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: YVJZ2

Calculation Name: 3B8O-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B8O

Chain ID: A

ChEMBL ID:

UniProt ID: P0AG01

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 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 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2379174.494562
FMO2-HF: Nuclear repulsion 2288947.983768
FMO2-HF: Total energy -90226.510794
FMO2-MP2: Total energy -90488.671092


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:55:GLU)


Summations of interaction energy for fragment #1(A:55: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.
-66.436-60.8421.806-14.462-12.9370.1
Interaction energy analysis for fragmet #1(A:55:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.821 / q_NPA : -0.896
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].
3A57SER0-0.021-0.0523.888-4.379-2.764-0.018-0.871-0.7260.002
4A58SER0-0.0020.0086.861-2.047-2.0470.0000.0000.0000.000
5A59THR0-0.038-0.04210.340-0.389-0.3890.0000.0000.0000.000
6A60ALA0-0.0110.00713.585-0.349-0.3490.0000.0000.0000.000
7A61ILE00.002-0.00616.952-0.007-0.0070.0000.0000.0000.000
8A62THR0-0.0240.00820.289-0.051-0.0510.0000.0000.0000.000
9A63ASP-1-0.811-0.89123.0879.8739.8730.0000.0000.0000.000
10A64ARG10.8170.87526.710-9.135-9.1350.0000.0000.0000.000
11A65PRO0-0.0470.00129.5480.0030.0030.0000.0000.0000.000
12A66THR00.002-0.03030.893-0.293-0.2930.0000.0000.0000.000
13A67VAL00.0650.00934.2570.0640.0640.0000.0000.0000.000
14A68ASN0-0.009-0.01035.806-0.176-0.1760.0000.0000.0000.000
15A69MET0-0.081-0.01628.645-0.033-0.0330.0000.0000.0000.000
16A70LEU00.0560.03232.6080.1290.1290.0000.0000.0000.000
17A71GLY00.0430.03234.865-0.067-0.0670.0000.0000.0000.000
18A72GLY0-0.014-0.02337.445-0.110-0.1100.0000.0000.0000.000
19A73TYR00.0520.03836.361-0.152-0.1520.0000.0000.0000.000
20A74TYR00.0200.00038.496-0.201-0.2010.0000.0000.0000.000
21A75SER0-0.035-0.03139.793-0.165-0.1650.0000.0000.0000.000
22A76GLN00.0360.03141.792-0.190-0.1900.0000.0000.0000.000
23A77GLN00.0580.03039.505-0.139-0.1390.0000.0000.0000.000
24A78GLN00.002-0.02242.316-0.011-0.0110.0000.0000.0000.000
25A79PHE0-0.035-0.00344.832-0.148-0.1480.0000.0000.0000.000
26A80LEU00.007-0.00443.945-0.130-0.1300.0000.0000.0000.000
27A81ARG10.8990.96240.466-7.213-7.2130.0000.0000.0000.000
28A82ASN0-0.073-0.02246.898-0.060-0.0600.0000.0000.0000.000
29A83LEU0-0.021-0.01749.833-0.148-0.1480.0000.0000.0000.000
30A84ASP-1-1.001-0.98646.9546.2826.2820.0000.0000.0000.000
31A85VAL0-0.022-0.00450.663-0.033-0.0330.0000.0000.0000.000
32A95PRO00.0200.01738.131-0.043-0.0430.0000.0000.0000.000
33A96SER0-0.007-0.04937.084-0.063-0.0630.0000.0000.0000.000
34A97VAL00.0570.02337.0430.0950.0950.0000.0000.0000.000
35A98MET00.0240.00033.8100.0970.0970.0000.0000.0000.000
36A99ASP-1-0.803-0.85232.7698.6438.6430.0000.0000.0000.000
37A100GLU-1-0.821-0.89932.5588.4918.4910.0000.0000.0000.000
38A101ALA0-0.0060.00331.8450.1430.1430.0000.0000.0000.000
39A102TYR0-0.021-0.02924.8650.3320.3320.0000.0000.0000.000
40A103LYS10.8360.90927.735-8.166-8.1660.0000.0000.0000.000
41A104GLU-1-0.817-0.89628.18510.05010.0500.0000.0000.0000.000
42A105PHE0-0.014-0.01121.3720.3250.3250.0000.0000.0000.000
43A106VAL0-0.0050.00023.4680.4890.4890.0000.0000.0000.000
44A107MET0-0.0140.00823.1450.3940.3940.0000.0000.0000.000
45A108GLN0-0.034-0.03923.6630.7050.7050.0000.0000.0000.000
46A109LEU0-0.030-0.01818.1490.5500.5500.0000.0000.0000.000
47A110ALA00.0090.01118.8530.7680.7680.0000.0000.0000.000
48A111SER00.0020.02219.8500.3520.3520.0000.0000.0000.000
49A112TRP00.0050.00216.9210.6420.6420.0000.0000.0000.000
50A113ASP-1-0.877-0.93919.49411.93511.9350.0000.0000.0000.000
51A114THR0-0.006-0.01119.7940.0550.0550.0000.0000.0000.000
52A115ARG10.8750.94414.870-15.285-15.2850.0000.0000.0000.000
53A116ARG10.9720.98416.485-11.902-11.9020.0000.0000.0000.000
54A117GLU-1-0.875-0.92518.38411.74211.7420.0000.0000.0000.000
55A118PHE0-0.0010.00112.775-0.045-0.0450.0000.0000.0000.000
56A119TRP00.0430.0078.9990.3040.3040.0000.0000.0000.000
57A120LEU0-0.016-0.00715.4540.1550.1550.0000.0000.0000.000
58A121GLN0-0.052-0.01218.4710.0420.0420.0000.0000.0000.000
59A122THR00.0070.01213.3020.1950.1950.0000.0000.0000.000
60A123ASP-1-0.864-0.92716.57015.21515.2150.0000.0000.0000.000
61A124TYR0-0.020-0.0336.4190.4920.4920.0000.0000.0000.000
62A125TYR00.050-0.00812.6470.4760.4760.0000.0000.0000.000
63A126LYS10.8270.89513.607-14.840-14.8400.0000.0000.0000.000
64A127GLN0-0.048-0.02213.8730.6740.6740.0000.0000.0000.000
65A128ARG10.8090.8808.243-28.635-28.6350.0000.0000.0000.000
66A129MET0-0.088-0.01213.592-0.301-0.3010.0000.0000.0000.000
67A130VAL0-0.040-0.03416.008-0.130-0.1300.0000.0000.0000.000
68A131GLY0-0.0060.00518.664-0.690-0.6900.0000.0000.0000.000
69A132ASN0-0.037-0.00720.267-0.720-0.7200.0000.0000.0000.000
70A133SER00.0370.01720.7300.3190.3190.0000.0000.0000.000
71A134LYS10.9880.98419.317-13.754-13.7540.0000.0000.0000.000
72A135ALA0-0.015-0.02317.1970.3410.3410.0000.0000.0000.000
73A136ASP-1-0.707-0.85016.38916.54016.5400.0000.0000.0000.000
74A137ALA0-0.020-0.00716.9210.4270.4270.0000.0000.0000.000
75A138ALA0-0.059-0.03415.5850.0920.0920.0000.0000.0000.000
76A139LEU00.0550.04210.5260.5340.5340.0000.0000.0000.000
77A140LEU0-0.014-0.00812.2700.8340.8340.0000.0000.0000.000
78A141ASP-1-0.929-0.97114.17716.48516.4850.0000.0000.0000.000
79A142GLU-1-0.914-0.9547.83126.83926.8390.0000.0000.0000.000
80A143MET0-0.028-0.0179.0520.8640.8640.0000.0000.0000.000
81A144ILE0-0.0200.00710.6530.0300.0300.0000.0000.0000.000
82A145ASN0-0.055-0.03211.562-0.771-0.7710.0000.0000.0000.000
83A146ASN00.0080.0136.3291.5311.5310.0000.0000.0000.000
84A147ILE0-0.0110.0088.9931.0411.0410.0000.0000.0000.000
85A148GLN0-0.046-0.0308.453-0.615-0.6150.0000.0000.0000.000
86A149PHE00.005-0.00113.3940.1470.1470.0000.0000.0000.000
87A150ILE0-0.027-0.01614.523-0.025-0.0250.0000.0000.0000.000
88A151PRO0-0.0090.00518.752-0.177-0.1770.0000.0000.0000.000
89A152GLY00.0150.00122.4710.1670.1670.0000.0000.0000.000
90A153ASP-1-0.808-0.91024.3029.5149.5140.0000.0000.0000.000
91A154PHE0-0.025-0.02827.347-0.004-0.0040.0000.0000.0000.000
92A155THR0-0.080-0.03130.298-0.307-0.3070.0000.0000.0000.000
93A156ARG10.9030.95425.997-10.512-10.5120.0000.0000.0000.000
94A157ALA0-0.030-0.00828.4550.1080.1080.0000.0000.0000.000
95A158VAL0-0.041-0.00922.2950.2460.2460.0000.0000.0000.000
96A159ASN00.0200.00723.711-0.470-0.4700.0000.0000.0000.000
97A160ASP-1-0.750-0.86422.00411.81211.8120.0000.0000.0000.000
98A161SER0-0.055-0.03417.3900.3170.3170.0000.0000.0000.000
99A162VAL00.0130.01614.457-0.006-0.0060.0000.0000.0000.000
100A163LYS10.8490.9246.690-28.138-28.1380.0000.0000.0000.000
101A164LEU0-0.015-0.0037.837-0.685-0.6850.0000.0000.0000.000
102A165ILE0-0.049-0.0263.1630.1680.9940.435-0.488-0.7720.005
103A166ALA00.0250.0144.109-3.081-2.786-0.001-0.044-0.2500.000
104A167GLU-1-0.771-0.8572.58536.82439.3191.091-1.775-1.810-0.019
105A168THR0-0.040-0.0433.08510.31111.5480.194-0.609-0.822-0.006
106A169ALA00.0630.0195.111-4.170-4.119-0.001-0.003-0.0470.000
107A170PRO00.0630.0227.433-2.579-2.5790.0000.0000.0000.000
108A171ASP-1-0.852-0.8987.51628.11028.1100.0000.0000.0000.000
109A172ALA00.0000.0016.401-2.348-2.3480.0000.0000.0000.000
110A173ASN00.0190.0078.328-3.044-3.0440.0000.0000.0000.000
111A174ASN0-0.033-0.03411.906-2.739-2.7390.0000.0000.0000.000
112A175LEU00.0050.0208.998-1.537-1.5370.0000.0000.0000.000
113A176LEU00.0080.01211.799-1.354-1.3540.0000.0000.0000.000
114A177ARG10.8070.88613.367-17.844-17.8440.0000.0000.0000.000
115A178GLN0-0.008-0.00815.705-0.926-0.9260.0000.0000.0000.000
116A179TYR0-0.021-0.01814.812-0.854-0.8540.0000.0000.0000.000
117A180VAL00.013-0.00216.805-0.833-0.8330.0000.0000.0000.000
118A181ALA0-0.017-0.00919.021-0.745-0.7450.0000.0000.0000.000
119A182PHE0-0.005-0.00419.479-0.662-0.6620.0000.0000.0000.000
120A183ALA00.0220.01220.348-0.550-0.5500.0000.0000.0000.000
121A184SER00.030-0.01122.163-0.601-0.6010.0000.0000.0000.000
122A185GLN0-0.037-0.01124.644-0.353-0.3530.0000.0000.0000.000
123A186ARG10.7980.88322.947-12.131-12.1310.0000.0000.0000.000
124A187ALA00.0310.01826.436-0.334-0.3340.0000.0000.0000.000
125A188ALA0-0.0090.00428.202-0.380-0.3800.0000.0000.0000.000
126A189SER0-0.077-0.04829.521-0.367-0.3670.0000.0000.0000.000
127A190HIS00.0880.05130.596-0.218-0.2180.0000.0000.0000.000
128A191LEU0-0.025-0.00631.471-0.308-0.3080.0000.0000.0000.000
129A192ASN0-0.055-0.05934.229-0.464-0.4640.0000.0000.0000.000
130A193ASP-1-0.927-0.95334.8567.9917.9910.0000.0000.0000.000
131A194GLU-1-0.932-0.95835.8497.6327.6320.0000.0000.0000.000
132A195LEU0-0.054-0.01838.271-0.263-0.2630.0000.0000.0000.000
133A196LYS10.9470.96739.955-7.619-7.6190.0000.0000.0000.000
134A197GLY00.0060.00241.017-0.209-0.2090.0000.0000.0000.000
135A198ALA00.0220.00942.463-0.181-0.1810.0000.0000.0000.000
136A199TRP00.008-0.01244.199-0.159-0.1590.0000.0000.0000.000
137A200ALA0-0.018-0.00545.695-0.193-0.1930.0000.0000.0000.000
138A201ALA00.0150.01546.859-0.168-0.1680.0000.0000.0000.000
139A202ARG10.9370.96848.386-5.881-5.8810.0000.0000.0000.000
140A203THR0-0.006-0.02249.736-0.167-0.1670.0000.0000.0000.000
141A204ILE00.004-0.00150.530-0.157-0.1570.0000.0000.0000.000
142A205GLN0-0.038-0.01252.279-0.186-0.1860.0000.0000.0000.000
143A206MET00.0170.01454.420-0.137-0.1370.0000.0000.0000.000
144A207LYS10.9100.94854.249-5.710-5.7100.0000.0000.0000.000
145A208ALA0-0.028-0.01857.569-0.114-0.1140.0000.0000.0000.000
146A209GLN0-0.041-0.02158.236-0.019-0.0190.0000.0000.0000.000
147A210VAL00.0600.02460.316-0.086-0.0860.0000.0000.0000.000
148A211LYS10.8420.92462.151-4.871-4.8710.0000.0000.0000.000
149A212ARG10.9750.98359.324-5.126-5.1260.0000.0000.0000.000
150A213GLN0-0.004-0.00463.621-0.020-0.0200.0000.0000.0000.000
151A214GLU-1-0.799-0.86965.8574.6554.6550.0000.0000.0000.000
152A215GLU-1-0.908-0.95368.2104.2654.2650.0000.0000.0000.000
153A216VAL0-0.022-0.01268.975-0.078-0.0780.0000.0000.0000.000
154A217ALA00.0200.01271.071-0.078-0.0780.0000.0000.0000.000
155A218LYS10.8990.94572.700-4.204-4.2040.0000.0000.0000.000
156A219ALA00.0160.01574.143-0.066-0.0660.0000.0000.0000.000
157A220ILE0-0.080-0.05574.158-0.078-0.0780.0000.0000.0000.000
158A221TYR0-0.058-0.03277.114-0.061-0.0610.0000.0000.0000.000
159A222ASP-1-0.785-0.88378.2913.9513.9510.0000.0000.0000.000
160A223ARG10.9250.97677.441-4.024-4.0240.0000.0000.0000.000
161A224ARG10.9380.96681.727-3.780-3.7800.0000.0000.0000.000
162A225MET00.0140.01682.997-0.045-0.0450.0000.0000.0000.000
163A226ASN00.0570.03684.620-0.064-0.0640.0000.0000.0000.000
164A227SER0-0.146-0.09186.193-0.044-0.0440.0000.0000.0000.000
165A228ILE0-0.073-0.04086.466-0.032-0.0320.0000.0000.0000.000
166A229GLU-1-0.912-0.95287.2813.5543.5540.0000.0000.0000.000
167A230GLN0-0.077-0.02389.912-0.069-0.0690.0000.0000.0000.000
168A266GLN00.020-0.00993.5390.0230.0230.0000.0000.0000.000
169A267ALA00.0780.04691.7000.0300.0300.0000.0000.0000.000
170A268ARG10.8880.93184.306-3.638-3.6380.0000.0000.0000.000
171A269LEU00.0710.04187.4260.0480.0480.0000.0000.0000.000
172A270GLU-1-0.858-0.92786.9333.4933.4930.0000.0000.0000.000
173A271ASN0-0.074-0.03384.3830.0250.0250.0000.0000.0000.000
174A272LEU0-0.004-0.00281.4080.0490.0490.0000.0000.0000.000
175A273GLN0-0.012-0.01282.2020.0360.0360.0000.0000.0000.000
176A274ALA0-0.009-0.00382.1170.0240.0240.0000.0000.0000.000
177A275VAL0-0.064-0.01378.5480.0320.0320.0000.0000.0000.000
178A276GLY00.0110.02276.8610.0580.0580.0000.0000.0000.000
179A277PRO0-0.030-0.03373.917-0.029-0.0290.0000.0000.0000.000
180A278ALA0-0.024-0.00274.7120.0260.0260.0000.0000.0000.000
181A279PHE00.010-0.01269.2130.0310.0310.0000.0000.0000.000
182A280ASP-1-0.886-0.93568.4944.5224.5220.0000.0000.0000.000
183A281LEU00.0310.00066.1920.0430.0430.0000.0000.0000.000
184A282ASP-1-0.818-0.90763.6464.9684.9680.0000.0000.0000.000
185A283TYR0-0.044-0.03263.6340.0900.0900.0000.0000.0000.000
186A284ASP-1-0.886-0.94663.9844.6744.6740.0000.0000.0000.000
187A285GLN0-0.056-0.04361.3690.0920.0920.0000.0000.0000.000
188A286ASN0-0.005-0.00859.5290.1760.1760.0000.0000.0000.000
189A287ARG10.9130.96859.081-4.749-4.7490.0000.0000.0000.000
190A288ALA0-0.014-0.01059.7180.0670.0670.0000.0000.0000.000
191A289MET00.0240.01754.4120.1320.1320.0000.0000.0000.000
192A290LEU0-0.021-0.03155.0410.1100.1100.0000.0000.0000.000
193A291ASN0-0.066-0.02655.3640.0840.0840.0000.0000.0000.000
194A292THR00.0350.01451.5990.0820.0820.0000.0000.0000.000
195A293LEU0-0.0030.00650.2580.1170.1170.0000.0000.0000.000
196A294ASN0-0.019-0.00850.5760.1570.1570.0000.0000.0000.000
197A295VAL0-0.057-0.00649.5970.0220.0220.0000.0000.0000.000
198A296GLY0-0.0200.01147.8120.0860.0860.0000.0000.0000.000
199A297PRO00.006-0.00243.028-0.008-0.0080.0000.0000.0000.000
200A298THR0-0.044-0.03242.0170.0020.0020.0000.0000.0000.000
201A299LEU0-0.005-0.00838.6460.1240.1240.0000.0000.0000.000
202A300ASP-1-0.798-0.86735.7668.2998.2990.0000.0000.0000.000
203A301PRO00.003-0.00232.7080.0980.0980.0000.0000.0000.000
204A302ARG10.8420.89131.557-7.894-7.8940.0000.0000.0000.000
205A303PHE0-0.0500.00231.3070.2130.2130.0000.0000.0000.000
206A304GLN0-0.020-0.00626.4910.2180.2180.0000.0000.0000.000
207A305THR00.0200.01026.598-0.388-0.3880.0000.0000.0000.000
208A306TYR00.004-0.01222.525-0.037-0.0370.0000.0000.0000.000
209A307ARG10.9440.97126.221-10.004-10.0040.0000.0000.0000.000
210A308TYR00.0760.02818.9900.3170.3170.0000.0000.0000.000
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