FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: V5M61

Calculation Name: 5CWB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5CWB

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-20

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 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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2265489.662254
FMO2-HF: Nuclear repulsion 2187900.467246
FMO2-HF: Total energy -77589.195008
FMO2-MP2: Total energy -77814.443699


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:5:ASP)


Summations of interaction energy for fragment #1(A:5: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.
106.316109.5140.029-1.543-1.6840.007
Interaction energy analysis for fragmet #1(A:5:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.923 / 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].
3A7CYS0-0.082-0.0193.264-10.059-6.8610.029-1.543-1.6840.007
4A8GLU-1-0.789-0.8684.82622.59922.5990.0000.0000.0000.000
5A9GLU-1-0.816-0.8966.32121.12621.1260.0000.0000.0000.000
6A10LYS10.7700.8627.427-24.699-24.6990.0000.0000.0000.000
7A11ALA00.0150.0109.018-2.365-2.3650.0000.0000.0000.000
8A12ARG10.8140.89310.178-24.603-24.6030.0000.0000.0000.000
9A13ARG10.7770.8768.471-28.081-28.0810.0000.0000.0000.000
10A14VAL00.0090.00213.020-1.286-1.2860.0000.0000.0000.000
11A15ALA00.0290.01614.960-1.262-1.2620.0000.0000.0000.000
12A16GLU-1-0.846-0.91316.52115.81715.8170.0000.0000.0000.000
13A17LYS10.7580.88017.528-15.725-15.7250.0000.0000.0000.000
14A18VAL00.0540.03119.252-0.731-0.7310.0000.0000.0000.000
15A19GLU-1-0.806-0.87320.99912.02712.0270.0000.0000.0000.000
16A20ARG10.7340.84317.483-15.879-15.8790.0000.0000.0000.000
17A21LEU00.0090.01522.580-0.472-0.4720.0000.0000.0000.000
18A22LYS10.8620.92025.274-11.118-11.1180.0000.0000.0000.000
19A23ARG10.7530.85324.430-12.010-12.0100.0000.0000.0000.000
20A24SER0-0.067-0.03728.112-0.224-0.2240.0000.0000.0000.000
21A25GLY0-0.034-0.01729.990-0.247-0.2470.0000.0000.0000.000
22A26THR0-0.079-0.03526.997-0.209-0.2090.0000.0000.0000.000
23A27SER0-0.040-0.05329.6970.0640.0640.0000.0000.0000.000
24A28GLU-1-0.859-0.94727.8269.9219.9210.0000.0000.0000.000
25A29ASP-1-0.909-0.95026.90910.56010.5600.0000.0000.0000.000
26A30GLU-1-0.868-0.89926.78010.26910.2690.0000.0000.0000.000
27A31ILE0-0.044-0.02523.0250.5820.5820.0000.0000.0000.000
28A32ALA00.0180.00922.5280.7030.7030.0000.0000.0000.000
29A33GLU-1-0.882-0.92022.28811.78911.7890.0000.0000.0000.000
30A34GLU-1-0.751-0.83620.05214.78714.7870.0000.0000.0000.000
31A35VAL0-0.008-0.01017.3200.9020.9020.0000.0000.0000.000
32A36ALA00.0100.00717.4250.9930.9930.0000.0000.0000.000
33A37ARG10.7640.84817.020-14.817-14.8170.0000.0000.0000.000
34A38GLU-1-0.819-0.92514.43918.75318.7530.0000.0000.0000.000
35A39ILE00.0130.00813.5211.6461.6460.0000.0000.0000.000
36A40SER0-0.006-0.01113.9160.8850.8850.0000.0000.0000.000
37A41GLU-1-0.865-0.91712.89919.66519.6650.0000.0000.0000.000
38A42VAL0-0.0020.0088.5121.0921.0920.0000.0000.0000.000
39A43ILE0-0.001-0.00410.2521.6001.6000.0000.0000.0000.000
40A44ARG10.7830.86312.266-14.986-14.9860.0000.0000.0000.000
41A45THR00.0190.0008.8670.2510.2510.0000.0000.0000.000
42A46LEU0-0.0060.0025.1871.6511.6510.0000.0000.0000.000
43A47LYS10.9020.9588.707-16.718-16.7180.0000.0000.0000.000
44A48GLU-1-0.967-0.98712.04918.28718.2870.0000.0000.0000.000
45A49SER0-0.088-0.0498.122-0.023-0.0230.0000.0000.0000.000
46A50GLY0-0.042-0.0179.7071.8891.8890.0000.0000.0000.000
47A51SER0-0.066-0.0357.4232.2032.2030.0000.0000.0000.000
48A52SER0-0.046-0.0469.394-1.548-1.5480.0000.0000.0000.000
49A53TYR00.0760.01510.6421.2551.2550.0000.0000.0000.000
50A54GLU-1-0.829-0.89011.61021.96121.9610.0000.0000.0000.000
51A55VAL0-0.027-0.0055.5980.6480.6480.0000.0000.0000.000
52A56ILE00.0020.0048.1501.2401.2400.0000.0000.0000.000
53A57CYS0-0.074-0.0349.9390.3590.3590.0000.0000.0000.000
54A58GLH0-0.024-0.0419.312-1.397-1.3970.0000.0000.0000.000
55A60VAL00.0350.0048.202-1.219-1.2190.0000.0000.0000.000
56A61ALA0-0.0050.00911.713-1.258-1.2580.0000.0000.0000.000
57A62ARG10.8690.9307.415-29.518-29.5180.0000.0000.0000.000
58A63ILE0-0.022-0.0209.326-1.146-1.1460.0000.0000.0000.000
59A64VAL00.0280.00812.363-1.230-1.2300.0000.0000.0000.000
60A65ALA0-0.0030.01114.208-1.120-1.1200.0000.0000.0000.000
61A66GLU-1-0.750-0.88412.82817.40217.4020.0000.0000.0000.000
62A67ILE0-0.0170.00315.676-0.934-0.9340.0000.0000.0000.000
63A68VAL00.0180.00718.240-0.852-0.8520.0000.0000.0000.000
64A69GLU-1-0.824-0.89517.69015.28215.2820.0000.0000.0000.000
65A70ALA0-0.041-0.02319.243-0.628-0.6280.0000.0000.0000.000
66A71LEU00.0010.02321.027-0.636-0.6360.0000.0000.0000.000
67A72LYS10.8320.90623.564-11.425-11.4250.0000.0000.0000.000
68A73ARG10.8160.90017.493-15.618-15.6180.0000.0000.0000.000
69A74SER0-0.072-0.04524.886-0.383-0.3830.0000.0000.0000.000
70A75GLY0-0.045-0.01927.134-0.337-0.3370.0000.0000.0000.000
71A76THR0-0.059-0.02726.879-0.306-0.3060.0000.0000.0000.000
72A77SER00.0050.00429.1030.0910.0910.0000.0000.0000.000
73A78GLU-1-0.863-0.95829.4909.8049.8040.0000.0000.0000.000
74A79ASP-1-0.893-0.93829.3569.3379.3370.0000.0000.0000.000
75A80GLU-1-0.728-0.84227.75610.64510.6450.0000.0000.0000.000
76A81ILE0-0.052-0.03724.1170.4830.4830.0000.0000.0000.000
77A82ALA00.0020.00125.3350.4770.4770.0000.0000.0000.000
78A83GLU-1-0.752-0.85226.85010.13910.1390.0000.0000.0000.000
79A84ILE0-0.044-0.01222.2630.3770.3770.0000.0000.0000.000
80A85VAL0-0.036-0.03120.8870.5440.5440.0000.0000.0000.000
81A86ALA0-0.021-0.00122.5250.3910.3910.0000.0000.0000.000
82A87ARG10.8480.89623.920-11.573-11.5730.0000.0000.0000.000
83A88VAL0-0.0110.00018.2540.3330.3330.0000.0000.0000.000
84A89ILE00.002-0.00119.3320.4900.4900.0000.0000.0000.000
85A90SER0-0.003-0.02821.4890.2580.2580.0000.0000.0000.000
86A91GLU-1-0.747-0.83520.07912.45212.4520.0000.0000.0000.000
87A92VAL0-0.0210.00916.6610.5720.5720.0000.0000.0000.000
88A93ILE0-0.021-0.01218.9230.1940.1940.0000.0000.0000.000
89A94ARG10.7970.86421.981-11.675-11.6750.0000.0000.0000.000
90A95THR0-0.0040.00116.734-0.067-0.0670.0000.0000.0000.000
91A96LEU00.0060.00115.5640.3150.3150.0000.0000.0000.000
92A97LYS10.8890.95719.109-12.146-12.1460.0000.0000.0000.000
93A98GLU-1-0.850-0.88320.56213.74613.7460.0000.0000.0000.000
94A99SER0-0.070-0.04317.6240.2100.2100.0000.0000.0000.000
95A100GLY00.006-0.01219.7240.3580.3580.0000.0000.0000.000
96A101SER0-0.037-0.00518.468-0.118-0.1180.0000.0000.0000.000
97A102SER0-0.032-0.03721.192-0.497-0.4970.0000.0000.0000.000
98A103TYR00.042-0.01822.6380.3950.3950.0000.0000.0000.000
99A104GLU-1-0.838-0.89322.46813.19513.1950.0000.0000.0000.000
100A105VAL00.0000.00417.5190.3640.3640.0000.0000.0000.000
101A106ILE0-0.016-0.00519.0660.6030.6030.0000.0000.0000.000
102A107CYS0-0.065-0.02520.4500.5410.5410.0000.0000.0000.000
103A108GLU-1-0.812-0.88318.33514.59914.5990.0000.0000.0000.000
104A110VAL00.0250.00617.3980.3460.3460.0000.0000.0000.000
105A111ALA00.0070.01219.988-0.082-0.0820.0000.0000.0000.000
106A112ARG10.7850.88614.586-18.176-18.1760.0000.0000.0000.000
107A113ILE0-0.018-0.01214.9280.2650.2650.0000.0000.0000.000
108A114VAL00.007-0.00717.073-0.188-0.1880.0000.0000.0000.000
109A115ALA0-0.0030.01119.451-0.471-0.4710.0000.0000.0000.000
110A116GLU-1-0.776-0.86512.93321.64821.6480.0000.0000.0000.000
111A117ILE0-0.0120.00317.716-0.071-0.0710.0000.0000.0000.000
112A118VAL00.0220.01120.203-0.446-0.4460.0000.0000.0000.000
113A119GLU-1-0.809-0.90318.24215.53115.5310.0000.0000.0000.000
114A120ALA0-0.019-0.01118.164-0.092-0.0920.0000.0000.0000.000
115A121LEU0-0.0070.00719.918-0.340-0.3400.0000.0000.0000.000
116A122LYS10.8040.87323.399-11.043-11.0430.0000.0000.0000.000
117A123ARG10.7840.88716.441-16.551-16.5510.0000.0000.0000.000
118A124SER0-0.038-0.02822.190-0.175-0.1750.0000.0000.0000.000
119A125GLY0-0.0380.00924.180-0.378-0.3780.0000.0000.0000.000
120A126THR0-0.046-0.05726.818-0.068-0.0680.0000.0000.0000.000
121A127SER0-0.055-0.06029.153-0.160-0.1600.0000.0000.0000.000
122A128GLU-1-0.895-0.96431.0878.9618.9610.0000.0000.0000.000
123A129ASP-1-0.768-0.86732.3548.8648.8640.0000.0000.0000.000
124A130GLU-1-0.807-0.85328.29810.68210.6820.0000.0000.0000.000
125A131ILE0-0.009-0.00826.9470.3560.3560.0000.0000.0000.000
126A132ALA0-0.010-0.00729.0530.2000.2000.0000.0000.0000.000
127A133GLU-1-0.795-0.86431.6338.7148.7140.0000.0000.0000.000
128A134ILE00.0340.02425.4200.1590.1590.0000.0000.0000.000
129A135VAL0-0.029-0.01626.0000.2610.2610.0000.0000.0000.000
130A136ALA0-0.020-0.00327.8630.0660.0660.0000.0000.0000.000
131A137ARG10.7730.83429.084-10.115-10.1150.0000.0000.0000.000
132A138VAL00.0330.01923.6160.0400.0400.0000.0000.0000.000
133A139ILE0-0.011-0.01826.8550.0500.0500.0000.0000.0000.000
134A140SER0-0.025-0.05928.445-0.228-0.2280.0000.0000.0000.000
135A141GLU-1-0.779-0.83625.85810.51210.5120.0000.0000.0000.000
136A142VAL0-0.0200.01024.690-0.044-0.0440.0000.0000.0000.000
137A143ILE0-0.025-0.01327.370-0.132-0.1320.0000.0000.0000.000
138A144ARG10.8490.91830.997-9.074-9.0740.0000.0000.0000.000
139A145THR00.035-0.00425.688-0.088-0.0880.0000.0000.0000.000
140A146LEU0-0.022-0.01026.4020.0470.0470.0000.0000.0000.000
141A147LYS10.7890.90129.438-8.432-8.4320.0000.0000.0000.000
142A148GLU-1-0.880-0.91528.47110.34010.3400.0000.0000.0000.000
143A149SER0-0.086-0.04927.9780.0400.0400.0000.0000.0000.000
144A150GLY00.001-0.00129.8860.0500.0500.0000.0000.0000.000
145A151SER0-0.055-0.02030.0000.0180.0180.0000.0000.0000.000
146A152SER0-0.049-0.04831.943-0.163-0.1630.0000.0000.0000.000
147A153TYR00.0450.00233.5900.2170.2170.0000.0000.0000.000
148A154GLU-1-0.868-0.92434.8088.5538.5530.0000.0000.0000.000
149A155VAL00.0680.04128.7610.1490.1490.0000.0000.0000.000
150A156ILE0-0.0170.00229.8230.3020.3020.0000.0000.0000.000
151A157LYS10.7880.88830.889-8.223-8.2230.0000.0000.0000.000
152A158GLU-1-0.931-0.96729.24310.15610.1560.0000.0000.0000.000
153A160VAL00.0130.00126.8760.2700.2700.0000.0000.0000.000
154A161GLN0-0.088-0.05028.735-0.108-0.1080.0000.0000.0000.000
155A162ARG10.8050.87222.083-12.878-12.8780.0000.0000.0000.000
156A163ILE00.011-0.00623.3600.3960.3960.0000.0000.0000.000
157A164VAL0-0.015-0.01525.0800.1170.1170.0000.0000.0000.000
158A165GLU-1-0.824-0.88526.42211.06611.0660.0000.0000.0000.000
159A166GLU-1-0.732-0.85619.67615.09015.0900.0000.0000.0000.000
160A167ILE00.0000.01723.3900.2290.2290.0000.0000.0000.000
161A168VAL00.0040.00025.287-0.134-0.1340.0000.0000.0000.000
162A169GLU-1-0.837-0.91524.18510.98810.9880.0000.0000.0000.000
163A170ALA00.0120.01822.0050.0970.0970.0000.0000.0000.000
164A171LEU00.0050.01223.388-0.080-0.0800.0000.0000.0000.000
165A172LYS10.8510.90926.752-10.645-10.6450.0000.0000.0000.000
166A173ARG10.7350.84719.941-14.708-14.7080.0000.0000.0000.000
167A174SER0-0.069-0.03024.1770.2100.2100.0000.0000.0000.000
168A175GLY0-0.048-0.01825.591-0.296-0.2960.0000.0000.0000.000
169A176THR0-0.079-0.03628.145-0.364-0.3640.0000.0000.0000.000
170A177SER0-0.008-0.00130.663-0.189-0.1890.0000.0000.0000.000
171A178GLU-1-0.826-0.93134.0069.0839.0830.0000.0000.0000.000
172A179ASP-1-0.848-0.92335.5917.7627.7620.0000.0000.0000.000
173A180GLU-1-0.852-0.90031.2949.6579.6570.0000.0000.0000.000
174A181ILE00.0190.00230.4760.1510.1510.0000.0000.0000.000
175A182ASN0-0.085-0.06532.870-0.011-0.0110.0000.0000.0000.000
176A183GLU-1-0.833-0.86836.0097.7237.7230.0000.0000.0000.000
177A184ILE00.0710.04329.9460.0010.0010.0000.0000.0000.000
178A185VAL0-0.031-0.01932.1220.0270.0270.0000.0000.0000.000
179A186ARG10.6790.80634.088-7.944-7.9440.0000.0000.0000.000
180A187ARG10.7480.82934.947-8.773-8.7730.0000.0000.0000.000
181A188VAL00.0500.02330.495-0.073-0.0730.0000.0000.0000.000
182A189LYS10.9290.95133.707-8.903-8.9030.0000.0000.0000.000
183A190SER0-0.043-0.01635.879-0.165-0.1650.0000.0000.0000.000
184A191GLU-1-0.756-0.81932.9868.6298.6290.0000.0000.0000.000
185A192VAL00.0020.01132.479-0.071-0.0710.0000.0000.0000.000
186A193GLU-1-0.814-0.91135.1588.0858.0850.0000.0000.0000.000
187A194ARG10.8380.93238.543-7.862-7.8620.0000.0000.0000.000
188A195THR00.0540.03133.628-0.237-0.2370.0000.0000.0000.000
189A196LEU0-0.027-0.00535.280-0.040-0.0400.0000.0000.0000.000
190A197LYS10.8550.91337.772-7.465-7.4650.0000.0000.0000.000
191A198GLU-1-0.839-0.91038.6537.7867.7860.0000.0000.0000.000
192A199SER0-0.028-0.01836.543-0.005-0.0050.0000.0000.0000.000
193A200GLY00.0100.01838.7620.0650.0650.0000.0000.0000.000
194A201SER0-0.017-0.01140.5250.0720.0720.0000.0000.0000.000