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: 76Z4K

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 OptAll
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 -2068240.181254
FMO2-HF: Nuclear repulsion 1996461.468807
FMO2-HF: Total energy -71778.712447
FMO2-MP2: Total energy -71994.238916


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.
126.974135.9461.728-4.488-6.2140.045
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 : -0.882 / q_NPA : -0.963
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].
3A13PRO0-0.0100.0363.860-2.642-0.843-0.022-0.844-0.9340.002
4A14GLY00.0070.0055.159-5.241-5.149-0.001-0.003-0.0880.000
5A15LEU0-0.021-0.0296.245-2.507-2.5070.0000.0000.0000.000
6A16LEU00.0300.0292.828-11.449-8.1980.540-1.629-2.1620.018
7A17GLU-1-0.826-0.9345.20842.80142.861-0.001-0.002-0.0570.000
8A18GLU-1-0.849-0.9147.92721.62921.6290.0000.0000.0000.000
9A19ILE0-0.0150.0046.821-3.540-3.5400.0000.0000.0000.000
10A20LYS10.8140.9206.981-38.650-38.6500.0000.0000.0000.000
11A21ALA0-0.031-0.01610.951-2.742-2.7420.0000.0000.0000.000
12A22LEU0-0.0180.00713.322-2.196-2.1960.0000.0000.0000.000
13A23PRO0-0.025-0.00315.637-0.519-0.5190.0000.0000.0000.000
14A24LEU0-0.006-0.01416.375-1.140-1.1400.0000.0000.0000.000
15A25ARG10.7880.89519.636-14.251-14.2510.0000.0000.0000.000
16A26LEU00.0340.03318.484-0.266-0.2660.0000.0000.0000.000
17A27ASP-1-0.844-0.93622.65810.76710.7670.0000.0000.0000.000
18A28GLU-1-0.824-0.88725.28512.16112.1610.0000.0000.0000.000
19A29GLU-1-0.921-0.95526.76410.08010.0800.0000.0000.0000.000
20A30ARG10.8170.88723.394-12.956-12.9560.0000.0000.0000.000
21A31PHE0-0.008-0.00718.1380.3240.3240.0000.0000.0000.000
22A32ARG10.8800.91123.240-11.220-11.2200.0000.0000.0000.000
23A33PHE0-0.0070.00525.5480.1620.1620.0000.0000.0000.000
24A34TRP0-0.050-0.03315.611-0.212-0.2120.0000.0000.0000.000
25A35LEU00.0370.02519.4320.6030.6030.0000.0000.0000.000
26A36GLN0-0.030-0.02122.2210.1550.1550.0000.0000.0000.000
27A37GLN0-0.098-0.06123.670-0.348-0.3480.0000.0000.0000.000
28A38ASP-1-0.798-0.89418.23817.73417.7340.0000.0000.0000.000
29A39TYR0-0.0110.01621.2670.2480.2480.0000.0000.0000.000
30A40PRO0-0.016-0.02923.2750.0830.0830.0000.0000.0000.000
31A41PHE0-0.025-0.01213.802-0.167-0.1670.0000.0000.0000.000
32A42VAL00.0840.04418.9060.3820.3820.0000.0000.0000.000
33A43GLU-1-0.868-0.93320.24812.03612.0360.0000.0000.0000.000
34A44ALA0-0.029-0.01819.955-0.137-0.1370.0000.0000.0000.000
35A45LEU00.0450.01614.7780.1740.1740.0000.0000.0000.000
36A46TYR00.0080.02718.829-0.058-0.0580.0000.0000.0000.000
37A47ARG10.8830.92922.099-12.089-12.0890.0000.0000.0000.000
38A48TYR0-0.047-0.02715.071-0.359-0.3590.0000.0000.0000.000
39A49GLN00.008-0.03118.687-0.125-0.1250.0000.0000.0000.000
40A50VAL0-0.023-0.00620.869-0.398-0.3980.0000.0000.0000.000
41A51GLY0-0.0010.00123.185-0.410-0.4100.0000.0000.0000.000
42A52LEU0-0.0320.00017.300-0.106-0.1060.0000.0000.0000.000
43A53LEU00.002-0.02221.203-0.373-0.3730.0000.0000.0000.000
44A54LEU0-0.067-0.01424.186-0.527-0.5270.0000.0000.0000.000
45A55GLU-1-0.824-0.90022.80513.26713.2670.0000.0000.0000.000
46A56ALA0-0.0070.01622.098-0.030-0.0300.0000.0000.0000.000
47A57PRO00.0070.00321.751-0.806-0.8060.0000.0000.0000.000
48A58GLN00.0260.00824.2730.2740.2740.0000.0000.0000.000
49A59ALA0-0.033-0.02723.7290.0080.0080.0000.0000.0000.000
50A60HIS00.0620.03719.3550.4480.4480.0000.0000.0000.000
51A61ARG10.8860.94321.247-10.969-10.9690.0000.0000.0000.000
52A62ALA0-0.0040.01323.8650.0550.0550.0000.0000.0000.000
53A63PRO00.0750.02618.675-0.143-0.1430.0000.0000.0000.000
54A64LEU00.0230.01117.8380.2330.2330.0000.0000.0000.000
55A65VAL0-0.017-0.00920.782-0.038-0.0380.0000.0000.0000.000
56A66GLN00.0040.00921.808-0.281-0.2810.0000.0000.0000.000
57A67ALA00.0090.01718.0930.0770.0770.0000.0000.0000.000
58A68LEU0-0.0140.00419.917-0.041-0.0410.0000.0000.0000.000
59A69MET0-0.033-0.02122.607-0.380-0.3800.0000.0000.0000.000
60A70ALA00.0610.03620.330-0.203-0.2030.0000.0000.0000.000
61A71THR00.0200.01419.7700.2500.2500.0000.0000.0000.000
62A72VAL0-0.038-0.02421.474-0.305-0.3050.0000.0000.0000.000
63A73GLU-1-0.927-0.96824.69511.55011.5500.0000.0000.0000.000
64A74GLU-1-0.890-0.93818.59116.56616.5660.0000.0000.0000.000
65A75LEU0-0.044-0.03423.162-0.240-0.2400.0000.0000.0000.000
66A76ASP-1-0.926-0.96625.2899.9209.9200.0000.0000.0000.000
67A77TRP0-0.014-0.01824.269-0.243-0.2430.0000.0000.0000.000
68A78LEU0-0.001-0.01022.208-0.336-0.3360.0000.0000.0000.000
69A79LEU0-0.063-0.02426.508-0.336-0.3360.0000.0000.0000.000
70A80LEU0-0.039-0.01530.060-0.394-0.3940.0000.0000.0000.000
71A81GLN0-0.0140.02026.831-0.203-0.2030.0000.0000.0000.000
72A82GLY0-0.014-0.00429.6610.0140.0140.0000.0000.0000.000
73A83ALA0-0.0120.00427.086-0.032-0.0320.0000.0000.0000.000
74A84SER0-0.008-0.01829.039-0.370-0.3700.0000.0000.0000.000
75A85PRO00.0140.00728.7480.1360.1360.0000.0000.0000.000
76A86SER0-0.071-0.02429.7910.1050.1050.0000.0000.0000.000
77A87ALA00.0180.01129.542-0.362-0.3620.0000.0000.0000.000
78A88PRO0-0.055-0.02729.6350.2070.2070.0000.0000.0000.000
79A89VAL00.0550.02823.7120.1760.1760.0000.0000.0000.000
80A90HIS00.0540.02823.0970.1570.1570.0000.0000.0000.000
81A91PRO00.017-0.00723.1160.5020.5020.0000.0000.0000.000
82A92VAL0-0.0100.00717.8800.2750.2750.0000.0000.0000.000
83A93ARG10.8500.91118.683-15.183-15.1830.0000.0000.0000.000
84A94ALA0-0.0070.00119.8390.2210.2210.0000.0000.0000.000
85A95GLY0-0.008-0.00219.804-0.036-0.0360.0000.0000.0000.000
86A96TYR0-0.025-0.04911.2180.6900.6900.0000.0000.0000.000
87A97ILE00.0280.01216.9060.5060.5060.0000.0000.0000.000
88A98ALA0-0.011-0.00319.524-0.057-0.0570.0000.0000.0000.000
89A99LEU0-0.0120.00213.018-0.175-0.1750.0000.0000.0000.000
90A100LEU00.0290.02214.3490.2900.2900.0000.0000.0000.000
91A101GLU-1-0.842-0.92217.19412.96812.9680.0000.0000.0000.000
92A102GLU-1-0.895-0.88117.85717.82717.8270.0000.0000.0000.000
93A103MET00.0010.00211.248-0.291-0.2910.0000.0000.0000.000
94A104GLY00.0080.00717.215-0.273-0.2730.0000.0000.0000.000
95A105ARG10.7810.87720.449-14.827-14.8270.0000.0000.0000.000
96A106LEU0-0.0320.01615.545-0.522-0.5220.0000.0000.0000.000
97A107PRO00.029-0.00218.343-0.451-0.4510.0000.0000.0000.000
98A108TYR00.027-0.00117.7371.0621.0620.0000.0000.0000.000
99A109ALA00.0090.00415.4640.6790.6790.0000.0000.0000.000
100A110TYR00.0430.01612.3210.3310.3310.0000.0000.0000.000
101A111ARG10.7400.86412.869-13.606-13.6060.0000.0000.0000.000
102A112VAL00.0280.01114.3790.8640.8640.0000.0000.0000.000
103A113VAL0-0.0030.0118.4561.1771.1770.0000.0000.0000.000
104A114PHE0-0.001-0.0249.1612.7282.7280.0000.0000.0000.000
105A115PHE00.0170.01810.4221.5411.5410.0000.0000.0000.000
106A116TYR0-0.039-0.0346.2211.9561.9560.0000.0000.0000.000
107A117PHE0-0.002-0.0022.495-6.846-4.2661.196-1.685-2.0910.024
108A118LEU0-0.015-0.0106.9462.7412.7410.0000.0000.0000.000
109A119ASN00.000-0.0119.356-0.677-0.6770.0000.0000.0000.000
110A120GLY00.0160.0057.528-1.318-1.3180.0000.0000.0000.000
111A121LEU0-0.0080.0004.3770.2640.465-0.001-0.016-0.1840.000
112A122PHE00.007-0.0056.630-1.828-1.8280.0000.0000.0000.000
113A123LEU00.0150.01710.173-1.568-1.5680.0000.0000.0000.000
114A124GLU-1-0.814-0.9116.04236.00036.0000.0000.0000.0000.000
115A125ALA0-0.047-0.0148.487-0.796-0.7960.0000.0000.0000.000
116A126TRP00.0350.0019.922-2.205-2.2050.0000.0000.0000.000
117A127ALA0-0.003-0.00211.756-1.510-1.5100.0000.0000.0000.000
118A128HIS0-0.0240.00311.0210.2750.2750.0000.0000.0000.000
119A129HIS10.7650.86013.092-23.293-23.2930.0000.0000.0000.000
120A130VAL0-0.0070.00415.724-1.184-1.1840.0000.0000.0000.000
121A131PRO0-0.028-0.00218.0750.3470.3470.0000.0000.0000.000
122A132GLU-1-0.900-0.96119.59815.63215.6320.0000.0000.0000.000
123A133GLU-1-0.963-0.98821.99112.96212.9620.0000.0000.0000.000
124A134GLY0-0.004-0.00325.304-0.585-0.5850.0000.0000.0000.000
125A135PRO00.0040.00726.2120.2470.2470.0000.0000.0000.000
126A136TRP00.0100.00122.0140.1970.1970.0000.0000.0000.000
127A137ALA00.0540.04722.2640.5520.5520.0000.0000.0000.000
128A138GLU-1-0.943-0.96723.20410.87110.8710.0000.0000.0000.000
129A139LEU0-0.027-0.01722.0090.1220.1220.0000.0000.0000.000
130A140SER0-0.031-0.03218.7930.3980.3980.0000.0000.0000.000
131A141GLN0-0.043-0.02320.2350.4160.4160.0000.0000.0000.000
132A142HIS0-0.029-0.01322.682-0.630-0.6300.0000.0000.0000.000
133A143TRP0-0.0180.00217.318-0.727-0.7270.0000.0000.0000.000
134A144PHE0-0.042-0.01514.0510.6550.6550.0000.0000.0000.000
135A145ALA00.0580.03319.247-0.580-0.5800.0000.0000.0000.000
136A146PRO00.004-0.00320.3080.6960.6960.0000.0000.0000.000
137A147GLU-1-0.899-0.95121.04113.41613.4160.0000.0000.0000.000
138A148PHE00.0090.01012.9660.4810.4810.0000.0000.0000.000
139A149GLN00.032-0.00714.1080.5270.5270.0000.0000.0000.000
140A150ALA0-0.043-0.00715.4430.5730.5730.0000.0000.0000.000
141A151VAL00.0400.00817.1970.2650.2650.0000.0000.0000.000
142A152LEU00.0090.00810.0020.3770.3770.0000.0000.0000.000
143A153TYR0-0.0110.00012.7131.2481.2480.0000.0000.0000.000
144A154ASP-1-0.894-0.95414.21815.73315.7330.0000.0000.0000.000
145A155LEU0-0.046-0.03613.076-0.226-0.2260.0000.0000.0000.000
146A156GLU-1-0.825-0.8659.02528.15428.1540.0000.0000.0000.000
147A157VAL0-0.062-0.03311.7000.0750.0750.0000.0000.0000.000
148A158LEU0-0.054-0.02114.406-0.603-0.6030.0000.0000.0000.000
149A159ALA00.0060.0009.810-0.274-0.2740.0000.0000.0000.000
150A160ARG10.8490.8899.131-22.768-22.7680.0000.0000.0000.000
151A161GLY00.0160.03411.002-0.307-0.3070.0000.0000.0000.000
152A162LEU0-0.068-0.04713.701-0.541-0.5410.0000.0000.0000.000
153A163TRP00.017-0.0025.814-0.204-0.2040.0000.0000.0000.000
154A164GLU-1-0.995-0.99411.34316.34516.3450.0000.0000.0000.000
155A165ASP-1-0.968-0.97713.80215.46515.4650.0000.0000.0000.000
156A166LEU0-0.0480.00010.643-0.616-0.6160.0000.0000.0000.000
157A167ASP-1-0.849-0.92912.91220.27220.2720.0000.0000.0000.000
158A168PRO00.0760.0189.2771.2991.2990.0000.0000.0000.000
159A169GLU-1-0.852-0.9099.34527.65427.6540.0000.0000.0000.000
160A170VAL0-0.0170.00011.7810.8840.8840.0000.0000.0000.000
161A171VAL00.0340.0176.6400.9880.9880.0000.0000.0000.000
162A172ARG10.8330.9056.984-26.030-26.0300.0000.0000.0000.000
163A173THR0-0.070-0.0528.2031.3711.3710.0000.0000.0000.000
164A174TYR0-0.058-0.05210.671-1.314-1.3140.0000.0000.0000.000
165A175LEU00.0400.0183.432-0.897-0.5780.012-0.059-0.2720.000
166A176ARG10.8060.8797.455-24.068-24.0680.0000.0000.0000.000
167A177ARG10.7880.8538.575-22.018-22.0180.0000.0000.0000.000
168A178ILE00.0640.0397.994-1.827-1.8270.0000.0000.0000.000
169A179LEU00.0100.0153.828-3.434-2.7640.005-0.250-0.4260.001
170A180GLU-1-0.836-0.9027.98922.36022.3600.0000.0000.0000.000
171A181ALA00.0100.01611.467-2.299-2.2990.0000.0000.0000.000
172A182GLU-1-0.749-0.8418.50025.80825.8080.0000.0000.0000.000
173A183LYS10.7800.88411.023-27.506-27.5060.0000.0000.0000.000
174A184ALA0-0.016-0.01012.496-1.927-1.9270.0000.0000.0000.000
175A185THR00.0320.00914.610-2.004-2.0040.0000.0000.0000.000
176A186TRP00.028-0.00211.717-2.466-2.4660.0000.0000.0000.000
177A187SER0-0.076-0.05615.711-1.503-1.5030.0000.0000.0000.000
178A188LEU0-0.054-0.01917.966-1.156-1.1560.0000.0000.0000.000
179A189LEU00.0440.02918.152-0.921-0.9210.0000.0000.0000.000
180A190LEU0-0.063-0.00818.676-0.678-0.6780.0000.0000.0000.000