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: P2KJR

Calculation Name: 4KEL-A-Xray13

Preferred Name: Kallikrein 4

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4KEL

Chain ID: A

ChEMBL ID: CHEMBL4446

UniProt ID: Q9Y5K2

Base Structure: X-ray

Registration Date: 2018-02-14

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water No
Procedure Auto-FMO protocol ver. 1.20181228
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 217
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -2604226.876904
FMO2-HF: Nuclear repulsion 2517106.16277
FMO2-HF: Total energy -87120.714134
FMO2-MP2: Total energy -87363.87734


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:17:ILE)


Summations of interaction energy for fragment #1(A:17:ILE)
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.
-345.813-326.38731.9-20.692-30.63-0.218
Interaction energy analysis for fragmet #1(A:17:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.738 / q_NPA : 0.871
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].
3A19ASN0-0.039-0.0463.6304.3235.9750.020-0.580-1.0930.001
4A20GLY00.0150.0092.5482.9913.8700.709-0.566-1.022-0.002
5A21GLU-1-0.975-0.9733.289-27.801-28.0990.0150.452-0.1680.000
6A22ASP-1-0.867-0.9325.345-33.118-33.1180.0000.0000.0000.000
7A153CYS0-0.062-0.0362.807-3.432-1.0490.486-1.180-1.689-0.015
8A24SER0-0.010-0.0088.1791.7411.7410.0000.0000.0000.000
9A25PRO00.0580.02411.448-0.657-0.6570.0000.0000.0000.000
10A26HIS00.0190.01312.4200.7730.7730.0000.0000.0000.000
11A27SER0-0.084-0.04010.9610.4530.4530.0000.0000.0000.000
12A28GLN0-0.018-0.0267.7690.1740.1740.0000.0000.0000.000
13A29PRO00.0100.00811.112-0.744-0.7440.0000.0000.0000.000
14A30TRP00.0660.0439.5251.3631.3630.0000.0000.0000.000
15A31GLN0-0.0260.0015.6200.2010.2010.0000.0000.0000.000
16A32ALA00.0080.00610.4311.2071.2070.0000.0000.0000.000
17A33ALA00.0060.00710.423-2.136-2.1360.0000.0000.0000.000
18A34LEU0-0.044-0.02011.6862.1942.1940.0000.0000.0000.000
19A35VAL00.0190.00113.175-1.441-1.4410.0000.0000.0000.000
20A36MET0-0.005-0.01515.4431.2681.2680.0000.0000.0000.000
21A37GLU-1-0.926-0.96118.023-14.292-14.2920.0000.0000.0000.000
22A38ASN0-0.102-0.05517.6820.0060.0060.0000.0000.0000.000
23A39GLU-1-0.870-0.91812.920-24.233-24.2330.0000.0000.0000.000
24A40LEU0-0.043-0.0128.1490.3130.3130.0000.0000.0000.000
25A41PHE0-0.029-0.02711.418-0.524-0.5240.0000.0000.0000.000
26A58CYS0-0.087-0.0359.438-1.635-1.6350.0000.0000.0000.000
27A43SER00.0570.0307.0830.0330.0330.0000.0000.0000.000
28A44GLY00.0270.0159.1961.5171.5170.0000.0000.0000.000
29A45VAL0-0.051-0.0189.648-1.205-1.2050.0000.0000.0000.000
30A46LEU0-0.0120.00512.1221.0951.0950.0000.0000.0000.000
31A47VAL0-0.004-0.01215.5210.0060.0060.0000.0000.0000.000
32A48HIS10.7960.87317.65813.39213.3920.0000.0000.0000.000
33A49PRO00.0840.04320.374-0.377-0.3770.0000.0000.0000.000
34A50GLN0-0.031-0.00822.3200.0890.0890.0000.0000.0000.000
35A51TRP00.0310.01120.373-0.016-0.0160.0000.0000.0000.000
36A52VAL00.0580.03114.281-0.390-0.3900.0000.0000.0000.000
37A53LEU0-0.034-0.01114.2300.5410.5410.0000.0000.0000.000
38A54SER00.0400.00111.883-1.232-1.2320.0000.0000.0000.000
39A55ALA00.0470.02311.7681.0751.0750.0000.0000.0000.000
40A56ALA0-0.034-0.01913.5830.4720.4720.0000.0000.0000.000
41A57HIS0-0.110-0.04911.960-0.724-0.7240.0000.0000.0000.000
42A59PHE0-0.037-0.03315.3670.4980.4980.0000.0000.0000.000
43A60GLN0-0.0030.00417.0510.7480.7480.0000.0000.0000.000
44A61ASN0-0.080-0.04920.9830.3320.3320.0000.0000.0000.000
45A62SER0-0.0070.00022.6230.6110.6110.0000.0000.0000.000
46A63TYR0-0.015-0.02117.397-0.906-0.9060.0000.0000.0000.000
47A64THR00.0440.02618.6410.6170.6170.0000.0000.0000.000
48A65ILE0-0.051-0.04215.219-1.221-1.2210.0000.0000.0000.000
49A66GLY00.0210.01915.0670.9770.9770.0000.0000.0000.000
50A67LEU0-0.014-0.02114.192-1.360-1.3600.0000.0000.0000.000
51A68GLY00.0520.01714.9570.7320.7320.0000.0000.0000.000
52A69LEU0-0.018-0.00712.3870.4630.4630.0000.0000.0000.000
53A70HIS00.0110.0209.642-1.290-1.2900.0000.0000.0000.000
54A71SER0-0.029-0.03310.250-3.194-3.1940.0000.0000.0000.000
55A72LEU0-0.018-0.0179.3000.9010.9010.0000.0000.0000.000
56A73GLU-1-0.938-0.97313.003-18.112-18.1120.0000.0000.0000.000
57A74ALA0-0.107-0.03615.5831.1281.1280.0000.0000.0000.000
58A75ASP-1-0.918-0.95017.905-14.271-14.2710.0000.0000.0000.000
59A76GLN0-0.023-0.03019.196-0.224-0.2240.0000.0000.0000.000
60A77GLU-1-0.794-0.90415.206-18.392-18.3920.0000.0000.0000.000
61A78PRO0-0.017-0.03219.7110.2520.2520.0000.0000.0000.000
62A79GLY0-0.019-0.00620.360-0.400-0.4000.0000.0000.0000.000
63A80SER0-0.072-0.01017.730-0.184-0.1840.0000.0000.0000.000
64A81GLN0-0.004-0.01918.6851.0181.0180.0000.0000.0000.000
65A82MET00.0080.02116.914-1.227-1.2270.0000.0000.0000.000
66A83VAL0-0.031-0.01519.3600.8250.8250.0000.0000.0000.000
67A84GLU-1-0.803-0.87820.699-14.262-14.2620.0000.0000.0000.000
68A85ALA0-0.017-0.01120.7310.1610.1610.0000.0000.0000.000
69A86SER0-0.031-0.04522.716-0.281-0.2810.0000.0000.0000.000
70A87LEU0-0.046-0.02224.2740.3890.3890.0000.0000.0000.000
71A88SER00.0150.02120.568-0.687-0.6870.0000.0000.0000.000
72A89VAL0-0.015-0.00521.9670.4810.4810.0000.0000.0000.000
73A90ARG10.9770.98320.11212.69712.6970.0000.0000.0000.000
74A91HIS00.0510.03420.8270.6120.6120.0000.0000.0000.000
75A92PRO0-0.010-0.00922.585-0.041-0.0410.0000.0000.0000.000
76A93GLU-1-0.892-0.95424.626-10.396-10.3960.0000.0000.0000.000
77A94TYR00.0230.01618.0470.0730.0730.0000.0000.0000.000
78A95ASN0-0.029-0.01320.6110.1020.1020.0000.0000.0000.000
79A96ARG10.7880.92922.46511.38711.3870.0000.0000.0000.000
80A97PRO00.021-0.00723.5410.2230.2230.0000.0000.0000.000
81A98LEU00.029-0.00421.095-0.342-0.3420.0000.0000.0000.000
82A99LEU00.000-0.00716.622-0.040-0.0400.0000.0000.0000.000
83A100ALA0-0.0060.01817.593-0.766-0.7660.0000.0000.0000.000
84A101ASN0-0.015-0.04019.590-0.026-0.0260.0000.0000.0000.000
85A102ASP-1-0.738-0.84714.345-19.503-19.5030.0000.0000.0000.000
86A103LEU0-0.038-0.00714.969-1.093-1.0930.0000.0000.0000.000
87A104MET0-0.045-0.01015.8391.4961.4960.0000.0000.0000.000
88A105LEU0-0.0370.00017.210-0.649-0.6490.0000.0000.0000.000
89A106ILE00.0180.00816.1240.6040.6040.0000.0000.0000.000
90A107LYS10.9020.96419.86410.62210.6220.0000.0000.0000.000
91A108LEU0-0.007-0.00718.920-0.005-0.0050.0000.0000.0000.000
92A109ASP-1-0.773-0.87022.763-11.311-11.3110.0000.0000.0000.000
93A110GLU-1-0.947-0.96725.059-9.820-9.8200.0000.0000.0000.000
94A111SER0-0.082-0.04524.434-0.519-0.5190.0000.0000.0000.000
95A112VAL00.0090.00920.3870.2060.2060.0000.0000.0000.000
96A113SER0-0.031-0.02223.7210.2890.2890.0000.0000.0000.000
97A114GLU-1-0.855-0.91321.318-13.628-13.6280.0000.0000.0000.000
98A115SER0-0.002-0.00721.4170.4210.4210.0000.0000.0000.000
99A116ASP-1-0.900-0.95521.262-12.545-12.5450.0000.0000.0000.000
100A117THR0-0.056-0.03817.064-0.306-0.3060.0000.0000.0000.000
101A118ILE0-0.0030.02216.389-1.045-1.0450.0000.0000.0000.000
102A119ARG10.8960.94416.85215.73715.7370.0000.0000.0000.000
103A120SER0-0.023-0.02316.398-1.015-1.0150.0000.0000.0000.000
104A121ILE0-0.048-0.01813.1520.2330.2330.0000.0000.0000.000
105A122SER0-0.028-0.01716.5830.3990.3990.0000.0000.0000.000
106A123ILE00.002-0.00216.353-0.697-0.6970.0000.0000.0000.000
107A124ALA0-0.013-0.00316.9210.7140.7140.0000.0000.0000.000
108A125SER0-0.013-0.00318.6230.0250.0250.0000.0000.0000.000
109A126GLN00.0030.00320.6830.5820.5820.0000.0000.0000.000
110A227CYS0-0.078-0.02216.8420.2030.2030.0000.0000.0000.000
111A128PRO00.0490.02615.7420.2330.2330.0000.0000.0000.000
112A129THR0-0.018-0.00717.7740.6360.6360.0000.0000.0000.000
113A130ALA00.008-0.01117.769-0.648-0.6480.0000.0000.0000.000
114A131GLY0-0.025-0.00817.0080.6570.6570.0000.0000.0000.000
115A132ASN0-0.050-0.02415.268-0.068-0.0680.0000.0000.0000.000
116A133SER00.0480.02713.241-1.324-1.3240.0000.0000.0000.000
117A199CYS0-0.040-0.0349.3620.3160.3160.0000.0000.0000.000
118A135LEU00.0110.0086.207-0.283-0.2830.0000.0000.0000.000
119A136VAL0-0.0140.0062.2181.1431.4651.675-0.393-1.6040.003
120A137SER00.003-0.0232.847-4.532-2.9290.496-0.775-1.323-0.007
121A138GLY0-0.007-0.0162.5531.3432.5341.166-0.560-1.798-0.008
122A139TRP00.0250.0073.121-7.293-6.2430.275-0.341-0.984-0.005
123A140GLY00.0240.0203.2016.2756.9140.055-0.227-0.466-0.001
124A141LEU0-0.072-0.0482.739-12.264-10.1770.596-1.429-1.254-0.016
125A142LEU00.0370.0241.971-30.854-30.8075.902-3.180-2.769-0.041
126A143ALA00.0300.0024.3865.6725.834-0.001-0.015-0.1450.000
127A144ASN0-0.052-0.0256.9421.7611.7610.0000.0000.0000.000
128A145GLY00.0070.0027.5513.4343.4340.0000.0000.0000.000
129A146ARG10.9080.9598.32926.14526.1450.0000.0000.0000.000
130A147MET00.0610.0216.300-6.144-6.1440.0000.0000.0000.000
131A148PRO0-0.0430.0084.0475.2175.343-0.001-0.010-0.1150.000
132A149THR00.0580.0227.1260.1920.1920.0000.0000.0000.000
133A150VAL00.0100.0148.4301.2341.2340.0000.0000.0000.000
134A151LEU0-0.0260.0115.212-5.368-5.3680.0000.0000.0000.000
135A152GLN0-0.048-0.0342.281-0.1070.3992.801-1.031-2.276-0.004
136A154VAL00.0550.0322.375-0.5610.0362.902-0.766-2.733-0.003
137A155ASN00.0240.0293.9020.3060.4230.0030.011-0.1310.000
138A156VAL00.0220.0075.736-0.368-0.3680.0000.0000.0000.000
139A157SER0-0.005-0.0098.4911.6541.6540.0000.0000.0000.000
140A158VAL00.0130.01112.176-0.586-0.5860.0000.0000.0000.000
141A159VAL0-0.021-0.00213.9371.0031.0030.0000.0000.0000.000
142A160SER0-0.003-0.01116.578-0.031-0.0310.0000.0000.0000.000
143A161GLU-1-0.855-0.93819.222-13.023-13.0230.0000.0000.0000.000
144A162GLU-1-0.908-0.95320.785-11.654-11.6540.0000.0000.0000.000
145A163VAL0-0.059-0.02517.6740.0390.0390.0000.0000.0000.000
146A178CYS00.0140.02412.649-1.558-1.5580.0000.0000.0000.000
147A165SER00.025-0.01018.154-0.235-0.2350.0000.0000.0000.000
148A166LYS10.9791.00021.36312.93912.9390.0000.0000.0000.000
149A167LEU0-0.074-0.03916.8480.1220.1220.0000.0000.0000.000
150A168TYR0-0.029-0.05012.523-0.364-0.3640.0000.0000.0000.000
151A169ASP-1-0.929-0.90918.911-12.013-12.0130.0000.0000.0000.000
152A170PRO0-0.023-0.02822.120-0.366-0.3660.0000.0000.0000.000
153A171LEU0-0.047-0.05220.1540.4350.4350.0000.0000.0000.000
154A172TYR0-0.022-0.00417.868-0.182-0.1820.0000.0000.0000.000
155A173HIS00.0880.05119.9460.3590.3590.0000.0000.0000.000
156A174PRO00.0650.02120.021-0.581-0.5810.0000.0000.0000.000
157A175SER0-0.043-0.02519.387-0.414-0.4140.0000.0000.0000.000
158A176MET0-0.0310.02015.921-0.815-0.8150.0000.0000.0000.000
159A177PHE0-0.019-0.01012.3101.0021.0020.0000.0000.0000.000
160A179ALA00.0140.0019.5761.2211.2210.0000.0000.0000.000
161A180GLY00.0410.0259.132-2.296-2.2960.0000.0000.0000.000
162A181GLY00.0220.0109.9451.9161.9160.0000.0000.0000.000
163A182GLY0-0.0020.00911.0281.6691.6690.0000.0000.0000.000
164A183GLN0-0.013-0.03112.165-0.978-0.9780.0000.0000.0000.000
165A184ASP-1-0.888-0.9549.803-24.620-24.6200.0000.0000.0000.000
166A185GLN0-0.096-0.0449.321-0.372-0.3720.0000.0000.0000.000
167A186LYS10.8840.9655.40024.12124.1210.0000.0000.0000.000
168A187ASP-1-0.826-0.9144.083-32.275-32.039-0.001-0.040-0.1950.000
169A188SER0-0.0370.0042.264-15.093-11.8962.047-2.604-2.640-0.018
170A214CYS00.0490.0093.15811.70012.0940.0280.286-0.708-0.002
171A190ASN00.035-0.0184.4460.1270.282-0.001-0.004-0.1490.000
172A191GLY00.0660.0365.422-5.127-5.1270.0000.0000.0000.000
173A192ASP-1-0.762-0.8751.823-123.481-121.25612.730-7.726-7.228-0.100
174A193SER00.004-0.0285.0253.1543.216-0.001-0.006-0.0550.000
175A194GLY0-0.017-0.0088.1480.4580.4580.0000.0000.0000.000
176A195GLY00.0180.0205.8461.9781.9780.0000.0000.0000.000
177A196PRO0-0.0070.0025.8201.5291.5290.0000.0000.0000.000
178A197LEU0-0.0010.0035.894-2.916-2.9160.0000.0000.0000.000
179A198ILE00.0000.0028.1042.5452.5450.0000.0000.0000.000
180A200ASN0-0.029-0.02912.9650.7060.7060.0000.0000.0000.000
181A201GLY00.0100.00414.1280.8050.8050.0000.0000.0000.000
182A202TYR0-0.0010.01615.1760.5700.5700.0000.0000.0000.000
183A203LEU00.0210.01611.072-0.982-0.9820.0000.0000.0000.000
184A204GLN0-0.045-0.03112.3141.1841.1840.0000.0000.0000.000
185A205GLY00.004-0.02511.3810.9440.9440.0000.0000.0000.000
186A206LEU0-0.0260.0089.157-0.513-0.5130.0000.0000.0000.000
187A207VAL0-0.0030.0114.2841.2741.368-0.001-0.008-0.0850.000
188A208SER0-0.055-0.0277.6751.3331.3330.0000.0000.0000.000
189A209PHE00.039-0.00310.763-0.071-0.0710.0000.0000.0000.000
190A210GLY00.0690.02410.580-0.751-0.7510.0000.0000.0000.000
191A211LYS10.8590.94411.60018.50218.5020.0000.0000.0000.000
192A212ALA00.0090.03811.336-2.150-2.1500.0000.0000.0000.000
193A213PRO0-0.051-0.04310.6681.8471.8470.0000.0000.0000.000
194A215GLY00.0180.0137.9150.2400.2400.0000.0000.0000.000
195A216GLN0-0.065-0.0288.4033.8773.8770.0000.0000.0000.000
196A217VAL00.0190.00112.156-0.111-0.1110.0000.0000.0000.000
197A218GLY0-0.030-0.00914.1480.9170.9170.0000.0000.0000.000
198A219VAL0-0.071-0.03912.6441.2371.2370.0000.0000.0000.000
199A220PRO0-0.0220.00611.100-1.588-1.5880.0000.0000.0000.000
200A221GLY00.0870.0658.4380.2250.2250.0000.0000.0000.000
201A222VAL0-0.013-0.0289.5161.9631.9630.0000.0000.0000.000
202A223TYR00.0210.0046.020-2.827-2.8270.0000.0000.0000.000
203A224THR00.000-0.02211.2871.3631.3630.0000.0000.0000.000
204A225ASN0-0.008-0.02613.704-0.550-0.5500.0000.0000.0000.000
205A226LEU00.0660.02313.1681.1301.1300.0000.0000.0000.000
206A228LYS10.8990.95419.70913.11913.1190.0000.0000.0000.000
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208A230THR00.0540.03320.551-0.038-0.0380.0000.0000.0000.000
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