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: K9VL3

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 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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1927777.825147
FMO2-HF: Nuclear repulsion 1856168.650248
FMO2-HF: Total energy -71609.174899
FMO2-MP2: Total energy -71814.333571


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.
-7.5230.4336.125-3.801-10.282-0.015
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 : -0.019 / q_NPA : -0.010
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].
3A275LYS10.9670.9553.102-0.8661.3030.140-1.158-1.1510.000
4A276ASP-1-0.793-0.8905.820-0.087-0.0870.0000.0000.0000.000
5A277ALA00.0160.0122.390-0.6950.0210.804-0.381-1.138-0.001
6A278VAL00.0140.0202.918-0.9560.0930.363-0.272-1.1400.000
7A279LYS10.8820.9264.4680.3980.492-0.001-0.012-0.0820.000
8A280LYS10.8610.9297.1680.1920.1920.0000.0000.0000.000
9A281MET00.0230.0132.2270.023-0.5972.566-0.283-1.6630.001
10A282PHE00.0240.0106.7410.0370.0370.0000.0000.0000.000
11A283ALA0-0.0270.0049.3050.0460.0460.0000.0000.0000.000
12A284VAL0-0.015-0.0149.5470.0300.0300.0000.0000.0000.000
13A285GLY00.0430.02510.7530.0220.0220.0000.0000.0000.000
14A286THR0-0.051-0.05412.1000.0140.0140.0000.0000.0000.000
15A287ALA00.0290.02014.8690.0170.0170.0000.0000.0000.000
16A288SER0-0.015-0.00716.9550.0090.0090.0000.0000.0000.000
17A289LEU0-0.061-0.02417.7280.0090.0090.0000.0000.0000.000
18A290GLY0-0.0140.00420.2200.0070.0070.0000.0000.0000.000
19A291HIS0-0.030-0.02019.650-0.011-0.0110.0000.0000.0000.000
20A292VAL00.0100.00615.657-0.001-0.0010.0000.0000.0000.000
21A293PRO0-0.041-0.00516.423-0.016-0.0160.0000.0000.0000.000
22A294VAL00.017-0.00511.718-0.016-0.0160.0000.0000.0000.000
23A295LEU0-0.049-0.03115.0720.0170.0170.0000.0000.0000.000
24A296ASP-1-0.817-0.90113.814-0.433-0.4330.0000.0000.0000.000
25A297VAL0-0.0050.0027.276-0.041-0.0410.0000.0000.0000.000
26A298GLY0-0.0040.00910.4010.0250.0250.0000.0000.0000.000
27A299ARG10.9120.9395.5410.7690.7690.0000.0000.0000.000
28A300PHE00.0020.0139.2820.1770.1770.0000.0000.0000.000
29A301SER00.012-0.00310.596-0.048-0.0480.0000.0000.0000.000
30A302SER00.0000.00012.6490.0380.0380.0000.0000.0000.000
31A303GLU-1-0.798-0.89815.146-0.076-0.0760.0000.0000.0000.000
32A304ILE00.0020.00117.4360.0080.0080.0000.0000.0000.000
33A305ALA0-0.028-0.02312.351-0.006-0.0060.0000.0000.0000.000
34A306GLU-1-0.917-0.95912.677-0.120-0.1200.0000.0000.0000.000
35A307ALA00.0080.00713.9030.0300.0300.0000.0000.0000.000
36A308ARG10.8390.90914.7220.2590.2590.0000.0000.0000.000
37A309LEU0-0.0170.0038.718-0.008-0.0080.0000.0000.0000.000
38A310ALA0-0.001-0.00712.4650.0450.0450.0000.0000.0000.000
39A311LEU0-0.024-0.00315.0670.0220.0220.0000.0000.0000.000
40A312PHE00.0200.00710.2550.0040.0040.0000.0000.0000.000
41A313GLN00.010-0.0239.8160.0770.0770.0000.0000.0000.000
42A314LYS10.8850.93313.904-0.050-0.0500.0000.0000.0000.000
43A315GLN00.0460.02716.7520.0240.0240.0000.0000.0000.000
44A316VAL0-0.0070.00212.0440.0030.0030.0000.0000.0000.000
45A317GLU-1-0.858-0.91515.4840.1240.1240.0000.0000.0000.000
46A318ILE0-0.023-0.00517.9970.0070.0070.0000.0000.0000.000
47A319THR00.0330.00717.729-0.003-0.0030.0000.0000.0000.000
48A320LYS10.9450.97516.247-0.161-0.1610.0000.0000.0000.000
49A321LYS10.8220.90519.097-0.077-0.0770.0000.0000.0000.000
50A322HIS0-0.0070.01622.5170.0090.0090.0000.0000.0000.000
51A323ARG10.7980.87420.6880.0540.0540.0000.0000.0000.000
52A324GLY0-0.0160.00921.6260.0010.0010.0000.0000.0000.000
53A325ASP-1-0.891-0.97415.4250.0250.0250.0000.0000.0000.000
54A326ALA0-0.036-0.01014.227-0.019-0.0190.0000.0000.0000.000
55A327ASN0-0.033-0.02013.242-0.065-0.0650.0000.0000.0000.000
56A328VAL0-0.009-0.0128.517-0.042-0.0420.0000.0000.0000.000
57A329ARG10.8880.9407.8280.2150.2150.0000.0000.0000.000
58A330TYR0-0.032-0.0302.715-3.620-1.1211.847-1.029-3.318-0.013
59A331ALA00.0100.0006.1630.1870.1870.0000.0000.0000.000
60A332TRP0-0.049-0.0396.833-0.163-0.1630.0000.0000.0000.000
61A333LEU00.0360.01710.3880.0750.0750.0000.0000.0000.000
62A334PRO00.001-0.01513.234-0.021-0.0210.0000.0000.0000.000
63A335ALA00.0030.00415.5340.0080.0080.0000.0000.0000.000
64A336LYS10.8460.93017.2690.2030.2030.0000.0000.0000.000
65A337ARG10.8960.91319.5980.1690.1690.0000.0000.0000.000
66A338GLU-1-0.889-0.95020.890-0.177-0.1770.0000.0000.0000.000
67A339VAL00.0040.01218.6830.0080.0080.0000.0000.0000.000
68A340LEU0-0.042-0.02015.490-0.015-0.0150.0000.0000.0000.000
69A341SER0-0.030-0.01418.335-0.008-0.0080.0000.0000.0000.000
70A342ALA00.0520.02220.7630.0030.0030.0000.0000.0000.000
71A343VAL0-0.055-0.02415.5230.0030.0030.0000.0000.0000.000
72A344MET00.0370.05012.2240.0250.0250.0000.0000.0000.000
73A345MET00.0180.01317.6140.0200.0200.0000.0000.0000.000
74A346GLN0-0.004-0.01221.0490.0110.0110.0000.0000.0000.000
75A347GLY00.0000.01319.5230.0120.0120.0000.0000.0000.000
76A348LEU00.0360.00615.150-0.009-0.0090.0000.0000.0000.000
77A349GLY00.0240.01219.2760.0040.0040.0000.0000.0000.000
78A350VAL00.0010.01821.4170.0160.0160.0000.0000.0000.000
79A351GLY00.004-0.02423.9170.0130.0130.0000.0000.0000.000
80A352GLY00.0060.00325.4990.0000.0000.0000.0000.0000.000
81A353ALA0-0.055-0.02323.466-0.006-0.0060.0000.0000.0000.000
82A354PHE0-0.001-0.00516.921-0.018-0.0180.0000.0000.0000.000
83A355ILE0-0.078-0.01220.629-0.006-0.0060.0000.0000.0000.000
84A356ARG10.9260.96620.8040.2090.2090.0000.0000.0000.000
85A357LYS10.9730.98924.2760.1010.1010.0000.0000.0000.000
86A358SER0-0.032-0.03323.9570.0030.0030.0000.0000.0000.000
87A359ILE0-0.041-0.04925.9550.0090.0090.0000.0000.0000.000
88A360TYR00.0360.00822.8570.0050.0050.0000.0000.0000.000
89A361GLY00.0890.08425.7800.0020.0020.0000.0000.0000.000
90A362VAL0-0.108-0.07225.600-0.009-0.0090.0000.0000.0000.000
91A363GLY00.0630.02822.2910.0060.0060.0000.0000.0000.000
92A364ILE0-0.021-0.01816.618-0.001-0.0010.0000.0000.0000.000
93A365HIS0-0.0090.02018.3390.0120.0120.0000.0000.0000.000
94A366LEU0-0.031-0.01511.960-0.021-0.0210.0000.0000.0000.000
95A367THR00.004-0.00213.1420.0410.0410.0000.0000.0000.000
96A368ALA00.0460.03611.107-0.081-0.0810.0000.0000.0000.000
97A369ALA00.006-0.0196.2520.0000.0000.0000.0000.0000.000
98A370ASP-1-0.847-0.8978.175-0.284-0.2840.0000.0000.0000.000
99A371CYS0-0.026-0.02710.4940.0560.0560.0000.0000.0000.000
100A372PRO00.0020.01110.1810.0170.0170.0000.0000.0000.000
101A373TYR0-0.002-0.01713.0580.0180.0180.0000.0000.0000.000
102A374PHE0-0.0330.00116.2680.0200.0200.0000.0000.0000.000
103A375SER00.0270.01815.3360.0090.0090.0000.0000.0000.000
104A376ALA00.0150.01116.094-0.003-0.0030.0000.0000.0000.000
105A377ARG10.9270.94317.4010.1560.1560.0000.0000.0000.000
106A378TYR0-0.021-0.00819.7030.0130.0130.0000.0000.0000.000
107A379CYS0-0.0500.00816.729-0.018-0.0180.0000.0000.0000.000
108A380ASP-1-0.820-0.90419.410-0.177-0.1770.0000.0000.0000.000
109A381VAL0-0.075-0.03121.684-0.015-0.0150.0000.0000.0000.000
110A382ASP-1-0.772-0.86722.855-0.199-0.1990.0000.0000.0000.000
111A383GLU-1-0.797-0.89824.885-0.153-0.1530.0000.0000.0000.000
112A384ASN0-0.0290.00224.9090.0180.0180.0000.0000.0000.000
113A385GLY0-0.022-0.02425.1300.0020.0020.0000.0000.0000.000
114A386VAL0-0.080-0.03619.217-0.006-0.0060.0000.0000.0000.000
115A387ARG10.8810.95118.5580.2080.2080.0000.0000.0000.000
116A388TYR0-0.018-0.05215.492-0.028-0.0280.0000.0000.0000.000
117A389MET00.0120.02611.5390.0370.0370.0000.0000.0000.000
118A390VAL0-0.022-0.01110.246-0.061-0.0610.0000.0000.0000.000
119A391LEU0-0.0350.0052.796-0.4130.0130.147-0.108-0.4660.000
120A392CYS0-0.024-0.0187.281-0.109-0.1090.0000.0000.0000.000
121A393ARG10.8560.9175.0120.7370.7370.0000.0000.0000.000
122A394VAL00.027-0.0028.0900.1390.1390.0000.0000.0000.000
123A395ILE0-0.032-0.00211.2490.0010.0010.0000.0000.0000.000
124A396MET0-0.020-0.01212.8000.0050.0050.0000.0000.0000.000
125A397GLY00.0280.02815.2240.0200.0200.0000.0000.0000.000
126A398ASN00.000-0.00317.5470.0020.0020.0000.0000.0000.000
127A399MET0-0.026-0.00114.815-0.006-0.0060.0000.0000.0000.000
128A400GLU-1-0.729-0.84319.640-0.083-0.0830.0000.0000.0000.000
129A401LEU0-0.018-0.00821.811-0.014-0.0140.0000.0000.0000.000
130A402LEU0-0.034-0.01321.7320.0070.0070.0000.0000.0000.000
131A403ARG10.9440.96424.9460.0640.0640.0000.0000.0000.000
132A404GLY0-0.021-0.00927.4480.0040.0040.0000.0000.0000.000
133A405ASP-1-0.843-0.90728.857-0.076-0.0760.0000.0000.0000.000
134A406LYS10.9150.94129.2830.0900.0900.0000.0000.0000.000
135A407ALA0-0.070-0.04030.526-0.006-0.0060.0000.0000.0000.000
136A408GLN0-0.0300.00126.8780.0000.0000.0000.0000.0000.000
137A409PHE0-0.027-0.03127.037-0.009-0.0090.0000.0000.0000.000
138A410PHE0-0.067-0.03826.157-0.006-0.0060.0000.0000.0000.000
139A411SER00.0170.00325.0150.0000.0000.0000.0000.0000.000
140A412GLY00.0240.00426.2410.0060.0060.0000.0000.0000.000
141A413GLY0-0.015-0.00427.6810.0070.0070.0000.0000.0000.000
142A414GLU-1-0.959-0.97027.333-0.038-0.0380.0000.0000.0000.000
143A415GLU-1-0.874-0.94326.961-0.045-0.0450.0000.0000.0000.000
144A416TYR0-0.054-0.02023.322-0.001-0.0010.0000.0000.0000.000
145A417ASP-1-0.823-0.86419.729-0.080-0.0800.0000.0000.0000.000
146A418ASN0-0.031-0.02417.1640.0020.0020.0000.0000.0000.000
147A419GLY00.0590.03119.7400.0120.0120.0000.0000.0000.000
148A420VAL0-0.047-0.03916.721-0.031-0.0310.0000.0000.0000.000
149A421ASP-1-0.742-0.86718.590-0.164-0.1640.0000.0000.0000.000
150A422ASP-1-0.862-0.92719.364-0.098-0.0980.0000.0000.0000.000
151A423ILE00.034-0.00818.409-0.015-0.0150.0000.0000.0000.000
152A424GLU-1-0.970-0.96217.764-0.067-0.0670.0000.0000.0000.000
153A425SER0-0.024-0.01716.347-0.005-0.0050.0000.0000.0000.000
154A426PRO0-0.036-0.00613.989-0.006-0.0060.0000.0000.0000.000
155A427LYS10.8390.90714.8240.1300.1300.0000.0000.0000.000
156A428ASN0-0.114-0.07115.520-0.038-0.0380.0000.0000.0000.000
157A429TYR00.0340.00610.7180.0280.0280.0000.0000.0000.000
158A430ILE0-0.016-0.00916.361-0.010-0.0100.0000.0000.0000.000
159A431VAL00.0090.00915.5130.0070.0070.0000.0000.0000.000
160A432TRP00.0370.03218.798-0.004-0.0040.0000.0000.0000.000
161A433ASN00.0680.00221.625-0.019-0.0190.0000.0000.0000.000
162A434ILE0-0.005-0.00623.131-0.008-0.0080.0000.0000.0000.000
163A435ASN00.0240.01019.5200.0150.0150.0000.0000.0000.000
164A436MET0-0.058-0.00118.466-0.024-0.0240.0000.0000.0000.000
165A437ASN0-0.001-0.02217.563-0.047-0.0470.0000.0000.0000.000
166A438THR0-0.031-0.02518.279-0.003-0.0030.0000.0000.0000.000
167A439HIS00.0900.05715.785-0.011-0.0110.0000.0000.0000.000
168A440ILE00.0030.00412.374-0.047-0.0470.0000.0000.0000.000
169A441PHE00.0010.0017.9770.0780.0780.0000.0000.0000.000
170A442PRO0-0.012-0.0069.477-0.180-0.1800.0000.0000.0000.000
171A443GLU-1-0.780-0.8564.779-2.688-2.531-0.001-0.006-0.1490.000
172A444PHE0-0.005-0.0292.739-0.7850.6810.260-0.552-1.175-0.002
173A445VAL0-0.0060.0117.9330.1510.1510.0000.0000.0000.000
174A446VAL00.0080.0108.893-0.029-0.0290.0000.0000.0000.000
175A447ARG10.8510.91311.5780.4090.4090.0000.0000.0000.000
176A448PHE0-0.006-0.01514.8010.0080.0080.0000.0000.0000.000
177A449LYS10.9150.96516.8010.1850.1850.0000.0000.0000.000
178A450LEU00.0220.00718.483-0.004-0.0040.0000.0000.0000.000
179A451SER00.0440.02821.7220.0050.0050.0000.0000.0000.000
180A452ASN00.0150.00825.280-0.006-0.0060.0000.0000.0000.000