FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: 14LJZ

Calculation Name: 3NXH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NXH

Chain ID: A

ChEMBL ID:

UniProt ID: P96499

Base Structure: X-ray

Registration Date: 2023-06-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 222
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2690333.725278
FMO2-HF: Nuclear repulsion 2602919.723809
FMO2-HF: Total energy -87414.001469
FMO2-MP2: Total energy -87669.579326


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:72:MET)


Summations of interaction energy for fragment #1(A:72:MET)
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.
-7.86-2.8879.546-3.24-11.279-0.017
Interaction energy analysis for fragmet #1(A:72:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.064 / q_NPA : 0.047
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].
3A74LYS10.9480.9552.572-1.2972.6421.242-2.482-2.699-0.010
4A75LYS10.8410.9144.7531.3161.529-0.001-0.015-0.1970.000
5A76PRO00.0730.0405.579-0.474-0.4740.0000.0000.0000.000
6A77PHE0-0.065-0.0203.944-0.0710.2300.001-0.039-0.2630.000
7A78SER00.0600.0078.433-0.073-0.0730.0000.0000.0000.000
8A79ILE0-0.028-0.0147.4600.1700.1700.0000.0000.0000.000
9A80LEU00.0150.00811.462-0.073-0.0730.0000.0000.0000.000
10A81PHE00.005-0.01011.2820.0810.0810.0000.0000.0000.000
11A82MET0-0.065-0.03316.320-0.038-0.0380.0000.0000.0000.000
12A83GLY00.0380.03519.8060.0280.0280.0000.0000.0000.000
13A84ILE0-0.042-0.04222.332-0.024-0.0240.0000.0000.0000.000
14A85GLU-1-0.774-0.86125.3170.0880.0880.0000.0000.0000.000
15A86ASP-1-0.825-0.92428.0070.1290.1290.0000.0000.0000.000
16A87TYR00.0800.05921.4830.0080.0080.0000.0000.0000.000
17A88ALA0-0.014-0.01426.8730.0050.0050.0000.0000.0000.000
18A89THR0-0.0360.03928.080-0.012-0.0120.0000.0000.0000.000
19A90LYS10.8800.90830.815-0.141-0.1410.0000.0000.0000.000
20A91GLY00.0630.04433.549-0.003-0.0030.0000.0000.0000.000
21A92GLN0-0.013-0.01734.271-0.001-0.0010.0000.0000.0000.000
22A93LYS10.8140.86833.071-0.112-0.1120.0000.0000.0000.000
23A94GLY00.007-0.00230.9420.0030.0030.0000.0000.0000.000
24A95ARG10.7990.87829.069-0.071-0.0710.0000.0000.0000.000
25A96SER00.0870.05324.5380.0070.0070.0000.0000.0000.000
26A97ASP-1-0.902-0.92125.6560.0350.0350.0000.0000.0000.000
27A98SER0-0.042-0.03022.143-0.017-0.0170.0000.0000.0000.000
28A99LEU00.003-0.00420.6660.0240.0240.0000.0000.0000.000
29A100ILE00.0160.01616.420-0.030-0.0300.0000.0000.0000.000
30A101VAL00.0150.01814.8020.0330.0330.0000.0000.0000.000
31A102VAL0-0.0030.00210.722-0.039-0.0390.0000.0000.0000.000
32A103THR00.008-0.01710.9910.0620.0620.0000.0000.0000.000
33A104LEU0-0.021-0.0105.676-0.073-0.0730.0000.0000.0000.000
34A105ASP-1-0.761-0.8618.020-1.579-1.5790.0000.0000.0000.000
35A106PRO00.0430.0163.482-0.2740.0080.008-0.045-0.2450.000
36A107LYS10.8300.9216.1721.6331.6330.0000.0000.0000.000
37A108ASN0-0.042-0.0338.4800.2450.2450.0000.0000.0000.000
38A109LYS10.8680.9359.0901.5771.5770.0000.0000.0000.000
39A110THR00.0200.02110.1610.2310.2310.0000.0000.0000.000
40A111MET00.0110.0039.037-0.141-0.1410.0000.0000.0000.000
41A112LYS10.8650.95712.0720.5580.5580.0000.0000.0000.000
42A113MET00.0120.00713.9650.0040.0040.0000.0000.0000.000
43A114LEU0-0.0040.00916.4260.0070.0070.0000.0000.0000.000
44A115SER00.0530.01319.1460.0160.0160.0000.0000.0000.000
45A116ILE0-0.050-0.02220.873-0.009-0.0090.0000.0000.0000.000
46A117PRO00.0030.00923.9080.0160.0160.0000.0000.0000.000
47A118ARG10.8860.95727.299-0.014-0.0140.0000.0000.0000.000
48A119ASP-1-0.832-0.92528.4180.0130.0130.0000.0000.0000.000
49A120THR0-0.026-0.03427.861-0.008-0.0080.0000.0000.0000.000
50A121ARG10.8130.89930.2190.0300.0300.0000.0000.0000.000
51A122VAL0-0.003-0.00727.479-0.009-0.0090.0000.0000.0000.000
52A123GLN00.0180.00430.7150.0050.0050.0000.0000.0000.000
53A124LEU0-0.038-0.02928.9920.0000.0000.0000.0000.0000.000
54A125ALA00.0430.04725.830-0.006-0.0060.0000.0000.0000.000
55A126GLY00.0360.01127.864-0.002-0.0020.0000.0000.0000.000
56A127ASP-1-0.834-0.89030.4860.0100.0100.0000.0000.0000.000
57A128THR0-0.048-0.03732.9650.0020.0020.0000.0000.0000.000
58A129THR0-0.093-0.04035.0410.0000.0000.0000.0000.0000.000
59A130GLY0-0.022-0.02437.666-0.001-0.0010.0000.0000.0000.000
60A131SER0-0.070-0.05434.8550.0020.0020.0000.0000.0000.000
61A132LYS10.8750.93537.436-0.033-0.0330.0000.0000.0000.000
62A133THR0-0.023-0.00533.956-0.001-0.0010.0000.0000.0000.000
63A134LYS10.8710.94033.691-0.038-0.0380.0000.0000.0000.000
64A135ILE00.0550.03431.571-0.002-0.0020.0000.0000.0000.000
65A136ASN00.0690.03225.0830.0000.0000.0000.0000.0000.000
66A137ALA0-0.030-0.01527.8010.0070.0070.0000.0000.0000.000
67A138ALA00.020-0.01026.1180.0050.0050.0000.0000.0000.000
68A139TYR0-0.0060.01022.341-0.003-0.0030.0000.0000.0000.000
69A140SER0-0.068-0.02326.7490.0070.0070.0000.0000.0000.000
70A141LYS10.8640.93930.123-0.063-0.0630.0000.0000.0000.000
71A142GLY00.0810.01827.879-0.008-0.0080.0000.0000.0000.000
72A143GLY0-0.0080.01725.4790.0160.0160.0000.0000.0000.000
73A144LYS10.8910.90617.375-0.368-0.3680.0000.0000.0000.000
74A145ASP-1-0.824-0.91120.1160.2770.2770.0000.0000.0000.000
75A146GLU-1-0.791-0.86321.8360.0590.0590.0000.0000.0000.000
76A147THR0-0.058-0.03222.046-0.025-0.0250.0000.0000.0000.000
77A148VAL00.0330.00317.459-0.023-0.0230.0000.0000.0000.000
78A149GLU-1-0.834-0.90620.1140.0380.0380.0000.0000.0000.000
79A150THR0-0.041-0.02722.255-0.029-0.0290.0000.0000.0000.000
80A151VAL0-0.025-0.02519.225-0.024-0.0240.0000.0000.0000.000
81A152GLU-1-0.816-0.90117.6380.0180.0180.0000.0000.0000.000
82A153ASN0-0.064-0.03420.555-0.042-0.0420.0000.0000.0000.000
83A154PHE0-0.0050.00423.907-0.019-0.0190.0000.0000.0000.000
84A155LEU00.003-0.00318.655-0.015-0.0150.0000.0000.0000.000
85A156GLN0-0.093-0.05021.083-0.040-0.0400.0000.0000.0000.000
86A157ILE0-0.0020.00515.374-0.039-0.0390.0000.0000.0000.000
87A158PRO00.0280.02414.3320.0360.0360.0000.0000.0000.000
88A159ILE0-0.029-0.00414.311-0.057-0.0570.0000.0000.0000.000
89A160ASP-1-0.864-0.9199.543-0.146-0.1460.0000.0000.0000.000
90A161LYS10.7660.8596.158-1.935-1.9350.0000.0000.0000.000
91A162TYR00.0430.03410.728-0.145-0.1450.0000.0000.0000.000
92A163VAL0-0.021-0.00812.4700.1330.1330.0000.0000.0000.000
93A164THR0-0.043-0.01515.124-0.080-0.0800.0000.0000.0000.000
94A165VAL00.0030.01418.8140.0350.0350.0000.0000.0000.000
95A166ASP-1-0.821-0.90920.6490.1660.1660.0000.0000.0000.000
96A167PHE00.017-0.01623.995-0.008-0.0080.0000.0000.0000.000
97A168ASP-1-0.832-0.91626.5440.1480.1480.0000.0000.0000.000
98A169GLY00.0270.00622.9340.0010.0010.0000.0000.0000.000
99A170PHE0-0.0130.00520.9760.0100.0100.0000.0000.0000.000
100A171LYS10.9040.96322.471-0.131-0.1310.0000.0000.0000.000
101A172ASP-1-0.904-0.93922.5970.2730.2730.0000.0000.0000.000
102A173VAL00.0450.02617.3230.0010.0010.0000.0000.0000.000
103A174ILE0-0.031-0.01020.071-0.005-0.0050.0000.0000.0000.000
104A175ASN00.018-0.00121.800-0.026-0.0260.0000.0000.0000.000
105A176GLU-1-0.881-0.94420.0240.2880.2880.0000.0000.0000.000
106A177VAL0-0.080-0.03216.615-0.005-0.0050.0000.0000.0000.000
107A178GLY0-0.035-0.01719.519-0.027-0.0270.0000.0000.0000.000
108A179GLY00.0040.01722.577-0.017-0.0170.0000.0000.0000.000
109A180ILE0-0.100-0.06220.380-0.003-0.0030.0000.0000.0000.000
110A181ASP-1-0.867-0.92623.309-0.014-0.0140.0000.0000.0000.000
111A182VAL0-0.094-0.08423.934-0.012-0.0120.0000.0000.0000.000
112A184VAL00.0470.02829.8840.0020.0020.0000.0000.0000.000
113A185PRO0-0.072-0.04131.2570.0010.0010.0000.0000.0000.000
114A206GLU-1-0.924-0.92128.941-0.068-0.0680.0000.0000.0000.000
115A207MET0-0.037-0.02329.5190.0040.0040.0000.0000.0000.000
116A208HIS0-0.032-0.01525.2110.0080.0080.0000.0000.0000.000
117A209LEU00.0130.00026.240-0.002-0.0020.0000.0000.0000.000
118A210ASN00.0040.00426.6940.0110.0110.0000.0000.0000.000
119A211GLY00.0630.03225.758-0.005-0.0050.0000.0000.0000.000
120A212GLU-1-0.944-0.98226.7390.0850.0850.0000.0000.0000.000
121A213GLU-1-0.855-0.92829.6620.0300.0300.0000.0000.0000.000
122A214ALA00.0640.02824.937-0.006-0.0060.0000.0000.0000.000
123A215LEU0-0.009-0.02026.347-0.005-0.0050.0000.0000.0000.000
124A216ALA0-0.009-0.00527.356-0.003-0.0030.0000.0000.0000.000
125A217TYR0-0.149-0.05426.707-0.008-0.0080.0000.0000.0000.000
126A218ALA0-0.079-0.04126.832-0.015-0.0150.0000.0000.0000.000
127A228ASP-1-0.723-0.86329.060-0.010-0.0100.0000.0000.0000.000
128A229PHE0-0.090-0.06428.027-0.003-0.0030.0000.0000.0000.000
129A230GLY00.0120.02430.001-0.008-0.0080.0000.0000.0000.000
130A231ARG10.8070.85828.926-0.031-0.0310.0000.0000.0000.000
131A232ASN00.012-0.01224.484-0.008-0.0080.0000.0000.0000.000
132A233ASP-1-0.823-0.90124.405-0.104-0.1040.0000.0000.0000.000
133A234ARG10.9120.95324.9010.0000.0000.0000.0000.0000.000
134A235GLN00.0430.04322.347-0.003-0.0030.0000.0000.0000.000
135A236LYS10.9150.96019.9200.1190.1190.0000.0000.0000.000
136A237GLN0-0.0290.00220.011-0.005-0.0050.0000.0000.0000.000
137A238ILE00.0330.02420.254-0.007-0.0070.0000.0000.0000.000
138A239LEU0-0.0090.00014.7550.0040.0040.0000.0000.0000.000
139A240ASN00.013-0.02716.621-0.034-0.0340.0000.0000.0000.000
140A241ALA00.0210.03217.624-0.024-0.0240.0000.0000.0000.000
141A242LEU00.0330.01014.9590.0030.0030.0000.0000.0000.000
142A243ILE0-0.039-0.03612.102-0.006-0.0060.0000.0000.0000.000
143A244ASP-1-0.766-0.84513.912-0.261-0.2610.0000.0000.0000.000
144A245ARG10.7970.91616.629-0.062-0.0620.0000.0000.0000.000
145A246MET0-0.090-0.03912.0800.0710.0710.0000.0000.0000.000
146A247SER0-0.059-0.02312.2800.0210.0210.0000.0000.0000.000
147A256ASP-1-0.878-0.94913.6430.5170.5170.0000.0000.0000.000
148A257LYS10.8070.86714.711-0.693-0.6930.0000.0000.0000.000
149A258ILE00.0670.03415.7930.0120.0120.0000.0000.0000.000
150A259ALA0-0.0120.00712.1110.0000.0000.0000.0000.0000.000
151A260GLU-1-0.825-0.91014.1451.0201.0200.0000.0000.0000.000
152A261LYS10.7940.89015.840-0.340-0.3400.0000.0000.0000.000
153A262ALA00.0380.00915.910-0.010-0.0100.0000.0000.0000.000
154A263SER0-0.111-0.05313.5900.0300.0300.0000.0000.0000.000
155A264GLU-1-0.946-0.96315.3870.6640.6640.0000.0000.0000.000
156A265ASN0-0.0100.00018.321-0.051-0.0510.0000.0000.0000.000
157A266VAL0-0.040-0.01115.267-0.059-0.0590.0000.0000.0000.000
158A267GLU-1-0.791-0.87617.4460.3680.3680.0000.0000.0000.000
159A268THR0-0.008-0.04912.1040.0350.0350.0000.0000.0000.000
160A269ASN00.0160.01611.2640.0510.0510.0000.0000.0000.000
161A270ILE0-0.032-0.0046.3830.3660.3660.0000.0000.0000.000
162A271ARG10.8830.9234.051-4.421-4.275-0.001-0.017-0.1290.000
163A272ILE00.1200.0477.2540.5070.5070.0000.0000.0000.000
164A273THR00.007-0.0094.428-0.402-0.303-0.001-0.014-0.0830.000
165A274GLU-1-0.806-0.8772.8793.2003.3014.729-2.027-2.8030.004
166A275GLY00.0740.0473.724-0.300-2.172-0.0062.513-0.636-0.005
167A276LEU00.0350.0146.461-0.789-0.7890.0000.0000.0000.000
168A277ALA0-0.041-0.0302.711-1.887-1.2161.402-0.535-1.538-0.001
169A278LEU0-0.032-0.0192.227-3.458-2.9041.911-0.432-2.033-0.005
170A279GLN00.0740.0414.189-0.0760.0050.001-0.030-0.0510.000
171A280GLN00.0070.0186.657-0.201-0.2010.0000.0000.0000.000
172A281ILE0-0.085-0.0482.818-0.703-0.2450.261-0.117-0.6020.000
173A282TYR0-0.082-0.0675.128-0.064-0.0640.0000.0000.0000.000
174A283SER00.0180.0288.7830.1620.1620.0000.0000.0000.000
175A284GLY00.0180.01911.7730.0790.0790.0000.0000.0000.000
176A285PHE00.001-0.03612.368-0.096-0.0960.0000.0000.0000.000
177A286THR0-0.010-0.00211.4370.0020.0020.0000.0000.0000.000
178A287SER0-0.018-0.04214.0920.0430.0430.0000.0000.0000.000
179A288LYS10.9260.96816.8170.1750.1750.0000.0000.0000.000
180A289LYS10.8210.91316.1100.5370.5370.0000.0000.0000.000
181A290ILE0-0.0280.00314.044-0.034-0.0340.0000.0000.0000.000
182A291ASP-1-0.829-0.90716.273-0.322-0.3220.0000.0000.0000.000
183A292THR0-0.040-0.02017.9720.0010.0010.0000.0000.0000.000
184A293LEU00.0010.01319.2660.0150.0150.0000.0000.0000.000
185A294SER0-0.025-0.04121.7610.0240.0240.0000.0000.0000.000
186A295ILE00.0220.02323.984-0.007-0.0070.0000.0000.0000.000
187A296THR0-0.010-0.02226.5080.0060.0060.0000.0000.0000.000
188A297GLY00.0680.03630.115-0.002-0.0020.0000.0000.0000.000
189A298SER0-0.044-0.00533.005-0.002-0.0020.0000.0000.0000.000
190A299ASP-1-0.827-0.88535.938-0.026-0.0260.0000.0000.0000.000
191A300LEU0-0.050-0.01538.058-0.001-0.0010.0000.0000.0000.000
192A301TYR0-0.030-0.02839.3230.0050.0050.0000.0000.0000.000
193A302LEU0-0.016-0.00939.878-0.001-0.0010.0000.0000.0000.000
194A303GLY00.002-0.00243.4050.0030.0030.0000.0000.0000.000
195A304PRO00.022-0.00646.343-0.001-0.0010.0000.0000.0000.000
196A305ASN0-0.026-0.01643.206-0.003-0.0030.0000.0000.0000.000
197A306ASN0-0.021-0.00744.506-0.002-0.0020.0000.0000.0000.000
198A307THR0-0.0140.00238.9050.0020.0020.0000.0000.0000.000
199A308TYR0-0.044-0.03434.405-0.001-0.0010.0000.0000.0000.000
200A309TYR0-0.041-0.02135.1090.0070.0070.0000.0000.0000.000
201A310PHE00.0090.00729.546-0.005-0.0050.0000.0000.0000.000
202A311GLU-1-0.772-0.88532.792-0.031-0.0310.0000.0000.0000.000
203A312PRO0-0.042-0.01029.554-0.005-0.0050.0000.0000.0000.000
204A313ASP-1-0.792-0.93231.518-0.096-0.0960.0000.0000.0000.000
205A314ALA0-0.0080.00230.934-0.008-0.0080.0000.0000.0000.000
206A315THR00.0430.03730.621-0.013-0.0130.0000.0000.0000.000
207A316ASN0-0.014-0.03126.710-0.008-0.0080.0000.0000.0000.000
208A317LEU00.0290.03425.277-0.019-0.0190.0000.0000.0000.000
209A318GLU-1-0.916-0.96625.569-0.135-0.1350.0000.0000.0000.000
210A319LYS10.8410.91825.8530.1260.1260.0000.0000.0000.000
211A320VAL0-0.0120.00521.458-0.030-0.0300.0000.0000.0000.000
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