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: YY3Q2

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 OptHSide
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 -2136346.289372
FMO2-HF: Nuclear repulsion 2056947.207433
FMO2-HF: Total energy -79399.08194
FMO2-MP2: Total energy -79630.593566


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.
-62.818-67.0149.863.286-8.953-0.065
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 : 0.866 / q_NPA : 0.940
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].
3A16ALA00.0300.0102.6339.8190.9710.1319.284-0.567-0.004
4A17PRO00.0500.0175.6920.5680.5680.0000.0000.0000.000
5A18ALA00.0110.0138.4980.9580.9580.0000.0000.0000.000
6A19ASP-1-0.984-0.9936.500-24.184-24.1840.0000.0000.0000.000
7A20LEU0-0.065-0.0276.916-2.077-2.0770.0000.0000.0000.000
8A21PRO00.0270.01510.0650.9260.9260.0000.0000.0000.000
9A22LEU0-0.027-0.0258.027-0.313-0.3130.0000.0000.0000.000
10A23GLY00.0810.02412.0761.2181.2180.0000.0000.0000.000
11A24LEU0-0.062-0.04214.826-0.933-0.9330.0000.0000.0000.000
12A25ASP-1-0.801-0.89417.431-13.099-13.0990.0000.0000.0000.000
13A26PRO0-0.033-0.03419.6210.0080.0080.0000.0000.0000.000
14A27PHE0-0.084-0.02622.7960.4630.4630.0000.0000.0000.000
15A28CYS00.0060.01320.6020.0250.0250.0000.0000.0000.000
16A29TYR0-0.057-0.03919.9980.8750.8750.0000.0000.0000.000
17A40SER00.0200.00921.247-0.056-0.0560.0000.0000.0000.000
18A41ARG10.9691.00323.10311.04211.0420.0000.0000.0000.000
19A42ILE00.0360.03220.957-0.039-0.0390.0000.0000.0000.000
20A43SER0-0.023-0.02624.7790.4560.4560.0000.0000.0000.000
21A44GLY0-0.004-0.00627.244-0.186-0.1860.0000.0000.0000.000
22A45VAL00.0290.02923.4460.0150.0150.0000.0000.0000.000
23A46THR0-0.029-0.02925.905-0.151-0.1510.0000.0000.0000.000
24A47LYS10.9510.95722.48211.56911.5690.0000.0000.0000.000
25A48GLU-1-0.840-0.89921.239-12.021-12.0210.0000.0000.0000.000
26A49GLU-1-0.835-0.90521.362-12.161-12.1610.0000.0000.0000.000
27A50PHE0-0.029-0.01317.244-0.621-0.6210.0000.0000.0000.000
28A51LEU00.0140.00615.296-0.782-0.7820.0000.0000.0000.000
29A52GLU-1-0.939-0.96016.539-14.702-14.7020.0000.0000.0000.000
30A53LYS10.9520.94917.63211.96611.9660.0000.0000.0000.000
31A54VAL0-0.050-0.01112.779-0.846-0.8460.0000.0000.0000.000
32A55ASN0-0.016-0.02112.713-2.568-2.5680.0000.0000.0000.000
33A56GLU-1-0.783-0.83813.460-16.265-16.2650.0000.0000.0000.000
34A57LEU0-0.033-0.03814.152-0.401-0.4010.0000.0000.0000.000
35A58VAL0-0.068-0.0328.254-1.110-1.1100.0000.0000.0000.000
36A59THR0-0.055-0.03310.066-0.870-0.8700.0000.0000.0000.000
37A60ARG10.7660.86611.65916.61916.6190.0000.0000.0000.000
38A61ASP-1-0.892-0.94012.097-22.722-22.7220.0000.0000.0000.000
39A62ALA0-0.004-0.0128.626-1.904-1.9040.0000.0000.0000.000
40A63GLY0-0.034-0.0127.820-2.890-2.8900.0000.0000.0000.000
41A64ILE0-0.051-0.0127.619-1.290-1.2900.0000.0000.0000.000
42A65GLU-1-0.804-0.8914.251-41.018-40.891-0.001-0.021-0.1050.000
43A66PHE00.0200.0062.1841.4682.9431.799-1.176-2.099-0.003
44A67PHE0-0.065-0.0461.878-38.508-37.2507.827-4.392-4.693-0.058
45A68GLN0-0.077-0.0653.5847.7838.2880.012-0.104-0.4140.001
46A69GLY00.0290.0215.5280.9881.019-0.001-0.001-0.0290.000
47A70TYR00.011-0.0039.0921.3921.3920.0000.0000.0000.000
48A71ALA00.0210.04211.1190.6230.6230.0000.0000.0000.000
49A72PRO00.001-0.0179.941-1.889-1.8890.0000.0000.0000.000
50A73PHE00.0290.01110.152-0.990-0.9900.0000.0000.0000.000
51A74CYS0-0.0220.01710.9530.5250.5250.0000.0000.0000.000
52A75ARG10.9220.9603.34143.29944.5550.093-0.304-1.046-0.001
53A76HIS10.8230.9076.82234.28434.2840.0000.0000.0000.000
54A77LEU00.0470.0456.505-5.987-5.9870.0000.0000.0000.000
55A78TYR0-0.045-0.0378.3922.3322.3320.0000.0000.0000.000
56A79ILE00.0540.03511.038-1.046-1.0460.0000.0000.0000.000
57A80PRO00.0530.00513.6680.8120.8120.0000.0000.0000.000
58A81ASN0-0.041-0.02717.212-0.004-0.0040.0000.0000.0000.000
59A82PHE0-0.008-0.00717.2450.8130.8130.0000.0000.0000.000
60A83VAL0-0.012-0.00421.2300.5310.5310.0000.0000.0000.000
61A84GLY00.0020.01223.5770.5110.5110.0000.0000.0000.000
62A85ALA0-0.0020.00722.1510.4070.4070.0000.0000.0000.000
63A86LEU00.0410.01823.859-0.257-0.2570.0000.0000.0000.000
64A87PRO0-0.023-0.00322.523-0.376-0.3760.0000.0000.0000.000
65A88GLY0-0.012-0.00823.1210.4490.4490.0000.0000.0000.000
66A89SER0-0.067-0.04423.4940.2510.2510.0000.0000.0000.000
67A90LEU00.0410.03125.913-0.221-0.2210.0000.0000.0000.000
68A91PRO00.0120.00826.677-0.073-0.0730.0000.0000.0000.000
69A92ILE0-0.041-0.01627.9760.3210.3210.0000.0000.0000.000
70A93THR0-0.039-0.03030.864-0.063-0.0630.0000.0000.0000.000
71A94ALA00.0360.00133.1840.1150.1150.0000.0000.0000.000
72A95ASP-1-0.898-0.93936.631-8.090-8.0900.0000.0000.0000.000
73A96ASN0-0.025-0.02932.1670.1690.1690.0000.0000.0000.000
74A97GLU-1-0.901-0.94235.502-8.693-8.6930.0000.0000.0000.000
75A98HIS00.008-0.00136.451-0.099-0.0990.0000.0000.0000.000
76A99LEU0-0.037-0.01837.2790.1770.1770.0000.0000.0000.000
77A100LEU0-0.058-0.01032.585-0.088-0.0880.0000.0000.0000.000
78A101ARG10.8510.93936.2768.0488.0480.0000.0000.0000.000
79A102SER00.027-0.00436.073-0.279-0.2790.0000.0000.0000.000
80A103GLY00.000-0.01636.6830.2990.2990.0000.0000.0000.000
81A104TYR00.0020.00436.502-0.304-0.3040.0000.0000.0000.000
82A105ILE00.0240.01434.1070.1600.1600.0000.0000.0000.000
83A106ALA00.0480.03134.450-0.191-0.1910.0000.0000.0000.000
84A107ARG10.7840.85126.12811.10111.1010.0000.0000.0000.000
85A108ARG10.9640.98428.54510.35110.3510.0000.0000.0000.000
86A109PRO00.0130.00534.2450.0680.0680.0000.0000.0000.000
87A110ASN0-0.008-0.00633.7440.1390.1390.0000.0000.0000.000
88A111GLU-1-0.810-0.85730.813-10.361-10.3610.0000.0000.0000.000
89A112LEU00.0350.01635.3090.2390.2390.0000.0000.0000.000
90A113PRO0-0.014-0.00634.990-0.302-0.3020.0000.0000.0000.000
91A114VAL0-0.013-0.01931.2530.0390.0390.0000.0000.0000.000
92A115LEU0-0.0300.00034.625-0.004-0.0040.0000.0000.0000.000
93A116THR0-0.053-0.02030.729-0.453-0.4530.0000.0000.0000.000
94A117ARG10.8950.93029.48610.25610.2560.0000.0000.0000.000
95A118TRP0-0.055-0.03631.330-0.407-0.4070.0000.0000.0000.000
96A119PHE00.0480.02230.4040.2890.2890.0000.0000.0000.000
97A120PRO00.0180.01033.769-0.242-0.2420.0000.0000.0000.000
98A121MET00.0590.02033.725-0.238-0.2380.0000.0000.0000.000
99A122SER0-0.087-0.05736.445-0.055-0.0550.0000.0000.0000.000
100A123TYR00.0360.02433.373-0.009-0.0090.0000.0000.0000.000
101A124ALA00.0290.00132.175-0.095-0.0950.0000.0000.0000.000
102A125LYS10.7470.86633.3387.7447.7440.0000.0000.0000.000
103A126ASP-1-0.829-0.88935.283-8.108-8.1080.0000.0000.0000.000
104A127ALA0-0.045-0.02732.5130.0180.0180.0000.0000.0000.000
105A128LEU0-0.059-0.02827.626-0.340-0.3400.0000.0000.0000.000
106A129MET00.0280.01727.9640.2900.2900.0000.0000.0000.000
107A130PRO0-0.027-0.02225.065-0.365-0.3650.0000.0000.0000.000
108A131ALA0-0.044-0.00220.753-0.036-0.0360.0000.0000.0000.000
109A132ALA00.0430.02118.946-0.056-0.0560.0000.0000.0000.000
110A133PHE0-0.055-0.03414.827-0.615-0.6150.0000.0000.0000.000
111A134LEU00.0170.01015.6330.9930.9930.0000.0000.0000.000
112A135ASP-1-0.800-0.86011.172-26.951-26.9510.0000.0000.0000.000
113A136LEU00.003-0.00811.3751.7291.7290.0000.0000.0000.000
114A137ILE0-0.014-0.02311.103-2.659-2.6590.0000.0000.0000.000
115A138LEU0-0.007-0.0147.4771.1611.1610.0000.0000.0000.000
116A139TYR00.020-0.01011.415-1.111-1.1110.0000.0000.0000.000
117A140SER0-0.031-0.03212.1340.2050.2050.0000.0000.0000.000
118A141ARG10.9380.97112.94517.92217.9220.0000.0000.0000.000
119A142GLU-1-0.851-0.91014.195-17.280-17.2800.0000.0000.0000.000
120A143GLN0-0.028-0.01715.9101.0811.0810.0000.0000.0000.000
121A144ILE00.0500.03515.6300.6070.6070.0000.0000.0000.000
122A145ALA0-0.0010.02018.9400.7620.7620.0000.0000.0000.000
123A146LYS10.8920.92719.47815.49015.4900.0000.0000.0000.000
124A147GLU-1-0.846-0.92419.798-14.794-14.7940.0000.0000.0000.000
125A148THR00.0160.01222.4180.4990.4990.0000.0000.0000.000
126A149ALA0-0.048-0.02324.8430.4860.4860.0000.0000.0000.000
127A150ALA0-0.002-0.00326.1370.4570.4570.0000.0000.0000.000
128A151GLU-1-0.956-0.97226.932-10.437-10.4370.0000.0000.0000.000
129A152SER0-0.060-0.03128.6970.4320.4320.0000.0000.0000.000
130A153ASN0-0.111-0.06330.2960.3100.3100.0000.0000.0000.000
131A154THR0-0.0260.00030.1310.3180.3180.0000.0000.0000.000
132A155ALA0-0.0080.00229.652-0.281-0.2810.0000.0000.0000.000
133A156VAL00.001-0.00923.440-0.027-0.0270.0000.0000.0000.000
134A157VAL0-0.017-0.00525.7100.0690.0690.0000.0000.0000.000
135A158ILE0-0.011-0.01119.259-0.310-0.3100.0000.0000.0000.000
136A159ASP-1-0.789-0.88821.123-12.200-12.2000.0000.0000.0000.000
137A160PRO0-0.050-0.03118.506-0.645-0.6450.0000.0000.0000.000
138A161ASN0-0.071-0.04417.417-0.677-0.6770.0000.0000.0000.000
139A162ALA0-0.0010.01817.770-0.200-0.2000.0000.0000.0000.000
140A163PRO00.0350.00913.565-0.560-0.5600.0000.0000.0000.000
141A164ALA0-0.0030.0059.8000.2060.2060.0000.0000.0000.000
142A165TRP0-0.058-0.0316.970-1.382-1.3820.0000.0000.0000.000
143A166SER00.0110.00511.0950.8580.8580.0000.0000.0000.000
144A167ILE00.003-0.01212.994-0.578-0.5780.0000.0000.0000.000
145A168ILE00.0360.01914.5001.0101.0100.0000.0000.0000.000
146A169ALA0-0.004-0.00416.0270.9660.9660.0000.0000.0000.000
147A170VAL00.0170.01315.883-1.218-1.2180.0000.0000.0000.000
148A171LYS10.8670.93116.33617.51817.5180.0000.0000.0000.000
149A172ALA00.0380.02817.103-0.889-0.8890.0000.0000.0000.000
150A173GLN0-0.074-0.05614.6141.2441.2440.0000.0000.0000.000
151A174ASN00.0620.02518.322-0.296-0.2960.0000.0000.0000.000
152A175GLU-1-0.797-0.87116.003-15.470-15.4700.0000.0000.0000.000
153A176LYS10.8490.9229.03729.84729.8470.0000.0000.0000.000
154A177TYR00.0140.00310.636-1.647-1.6470.0000.0000.0000.000
155A178SER00.0330.01411.0680.5150.5150.0000.0000.0000.000
156A179LEU0-0.0130.00712.7390.5390.5390.0000.0000.0000.000
157A180PRO0-0.0070.01416.429-0.073-0.0730.0000.0000.0000.000
158A181MET00.0450.03117.9400.9250.9250.0000.0000.0000.000
159A182ALA00.0350.02820.4860.1380.1380.0000.0000.0000.000
160A183PRO00.0540.01324.052-0.059-0.0590.0000.0000.0000.000
161A184ILE00.0670.02625.472-0.026-0.0260.0000.0000.0000.000
162A185THR0-0.020-0.00523.5620.3080.3080.0000.0000.0000.000
163A186MET0-0.009-0.00920.714-0.102-0.1020.0000.0000.0000.000
164A187LEU0-0.0110.00324.2960.0480.0480.0000.0000.0000.000
165A188ARG10.9020.96227.91510.18010.1800.0000.0000.0000.000
166A189ASN0-0.010-0.01122.7320.3740.3740.0000.0000.0000.000
167A190THR0-0.084-0.04726.112-0.079-0.0790.0000.0000.0000.000
168A191LEU00.0080.01127.9560.2360.2360.0000.0000.0000.000
169A192ILE00.0660.03229.554-0.056-0.0560.0000.0000.0000.000
170A193GLU-1-1.000-0.99731.384-8.605-8.6050.0000.0000.0000.000
171A194GLU-1-0.822-0.90232.277-9.124-9.1240.0000.0000.0000.000
172A195GLY0-0.0430.01929.084-0.216-0.2160.0000.0000.0000.000
173A196GLY0-0.015-0.03126.0290.1270.1270.0000.0000.0000.000
174A197SER0-0.041-0.05122.2030.2580.2580.0000.0000.0000.000
175A198GLY00.0630.04325.3540.2570.2570.0000.0000.0000.000
176A199VAL0-0.085-0.03921.9790.2120.2120.0000.0000.0000.000
177A200ALA00.008-0.00125.2290.1050.1050.0000.0000.0000.000
178A201LEU00.0090.00023.881-0.488-0.4880.0000.0000.0000.000
179A202ASP-1-0.816-0.89718.271-15.437-15.4370.0000.0000.0000.000
180A203ARG10.9630.94621.88210.55210.5520.0000.0000.0000.000
181A204GLU-1-0.807-0.88719.754-12.941-12.9410.0000.0000.0000.000
182A205ALA00.0340.03517.890-0.160-0.1600.0000.0000.0000.000
183A206TYR0-0.016-0.01619.3420.0990.0990.0000.0000.0000.000
184A207LYS10.8150.89322.78012.88512.8850.0000.0000.0000.000
185A208ALA00.0260.01918.3280.2380.2380.0000.0000.0000.000
186A209SER0-0.022-0.03320.4490.2360.2360.0000.0000.0000.000
187A210VAL0-0.004-0.02121.3860.3210.3210.0000.0000.0000.000
188A211ALA0-0.057-0.03422.1330.4030.4030.0000.0000.0000.000
189A212TYR0-0.029-0.03019.5820.3230.3230.0000.0000.0000.000
190A213TRP0-0.033-0.03121.5370.6230.6230.0000.0000.0000.000
191A214LYS10.9480.98225.36511.17211.1720.0000.0000.0000.000
192A215THR00.0180.00825.2440.2940.2940.0000.0000.0000.000
193A216HIS10.8820.95522.07513.14813.1480.0000.0000.0000.000
194A217ALA00.0030.01026.7030.0290.0290.0000.0000.0000.000
195A218ILE00.0160.00825.816-0.187-0.1870.0000.0000.0000.000
196A219VAL00.0230.02028.1100.3450.3450.0000.0000.0000.000
197A220MET0-0.040-0.02630.399-0.101-0.1010.0000.0000.0000.000
198A221ASP-1-0.915-0.95433.071-8.205-8.2050.0000.0000.0000.000
199A222LYS10.9550.97836.1868.1008.1000.0000.0000.0000.000
200A223GLU-1-0.768-0.85938.644-8.014-8.0140.0000.0000.0000.000
201A224SER0-0.012-0.01041.2130.0350.0350.0000.0000.0000.000
202A225SER0-0.029-0.02240.337-0.045-0.0450.0000.0000.0000.000
203A226LEU0-0.055-0.01641.7080.0030.0030.0000.0000.0000.000
204A227GLU-1-0.947-0.96143.343-7.251-7.2510.0000.0000.0000.000