490.0000.0000.0000.0000.0000.000
149A52HOH0-0.043-0.03010.4870.0330.0330.0000.0000.0000.000
150A53HOH0-0.018-0.02311.980-0.023-0.0230.0000.0000.0000.000
151A54HOH0-0.016-0.02024.005-0.003-0.0030.0000.0000.0000.000
152A55HOH0-0.052-0.03828.4490.0000.0000.0000.0000.0000.000
153A57HOH00.0120.01715.6870.0050.0050.0000.0000.0000.000
154A58HOH00.0190.00622.2400.0060.0060.0000.0000.0000.000
155A59HOH0-0.039-0.03516.7200.0010.0010.0000.0000.0000.000
156A61HOH0-0.064-0.05247.5950.0000.0000.0000.0000.0000.000
157A62HOH00.0250.01017.6420.0060.0060.0000.0000.0000.000
158A65HOH0-0.037-0.02212.7150.0190.0190.0000.0000.0000.000
159A72HOH0-0.039-0.02217.5880.0010.0010.0000.0000.0000.000
160A74HOH0-0.027-0.01423.227-0.001-0.0010.0000.0000.0000.000
161A75HOH0-0.042-0.03127.5510.0020.0020.0000.0000.0000.000
162A76HOH0-0.021-0.01733.7540.0010.0010.0000.0000.0000.000
163A81HOH0-0.036-0.02116.9710.0020.0020.0000.0000.0000.000
164A82HOH0-0.033-0.01912.9250.0290.0290.0000.0000.0000.000
165A83HOH0-0.003-0.00416.0320.0110.0110.0000.0000.0000.000
166A89HOH00.0290.01924.485-0.005-0.0050.0000.0000.0000.000
167A91HOH00.0070.00323.164-0.005-0.0050.0000.0000.0000.000
168A93HOH0-0.011-0.01119.086-0.010-0.0100.0000.0000.0000.000
169A95HOH0-0.030-0.02840.281-0.001-0.0010.0000.0000.0000.000
170A98HOH00.0230.01913.438-0.049-0.0490.0000.0000.0000.000
171A99HOH00.0550.0242.928-0.724-0.1720.505-0.622-0.436-0.005
172A100HOH0-0.034-0.02122.6250.0020.0020.0000.0000.0000.000
173A101HOH0-0.041-0.03526.0290.0020.0020.0000.0000.0000.000
174A102HOH00.007-0.00236.929-0.001-0.0010.0000.0000.0000.000
175A103HOH0-0.020-0.03244.455-0.001-0.0010.0000.0000.0000.000
176A104HOH00.0210.01237.496-0.001-0.0010.0000.0000.0000.000
177A105HOH00.0290.01626.150-0.003-0.0030.0000.0000.0000.000