Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 1NKKZ

Calculation Name: 4BJI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4BJI

Chain ID: A

ChEMBL ID:

UniProt ID: O14229

Base Structure: X-ray

Registration Date: 2023-09-23

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 OptH
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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2394430.153986
FMO2-HF: Nuclear repulsion 2312736.331508
FMO2-HF: Total energy -81693.822478
FMO2-MP2: Total energy -81933.142476


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:190:ARG)


Summations of interaction energy for fragment #1(A:190:ARG)
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.
123.093127.2478.377-3.68-8.852-0.027
Interaction energy analysis for fragmet #1(A:190:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.943 / q_NPA : 0.957
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].
3A192TRP00.002-0.0082.356-9.444-5.5788.377-3.623-8.620-0.027
4A193ILE00.0310.0294.2013.3373.5090.001-0.042-0.1320.000
5A194ILE00.0200.0157.267-2.233-2.2330.0000.0000.0000.000
6A195THR0-0.030-0.0209.7291.3131.3130.0000.0000.0000.000
7A196THR00.0590.03612.058-0.159-0.1590.0000.0000.0000.000
8A197ASN00.012-0.00115.7900.6350.6350.0000.0000.0000.000
9A198MET00.028-0.00218.945-0.018-0.0180.0000.0000.0000.000
10A199GLY0-0.0020.01621.7410.5110.5110.0000.0000.0000.000
11A200VAL0-0.061-0.01117.8470.0250.0250.0000.0000.0000.000
12A201GLU-1-0.866-0.92620.617-11.874-11.8740.0000.0000.0000.000
13A202SER00.000-0.00721.1080.7060.7060.0000.0000.0000.000
14A203VAL0-0.072-0.02318.828-0.761-0.7610.0000.0000.0000.000
15A204PRO00.0180.00114.4870.1080.1080.0000.0000.0000.000
16A205THR00.0420.01016.6670.1920.1920.0000.0000.0000.000
17A206CYS00.0060.00414.7240.6240.6240.0000.0000.0000.000
18A207ARG10.8850.96511.09219.16919.1690.0000.0000.0000.000
19A208HIS00.0410.0136.6290.4220.4220.0000.0000.0000.000
20A209SER00.0500.0229.608-0.837-0.8370.0000.0000.0000.000
21A210LYS10.9260.9525.14243.81743.8170.0000.0000.0000.000
22A211LEU0-0.066-0.0076.668-1.960-1.9600.0000.0000.0000.000
23A212GLY00.0630.0358.5671.8971.8970.0000.0000.0000.000
24A213GLU-1-0.885-0.94311.028-17.559-17.5590.0000.0000.0000.000
25A214PRO0-0.0190.01611.398-1.071-1.0710.0000.0000.0000.000
26A215SER00.0540.01911.9721.2061.2060.0000.0000.0000.000
27A216LYS11.0380.99613.89012.53512.5350.0000.0000.0000.000
28A217THR00.0110.01914.2440.2190.2190.0000.0000.0000.000
29A218ILE0-0.016-0.01510.3110.1270.1270.0000.0000.0000.000
30A219GLN0-0.015-0.01513.687-0.439-0.4390.0000.0000.0000.000
31A220GLU-1-0.840-0.88016.521-12.092-12.0920.0000.0000.0000.000
32A221VAL0-0.008-0.00614.9710.2390.2390.0000.0000.0000.000
33A222ILE0-0.029-0.02013.3890.2440.2440.0000.0000.0000.000
34A223GLU-1-0.807-0.90617.101-12.540-12.5400.0000.0000.0000.000
35A224ALA00.0110.01720.1660.5140.5140.0000.0000.0000.000
36A225LEU0-0.046-0.03515.4030.2250.2250.0000.0000.0000.000
37A226LYS10.8670.93819.41713.47713.4770.0000.0000.0000.000
38A227PRO00.0690.03621.6920.2450.2450.0000.0000.0000.000
39A228LEU0-0.033-0.01421.3210.3790.3790.0000.0000.0000.000
40A229PHE0-0.012-0.00916.8400.0330.0330.0000.0000.0000.000
41A230GLU-1-0.914-0.94322.482-10.831-10.8310.0000.0000.0000.000
42A231LYS10.8780.94725.79910.14610.1460.0000.0000.0000.000
43A232ARG10.7490.85623.84711.26211.2620.0000.0000.0000.000
44A233PRO00.0230.02322.921-0.463-0.4630.0000.0000.0000.000
45A234VAL00.0260.01520.746-0.626-0.6260.0000.0000.0000.000
46A235TRP00.0180.00719.0510.5670.5670.0000.0000.0000.000
47A236THR00.0510.03318.150-0.777-0.7770.0000.0000.0000.000
48A237ARG10.9590.97412.77116.83116.8310.0000.0000.0000.000
49A238ARG10.8880.95316.56612.89512.8950.0000.0000.0000.000
50A239ALA00.0820.03319.6370.3110.3110.0000.0000.0000.000
51A240LEU00.0330.02717.0680.2220.2220.0000.0000.0000.000
52A241LEU0-0.062-0.02616.2520.1450.1450.0000.0000.0000.000
53A242ASN0-0.078-0.04519.8160.1050.1050.0000.0000.0000.000
54A243HIS0-0.078-0.03822.6360.7450.7450.0000.0000.0000.000
55A244LEU0-0.043-0.02018.115-0.047-0.0470.0000.0000.0000.000
56A245ASP-1-0.745-0.82221.639-11.163-11.1630.0000.0000.0000.000
57A246PRO00.0500.00820.756-0.589-0.5890.0000.0000.0000.000
58A247SER0-0.072-0.05219.824-0.595-0.5950.0000.0000.0000.000
59A248TYR0-0.037-0.06816.624-0.852-0.8520.0000.0000.0000.000
60A249THR0-0.060-0.03915.432-0.851-0.8510.0000.0000.0000.000
61A250HIS0-0.049-0.04912.016-1.150-1.1500.0000.0000.0000.000
62A251TYR00.0630.02511.003-1.524-1.5240.0000.0000.0000.000
63A252LEU00.0410.03611.416-1.137-1.1370.0000.0000.0000.000
64A253LYS10.8930.9436.33524.01624.0160.0000.0000.0000.000
65A254PHE0-0.001-0.0154.262-1.929-1.813-0.001-0.015-0.1000.000
66A255ALA00.0570.0418.477-0.683-0.6830.0000.0000.0000.000
67A256LEU00.0070.00311.1870.1800.1800.0000.0000.0000.000
68A257PRO0-0.014-0.0067.3410.8950.8950.0000.0000.0000.000
69A258TYR0-0.045-0.0489.679-0.542-0.5420.0000.0000.0000.000
70A259LEU0-0.064-0.02212.4710.9800.9800.0000.0000.0000.000
71A260SER0-0.031-0.01113.5070.9320.9320.0000.0000.0000.000
72A261TYR0-0.011-0.01012.396-1.596-1.5960.0000.0000.0000.000
73A262LEU0-0.034-0.01910.7230.8110.8110.0000.0000.0000.000
74A263TRP00.0030.01713.788-0.819-0.8190.0000.0000.0000.000
75A264THR0-0.008-0.02812.7860.0060.0060.0000.0000.0000.000
76A265SER0-0.062-0.03915.8750.4430.4430.0000.0000.0000.000
77A266GLY00.0550.03719.629-0.099-0.0990.0000.0000.0000.000
78A267PRO00.0140.00622.787-0.222-0.2220.0000.0000.0000.000
79A268PHE00.0500.01721.2930.2630.2630.0000.0000.0000.000
80A269ARG10.8930.97218.42613.44513.4450.0000.0000.0000.000
81A270ASP-1-0.887-0.94915.889-15.164-15.1640.0000.0000.0000.000
82A271THR0-0.094-0.05716.9700.2800.2800.0000.0000.0000.000
83A272TYR0-0.009-0.02310.458-0.538-0.5380.0000.0000.0000.000
84A273THR00.0040.00216.1881.1291.1290.0000.0000.0000.000
85A274ARG10.9260.96617.07110.59910.5990.0000.0000.0000.000
86A275PHE0-0.013-0.02312.2600.2230.2230.0000.0000.0000.000
87A276GLY00.0120.00418.2020.5550.5550.0000.0000.0000.000
88A277TYR0-0.074-0.03221.0690.4190.4190.0000.0000.0000.000
89A278ASP-1-0.736-0.86921.614-12.662-12.6620.0000.0000.0000.000
90A279PRO00.0190.01622.4000.5020.5020.0000.0000.0000.000
91A280ARG10.7640.83723.08512.85512.8550.0000.0000.0000.000
92A281LYS10.9010.94826.29111.11011.1100.0000.0000.0000.000
93A282ASP-1-0.784-0.86828.554-9.297-9.2970.0000.0000.0000.000
94A283SER00.0290.01029.888-0.193-0.1930.0000.0000.0000.000
95A284ASN00.0500.02731.3980.2170.2170.0000.0000.0000.000
96A285ALA0-0.045-0.02326.614-0.082-0.0820.0000.0000.0000.000
97A286ALA00.0280.01327.972-0.291-0.2910.0000.0000.0000.000
98A287ALA0-0.0030.00629.946-0.036-0.0360.0000.0000.0000.000
99A288TYR00.012-0.00724.660-0.122-0.1220.0000.0000.0000.000
100A289GLN00.0070.01824.569-0.314-0.3140.0000.0000.0000.000
101A290ALA0-0.004-0.00222.3650.2100.2100.0000.0000.0000.000
102A291LEU0-0.0120.00324.2850.0030.0030.0000.0000.0000.000
103A292PHE0-0.011-0.00921.062-0.115-0.1150.0000.0000.0000.000
104A293PHE0-0.017-0.01124.1480.3040.3040.0000.0000.0000.000
105A294LYS10.9570.97824.52311.24911.2490.0000.0000.0000.000
106A295LEU00.0290.01225.8400.2700.2700.0000.0000.0000.000
107A296LYS10.9780.98626.0498.8448.8440.0000.0000.0000.000
108A297LEU00.0250.03522.2690.2520.2520.0000.0000.0000.000
109A298ASN0-0.009-0.01225.847-0.379-0.3790.0000.0000.0000.000
110A299GLY00.0450.02226.838-0.119-0.1190.0000.0000.0000.000
111A300LYS10.9450.96027.6749.0059.0050.0000.0000.0000.000
112A301HIS00.0390.03829.3950.2800.2800.0000.0000.0000.000
113A302LYS10.9130.94928.5228.8518.8510.0000.0000.0000.000
114A303GLY00.0860.05428.3680.2700.2700.0000.0000.0000.000
115A304THR00.0170.03328.093-0.348-0.3480.0000.0000.0000.000
116A305LYS10.9500.96222.44511.11011.1100.0000.0000.0000.000
117A306THR00.0410.01824.406-0.456-0.4560.0000.0000.0000.000
118A307HIS00.0290.01023.791-0.363-0.3630.0000.0000.0000.000
119A308VAL0-0.0210.00425.528-0.011-0.0110.0000.0000.0000.000
120A309PHE0-0.013-0.00429.246-0.009-0.0090.0000.0000.0000.000
121A310ASP-1-0.758-0.87831.230-8.072-8.0720.0000.0000.0000.000
122A311GLY0-0.0020.00434.2480.2200.2200.0000.0000.0000.000
123A312LYS10.9200.94735.8577.3917.3910.0000.0000.0000.000
124A313THR0-0.062-0.05532.8870.1160.1160.0000.0000.0000.000
125A314LEU00.0240.01433.651-0.197-0.1970.0000.0000.0000.000
126A315PHE0-0.036-0.00531.168-0.210-0.2100.0000.0000.0000.000
127A316PRO00.0210.02228.349-0.304-0.3040.0000.0000.0000.000
128A317THR0-0.035-0.03523.959-0.284-0.2840.0000.0000.0000.000
129A318ASN0-0.025-0.01922.289-0.924-0.9240.0000.0000.0000.000
130A319ARG10.8260.89422.21210.94310.9430.0000.0000.0000.000
131A320VAL00.0120.01019.6230.0560.0560.0000.0000.0000.000
132A321TYR0-0.0030.01822.806-0.040-0.0400.0000.0000.0000.000
133A322GLN00.022-0.00522.708-0.246-0.2460.0000.0000.0000.000
134A323VAL00.0190.00825.9310.2510.2510.0000.0000.0000.000
135A324CYS0-0.040-0.01227.7440.1470.1470.0000.0000.0000.000
136A325ASP-1-0.809-0.87725.966-10.281-10.2810.0000.0000.0000.000
137A326ILE0-0.031-0.02129.4730.0610.0610.0000.0000.0000.000
138A327VAL00.0180.00532.1180.1600.1600.0000.0000.0000.000
139A328ASP-1-0.761-0.85535.067-7.400-7.4000.0000.0000.0000.000
140A329PRO00.0260.00937.111-0.040-0.0400.0000.0000.0000.000
141A330THR0-0.051-0.03639.8790.1050.1050.0000.0000.0000.000
142A331ILE0-0.013-0.01534.884-0.009-0.0090.0000.0000.0000.000
143A332ALA00.0030.00236.160-0.041-0.0410.0000.0000.0000.000
144A333PRO00.0440.01637.151-0.089-0.0890.0000.0000.0000.000
145A334LEU0-0.0120.00938.1240.0240.0240.0000.0000.0000.000
146A335LEU00.003-0.01332.584-0.045-0.0450.0000.0000.0000.000
147A336LYS10.9230.96836.6177.2067.2060.0000.0000.0000.000
148A337ASP-1-0.873-0.93438.280-6.945-6.9450.0000.0000.0000.000
149A338THR0-0.119-0.04037.2210.1390.1390.0000.0000.0000.000
150A339GLN0-0.001-0.00139.275-0.005-0.0050.0000.0000.0000.000
151A340LEU0-0.035-0.01534.408-0.094-0.0940.0000.0000.0000.000
152A341ARG10.8630.92533.9528.9338.9330.0000.0000.0000.000
153A342SER00.0330.00736.225-0.043-0.0430.0000.0000.0000.000
154A343GLU-1-0.935-0.96231.926-9.284-9.2840.0000.0000.0000.000
155A344CYS0-0.0730.01028.063-0.061-0.0610.0000.0000.0000.000
156A345HIS00.0510.02829.579-0.349-0.3490.0000.0000.0000.000
157A346ARG10.9690.96726.17110.73710.7370.0000.0000.0000.000
158A347ASP-1-0.887-0.94426.146-11.096-11.0960.0000.0000.0000.000
159A348THR0-0.027-0.04327.832-0.144-0.1440.0000.0000.0000.000
160A349GLY00.0200.00828.9260.1340.1340.0000.0000.0000.000
161A350TRP00.006-0.00628.9620.3410.3410.0000.0000.0000.000
162A351TYR00.0120.02030.6860.4330.4330.0000.0000.0000.000
163A352ARG10.9190.94234.3417.2147.2140.0000.0000.0000.000
164A353SER00.0270.00735.2550.0370.0370.0000.0000.0000.000
165A354GLY00.0750.03336.306-0.099-0.0990.0000.0000.0000.000
166A355ARG10.8310.91037.2317.3587.3580.0000.0000.0000.000
167A356TYR0-0.019-0.01827.743-0.116-0.1160.0000.0000.0000.000
168A357TYR00.002-0.02331.073-0.259-0.2590.0000.0000.0000.000
169A358LYS10.9350.99535.1406.9746.9740.0000.0000.0000.000
170A359VAL00.0270.01033.0030.0090.0090.0000.0000.0000.000
171A360ARG10.8370.91030.3489.0369.0360.0000.0000.0000.000
172A361ASP-1-0.831-0.92432.900-8.475-8.4750.0000.0000.0000.000
173A362LEU00.0150.01435.6550.0330.0330.0000.0000.0000.000
174A363MET0-0.022-0.00729.537-0.021-0.0210.0000.0000.0000.000
175A364ARG10.8850.94731.5838.4828.4820.0000.0000.0000.000
176A365GLU-1-0.896-0.94632.957-7.714-7.7140.0000.0000.0000.000
177A366LYS10.8660.91935.3167.5677.5670.0000.0000.0000.000
178A367LEU0-0.036-0.02329.004-0.056-0.0560.0000.0000.0000.000
179A368PHE0-0.020-0.01332.889-0.210-0.2100.0000.0000.0000.000
180A369ALA00.0590.04634.522-0.002-0.0020.0000.0000.0000.000
181A370LEU00.0180.02133.446-0.023-0.0230.0000.0000.0000.000
182A371ILE0-0.146-0.08129.784-0.142-0.1420.0000.0000.0000.000
183A372GLU-1-0.925-0.96932.552-8.484-8.4840.0000.0000.0000.000
184A373GLY0-0.069-0.03035.5900.1440.1440.0000.0000.0000.000
185A374GLU-1-0.951-0.96537.208-7.017-7.0170.0000.0000.0000.000
186A375MET0-0.019-0.02538.586-0.219-0.2190.0000.0000.0000.000
187A376PRO0-0.018-0.01337.9560.0850.0850.0000.0000.0000.000
188A377SER00.0440.03640.7200.1480.1480.0000.0000.0000.000
189A378GLU-1-0.891-0.95443.993-6.309-6.3090.0000.0000.0000.000
190A379VAL00.0370.02045.526-0.015-0.0150.0000.0000.0000.000
191A380ALA00.007-0.00744.0080.0040.0040.0000.0000.0000.000
192A381VAL00.012-0.00640.409-0.084-0.0840.0000.0000.0000.000
193A382ASN0-0.009-0.01442.924-0.177-0.1770.0000.0000.0000.000
194A383MET0-0.049-0.01445.5160.0300.0300.0000.0000.0000.000
195A384ILE0-0.014-0.00139.312-0.023-0.0230.0000.0000.0000.000
196A385LEU0-0.037-0.01941.904-0.086-0.0860.0000.0000.0000.000
197A386ASN0-0.007-0.02143.311-0.042-0.0420.0000.0000.0000.000
198A387ALA0-0.0090.02943.7950.1070.1070.0000.0000.0000.000
199A388GLU-1-0.901-0.95045.122-6.261-6.2610.0000.0000.0000.000
200A389GLU-1-0.844-0.89041.783-7.443-7.4430.0000.0000.0000.000
201A390VAL00.002-0.00140.642-0.007-0.0070.0000.0000.0000.000