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

tag_button

FMODB ID: QV15Y

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 OptAll
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 -2016564.793831
FMO2-HF: Nuclear repulsion 1935367.344744
FMO2-HF: Total energy -81197.449088
FMO2-MP2: Total energy -81429.375452


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.
-6.976-6.7626.853-3.34-3.724-0.032
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 : -0.031 / q_NPA : -0.031
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].
3A27GLY00.0140.0093.860-0.6020.406-0.001-0.469-0.5370.002
4A28SER0-0.036-0.0246.4340.3070.3070.0000.0000.0000.000
5A29VAL0-0.041-0.0139.051-0.003-0.0030.0000.0000.0000.000
6A30THR0-0.031-0.01311.6020.1220.1220.0000.0000.0000.000
7A31VAL00.0320.00315.304-0.054-0.0540.0000.0000.0000.000
8A32HIS0-0.044-0.01917.8460.0480.0480.0000.0000.0000.000
9A33SER00.027-0.01621.629-0.013-0.0130.0000.0000.0000.000
10A34SER00.0020.00525.0330.0060.0060.0000.0000.0000.000
11A35GLU-1-0.881-0.93528.028-0.057-0.0570.0000.0000.0000.000
12A36PRO0-0.006-0.00228.497-0.005-0.0050.0000.0000.0000.000
13A37GLU-1-0.857-0.91529.810-0.038-0.0380.0000.0000.0000.000
14A38VAL00.0470.03731.6400.0030.0030.0000.0000.0000.000
15A39ARG10.8890.93034.3860.0430.0430.0000.0000.0000.000
16A40ILE0-0.0020.00737.6600.0000.0000.0000.0000.0000.000
17A41PRO0-0.0110.01040.0730.0000.0000.0000.0000.0000.000
18A42GLU-1-0.756-0.85941.959-0.048-0.0480.0000.0000.0000.000
19A43ASN0-0.047-0.03442.3030.0030.0030.0000.0000.0000.000
20A44ASN0-0.064-0.01640.796-0.002-0.0020.0000.0000.0000.000
21A45PRO0-0.007-0.00637.637-0.003-0.0030.0000.0000.0000.000
22A46VAL00.0100.01033.8340.0030.0030.0000.0000.0000.000
23A47LYS10.8330.92126.7370.1400.1400.0000.0000.0000.000
24A48LEU00.0210.02828.3100.0050.0050.0000.0000.0000.000
25A49SER0-0.012-0.01826.445-0.010-0.0100.0000.0000.0000.000
26A50CYS0-0.077-0.01220.713-0.017-0.0170.0000.0000.0000.000
27A51ALA00.0070.01120.562-0.010-0.0100.0000.0000.0000.000
28A52TYR00.0200.01614.5940.0040.0040.0000.0000.0000.000
29A53SER0-0.015-0.01514.457-0.010-0.0100.0000.0000.0000.000
30A54GLY00.0530.01910.7310.0180.0180.0000.0000.0000.000
31A55PHE0-0.048-0.0168.738-0.215-0.2150.0000.0000.0000.000
32A56SER0-0.059-0.0636.8840.1020.1020.0000.0000.0000.000
33A57SER0-0.064-0.0428.6180.1580.1580.0000.0000.0000.000
34A58PRO0-0.0100.01910.275-0.076-0.0760.0000.0000.0000.000
35A59ARG10.7710.86012.3560.5290.5290.0000.0000.0000.000
36A60VAL0-0.015-0.01414.6410.0070.0070.0000.0000.0000.000
37A61GLU-1-0.804-0.87917.536-0.274-0.2740.0000.0000.0000.000
38A62TRP0-0.002-0.02620.1020.0070.0070.0000.0000.0000.000
39A63LYS10.8560.91521.2120.1270.1270.0000.0000.0000.000
40A64PHE0-0.049-0.01525.283-0.001-0.0010.0000.0000.0000.000
41A65ASP-1-0.762-0.86027.082-0.075-0.0750.0000.0000.0000.000
42A66GLN0-0.028-0.03930.2930.0000.0000.0000.0000.0000.000
43A67GLY00.0220.01634.1090.0020.0020.0000.0000.0000.000
44A68ASP-1-0.907-0.95533.450-0.029-0.0290.0000.0000.0000.000
45A69THR0-0.063-0.01733.571-0.003-0.0030.0000.0000.0000.000
46A70THR0-0.003-0.02526.8820.0010.0010.0000.0000.0000.000
47A71ARG10.8170.90929.2410.0700.0700.0000.0000.0000.000
48A72LEU00.0130.00423.138-0.003-0.0030.0000.0000.0000.000
49A73VAL0-0.0200.01226.4510.0060.0060.0000.0000.0000.000
50A74CYS0-0.088-0.05222.776-0.008-0.0080.0000.0000.0000.000
51A75TYR00.0320.01520.0300.0040.0040.0000.0000.0000.000
52A76ASN00.002-0.01518.169-0.003-0.0030.0000.0000.0000.000
53A77ASN0-0.0180.00515.8820.0100.0100.0000.0000.0000.000
54A78LYS10.8460.91320.0600.1630.1630.0000.0000.0000.000
55A79ILE0-0.0030.01623.872-0.001-0.0010.0000.0000.0000.000
56A80THR0-0.016-0.02726.2760.0000.0000.0000.0000.0000.000
57A81ALA00.0710.01028.4470.0060.0060.0000.0000.0000.000
58A82SER0-0.058-0.02031.9060.0040.0040.0000.0000.0000.000
59A83TYR00.0480.02830.9830.0050.0050.0000.0000.0000.000
60A84GLU-1-0.834-0.89830.380-0.128-0.1280.0000.0000.0000.000
61A85ASP-1-0.870-0.93332.660-0.083-0.0830.0000.0000.0000.000
62A86ARG10.7690.86535.2380.0780.0780.0000.0000.0000.000
63A87VAL0-0.0070.00729.6470.0010.0010.0000.0000.0000.000
64A88THR0-0.028-0.01329.771-0.004-0.0040.0000.0000.0000.000
65A89PHE00.0720.01719.9500.0040.0040.0000.0000.0000.000
66A90LEU00.0010.00224.5150.0030.0030.0000.0000.0000.000
67A91PRO00.010-0.00119.757-0.001-0.0010.0000.0000.0000.000
68A92THR00.0400.02820.824-0.008-0.0080.0000.0000.0000.000
69A93GLY00.0380.02123.4990.0160.0160.0000.0000.0000.000
70A94ILE0-0.0030.01524.7200.0010.0010.0000.0000.0000.000
71A95THR0-0.024-0.03027.3170.0070.0070.0000.0000.0000.000
72A96PHE0-0.0040.00730.680-0.002-0.0020.0000.0000.0000.000
73A97LYS10.8180.88733.9930.0960.0960.0000.0000.0000.000
74A98SER00.0560.02037.3430.0050.0050.0000.0000.0000.000
75A99VAL0-0.0490.00236.047-0.004-0.0040.0000.0000.0000.000
76A100THR00.036-0.00138.6560.0030.0030.0000.0000.0000.000
77A101ARG10.8610.88839.5470.0360.0360.0000.0000.0000.000
78A102GLU-1-0.885-0.93839.199-0.047-0.0470.0000.0000.0000.000
79A103ASP-1-0.805-0.86135.358-0.076-0.0760.0000.0000.0000.000
80A104THR00.0270.00835.243-0.004-0.0040.0000.0000.0000.000
81A105GLY00.0250.01533.9810.0030.0030.0000.0000.0000.000
82A106THR0-0.060-0.03328.3890.0000.0000.0000.0000.0000.000
83A107TYR00.0240.01527.493-0.006-0.0060.0000.0000.0000.000
84A108THR0-0.024-0.01822.0640.0110.0110.0000.0000.0000.000
85A110MET00.0050.00617.7730.0230.0230.0000.0000.0000.000
86A111VAL00.0200.00813.345-0.008-0.0080.0000.0000.0000.000
87A112SER00.0120.01510.9880.0300.0300.0000.0000.0000.000
88A113GLU-1-0.750-0.8525.539-1.388-1.3880.0000.0000.0000.000
89A114GLU-1-0.828-0.9128.490-0.624-0.6240.0000.0000.0000.000
90A115GLY0-0.061-0.0336.977-0.366-0.3660.0000.0000.0000.000
91A116GLY0-0.010-0.0117.6710.1000.1000.0000.0000.0000.000
92A117ASN0-0.044-0.0141.982-5.621-6.4186.855-2.855-3.202-0.034
93A118SER00.0900.0224.5440.6680.671-0.001-0.0160.0150.000
94A119TYR0-0.058-0.0597.665-0.016-0.0160.0000.0000.0000.000
95A120GLY00.0230.01611.3910.0700.0700.0000.0000.0000.000
96A121GLU-1-0.809-0.87214.979-0.155-0.1550.0000.0000.0000.000
97A122VAL0-0.023-0.01318.6680.0170.0170.0000.0000.0000.000
98A123LYS10.8000.88522.1440.0690.0690.0000.0000.0000.000
99A124VAL00.0060.02325.3500.0090.0090.0000.0000.0000.000
100A125LYS10.8720.91928.2510.0420.0420.0000.0000.0000.000
101A126LEU0-0.030-0.01231.695-0.003-0.0030.0000.0000.0000.000
102A127ILE0-0.019-0.00834.4220.0030.0030.0000.0000.0000.000
103A128VAL00.0390.01637.857-0.001-0.0010.0000.0000.0000.000
104A129LEU0-0.029-0.00740.1200.0030.0030.0000.0000.0000.000
105A130VAL00.017-0.00143.527-0.002-0.0020.0000.0000.0000.000
106A131PRO0-0.017-0.01246.8210.0010.0010.0000.0000.0000.000
107A132PRO0-0.0050.02150.3820.0000.0000.0000.0000.0000.000
108A133SER0-0.006-0.04152.3250.0000.0000.0000.0000.0000.000
109A134LYS10.8180.90254.8120.0190.0190.0000.0000.0000.000
110A135PRO0-0.0120.00157.2420.0000.0000.0000.0000.0000.000
111A136THR0-0.027-0.01158.1220.0010.0010.0000.0000.0000.000
112A137VAL0-0.008-0.02859.6640.0000.0000.0000.0000.0000.000
113A138ASN0-0.052-0.01962.3710.0000.0000.0000.0000.0000.000
114A139ILE00.0240.01864.6380.0000.0000.0000.0000.0000.000
115A140PRO00.0120.02167.5880.0000.0000.0000.0000.0000.000
116A141SER00.0490.00270.5780.0000.0000.0000.0000.0000.000
117A142SER0-0.051-0.02873.8640.0000.0000.0000.0000.0000.000
118A143ALA0-0.0100.00472.2190.0000.0000.0000.0000.0000.000
119A144THR0-0.009-0.00274.3260.0000.0000.0000.0000.0000.000
120A145ILE0-0.022-0.00974.9210.0000.0000.0000.0000.0000.000
121A146GLY0-0.006-0.00175.2380.0000.0000.0000.0000.0000.000
122A147ASN0-0.065-0.03171.9760.0010.0010.0000.0000.0000.000
123A148ARG10.8850.93761.1820.0050.0050.0000.0000.0000.000
124A149ALA0-0.010-0.00768.2990.0000.0000.0000.0000.0000.000
125A150VAL0-0.046-0.01862.2920.0000.0000.0000.0000.0000.000
126A151LEU00.0070.01864.2770.0000.0000.0000.0000.0000.000
127A152THR0-0.017-0.02359.7010.0000.0000.0000.0000.0000.000
128A153CYS0-0.014-0.00658.7450.0000.0000.0000.0000.0000.000
129A154SER00.0000.00254.8440.0000.0000.0000.0000.0000.000
130A155GLU-1-0.754-0.85151.752-0.026-0.0260.0000.0000.0000.000
131A156GLN0-0.048-0.01848.8260.0010.0010.0000.0000.0000.000
132A157ASP-1-0.795-0.84549.130-0.032-0.0320.0000.0000.0000.000
133A158GLY0-0.039-0.01947.873-0.002-0.0020.0000.0000.0000.000
134A159SER0-0.071-0.02642.4760.0000.0000.0000.0000.0000.000
135A160PRO00.009-0.02542.852-0.002-0.0020.0000.0000.0000.000
136A161PRO00.0370.01043.7720.0010.0010.0000.0000.0000.000
137A162SER0-0.028-0.03146.9650.0010.0010.0000.0000.0000.000
138A163GLU-1-0.965-0.96749.987-0.015-0.0150.0000.0000.0000.000
139A164TYR0-0.028-0.04652.2210.0000.0000.0000.0000.0000.000
140A165THR0-0.054-0.02555.9510.0010.0010.0000.0000.0000.000
141A166TRP00.006-0.00958.9270.0000.0000.0000.0000.0000.000
142A167PHE0-0.026-0.01762.2040.0000.0000.0000.0000.0000.000
143A168LYS10.8350.90865.7210.0070.0070.0000.0000.0000.000
144A169ASP-1-0.834-0.90969.300-0.008-0.0080.0000.0000.0000.000
145A170GLY0-0.0090.00468.9360.0000.0000.0000.0000.0000.000
146A171ILE0-0.048-0.02068.1160.0000.0000.0000.0000.0000.000
147A172VAL00.0100.00262.0290.0000.0000.0000.0000.0000.000
148A173MET0-0.0010.01063.2830.0010.0010.0000.0000.0000.000
149A174PRO0-0.039-0.01062.3880.0000.0000.0000.0000.0000.000
150A175THR00.0430.02156.7600.0000.0000.0000.0000.0000.000
151A176ASN00.0010.02260.2310.0000.0000.0000.0000.0000.000
152A177PRO00.0780.06362.4600.0000.0000.0000.0000.0000.000
153A178LYS10.9190.93965.4130.0020.0020.0000.0000.0000.000
154A179SER0-0.045-0.02165.6440.0000.0000.0000.0000.0000.000
155A180THR00.0050.00367.6550.0000.0000.0000.0000.0000.000
156A181ARG10.8980.92961.9970.0050.0050.0000.0000.0000.000
157A182ALA00.0290.03069.2990.0000.0000.0000.0000.0000.000
158A183PHE00.0740.02168.5890.0000.0000.0000.0000.0000.000
159A184SER0-0.026-0.01970.0780.0000.0000.0000.0000.0000.000
160A185ASN0-0.058-0.03171.0790.0000.0000.0000.0000.0000.000
161A186SER00.016-0.00669.8410.0000.0000.0000.0000.0000.000
162A187SER0-0.061-0.04968.6860.0010.0010.0000.0000.0000.000
163A188TYR0-0.024-0.02563.4000.0000.0000.0000.0000.0000.000
164A189VAL0-0.017-0.01159.5930.0000.0000.0000.0000.0000.000
165A190LEU00.0090.00158.941-0.001-0.0010.0000.0000.0000.000
166A191ASN00.0320.01753.2320.0000.0000.0000.0000.0000.000
167A192PRO00.0320.00953.009-0.001-0.0010.0000.0000.0000.000
168A193THR00.0500.02848.165-0.001-0.0010.0000.0000.0000.000
169A194THR0-0.033-0.01651.129-0.001-0.0010.0000.0000.0000.000
170A195GLY00.0200.01853.5620.0000.0000.0000.0000.0000.000
171A196GLU-1-0.881-0.93356.824-0.007-0.0070.0000.0000.0000.000
172A197LEU0-0.044-0.01358.9900.0000.0000.0000.0000.0000.000
173A198VAL0-0.028-0.01361.1600.0000.0000.0000.0000.0000.000
174A199PHE00.0250.01263.9890.0010.0010.0000.0000.0000.000
175A200ASP-1-0.868-0.94166.793-0.003-0.0030.0000.0000.0000.000
176A201PRO0-0.0310.01368.6740.0000.0000.0000.0000.0000.000
177A202LEU0-0.020-0.00971.3120.0000.0000.0000.0000.0000.000
178A203SER00.017-0.00772.6650.0000.0000.0000.0000.0000.000
179A204ALA00.0800.02975.5350.0000.0000.0000.0000.0000.000
180A205SER0-0.028-0.02375.2640.0000.0000.0000.0000.0000.000
181A206ASP-1-0.759-0.84671.765-0.005-0.0050.0000.0000.0000.000
182A207THR00.0100.02472.877-0.001-0.0010.0000.0000.0000.000
183A208GLY0-0.023-0.00773.4600.0000.0000.0000.0000.0000.000
184A209GLU-1-0.910-0.96671.248-0.011-0.0110.0000.0000.0000.000
185A210TYR0-0.022-0.03567.0600.0000.0000.0000.0000.0000.000
186A211SER0-0.008-0.00665.1770.0000.0000.0000.0000.0000.000
187A213GLU-1-0.822-0.89857.655-0.018-0.0180.0000.0000.0000.000
188A214ALA00.0200.01454.4940.0010.0010.0000.0000.0000.000
189A215ARG10.8700.91053.2510.0150.0150.0000.0000.0000.000
190A216ASN00.0300.01247.5940.0020.0020.0000.0000.0000.000
191A217GLY0-0.0080.00447.644-0.001-0.0010.0000.0000.0000.000
192A218TYR0-0.012-0.01447.029-0.001-0.0010.0000.0000.0000.000
193A219GLY00.0200.01149.1690.0010.0010.0000.0000.0000.000
194A220THR0-0.055-0.03851.5390.0010.0010.0000.0000.0000.000
195A221PRO0-0.0030.02254.928-0.001-0.0010.0000.0000.0000.000
196A222MET00.0140.01356.3130.0010.0010.0000.0000.0000.000
197A223THR0-0.015-0.01058.3900.0010.0010.0000.0000.0000.000
198A224SER00.0300.00461.5530.0000.0000.0000.0000.0000.000
199A225ASN0-0.047-0.03162.786-0.001-0.0010.0000.0000.0000.000
200A226ALA00.0210.02866.2330.0000.0000.0000.0000.0000.000
201A227VAL0-0.021-0.01567.8880.0000.0000.0000.0000.0000.000
202A228ARG10.8480.90370.3540.0080.0080.0000.0000.0000.000
203A229MET0-0.043-0.00770.3690.0000.0000.0000.0000.0000.000
204A230GLU-1-0.797-0.87273.593-0.007-0.0070.0000.0000.0000.000
205A231ALA00.012-0.00175.4910.0000.0000.0000.0000.0000.000
206A232VAL0-0.027-0.01876.8500.0000.0000.0000.0000.0000.000
207A233GLU-1-0.952-0.96979.245-0.003-0.0030.0000.0000.0000.000