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: G5NY1

Calculation Name: 1BVO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1BVO

Chain ID: A

ChEMBL ID:

UniProt ID: Q17034

Base Structure: X-ray

Registration Date: 2023-09-21

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 OptH
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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1831367.290179
FMO2-HF: Nuclear repulsion 1762283.329352
FMO2-HF: Total energy -69083.960827
FMO2-MP2: Total energy -69284.574147


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:48:PRO)


Summations of interaction energy for fragment #1(A:48:PRO)
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.
-3.248-3.37822.067-11.428-10.505-0.029
Interaction energy analysis for fragmet #1(A:48:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : -0.012
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].
3A50VAL00.0360.0083.7950.2462.326-0.026-1.006-1.0460.005
4A51GLU-1-0.852-0.9097.0070.2560.2560.0000.0000.0000.000
5A52ILE0-0.030-0.0269.6130.0270.0270.0000.0000.0000.000
6A53THR00.0140.00812.1130.0190.0190.0000.0000.0000.000
7A54GLU-1-0.845-0.90414.6410.0260.0260.0000.0000.0000.000
8A55GLN00.1000.04816.791-0.041-0.0410.0000.0000.0000.000
9A56PRO0-0.012-0.00619.4030.0230.0230.0000.0000.0000.000
10A57HIS00.0500.03622.186-0.009-0.0090.0000.0000.0000.000
11A58PRO00.0250.01225.440-0.007-0.0070.0000.0000.0000.000
12A59LYS10.9200.95026.9430.0690.0690.0000.0000.0000.000
13A60ALA00.0070.00329.0580.0080.0080.0000.0000.0000.000
14A61LEU0-0.027-0.01227.9600.0050.0050.0000.0000.0000.000
15A62ARG10.8890.96531.0450.0530.0530.0000.0000.0000.000
16A63PHE00.0050.01728.311-0.001-0.0010.0000.0000.0000.000
17A64ARG10.8180.89132.0630.0630.0630.0000.0000.0000.000
18A65TYR00.0740.02633.191-0.008-0.0080.0000.0000.0000.000
19A66GLU-1-0.876-0.93034.596-0.085-0.0850.0000.0000.0000.000
20A67CYS0-0.059-0.03735.7350.0040.0040.0000.0000.0000.000
21A68GLU-1-0.845-0.93337.385-0.057-0.0570.0000.0000.0000.000
22A69GLY0-0.0050.02237.2920.0040.0040.0000.0000.0000.000
23A70ARG10.9240.96935.3520.0500.0500.0000.0000.0000.000
24A71SER00.0370.00631.909-0.002-0.0020.0000.0000.0000.000
25A72ALA0-0.023-0.00829.662-0.004-0.0040.0000.0000.0000.000
26A73GLY0-0.045-0.01930.6330.0010.0010.0000.0000.0000.000
27A74SER0-0.009-0.01126.350-0.006-0.0060.0000.0000.0000.000
28A75ILE0-0.0130.01023.2730.0060.0060.0000.0000.0000.000
29A76PRO0-0.0040.01224.4820.0020.0020.0000.0000.0000.000
30A77GLY00.0640.02522.831-0.015-0.0150.0000.0000.0000.000
31A78VAL0-0.004-0.03121.7610.0030.0030.0000.0000.0000.000
32A79ASN0-0.050-0.03521.9120.0020.0020.0000.0000.0000.000
33A80THR0-0.0760.00025.5180.0100.0100.0000.0000.0000.000
34A81THR00.006-0.00227.456-0.002-0.0020.0000.0000.0000.000
35A82ALA0-0.079-0.03930.395-0.003-0.0030.0000.0000.0000.000
36A83GLU-1-0.887-0.94933.5910.0190.0190.0000.0000.0000.000
37A84GLN0-0.007-0.00326.5330.0000.0000.0000.0000.0000.000
38A85LYS10.9620.98328.4100.0040.0040.0000.0000.0000.000
39A86THR00.0160.01623.0990.0050.0050.0000.0000.0000.000
40A87PHE0-0.028-0.03122.023-0.010-0.0100.0000.0000.0000.000
41A88PRO00.0140.01518.8720.0120.0120.0000.0000.0000.000
42A89SER0-0.002-0.00315.6560.0120.0120.0000.0000.0000.000
43A90ILE0-0.0110.00910.005-0.030-0.0300.0000.0000.0000.000
44A91GLN0-0.004-0.0178.9600.1840.1840.0000.0000.0000.000
45A92VAL00.0000.0154.006-0.346-0.1680.002-0.039-0.1410.000
46A93HIS10.8410.9093.951-1.537-0.8020.001-0.428-0.308-0.001
47A94GLY00.0310.0141.9171.982-2.67818.050-8.854-4.536-0.027
48A95TYR0-0.014-0.0222.498-2.127-1.3960.6180.019-1.367-0.002
49A96ARG10.9440.9734.114-1.089-0.9910.001-0.029-0.0700.000
50A97GLY00.0630.0277.666-0.065-0.0650.0000.0000.0000.000
51A98ARG10.8430.9169.4920.0120.0120.0000.0000.0000.000
52A99ALA00.0460.0057.383-0.040-0.0400.0000.0000.0000.000
53A100VAL00.0170.0399.3750.0700.0700.0000.0000.0000.000
54A101VAL0-0.023-0.0199.990-0.124-0.1240.0000.0000.0000.000
55A102VAL00.0240.01412.0000.0800.0800.0000.0000.0000.000
56A103VAL00.0070.00114.200-0.055-0.0550.0000.0000.0000.000
57A104SER0-0.007-0.01416.6070.0370.0370.0000.0000.0000.000
58A105CYS00.0300.03019.076-0.012-0.0120.0000.0000.0000.000
59A106VAL00.0240.02318.302-0.006-0.0060.0000.0000.0000.000
60A107THR00.0310.00521.5740.0160.0160.0000.0000.0000.000
61A108LYS10.8870.94022.7230.1180.1180.0000.0000.0000.000
62A109GLU-1-0.888-0.98323.859-0.183-0.1830.0000.0000.0000.000
63A110GLY00.0810.04223.363-0.016-0.0160.0000.0000.0000.000
64A111PRO00.0110.00919.038-0.008-0.0080.0000.0000.0000.000
65A112GLU-1-0.896-0.94218.106-0.497-0.4970.0000.0000.0000.000
66A113HIS10.7890.90818.1820.3680.3680.0000.0000.0000.000
67A114LYS11.0501.01720.2170.2040.2040.0000.0000.0000.000
68A115PRO0-0.0080.01021.5630.0100.0100.0000.0000.0000.000
69A116HIS00.0220.01323.0900.0140.0140.0000.0000.0000.000
70A117PRO00.0380.01925.272-0.005-0.0050.0000.0000.0000.000
71A118HIS00.0070.01926.9340.0020.0020.0000.0000.0000.000
72A119ASN00.0260.02725.640-0.026-0.0260.0000.0000.0000.000
73A120LEU0-0.010-0.00520.5550.0100.0100.0000.0000.0000.000
74A121VAL0-0.022-0.01924.5830.0000.0000.0000.0000.0000.000
75A122GLY00.0610.00024.8160.0010.0010.0000.0000.0000.000
76A123LYS10.8570.92425.5870.0380.0380.0000.0000.0000.000
77A124GLU-1-0.939-0.97020.900-0.059-0.0590.0000.0000.0000.000
78A125GLY00.1320.06520.712-0.012-0.0120.0000.0000.0000.000
79A126CYS0-0.112-0.02921.418-0.025-0.0250.0000.0000.0000.000
80A127LYS10.9900.98523.1380.1350.1350.0000.0000.0000.000
81A128LYS10.9630.97723.8090.1210.1210.0000.0000.0000.000
82A129GLY0-0.010-0.00125.025-0.011-0.0110.0000.0000.0000.000
83A130VAL00.0220.02919.081-0.012-0.0120.0000.0000.0000.000
84A131CYS0-0.034-0.00819.6810.0270.0270.0000.0000.0000.000
85A132THR0-0.034-0.01015.697-0.040-0.0400.0000.0000.0000.000
86A133VAL00.0100.02015.1870.0280.0280.0000.0000.0000.000
87A134GLU-1-0.829-0.91013.447-0.093-0.0930.0000.0000.0000.000
88A135ILE0-0.046-0.0158.7510.0230.0230.0000.0000.0000.000
89A136ASN00.0440.04412.6210.0670.0670.0000.0000.0000.000
90A137SER00.065-0.00311.5280.0510.0510.0000.0000.0000.000
91A138THR0-0.021-0.01411.6240.0760.0760.0000.0000.0000.000
92A139THR0-0.007-0.03012.0110.1030.1030.0000.0000.0000.000
93A140MET0-0.0590.0377.6860.0470.0470.0000.0000.0000.000
94A141SER00.001-0.0089.663-0.027-0.0270.0000.0000.0000.000
95A142TYR0-0.007-0.00212.374-0.011-0.0110.0000.0000.0000.000
96A143THR00.0050.00314.857-0.006-0.0060.0000.0000.0000.000
97A144PHE0-0.002-0.00814.5110.0010.0010.0000.0000.0000.000
98A145ASN00.0640.02919.6940.0010.0010.0000.0000.0000.000
99A146ASN0-0.085-0.06622.9360.0060.0060.0000.0000.0000.000
100A147LEU00.0690.03719.581-0.007-0.0070.0000.0000.0000.000
101A148GLY00.0270.01323.6190.0070.0070.0000.0000.0000.000
102A149ILE00.002-0.00124.579-0.011-0.0110.0000.0000.0000.000
103A150GLN0-0.019-0.01727.4700.0090.0090.0000.0000.0000.000
104A151CYS0-0.051-0.03029.669-0.008-0.0080.0000.0000.0000.000
105A152VAL00.0650.04530.3300.0080.0080.0000.0000.0000.000
106A153LYS10.9460.96532.9870.0760.0760.0000.0000.0000.000
107A154LYS10.9790.96436.1170.0890.0890.0000.0000.0000.000
108A155LYS10.9090.95937.1310.0690.0690.0000.0000.0000.000
109A156ASP-1-0.788-0.90235.220-0.091-0.0910.0000.0000.0000.000
110A157VAL0-0.039-0.00231.531-0.006-0.0060.0000.0000.0000.000
111A158GLU-1-0.868-0.93732.017-0.133-0.1330.0000.0000.0000.000
112A159GLU-1-0.926-0.96632.449-0.115-0.1150.0000.0000.0000.000
113A160ALA00.0480.02129.976-0.006-0.0060.0000.0000.0000.000
114A161LEU0-0.016-0.02026.985-0.012-0.0120.0000.0000.0000.000
115A162ARG10.8520.93728.1280.1150.1150.0000.0000.0000.000
116A163LEU0-0.017-0.02728.572-0.008-0.0080.0000.0000.0000.000
117A164ARG10.8040.90722.0710.2080.2080.0000.0000.0000.000
118A165GLN00.0380.01123.908-0.026-0.0260.0000.0000.0000.000
119A166GLU-1-0.923-0.95625.016-0.148-0.1480.0000.0000.0000.000
120A167ILE0-0.067-0.02821.550-0.003-0.0030.0000.0000.0000.000
121A168ARG10.9140.96520.4830.2660.2660.0000.0000.0000.000
122A169VAL0-0.0140.00218.241-0.031-0.0310.0000.0000.0000.000
123A170ASP-1-0.785-0.91018.532-0.328-0.3280.0000.0000.0000.000
124A171PRO0-0.079-0.04915.269-0.030-0.0300.0000.0000.0000.000
125A172PHE00.049-0.00514.416-0.068-0.0680.0000.0000.0000.000
126A173ARG10.9071.00014.6210.5540.5540.0000.0000.0000.000
127A174THR00.0360.02019.0250.0240.0240.0000.0000.0000.000
128A175GLY0-0.047-0.01622.1860.0280.0280.0000.0000.0000.000
129A176PHE00.021-0.02723.4300.0000.0000.0000.0000.0000.000
130A177GLY0-0.0190.00227.4550.0150.0150.0000.0000.0000.000
131A178HIS0-0.013-0.03726.2890.0150.0150.0000.0000.0000.000
132A179ALA0-0.015-0.00530.2570.0070.0070.0000.0000.0000.000
133A180LYS11.0031.01031.9540.1550.1550.0000.0000.0000.000
134A181GLU-1-0.970-0.96733.857-0.124-0.1240.0000.0000.0000.000
135A182PRO00.0380.00333.779-0.005-0.0050.0000.0000.0000.000
136A183GLY0-0.073-0.03734.5900.0000.0000.0000.0000.0000.000
137A184SER0-0.0020.00232.6940.0020.0020.0000.0000.0000.000
138A185ILE0-0.0230.00329.012-0.007-0.0070.0000.0000.0000.000
139A186ASP-1-0.791-0.90230.394-0.108-0.1080.0000.0000.0000.000
140A187LEU0-0.066-0.03430.295-0.005-0.0050.0000.0000.0000.000
141A188ASN0-0.039-0.03331.9990.0100.0100.0000.0000.0000.000
142A189ALA0-0.010-0.00127.8970.0060.0060.0000.0000.0000.000
143A190VAL0-0.0270.00524.082-0.006-0.0060.0000.0000.0000.000
144A191ARG10.8450.93520.0340.2580.2580.0000.0000.0000.000
145A192LEU00.0110.00918.254-0.001-0.0010.0000.0000.0000.000
146A193CYS0-0.071-0.02115.368-0.051-0.0510.0000.0000.0000.000
147A194PHE00.0400.01311.7820.0600.0600.0000.0000.0000.000
148A195GLN00.0230.00110.616-0.085-0.0850.0000.0000.0000.000
149A196VAL00.0280.0155.7360.1510.1510.0000.0000.0000.000
150A197PHE0-0.015-0.0017.577-0.233-0.2330.0000.0000.0000.000
151A198LEU00.027-0.0042.641-0.4360.1490.316-0.214-0.687-0.001
152A199GLU-1-0.851-0.9467.056-0.039-0.0390.0000.0000.0000.000
153A200GLY0-0.004-0.0049.049-0.036-0.0360.0000.0000.0000.000
154A201GLN00.0390.02610.5790.0590.0590.0000.0000.0000.000
155A202GLN0-0.019-0.00313.2120.0170.0170.0000.0000.0000.000
156A203ARG10.9930.97615.6570.0040.0040.0000.0000.0000.000
157A204GLY0-0.046-0.01915.5370.0040.0040.0000.0000.0000.000
158A205ARG10.8960.95515.4460.1600.1600.0000.0000.0000.000
159A206PHE0-0.034-0.02610.5110.0000.0000.0000.0000.0000.000
160A207THR0-0.032-0.01810.5980.0060.0060.0000.0000.0000.000
161A208GLU-1-0.846-0.9056.078-0.797-0.7970.0000.0000.0000.000
162A209PRO0-0.063-0.0057.153-0.046-0.0460.0000.0000.0000.000
163A210LEU0-0.0060.0042.152-1.155-1.0323.105-0.877-2.350-0.003
164A211THR0-0.018-0.0235.5050.5740.5740.0000.0000.0000.000
165A212PRO0-0.052-0.0237.966-0.017-0.0170.0000.0000.0000.000
166A213VAL00.0360.0359.394-0.018-0.0180.0000.0000.0000.000
167A214VAL0-0.044-0.03112.0660.0890.0890.0000.0000.0000.000
168A215SER00.0250.02815.7510.0040.0040.0000.0000.0000.000
169A216ASP-1-0.889-0.95417.803-0.176-0.1760.0000.0000.0000.000
170A217ILE0-0.094-0.05820.904-0.006-0.0060.0000.0000.0000.000
171A218ILE00.0040.01722.2390.0170.0170.0000.0000.0000.000
172A219TYR0-0.037-0.04325.790-0.007-0.0070.0000.0000.0000.000
173A220ASP-1-0.859-0.93629.548-0.075-0.0750.0000.0000.0000.000
174A221LYS10.9270.98131.9670.0490.0490.0000.0000.0000.000
175A222LYS10.9420.96134.1870.0520.0520.0000.0000.0000.000