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: XMYZX

Calculation Name: 3ZSG-A-Xray12

Preferred Name: MAP kinase p38 alpha

Target Type: SINGLE PROTEIN

Ligand Name: tak-715

ligand 3-letter code: T75

PDB ID: 3ZSG

Chain ID: A

ChEMBL ID: CHEMBL260

UniProt ID: Q16539

Base Structure: X-ray

Registration Date: 2017-08-22

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Homology modeling
Water No
Procedure Auto-FMO protocol ver. 1.20160629
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 347
LigandResidueName T75
LigandFragmentNumber 347
LigandCharge
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5682479.044189
FMO2-HF: Nuclear repulsion 5541965.723878
FMO2-HF: Total energy -140513.320311
FMO2-MP2: Total energy -140922.629985


3D Structure
Snapshot
 
Ligand structure

T75

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.
-117.687-87.836109.444-39.157-100.1440.023


Interactive mode: IFIE and PIEDA for fragment #347(A:400:T75)


Summations of interaction energy for fragment #347(A:400:T75)
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.
-117.687-87.836109.444-39.157-100.144-0.023
Interaction energy analysis for fragmet #347(A:400:T75)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / q_NPA : 0.002
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].
1A6PRO10.8640.90315.264-0.045-0.0450.0000.0000.0000.000
2A7THR00.0980.07018.3090.0180.0180.0000.0000.0000.000
3A8PHE00.0170.01713.385-0.028-0.0280.0000.0000.0000.000
4A9TYR0-0.047-0.03213.3220.0080.0080.0000.0000.0000.000
5A10ARG10.9580.97615.755-0.350-0.3500.0000.0000.0000.000
6A11GLN00.0340.01014.881-0.061-0.0610.0000.0000.0000.000
7A12GLU-1-0.988-0.98315.4850.7410.7410.0000.0000.0000.000
8A13LEU00.0430.00811.306-0.017-0.0170.0000.0000.0000.000
9A14ASN00.009-0.0149.453-0.298-0.2980.0000.0000.0000.000
10A15LYS10.9270.95913.168-0.771-0.7710.0000.0000.0000.000
11A16THR00.0050.02813.715-0.054-0.0540.0000.0000.0000.000
12A17ILE00.0520.01015.5540.0220.0220.0000.0000.0000.000
13A18TRP0-0.027-0.0076.733-0.008-0.0080.0000.0000.0000.000
14A19GLU-1-0.912-0.97113.0050.3290.3290.0000.0000.0000.000
15A20VAL0-0.0070.0019.5590.0220.0220.0000.0000.0000.000
16A21PRO0-0.020-0.00410.967-0.032-0.0320.0000.0000.0000.000
17A22GLU-1-0.879-0.95513.1270.0900.0900.0000.0000.0000.000
18A23ARG10.7810.89511.9200.3820.3820.0000.0000.0000.000
19A24TYR0-0.044-0.0468.932-0.067-0.0670.0000.0000.0000.000
20A25GLN0-0.013-0.00211.5070.1120.1120.0000.0000.0000.000
21A26ASN0-0.013-0.01912.0720.0390.0390.0000.0000.0000.000
22A27LEU00.0090.0148.5860.0580.0580.0000.0000.0000.000
23A28SER0-0.003-0.0057.891-0.074-0.0740.0000.0000.0000.000
24A29PRO0-0.030-0.0177.3440.4290.4290.0000.0000.0000.000
25A30VAL0-0.0220.0042.406-1.701-2.5038.038-1.779-5.4570.012
26A31GLY00.0420.0105.555-0.792-0.553-0.001-0.010-0.2290.000
27A32SER0-0.068-0.0455.4800.1970.1970.0000.0000.0000.000
28A33GLY00.0410.0216.150-0.560-0.5600.0000.0000.0000.000
29A34ALA0-0.026-0.0186.8930.2260.2260.0000.0000.0000.000
30A35TYR00.0460.0362.810-2.551-0.2071.232-0.635-2.941-0.006
31A36GLY00.0450.0185.9150.3000.3000.0000.0000.0000.000
32A37SER0-0.088-0.0415.491-0.695-0.6950.0000.0000.0000.000
33A38VAL00.0570.0302.407-4.756-0.6762.921-1.298-5.7030.008
34A39CYS0-0.0360.0094.782-0.709-0.468-0.001-0.014-0.2270.000
35A40ALA00.0310.0274.149-0.330-0.0870.000-0.020-0.2230.000
36A41ALA00.0040.0016.000-0.187-0.1870.0000.0000.0000.000
37A42PHE0-0.030-0.0138.938-0.122-0.1220.0000.0000.0000.000
38A43ASP-1-0.708-0.8319.966-0.348-0.3480.0000.0000.0000.000
39A44THR0-0.037-0.03811.806-0.037-0.0370.0000.0000.0000.000
40A45LYS10.8880.95614.5170.1220.1220.0000.0000.0000.000
41A46THR00.015-0.01712.1890.0090.0090.0000.0000.0000.000
42A47GLY00.0010.01614.725-0.007-0.0070.0000.0000.0000.000
43A48LEU00.0230.0239.296-0.011-0.0110.0000.0000.0000.000
44A49ARG10.9490.9735.0250.7170.7170.0000.0000.0000.000
45A50VAL00.0240.0065.399-0.067-0.0670.0000.0000.0000.000
46A51ALA0-0.0080.0002.475-1.5590.2404.267-1.818-4.2490.012
47A52VAL00.004-0.0052.442-6.276-4.6621.784-1.220-2.178-0.019
48A53LYS10.8970.9551.988-33.316-28.51911.758-5.055-11.5000.069
49A54LYS10.8920.9704.175-2.955-2.6690.007-0.066-0.2280.001
50A55LEU00.006-0.0065.5950.5910.5910.0000.0000.0000.000
51A56SER0-0.008-0.0057.947-0.642-0.6420.0000.0000.0000.000
52A57ARG10.8640.9239.894-1.020-1.0200.0000.0000.0000.000
53A58PRO00.0780.05311.195-0.076-0.0760.0000.0000.0000.000
54A59PHE00.062-0.00112.263-0.103-0.1030.0000.0000.0000.000
55A60GLN00.0050.02715.195-0.033-0.0330.0000.0000.0000.000
56A61SER00.016-0.01816.707-0.052-0.0520.0000.0000.0000.000
57A62ILE00.1110.05017.2640.0520.0520.0000.0000.0000.000
58A63ILE00.0000.00314.4520.0200.0200.0000.0000.0000.000
59A64HIS0-0.087-0.03711.4470.0780.0780.0000.0000.0000.000
60A65ALA00.0540.03512.8160.1030.1030.0000.0000.0000.000
61A66LYS10.8240.90913.905-0.233-0.2330.0000.0000.0000.000
62A67ARG10.8850.93310.339-0.719-0.7190.0000.0000.0000.000
63A68THR00.0350.0239.2250.1820.1820.0000.0000.0000.000
64A69TYR00.0210.0239.136-0.071-0.0710.0000.0000.0000.000
65A70ARG10.7820.85710.685-0.477-0.4770.0000.0000.0000.000
66A71GLU-1-0.911-0.9584.5154.3314.502-0.001-0.013-0.1570.000
67A72LEU0-0.008-0.0086.391-0.315-0.3150.0000.0000.0000.000
68A73ARG10.8860.9337.424-0.234-0.2340.0000.0000.0000.000
69A74LEU00.0130.0177.735-0.097-0.0970.0000.0000.0000.000
70A75LEU0-0.006-0.0182.342-0.487-0.9512.850-0.348-2.038-0.005
71A76LYS10.7760.8706.1930.0620.0620.0000.0000.0000.000
72A77HIS0-0.038-0.0168.9700.0100.0100.0000.0000.0000.000
73A78MET0-0.065-0.0207.8180.0800.0800.0000.0000.0000.000
74A79LYS10.9180.9648.7900.2850.2850.0000.0000.0000.000
75A80HIS00.1010.05010.9500.0500.0500.0000.0000.0000.000
76A81GLU-1-0.822-0.90511.330-0.516-0.5160.0000.0000.0000.000
77A82ASN0-0.013-0.00711.939-0.014-0.0140.0000.0000.0000.000
78A83VAL0-0.011-0.0028.5670.0510.0510.0000.0000.0000.000
79A84ILE0-0.055-0.0152.638-1.220-0.4561.312-0.347-1.7280.000
80A85GLY00.0910.0415.5060.1970.1970.0000.0000.0000.000
81A86LEU0-0.080-0.0243.384-1.693-1.0430.031-0.150-0.531-0.001
82A87LEU00.000-0.0065.2430.4800.567-0.001-0.003-0.0840.000
83A88ASP-1-0.832-0.9125.937-0.073-0.0730.0000.0000.0000.000
84A89VAL0-0.0090.0065.590-0.580-0.5800.0000.0000.0000.000
85A90PHE0-0.023-0.0087.6550.1670.1670.0000.0000.0000.000
86A91THR00.005-0.02910.1570.1830.1830.0000.0000.0000.000
87A92PRO0-0.012-0.00312.952-0.075-0.0750.0000.0000.0000.000
88A93ALA0-0.0410.00715.834-0.038-0.0380.0000.0000.0000.000
89A94ARG10.9380.95817.956-0.238-0.2380.0000.0000.0000.000
90A95SER00.0040.00620.741-0.024-0.0240.0000.0000.0000.000
91A96LEU00.0780.03419.2080.0370.0370.0000.0000.0000.000
92A97GLU-1-0.943-0.98420.9190.2390.2390.0000.0000.0000.000
93A98GLU-1-0.936-0.96321.1510.2880.2880.0000.0000.0000.000
94A99PHE0-0.077-0.02212.8360.0620.0620.0000.0000.0000.000
95A100ASN0-0.037-0.03916.844-0.002-0.0020.0000.0000.0000.000
96A101ASP-1-0.917-0.94412.6561.0861.0860.0000.0000.0000.000
97A102VAL00.0210.0017.574-0.198-0.1980.0000.0000.0000.000
98A103TYR00.0160.0076.9710.6930.6930.0000.0000.0000.000
99A104LEU00.0140.0112.685-2.253-0.5590.720-0.553-1.8610.001
100A105VAL00.0090.0052.894-3.254-0.9690.698-1.000-1.984-0.010
101A106THR00.0200.0002.408-3.714-0.2583.277-1.341-5.3920.000
102A107HIS00.0910.0364.0950.1340.6490.003-0.095-0.4230.000
103A108LEU0-0.089-0.0402.267-9.675-5.0974.502-2.897-6.184-0.010
104A109MET0-0.004-0.0032.045-10.480-11.49912.933-4.145-7.7690.034
105A110GLY00.0160.0001.798-14.235-17.47513.615-4.726-5.649-0.048
106A111ALA0-0.013-0.0024.277-0.583-0.0080.0090.015-0.6000.000
107A112ASP-1-0.770-0.8916.451-0.861-0.8610.0000.0000.0000.000
108A113LEU00.0320.0138.464-0.014-0.0140.0000.0000.0000.000
109A114ASN00.0180.00310.4770.1080.1080.0000.0000.0000.000
110A115ASN0-0.062-0.0226.558-0.200-0.2000.0000.0000.0000.000
111A116ILE00.0260.0109.9410.0360.0360.0000.0000.0000.000
112A117VAL0-0.0240.00312.8040.0540.0540.0000.0000.0000.000
113A118LYS10.9100.95611.9860.6870.6870.0000.0000.0000.000
114A119CYS0-0.018-0.01715.0780.0300.0300.0000.0000.0000.000
115A120GLN0-0.0340.00418.1990.0550.0550.0000.0000.0000.000
116A121LYS10.9170.96320.3060.1950.1950.0000.0000.0000.000
117A122LEU00.0150.01917.978-0.011-0.0110.0000.0000.0000.000
118A123THR0-0.011-0.01922.0390.0160.0160.0000.0000.0000.000
119A124ASP-1-0.745-0.87224.511-0.209-0.2090.0000.0000.0000.000
120A125ASP-1-0.848-0.92026.271-0.215-0.2150.0000.0000.0000.000
121A126HIS0-0.004-0.01517.7640.0070.0070.0000.0000.0000.000
122A127VAL0-0.012-0.01521.507-0.017-0.0170.0000.0000.0000.000
123A128GLN0-0.0130.00322.727-0.008-0.0080.0000.0000.0000.000
124A129PHE00.0630.03917.9390.0000.0000.0000.0000.0000.000
125A130LEU0-0.005-0.00616.130-0.017-0.0170.0000.0000.0000.000
126A131ILE0-0.021-0.03218.436-0.008-0.0080.0000.0000.0000.000
127A132TYR0-0.032-0.02420.675-0.005-0.0050.0000.0000.0000.000
128A133GLN00.0390.01515.481-0.023-0.0230.0000.0000.0000.000
129A134ILE0-0.031-0.00516.148-0.014-0.0140.0000.0000.0000.000
130A135LEU0-0.018-0.02117.2910.0040.0040.0000.0000.0000.000
131A136ARG10.8030.90017.4670.3590.3590.0000.0000.0000.000
132A137GLY00.0320.01014.820-0.003-0.0030.0000.0000.0000.000
133A138LEU0-0.057-0.04015.2370.0050.0050.0000.0000.0000.000
134A139LYS10.8810.94116.9050.2330.2330.0000.0000.0000.000
135A140TYR00.0250.03112.4310.0160.0160.0000.0000.0000.000
136A141ILE00.0210.01911.6250.0200.0200.0000.0000.0000.000
137A142HIS0-0.096-0.06614.8410.0330.0330.0000.0000.0000.000
138A143SER0-0.061-0.03117.9270.0240.0240.0000.0000.0000.000
139A144ALA0-0.0010.00515.2900.0130.0130.0000.0000.0000.000
140A145ASP-1-0.972-0.99817.310-0.049-0.0490.0000.0000.0000.000
141A146ILE0-0.044-0.00612.3060.0270.0270.0000.0000.0000.000
142A147ILE0-0.037-0.03216.113-0.017-0.0170.0000.0000.0000.000
143A148HIS0-0.031-0.0289.8250.0710.0710.0000.0000.0000.000
144A149ARG10.8970.93113.1500.0420.0420.0000.0000.0000.000
145A150ASP-1-0.839-0.92411.843-0.196-0.1960.0000.0000.0000.000
146A151LEU00.0310.02612.369-0.050-0.0500.0000.0000.0000.000
147A152LYS10.8320.91310.9580.3460.3460.0000.0000.0000.000
148A153PRO00.0460.01712.938-0.028-0.0280.0000.0000.0000.000
149A154SER0-0.056-0.0399.244-0.034-0.0340.0000.0000.0000.000
150A155ASN00.0090.0018.097-0.144-0.1440.0000.0000.0000.000
151A156LEU0-0.032-0.0099.6590.0360.0360.0000.0000.0000.000
152A157ALA00.0460.0256.790-0.050-0.0500.0000.0000.0000.000
153A158VAL0-0.012-0.0128.7200.0220.0220.0000.0000.0000.000
154A159ASN0-0.068-0.0259.351-0.085-0.0850.0000.0000.0000.000
155A160GLU-1-0.927-0.99210.251-0.650-0.6500.0000.0000.0000.000
156A161ASP-1-0.935-0.93512.877-0.382-0.3820.0000.0000.0000.000
157A162CYS0-0.109-0.06713.8110.0250.0250.0000.0000.0000.000
158A163GLU-1-0.847-0.88912.373-0.441-0.4410.0000.0000.0000.000
159A164LEU0-0.039-0.02711.631-0.031-0.0310.0000.0000.0000.000
160A165LYS10.8410.9267.2920.9310.9310.0000.0000.0000.000
161A166ILE0-0.026-0.0209.9370.0440.0440.0000.0000.0000.000
162A167LEU0-0.030-0.0115.586-0.099-0.0990.0000.0000.0000.000
163A168ASP-1-0.900-0.9415.5900.0100.0100.0000.0000.0000.000
164A169PHE0-0.040-0.0372.674-9.253-2.1468.792-3.374-12.525-0.030
165A170GLY00.1020.0544.2210.2000.4060.000-0.062-0.1430.000
166A171LEU0-0.087-0.0802.049-4.043-10.55628.971-6.398-16.061-0.011
167A172ALA0-0.059-0.0134.0220.2070.9590.001-0.068-0.6840.000
168A173ARG10.7830.8482.417-2.4460.4181.727-1.683-2.908-0.020
169A174HIS00.0190.0784.4340.6141.1560.000-0.054-0.4880.000
170A175THR0-0.004-0.0314.910-0.072-0.0720.0000.0000.0000.000
171A176ASP-1-0.808-0.8926.060-1.069-1.0690.0000.0000.0000.000
172A177ASP-1-0.767-0.8737.830-1.056-1.0560.0000.0000.0000.000
173A178GLU-1-0.834-0.90910.170-0.292-0.2920.0000.0000.0000.000
174A179MET0-0.043-0.01711.5850.1180.1180.0000.0000.0000.000
175A180THR0-0.038-0.04011.4260.0670.0670.0000.0000.0000.000
176A181GLY00.0260.01814.0210.0370.0370.0000.0000.0000.000
177A182TYR0-0.028-0.00113.4260.0150.0150.0000.0000.0000.000
178A183VAL0-0.059-0.02016.0520.0180.0180.0000.0000.0000.000
179A184ALA00.0460.01815.5630.0160.0160.0000.0000.0000.000
180A185THR0-0.042-0.03013.1610.0090.0090.0000.0000.0000.000
181A186ARG10.7970.89215.3820.1350.1350.0000.0000.0000.000
182A187TRP0-0.032-0.01218.356-0.004-0.0040.0000.0000.0000.000
183A188TYR00.002-0.02716.5940.0010.0010.0000.0000.0000.000
184A189ARG10.8590.94913.6850.1210.1210.0000.0000.0000.000
185A190ALA00.0370.02419.3340.0050.0050.0000.0000.0000.000
186A191PRO00.0410.01322.1310.0120.0120.0000.0000.0000.000
187A192GLU-1-0.771-0.87623.627-0.076-0.0760.0000.0000.0000.000
188A193ILE0-0.011-0.00918.1040.0150.0150.0000.0000.0000.000
189A194MET0-0.062-0.02920.5990.0120.0120.0000.0000.0000.000
190A195LEU0-0.057-0.01822.3370.0100.0100.0000.0000.0000.000
191A196ASN0-0.060-0.02322.5520.0100.0100.0000.0000.0000.000
192A197TRP0-0.0180.00023.8860.0060.0060.0000.0000.0000.000
193A198MET0-0.031-0.02321.0240.0040.0040.0000.0000.0000.000
194A199HIS0-0.016-0.01724.621-0.009-0.0090.0000.0000.0000.000
195A200TYR0-0.0100.00720.796-0.007-0.0070.0000.0000.0000.000
196A201ASN00.0600.02523.7060.0030.0030.0000.0000.0000.000
197A202GLN00.0860.01320.386-0.007-0.0070.0000.0000.0000.000
198A203THR0-0.014-0.01321.080-0.015-0.0150.0000.0000.0000.000
199A204VAL0-0.071-0.03318.994-0.004-0.0040.0000.0000.0000.000
200A205ASP-1-0.698-0.84416.991-0.193-0.1930.0000.0000.0000.000
201A206ILE0-0.0050.00719.227-0.020-0.0200.0000.0000.0000.000
202A207TRP00.0010.00821.8550.0010.0010.0000.0000.0000.000
203A208SER0-0.003-0.01417.791-0.001-0.0010.0000.0000.0000.000
204A209VAL0-0.0060.00319.588-0.017-0.0170.0000.0000.0000.000
205A210GLY00.0490.02320.957-0.008-0.0080.0000.0000.0000.000
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