Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 8244Y

Calculation Name: 1WYZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WYZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q8A031

Base Structure: X-ray

Registration Date: 2023-06-19

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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2614152.925013
FMO2-HF: Nuclear repulsion 2525492.813828
FMO2-HF: Total energy -88660.111185
FMO2-MP2: Total energy -88919.959584


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:2:GLU)


Summations of interaction energy for fragment #1(A:2: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.
-83.233-87.46231.149-15.107-11.8120.122
Interaction energy analysis for fragmet #1(A:2:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.866 / q_NPA : -0.905
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].
3A4ALA0-0.012-0.0233.678-9.031-7.8270.004-0.462-0.7450.002
4A5LEU00.0160.0126.0432.6282.6280.0000.0000.0000.000
5A6TYR00.006-0.0371.723-34.898-36.96915.776-7.546-6.1590.053
6A7LEU0-0.050-0.0358.003-2.631-2.6310.0000.0000.0000.000
7A8LEU0-0.023-0.0188.3440.8950.8950.0000.0000.0000.000
8A9PRO0-0.0310.00212.294-1.540-1.5400.0000.0000.0000.000
9A10VAL00.0370.00915.5020.7680.7680.0000.0000.0000.000
10A11THR00.0060.00018.1790.0720.0720.0000.0000.0000.000
11A12LEU0-0.053-0.02921.454-0.147-0.1470.0000.0000.0000.000
12A13GLY00.026-0.00424.351-0.603-0.6030.0000.0000.0000.000
13A14ASP-1-0.985-0.98225.49311.68711.6870.0000.0000.0000.000
14A15THR0-0.001-0.00124.710-0.148-0.1480.0000.0000.0000.000
15A16PRO0-0.015-0.00723.7870.3790.3790.0000.0000.0000.000
16A17LEU00.0490.01416.9780.2090.2090.0000.0000.0000.000
17A18GLU-1-0.888-0.95419.08115.44815.4480.0000.0000.0000.000
18A19GLN0-0.063-0.02420.072-0.179-0.1790.0000.0000.0000.000
19A20VAL0-0.041-0.03320.305-0.258-0.2580.0000.0000.0000.000
20A21LEU0-0.028-0.01115.4550.6400.6400.0000.0000.0000.000
21A22PRO0-0.013-0.00512.987-0.400-0.4000.0000.0000.0000.000
22A23SER00.007-0.00812.5620.4740.4740.0000.0000.0000.000
23A24TYR00.0310.0164.818-0.565-0.5650.0000.0000.0000.000
24A25ASN00.0160.0008.2765.3025.3020.0000.0000.0000.000
25A26THR00.0440.0129.4552.3082.3080.0000.0000.0000.000
26A27GLU-1-0.964-0.9767.44230.56130.5610.0000.0000.0000.000
27A28ILE00.0250.0163.8711.1121.7110.005-0.150-0.4540.001
28A29ILE0-0.017-0.0105.4382.5762.591-0.0010.000-0.0140.000
29A30ARG10.8130.8888.196-26.911-26.9110.0000.0000.0000.000
30A31GLY0-0.0180.0085.294-2.487-2.4870.0000.0000.0000.000
31A32ILE0-0.079-0.0264.449-0.507-0.348-0.001-0.010-0.1480.000
32A33ARG10.9590.9856.848-33.669-33.6690.0000.0000.0000.000
33A34HIS00.0160.0299.655-1.581-1.5810.0000.0000.0000.000
34A35PHE00.0410.02010.2642.5752.5750.0000.0000.0000.000
35A36ILE00.0020.00812.843-1.976-1.9760.0000.0000.0000.000
36A37VAL0-0.025-0.01815.1710.4830.4830.0000.0000.0000.000
37A38GLU-1-0.801-0.89817.76814.53614.5360.0000.0000.0000.000
38A39ASP-1-0.777-0.89020.85612.25512.2550.0000.0000.0000.000
39A40VAL00.0050.01019.9410.6200.6200.0000.0000.0000.000
40A41ARG10.8840.93020.918-11.220-11.2200.0000.0000.0000.000
41A42SER0-0.030-0.03122.2460.2520.2520.0000.0000.0000.000
42A43ALA00.0700.03916.9410.3470.3470.0000.0000.0000.000
43A44ARG10.8430.92717.646-15.080-15.0800.0000.0000.0000.000
44A45ARG10.8880.94319.187-12.319-12.3190.0000.0000.0000.000
45A46PHE00.0560.03314.331-0.066-0.0660.0000.0000.0000.000
46A47LEU00.0240.00312.6920.3240.3240.0000.0000.0000.000
47A48LYS10.7490.86416.203-17.293-17.2930.0000.0000.0000.000
48A49LYN0-0.0230.01919.114-0.448-0.4480.0000.0000.0000.000
49A50VAL0-0.049-0.01412.6930.2230.2230.0000.0000.0000.000
50A51ASP-1-0.750-0.86714.27121.05021.0500.0000.0000.0000.000
51A52ARG10.8230.91516.368-16.738-16.7380.0000.0000.0000.000
52A53GLU-1-0.840-0.93216.51716.00716.0070.0000.0000.0000.000
53A54ILE0-0.0310.00811.6740.3130.3130.0000.0000.0000.000
54A55ASP-1-0.826-0.90915.28215.22215.2220.0000.0000.0000.000
55A56ILE0-0.008-0.00816.4770.7750.7750.0000.0000.0000.000
56A57ASP-1-0.928-0.96318.41614.08014.0800.0000.0000.0000.000
57A58SER00.0100.01714.3590.1040.1040.0000.0000.0000.000
58A59LEU0-0.069-0.03416.2250.6890.6890.0000.0000.0000.000
59A60THR0-0.051-0.06413.608-0.954-0.9540.0000.0000.0000.000
60A61PHE00.002-0.00315.3280.9550.9550.0000.0000.0000.000
61A62TYR00.0190.00114.654-0.766-0.7660.0000.0000.0000.000
62A63PRO0-0.003-0.00318.4350.3530.3530.0000.0000.0000.000
63A64LEU0-0.0040.01818.864-0.170-0.1700.0000.0000.0000.000
64A65ASN00.0350.00021.512-0.494-0.4940.0000.0000.0000.000
65A66LYS10.9520.96824.733-10.927-10.9270.0000.0000.0000.000
66A67HIS0-0.034-0.01426.144-0.445-0.4450.0000.0000.0000.000
67A68THR00.0160.02822.616-0.212-0.2120.0000.0000.0000.000
68A69SER00.0210.02425.740-0.096-0.0960.0000.0000.0000.000
69A70PRO00.013-0.02123.4460.5650.5650.0000.0000.0000.000
70A71GLU-1-0.839-0.92722.59714.13414.1340.0000.0000.0000.000
71A72ASP-1-0.831-0.91922.77212.72612.7260.0000.0000.0000.000
72A73ILE0-0.0220.00018.0880.7800.7800.0000.0000.0000.000
73A74SER00.0000.00318.1231.3331.3330.0000.0000.0000.000
74A75GLY0-0.081-0.05218.4850.5930.5930.0000.0000.0000.000
75A76TYR0-0.021-0.03416.4880.4950.4950.0000.0000.0000.000
76A77LEU00.0130.00413.8721.4271.4270.0000.0000.0000.000
77A78LYS10.8450.93613.557-13.698-13.6980.0000.0000.0000.000
78A79PRO00.0140.00511.5690.2260.2260.0000.0000.0000.000
79A80LEU00.0060.0217.5930.9630.9630.0000.0000.0000.000
80A81ALA0-0.057-0.02610.0140.7370.7370.0000.0000.0000.000
81A82GLY0-0.0160.00411.986-0.959-0.9590.0000.0000.0000.000
82A83GLY0-0.012-0.0048.052-0.182-0.1820.0000.0000.0000.000
83A84ALA0-0.035-0.0036.0164.8644.8640.0000.0000.0000.000
84A85SER0-0.017-0.0381.692-26.897-31.23915.368-6.914-4.1120.066
85A86MET0-0.050-0.0094.913-5.732-5.633-0.001-0.012-0.0860.000
86A87GLY00.0390.0227.2753.3423.3420.0000.0000.0000.000
87A88VAL0-0.035-0.0209.520-2.450-2.4500.0000.0000.0000.000
88A89ILE0-0.0110.00113.0210.5610.5610.0000.0000.0000.000
89A90SER00.0330.00615.575-0.497-0.4970.0000.0000.0000.000
90A91GLU-1-0.981-0.98019.13913.25713.2570.0000.0000.0000.000
91A99ASP-1-0.900-0.96022.71512.61212.6120.0000.0000.0000.000
92A100PRO0-0.039-0.01821.7150.2140.2140.0000.0000.0000.000
93A101GLY00.0660.03518.0100.3780.3780.0000.0000.0000.000
94A102ALA0-0.027-0.02117.7740.9010.9010.0000.0000.0000.000
95A103ASP-1-0.877-0.94419.72413.41713.4170.0000.0000.0000.000
96A104VAL0-0.024-0.01615.0790.1390.1390.0000.0000.0000.000
97A105VAL00.0050.00714.4810.6840.6840.0000.0000.0000.000
98A106ALA0-0.0030.00016.2290.2180.2180.0000.0000.0000.000
99A107ILE0-0.023-0.00518.761-0.323-0.3230.0000.0000.0000.000
100A108ALA00.0460.01913.166-0.008-0.0080.0000.0000.0000.000
101A109GLN0-0.004-0.00412.4980.1010.1010.0000.0000.0000.000
102A110ARG10.9050.96315.617-13.145-13.1450.0000.0000.0000.000
103A111GLN0-0.029-0.01616.2530.1700.1700.0000.0000.0000.000
104A112LYS10.8720.92813.199-19.243-19.2430.0000.0000.0000.000
105A113LEU00.0340.03311.1550.8370.8370.0000.0000.0000.000
106A114LYS10.9320.9783.974-37.299-37.191-0.001-0.013-0.0940.000
107A115VAL00.0230.0108.2971.4921.4920.0000.0000.0000.000
108A116ILE0-0.031-0.0185.112-0.793-0.7930.0000.0000.0000.000
109A117PRO00.0080.0178.1780.7800.7800.0000.0000.0000.000
110A118LEU00.0070.0097.7171.2541.2540.0000.0000.0000.000
111A119VAL0-0.002-0.00711.638-1.763-1.7630.0000.0000.0000.000
112A120GLY00.0610.02214.9421.1201.1200.0000.0000.0000.000
113A121PRO0-0.0090.02517.658-0.619-0.6190.0000.0000.0000.000
114A122SER00.021-0.00221.034-0.060-0.0600.0000.0000.0000.000
115A123SER00.0750.03022.892-0.288-0.2880.0000.0000.0000.000
116A124ILE00.0130.02325.499-0.516-0.5160.0000.0000.0000.000
117A125ILE00.0410.00821.667-0.449-0.4490.0000.0000.0000.000
118A126LEU00.0350.02524.365-0.329-0.3290.0000.0000.0000.000
119A127SER00.011-0.01427.419-0.508-0.5080.0000.0000.0000.000
120A128VAL0-0.046-0.01728.630-0.393-0.3930.0000.0000.0000.000
121A129MET0-0.033-0.01325.921-0.194-0.1940.0000.0000.0000.000
122A130ALA00.0340.02530.245-0.292-0.2920.0000.0000.0000.000
123A131SER0-0.048-0.02932.959-0.387-0.3870.0000.0000.0000.000
124A132GLY00.0210.02634.448-0.335-0.3350.0000.0000.0000.000
125A133PHE0-0.078-0.04734.725-0.320-0.3200.0000.0000.0000.000
126A134ASN0-0.010-0.00733.1230.3980.3980.0000.0000.0000.000
127A135GLY00.1020.03829.7390.1030.1030.0000.0000.0000.000
128A136GLN0-0.046-0.01528.2280.5190.5190.0000.0000.0000.000
129A137SER0-0.019-0.01029.9070.0470.0470.0000.0000.0000.000
130A138PHE0-0.016-0.01425.414-0.292-0.2920.0000.0000.0000.000
131A139ALA00.0260.02729.8720.2160.2160.0000.0000.0000.000
132A140PHE00.026-0.00327.706-0.222-0.2220.0000.0000.0000.000
133A141HIS00.004-0.01330.350-0.026-0.0260.0000.0000.0000.000
134A142GLY00.0330.03331.074-0.116-0.1160.0000.0000.0000.000
135A143TYR00.0210.00730.639-0.312-0.3120.0000.0000.0000.000
136A144LEU0-0.005-0.00534.976-0.091-0.0910.0000.0000.0000.000
137A145PRO00.002-0.00438.386-0.001-0.0010.0000.0000.0000.000
138A146ILE00.0590.03238.773-0.105-0.1050.0000.0000.0000.000
139A147GLU-1-0.910-0.93942.3426.8446.8440.0000.0000.0000.000
140A148PRO00.036-0.01246.0320.0710.0710.0000.0000.0000.000
141A149GLY00.0490.03948.476-0.038-0.0380.0000.0000.0000.000
142A150GLU-1-0.790-0.87843.6777.1587.1580.0000.0000.0000.000
143A151ARG10.7750.86640.954-7.533-7.5330.0000.0000.0000.000
144A152ALA00.0230.01943.9520.1060.1060.0000.0000.0000.000
145A153LYS10.8510.90045.749-6.900-6.9000.0000.0000.0000.000
146A154LYS10.8800.96736.070-8.557-8.5570.0000.0000.0000.000
147A155LEU00.0410.01341.0890.1160.1160.0000.0000.0000.000
148A156LYS10.8250.90342.830-6.534-6.5340.0000.0000.0000.000
149A157THR00.012-0.00640.575-0.017-0.0170.0000.0000.0000.000
150A158LEU0-0.028-0.01036.9300.0950.0950.0000.0000.0000.000
151A159GLU-1-0.742-0.83540.0736.8786.8780.0000.0000.0000.000
152A160GLN0-0.033-0.03242.800-0.011-0.0110.0000.0000.0000.000
153A161ARG10.8620.90836.075-8.594-8.5940.0000.0000.0000.000
154A162VAL0-0.0320.00038.5860.0760.0760.0000.0000.0000.000
155A163TYR0-0.095-0.07139.829-0.023-0.0230.0000.0000.0000.000
156A164ALA0-0.019-0.00541.490-0.027-0.0270.0000.0000.0000.000
157A165GLU-1-0.774-0.85235.7828.5178.5170.0000.0000.0000.000
158A166SER0-0.042-0.01736.7470.1190.1190.0000.0000.0000.000
159A167GLN00.0280.04133.1510.1590.1590.0000.0000.0000.000
160A168THR0-0.008-0.01733.014-0.309-0.3090.0000.0000.0000.000
161A169GLN0-0.047-0.02733.5180.3180.3180.0000.0000.0000.000
162A170LEU00.0050.00629.877-0.181-0.1810.0000.0000.0000.000
163A171PHE0-0.005-0.02233.1410.0400.0400.0000.0000.0000.000
164A172ILE00.0230.02429.9780.0320.0320.0000.0000.0000.000
165A173GLU-1-0.737-0.88434.0798.0108.0100.0000.0000.0000.000
166A174THR00.0130.01635.2370.2370.2370.0000.0000.0000.000
167A175PRO00.041-0.00534.374-0.243-0.2430.0000.0000.0000.000
168A176TYR00.0340.02437.014-0.160-0.1600.0000.0000.0000.000
169A177ARG10.8140.90839.716-7.797-7.7970.0000.0000.0000.000
170A178ASN0-0.028-0.00936.985-0.094-0.0940.0000.0000.0000.000
171A179HIS00.0560.01440.786-0.168-0.1680.0000.0000.0000.000
172A180LYS10.8410.91244.293-6.992-6.9920.0000.0000.0000.000
173A181MET0-0.0310.00639.796-0.047-0.0470.0000.0000.0000.000
174A182ILE00.0210.01242.414-0.053-0.0530.0000.0000.0000.000
175A183GLU-1-0.820-0.90144.5246.2676.2670.0000.0000.0000.000
176A184ASP-1-0.812-0.89544.8256.9646.9640.0000.0000.0000.000
177A185ILE00.002-0.00141.589-0.070-0.0700.0000.0000.0000.000
178A186LEU0-0.025-0.00245.467-0.123-0.1230.0000.0000.0000.000
179A187GLN0-0.025-0.02148.633-0.193-0.1930.0000.0000.0000.000
180A188ASN0-0.061-0.03047.270-0.167-0.1670.0000.0000.0000.000
181A189CYS0-0.048-0.00844.7490.0280.0280.0000.0000.0000.000
182A190ARG10.8840.93745.702-6.880-6.8800.0000.0000.0000.000
183A191PRO00.0300.00248.4510.1220.1220.0000.0000.0000.000
184A192GLN00.001-0.01048.9840.0890.0890.0000.0000.0000.000
185A193THR0-0.048-0.02043.2580.0580.0580.0000.0000.0000.000
186A194LYS10.9340.97841.798-7.411-7.4110.0000.0000.0000.000
187A195LEU00.0250.01039.9630.1070.1070.0000.0000.0000.000
188A196CYS0-0.0540.00136.860-0.022-0.0220.0000.0000.0000.000
189A197ILE00.0080.00337.7370.0710.0710.0000.0000.0000.000
190A198ALA00.0730.02632.866-0.052-0.0520.0000.0000.0000.000
191A199ALA0-0.001-0.01833.5060.2090.2090.0000.0000.0000.000
192A200ASN0-0.003-0.00631.9640.1120.1120.0000.0000.0000.000
193A201ILE00.0190.01527.8420.0830.0830.0000.0000.0000.000
194A202THR0-0.048-0.02425.3640.6450.6450.0000.0000.0000.000
195A203CYS0-0.0020.00027.9860.2800.2800.0000.0000.0000.000
196A204GLU-1-0.859-0.93130.08810.40010.4000.0000.0000.0000.000
197A205GLY0-0.053-0.01732.847-0.347-0.3470.0000.0000.0000.000
198A206GLU-1-0.899-0.94831.11610.24410.2440.0000.0000.0000.000
199A207PHE0-0.034-0.02434.600-0.384-0.3840.0000.0000.0000.000
200A208ILE00.0380.02331.6580.0750.0750.0000.0000.0000.000
201A209GLN00.0320.02736.302-0.285-0.2850.0000.0000.0000.000
202A210THR0-0.012-0.03138.2490.0460.0460.0000.0000.0000.000
203A211ARG10.7860.87140.664-7.192-7.1920.0000.0000.0000.000
204A212THR0-0.0050.00043.9850.1340.1340.0000.0000.0000.000
205A213VAL00.0430.02445.353-0.050-0.0500.0000.0000.0000.000
206A214LYS10.8210.88047.610-6.199-6.1990.0000.0000.0000.000
207A215ASP-1-0.820-0.90249.0736.1986.1980.0000.0000.0000.000
208A216TRP0-0.037-0.01941.822-0.030-0.0300.0000.0000.0000.000
209A217LYS10.8280.93348.086-6.214-6.2140.0000.0000.0000.000
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