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: 982Q2

Calculation Name: 1WWM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WWM

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SLX4

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 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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2064171.79718
FMO2-HF: Nuclear repulsion 1992395.028373
FMO2-HF: Total energy -71776.768807
FMO2-MP2: Total energy -71992.52992


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:11:GLU)


Summations of interaction energy for fragment #1(A:11:GLU)
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.
148.556154.4060.177-2.17-3.8520.02
Interaction energy analysis for fragmet #1(A:11:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.928 / q_NPA : -0.970
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].
3A13PRO0-0.092-0.0313.5891.2683.1660.003-0.596-1.3040.008
4A14GLY00.0470.0235.313-6.799-6.692-0.001-0.004-0.1020.000
5A15LEU00.0030.0006.774-1.509-1.5090.0000.0000.0000.000
6A16LEU00.0490.0373.325-11.396-9.1070.092-1.092-1.2880.009
7A17GLU-1-0.840-0.9515.37244.12744.180-0.0010.001-0.0510.000
8A18GLU-1-0.911-0.9507.72420.49120.4910.0000.0000.0000.000
9A19ILE00.0380.0067.897-3.246-3.2460.0000.0000.0000.000
10A20LYS10.9280.9837.266-40.176-40.1760.0000.0000.0000.000
11A21ALA0-0.023-0.00611.085-2.525-2.5250.0000.0000.0000.000
12A22LEU0-0.070-0.01313.375-2.134-2.1340.0000.0000.0000.000
13A23PRO0-0.030-0.01215.745-0.356-0.3560.0000.0000.0000.000
14A24LEU0-0.001-0.01016.665-0.858-0.8580.0000.0000.0000.000
15A25ARG10.8740.93919.977-13.773-13.7730.0000.0000.0000.000
16A26LEU00.0060.01418.821-0.258-0.2580.0000.0000.0000.000
17A27ASP-1-0.860-0.93222.86810.81710.8170.0000.0000.0000.000
18A28GLU-1-0.869-0.93625.67311.64511.6450.0000.0000.0000.000
19A29GLU-1-0.934-0.96626.75010.25010.2500.0000.0000.0000.000
20A30ARG10.8540.93223.598-12.818-12.8180.0000.0000.0000.000
21A31PHE0-0.037-0.01618.5540.2940.2940.0000.0000.0000.000
22A32ARG11.0110.98823.496-11.206-11.2060.0000.0000.0000.000
23A33PHE00.0140.02125.7230.1530.1530.0000.0000.0000.000
24A34TRP0-0.080-0.06316.002-0.185-0.1850.0000.0000.0000.000
25A35LEU00.0070.00419.8740.4380.4380.0000.0000.0000.000
26A36GLN0-0.026-0.01922.5840.1020.1020.0000.0000.0000.000
27A37GLN0-0.130-0.06423.999-0.490-0.4900.0000.0000.0000.000
28A38ASP-1-0.843-0.93818.80117.27517.2750.0000.0000.0000.000
29A39TYR00.0280.02821.8440.1930.1930.0000.0000.0000.000
30A40PRO0-0.014-0.02424.1690.0790.0790.0000.0000.0000.000
31A41PHE0-0.015-0.00615.154-0.199-0.1990.0000.0000.0000.000
32A42VAL00.0780.04619.7480.3630.3630.0000.0000.0000.000
33A43GLU-1-0.908-0.94821.12311.75711.7570.0000.0000.0000.000
34A44ALA0-0.039-0.02420.973-0.170-0.1700.0000.0000.0000.000
35A45LEU00.0470.00915.7730.1290.1290.0000.0000.0000.000
36A46TYR00.0200.02219.743-0.081-0.0810.0000.0000.0000.000
37A47ARG10.8960.94822.739-11.940-11.9400.0000.0000.0000.000
38A48TYR0-0.053-0.03614.620-0.294-0.2940.0000.0000.0000.000
39A49GLN00.012-0.03018.942-0.169-0.1690.0000.0000.0000.000
40A50VAL0-0.0040.00820.879-0.318-0.3180.0000.0000.0000.000
41A51GLY0-0.019-0.00723.074-0.431-0.4310.0000.0000.0000.000
42A52LEU0-0.053-0.02016.999-0.193-0.1930.0000.0000.0000.000
43A53LEU00.012-0.00221.212-0.349-0.3490.0000.0000.0000.000
44A54LEU0-0.063-0.01724.241-0.520-0.5200.0000.0000.0000.000
45A55GLU-1-0.866-0.91922.58012.77812.7780.0000.0000.0000.000
46A56ALA0-0.0340.00421.962-0.023-0.0230.0000.0000.0000.000
47A57PRO00.0160.01521.827-0.750-0.7500.0000.0000.0000.000
48A58GLN00.051-0.00424.4840.3020.3020.0000.0000.0000.000
49A59ALA0-0.051-0.04223.7440.1260.1260.0000.0000.0000.000
50A60HIS00.0530.03418.7420.5090.5090.0000.0000.0000.000
51A61ARG10.8800.95221.455-10.666-10.6660.0000.0000.0000.000
52A62ALA00.0280.02223.6400.1180.1180.0000.0000.0000.000
53A63PRO00.0660.02518.841-0.147-0.1470.0000.0000.0000.000
54A64LEU00.0340.01417.8010.2520.2520.0000.0000.0000.000
55A65VAL0-0.035-0.01120.928-0.087-0.0870.0000.0000.0000.000
56A66GLN0-0.0070.00121.828-0.056-0.0560.0000.0000.0000.000
57A67ALA00.0080.01618.2770.0690.0690.0000.0000.0000.000
58A68LEU00.0030.00220.085-0.084-0.0840.0000.0000.0000.000
59A69MET0-0.036-0.02022.758-0.372-0.3720.0000.0000.0000.000
60A70ALA00.0560.03920.192-0.233-0.2330.0000.0000.0000.000
61A71THR00.0190.02120.1750.2520.2520.0000.0000.0000.000
62A72VAL0-0.033-0.02621.816-0.287-0.2870.0000.0000.0000.000
63A73GLU-1-0.925-0.97024.78911.78011.7800.0000.0000.0000.000
64A74GLU-1-0.918-0.95519.23115.88615.8860.0000.0000.0000.000
65A75LEU0-0.034-0.02623.706-0.231-0.2310.0000.0000.0000.000
66A76ASP-1-0.884-0.94625.93110.00910.0090.0000.0000.0000.000
67A77TRP0-0.027-0.01323.849-0.260-0.2600.0000.0000.0000.000
68A78LEU00.019-0.00122.808-0.365-0.3650.0000.0000.0000.000
69A79LEU0-0.073-0.02027.046-0.356-0.3560.0000.0000.0000.000
70A80LEU0-0.075-0.03330.562-0.376-0.3760.0000.0000.0000.000
71A81GLN0-0.063-0.01827.478-0.301-0.3010.0000.0000.0000.000
72A82GLY0-0.018-0.01130.0170.1590.1590.0000.0000.0000.000
73A83ALA0-0.0090.01427.900-0.106-0.1060.0000.0000.0000.000
74A84SER0-0.006-0.03829.899-0.405-0.4050.0000.0000.0000.000
75A85PRO00.0030.02629.7750.1390.1390.0000.0000.0000.000
76A86SER0-0.080-0.05230.6290.0700.0700.0000.0000.0000.000
77A87ALA00.0510.03730.925-0.311-0.3110.0000.0000.0000.000
78A88PRO0-0.062-0.01630.5010.2340.2340.0000.0000.0000.000
79A89VAL00.0740.03424.8830.1760.1760.0000.0000.0000.000
80A90HIS00.0320.02724.2070.0690.0690.0000.0000.0000.000
81A91PRO00.0410.00224.5360.4120.4120.0000.0000.0000.000
82A92VAL0-0.011-0.00819.5860.2590.2590.0000.0000.0000.000
83A93ARG10.9560.98419.548-14.862-14.8620.0000.0000.0000.000
84A94ALA0-0.0100.00221.1210.2340.2340.0000.0000.0000.000
85A95GLY0-0.008-0.00520.828-0.048-0.0480.0000.0000.0000.000
86A96TYR0-0.033-0.03312.4380.5490.5490.0000.0000.0000.000
87A97ILE00.0340.00817.7890.4720.4720.0000.0000.0000.000
88A98ALA00.0080.00920.405-0.060-0.0600.0000.0000.0000.000
89A99LEU0-0.020-0.00313.687-0.034-0.0340.0000.0000.0000.000
90A100LEU00.0250.03015.2470.1970.1970.0000.0000.0000.000
91A101GLU-1-0.888-0.96217.61712.89412.8940.0000.0000.0000.000
92A102GLU-1-0.883-0.90918.16616.38916.3890.0000.0000.0000.000
93A103MET0-0.022-0.00611.316-0.145-0.1450.0000.0000.0000.000
94A104GLY0-0.028-0.00917.017-0.112-0.1120.0000.0000.0000.000
95A105ARG10.8470.92119.932-13.904-13.9040.0000.0000.0000.000
96A106LEU0-0.0400.00614.813-0.494-0.4940.0000.0000.0000.000
97A107PRO00.0480.00717.418-0.329-0.3290.0000.0000.0000.000
98A108TYR00.0480.01117.2430.9290.9290.0000.0000.0000.000
99A109ALA00.034-0.00415.2970.6700.6700.0000.0000.0000.000
100A110TYR00.0220.01012.1280.4390.4390.0000.0000.0000.000
101A111ARG10.8210.91712.472-13.232-13.2320.0000.0000.0000.000
102A112VAL00.0180.01313.8900.9180.9180.0000.0000.0000.000
103A113VAL00.0100.0158.0621.1171.1170.0000.0000.0000.000
104A114PHE00.004-0.0188.7872.4352.4350.0000.0000.0000.000
105A115PHE00.0040.01010.5091.4841.4840.0000.0000.0000.000
106A116TYR00.0050.0196.4831.7251.7250.0000.0000.0000.000
107A117PHE00.006-0.0082.917-0.3060.4720.061-0.268-0.5700.001
108A118LEU0-0.015-0.0157.4042.6352.6350.0000.0000.0000.000
109A119ASN0-0.009-0.0069.782-0.736-0.7360.0000.0000.0000.000
110A120GLY00.0310.0156.876-0.685-0.6850.0000.0000.0000.000
111A121LEU0-0.024-0.0105.3802.1582.1580.0000.0000.0000.000
112A122PHE0-0.002-0.0086.854-1.734-1.7340.0000.0000.0000.000
113A123LEU0-0.0040.0009.502-1.327-1.3270.0000.0000.0000.000
114A124GLU-1-0.934-0.9644.74742.66042.748-0.001-0.003-0.0840.000
115A125ALA0-0.059-0.0318.099-1.984-1.9840.0000.0000.0000.000
116A126TRP00.001-0.01310.160-2.422-2.4220.0000.0000.0000.000
117A127ALA00.0280.01111.326-1.640-1.6400.0000.0000.0000.000
118A128HIS0-0.056-0.01610.9350.0270.0270.0000.0000.0000.000
119A129HIS10.7700.87812.783-24.495-24.4950.0000.0000.0000.000
120A130VAL0-0.0220.00115.606-1.332-1.3320.0000.0000.0000.000
121A131PRO0-0.0180.00517.7390.3100.3100.0000.0000.0000.000
122A132GLU-1-0.890-0.96118.44616.91016.9100.0000.0000.0000.000
123A133GLU-1-0.981-1.01421.12013.41213.4120.0000.0000.0000.000
124A134GLY0-0.0120.00724.792-0.277-0.2770.0000.0000.0000.000
125A135PRO00.0220.00926.3790.1390.1390.0000.0000.0000.000
126A136TRP00.0400.01621.8380.1610.1610.0000.0000.0000.000
127A137ALA00.0810.05422.2450.5380.5380.0000.0000.0000.000
128A138GLU-1-0.957-0.96923.16610.95610.9560.0000.0000.0000.000
129A139LEU0-0.058-0.01922.1790.0540.0540.0000.0000.0000.000
130A140SER00.021-0.01918.7610.3120.3120.0000.0000.0000.000
131A141GLN0-0.086-0.03220.1420.4200.4200.0000.0000.0000.000
132A142HIS0-0.046-0.03222.260-0.515-0.5150.0000.0000.0000.000
133A143TRP0-0.028-0.00416.554-0.808-0.8080.0000.0000.0000.000
134A144PHE0-0.0140.00314.0690.7120.7120.0000.0000.0000.000
135A145ALA00.0570.02918.938-0.598-0.5980.0000.0000.0000.000
136A146PRO00.027-0.00119.7290.7140.7140.0000.0000.0000.000
137A147GLU-1-0.933-0.97220.39913.25513.2550.0000.0000.0000.000
138A148PHE00.0060.02412.2980.4460.4460.0000.0000.0000.000
139A149GLN00.041-0.00613.7001.0611.0610.0000.0000.0000.000
140A150ALA0-0.0360.00015.2520.4990.4990.0000.0000.0000.000
141A151VAL00.0510.00916.8660.1240.1240.0000.0000.0000.000
142A152LEU0-0.005-0.0069.7290.2940.2940.0000.0000.0000.000
143A153TYR0-0.023-0.00512.9840.6060.6060.0000.0000.0000.000
144A154ASP-1-0.874-0.94414.31315.78015.7800.0000.0000.0000.000
145A155LEU0-0.043-0.03112.870-0.324-0.3240.0000.0000.0000.000
146A156GLU-1-0.951-0.9669.07527.96227.9620.0000.0000.0000.000
147A157VAL0-0.036-0.01711.4620.0720.0720.0000.0000.0000.000
148A158LEU0-0.059-0.01814.420-0.776-0.7760.0000.0000.0000.000
149A159ALA00.011-0.0019.848-0.434-0.4340.0000.0000.0000.000
150A160ARG10.9290.9539.958-23.517-23.5170.0000.0000.0000.000
151A161GLY0-0.0170.00511.269-0.354-0.3540.0000.0000.0000.000
152A162LEU0-0.031-0.02713.380-0.546-0.5460.0000.0000.0000.000
153A163TRP0-0.075-0.0275.394-0.664-0.6640.0000.0000.0000.000
154A164GLU-1-0.990-1.00311.00415.31915.3190.0000.0000.0000.000
155A165ASP-1-0.953-0.96212.79615.56015.5600.0000.0000.0000.000
156A166LEU0-0.019-0.00210.040-0.548-0.5480.0000.0000.0000.000
157A167ASP-1-0.859-0.93911.85319.05419.0540.0000.0000.0000.000
158A168PRO00.0600.0128.9331.1351.1350.0000.0000.0000.000
159A169GLU-1-0.956-0.9818.87424.49524.4950.0000.0000.0000.000
160A170VAL0-0.042-0.01511.3680.6100.6100.0000.0000.0000.000
161A171VAL00.0410.0116.6320.5230.5230.0000.0000.0000.000
162A172ARG11.0001.0086.647-24.044-24.0440.0000.0000.0000.000
163A173THR0-0.108-0.0358.0900.8790.8790.0000.0000.0000.000
164A174TYR0-0.010-0.01810.804-0.453-0.4530.0000.0000.0000.000
165A175LEU00.0340.0233.693-1.153-0.6470.025-0.206-0.3250.002
166A176ARG10.8870.9487.424-22.009-22.0090.0000.0000.0000.000
167A177ARG10.8270.8748.276-19.847-19.8470.0000.0000.0000.000
168A178ILE00.0150.0198.631-1.366-1.3660.0000.0000.0000.000
169A179LEU00.0130.0134.754-1.159-1.028-0.001-0.002-0.1280.000
170A180GLU-1-0.904-0.9699.03522.87022.8700.0000.0000.0000.000
171A181ALA0-0.030-0.00812.429-1.616-1.6160.0000.0000.0000.000
172A182GLU-1-0.766-0.8909.78224.92124.9210.0000.0000.0000.000
173A183LYS10.8520.93211.916-24.569-24.5690.0000.0000.0000.000
174A184ALA0-0.038-0.01913.352-1.629-1.6290.0000.0000.0000.000
175A185THR00.0430.01215.829-1.716-1.7160.0000.0000.0000.000
176A186TRP00.0510.03112.403-2.021-2.0210.0000.0000.0000.000
177A187SER0-0.046-0.02016.468-1.301-1.3010.0000.0000.0000.000
178A188LEU0-0.050-0.01618.565-1.075-1.0750.0000.0000.0000.000
179A189LEU00.0160.00018.387-0.919-0.9190.0000.0000.0000.000
180A190LEU0-0.101-0.03419.302-0.531-0.5310.0000.0000.0000.000