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: VRM21

Calculation Name: 4FBD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4FBD

Chain ID: A

ChEMBL ID:

UniProt ID:

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 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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2137619.709568
FMO2-HF: Nuclear repulsion 2058220.024456
FMO2-HF: Total energy -79399.685111
FMO2-MP2: Total energy -79631.211125


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:14:ARG)


Summations of interaction energy for fragment #1(A:14:ARG)
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.
-72.099-76.39211.4521.72-8.88-0.079
Interaction energy analysis for fragmet #1(A:14:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.867 / q_NPA : 0.945
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].
3A16ALA00.0330.0072.6356.422-0.560-0.2137.939-0.744-0.009
4A17PRO00.027-0.0125.5140.3710.3710.0000.0000.0000.000
5A18ALA00.0140.0158.3401.0541.0540.0000.0000.0000.000
6A19ASP-1-0.911-0.9476.525-26.591-26.5910.0000.0000.0000.000
7A20LEU0-0.049-0.0186.762-0.948-0.9480.0000.0000.0000.000
8A21PRO00.0310.01510.3060.9340.9340.0000.0000.0000.000
9A22LEU0-0.015-0.0167.852-0.255-0.2550.0000.0000.0000.000
10A23GLY00.0760.02711.8631.2811.2810.0000.0000.0000.000
11A24LEU0-0.053-0.03514.506-1.000-1.0000.0000.0000.0000.000
12A25ASP-1-0.757-0.87317.219-12.989-12.9890.0000.0000.0000.000
13A26PRO0-0.069-0.02819.5660.0570.0570.0000.0000.0000.000
14A27PHE0-0.048-0.01522.9830.4290.4290.0000.0000.0000.000
15A28CYS00.0040.01420.3820.2340.2340.0000.0000.0000.000
16A29TYR0-0.097-0.07420.0730.5450.5450.0000.0000.0000.000
17A40SER00.022-0.01020.7060.1330.1330.0000.0000.0000.000
18A41ARG10.8990.95723.54511.52311.5230.0000.0000.0000.000
19A42ILE00.0800.06020.929-0.022-0.0220.0000.0000.0000.000
20A43SER0-0.050-0.04924.7630.5570.5570.0000.0000.0000.000
21A44GLY00.0070.00427.260-0.199-0.1990.0000.0000.0000.000
22A45VAL0-0.0070.02423.5630.0530.0530.0000.0000.0000.000
23A46THR0-0.032-0.04125.775-0.049-0.0490.0000.0000.0000.000
24A47LYS10.9150.94222.55911.53211.5320.0000.0000.0000.000
25A48GLU-1-0.830-0.89521.166-12.232-12.2320.0000.0000.0000.000
26A49GLU-1-0.785-0.87921.243-12.110-12.1100.0000.0000.0000.000
27A50PHE0-0.019-0.01217.579-0.622-0.6220.0000.0000.0000.000
28A51LEU00.003-0.00115.101-0.790-0.7900.0000.0000.0000.000
29A52GLU-1-0.934-0.96116.488-14.625-14.6250.0000.0000.0000.000
30A53LYS10.9400.94217.34311.76611.7660.0000.0000.0000.000
31A54VAL0-0.035-0.01112.837-0.783-0.7830.0000.0000.0000.000
32A55ASN0-0.033-0.02512.664-2.650-2.6500.0000.0000.0000.000
33A56GLU-1-0.784-0.82713.428-16.448-16.4480.0000.0000.0000.000
34A57LEU0-0.023-0.02213.743-0.321-0.3210.0000.0000.0000.000
35A58VAL0-0.038-0.0268.000-0.888-0.8880.0000.0000.0000.000
36A59THR0-0.075-0.0529.498-1.130-1.1300.0000.0000.0000.000
37A60ARG10.7690.85711.44916.90116.9010.0000.0000.0000.000
38A61ASP-1-0.900-0.94211.668-22.449-22.4490.0000.0000.0000.000
39A62ALA00.002-0.0067.690-1.913-1.9130.0000.0000.0000.000
40A63GLY0-0.033-0.0097.468-2.739-2.7390.0000.0000.0000.000
41A64ILE0-0.061-0.0257.821-1.032-1.0320.0000.0000.0000.000
42A65GLU-1-0.802-0.8844.568-39.520-39.421-0.001-0.009-0.0890.000
43A66PHE00.0210.0052.3061.1762.6251.831-1.188-2.092-0.003
44A67PHE0-0.064-0.0381.829-41.325-41.1079.814-4.865-5.167-0.066
45A68GLN0-0.023-0.0373.8237.0357.2480.000-0.013-0.2000.000
46A69GLY00.0240.0156.0560.6910.6910.0000.0000.0000.000
47A70TYR0-0.002-0.0179.6211.2211.2210.0000.0000.0000.000
48A71ALA00.0300.03111.7531.0581.0580.0000.0000.0000.000
49A72PRO0-0.005-0.0049.779-1.448-1.4480.0000.0000.0000.000
50A73PHE00.0350.0209.764-1.697-1.6970.0000.0000.0000.000
51A74CYS0-0.0270.00911.0200.2950.2950.0000.0000.0000.000
52A75ARG10.9140.9633.52541.42742.1370.021-0.144-0.588-0.001
53A76HIS10.8150.9077.01234.35634.3560.0000.0000.0000.000
54A77LEU00.0340.0336.518-6.189-6.1890.0000.0000.0000.000
55A78TYR0-0.064-0.0478.3532.5252.5250.0000.0000.0000.000
56A79ILE00.0570.03711.050-0.733-0.7330.0000.0000.0000.000
57A80PRO00.0540.00913.6450.7870.7870.0000.0000.0000.000
58A81ASN0-0.026-0.01417.256-0.047-0.0470.0000.0000.0000.000
59A82PHE0-0.043-0.02517.2630.8970.8970.0000.0000.0000.000
60A83VAL0-0.011-0.00621.3160.4930.4930.0000.0000.0000.000
61A84GLY00.0040.01023.6730.4560.4560.0000.0000.0000.000
62A85ALA00.0040.00822.3690.3850.3850.0000.0000.0000.000
63A86LEU00.0410.02423.975-0.284-0.2840.0000.0000.0000.000
64A87PRO0-0.022-0.00322.730-0.422-0.4220.0000.0000.0000.000
65A88GLY00.010-0.00223.5400.4740.4740.0000.0000.0000.000
66A89SER0-0.068-0.04323.5690.2520.2520.0000.0000.0000.000
67A90LEU00.0440.03326.343-0.174-0.1740.0000.0000.0000.000
68A91PRO0-0.001-0.00426.799-0.104-0.1040.0000.0000.0000.000
69A92ILE0-0.035-0.01128.1290.3390.3390.0000.0000.0000.000
70A93THR0-0.032-0.02430.987-0.116-0.1160.0000.0000.0000.000
71A94ALA00.0300.00333.7050.1250.1250.0000.0000.0000.000
72A95ASP-1-0.899-0.94136.917-8.131-8.1310.0000.0000.0000.000
73A96ASN0-0.018-0.02632.4210.1360.1360.0000.0000.0000.000
74A97GLU-1-0.850-0.91934.653-8.979-8.9790.0000.0000.0000.000
75A98HIS00.002-0.00236.530-0.086-0.0860.0000.0000.0000.000
76A99LEU0-0.024-0.00937.5110.1930.1930.0000.0000.0000.000
77A100LEU0-0.043-0.00732.906-0.061-0.0610.0000.0000.0000.000
78A101ARG10.8270.92136.6428.0428.0420.0000.0000.0000.000
79A102SER00.0350.00536.347-0.286-0.2860.0000.0000.0000.000
80A103GLY0-0.006-0.00837.0780.3080.3080.0000.0000.0000.000
81A104TYR0-0.0020.00136.820-0.295-0.2950.0000.0000.0000.000
82A105ILE00.0300.01834.1320.1570.1570.0000.0000.0000.000
83A106ALA00.0350.02534.435-0.177-0.1770.0000.0000.0000.000
84A107ARG10.7970.86426.56411.00311.0030.0000.0000.0000.000
85A108ARG10.9770.98928.60110.30010.3000.0000.0000.0000.000
86A109PRO0-0.0010.00034.5670.0390.0390.0000.0000.0000.000
87A110ASN0-0.013-0.01733.7830.1420.1420.0000.0000.0000.000
88A111GLU-1-0.809-0.85731.064-10.329-10.3290.0000.0000.0000.000
89A112LEU00.0530.01835.6710.2550.2550.0000.0000.0000.000
90A113PRO0-0.0190.00535.551-0.300-0.3000.0000.0000.0000.000
91A114VAL0-0.008-0.02231.9840.1010.1010.0000.0000.0000.000
92A115LEU0-0.034-0.00334.896-0.050-0.0500.0000.0000.0000.000
93A116THR0-0.050-0.01931.044-0.447-0.4470.0000.0000.0000.000
94A117ARG10.8510.90730.22610.04510.0450.0000.0000.0000.000
95A118TRP0-0.026-0.02531.619-0.404-0.4040.0000.0000.0000.000
96A119PHE00.0470.01030.5030.3100.3100.0000.0000.0000.000
97A120PRO0-0.0060.00334.130-0.194-0.1940.0000.0000.0000.000
98A121MET00.0550.02934.319-0.259-0.2590.0000.0000.0000.000
99A122SER0-0.099-0.08336.745-0.065-0.0650.0000.0000.0000.000
100A123TYR00.0570.03233.811-0.009-0.0090.0000.0000.0000.000
101A124ALA00.022-0.00232.487-0.119-0.1190.0000.0000.0000.000
102A125LYS10.7740.87333.3817.6707.6700.0000.0000.0000.000
103A126ASP-1-0.848-0.89435.670-8.075-8.0750.0000.0000.0000.000
104A127ALA0-0.031-0.01732.8290.0070.0070.0000.0000.0000.000
105A128LEU0-0.065-0.02227.952-0.391-0.3910.0000.0000.0000.000
106A129MET00.0190.00628.2250.3380.3380.0000.0000.0000.000
107A130PRO0-0.031-0.02225.485-0.359-0.3590.0000.0000.0000.000
108A131ALA0-0.0210.01121.071-0.052-0.0520.0000.0000.0000.000
109A132ALA00.0150.00819.283-0.064-0.0640.0000.0000.0000.000
110A133PHE0-0.046-0.03115.079-0.566-0.5660.0000.0000.0000.000
111A134LEU00.0090.00015.8200.9690.9690.0000.0000.0000.000
112A135ASP-1-0.749-0.84111.239-26.860-26.8600.0000.0000.0000.000
113A136LEU00.0120.00011.5301.6961.6960.0000.0000.0000.000
114A137ILE0-0.014-0.01611.288-2.462-2.4620.0000.0000.0000.000
115A138LEU00.0220.0047.7921.3861.3860.0000.0000.0000.000
116A139TYR00.011-0.00711.567-1.356-1.3560.0000.0000.0000.000
117A140SER0-0.031-0.03411.836-0.009-0.0090.0000.0000.0000.000
118A141ARG10.8880.93612.72118.09518.0950.0000.0000.0000.000
119A142GLU-1-0.822-0.89214.586-17.319-17.3190.0000.0000.0000.000
120A143GLN0-0.049-0.02516.0760.9670.9670.0000.0000.0000.000
121A144ILE00.0440.03115.3310.7540.7540.0000.0000.0000.000
122A145ALA00.0100.02318.9360.7290.7290.0000.0000.0000.000
123A146LYS10.8760.92719.51915.48115.4810.0000.0000.0000.000
124A147GLU-1-0.861-0.92919.464-14.824-14.8240.0000.0000.0000.000
125A148THR0-0.007-0.01422.3700.5020.5020.0000.0000.0000.000
126A149ALA0-0.041-0.01424.7900.4600.4600.0000.0000.0000.000
127A150ALA0-0.005-0.01126.1370.4420.4420.0000.0000.0000.000
128A151GLU-1-0.932-0.95327.000-10.406-10.4060.0000.0000.0000.000
129A152SER0-0.085-0.05228.8760.3890.3890.0000.0000.0000.000
130A153ASN0-0.104-0.05130.8990.2710.2710.0000.0000.0000.000
131A154THR00.0070.01629.7510.3110.3110.0000.0000.0000.000
132A155ALA0-0.004-0.00129.750-0.244-0.2440.0000.0000.0000.000
133A156VAL00.001-0.00723.407-0.086-0.0860.0000.0000.0000.000
134A157VAL0-0.015-0.00325.8260.1580.1580.0000.0000.0000.000
135A158ILE0-0.016-0.01619.442-0.342-0.3420.0000.0000.0000.000
136A159ASP-1-0.786-0.88421.373-12.464-12.4640.0000.0000.0000.000
137A160PRO0-0.045-0.03218.422-0.619-0.6190.0000.0000.0000.000
138A161ASN0-0.069-0.05117.261-0.738-0.7380.0000.0000.0000.000
139A162ALA00.0170.03117.634-0.413-0.4130.0000.0000.0000.000
140A163PRO00.0260.00713.470-0.493-0.4930.0000.0000.0000.000
141A164ALA00.0030.0159.9590.1570.1570.0000.0000.0000.000
142A165TRP0-0.072-0.0497.070-1.585-1.5850.0000.0000.0000.000
143A166SER00.0080.00310.8790.7880.7880.0000.0000.0000.000
144A167ILE0-0.012-0.01613.291-0.438-0.4380.0000.0000.0000.000
145A168ILE00.0210.01114.5081.0371.0370.0000.0000.0000.000
146A169ALA00.0170.00916.2191.0091.0090.0000.0000.0000.000
147A170VAL00.0220.01916.086-1.247-1.2470.0000.0000.0000.000
148A171LYS10.8520.92716.25517.50817.5080.0000.0000.0000.000
149A172ALA00.0450.03817.151-0.861-0.8610.0000.0000.0000.000
150A173GLN0-0.078-0.05314.7600.9440.9440.0000.0000.0000.000
151A174ASN00.0720.03118.802-0.297-0.2970.0000.0000.0000.000
152A175GLU-1-0.780-0.85816.429-15.296-15.2960.0000.0000.0000.000
153A176LYS10.8480.9259.20929.46729.4670.0000.0000.0000.000
154A177TYR00.010-0.01211.127-1.493-1.4930.0000.0000.0000.000
155A178SER0-0.006-0.00411.5230.7250.7250.0000.0000.0000.000
156A179LEU0-0.024-0.00113.3330.3410.3410.0000.0000.0000.000
157A180PRO00.0070.02617.039-0.139-0.1390.0000.0000.0000.000
158A181MET00.0410.02218.3940.9700.9700.0000.0000.0000.000
159A182ALA00.0520.04121.0930.1360.1360.0000.0000.0000.000
160A183PRO00.0470.00924.639-0.008-0.0080.0000.0000.0000.000
161A184ILE00.0530.01925.923-0.065-0.0650.0000.0000.0000.000
162A185THR0-0.009-0.00224.1560.3500.3500.0000.0000.0000.000
163A186MET0-0.020-0.00820.997-0.116-0.1160.0000.0000.0000.000
164A187LEU0-0.0110.00124.7250.0600.0600.0000.0000.0000.000
165A188ARG10.8580.93928.3399.9779.9770.0000.0000.0000.000
166A189ASN0-0.008-0.01322.9370.3790.3790.0000.0000.0000.000
167A190THR0-0.080-0.05226.477-0.046-0.0460.0000.0000.0000.000
168A191LEU00.0060.00828.2650.1970.1970.0000.0000.0000.000
169A192ILE00.0310.00730.007-0.025-0.0250.0000.0000.0000.000
170A193GLU-1-0.988-0.98031.919-8.625-8.6250.0000.0000.0000.000
171A194GLU-1-0.802-0.88832.738-9.014-9.0140.0000.0000.0000.000
172A195GLY0-0.004-0.01329.435-0.221-0.2210.0000.0000.0000.000
173A196GLY00.014-0.00527.1110.1110.1110.0000.0000.0000.000
174A197SER0-0.059-0.01922.4710.2020.2020.0000.0000.0000.000
175A198GLY00.0090.01325.5790.0080.0080.0000.0000.0000.000
176A199VAL0-0.058-0.01722.4580.2000.2000.0000.0000.0000.000
177A200ALA00.0140.00125.7720.1920.1920.0000.0000.0000.000
178A201LEU0-0.006-0.00924.370-0.494-0.4940.0000.0000.0000.000
179A202ASP-1-0.799-0.89518.666-15.189-15.1890.0000.0000.0000.000
180A203ARG10.9750.95922.28310.64410.6440.0000.0000.0000.000
181A204GLU-1-0.822-0.88419.866-12.619-12.6190.0000.0000.0000.000
182A205ALA00.0410.02118.006-0.048-0.0480.0000.0000.0000.000
183A206TYR0-0.022-0.01319.5210.1510.1510.0000.0000.0000.000
184A207LYS10.8190.88823.14112.66312.6630.0000.0000.0000.000
185A208ALA00.0170.01618.6660.2480.2480.0000.0000.0000.000
186A209SER0-0.011-0.02820.7780.2310.2310.0000.0000.0000.000
187A210VAL00.006-0.00922.0470.3420.3420.0000.0000.0000.000
188A211ALA0-0.050-0.02622.5190.4340.4340.0000.0000.0000.000
189A212TYR0-0.018-0.03019.8830.3490.3490.0000.0000.0000.000
190A213TRP0-0.032-0.03222.1540.5410.5410.0000.0000.0000.000
191A214LYS10.9290.97326.05311.18911.1890.0000.0000.0000.000
192A215THR00.0050.00625.2310.2130.2130.0000.0000.0000.000
193A216HIS10.8340.92522.30513.05013.0500.0000.0000.0000.000
194A217ALA00.0170.01826.9290.1160.1160.0000.0000.0000.000
195A218ILE00.0160.00326.333-0.237-0.2370.0000.0000.0000.000
196A219VAL00.0190.01828.5310.3550.3550.0000.0000.0000.000
197A220MET0-0.047-0.02730.791-0.095-0.0950.0000.0000.0000.000
198A221ASP-1-0.893-0.94333.577-8.130-8.1300.0000.0000.0000.000
199A222LYS10.8270.90936.7627.8777.8770.0000.0000.0000.000
200A223GLU-1-0.740-0.84039.055-7.975-7.9750.0000.0000.0000.000
201A224SER0-0.006-0.00741.4110.0600.0600.0000.0000.0000.000
202A225SER0-0.007-0.00640.1480.0110.0110.0000.0000.0000.000
203A226LEU0-0.0040.01041.654-0.017-0.0170.0000.0000.0000.000
204A227GLU-1-0.942-0.96343.406-7.314-7.3140.0000.0000.0000.000