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: QY7VY

Calculation Name: 3NB6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NB6

Chain ID: A

ChEMBL ID:

UniProt ID: O66874

Base Structure: X-ray

Registration Date: 2023-06-21

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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2062055.294852
FMO2-HF: Nuclear repulsion 1989803.514071
FMO2-HF: Total energy -72251.780781
FMO2-MP2: Total energy -72468.445862


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:61:GLN)


Summations of interaction energy for fragment #1(A:61:GLN)
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.
-32.968-26.8912.393-6.981-11.490.002
Interaction energy analysis for fragmet #1(A:61:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.014 / q_NPA : -0.005
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].
3A63ARG10.9090.9512.128-21.048-19.2497.453-4.305-4.9470.025
4A64PHE00.0650.0355.375-0.226-0.095-0.001-0.006-0.1230.000
5A65TYR0-0.020-0.0247.759-0.889-0.8890.0000.0000.0000.000
6A66VAL0-0.052-0.0309.8750.4610.4610.0000.0000.0000.000
7A67SER0-0.015-0.02513.205-0.186-0.1860.0000.0000.0000.000
8A68ILE00.009-0.02815.3980.0370.0370.0000.0000.0000.000
9A69ASP-1-0.873-0.90516.805-0.684-0.6840.0000.0000.0000.000
10A70LYS10.8950.95916.3600.7170.7170.0000.0000.0000.000
11A71ILE0-0.059-0.02113.711-0.036-0.0360.0000.0000.0000.000
12A72PRO00.0390.03017.9380.0480.0480.0000.0000.0000.000
13A73GLU-1-0.868-0.94919.978-0.541-0.5410.0000.0000.0000.000
14A74HIS00.0370.01622.382-0.028-0.0280.0000.0000.0000.000
15A75VAL00.0090.00115.960-0.010-0.0100.0000.0000.0000.000
16A76ILE00.0050.00017.417-0.058-0.0580.0000.0000.0000.000
17A77ASN00.0270.00518.739-0.033-0.0330.0000.0000.0000.000
18A78ALA00.0430.02819.4780.0310.0310.0000.0000.0000.000
19A79PHE0-0.012-0.01812.505-0.004-0.0040.0000.0000.0000.000
20A80VAL0-0.0160.00317.7600.0200.0200.0000.0000.0000.000
21A81ALA00.0240.01419.9570.0440.0440.0000.0000.0000.000
22A82THR0-0.082-0.04619.0350.0810.0810.0000.0000.0000.000
23A83GLU-1-0.884-0.95915.468-0.653-0.6530.0000.0000.0000.000
24A84ASP-1-0.773-0.87018.276-0.604-0.6040.0000.0000.0000.000
25A85ARG10.9070.95320.1570.3260.3260.0000.0000.0000.000
26A86ASN0-0.023-0.02523.3670.0160.0160.0000.0000.0000.000
27A87PHE0-0.0410.00217.146-0.002-0.0020.0000.0000.0000.000
28A88TRP00.029-0.01320.253-0.032-0.0320.0000.0000.0000.000
29A89HIS00.0070.00823.5120.0190.0190.0000.0000.0000.000
30A90HIS0-0.078-0.02319.4900.0570.0570.0000.0000.0000.000
31A91PHE00.0480.01723.466-0.019-0.0190.0000.0000.0000.000
32A92GLY00.0470.01419.4450.0030.0030.0000.0000.0000.000
33A93ILE0-0.064-0.01919.545-0.015-0.0150.0000.0000.0000.000
34A94ASP-1-0.734-0.87122.188-0.344-0.3440.0000.0000.0000.000
35A95PRO00.0200.00024.2760.0150.0150.0000.0000.0000.000
36A96VAL00.0670.03427.5340.0170.0170.0000.0000.0000.000
37A97ALA00.0080.01524.0680.0160.0160.0000.0000.0000.000
38A98ILE00.003-0.00724.2540.0090.0090.0000.0000.0000.000
39A99VAL00.0190.01126.2520.0220.0220.0000.0000.0000.000
40A100ARG10.9360.95828.4760.2220.2220.0000.0000.0000.000
41A101ALA0-0.007-0.01925.2170.0050.0050.0000.0000.0000.000
42A102ALA00.0010.00527.2480.0150.0150.0000.0000.0000.000
43A103ILE0-0.016-0.02329.9530.0140.0140.0000.0000.0000.000
44A104VAL0-0.080-0.02629.5600.0110.0110.0000.0000.0000.000
45A105ASN00.0390.02227.9670.0080.0080.0000.0000.0000.000
46A106TYR00.0460.01230.6100.0050.0050.0000.0000.0000.000
47A107ARG10.8800.95234.0440.1320.1320.0000.0000.0000.000
48A108ALA0-0.0020.00031.144-0.002-0.0020.0000.0000.0000.000
49A109GLY00.0380.03731.8960.0000.0000.0000.0000.0000.000
50A110ARG10.9100.93929.0820.0730.0730.0000.0000.0000.000
51A111ILE0-0.047-0.02724.5130.0020.0020.0000.0000.0000.000
52A112ALA00.0350.02226.4090.0020.0020.0000.0000.0000.000
53A113GLN0-0.051-0.00424.301-0.006-0.0060.0000.0000.0000.000
54A114GLY00.0550.02820.5250.0140.0140.0000.0000.0000.000
55A115GLY0-0.029-0.01121.0610.0140.0140.0000.0000.0000.000
56A116SER0-0.097-0.04716.5990.0030.0030.0000.0000.0000.000
57A117THR00.0320.02617.963-0.053-0.0530.0000.0000.0000.000
58A118ILE00.018-0.01113.438-0.040-0.0400.0000.0000.0000.000
59A119THR0-0.034-0.04013.263-0.188-0.1880.0000.0000.0000.000
60A120GLN00.0440.02513.748-0.039-0.0390.0000.0000.0000.000
61A121GLN0-0.094-0.03411.252-0.089-0.0890.0000.0000.0000.000
62A122LEU00.0400.0228.306-0.132-0.1320.0000.0000.0000.000
63A123ALA00.0180.0009.050-0.090-0.0900.0000.0000.0000.000
64A124LYS10.8750.9569.9780.9290.9290.0000.0000.0000.000
65A125ASN0-0.064-0.0445.3840.5090.5090.0000.0000.0000.000
66A126LEU0-0.020-0.0015.969-0.052-0.0520.0000.0000.0000.000
67A127PHE0-0.082-0.0328.3170.2330.2330.0000.0000.0000.000
68A128LEU00.0290.0237.6160.2770.2770.0000.0000.0000.000
69A129THR00.017-0.0028.5390.4420.4420.0000.0000.0000.000
70A130ARG10.9870.9759.619-1.151-1.1510.0000.0000.0000.000
71A131GLU-1-0.827-0.87011.6520.2670.2670.0000.0000.0000.000
72A132ARG10.8180.83714.3050.0370.0370.0000.0000.0000.000
73A133THR00.0640.02817.069-0.053-0.0530.0000.0000.0000.000
74A134LEU00.0460.02219.836-0.030-0.0300.0000.0000.0000.000
75A135GLU-1-0.797-0.90520.8900.0290.0290.0000.0000.0000.000
76A136ARG10.7980.90812.337-0.298-0.2980.0000.0000.0000.000
77A137LYS10.9250.96717.2210.0300.0300.0000.0000.0000.000
78A138ILE00.0130.01218.474-0.052-0.0520.0000.0000.0000.000
79A139LYS10.9020.93817.627-0.069-0.0690.0000.0000.0000.000
80A140GLU-1-0.764-0.84613.551-0.249-0.2490.0000.0000.0000.000
81A141ALA00.0090.00116.107-0.082-0.0820.0000.0000.0000.000
82A142LEU0-0.009-0.00719.147-0.022-0.0220.0000.0000.0000.000
83A143LEU00.0000.01012.924-0.016-0.0160.0000.0000.0000.000
84A144ALA00.0310.00116.108-0.051-0.0510.0000.0000.0000.000
85A145ILE00.0230.01517.017-0.019-0.0190.0000.0000.0000.000
86A146LYS10.9130.96919.0190.3590.3590.0000.0000.0000.000
87A147ILE00.003-0.00413.303-0.002-0.0020.0000.0000.0000.000
88A148GLU-1-0.758-0.86017.572-0.661-0.6610.0000.0000.0000.000
89A149ARG10.8910.96020.0470.3200.3200.0000.0000.0000.000
90A150THR0-0.099-0.04918.9240.0500.0500.0000.0000.0000.000
91A151PHE0-0.019-0.01415.813-0.017-0.0170.0000.0000.0000.000
92A152ASP-1-0.789-0.89619.465-0.677-0.6770.0000.0000.0000.000
93A153LYS10.8230.89218.8590.4870.4870.0000.0000.0000.000
94A154LYS11.0051.00018.0370.5170.5170.0000.0000.0000.000
95A155LYS10.8780.93714.8130.9600.9600.0000.0000.0000.000
96A156ILE00.0030.00414.224-0.235-0.2350.0000.0000.0000.000
97A157MET0-0.0100.00313.183-0.293-0.2930.0000.0000.0000.000
98A158GLU-1-0.763-0.84112.548-1.506-1.5060.0000.0000.0000.000
99A159LEU00.0080.0089.923-0.377-0.3770.0000.0000.0000.000
100A160TYR0-0.030-0.0338.508-0.876-0.8760.0000.0000.0000.000
101A161LEU00.0430.0048.822-0.560-0.5600.0000.0000.0000.000
102A162ASN0-0.046-0.0247.629-0.035-0.0350.0000.0000.0000.000
103A163GLN0-0.055-0.0224.147-1.999-1.894-0.001-0.014-0.0900.000
104A164ILE0-0.031-0.0024.269-1.684-1.528-0.001-0.022-0.1340.000
105A165TYR0-0.0180.0045.3690.0990.0990.0000.0000.0000.000
106A166LEU0-0.002-0.0036.9360.6470.6470.0000.0000.0000.000
107A167GLY00.0370.0208.9260.3040.3040.0000.0000.0000.000
108A168SER00.0510.0109.579-0.104-0.1040.0000.0000.0000.000
109A169GLY0-0.0070.0046.3560.1210.1210.0000.0000.0000.000
110A170ALA00.0020.0095.475-0.093-0.0930.0000.0000.0000.000
111A171TYR0-0.049-0.0472.651-6.821-2.9444.944-2.622-6.199-0.023
112A172GLY00.0500.0404.765-0.159-0.149-0.001-0.0120.0030.000
113A173VAL00.017-0.0147.7050.5560.5560.0000.0000.0000.000
114A174GLU-1-0.772-0.8649.698-0.561-0.5610.0000.0000.0000.000
115A175ALA00.015-0.0046.1890.3470.3470.0000.0000.0000.000
116A176ALA0-0.007-0.0038.1870.3610.3610.0000.0000.0000.000
117A177ALA00.0210.01510.6630.2180.2180.0000.0000.0000.000
118A178GLN0-0.067-0.02510.9170.3000.3000.0000.0000.0000.000
119A179VAL0-0.057-0.0348.9630.1270.1270.0000.0000.0000.000
120A180TYR0-0.089-0.05811.8250.1430.1430.0000.0000.0000.000
121A181PHE00.003-0.00415.0950.0360.0360.0000.0000.0000.000
122A182GLY0-0.0160.01415.8630.0320.0320.0000.0000.0000.000
123A183LYS10.8110.89816.2770.4010.4010.0000.0000.0000.000
124A184HIS10.8500.89614.6670.3260.3260.0000.0000.0000.000
125A185VAL00.031-0.01513.7220.0280.0280.0000.0000.0000.000
126A186TRP0-0.016-0.02715.108-0.014-0.0140.0000.0000.0000.000
127A187GLU-1-0.849-0.90118.667-0.315-0.3150.0000.0000.0000.000
128A188LEU0-0.066-0.01715.8480.0250.0250.0000.0000.0000.000
129A189SER00.005-0.02020.3040.0000.0000.0000.0000.0000.000
130A190LEU00.009-0.00222.295-0.047-0.0470.0000.0000.0000.000
131A191ASP-1-0.808-0.90623.257-0.367-0.3670.0000.0000.0000.000
132A192GLU-1-0.784-0.85319.433-0.413-0.4130.0000.0000.0000.000
133A193ALA0-0.023-0.01718.633-0.081-0.0810.0000.0000.0000.000
134A194ALA0-0.002-0.01718.647-0.077-0.0770.0000.0000.0000.000
135A195LEU0-0.013-0.00417.934-0.008-0.0080.0000.0000.0000.000
136A196LEU00.0300.01313.568-0.052-0.0520.0000.0000.0000.000
137A197ALA00.0340.02415.129-0.090-0.0900.0000.0000.0000.000
138A198ALA0-0.007-0.00317.0440.0220.0220.0000.0000.0000.000
139A199LEU0-0.031-0.00213.4500.0710.0710.0000.0000.0000.000
140A200PRO00.0200.02011.9560.0730.0730.0000.0000.0000.000
141A201LYS10.9080.96312.8220.4000.4000.0000.0000.0000.000
142A202ALA0-0.076-0.05614.6770.1140.1140.0000.0000.0000.000
143A203PRO00.0530.03710.7870.0900.0900.0000.0000.0000.000
144A204ALA00.0270.02213.7050.0350.0350.0000.0000.0000.000
145A205LYS10.8940.95215.6780.2060.2060.0000.0000.0000.000
146A206TYR00.033-0.01217.5900.0460.0460.0000.0000.0000.000
147A207ASN00.0480.04014.037-0.066-0.0660.0000.0000.0000.000
148A208PRO00.0590.01016.1940.0640.0640.0000.0000.0000.000
149A209PHE0-0.010-0.00813.7520.0310.0310.0000.0000.0000.000
150A210TYR0-0.047-0.02714.8280.0180.0180.0000.0000.0000.000
151A211HIS0-0.0060.01219.4960.0520.0520.0000.0000.0000.000
152A212PRO00.0410.02822.290-0.034-0.0340.0000.0000.0000.000
153A213GLU-1-0.782-0.87323.362-0.135-0.1350.0000.0000.0000.000
154A214ARG10.7970.86722.1930.1040.1040.0000.0000.0000.000
155A215ALA0-0.044-0.00420.340-0.026-0.0260.0000.0000.0000.000
156A216LEU00.0520.02921.810-0.036-0.0360.0000.0000.0000.000
157A217GLN00.0080.00424.615-0.016-0.0160.0000.0000.0000.000
158A218ARG10.7820.87517.6050.5170.5170.0000.0000.0000.000
159A219ARG10.8790.93622.0000.2710.2710.0000.0000.0000.000
160A220ASN00.0580.02423.073-0.034-0.0340.0000.0000.0000.000
161A221LEU0-0.036-0.00324.4920.0090.0090.0000.0000.0000.000
162A222VAL0-0.029-0.00720.3440.0030.0030.0000.0000.0000.000
163A223LEU00.0470.01423.628-0.008-0.0080.0000.0000.0000.000
164A224LYS10.9000.95126.4250.2420.2420.0000.0000.0000.000
165A225ARG10.6650.81124.4890.3790.3790.0000.0000.0000.000
166A226MET0-0.0030.00823.485-0.006-0.0060.0000.0000.0000.000
167A227LEU00.0070.01826.6010.0080.0080.0000.0000.0000.000
168A228GLU-1-0.877-0.92229.533-0.259-0.2590.0000.0000.0000.000
169A229GLU-1-0.857-0.91625.924-0.344-0.3440.0000.0000.0000.000
170A230GLY00.0170.02129.147-0.004-0.0040.0000.0000.0000.000
171A231TYR0-0.065-0.03824.870-0.015-0.0150.0000.0000.0000.000
172A232ILE0-0.037-0.00927.310-0.010-0.0100.0000.0000.0000.000
173A233THR0-0.006-0.03630.0740.0060.0060.0000.0000.0000.000
174A234PRO00.0460.00533.258-0.008-0.0080.0000.0000.0000.000
175A235GLU-1-0.836-0.89035.284-0.204-0.2040.0000.0000.0000.000
176A236GLN00.0360.01130.652-0.010-0.0100.0000.0000.0000.000
177A237TYR0-0.022-0.00730.147-0.017-0.0170.0000.0000.0000.000
178A238GLU-1-0.900-0.96031.454-0.185-0.1850.0000.0000.0000.000
179A239GLU-1-0.823-0.88330.940-0.209-0.2090.0000.0000.0000.000
180A240ALA0-0.016-0.01327.3280.0000.0000.0000.0000.0000.000
181A241VAL0-0.052-0.02528.506-0.005-0.0050.0000.0000.0000.000
182A242ASN0-0.017-0.02129.8800.0170.0170.0000.0000.0000.000
183A243LYS10.7290.88927.3040.2280.2280.0000.0000.0000.000