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: VQQN1

Calculation Name: 4R3O-N-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4R3O

Chain ID: N

ChEMBL ID:

UniProt ID: P25786

Base Structure: X-ray

Registration Date: 2023-09-21

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2539228.0154
FMO2-HF: Nuclear repulsion 2453109.682817
FMO2-HF: Total energy -86118.332583
FMO2-MP2: Total energy -86364.244875


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(N:1:THR)


Summations of interaction energy for fragment #1(N:1:THR)
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.
-32.957-27.06222.242-12.556-15.58-0.095
Interaction energy analysis for fragmet #1(N:1:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.063 / q_NPA : -0.054
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].
3N3ASN0-0.012-0.0103.195-2.941-0.4110.116-1.136-1.5100.003
4N4PRO00.0140.0202.756-0.8970.6440.676-0.679-1.537-0.004
5N5MET0-0.001-0.0103.6640.3030.2090.0240.231-0.1620.000
6N6VAL0-0.052-0.0236.359-0.113-0.1130.0000.0000.0000.000
7N7THR0-0.0070.0036.344-0.279-0.2790.0000.0000.0000.000
8N8GLY00.0240.0298.6430.2460.2460.0000.0000.0000.000
9N9THR0-0.035-0.02611.072-0.200-0.2000.0000.0000.0000.000
10N10SER00.0200.02313.719-0.100-0.1000.0000.0000.0000.000
11N11VAL0-0.0220.01414.7440.0190.0190.0000.0000.0000.000
12N12LEU0-0.013-0.01117.3720.0040.0040.0000.0000.0000.000
13N13GLY00.0360.01221.025-0.013-0.0130.0000.0000.0000.000
14N14VAL00.001-0.00423.1410.0040.0040.0000.0000.0000.000
15N15LYS10.8490.93126.7990.3250.3250.0000.0000.0000.000
16N16PHE0-0.037-0.01729.2390.0040.0040.0000.0000.0000.000
17N17GLU-1-0.912-0.97232.657-0.181-0.1810.0000.0000.0000.000
18N18GLY00.0050.01334.5290.0040.0040.0000.0000.0000.000
19N19GLY00.012-0.01330.7370.0030.0030.0000.0000.0000.000
20N20VAL0-0.064-0.02625.025-0.011-0.0110.0000.0000.0000.000
21N21VAL00.0060.01526.3430.0010.0010.0000.0000.0000.000
22N22ILE0-0.007-0.00819.782-0.023-0.0230.0000.0000.0000.000
23N23ALA00.0080.01121.7590.0280.0280.0000.0000.0000.000
24N24ALA00.012-0.00817.033-0.061-0.0610.0000.0000.0000.000
25N25ASP-1-0.797-0.90317.080-0.518-0.5180.0000.0000.0000.000
26N26MET0-0.049-0.02517.213-0.049-0.0490.0000.0000.0000.000
27N27LEU0-0.067-0.01815.5260.0600.0600.0000.0000.0000.000
28N28GLY00.0210.01012.395-0.105-0.1050.0000.0000.0000.000
29N29SER0-0.031-0.02912.0910.1440.1440.0000.0000.0000.000
30N30TYR0-0.014-0.0229.505-0.093-0.0930.0000.0000.0000.000
31N31GLY00.0690.03811.0430.0700.0700.0000.0000.0000.000
32N32SER00.0310.00612.704-0.070-0.0700.0000.0000.0000.000
33N33LEU00.0030.01515.5410.0040.0040.0000.0000.0000.000
34N34ALA00.0870.03515.388-0.041-0.0410.0000.0000.0000.000
35N35ARG10.8820.95313.106-0.047-0.0470.0000.0000.0000.000
36N36PHE0-0.003-0.01212.9760.0460.0460.0000.0000.0000.000
37N37ARG10.9530.97816.4960.1040.1040.0000.0000.0000.000
38N38ASN00.005-0.01518.4150.0030.0030.0000.0000.0000.000
39N39ILE0-0.0070.02512.9550.0310.0310.0000.0000.0000.000
40N40SER00.0350.01017.105-0.036-0.0360.0000.0000.0000.000
41N41ARG10.7930.89912.7920.7320.7320.0000.0000.0000.000
42N42ILE00.0250.00715.108-0.092-0.0920.0000.0000.0000.000
43N43MET0-0.0630.00814.2140.0550.0550.0000.0000.0000.000
44N44ARG10.9490.96717.7050.2480.2480.0000.0000.0000.000
45N45VAL0-0.044-0.02617.4090.0010.0010.0000.0000.0000.000
46N46ASN00.1150.04720.4630.0050.0050.0000.0000.0000.000
47N47ASN00.0440.02024.044-0.017-0.0170.0000.0000.0000.000
48N48SER00.0450.03926.171-0.002-0.0020.0000.0000.0000.000
49N49THR0-0.052-0.02821.464-0.035-0.0350.0000.0000.0000.000
50N50MET0-0.0020.01720.3960.0100.0100.0000.0000.0000.000
51N51LEU0-0.012-0.01113.217-0.035-0.0350.0000.0000.0000.000
52N52GLY00.0620.03615.9810.0410.0410.0000.0000.0000.000
53N53ALA0-0.015-0.01510.528-0.091-0.0910.0000.0000.0000.000
54N54SER00.001-0.00611.1780.1530.1530.0000.0000.0000.000
55N55GLY0-0.011-0.0057.306-0.335-0.3350.0000.0000.0000.000
56N56ASP-1-0.794-0.9253.136-1.822-1.1810.074-0.171-0.544-0.001
57N57TYR0-0.020-0.0315.070-0.336-0.313-0.001-0.001-0.0210.000
58N58ALA0-0.019-0.0055.0220.2420.2420.0000.0000.0000.000
59N59ASP-1-0.770-0.8741.737-28.873-32.19314.201-6.324-4.557-0.061
60N60PHE00.0070.0074.7220.8860.925-0.001-0.010-0.0270.000
61N61GLN0-0.043-0.0308.2480.4410.4410.0000.0000.0000.000
62N62TYR0-0.0030.0026.7260.2870.2870.0000.0000.0000.000
63N63LEU00.027-0.0018.0520.2710.2710.0000.0000.0000.000
64N64LYS10.9540.97110.1820.7390.7390.0000.0000.0000.000
65N65GLN0-0.032-0.01112.1310.1440.1440.0000.0000.0000.000
66N66VAL0-0.017-0.00911.6050.0800.0800.0000.0000.0000.000
67N67LEU00.0170.00213.8340.0530.0530.0000.0000.0000.000
68N68GLY00.0070.01215.9650.0550.0550.0000.0000.0000.000
69N69GLN0-0.067-0.04217.2990.0490.0490.0000.0000.0000.000
70N70MET0-0.0270.00117.3430.0000.0000.0000.0000.0000.000
71N71VAL0-0.018-0.01319.9880.0170.0170.0000.0000.0000.000
72N72ILE00.0040.00321.3020.0210.0210.0000.0000.0000.000
73N73ASP-1-0.873-0.95321.771-0.084-0.0840.0000.0000.0000.000
74N74GLU-1-0.868-0.92924.218-0.213-0.2130.0000.0000.0000.000
75N75GLU-1-0.973-1.00426.086-0.186-0.1860.0000.0000.0000.000
76N76LEU0-0.080-0.02826.6630.0150.0150.0000.0000.0000.000
77N77LEU0-0.063-0.01628.7540.0140.0140.0000.0000.0000.000
78N78GLY0-0.0050.00531.2450.0070.0070.0000.0000.0000.000
79N79ASP-1-0.893-0.95731.832-0.112-0.1120.0000.0000.0000.000
80N80GLY0-0.047-0.01834.1150.0000.0000.0000.0000.0000.000
81N81HIS0-0.105-0.05030.649-0.001-0.0010.0000.0000.0000.000
82N82SER00.0380.02227.6880.0030.0030.0000.0000.0000.000
83N83TYR0-0.072-0.03922.481-0.017-0.0170.0000.0000.0000.000
84N84SER00.0340.02125.251-0.020-0.0200.0000.0000.0000.000
85N85PRO00.0800.02222.978-0.028-0.0280.0000.0000.0000.000
86N86ARG10.8950.94222.0950.2580.2580.0000.0000.0000.000
87N87ALA00.0030.01322.610-0.026-0.0260.0000.0000.0000.000
88N88ILE00.0540.02817.932-0.031-0.0310.0000.0000.0000.000
89N89HIS0-0.007-0.00517.878-0.046-0.0460.0000.0000.0000.000
90N90SER0-0.0070.01017.916-0.076-0.0760.0000.0000.0000.000
91N91TRP00.0290.00812.699-0.078-0.0780.0000.0000.0000.000
92N92LEU00.0490.01411.479-0.042-0.0420.0000.0000.0000.000
93N93THR0-0.012-0.02413.217-0.163-0.1630.0000.0000.0000.000
94N94ARG10.8830.94613.8570.4160.4160.0000.0000.0000.000
95N95ALA00.0100.01611.3090.0400.0400.0000.0000.0000.000
96N96MET00.0030.0177.513-0.041-0.0410.0000.0000.0000.000
97N97TYR00.0340.0129.259-0.050-0.0500.0000.0000.0000.000
98N98SER0-0.0170.00611.1260.1730.1730.0000.0000.0000.000
99N99ARG10.8770.9222.8661.6462.1870.046-0.163-0.4240.001
100N100ARG10.9390.9836.7560.7990.7990.0000.0000.0000.000
101N101SER0-0.066-0.0398.2160.2360.2360.0000.0000.0000.000
102N102LYS10.8650.9448.068-0.037-0.0370.0000.0000.0000.000
103N103MET0-0.0160.0027.6450.3600.3600.0000.0000.0000.000
104N104ASN00.0020.0063.1855.0185.8300.807-0.493-1.1270.000
105N105PRO00.0420.0313.362-1.309-0.2900.043-0.313-0.7490.000
106N106LEU00.0000.0052.044-7.967-7.9525.415-2.653-2.777-0.031
107N107TRP00.0300.0132.7021.2963.2950.841-0.822-2.018-0.002
108N108ASN0-0.058-0.0644.2230.3980.5470.001-0.022-0.1270.000
109N109THR0-0.0130.0017.7140.1780.1780.0000.0000.0000.000
110N110MET0-0.056-0.0259.6000.0800.0800.0000.0000.0000.000
111N111VAL00.0260.01913.6570.0800.0800.0000.0000.0000.000
112N112ILE0-0.0090.00116.4220.0000.0000.0000.0000.0000.000
113N113GLY00.0300.01519.1500.0330.0330.0000.0000.0000.000
114N114GLY0-0.013-0.03122.683-0.007-0.0070.0000.0000.0000.000
115N115TYR0-0.022-0.00125.3850.0090.0090.0000.0000.0000.000
116N116ALA00.010-0.01229.1090.0030.0030.0000.0000.0000.000
117N117ASP-1-0.918-0.95030.900-0.192-0.1920.0000.0000.0000.000
118N118GLY0-0.0120.00134.3490.0040.0040.0000.0000.0000.000
119N119GLU-1-0.903-0.93732.071-0.208-0.2080.0000.0000.0000.000
120N120SER0-0.023-0.00929.384-0.012-0.0120.0000.0000.0000.000
121N121PHE0-0.038-0.02121.5020.0000.0000.0000.0000.0000.000
122N122LEU0-0.010-0.01722.073-0.015-0.0150.0000.0000.0000.000
123N123GLY00.0190.02320.7540.0230.0230.0000.0000.0000.000
124N124TYR0-0.040-0.03814.458-0.044-0.0440.0000.0000.0000.000
125N125VAL0-0.003-0.00912.8700.0650.0650.0000.0000.0000.000
126N126ASP-1-0.834-0.88911.602-1.502-1.5020.0000.0000.0000.000
127N127MET00.004-0.0016.704-0.335-0.3350.0000.0000.0000.000
128N128LEU0-0.042-0.0448.527-0.025-0.0250.0000.0000.0000.000
129N129GLY0-0.002-0.00611.0890.2240.2240.0000.0000.0000.000
130N130VAL0-0.036-0.01213.3830.1390.1390.0000.0000.0000.000
131N131ALA00.0400.00715.618-0.090-0.0900.0000.0000.0000.000
132N132TYR0-0.066-0.02417.9440.0820.0820.0000.0000.0000.000
133N133GLU-1-0.802-0.90421.210-0.381-0.3810.0000.0000.0000.000
134N134ALA0-0.019-0.01523.9680.0190.0190.0000.0000.0000.000
135N135PRO00.0390.02125.728-0.014-0.0140.0000.0000.0000.000
136N136SER00.0500.00525.8590.0120.0120.0000.0000.0000.000
137N137LEU0-0.058-0.01619.787-0.025-0.0250.0000.0000.0000.000
138N138ALA00.0220.00819.9770.0160.0160.0000.0000.0000.000
139N139THR00.014-0.00214.4040.0320.0320.0000.0000.0000.000
140N140GLY00.0140.00215.1330.0420.0420.0000.0000.0000.000
141N141TYR00.0500.01715.6570.0470.0470.0000.0000.0000.000
142N142GLY00.0560.03318.4970.0600.0600.0000.0000.0000.000
143N143ALA0-0.036-0.01518.8930.0460.0460.0000.0000.0000.000
144N144TYR0-0.043-0.03118.0650.0200.0200.0000.0000.0000.000
145N145LEU0-0.051-0.01422.1290.0370.0370.0000.0000.0000.000
146N146ALA00.0370.01323.0760.0220.0220.0000.0000.0000.000
147N147GLN00.0210.00023.2860.0390.0390.0000.0000.0000.000
148N148PRO0-0.017-0.00525.2810.0170.0170.0000.0000.0000.000
149N149LEU00.0310.02528.3060.0180.0180.0000.0000.0000.000
150N150LEU00.008-0.00524.9860.0120.0120.0000.0000.0000.000
151N151ARG10.9540.97424.6740.3640.3640.0000.0000.0000.000
152N152GLU-1-0.867-0.90030.427-0.183-0.1830.0000.0000.0000.000
153N153VAL0-0.007-0.01432.7990.0140.0140.0000.0000.0000.000
154N154LEU00.0200.00129.6930.0090.0090.0000.0000.0000.000
155N155GLU-1-0.972-0.97932.188-0.238-0.2380.0000.0000.0000.000
156N156LYS10.7570.86135.8400.1910.1910.0000.0000.0000.000
157N157GLN0-0.096-0.05837.1550.0140.0140.0000.0000.0000.000
158N158PRO0-0.0140.00035.231-0.008-0.0080.0000.0000.0000.000
159N159VAL0-0.0060.01134.825-0.013-0.0130.0000.0000.0000.000
160N160LEU00.0250.01932.1530.0060.0060.0000.0000.0000.000
161N161SER00.042-0.02235.795-0.003-0.0030.0000.0000.0000.000
162N162GLN00.0560.01232.387-0.003-0.0030.0000.0000.0000.000
163N163THR00.001-0.00533.321-0.009-0.0090.0000.0000.0000.000
164N164GLU-1-0.789-0.83634.717-0.180-0.1800.0000.0000.0000.000
165N165ALA00.0180.01830.432-0.009-0.0090.0000.0000.0000.000
166N166ARG10.7650.83929.9940.2110.2110.0000.0000.0000.000
167N167ASP-1-0.820-0.90230.458-0.207-0.2070.0000.0000.0000.000
168N168LEU00.0090.00129.304-0.007-0.0070.0000.0000.0000.000
169N169VAL00.0090.00025.483-0.015-0.0150.0000.0000.0000.000
170N170GLU-1-0.834-0.91126.799-0.251-0.2510.0000.0000.0000.000
171N171ARG10.8170.89528.5740.2080.2080.0000.0000.0000.000
172N172CYS0-0.059-0.02125.310-0.003-0.0030.0000.0000.0000.000
173N173MET0-0.013-0.01020.670-0.029-0.0290.0000.0000.0000.000
174N174ARG10.8640.93424.8050.2040.2040.0000.0000.0000.000
175N175VAL0-0.013-0.00926.1080.0060.0060.0000.0000.0000.000
176N176LEU0-0.022-0.02420.074-0.004-0.0040.0000.0000.0000.000
177N177TYR0-0.0070.00122.8030.0000.0000.0000.0000.0000.000
178N178TYR0-0.0180.00124.3250.0190.0190.0000.0000.0000.000
179N179ARG10.8900.93524.6850.2250.2250.0000.0000.0000.000
180N180ASP-1-0.780-0.86517.905-0.515-0.5150.0000.0000.0000.000
181N181ALA0-0.013-0.00519.7890.0080.0080.0000.0000.0000.000
182N182ARG10.8000.88710.7720.6450.6450.0000.0000.0000.000
183N183SER00.0080.01316.321-0.049-0.0490.0000.0000.0000.000
184N184TYR00.022-0.01518.9130.0520.0520.0000.0000.0000.000
185N185ASN00.0370.06121.089-0.029-0.0290.0000.0000.0000.000
186N186ARG10.8910.94022.5100.2440.2440.0000.0000.0000.000
187N187PHE0-0.023-0.00321.548-0.044-0.0440.0000.0000.0000.000
188N188GLN00.0590.05020.602-0.009-0.0090.0000.0000.0000.000
189N189ILE00.0580.02822.633-0.036-0.0360.0000.0000.0000.000
190N190ALA0-0.030-0.00522.5710.0180.0180.0000.0000.0000.000
191N191THR00.025-0.00124.528-0.014-0.0140.0000.0000.0000.000
192N192VAL0-0.030-0.00525.1990.0060.0060.0000.0000.0000.000
193N193THR00.0600.02827.9730.0090.0090.0000.0000.0000.000
194N194GLU-1-0.816-0.89931.050-0.162-0.1620.0000.0000.0000.000
195N195LYS10.7930.88033.5910.1560.1560.0000.0000.0000.000
196N196GLY00.0100.02529.7870.0070.0070.0000.0000.0000.000
197N197VAL0-0.045-0.02923.589-0.012-0.0120.0000.0000.0000.000
198N198GLU-1-0.948-0.95627.061-0.196-0.1960.0000.0000.0000.000
199N199ILE0-0.043-0.04321.394-0.025-0.0250.0000.0000.0000.000
200N200GLU-1-0.770-0.84325.505-0.214-0.2140.0000.0000.0000.000
201N201GLY0-0.036-0.02825.917-0.020-0.0200.0000.0000.0000.000
202N202PRO0-0.050-0.04324.913-0.007-0.0070.0000.0000.0000.000
203N203LEU00.0480.05525.8030.0240.0240.0000.0000.0000.000
204N204SER0-0.043-0.03626.232-0.012-0.0120.0000.0000.0000.000
205N205THR0-0.003-0.01826.4810.0010.0010.0000.0000.0000.000
206N206GLU-1-0.823-0.89829.148-0.176-0.1760.0000.0000.0000.000
207N207THR0-0.043-0.02429.368-0.006-0.0060.0000.0000.0000.000
208N208ASN0-0.029-0.03632.5130.0130.0130.0000.0000.0000.000
209N209TRP00.003-0.01328.895-0.008-0.0080.0000.0000.0000.000
210N210ASP-1-0.794-0.87835.962-0.108-0.1080.0000.0000.0000.000
211N211ILE0-0.046-0.04434.0540.0050.0050.0000.0000.0000.000
212N212ALA0-0.029-0.00636.8580.0010.0010.0000.0000.0000.000
213N213HIS0-0.042-0.02438.3010.0080.0080.0000.0000.0000.000
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216N216SER0-0.022-0.00942.129-0.001-0.0010.0000.0000.0000.000
217N217GLY00.0210.02144.5290.0010.0010.0000.0000.0000.000