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: M3YMZ

Calculation Name: 1WJ9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WJ9

Chain ID: A

ChEMBL ID:

UniProt ID: Q53WG9

Base Structure: X-ray

Registration Date: 2023-06-20

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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2085257.37131
FMO2-HF: Nuclear repulsion 2012244.282817
FMO2-HF: Total energy -73013.088493
FMO2-MP2: Total energy -73231.644584


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:1:MET)


Summations of interaction energy for fragment #1(A:1: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.
-28.893-17.00728.203-12.689-27.397-0.087
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.047 / q_NPA : -0.009
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].
3A3LEU0-0.035-0.0213.7770.4702.835-0.008-1.119-1.2370.005
4A4THR00.0460.0235.574-0.180-0.1800.0000.0000.0000.000
5A5LYS10.9120.9649.0950.6020.6020.0000.0000.0000.000
6A6LEU00.0470.03012.123-0.067-0.0670.0000.0000.0000.000
7A7VAL00.0010.00614.8670.0820.0820.0000.0000.0000.000
8A8LEU00.013-0.00117.248-0.017-0.0170.0000.0000.0000.000
9A9ASN00.0760.04320.3100.0250.0250.0000.0000.0000.000
10A10PRO00.015-0.00723.9140.0090.0090.0000.0000.0000.000
11A11ALA00.0360.02826.4010.0130.0130.0000.0000.0000.000
12A12SER00.0240.02824.8120.0110.0110.0000.0000.0000.000
13A13ARG10.9650.97426.738-0.011-0.0110.0000.0000.0000.000
14A14ALA00.0280.00224.4550.0200.0200.0000.0000.0000.000
15A15ALA00.0820.04022.3450.0180.0180.0000.0000.0000.000
16A16ARG10.8710.92423.0120.0340.0340.0000.0000.0000.000
17A17ARG10.8050.90123.325-0.015-0.0150.0000.0000.0000.000
18A18ASP-1-0.739-0.85620.1420.0520.0520.0000.0000.0000.000
19A19LEU0-0.047-0.02920.0970.0330.0330.0000.0000.0000.000
20A20ALA0-0.0240.00122.2270.0240.0240.0000.0000.0000.000
21A21ASN00.0320.02123.4370.0390.0390.0000.0000.0000.000
22A22PRO00.0560.01619.166-0.008-0.0080.0000.0000.0000.000
23A23TYR00.0090.00718.8640.0080.0080.0000.0000.0000.000
24A24GLU-1-0.901-0.94520.0720.0980.0980.0000.0000.0000.000
25A25MET00.0200.02616.172-0.016-0.0160.0000.0000.0000.000
26A26HIS00.0270.02912.172-0.049-0.0490.0000.0000.0000.000
27A27ARG10.9050.97315.929-0.145-0.1450.0000.0000.0000.000
28A28THR0-0.040-0.04517.692-0.034-0.0340.0000.0000.0000.000
29A29LEU0-0.013-0.01412.383-0.062-0.0620.0000.0000.0000.000
30A30SER0-0.021-0.03213.361-0.055-0.0550.0000.0000.0000.000
31A31LYS10.9140.96214.3080.0210.0210.0000.0000.0000.000
32A32ALA00.0280.03412.200-0.020-0.0200.0000.0000.0000.000
33A33VAL00.0090.0088.305-0.134-0.1340.0000.0000.0000.000
34A34SER00.0100.00611.7090.1110.1110.0000.0000.0000.000
35A35ARG11.0301.02014.6320.2240.2240.0000.0000.0000.000
36A36ALA00.0010.0029.7860.0550.0550.0000.0000.0000.000
37A37LEU0-0.064-0.04411.1300.1620.1620.0000.0000.0000.000
38A38GLU-1-0.984-0.97113.1670.0920.0920.0000.0000.0000.000
39A39GLU-1-0.919-0.96814.362-0.029-0.0290.0000.0000.0000.000
40A40GLY0-0.0220.00013.7010.0350.0350.0000.0000.0000.000
41A41ARG10.8880.94410.1180.2450.2450.0000.0000.0000.000
42A42GLU-1-0.698-0.8256.4490.0890.0890.0000.0000.0000.000
43A43ARG10.8190.8975.933-1.654-1.6540.0000.0000.0000.000
44A44LEU00.0300.0366.1100.2840.2840.0000.0000.0000.000
45A45LEU0-0.055-0.0285.8500.0810.0810.0000.0000.0000.000
46A46TRP00.002-0.0028.276-0.182-0.1820.0000.0000.0000.000
47A47ARG10.7920.86710.589-0.732-0.7320.0000.0000.0000.000
48A48LEU00.0470.04713.247-0.090-0.0900.0000.0000.0000.000
49A49GLU-1-0.793-0.88013.5340.4430.4430.0000.0000.0000.000
50A50PRO0-0.039-0.02617.047-0.023-0.0230.0000.0000.0000.000
51A51ALA00.0240.02220.575-0.028-0.0280.0000.0000.0000.000
52A52ARG10.9610.98221.7790.0030.0030.0000.0000.0000.000
53A53GLY00.0310.01025.282-0.018-0.0180.0000.0000.0000.000
54A54LEU00.008-0.00627.9010.0120.0120.0000.0000.0000.000
55A55GLU-1-0.964-0.96325.119-0.061-0.0610.0000.0000.0000.000
56A56PRO0-0.011-0.00622.6300.0170.0170.0000.0000.0000.000
57A57PRO0-0.0010.00620.4820.0020.0020.0000.0000.0000.000
58A58VAL00.0020.00314.980-0.039-0.0390.0000.0000.0000.000
59A59VAL00.007-0.00412.7920.0910.0910.0000.0000.0000.000
60A60LEU0-0.063-0.0188.501-0.143-0.1430.0000.0000.0000.000
61A61VAL00.014-0.0128.0590.2850.2850.0000.0000.0000.000
62A62GLN0-0.017-0.0322.596-1.4000.0742.828-1.057-3.245-0.010
63A63THR0-0.023-0.0103.9550.3050.6150.000-0.065-0.2440.000
64A64LEU0-0.064-0.0592.335-4.791-2.3173.561-2.800-3.235-0.024
65A65THR0-0.063-0.0383.329-1.216-0.8900.0140.008-0.347-0.002
66A66GLU-1-0.926-0.9645.760-2.340-2.3400.0000.0000.0000.000
67A67PRO0-0.050-0.0196.8940.4280.4280.0000.0000.0000.000
68A68ASP-1-0.788-0.8789.779-0.654-0.6540.0000.0000.0000.000
69A69TRP0-0.023-0.0619.8440.2350.2350.0000.0000.0000.000
70A70SER0-0.062-0.03015.1230.0950.0950.0000.0000.0000.000
71A71VAL0-0.020-0.00416.2440.0590.0590.0000.0000.0000.000
72A72LEU0-0.115-0.05315.9650.0590.0590.0000.0000.0000.000
73A73ASP-1-0.888-0.93219.817-0.134-0.1340.0000.0000.0000.000
74A74GLU-1-0.895-0.95122.667-0.196-0.1960.0000.0000.0000.000
75A75GLY0-0.026-0.02124.2630.0240.0240.0000.0000.0000.000
76A76TYR0-0.096-0.06317.9060.0240.0240.0000.0000.0000.000
77A77ALA00.000-0.02818.3420.0300.0300.0000.0000.0000.000
78A78GLN00.0140.03719.1350.0060.0060.0000.0000.0000.000
79A79VAL00.018-0.00814.1430.0060.0060.0000.0000.0000.000
80A80PHE0-0.067-0.02713.908-0.020-0.0200.0000.0000.0000.000
81A81PRO00.010-0.00712.997-0.081-0.0810.0000.0000.0000.000
82A82PRO00.0070.0128.818-0.035-0.0350.0000.0000.0000.000
83A83LYS10.9450.9708.1291.3461.3460.0000.0000.0000.000
84A84PRO00.0400.0324.788-0.808-0.738-0.001-0.026-0.0420.000
85A85PHE0-0.034-0.0342.304-1.4021.1503.938-1.816-4.674-0.001
86A86HIS00.0520.0181.984-12.065-11.27010.130-4.955-5.970-0.057
87A87PRO0-0.044-0.0072.7190.2941.0660.585-0.248-1.1100.000
88A88ALA00.0750.0385.6200.3080.3080.0000.0000.0000.000
89A89LEU0-0.029-0.0275.3360.0780.0780.0000.0000.0000.000
90A90LYS10.9100.9519.2870.1960.1960.0000.0000.0000.000
91A91PRO00.0500.01512.9160.0420.0420.0000.0000.0000.000
92A92GLY00.0390.03715.310-0.054-0.0540.0000.0000.0000.000
93A93GLN0-0.022-0.00210.6700.0210.0210.0000.0000.0000.000
94A94ARG10.9660.98013.727-0.112-0.1120.0000.0000.0000.000
95A95LEU0-0.068-0.0318.942-0.068-0.0680.0000.0000.0000.000
96A96ARG10.9080.95013.172-0.064-0.0640.0000.0000.0000.000
97A97PHE0-0.004-0.00811.5480.0650.0650.0000.0000.0000.000
98A98ARG10.8450.90712.018-0.471-0.4710.0000.0000.0000.000
99A99LEU0-0.033-0.00911.3830.2140.2140.0000.0000.0000.000
100A100ARG10.9200.97213.623-0.552-0.5520.0000.0000.0000.000
101A101ALA00.000-0.01414.7080.1240.1240.0000.0000.0000.000
102A102ASN00.0580.03416.613-0.082-0.0820.0000.0000.0000.000
103A103PRO0-0.017-0.02419.2440.0470.0470.0000.0000.0000.000
104A104ALA00.0520.03220.325-0.057-0.0570.0000.0000.0000.000
105A105LYS10.9070.95320.075-0.452-0.4520.0000.0000.0000.000
106A106ARG10.9610.96420.168-0.463-0.4630.0000.0000.0000.000
107A107LEU00.0680.05119.911-0.021-0.0210.0000.0000.0000.000
108A117LYS10.9980.98530.795-0.233-0.2330.0000.0000.0000.000
109A118THR00.1430.07228.4610.0180.0180.0000.0000.0000.000
110A119PRO00.0400.01327.3010.0250.0250.0000.0000.0000.000
111A120ALA00.0360.00026.2030.0190.0190.0000.0000.0000.000
112A121GLU-1-0.947-0.96326.3800.3070.3070.0000.0000.0000.000
113A122LYS10.7950.89423.120-0.288-0.2880.0000.0000.0000.000
114A123VAL00.0220.01221.7780.0530.0530.0000.0000.0000.000
115A124ALA00.0600.03821.5230.0360.0360.0000.0000.0000.000
116A125TRP0-0.068-0.03016.2750.0530.0530.0000.0000.0000.000
117A126LEU0-0.033-0.02415.3490.0730.0730.0000.0000.0000.000
118A127GLU-1-0.896-0.94917.1640.4920.4920.0000.0000.0000.000
119A128ARG10.9740.99018.227-0.471-0.4710.0000.0000.0000.000
120A129ARG10.8240.92515.233-0.692-0.6920.0000.0000.0000.000
121A130LEU00.0220.00512.2630.1420.1420.0000.0000.0000.000
122A131GLU-1-0.903-0.93613.7860.5610.5610.0000.0000.0000.000
123A132GLU-1-1.011-1.01615.8760.6540.6540.0000.0000.0000.000
124A133GLY0-0.073-0.03111.8650.0570.0570.0000.0000.0000.000
125A134GLY00.0090.01910.6510.1810.1810.0000.0000.0000.000
126A135PHE0-0.008-0.0146.796-0.047-0.0470.0000.0000.0000.000
127A136ARG10.9920.99512.842-0.423-0.4230.0000.0000.0000.000
128A137LEU00.0290.01716.1580.0000.0000.0000.0000.0000.000
129A138LEU0-0.029-0.01117.663-0.042-0.0420.0000.0000.0000.000
130A139GLU-1-0.905-0.95119.8470.2760.2760.0000.0000.0000.000
131A140GLY0-0.032-0.02423.602-0.020-0.0200.0000.0000.0000.000
132A141GLU-1-0.952-0.97925.9140.1220.1220.0000.0000.0000.000
133A142ARG10.9210.95028.362-0.149-0.1490.0000.0000.0000.000
134A143GLY00.0370.04027.1880.0080.0080.0000.0000.0000.000
135A144PRO00.0420.01722.237-0.003-0.0030.0000.0000.0000.000
136A145TRP00.0050.00920.101-0.019-0.0190.0000.0000.0000.000
137A146VAL0-0.056-0.04918.9270.0440.0440.0000.0000.0000.000
138A147GLN0-0.0130.00420.883-0.039-0.0390.0000.0000.0000.000
139A148ILE0-0.010-0.01021.2300.0410.0410.0000.0000.0000.000
140A149LEU0-0.020-0.00420.002-0.030-0.0300.0000.0000.0000.000
141A150GLN00.008-0.01022.1830.0010.0010.0000.0000.0000.000
142A151ASP-1-0.827-0.90322.8280.3680.3680.0000.0000.0000.000
143A152THR00.0160.01223.634-0.034-0.0340.0000.0000.0000.000
144A153PHE00.014-0.00124.9310.0360.0360.0000.0000.0000.000
145A154LEU0-0.035-0.01119.466-0.013-0.0130.0000.0000.0000.000
146A155GLU-1-0.914-0.96024.2010.1750.1750.0000.0000.0000.000
147A170GLN00.0180.00727.6440.0090.0090.0000.0000.0000.000
148A171VAL0-0.0130.00121.3500.0170.0170.0000.0000.0000.000
149A172GLN0-0.0040.00423.763-0.019-0.0190.0000.0000.0000.000
150A173ALA00.008-0.00320.3600.0590.0590.0000.0000.0000.000
151A174VAL00.0060.00020.032-0.043-0.0430.0000.0000.0000.000
152A175LEU0-0.061-0.03016.7640.0890.0890.0000.0000.0000.000
153A176PHE00.0210.00016.753-0.060-0.0600.0000.0000.0000.000
154A177GLU-1-0.815-0.91716.6500.3730.3730.0000.0000.0000.000
155A178GLY00.0420.01916.565-0.044-0.0440.0000.0000.0000.000
156A179ARG10.8650.94315.962-0.204-0.2040.0000.0000.0000.000
157A180LEU00.0220.02110.9460.0170.0170.0000.0000.0000.000
158A181GLU-1-0.889-0.96814.2350.2560.2560.0000.0000.0000.000
159A182VAL0-0.021-0.0069.7560.1060.1060.0000.0000.0000.000
160A183VAL0-0.026-0.00412.420-0.090-0.0900.0000.0000.0000.000
161A184ASP-1-0.857-0.94713.0280.6110.6110.0000.0000.0000.000
162A185PRO00.006-0.0099.7840.1620.1620.0000.0000.0000.000
163A186GLU-1-0.854-0.9218.3510.9400.9400.0000.0000.0000.000
164A187ARG10.9170.9628.512-0.442-0.4420.0000.0000.0000.000
165A188ALA00.0030.0188.0110.3490.3490.0000.0000.0000.000
166A189LEU00.0380.0072.5660.3320.4811.032-0.114-1.068-0.001
167A190ALA0-0.019-0.0134.2821.7631.9530.000-0.027-0.1630.000
168A191THR0-0.055-0.0536.6770.7010.7010.0000.0000.0000.000
169A192LEU0-0.0330.0022.835-1.313-0.2630.504-0.306-1.247-0.001
170A193ARG11.0041.0112.297-3.720-3.0685.588-1.767-4.4740.003
171A194ARG10.8920.9633.925-3.718-5.0110.0321.603-0.3410.001
172A195GLY00.1010.0487.239-0.727-0.7270.0000.0000.0000.000
173A196VAL0-0.083-0.0618.637-0.282-0.2820.0000.0000.0000.000
174A197GLY00.0190.00611.924-0.141-0.1410.0000.0000.0000.000
175A198PRO0-0.036-0.01914.4150.1260.1260.0000.0000.0000.000
176A199GLY00.0830.02616.4860.0120.0120.0000.0000.0000.000
177A200LYS10.8210.91810.648-1.782-1.7820.0000.0000.0000.000
178A201ALA0-0.0230.00312.7790.0190.0190.0000.0000.0000.000
179A202LEU0-0.024-0.02415.205-0.094-0.0940.0000.0000.0000.000
180A203GLY00.0470.03514.030-0.053-0.0530.0000.0000.0000.000
181A204LEU0-0.064-0.02914.653-0.002-0.0020.0000.0000.0000.000
182A205GLY0-0.002-0.00111.9360.0890.0890.0000.0000.0000.000
183A206LEU00.0140.0136.3110.3690.3690.0000.0000.0000.000
184A207LEU0-0.0190.0007.879-0.405-0.4050.0000.0000.0000.000
185A208SER00.0190.0117.0330.5050.5050.0000.0000.0000.000
186A209VAL00.0410.0166.336-0.252-0.2520.0000.0000.0000.000
187A210ALA00.000-0.0078.913-0.156-0.1560.0000.0000.0000.000
188A211PRO00.0700.05711.1830.0650.0650.0000.0000.0000.000