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: 892NY

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 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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1832150.213933
FMO2-HF: Nuclear repulsion 1763064.801961
FMO2-HF: Total energy -69085.411972
FMO2-MP2: Total energy -69285.886752


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.
-3.195-2.77722.562-11.499-11.483-0.039
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 : 0.003 / q_NPA : -0.032
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].
3A50VAL00.0170.0043.7950.1791.939-0.028-0.825-0.9060.003
4A51GLU-1-0.846-0.9016.9600.5300.5300.0000.0000.0000.000
5A52ILE0-0.035-0.0319.516-0.022-0.0220.0000.0000.0000.000
6A53THR00.0160.00212.1760.0210.0210.0000.0000.0000.000
7A54GLU-1-0.814-0.85114.5670.0620.0620.0000.0000.0000.000
8A55GLN00.0810.02617.501-0.047-0.0470.0000.0000.0000.000
9A56PRO0-0.013-0.00419.3040.0110.0110.0000.0000.0000.000
10A57HIS00.0430.02822.134-0.005-0.0050.0000.0000.0000.000
11A58PRO00.0270.01025.177-0.009-0.0090.0000.0000.0000.000
12A59LYS10.8670.92826.8650.0280.0280.0000.0000.0000.000
13A60ALA0-0.023-0.01028.9740.0050.0050.0000.0000.0000.000
14A61LEU0-0.018-0.00728.0960.0030.0030.0000.0000.0000.000
15A62ARG10.8650.96231.1280.0300.0300.0000.0000.0000.000
16A63PHE00.0260.00328.174-0.001-0.0010.0000.0000.0000.000
17A64ARG10.8060.88832.1590.0390.0390.0000.0000.0000.000
18A65TYR00.0600.01333.285-0.006-0.0060.0000.0000.0000.000
19A66GLU-1-0.889-0.93834.618-0.066-0.0660.0000.0000.0000.000
20A67CYS0-0.034-0.02935.8230.0020.0020.0000.0000.0000.000
21A68GLU-1-0.856-0.92237.371-0.036-0.0360.0000.0000.0000.000
22A69GLY00.0030.02037.3640.0030.0030.0000.0000.0000.000
23A70ARG10.9330.96935.4720.0320.0320.0000.0000.0000.000
24A71SER00.0330.00631.762-0.002-0.0020.0000.0000.0000.000
25A72ALA0-0.019-0.00829.778-0.003-0.0030.0000.0000.0000.000
26A73GLY0-0.040-0.01430.6940.0020.0020.0000.0000.0000.000
27A74SER0-0.016-0.02926.474-0.007-0.0070.0000.0000.0000.000
28A75ILE0-0.025-0.00123.3510.0050.0050.0000.0000.0000.000
29A76PRO00.0030.01024.5420.0020.0020.0000.0000.0000.000
30A77GLY00.0540.02722.793-0.009-0.0090.0000.0000.0000.000
31A78VAL0-0.019-0.03421.635-0.002-0.0020.0000.0000.0000.000
32A79ASN0-0.057-0.04522.0600.0010.0010.0000.0000.0000.000
33A80THR0-0.074-0.00225.4440.0040.0040.0000.0000.0000.000
34A81THR00.021-0.00627.410-0.002-0.0020.0000.0000.0000.000
35A82ALA0-0.079-0.03330.346-0.004-0.0040.0000.0000.0000.000
36A83GLU-1-0.882-0.94333.5600.0300.0300.0000.0000.0000.000
37A84GLN0-0.047-0.01426.8130.0030.0030.0000.0000.0000.000
38A85LYS10.9730.99228.456-0.012-0.0120.0000.0000.0000.000
39A86THR0-0.014-0.03023.0570.0030.0030.0000.0000.0000.000
40A87PHE0-0.010-0.02822.069-0.011-0.0110.0000.0000.0000.000
41A88PRO00.0120.01618.9620.0140.0140.0000.0000.0000.000
42A89SER0-0.0040.00515.7500.0060.0060.0000.0000.0000.000
43A90ILE00.0070.01110.351-0.009-0.0090.0000.0000.0000.000
44A91GLN00.016-0.0179.0980.1820.1820.0000.0000.0000.000
45A92VAL00.0070.0213.930-0.257-0.0620.003-0.044-0.1540.000
46A93HIS10.7940.8763.949-1.806-1.1430.001-0.356-0.3090.000
47A94GLY00.0600.0311.9693.553-1.26118.090-8.634-4.642-0.031
48A95TYR0-0.019-0.0292.322-3.890-2.5281.826-0.657-2.532-0.008
49A96ARG10.9030.9433.749-0.392-0.2750.006-0.018-0.1050.000
50A97GLY00.0420.0227.312-0.075-0.0750.0000.0000.0000.000
51A98ARG10.7890.8689.2620.1610.1610.0000.0000.0000.000
52A99ALA00.0570.0247.341-0.080-0.0800.0000.0000.0000.000
53A100VAL00.0120.0379.3430.0810.0810.0000.0000.0000.000
54A101VAL0-0.023-0.02210.025-0.096-0.0960.0000.0000.0000.000
55A102VAL00.0000.00812.0520.0600.0600.0000.0000.0000.000
56A103VAL00.0150.00514.295-0.035-0.0350.0000.0000.0000.000
57A104SER0-0.005-0.01716.6980.0220.0220.0000.0000.0000.000
58A105CYS00.0220.02919.191-0.003-0.0030.0000.0000.0000.000
59A106VAL00.0090.01818.654-0.008-0.0080.0000.0000.0000.000
60A107THR0-0.001-0.00621.7070.0130.0130.0000.0000.0000.000
61A108LYS10.7840.87922.8630.0680.0680.0000.0000.0000.000
62A109GLU-1-0.781-0.92623.953-0.109-0.1090.0000.0000.0000.000
63A110GLY00.0530.02323.668-0.014-0.0140.0000.0000.0000.000
64A111PRO00.0110.00719.081-0.006-0.0060.0000.0000.0000.000
65A112GLU-1-0.894-0.93418.630-0.338-0.3380.0000.0000.0000.000
66A113HIS10.8040.91318.3160.2300.2300.0000.0000.0000.000
67A114LYS10.9700.96020.6530.1530.1530.0000.0000.0000.000
68A115PRO00.0000.00821.6010.0110.0110.0000.0000.0000.000
69A116HIS00.0210.00423.2220.0100.0100.0000.0000.0000.000
70A117PRO00.012-0.00125.394-0.004-0.0040.0000.0000.0000.000
71A118HIS00.0120.01326.958-0.002-0.0020.0000.0000.0000.000
72A119ASN00.0210.02825.750-0.022-0.0220.0000.0000.0000.000
73A120LEU0-0.0080.00020.6470.0100.0100.0000.0000.0000.000
74A121VAL0-0.014-0.01524.670-0.004-0.0040.0000.0000.0000.000
75A122GLY00.064-0.00624.8700.0040.0040.0000.0000.0000.000
76A123LYS10.8360.90525.6310.0280.0280.0000.0000.0000.000
77A124GLU-1-0.909-0.95220.881-0.067-0.0670.0000.0000.0000.000
78A125GLY00.1420.06720.745-0.008-0.0080.0000.0000.0000.000
79A126CYS0-0.156-0.01621.465-0.019-0.0190.0000.0000.0000.000
80A127LYS11.0000.98123.2010.1260.1260.0000.0000.0000.000
81A128LYS10.9400.97323.8820.1100.1100.0000.0000.0000.000
82A129GLY0-0.0150.00325.115-0.008-0.0080.0000.0000.0000.000
83A130VAL00.0030.02119.174-0.006-0.0060.0000.0000.0000.000
84A131CYS0-0.013-0.01719.7600.0150.0150.0000.0000.0000.000
85A132THR0-0.023-0.00815.624-0.032-0.0320.0000.0000.0000.000
86A133VAL00.0090.01415.2360.0220.0220.0000.0000.0000.000
87A134GLU-1-0.790-0.87313.496-0.161-0.1610.0000.0000.0000.000
88A135ILE0-0.048-0.0188.7750.0340.0340.0000.0000.0000.000
89A136ASN00.0550.04012.5950.0210.0210.0000.0000.0000.000
90A137SER00.0590.00611.1380.0470.0470.0000.0000.0000.000
91A138THR00.0010.00311.2480.0310.0310.0000.0000.0000.000
92A139THR00.000-0.02511.5240.0720.0720.0000.0000.0000.000
93A140MET0-0.0650.0287.3950.0450.0450.0000.0000.0000.000
94A141SER00.0160.0139.6680.0230.0230.0000.0000.0000.000
95A142TYR00.0090.00212.419-0.028-0.0280.0000.0000.0000.000
96A143THR00.0280.00714.8580.0100.0100.0000.0000.0000.000
97A144PHE0-0.014-0.01114.334-0.007-0.0070.0000.0000.0000.000
98A145ASN00.0550.02519.731-0.002-0.0020.0000.0000.0000.000
99A146ASN0-0.062-0.03522.9880.0010.0010.0000.0000.0000.000
100A147LEU00.0720.04319.645-0.008-0.0080.0000.0000.0000.000
101A148GLY00.0310.01523.6810.0090.0090.0000.0000.0000.000
102A149ILE0-0.0030.00024.838-0.010-0.0100.0000.0000.0000.000
103A150GLN0-0.019-0.01727.5620.0050.0050.0000.0000.0000.000
104A151CYS0-0.041-0.01529.770-0.006-0.0060.0000.0000.0000.000
105A152VAL00.0530.03530.5890.0050.0050.0000.0000.0000.000
106A153LYS10.8970.95833.0990.0580.0580.0000.0000.0000.000
107A154LYS10.9790.96336.2370.0580.0580.0000.0000.0000.000
108A155LYS10.9200.96337.2560.0480.0480.0000.0000.0000.000
109A156ASP-1-0.763-0.89935.331-0.068-0.0680.0000.0000.0000.000
110A157VAL0-0.036-0.00331.821-0.005-0.0050.0000.0000.0000.000
111A158GLU-1-0.865-0.93332.140-0.102-0.1020.0000.0000.0000.000
112A159GLU-1-0.827-0.91032.570-0.099-0.0990.0000.0000.0000.000
113A160ALA00.0470.02630.093-0.006-0.0060.0000.0000.0000.000
114A161LEU0-0.016-0.01827.082-0.010-0.0100.0000.0000.0000.000
115A162ARG10.7750.87728.2470.0950.0950.0000.0000.0000.000
116A163LEU0-0.020-0.02128.586-0.010-0.0100.0000.0000.0000.000
117A164ARG10.8010.89522.3100.1500.1500.0000.0000.0000.000
118A165GLN00.0400.01424.016-0.021-0.0210.0000.0000.0000.000
119A166GLU-1-0.878-0.93025.121-0.130-0.1300.0000.0000.0000.000
120A167ILE0-0.050-0.03021.714-0.005-0.0050.0000.0000.0000.000
121A168ARG10.9100.96920.9960.2220.2220.0000.0000.0000.000
122A169VAL0-0.0120.00118.195-0.026-0.0260.0000.0000.0000.000
123A170ASP-1-0.780-0.91018.645-0.247-0.2470.0000.0000.0000.000
124A171PRO0-0.076-0.04115.227-0.026-0.0260.0000.0000.0000.000
125A172PHE00.0500.00215.038-0.053-0.0530.0000.0000.0000.000
126A173ARG10.9040.99214.7480.4690.4690.0000.0000.0000.000
127A174THR00.0560.04319.7120.0260.0260.0000.0000.0000.000
128A175GLY0-0.030-0.00322.9120.0220.0220.0000.0000.0000.000
129A176PHE00.039-0.01323.6020.0020.0020.0000.0000.0000.000
130A177GLY00.0100.01427.9000.0130.0130.0000.0000.0000.000
131A178HIS00.028-0.01926.0060.0130.0130.0000.0000.0000.000
132A179ALA0-0.043-0.01830.6930.0060.0060.0000.0000.0000.000
133A180LYS10.9060.96532.1550.1190.1190.0000.0000.0000.000
134A181GLU-1-0.916-0.93834.282-0.081-0.0810.0000.0000.0000.000
135A182PRO00.0320.00634.082-0.003-0.0030.0000.0000.0000.000
136A183GLY0-0.069-0.03934.7270.0000.0000.0000.0000.0000.000
137A184SER0-0.027-0.01132.9840.0010.0010.0000.0000.0000.000
138A185ILE0-0.030-0.00629.124-0.004-0.0040.0000.0000.0000.000
139A186ASP-1-0.759-0.87030.529-0.062-0.0620.0000.0000.0000.000
140A187LEU0-0.061-0.02930.426-0.004-0.0040.0000.0000.0000.000
141A188ASN0-0.044-0.03332.1070.0070.0070.0000.0000.0000.000
142A189ALA0-0.0110.00028.0590.0070.0070.0000.0000.0000.000
143A190VAL0-0.0070.01024.283-0.006-0.0060.0000.0000.0000.000
144A191ARG10.8500.93920.1110.1370.1370.0000.0000.0000.000
145A192LEU00.0190.01318.349-0.007-0.0070.0000.0000.0000.000
146A193CYS0-0.046-0.02114.539-0.019-0.0190.0000.0000.0000.000
147A194PHE00.0270.01211.9170.0340.0340.0000.0000.0000.000
148A195GLN00.017-0.00210.746-0.056-0.0560.0000.0000.0000.000
149A196VAL00.0350.0145.9740.1120.1120.0000.0000.0000.000
150A197PHE0-0.005-0.0017.670-0.200-0.2000.0000.0000.0000.000
151A198LEU00.008-0.0092.495-0.5180.0670.539-0.263-0.8610.000
152A199GLU-1-0.851-0.9427.036-0.165-0.1650.0000.0000.0000.000
153A200GLY00.0160.0098.856-0.070-0.0700.0000.0000.0000.000
154A201GLN00.0200.01710.3510.0300.0300.0000.0000.0000.000
155A202GLN0-0.011-0.00113.0260.0280.0280.0000.0000.0000.000
156A203ARG10.9850.97215.3390.0950.0950.0000.0000.0000.000
157A204GLY0-0.022-0.01015.4340.0180.0180.0000.0000.0000.000
158A205ARG10.8760.94715.4280.2080.2080.0000.0000.0000.000
159A206PHE0-0.026-0.01610.584-0.016-0.0160.0000.0000.0000.000
160A207THR0-0.016-0.00611.2440.0280.0280.0000.0000.0000.000
161A208GLU-1-0.874-0.9276.508-0.813-0.8130.0000.0000.0000.000
162A209PRO0-0.0450.0137.200-0.035-0.0350.0000.0000.0000.000
163A210LEU00.002-0.0032.241-1.307-0.7572.125-0.702-1.974-0.003
164A211THR0-0.019-0.0215.7280.5310.5310.0000.0000.0000.000
165A212PRO0-0.041-0.0198.6670.0080.0080.0000.0000.0000.000
166A213VAL00.0150.0259.2590.0050.0050.0000.0000.0000.000
167A214VAL0-0.040-0.02612.2010.0500.0500.0000.0000.0000.000
168A215SER00.0390.02915.7970.0160.0160.0000.0000.0000.000
169A216ASP-1-0.887-0.93617.803-0.051-0.0510.0000.0000.0000.000
170A217ILE0-0.077-0.04320.887-0.010-0.0100.0000.0000.0000.000
171A218ILE00.0080.01422.3420.0140.0140.0000.0000.0000.000
172A219TYR00.001-0.02825.900-0.010-0.0100.0000.0000.0000.000
173A220ASP-1-0.826-0.91129.661-0.041-0.0410.0000.0000.0000.000
174A221LYS10.9290.97932.0750.0170.0170.0000.0000.0000.000
175A222LYS10.9680.97834.2860.0230.0230.0000.0000.0000.000