FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 49YVN

Calculation Name: 5NGO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5NGO

Chain ID: A

ChEMBL ID:

UniProt ID: Q8RY59

Base Structure: X-ray

Registration Date: 2023-06-22

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 180
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1934435.615803
FMO2-HF: Nuclear repulsion 1862826.015365
FMO2-HF: Total energy -71609.600438
FMO2-MP2: Total energy -71814.906294


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:273:LEU)


Summations of interaction energy for fragment #1(A:273:LEU)
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.
-7.6780.1895.239-3.364-9.745-0.014
Interaction energy analysis for fragmet #1(A:273:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : -0.003
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].
3A275LYS10.9630.9563.155-1.2070.8350.106-1.074-1.0750.000
4A276ASP-1-0.794-0.8885.6620.0040.0040.0000.0000.0000.000
5A277ALA0-0.008-0.0062.971-0.5090.1290.133-0.164-0.6080.000
6A278VAL00.0090.0112.460-0.931-0.0731.063-0.394-1.5270.000
7A279LYS10.8650.9244.3980.2630.3770.000-0.021-0.0940.000
8A280LYS10.8560.9317.3230.0900.0900.0000.0000.0000.000
9A281MET00.0070.0072.383-0.495-0.2741.423-0.212-1.4320.001
10A282PHE00.0420.0186.8260.0380.0380.0000.0000.0000.000
11A283ALA0-0.0050.0189.1330.0440.0440.0000.0000.0000.000
12A284VAL0-0.009-0.0189.6860.0270.0270.0000.0000.0000.000
13A285GLY00.0460.03710.7840.0190.0190.0000.0000.0000.000
14A286THR0-0.079-0.07212.0110.0080.0080.0000.0000.0000.000
15A287ALA00.0340.02514.8160.0170.0170.0000.0000.0000.000
16A288SER0-0.012-0.00217.0200.0100.0100.0000.0000.0000.000
17A289LEU0-0.064-0.02517.7930.0080.0080.0000.0000.0000.000
18A290GLY0-0.024-0.00520.4760.0070.0070.0000.0000.0000.000
19A291HIS0-0.012-0.01519.810-0.010-0.0100.0000.0000.0000.000
20A292VAL00.0210.01015.558-0.002-0.0020.0000.0000.0000.000
21A293PRO0-0.044-0.00816.259-0.015-0.0150.0000.0000.0000.000
22A294VAL00.016-0.00311.640-0.010-0.0100.0000.0000.0000.000
23A295LEU0-0.065-0.03714.8990.0240.0240.0000.0000.0000.000
24A296ASP-1-0.811-0.89313.682-0.370-0.3700.0000.0000.0000.000
25A297VAL0-0.020-0.0107.231-0.024-0.0240.0000.0000.0000.000
26A298GLY00.0480.0369.979-0.029-0.0290.0000.0000.0000.000
27A299ARG10.8710.9086.2110.6800.6800.0000.0000.0000.000
28A300PHE0-0.0200.0019.2240.1550.1550.0000.0000.0000.000
29A301SER0-0.014-0.03710.898-0.087-0.0870.0000.0000.0000.000
30A302SER0-0.029-0.01413.0650.0230.0230.0000.0000.0000.000
31A303GLU-1-0.865-0.92515.780-0.119-0.1190.0000.0000.0000.000
32A304ILE00.0080.00617.7990.0010.0010.0000.0000.0000.000
33A305ALA00.004-0.00212.815-0.016-0.0160.0000.0000.0000.000
34A306GLU-1-0.794-0.88712.438-0.277-0.2770.0000.0000.0000.000
35A307ALA00.0030.00613.9380.0180.0180.0000.0000.0000.000
36A308ARG10.8380.90714.9750.2990.2990.0000.0000.0000.000
37A309LEU0-0.0100.0098.774-0.014-0.0140.0000.0000.0000.000
38A310ALA0-0.004-0.00712.4000.0270.0270.0000.0000.0000.000
39A311LEU0-0.021-0.00214.9290.0210.0210.0000.0000.0000.000
40A312PHE00.0190.00710.171-0.005-0.0050.0000.0000.0000.000
41A313GLN00.020-0.0089.354-0.004-0.0040.0000.0000.0000.000
42A314LYS10.8900.93713.7250.0480.0480.0000.0000.0000.000
43A315GLN00.0440.03016.7030.0330.0330.0000.0000.0000.000
44A316VAL0-0.013-0.00511.9660.0070.0070.0000.0000.0000.000
45A317GLU-1-0.842-0.90315.3630.0430.0430.0000.0000.0000.000
46A318ILE0-0.029-0.00518.1110.0140.0140.0000.0000.0000.000
47A319THR00.0300.00117.5680.0030.0030.0000.0000.0000.000
48A320LYS10.8310.91215.655-0.025-0.0250.0000.0000.0000.000
49A321LYS10.8180.88818.9990.0050.0050.0000.0000.0000.000
50A322HIS0-0.0130.01322.3080.0140.0140.0000.0000.0000.000
51A323ARG10.7900.86620.4420.0970.0970.0000.0000.0000.000
52A324GLY00.0060.02421.7050.0040.0040.0000.0000.0000.000
53A325ASP-1-0.843-0.94815.163-0.043-0.0430.0000.0000.0000.000
54A326ALA00.0010.00514.310-0.014-0.0140.0000.0000.0000.000
55A327ASN0-0.032-0.01913.486-0.061-0.0610.0000.0000.0000.000
56A328VAL0-0.014-0.0088.614-0.040-0.0400.0000.0000.0000.000
57A329ARG10.8770.9347.6010.2810.2810.0000.0000.0000.000
58A330TYR0-0.039-0.0482.714-3.244-0.9631.839-0.910-3.210-0.012
59A331ALA00.0020.0015.8900.1920.1920.0000.0000.0000.000
60A332TRP0-0.044-0.0376.541-0.144-0.1440.0000.0000.0000.000
61A333LEU00.0410.01910.1410.0710.0710.0000.0000.0000.000
62A334PRO00.005-0.02013.047-0.014-0.0140.0000.0000.0000.000
63A335ALA00.0040.00315.4670.0030.0030.0000.0000.0000.000
64A336LYS10.8300.90917.2250.2000.2000.0000.0000.0000.000
65A337ARG10.8400.88219.5730.1540.1540.0000.0000.0000.000
66A338GLU-1-0.824-0.90721.056-0.186-0.1860.0000.0000.0000.000
67A339VAL0-0.016-0.00318.3260.0010.0010.0000.0000.0000.000
68A340LEU0-0.017-0.01715.004-0.015-0.0150.0000.0000.0000.000
69A341SER0-0.0230.00217.774-0.014-0.0140.0000.0000.0000.000
70A342ALA00.0610.02720.531-0.001-0.0010.0000.0000.0000.000
71A343VAL0-0.0150.00115.5080.0020.0020.0000.0000.0000.000
72A344MET00.0090.02912.5830.0160.0160.0000.0000.0000.000
73A345MET00.0170.01517.5490.0150.0150.0000.0000.0000.000
74A346GLN0-0.019-0.02321.2720.0100.0100.0000.0000.0000.000
75A347GLY00.0100.01618.6040.0100.0100.0000.0000.0000.000
76A348LEU0-0.005-0.01814.8800.0010.0010.0000.0000.0000.000
77A349GLY00.0340.01618.8260.0110.0110.0000.0000.0000.000
78A350VAL0-0.052-0.02220.8450.0160.0160.0000.0000.0000.000
79A351GLY00.0250.00723.6590.0130.0130.0000.0000.0000.000
80A352GLY00.015-0.00224.999-0.005-0.0050.0000.0000.0000.000
81A353ALA0-0.036-0.01222.847-0.005-0.0050.0000.0000.0000.000
82A354PHE00.0120.00716.737-0.017-0.0170.0000.0000.0000.000
83A355ILE0-0.054-0.01220.013-0.010-0.0100.0000.0000.0000.000
84A356ARG10.9250.96720.1150.2230.2230.0000.0000.0000.000
85A357LYS10.9120.95624.2810.1070.1070.0000.0000.0000.000
86A358SER0-0.028-0.03023.5710.0050.0050.0000.0000.0000.000
87A359ILE0-0.031-0.04225.5610.0090.0090.0000.0000.0000.000
88A360TYR00.0370.01122.5970.0050.0050.0000.0000.0000.000
89A361GLY00.0940.07625.105-0.002-0.0020.0000.0000.0000.000
90A362VAL0-0.095-0.06925.525-0.005-0.0050.0000.0000.0000.000
91A363GLY00.0590.02622.0130.0040.0040.0000.0000.0000.000
92A364ILE0-0.0020.01016.2180.0010.0010.0000.0000.0000.000
93A365HIS0-0.0220.00517.9530.0090.0090.0000.0000.0000.000
94A366LEU0-0.016-0.00811.447-0.019-0.0190.0000.0000.0000.000
95A367THR0-0.0080.01713.0590.0310.0310.0000.0000.0000.000
96A368ALA00.0440.03410.795-0.080-0.0800.0000.0000.0000.000
97A369ALA00.003-0.0175.9480.0110.0110.0000.0000.0000.000
98A370ASP-1-0.820-0.8947.927-0.294-0.2940.0000.0000.0000.000
99A371CYS0-0.019-0.01710.4170.0590.0590.0000.0000.0000.000
100A372PRO0-0.0050.00410.0610.0190.0190.0000.0000.0000.000
101A373TYR00.0350.00613.0480.0200.0200.0000.0000.0000.000
102A374PHE0-0.045-0.01016.2610.0180.0180.0000.0000.0000.000
103A375SER0-0.034-0.03215.1790.0050.0050.0000.0000.0000.000
104A376ALA00.0430.02015.432-0.001-0.0010.0000.0000.0000.000
105A377ARG10.8840.91216.9450.1470.1470.0000.0000.0000.000
106A378TYR0-0.030-0.01419.4100.0140.0140.0000.0000.0000.000
107A379CYS0-0.0700.00716.242-0.018-0.0180.0000.0000.0000.000
108A380ASP-1-0.807-0.89918.808-0.158-0.1580.0000.0000.0000.000
109A381VAL0-0.077-0.03421.018-0.014-0.0140.0000.0000.0000.000
110A382ASP-1-0.753-0.85522.766-0.177-0.1770.0000.0000.0000.000
111A383GLU-1-0.768-0.86224.599-0.141-0.1410.0000.0000.0000.000
112A384ASN0-0.053-0.01424.4880.0190.0190.0000.0000.0000.000
113A385GLY0-0.008-0.00825.2460.0040.0040.0000.0000.0000.000
114A386VAL0-0.094-0.05119.137-0.002-0.0020.0000.0000.0000.000
115A387ARG10.8880.95218.5330.1890.1890.0000.0000.0000.000
116A388TYR0-0.019-0.04715.555-0.023-0.0230.0000.0000.0000.000
117A389MET00.0170.02811.1660.0200.0200.0000.0000.0000.000
118A390VAL0-0.020-0.01010.272-0.050-0.0500.0000.0000.0000.000
119A391LEU0-0.0440.0022.609-0.458-0.0330.313-0.135-0.6030.000
120A392CYS0-0.014-0.0107.145-0.071-0.0710.0000.0000.0000.000
121A393ARG10.8460.9055.4401.1601.1600.0000.0000.0000.000
122A394VAL00.015-0.0107.7140.1620.1620.0000.0000.0000.000
123A395ILE0-0.031-0.00510.861-0.015-0.0150.0000.0000.0000.000
124A396MET0-0.021-0.01012.2790.0210.0210.0000.0000.0000.000
125A397GLY00.0260.02414.7990.0280.0280.0000.0000.0000.000
126A398ASN0-0.019-0.00817.377-0.004-0.0040.0000.0000.0000.000
127A399MET0-0.0180.00614.897-0.007-0.0070.0000.0000.0000.000
128A400GLU-1-0.731-0.85019.348-0.105-0.1050.0000.0000.0000.000
129A401LEU0-0.009-0.00421.473-0.014-0.0140.0000.0000.0000.000
130A402LEU0-0.046-0.00721.3530.0100.0100.0000.0000.0000.000
131A403ARG10.9590.96524.7630.0800.0800.0000.0000.0000.000
132A404GLY0-0.0090.01127.3810.0050.0050.0000.0000.0000.000
133A405ASP-1-0.805-0.89928.772-0.089-0.0890.0000.0000.0000.000
134A406LYS10.9080.95228.9590.0970.0970.0000.0000.0000.000
135A407ALA0-0.088-0.05830.456-0.004-0.0040.0000.0000.0000.000
136A408GLN0-0.0100.00426.5180.0010.0010.0000.0000.0000.000
137A409PHE0-0.043-0.03526.475-0.008-0.0080.0000.0000.0000.000
138A410PHE0-0.047-0.02525.644-0.007-0.0070.0000.0000.0000.000
139A411SER00.0100.00524.3410.0010.0010.0000.0000.0000.000
140A412GLY00.0240.00025.7340.0080.0080.0000.0000.0000.000
141A413GLY0-0.0010.00127.4070.0090.0090.0000.0000.0000.000
142A414GLU-1-0.944-0.95927.047-0.066-0.0660.0000.0000.0000.000
143A415GLU-1-0.847-0.91626.690-0.072-0.0720.0000.0000.0000.000
144A416TYR0-0.078-0.04922.781-0.003-0.0030.0000.0000.0000.000
145A417ASP-1-0.829-0.86819.422-0.126-0.1260.0000.0000.0000.000
146A418ASN0-0.016-0.02116.9090.0030.0030.0000.0000.0000.000
147A419GLY00.0530.03519.3430.0110.0110.0000.0000.0000.000
148A420VAL0-0.059-0.03716.192-0.035-0.0350.0000.0000.0000.000
149A421ASP-1-0.746-0.87418.248-0.180-0.1800.0000.0000.0000.000
150A422ASP-1-0.817-0.89318.675-0.112-0.1120.0000.0000.0000.000
151A423ILE00.035-0.00218.012-0.019-0.0190.0000.0000.0000.000
152A424GLU-1-0.970-0.96518.088-0.068-0.0680.0000.0000.0000.000
153A425SER0-0.044-0.03416.1400.0010.0010.0000.0000.0000.000
154A426PRO0-0.0270.00013.497-0.005-0.0050.0000.0000.0000.000
155A427LYS10.8070.88214.4620.1460.1460.0000.0000.0000.000
156A428ASN0-0.131-0.08415.220-0.038-0.0380.0000.0000.0000.000
157A429TYR00.0430.01210.4240.0260.0260.0000.0000.0000.000
158A430ILE0-0.029-0.01715.898-0.007-0.0070.0000.0000.0000.000
159A431VAL00.0000.00715.2230.0060.0060.0000.0000.0000.000
160A432TRP00.0500.03718.5410.0010.0010.0000.0000.0000.000
161A433ASN00.056-0.00421.358-0.022-0.0220.0000.0000.0000.000
162A434ILE0-0.007-0.00523.011-0.007-0.0070.0000.0000.0000.000
163A435ASN00.0370.01819.2250.0160.0160.0000.0000.0000.000
164A436MET0-0.051-0.00418.245-0.029-0.0290.0000.0000.0000.000
165A437ASN00.009-0.00617.529-0.047-0.0470.0000.0000.0000.000
166A438THR0-0.031-0.02217.9580.0020.0020.0000.0000.0000.000
167A439HIS00.0760.04115.419-0.024-0.0240.0000.0000.0000.000
168A440ILE00.0020.00412.328-0.050-0.0500.0000.0000.0000.000
169A441PHE00.002-0.0028.3410.0830.0830.0000.0000.0000.000
170A442PRO00.0020.0089.107-0.182-0.1820.0000.0000.0000.000
171A443GLU-1-0.784-0.8475.338-2.527-2.5270.0000.0000.0000.000
172A444PHE00.002-0.0252.817-0.7990.4890.362-0.454-1.196-0.003
173A445VAL0-0.019-0.0067.7930.1080.1080.0000.0000.0000.000
174A446VAL0-0.0060.0128.8430.0160.0160.0000.0000.0000.000
175A447ARG10.8570.91511.4840.3460.3460.0000.0000.0000.000
176A448PHE00.004-0.01114.6080.0060.0060.0000.0000.0000.000
177A449LYS10.9040.95616.6150.1600.1600.0000.0000.0000.000
178A450LEU00.0190.00118.387-0.006-0.0060.0000.0000.0000.000
179A451SER00.0510.03421.4580.0040.0040.0000.0000.0000.000
180A452ASN00.0270.02824.991-0.009-0.0090.0000.0000.0000.000