Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: Q1QVY

Calculation Name: 3NFQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NFQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q06505

Base Structure: X-ray

Registration Date: 2023-06-20

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 147
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1373008.800325
FMO2-HF: Nuclear repulsion 1315781.904017
FMO2-HF: Total energy -57226.896308
FMO2-MP2: Total energy -57397.220038


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:8:ASP)


Summations of interaction energy for fragment #1(A:8:ASP)
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.
8.89114.1147.133-5.455-6.9020.035
Interaction energy analysis for fragmet #1(A:8:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.894 / q_NPA : -0.960
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].
3A10LEU0-0.025-0.0232.818-10.780-7.3890.772-1.852-2.3110.012
4A11GLU-1-0.874-0.9542.07032.86933.8276.350-3.304-4.0050.022
5A12GLN0-0.035-0.0153.841-12.192-11.3180.011-0.299-0.5860.001
6A13TYR0-0.027-0.0085.582-5.784-5.7840.0000.0000.0000.000
7A14LEU0-0.026-0.0136.949-4.860-4.8600.0000.0000.0000.000
8A15ASP-1-0.772-0.8797.24529.91329.9130.0000.0000.0000.000
9A16GLU-1-0.841-0.8849.26617.84417.8440.0000.0000.0000.000
10A17LYS10.8860.94911.311-20.375-20.3750.0000.0000.0000.000
11A18ILE0-0.049-0.03912.385-2.319-2.3190.0000.0000.0000.000
12A19LEU00.0260.00612.025-1.768-1.7680.0000.0000.0000.000
13A20ARG10.8470.90915.135-18.609-18.6090.0000.0000.0000.000
14A21LEU0-0.053-0.01917.066-0.987-0.9870.0000.0000.0000.000
15A22LYS10.9000.95617.387-17.209-17.2090.0000.0000.0000.000
16A23ASP-1-0.889-0.94319.36313.83213.8320.0000.0000.0000.000
17A24GLU-1-0.863-0.92821.23512.68212.6820.0000.0000.0000.000
18A25MET0-0.055-0.02922.515-0.470-0.4700.0000.0000.0000.000
19A26ASN00.0410.04322.300-0.755-0.7550.0000.0000.0000.000
20A27ILE00.0190.01924.607-0.560-0.5600.0000.0000.0000.000
21A28ALA0-0.016-0.01227.099-0.490-0.4900.0000.0000.0000.000
22A29ALA0-0.012-0.01528.460-0.434-0.4340.0000.0000.0000.000
23A30GLN0-0.030-0.01029.894-0.196-0.1960.0000.0000.0000.000
24A31LEU00.0440.01330.829-0.324-0.3240.0000.0000.0000.000
25A32ASP-1-0.770-0.87433.0758.8498.8490.0000.0000.0000.000
26A33ILE00.0090.01234.224-0.300-0.3000.0000.0000.0000.000
27A34ASP-1-0.852-0.91435.5038.3128.3120.0000.0000.0000.000
28A35THR0-0.078-0.04637.297-0.288-0.2880.0000.0000.0000.000
29A36LEU0-0.049-0.01738.965-0.250-0.2500.0000.0000.0000.000
30A37ASN00.0400.01039.300-0.266-0.2660.0000.0000.0000.000
31A38LYS11.0351.03642.075-7.303-7.3030.0000.0000.0000.000
32A39ARG10.8230.91643.496-7.159-7.1590.0000.0000.0000.000
33A40ILE0-0.065-0.03543.518-0.174-0.1740.0000.0000.0000.000
34A41GLU-1-0.966-0.98245.0396.7896.7890.0000.0000.0000.000
35A42THR0-0.082-0.07447.451-0.147-0.1470.0000.0000.0000.000
36A43GLY00.0060.01649.262-0.128-0.1280.0000.0000.0000.000
37A44ASP-1-0.827-0.87648.2996.3686.3680.0000.0000.0000.000
38A45THR0-0.025-0.02947.4140.1350.1350.0000.0000.0000.000
39A46SER0-0.117-0.08646.9920.1270.1270.0000.0000.0000.000
40A47LEU00.0040.02143.3590.1870.1870.0000.0000.0000.000
41A48ILE00.0130.00140.312-0.046-0.0460.0000.0000.0000.000
42A49ALA00.0110.01836.4230.0920.0920.0000.0000.0000.000
43A50MET00.005-0.00835.6840.0220.0220.0000.0000.0000.000
44A51GLN0-0.022-0.00930.886-0.020-0.0200.0000.0000.0000.000
45A52LYS10.9010.93729.368-9.201-9.2010.0000.0000.0000.000
46A53VAL00.0080.00029.7700.2690.2690.0000.0000.0000.000
47A54LYS10.8880.94430.945-8.833-8.8330.0000.0000.0000.000
48A55LEU0-0.0070.01323.7460.1970.1970.0000.0000.0000.000
49A56LEU00.005-0.00126.1280.4400.4400.0000.0000.0000.000
50A57PRO00.0140.00826.4890.3720.3720.0000.0000.0000.000
51A58LYS10.8260.90720.645-13.170-13.1700.0000.0000.0000.000
52A59VAL00.0270.01222.0750.6340.6340.0000.0000.0000.000
53A60VAL00.0290.01222.2430.4760.4760.0000.0000.0000.000
54A61SER00.0030.00922.0880.5380.5380.0000.0000.0000.000
55A62VAL0-0.017-0.00816.7320.4400.4400.0000.0000.0000.000
56A63LEU00.005-0.00218.4140.6270.6270.0000.0000.0000.000
57A64SER0-0.052-0.01920.3610.0310.0310.0000.0000.0000.000
58A65LYS10.8520.92716.474-15.273-15.2730.0000.0000.0000.000
59A66ALA00.0860.03816.6170.7320.7320.0000.0000.0000.000
60A67ASN0-0.031-0.02611.826-0.201-0.2010.0000.0000.0000.000
61A68LEU00.0230.01811.5961.4921.4920.0000.0000.0000.000
62A69ALA0-0.018-0.00813.4660.0790.0790.0000.0000.0000.000
63A70ASP-1-0.843-0.91710.75124.19724.1970.0000.0000.0000.000
64A71THR00.0590.0498.982-0.976-0.9760.0000.0000.0000.000
65A72ILE0-0.065-0.04011.021-1.255-1.2550.0000.0000.0000.000
66A73LEU0-0.089-0.05914.641-1.176-1.1760.0000.0000.0000.000
67A74ASP-1-0.886-0.93310.44125.81825.8180.0000.0000.0000.000
68A75ASN0-0.089-0.0639.723-1.047-1.0470.0000.0000.0000.000
69A76ASN0-0.021-0.03313.701-1.740-1.7400.0000.0000.0000.000
70A77LEU00.0360.02116.736-1.083-1.0830.0000.0000.0000.000
71A78LEU00.001-0.01518.382-0.987-0.9870.0000.0000.0000.000
72A79GLN00.0080.00920.856-0.515-0.5150.0000.0000.0000.000
73A80SER00.008-0.01821.821-0.397-0.3970.0000.0000.0000.000
74A81VAL0-0.025-0.00922.278-0.563-0.5630.0000.0000.0000.000
75A82ARG10.7700.85924.861-11.598-11.5980.0000.0000.0000.000
76A83ILE0-0.010-0.00425.374-0.463-0.4630.0000.0000.0000.000
77A84TRP0-0.061-0.04926.576-0.463-0.4630.0000.0000.0000.000
78A85LEU0-0.039-0.00428.413-0.386-0.3860.0000.0000.0000.000
79A86GLU-1-0.806-0.86230.7909.8429.8420.0000.0000.0000.000
80A87PRO0-0.044-0.01432.816-0.092-0.0920.0000.0000.0000.000
81A88LEU00.0250.01935.9880.1120.1120.0000.0000.0000.000
82A89PRO00.0550.01138.092-0.105-0.1050.0000.0000.0000.000
83A90ASP-1-0.793-0.86440.5937.2617.2610.0000.0000.0000.000
84A91GLY0-0.037-0.01940.945-0.163-0.1630.0000.0000.0000.000
85A92SER0-0.123-0.08740.9880.1000.1000.0000.0000.0000.000
86A93LEU00.005-0.00336.2560.1700.1700.0000.0000.0000.000
87A94PRO00.0120.02033.182-0.172-0.1720.0000.0000.0000.000
88A95SER00.021-0.01336.088-0.049-0.0490.0000.0000.0000.000
89A96PHE00.0590.01835.8840.2620.2620.0000.0000.0000.000
90A97GLU-1-0.830-0.90435.0538.4048.4040.0000.0000.0000.000
91A98ILE00.0070.01830.5790.3330.3330.0000.0000.0000.000
92A99GLN0-0.036-0.02231.2120.3250.3250.0000.0000.0000.000
93A100LYS10.9460.96332.002-8.297-8.2970.0000.0000.0000.000
94A101SER0-0.054-0.03429.4580.2070.2070.0000.0000.0000.000
95A102LEU00.0100.00025.8890.4000.4000.0000.0000.0000.000
96A103PHE0-0.017-0.01427.2400.3680.3680.0000.0000.0000.000
97A104ALA0-0.033-0.01528.8720.1370.1370.0000.0000.0000.000
98A105ALA00.0080.00524.0710.2220.2220.0000.0000.0000.000
99A106LEU0-0.018-0.01623.4550.4450.4450.0000.0000.0000.000
100A107ASN0-0.071-0.04425.145-0.124-0.1240.0000.0000.0000.000
101A108ASP-1-0.871-0.92223.43511.97511.9750.0000.0000.0000.000
102A109LEU0-0.0010.01118.5270.6600.6600.0000.0000.0000.000
103A110PRO0-0.0070.00718.164-0.711-0.7110.0000.0000.0000.000
104A111VAL0-0.047-0.03120.2880.5310.5310.0000.0000.0000.000
105A112LYS10.9450.98720.160-15.441-15.4410.0000.0000.0000.000
106A113THR00.026-0.01122.812-0.199-0.1990.0000.0000.0000.000
107A114GLU-1-0.857-0.94319.08914.91014.9100.0000.0000.0000.000
108A115HIS00.1690.08116.773-1.066-1.0660.0000.0000.0000.000
109A116LEU0-0.0370.00821.160-0.426-0.4260.0000.0000.0000.000
110A117LYS10.8630.92824.400-11.445-11.4450.0000.0000.0000.000
111A118GLU-1-0.830-0.89818.36216.31816.3180.0000.0000.0000.000
112A119SER0-0.011-0.01121.860-0.361-0.3610.0000.0000.0000.000
113A120GLY0-0.009-0.01923.353-0.431-0.4310.0000.0000.0000.000
114A121LEU00.0390.01024.552-0.566-0.5660.0000.0000.0000.000
115A122GLY00.0270.02727.178-0.351-0.3510.0000.0000.0000.000
116A123ARG10.9040.93929.169-9.702-9.7020.0000.0000.0000.000
117A124VAL00.0270.03030.191-0.378-0.3780.0000.0000.0000.000
118A125VAL00.0580.02528.994-0.346-0.3460.0000.0000.0000.000
119A126ILE00.0160.00132.086-0.368-0.3680.0000.0000.0000.000
120A127PHE0-0.0230.00834.895-0.327-0.3270.0000.0000.0000.000
121A128TYR00.001-0.03333.920-0.294-0.2940.0000.0000.0000.000
122A129THR0-0.077-0.03435.781-0.255-0.2550.0000.0000.0000.000
123A130LYS10.9280.95438.330-8.335-8.3350.0000.0000.0000.000
124A131SER0-0.0220.00340.189-0.333-0.3330.0000.0000.0000.000
125A132LYS10.9580.95641.867-6.865-6.8650.0000.0000.0000.000
126A133ARG10.8660.94241.889-7.332-7.3320.0000.0000.0000.000
127A134VAL0-0.0270.01338.0040.0630.0630.0000.0000.0000.000
128A135GLU-1-0.855-0.92940.2957.1347.1340.0000.0000.0000.000
129A136ALA00.0310.01040.3530.1960.1960.0000.0000.0000.000
130A137GLN00.0260.00338.3630.3030.3030.0000.0000.0000.000
131A138LEU00.0120.00434.7410.1990.1990.0000.0000.0000.000
132A139ALA00.0240.02536.0180.2140.2140.0000.0000.0000.000
133A140ARG10.8240.89237.491-7.725-7.7250.0000.0000.0000.000
134A141LEU00.0240.03431.7050.1030.1030.0000.0000.0000.000
135A142ALA0-0.002-0.00832.7510.2870.2870.0000.0000.0000.000
136A143GLU-1-0.900-0.94433.3048.2888.2880.0000.0000.0000.000
137A144LYS10.8530.92629.846-10.542-10.5420.0000.0000.0000.000
138A145LEU0-0.010-0.00528.0180.1770.1770.0000.0000.0000.000
139A146ILE00.0020.00429.6560.3150.3150.0000.0000.0000.000
140A147ALA0-0.0010.01930.9690.1680.1680.0000.0000.0000.000
141A148GLU-1-0.858-0.92527.63711.55011.5500.0000.0000.0000.000
142A149TRP0-0.011-0.01125.5640.1140.1140.0000.0000.0000.000
143A150THR0-0.089-0.05426.4630.2710.2710.0000.0000.0000.000
144A151ARG10.8690.94225.945-12.247-12.2470.0000.0000.0000.000
145A152PRO00.008-0.02028.3950.3420.3420.0000.0000.0000.000
146A153ILE0-0.0370.00324.4160.2670.2670.0000.0000.0000.000
147A154ILE00.0130.01727.8170.1230.1230.0000.0000.0000.000