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: 89L8Y

Calculation Name: 1W8A-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1W8A

Chain ID: A

ChEMBL ID:

UniProt ID: P24014

Base Structure: X-ray

Registration Date: 2023-09-24

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 187
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2065306.740709
FMO2-HF: Nuclear repulsion 1988495.492365
FMO2-HF: Total energy -76811.248344
FMO2-MP2: Total energy -77028.074461


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:542:ASP)


Summations of interaction energy for fragment #1(A:542:ASP)
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.
28.87332.6870.177-1.78-2.2110.014
Interaction energy analysis for fragmet #1(A:542:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.973 / q_NPA : -0.997
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].
3A544PRO00.0030.0103.813-2.791-1.292-0.021-0.652-0.8260.002
4A545ALA00.004-0.0046.277-2.167-2.1670.0000.0000.0000.000
5A546MET0-0.048-0.0157.679-1.035-1.0350.0000.0000.0000.000
6A547CYS0-0.075-0.0459.007-0.948-0.9480.0000.0000.0000.000
7A548HIS0-0.033-0.0389.1801.4501.4500.0000.0000.0000.000
8A550GLU-1-0.820-0.8658.48921.77521.7750.0000.0000.0000.000
9A551GLY00.0190.0099.782-0.737-0.7370.0000.0000.0000.000
10A552THR0-0.020-0.0138.2662.7112.7110.0000.0000.0000.000
11A553THR0-0.017-0.02810.1940.2540.2540.0000.0000.0000.000
12A554VAL00.0200.0037.9361.6261.6260.0000.0000.0000.000
13A555ASP-1-0.832-0.89210.89816.59416.5940.0000.0000.0000.000
14A557THR0-0.045-0.03414.003-1.261-1.2610.0000.0000.0000.000
15A558GLY00.0450.03117.4470.2470.2470.0000.0000.0000.000
16A559ARG10.7660.87912.534-19.903-19.9030.0000.0000.0000.000
17A560GLY00.0230.02117.4170.0580.0580.0000.0000.0000.000
18A561LEU0-0.039-0.02213.796-0.275-0.2750.0000.0000.0000.000
19A562LYS10.8600.91617.925-13.946-13.9460.0000.0000.0000.000
20A563GLU-1-0.933-0.96716.04516.35616.3560.0000.0000.0000.000
21A564ILE0-0.030-0.01613.0120.5710.5710.0000.0000.0000.000
22A565PRO00.0310.0119.736-0.009-0.0090.0000.0000.0000.000
23A566ARG10.9930.97510.576-20.711-20.7110.0000.0000.0000.000
24A567ASP-1-0.944-0.9605.21236.10136.1010.0000.0000.0000.000
25A568ILE00.0190.0175.4224.3784.3780.0000.0000.0000.000
26A569PRO00.0410.0162.913-5.465-3.2420.199-1.111-1.3110.012
27A570LEU00.006-0.0074.583-8.184-8.092-0.001-0.017-0.0740.000
28A571HIS0-0.025-0.0306.529-7.626-7.6260.0000.0000.0000.000
29A572THR0-0.0160.0167.302-1.687-1.6870.0000.0000.0000.000
30A573THR0-0.018-0.0189.527-2.111-2.1110.0000.0000.0000.000
31A574GLU-1-0.852-0.90412.85815.91615.9160.0000.0000.0000.000
32A575LEU00.0150.00811.2161.5561.5560.0000.0000.0000.000
33A576LEU0-0.029-0.01713.916-1.676-1.6760.0000.0000.0000.000
34A577LEU00.0420.01613.8790.6490.6490.0000.0000.0000.000
35A578ASN0-0.001-0.01417.225-1.073-1.0730.0000.0000.0000.000
36A579ASP-1-0.787-0.85319.90513.23413.2340.0000.0000.0000.000
37A580ASN0-0.038-0.01717.2100.3290.3290.0000.0000.0000.000
38A581GLU-1-0.908-0.97520.92511.95111.9510.0000.0000.0000.000
39A582LEU0-0.0140.00317.720-0.284-0.2840.0000.0000.0000.000
40A583GLY00.0340.03821.661-0.142-0.1420.0000.0000.0000.000
41A584ARG10.8300.87323.665-12.028-12.0280.0000.0000.0000.000
42A585ILE0-0.0140.01120.9720.4430.4430.0000.0000.0000.000
43A586SER00.0450.01820.160-0.717-0.7170.0000.0000.0000.000
44A587SER0-0.060-0.04921.3010.6030.6030.0000.0000.0000.000
45A588ASP-1-0.794-0.90416.42218.06218.0620.0000.0000.0000.000
46A589GLY00.0030.00518.5230.4550.4550.0000.0000.0000.000
47A590LEU0-0.007-0.00611.1670.4710.4710.0000.0000.0000.000
48A591PHE00.0790.02614.2300.9350.9350.0000.0000.0000.000
49A592GLY0-0.0480.00415.9270.4200.4200.0000.0000.0000.000
50A593ARG10.8100.89112.651-20.453-20.4530.0000.0000.0000.000
51A594LEU0-0.0210.0019.4541.6691.6690.0000.0000.0000.000
52A595PRO0-0.003-0.01411.822-1.053-1.0530.0000.0000.0000.000
53A596HIS00.0010.00711.249-2.037-2.0370.0000.0000.0000.000
54A597LEU0-0.0340.00913.232-0.335-0.3350.0000.0000.0000.000
55A598VAL00.0370.00814.762-1.300-1.3000.0000.0000.0000.000
56A599LYS10.8260.91717.092-16.612-16.6120.0000.0000.0000.000
57A600LEU00.0140.01116.2381.0881.0880.0000.0000.0000.000
58A601GLU-1-0.844-0.89918.08313.45113.4510.0000.0000.0000.000
59A602LEU00.0190.00818.4590.6040.6040.0000.0000.0000.000
60A603LYS10.9040.94521.502-13.708-13.7080.0000.0000.0000.000
61A604ARG10.7510.83823.628-11.316-11.3160.0000.0000.0000.000
62A605ASN00.003-0.02420.9070.5490.5490.0000.0000.0000.000
63A606GLN0-0.026-0.00424.645-0.503-0.5030.0000.0000.0000.000
64A607LEU0-0.0040.02023.078-0.164-0.1640.0000.0000.0000.000
65A608THR0-0.027-0.01027.233-0.412-0.4120.0000.0000.0000.000
66A609GLY00.010-0.00528.632-0.325-0.3250.0000.0000.0000.000
67A610ILE0-0.036-0.01924.5870.4180.4180.0000.0000.0000.000
68A611GLU-1-0.819-0.88624.69611.93811.9380.0000.0000.0000.000
69A612PRO00.016-0.01026.1870.2170.2170.0000.0000.0000.000
70A613ASN0-0.017-0.00326.1490.0740.0740.0000.0000.0000.000
71A614ALA00.0590.04622.0860.3750.3750.0000.0000.0000.000
72A615PHE0-0.044-0.03019.9580.7100.7100.0000.0000.0000.000
73A616GLU-1-0.872-0.93622.36411.87611.8760.0000.0000.0000.000
74A617GLY00.004-0.00121.0270.6460.6460.0000.0000.0000.000
75A618ALA0-0.029-0.02219.2390.7280.7280.0000.0000.0000.000
76A619SER0-0.031-0.00820.180-0.071-0.0710.0000.0000.0000.000
77A620HIS00.0010.00116.480-1.012-1.0120.0000.0000.0000.000
78A621ILE0-0.020-0.00118.049-0.194-0.1940.0000.0000.0000.000
79A622GLN0-0.060-0.04020.255-0.598-0.5980.0000.0000.0000.000
80A623GLU-1-0.870-0.93421.65412.17612.1760.0000.0000.0000.000
81A624LEU00.0170.01621.4400.6460.6460.0000.0000.0000.000
82A625GLN0-0.040-0.02722.591-1.139-1.1390.0000.0000.0000.000
83A626LEU00.0420.00923.6620.3910.3910.0000.0000.0000.000
84A627GLY0-0.0040.01826.123-0.343-0.3430.0000.0000.0000.000
85A628GLU-1-0.842-0.91727.76911.12711.1270.0000.0000.0000.000
86A629ASN0-0.044-0.02525.5180.3320.3320.0000.0000.0000.000
87A630LYS10.8860.93229.544-10.104-10.1040.0000.0000.0000.000
88A631ILE00.0300.02528.129-0.135-0.1350.0000.0000.0000.000
89A632LYS10.9910.98032.507-8.742-8.7420.0000.0000.0000.000
90A633GLU-1-0.857-0.95335.0628.1128.1120.0000.0000.0000.000
91A634ILE0-0.010-0.00432.7140.3110.3110.0000.0000.0000.000
92A635SER00.0550.01632.526-0.162-0.1620.0000.0000.0000.000
93A636ASN00.0020.01133.5960.2730.2730.0000.0000.0000.000
94A637LYS10.9030.95730.827-8.938-8.9380.0000.0000.0000.000
95A638MET0-0.0130.00428.5490.2320.2320.0000.0000.0000.000
96A639PHE00.0560.00926.6930.3590.3590.0000.0000.0000.000
97A640LEU0-0.032-0.01027.706-0.021-0.0210.0000.0000.0000.000
98A641GLY00.0880.04425.2070.3420.3420.0000.0000.0000.000
99A642LEU0-0.0310.00122.2630.2500.2500.0000.0000.0000.000
100A643HIS0-0.018-0.01725.576-0.102-0.1020.0000.0000.0000.000
101A644GLN00.0020.00724.273-0.744-0.7440.0000.0000.0000.000
102A645LEU0-0.0070.01623.8990.0870.0870.0000.0000.0000.000
103A646LYS10.8670.93525.938-11.122-11.1220.0000.0000.0000.000
104A647THR00.006-0.01026.243-0.686-0.6860.0000.0000.0000.000
105A648LEU00.0310.02426.3670.4280.4280.0000.0000.0000.000
106A649ASN0-0.042-0.03227.351-0.832-0.8320.0000.0000.0000.000
107A650LEU00.0390.00528.3490.2880.2880.0000.0000.0000.000
108A651TYR0-0.082-0.03530.916-0.231-0.2310.0000.0000.0000.000
109A652ASP-1-0.829-0.92731.9139.1019.1010.0000.0000.0000.000
110A653ASN0-0.0260.00329.8000.3180.3180.0000.0000.0000.000
111A654GLN0-0.042-0.04233.704-0.088-0.0880.0000.0000.0000.000
112A655ILE0-0.0250.00133.034-0.166-0.1660.0000.0000.0000.000
113A656SER00.0260.01037.067-0.210-0.2100.0000.0000.0000.000
114A733CYS0-0.0950.02339.519-0.183-0.1830.0000.0000.0000.000
115A658VAL00.029-0.00336.5890.2470.2470.0000.0000.0000.000
116A659MET00.0050.02637.273-0.162-0.1620.0000.0000.0000.000
117A660PRO00.0390.00038.3730.1470.1470.0000.0000.0000.000
118A661GLY00.0690.03338.1230.0810.0810.0000.0000.0000.000
119A662SER0-0.041-0.05934.3950.1380.1380.0000.0000.0000.000
120A663PHE0-0.028-0.01832.0840.2680.2680.0000.0000.0000.000
121A664GLU-1-0.954-0.96934.1028.4778.4770.0000.0000.0000.000
122A665HIS00.0460.02929.4750.2180.2180.0000.0000.0000.000
123A666LEU0-0.033-0.00228.3800.3430.3430.0000.0000.0000.000
124A667ASN00.022-0.00131.208-0.338-0.3380.0000.0000.0000.000
125A668SER0-0.025-0.01928.958-0.341-0.3410.0000.0000.0000.000
126A669LEU0-0.057-0.00229.991-0.001-0.0010.0000.0000.0000.000
127A670THR00.002-0.02031.198-0.273-0.2730.0000.0000.0000.000
128A671SER0-0.037-0.00930.613-0.367-0.3670.0000.0000.0000.000
129A672LEU00.0310.01731.1650.2850.2850.0000.0000.0000.000
130A673ASN0-0.030-0.00531.881-0.538-0.5380.0000.0000.0000.000
131A674LEU00.035-0.00333.0950.1760.1760.0000.0000.0000.000
132A675ALA00.0410.02635.820-0.238-0.2380.0000.0000.0000.000
133A676SER0-0.027-0.01636.3410.1450.1450.0000.0000.0000.000
134A677ASN00.0040.00534.5610.1530.1530.0000.0000.0000.000
135A678PRO00.0040.02038.721-0.200-0.2000.0000.0000.0000.000
136A679PHE00.0030.01237.567-0.002-0.0020.0000.0000.0000.000
137A680ASN00.012-0.01542.523-0.308-0.3080.0000.0000.0000.000
138A681CYS0-0.086-0.03243.3140.1860.1860.0000.0000.0000.000
139A682ASN00.0540.01447.543-0.176-0.1760.0000.0000.0000.000
140A683CYS00.0110.01048.7510.0690.0690.0000.0000.0000.000
141A684HIS0-0.007-0.00545.1860.0730.0730.0000.0000.0000.000
142A685LEU0-0.080-0.02541.3640.1740.1740.0000.0000.0000.000
143A686ALA00.0360.01245.0730.0420.0420.0000.0000.0000.000
144A687TRP0-0.033-0.01538.551-0.016-0.0160.0000.0000.0000.000
145A688PHE00.0270.00638.0500.0690.0690.0000.0000.0000.000
146A689ALA00.0540.03542.6180.1060.1060.0000.0000.0000.000
147A690GLU-1-0.815-0.91444.8266.5496.5490.0000.0000.0000.000
148A691TRP0-0.021-0.01235.4360.0330.0330.0000.0000.0000.000
149A692LEU0-0.012-0.00438.7980.1430.1430.0000.0000.0000.000
150A693ARG10.7330.83141.665-6.511-6.5110.0000.0000.0000.000
151A694LYS10.9671.00242.784-7.273-7.2730.0000.0000.0000.000
152A695LYS10.8710.92734.632-9.005-9.0050.0000.0000.0000.000
153A696SER0-0.053-0.00340.0010.0120.0120.0000.0000.0000.000
154A697LEU00.0280.01635.6210.2040.2040.0000.0000.0000.000
155A698ASN0-0.021-0.00335.684-0.341-0.3410.0000.0000.0000.000
156A699GLY0-0.002-0.02039.248-0.115-0.1150.0000.0000.0000.000
157A700GLY00.0450.02336.945-0.031-0.0310.0000.0000.0000.000
158A701ALA0-0.033-0.01737.5570.1130.1130.0000.0000.0000.000
159A702ALA00.0030.02339.254-0.049-0.0490.0000.0000.0000.000
160A703ARG10.9080.92640.660-7.233-7.2330.0000.0000.0000.000
161A705GLY00.0270.00344.884-0.063-0.0630.0000.0000.0000.000
162A706ALA0-0.013-0.00445.8540.0200.0200.0000.0000.0000.000
163A707PRO00.0380.03248.244-0.127-0.1270.0000.0000.0000.000
164A708SER00.001-0.01851.407-0.008-0.0080.0000.0000.0000.000
165A709LYS10.8580.93853.361-5.732-5.7320.0000.0000.0000.000
166A710VAL00.0470.01849.882-0.023-0.0230.0000.0000.0000.000
167A711ARG10.8610.92448.546-6.365-6.3650.0000.0000.0000.000
168A712ASP-1-0.798-0.88646.8426.6786.6780.0000.0000.0000.000
169A713VAL0-0.0260.00947.9100.0520.0520.0000.0000.0000.000
170A714GLN0-0.037-0.01744.5860.3110.3110.0000.0000.0000.000
171A715ILE00.0290.01742.516-0.132-0.1320.0000.0000.0000.000
172A716LYS10.9070.93143.865-7.166-7.1660.0000.0000.0000.000
173A717ASP-1-0.892-0.92246.1916.6186.6180.0000.0000.0000.000
174A718LEU00.0070.00648.927-0.168-0.1680.0000.0000.0000.000
175A719PRO00.0420.04650.1310.1280.1280.0000.0000.0000.000
176A720HIS00.0540.02050.262-0.030-0.0300.0000.0000.0000.000
177A721SER0-0.007-0.02151.615-0.007-0.0070.0000.0000.0000.000
178A722GLU-1-0.852-0.91953.7755.5145.5140.0000.0000.0000.000
179A723PHE0-0.082-0.02446.6690.0560.0560.0000.0000.0000.000
180A724LYS10.8190.90651.688-5.630-5.6300.0000.0000.0000.000
181A726SER00.018-0.02053.088-0.095-0.0950.0000.0000.0000.000
182A727SER0-0.006-0.00256.105-0.007-0.0070.0000.0000.0000.000
183A728GLU-1-0.798-0.86354.9935.7875.7870.0000.0000.0000.000
184A729ASN0-0.113-0.06951.1360.1530.1530.0000.0000.0000.000
185A730SER0-0.037-0.03551.0340.1080.1080.0000.0000.0000.000
186A731GLU-1-0.874-0.94447.3086.6416.6410.0000.0000.0000.000
187A732GLY00.021-0.00344.958-0.017-0.0170.0000.0000.0000.000