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: 37NZL

Calculation Name: 1K1B-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1K1B

Chain ID: A

ChEMBL ID:

UniProt ID: P20749

Base Structure: X-ray

Registration Date: 2023-09-26

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 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 228
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2451637.053777
FMO2-HF: Nuclear repulsion 2365449.080065
FMO2-HF: Total energy -86187.973712
FMO2-MP2: Total energy -86438.332153


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:125:GLU)


Summations of interaction energy for fragment #1(A:125:GLU)
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.
10.67413.2930.041-0.719-1.943-0.002
Interaction energy analysis for fragmet #1(A:125:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.960 / q_NPA : -1.005
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].
3A127GLY00.0370.0093.6340.6831.698-0.025-0.104-0.8870.001
4A128ASP-1-0.979-0.9833.34445.57147.1740.067-0.564-1.107-0.003
5A129THR0-0.013-0.0274.051-0.802-0.801-0.001-0.0510.0510.000
6A130PRO00.0190.0165.514-3.187-3.1870.0000.0000.0000.000
7A131LEU00.0070.0038.661-2.042-2.0420.0000.0000.0000.000
8A132HIS00.004-0.0269.383-0.633-0.6330.0000.0000.0000.000
9A133ILE0-0.005-0.00110.547-1.473-1.4730.0000.0000.0000.000
10A134ALA0-0.007-0.00412.594-1.222-1.2220.0000.0000.0000.000
11A135VAL0-0.040-0.01814.441-1.148-1.1480.0000.0000.0000.000
12A136VAL00.0290.01815.678-0.806-0.8060.0000.0000.0000.000
13A137GLN0-0.067-0.02915.501-0.622-0.6220.0000.0000.0000.000
14A138GLY00.0110.01318.648-0.533-0.5330.0000.0000.0000.000
15A139ASN0-0.009-0.00218.015-0.850-0.8500.0000.0000.0000.000
16A140LEU00.0500.01818.7450.5390.5390.0000.0000.0000.000
17A141PRO00.010-0.00819.9610.3390.3390.0000.0000.0000.000
18A142ALA0-0.020-0.00915.7790.3420.3420.0000.0000.0000.000
19A143VAL00.0420.02615.4240.9250.9250.0000.0000.0000.000
20A144HIS00.0050.00816.1360.8140.8140.0000.0000.0000.000
21A145ARG10.9540.97915.455-16.074-16.0740.0000.0000.0000.000
22A146LEU0-0.004-0.00910.2400.5920.5920.0000.0000.0000.000
23A147VAL00.0310.02613.0580.8480.8480.0000.0000.0000.000
24A148ASN00.0110.00115.219-0.041-0.0410.0000.0000.0000.000
25A149LEU0-0.025-0.01811.9370.0930.0930.0000.0000.0000.000
26A150PHE0-0.062-0.0407.6071.6111.6110.0000.0000.0000.000
27A151GLN00.0160.02012.0570.0910.0910.0000.0000.0000.000
28A152GLN0-0.017-0.00115.520-0.813-0.8130.0000.0000.0000.000
29A153GLY0-0.046-0.01311.968-0.074-0.0740.0000.0000.0000.000
30A154GLY0-0.019-0.01112.3990.8790.8790.0000.0000.0000.000
31A155ARG10.8780.9405.009-31.880-31.8800.0000.0000.0000.000
32A156GLU-1-0.827-0.92510.91816.04216.0420.0000.0000.0000.000
33A157LEU0-0.007-0.01210.9661.3701.3700.0000.0000.0000.000
34A158ASP-1-0.864-0.90812.78115.40615.4060.0000.0000.0000.000
35A159ILE0-0.048-0.0147.2300.2410.2410.0000.0000.0000.000
36A160TYR0-0.042-0.05510.456-0.496-0.4960.0000.0000.0000.000
37A161ASN00.0530.0378.8901.4681.4680.0000.0000.0000.000
38A162ASN00.0670.0029.3520.2760.2760.0000.0000.0000.000
39A163LEU0-0.097-0.02911.771-1.026-1.0260.0000.0000.0000.000
40A164ARG10.9090.95113.478-15.992-15.9920.0000.0000.0000.000
41A165GLN00.0740.03513.796-0.273-0.2730.0000.0000.0000.000
42A166THR00.0660.04912.8291.1981.1980.0000.0000.0000.000
43A167PRO00.037-0.00111.734-0.755-0.7550.0000.0000.0000.000
44A168LEU00.0450.02314.380-0.674-0.6740.0000.0000.0000.000
45A169HIS00.0040.00717.086-0.057-0.0570.0000.0000.0000.000
46A170LEU00.0210.00613.940-0.507-0.5070.0000.0000.0000.000
47A171ALA0-0.0140.01417.925-0.427-0.4270.0000.0000.0000.000
48A172VAL0-0.042-0.02019.980-0.578-0.5780.0000.0000.0000.000
49A173ILE0-0.0140.00019.359-0.325-0.3250.0000.0000.0000.000
50A174THR0-0.031-0.02219.836-0.155-0.1550.0000.0000.0000.000
51A175THR0-0.080-0.04622.500-0.531-0.5310.0000.0000.0000.000
52A176LEU00.0160.01520.578-0.236-0.2360.0000.0000.0000.000
53A177PRO00.0490.00723.7870.2890.2890.0000.0000.0000.000
54A178SER00.003-0.01425.538-0.065-0.0650.0000.0000.0000.000
55A179VAL00.0370.01318.8980.1290.1290.0000.0000.0000.000
56A180VAL0-0.0030.00621.1310.3300.3300.0000.0000.0000.000
57A181ARG10.9200.96422.819-9.429-9.4290.0000.0000.0000.000
58A182LEU0-0.0190.01019.270-0.015-0.0150.0000.0000.0000.000
59A183LEU00.0160.00016.2320.2340.2340.0000.0000.0000.000
60A184VAL00.0120.01919.6970.1880.1880.0000.0000.0000.000
61A185THR0-0.073-0.04022.366-0.022-0.0220.0000.0000.0000.000
62A186ALA0-0.053-0.02018.930-0.080-0.0800.0000.0000.0000.000
63A187GLY00.004-0.00519.6250.4510.4510.0000.0000.0000.000
64A188ALA0-0.052-0.00917.6200.2040.2040.0000.0000.0000.000
65A189SER00.025-0.00518.790-0.928-0.9280.0000.0000.0000.000
66A190PRO0-0.011-0.02320.5300.2540.2540.0000.0000.0000.000
67A191MET00.0060.01722.863-0.301-0.3010.0000.0000.0000.000
68A192ALA00.0040.02617.8890.0250.0250.0000.0000.0000.000
69A193LEU0-0.0180.00019.956-0.223-0.2230.0000.0000.0000.000
70A194ASP-1-0.741-0.86918.35413.22113.2210.0000.0000.0000.000
71A195ARG10.8780.93618.127-13.722-13.7220.0000.0000.0000.000
72A196HIS0-0.026-0.01919.990-0.324-0.3240.0000.0000.0000.000
73A197GLY00.0300.00122.435-0.513-0.5130.0000.0000.0000.000
74A198GLN00.0390.03323.234-0.658-0.6580.0000.0000.0000.000
75A199THR00.0400.00522.4990.4720.4720.0000.0000.0000.000
76A200ALA00.026-0.00222.230-0.056-0.0560.0000.0000.0000.000
77A201ALA00.0420.01123.706-0.181-0.1810.0000.0000.0000.000
78A202HIS00.0020.01626.1560.0220.0220.0000.0000.0000.000
79A203LEU00.0050.00821.225-0.188-0.1880.0000.0000.0000.000
80A204ALA00.006-0.00225.633-0.115-0.1150.0000.0000.0000.000
81A205CYS0-0.069-0.02027.688-0.354-0.3540.0000.0000.0000.000
82A206GLU-1-0.919-0.95526.42510.47710.4770.0000.0000.0000.000
83A207HIS0-0.056-0.03524.352-0.013-0.0130.0000.0000.0000.000
84A208ARG10.8830.95628.842-8.557-8.5570.0000.0000.0000.000
85A209SER00.0570.02628.210-0.208-0.2080.0000.0000.0000.000
86A210PRO00.0560.01430.5410.1560.1560.0000.0000.0000.000
87A211THR0-0.032-0.01730.8540.0490.0490.0000.0000.0000.000
88A212CYS0-0.0200.01025.5360.1250.1250.0000.0000.0000.000
89A213LEU00.0500.03427.8400.1960.1960.0000.0000.0000.000
90A214ARG10.9650.98229.976-8.004-8.0040.0000.0000.0000.000
91A215ALA0-0.036-0.01427.169-0.018-0.0180.0000.0000.0000.000
92A216LEU00.0090.01823.7580.1290.1290.0000.0000.0000.000
93A217LEU00.005-0.00627.4150.0180.0180.0000.0000.0000.000
94A218ASP-1-0.892-0.94030.7518.3678.3670.0000.0000.0000.000
95A219SER0-0.085-0.06326.637-0.049-0.0490.0000.0000.0000.000
96A220ALA0-0.0070.01326.8380.2420.2420.0000.0000.0000.000
97A221ALA00.0240.02727.327-0.326-0.3260.0000.0000.0000.000
98A222PRO00.0360.01229.2340.0600.0600.0000.0000.0000.000
99A223GLY00.0020.00431.2150.0920.0920.0000.0000.0000.000
100A224THR0-0.074-0.05026.0710.2350.2350.0000.0000.0000.000
101A225LEU0-0.013-0.01427.0580.3090.3090.0000.0000.0000.000
102A226ASP-1-0.851-0.94328.7938.4668.4660.0000.0000.0000.000
103A227LEU0-0.026-0.02530.3590.2400.2400.0000.0000.0000.000
104A228GLU-1-0.830-0.90432.5507.8857.8850.0000.0000.0000.000
105A229ALA0-0.032-0.01228.2730.0160.0160.0000.0000.0000.000
106A230ARG10.8230.90430.253-8.319-8.3190.0000.0000.0000.000
107A231ASN0-0.0020.00627.2150.0290.0290.0000.0000.0000.000
108A232TYR0-0.036-0.03522.264-0.022-0.0220.0000.0000.0000.000
109A233ASP-1-0.964-0.96528.0489.3259.3250.0000.0000.0000.000
110A234GLY0-0.039-0.02431.007-0.344-0.3440.0000.0000.0000.000
111A235LEU0-0.051-0.02432.198-0.245-0.2450.0000.0000.0000.000
112A236THR00.0900.05131.6690.2830.2830.0000.0000.0000.000
113A237ALA00.039-0.00230.6430.0020.0020.0000.0000.0000.000
114A238LEU00.0590.03232.139-0.048-0.0480.0000.0000.0000.000
115A239HIS00.0010.01035.1410.0530.0530.0000.0000.0000.000
116A240VAL0-0.017-0.00130.520-0.085-0.0850.0000.0000.0000.000
117A241ALA00.0110.00033.779-0.059-0.0590.0000.0000.0000.000
118A242VAL00.001-0.00235.266-0.142-0.1420.0000.0000.0000.000
119A243ASN00.000-0.00735.816-0.303-0.3030.0000.0000.0000.000
120A244THR0-0.101-0.03833.069-0.021-0.0210.0000.0000.0000.000
121A245GLU-1-0.825-0.90136.3806.9806.9800.0000.0000.0000.000
122A246CYS0-0.078-0.00336.268-0.044-0.0440.0000.0000.0000.000
123A247GLN00.053-0.00738.223-0.032-0.0320.0000.0000.0000.000
124A248GLU-1-0.892-0.94937.4057.4037.4030.0000.0000.0000.000
125A249THR0-0.001-0.01833.055-0.024-0.0240.0000.0000.0000.000
126A250VAL00.0350.02135.8350.0340.0340.0000.0000.0000.000
127A251GLN0-0.041-0.02238.392-0.049-0.0490.0000.0000.0000.000
128A252LEU0-0.037-0.00934.058-0.019-0.0190.0000.0000.0000.000
129A253LEU0-0.011-0.02232.7630.0560.0560.0000.0000.0000.000
130A254LEU00.0050.00536.564-0.023-0.0230.0000.0000.0000.000
131A255GLU-1-0.913-0.94839.8147.0257.0250.0000.0000.0000.000
132A256ARG10.7450.85934.729-8.087-8.0870.0000.0000.0000.000
133A257GLY00.0000.00436.9810.1510.1510.0000.0000.0000.000
134A258ALA0-0.045-0.00636.3940.0160.0160.0000.0000.0000.000
135A259ASP-1-0.887-0.95037.8596.8586.8580.0000.0000.0000.000
136A260ILE0-0.027-0.02040.0770.0950.0950.0000.0000.0000.000
137A261ASP-1-0.889-0.94842.3606.3906.3900.0000.0000.0000.000
138A262ALA00.0030.01238.225-0.017-0.0170.0000.0000.0000.000
139A263VAL0-0.016-0.01640.3480.0030.0030.0000.0000.0000.000
140A264ASP-1-0.795-0.86036.2577.7917.7910.0000.0000.0000.000
141A265ILE00.0270.00435.345-0.153-0.1530.0000.0000.0000.000
142A266LYS10.9861.00534.393-8.604-8.6040.0000.0000.0000.000
143A267SER0-0.079-0.07337.767-0.234-0.2340.0000.0000.0000.000
144A268GLY00.0400.01040.567-0.198-0.1980.0000.0000.0000.000
145A269ARG10.8010.89741.721-6.964-6.9640.0000.0000.0000.000
146A270SER00.0960.05241.4600.1560.1560.0000.0000.0000.000
147A271PRO00.0510.01439.692-0.038-0.0380.0000.0000.0000.000
148A272LEU00.0210.02541.839-0.037-0.0370.0000.0000.0000.000
149A273ILE0-0.025-0.03045.234-0.083-0.0830.0000.0000.0000.000
150A274HIS00.0190.01538.969-0.061-0.0610.0000.0000.0000.000
151A275ALA00.0210.02142.903-0.005-0.0050.0000.0000.0000.000
152A276VAL0-0.064-0.03744.324-0.109-0.1090.0000.0000.0000.000
153A277GLU-1-0.919-0.95644.6526.5196.5190.0000.0000.0000.000
154A278ASN0-0.018-0.00340.268-0.038-0.0380.0000.0000.0000.000
155A279ASN0-0.097-0.05844.354-0.115-0.1150.0000.0000.0000.000
156A280SER00.009-0.00643.961-0.102-0.1020.0000.0000.0000.000
157A281LEU0-0.041-0.04146.441-0.044-0.0440.0000.0000.0000.000
158A282SER00.0250.00845.787-0.110-0.1100.0000.0000.0000.000
159A283MET00.0420.03641.7800.0220.0220.0000.0000.0000.000
160A284VAL0-0.015-0.00444.919-0.032-0.0320.0000.0000.0000.000
161A285GLN0-0.052-0.04047.917-0.018-0.0180.0000.0000.0000.000
162A286LEU00.0060.01642.574-0.059-0.0590.0000.0000.0000.000
163A287LEU00.0350.00642.101-0.007-0.0070.0000.0000.0000.000
164A288LEU0-0.020-0.02046.062-0.050-0.0500.0000.0000.0000.000
165A289GLN0-0.072-0.02148.641-0.022-0.0220.0000.0000.0000.000
166A290HIS0-0.048-0.02945.0370.0010.0010.0000.0000.0000.000
167A291GLY00.0030.01146.9200.0710.0710.0000.0000.0000.000
168A292ALA0-0.0160.00446.4340.0020.0020.0000.0000.0000.000
169A293ASN00.0250.01147.865-0.260-0.2600.0000.0000.0000.000
170A294VAL0-0.024-0.02449.6460.0640.0640.0000.0000.0000.000
171A295ASN0-0.024-0.01551.979-0.040-0.0400.0000.0000.0000.000
172A296ALA00.0110.02247.591-0.013-0.0130.0000.0000.0000.000
173A297GLN0-0.070-0.05249.539-0.038-0.0380.0000.0000.0000.000
174A298MET0-0.0080.00346.6100.1300.1300.0000.0000.0000.000
175A299TYR00.009-0.00640.857-0.178-0.1780.0000.0000.0000.000
176A300SER0-0.028-0.01047.626-0.095-0.0950.0000.0000.0000.000
177A301GLY00.0800.02850.616-0.146-0.1460.0000.0000.0000.000
178A302SER0-0.043-0.01751.313-0.136-0.1360.0000.0000.0000.000
179A303SER00.1070.04950.8080.1100.1100.0000.0000.0000.000
180A304ALA00.0760.02349.5500.0060.0060.0000.0000.0000.000
181A305LEU00.0180.00751.041-0.021-0.0210.0000.0000.0000.000
182A306HIS00.0110.00353.5930.0180.0180.0000.0000.0000.000
183A307SER00.0280.02250.200-0.026-0.0260.0000.0000.0000.000
184A308ALA0-0.006-0.00552.224-0.015-0.0150.0000.0000.0000.000
185A309SER0-0.059-0.04853.618-0.078-0.0780.0000.0000.0000.000
186A310GLY00.0600.02955.749-0.069-0.0690.0000.0000.0000.000
187A311ARG10.8860.93647.223-6.258-6.2580.0000.0000.0000.000
188A312GLY0-0.046-0.01654.567-0.002-0.0020.0000.0000.0000.000
189A313LEU00.0010.01450.337-0.046-0.0460.0000.0000.0000.000
190A314LEU0-0.013-0.02054.868-0.025-0.0250.0000.0000.0000.000
191A315PRO00.000-0.01054.115-0.062-0.0620.0000.0000.0000.000
192A316LEU00.0800.04449.405-0.042-0.0420.0000.0000.0000.000
193A317VAL00.0170.01753.888-0.020-0.0200.0000.0000.0000.000
194A318ARG10.9040.94756.934-5.112-5.1120.0000.0000.0000.000
195A319THR00.0290.01652.928-0.054-0.0540.0000.0000.0000.000
196A320LEU00.0270.01551.460-0.017-0.0170.0000.0000.0000.000
197A321VAL00.0200.01155.421-0.028-0.0280.0000.0000.0000.000
198A322ARG10.8950.94258.720-4.916-4.9160.0000.0000.0000.000
199A323SER0-0.024-0.01154.850-0.023-0.0230.0000.0000.0000.000
200A324GLY00.0080.01856.5900.0420.0420.0000.0000.0000.000
201A325ALA0-0.051-0.02155.7660.0070.0070.0000.0000.0000.000
202A326ASP-1-0.806-0.88757.1804.9634.9630.0000.0000.0000.000
203A327SER0-0.054-0.03858.7670.0470.0470.0000.0000.0000.000
204A328SER0-0.087-0.06061.042-0.050-0.0500.0000.0000.0000.000
205A329LEU00.0550.03354.823-0.021-0.0210.0000.0000.0000.000
206A330LYS10.8290.89859.045-4.894-4.8940.0000.0000.0000.000
207A331ASN00.0010.01954.691-0.003-0.0030.0000.0000.0000.000
208A332CYS00.017-0.00654.002-0.053-0.0530.0000.0000.0000.000
209A333HIS0-0.122-0.06556.011-0.061-0.0610.0000.0000.0000.000
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211A335ASP-1-0.779-0.86958.8724.9844.9840.0000.0000.0000.000
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