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: R8548

Calculation Name: 1NBQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NBQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y624

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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2015292.773665
FMO2-HF: Nuclear repulsion 1934097.421051
FMO2-HF: Total energy -81195.352614
FMO2-MP2: Total energy -81427.571036


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:25:ALA)


Summations of interaction energy for fragment #1(A:25:ALA)
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.
-6.335-3.442.441-2.281-3.054-0.022
Interaction energy analysis for fragmet #1(A:25:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.025 / q_NPA : -0.025
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].
3A27GLY00.0100.0193.888-0.3140.699-0.004-0.419-0.5900.002
4A28SER0-0.010-0.0236.3740.3410.3410.0000.0000.0000.000
5A29VAL0-0.061-0.0289.277-0.032-0.0320.0000.0000.0000.000
6A30THR0-0.045-0.02012.0350.1010.1010.0000.0000.0000.000
7A31VAL00.0570.03115.640-0.045-0.0450.0000.0000.0000.000
8A32HIS0-0.052-0.01618.2160.0450.0450.0000.0000.0000.000
9A33SER00.034-0.01121.949-0.011-0.0110.0000.0000.0000.000
10A34SER0-0.011-0.00325.2630.0070.0070.0000.0000.0000.000
11A35GLU-1-0.915-0.97427.997-0.066-0.0660.0000.0000.0000.000
12A36PRO00.0090.01228.465-0.002-0.0020.0000.0000.0000.000
13A37GLU-1-0.911-0.94729.713-0.048-0.0480.0000.0000.0000.000
14A38VAL00.0190.03431.9520.0030.0030.0000.0000.0000.000
15A39ARG10.9430.95934.6580.0500.0500.0000.0000.0000.000
16A40ILE0-0.0190.00237.9300.0000.0000.0000.0000.0000.000
17A41PRO00.0000.01540.3350.0000.0000.0000.0000.0000.000
18A42GLU-1-0.827-0.89442.511-0.053-0.0530.0000.0000.0000.000
19A43ASN0-0.034-0.03042.7850.0030.0030.0000.0000.0000.000
20A44ASN0-0.0420.00941.447-0.001-0.0010.0000.0000.0000.000
21A45PRO00.0010.00537.694-0.002-0.0020.0000.0000.0000.000
22A46VAL00.0080.00434.3070.0020.0020.0000.0000.0000.000
23A47LYS10.8970.96226.9640.1430.1430.0000.0000.0000.000
24A48LEU00.0410.04528.5400.0050.0050.0000.0000.0000.000
25A49SER0-0.040-0.02926.311-0.009-0.0090.0000.0000.0000.000
26A50CYS0-0.043-0.01321.100-0.017-0.0170.0000.0000.0000.000
27A51ALA0-0.0010.02320.953-0.014-0.0140.0000.0000.0000.000
28A52TYR00.017-0.00114.7610.0050.0050.0000.0000.0000.000
29A53SER0-0.040-0.03214.653-0.016-0.0160.0000.0000.0000.000
30A54GLY00.0790.03211.0020.0360.0360.0000.0000.0000.000
31A55PHE0-0.056-0.0368.934-0.203-0.2030.0000.0000.0000.000
32A56SER0-0.038-0.0397.1130.0850.0850.0000.0000.0000.000
33A57SER0-0.047-0.0309.3660.1750.1750.0000.0000.0000.000
34A58PRO0-0.022-0.00210.788-0.080-0.0800.0000.0000.0000.000
35A59ARG10.7910.89112.6210.5190.5190.0000.0000.0000.000
36A60VAL0-0.018-0.01214.9630.0090.0090.0000.0000.0000.000
37A61GLU-1-0.807-0.88117.893-0.275-0.2750.0000.0000.0000.000
38A62TRP00.0380.00620.6550.0070.0070.0000.0000.0000.000
39A63LYS10.8640.93221.5920.1510.1510.0000.0000.0000.000
40A64PHE0-0.023-0.01625.7560.0010.0010.0000.0000.0000.000
41A65ASP-1-0.834-0.90427.674-0.089-0.0890.0000.0000.0000.000
42A66GLN0-0.062-0.05230.9190.0010.0010.0000.0000.0000.000
43A67GLY0-0.0040.00834.5000.0000.0000.0000.0000.0000.000
44A68ASP-1-0.872-0.93134.357-0.038-0.0380.0000.0000.0000.000
45A69THR0-0.080-0.03434.044-0.003-0.0030.0000.0000.0000.000
46A70THR00.027-0.01327.7150.0020.0020.0000.0000.0000.000
47A71ARG10.8650.94329.5770.0800.0800.0000.0000.0000.000
48A72LEU00.0200.00223.405-0.002-0.0020.0000.0000.0000.000
49A73VAL00.0060.03026.9170.0040.0040.0000.0000.0000.000
50A74CYS0-0.110-0.05023.211-0.006-0.0060.0000.0000.0000.000
51A75TYR00.0310.00621.077-0.001-0.0010.0000.0000.0000.000
52A76ASN00.004-0.01318.811-0.004-0.0040.0000.0000.0000.000
53A77ASN0-0.0100.00816.5090.0090.0090.0000.0000.0000.000
54A78LYS10.8590.93320.7850.1670.1670.0000.0000.0000.000
55A79ILE0-0.0210.00524.372-0.003-0.0030.0000.0000.0000.000
56A80THR0-0.041-0.05126.7350.0050.0050.0000.0000.0000.000
57A81ALA00.0620.00328.7890.0050.0050.0000.0000.0000.000
58A82SER0-0.027-0.01432.3440.0020.0020.0000.0000.0000.000
59A83TYR00.0390.02331.2680.0050.0050.0000.0000.0000.000
60A84GLU-1-0.833-0.89630.854-0.127-0.1270.0000.0000.0000.000
61A85ASP-1-0.910-0.92532.953-0.087-0.0870.0000.0000.0000.000
62A86ARG10.8130.86035.7690.0820.0820.0000.0000.0000.000
63A87VAL0-0.069-0.02629.931-0.001-0.0010.0000.0000.0000.000
64A88THR00.0270.01230.586-0.006-0.0060.0000.0000.0000.000
65A89PHE00.055-0.00620.6620.0020.0020.0000.0000.0000.000
66A90LEU0-0.022-0.01624.9160.0010.0010.0000.0000.0000.000
67A91PRO00.0100.01020.227-0.005-0.0050.0000.0000.0000.000
68A92THR00.0550.02321.091-0.008-0.0080.0000.0000.0000.000
69A93GLY00.0330.00123.6400.0120.0120.0000.0000.0000.000
70A94ILE0-0.028-0.00225.529-0.003-0.0030.0000.0000.0000.000
71A95THR00.0110.00028.0190.0070.0070.0000.0000.0000.000
72A96PHE0-0.034-0.00530.969-0.001-0.0010.0000.0000.0000.000
73A97LYS10.8290.90534.5000.0970.0970.0000.0000.0000.000
74A98SER00.0610.01737.9570.0050.0050.0000.0000.0000.000
75A99VAL0-0.0180.00236.806-0.004-0.0040.0000.0000.0000.000
76A100THR00.0710.02139.4770.0020.0020.0000.0000.0000.000
77A101ARG10.8110.88340.3690.0400.0400.0000.0000.0000.000
78A102GLU-1-0.896-0.93839.478-0.053-0.0530.0000.0000.0000.000
79A103ASP-1-0.811-0.86935.959-0.080-0.0800.0000.0000.0000.000
80A104THR00.0500.02335.684-0.004-0.0040.0000.0000.0000.000
81A105GLY00.0570.01834.1460.0030.0030.0000.0000.0000.000
82A106THR0-0.050-0.02728.5990.0000.0000.0000.0000.0000.000
83A107TYR0-0.043-0.02527.958-0.006-0.0060.0000.0000.0000.000
84A108THR0-0.040-0.02522.3880.0060.0060.0000.0000.0000.000
85A110MET0-0.004-0.00418.0840.0180.0180.0000.0000.0000.000
86A111VAL00.0000.01413.609-0.006-0.0060.0000.0000.0000.000
87A112SER00.0790.04511.9260.0380.0380.0000.0000.0000.000
88A113GLU-1-0.797-0.8716.017-1.347-1.3470.0000.0000.0000.000
89A114GLU-1-0.833-0.9229.106-0.630-0.6300.0000.0000.0000.000
90A115GLY0-0.072-0.0287.393-0.338-0.3380.0000.0000.0000.000
91A116GLY0-0.036-0.0328.0300.1450.1450.0000.0000.0000.000
92A117ASN0-0.038-0.0152.220-5.222-3.4002.446-1.854-2.414-0.024
93A118SER00.0660.0104.9990.4570.517-0.001-0.008-0.0500.000
94A119TYR0-0.067-0.0838.0540.0390.0390.0000.0000.0000.000
95A120GLY0-0.025-0.00411.8130.0790.0790.0000.0000.0000.000
96A121GLU-1-0.807-0.90515.241-0.171-0.1710.0000.0000.0000.000
97A122VAL0-0.0090.01518.9560.0250.0250.0000.0000.0000.000
98A123LYS10.8550.91722.3620.0890.0890.0000.0000.0000.000
99A124VAL00.0310.03325.5040.0080.0080.0000.0000.0000.000
100A125LYS10.8320.91328.6070.0540.0540.0000.0000.0000.000
101A126LEU00.0000.01132.1180.0000.0000.0000.0000.0000.000
102A127ILE00.0010.00534.8780.0040.0040.0000.0000.0000.000
103A128VAL00.0330.00338.514-0.002-0.0020.0000.0000.0000.000
104A129LEU0-0.026-0.02140.7040.0030.0030.0000.0000.0000.000
105A130VAL0-0.004-0.00744.143-0.001-0.0010.0000.0000.0000.000
106A131PRO0-0.0190.00547.3650.0010.0010.0000.0000.0000.000
107A132PRO00.0170.02750.7290.0000.0000.0000.0000.0000.000
108A133SER0-0.029-0.03552.7200.0000.0000.0000.0000.0000.000
109A134LYS10.8090.88755.3580.0220.0220.0000.0000.0000.000
110A135PRO00.0290.00657.7470.0000.0000.0000.0000.0000.000
111A136THR0-0.061-0.01858.7070.0010.0010.0000.0000.0000.000
112A137VAL0-0.010-0.02560.3160.0000.0000.0000.0000.0000.000
113A138ASN0-0.047-0.01563.0430.0000.0000.0000.0000.0000.000
114A139ILE00.0000.01565.1550.0000.0000.0000.0000.0000.000
115A140PRO00.0110.02267.7600.0000.0000.0000.0000.0000.000
116A141SER00.033-0.01470.6410.0000.0000.0000.0000.0000.000
117A142SER0-0.031-0.01574.2090.0000.0000.0000.0000.0000.000
118A143ALA00.0170.01172.4970.0000.0000.0000.0000.0000.000
119A144THR0-0.038-0.01674.6260.0000.0000.0000.0000.0000.000
120A145ILE0-0.013-0.00775.5460.0000.0000.0000.0000.0000.000
121A146GLY0-0.0090.00075.4450.0000.0000.0000.0000.0000.000
122A147ASN0-0.034-0.02072.4540.0000.0000.0000.0000.0000.000
123A148ARG10.9340.97961.6140.0090.0090.0000.0000.0000.000
124A149ALA0-0.037-0.03068.2510.0000.0000.0000.0000.0000.000
125A150VAL0-0.043-0.01562.4390.0000.0000.0000.0000.0000.000
126A151LEU00.0130.01664.2760.0000.0000.0000.0000.0000.000
127A152THR0-0.019-0.03359.9810.0000.0000.0000.0000.0000.000
128A153CYS0-0.012-0.00358.7300.0000.0000.0000.0000.0000.000
129A154SER00.0380.00955.2220.0000.0000.0000.0000.0000.000
130A155GLU-1-0.724-0.83252.005-0.030-0.0300.0000.0000.0000.000
131A156GLN0-0.073-0.03248.9790.0020.0020.0000.0000.0000.000
132A157ASP-1-0.805-0.86849.337-0.035-0.0350.0000.0000.0000.000
133A158GLY0-0.058-0.04248.436-0.002-0.0020.0000.0000.0000.000
134A159SER0-0.086-0.00942.9540.0010.0010.0000.0000.0000.000
135A160PRO00.019-0.03743.486-0.002-0.0020.0000.0000.0000.000
136A161PRO00.0370.01444.4620.0010.0010.0000.0000.0000.000
137A162SER00.003-0.01547.5980.0000.0000.0000.0000.0000.000
138A163GLU-1-0.948-0.94150.191-0.021-0.0210.0000.0000.0000.000
139A164TYR0-0.047-0.05452.7150.0000.0000.0000.0000.0000.000
140A165THR0-0.052-0.02956.3980.0010.0010.0000.0000.0000.000
141A166TRP0-0.015-0.01159.5350.0000.0000.0000.0000.0000.000
142A167PHE0-0.024-0.01162.4530.0000.0000.0000.0000.0000.000
143A168LYS10.9390.97666.1740.0090.0090.0000.0000.0000.000
144A169ASP-1-0.864-0.93269.760-0.010-0.0100.0000.0000.0000.000
145A170GLY0-0.006-0.00868.6920.0000.0000.0000.0000.0000.000
146A171ILE0-0.060-0.02968.3170.0000.0000.0000.0000.0000.000
147A172VAL0-0.044-0.02362.3700.0000.0000.0000.0000.0000.000
148A173MET00.0210.01763.2870.0010.0010.0000.0000.0000.000
149A174PRO0-0.060-0.00762.4060.0000.0000.0000.0000.0000.000
150A175THR00.0420.01857.2900.0000.0000.0000.0000.0000.000
151A176ASN0-0.0220.00660.7270.0000.0000.0000.0000.0000.000
152A177PRO00.0690.06262.8500.0000.0000.0000.0000.0000.000
153A178LYS10.9360.95465.8410.0040.0040.0000.0000.0000.000
154A179SER0-0.039-0.01965.7700.0000.0000.0000.0000.0000.000
155A180THR00.0500.03067.7980.0000.0000.0000.0000.0000.000
156A181ARG10.9040.93262.3030.0080.0080.0000.0000.0000.000
157A182ALA00.0290.02669.6650.0000.0000.0000.0000.0000.000
158A183PHE00.0610.00968.7350.0000.0000.0000.0000.0000.000
159A184SER00.0160.01270.3140.0000.0000.0000.0000.0000.000
160A185ASN0-0.094-0.05471.2560.0000.0000.0000.0000.0000.000
161A186SER0-0.016-0.01069.8870.0000.0000.0000.0000.0000.000
162A187SER0-0.042-0.02769.0230.0000.0000.0000.0000.0000.000
163A188TYR0-0.061-0.04563.7160.0000.0000.0000.0000.0000.000
164A189VAL00.0220.01159.8340.0010.0010.0000.0000.0000.000
165A190LEU00.0070.00959.329-0.001-0.0010.0000.0000.0000.000
166A191ASN00.0650.01153.7410.0000.0000.0000.0000.0000.000
167A192PRO00.0360.00953.266-0.001-0.0010.0000.0000.0000.000
168A193THR00.0440.02948.777-0.001-0.0010.0000.0000.0000.000
169A194THR0-0.023-0.00551.881-0.001-0.0010.0000.0000.0000.000
170A195GLY0-0.042-0.00154.3700.0000.0000.0000.0000.0000.000
171A196GLU-1-0.881-0.95157.298-0.011-0.0110.0000.0000.0000.000
172A197LEU0-0.0140.01559.2790.0000.0000.0000.0000.0000.000
173A198VAL0-0.053-0.03261.6400.0000.0000.0000.0000.0000.000
174A199PHE0-0.016-0.00764.4210.0010.0010.0000.0000.0000.000
175A200ASP-1-0.856-0.93467.157-0.006-0.0060.0000.0000.0000.000
176A201PRO0-0.0050.00769.2900.0000.0000.0000.0000.0000.000
177A202LEU0-0.0100.00771.5500.0000.0000.0000.0000.0000.000
178A203SER00.007-0.01173.1440.0010.0010.0000.0000.0000.000
179A204ALA00.0880.03175.8740.0000.0000.0000.0000.0000.000
180A205SER0-0.043-0.03375.7840.0000.0000.0000.0000.0000.000
181A206ASP-1-0.816-0.90972.248-0.008-0.0080.0000.0000.0000.000
182A207THR00.0160.02573.416-0.001-0.0010.0000.0000.0000.000
183A208GLY0-0.037-0.03173.6230.0000.0000.0000.0000.0000.000
184A209GLU-1-0.892-0.95071.730-0.013-0.0130.0000.0000.0000.000
185A210TYR0-0.069-0.04367.3580.0000.0000.0000.0000.0000.000
186A211SER00.0190.00165.7080.0000.0000.0000.0000.0000.000
187A213GLU-1-0.820-0.89858.211-0.021-0.0210.0000.0000.0000.000
188A214ALA00.0030.00054.9010.0000.0000.0000.0000.0000.000
189A215ARG10.8570.91153.7240.0190.0190.0000.0000.0000.000
190A216ASN00.1000.05948.2800.0020.0020.0000.0000.0000.000
191A217GLY0-0.063-0.03348.270-0.001-0.0010.0000.0000.0000.000
192A218TYR0-0.024-0.03147.474-0.001-0.0010.0000.0000.0000.000
193A219GLY00.0340.01649.5980.0010.0010.0000.0000.0000.000
194A220THR0-0.060-0.04352.1300.0010.0010.0000.0000.0000.000
195A221PRO00.0120.01855.714-0.001-0.0010.0000.0000.0000.000
196A222MET00.0280.03156.8590.0010.0010.0000.0000.0000.000
197A223THR0-0.010-0.00158.9260.0010.0010.0000.0000.0000.000
198A224SER00.0320.01162.0500.0000.0000.0000.0000.0000.000
199A225ASN0-0.042-0.02463.2870.0000.0000.0000.0000.0000.000
200A226ALA00.0400.01766.8800.0000.0000.0000.0000.0000.000
201A227VAL0-0.037-0.02268.3850.0000.0000.0000.0000.0000.000
202A228ARG10.8510.91270.7700.0100.0100.0000.0000.0000.000
203A229MET0-0.039-0.00770.3520.0000.0000.0000.0000.0000.000
204A230GLU-1-0.830-0.89774.107-0.009-0.0090.0000.0000.0000.000
205A231ALA0-0.0090.01276.1950.0000.0000.0000.0000.0000.000
206A232VAL0-0.002-0.00877.6360.0000.0000.0000.0000.0000.000
207A233GLU-1-0.941-0.96779.839-0.005-0.0050.0000.0000.0000.000