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: XY72X

Calculation Name: 2WMR-A-Xray10

Preferred Name: Serine/threonine-protein kinase Chk1

Target Type: SINGLE PROTEIN

Ligand Name: 5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4(3h)-one

ligand 3-letter code: ZYR

PDB ID: 2WMR

Chain ID: A

ChEMBL ID: CHEMBL4630

UniProt ID: O14757

Base Structure: X-ray

Registration Date: 2017-06-23

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 262
LigandResidueName ZYR
LigandFragmentNumber 262
LigandCharge
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3699939.66552
FMO2-HF: Nuclear repulsion 3592681.1938
FMO2-HF: Total energy -107258.471719
FMO2-MP2: Total energy -107568.495259


3D Structure
Snapshot
 
Ligand structure

ZYR

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.
-64.955-72.92773.445-26.717-38.7550.015


Interactive mode: IFIE and PIEDA for fragment #262(A:1271:ZYR)


Summations of interaction energy for fragment #262(A:1271:ZYR)
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.
-64.955-72.92773.445-26.717-38.755-0.015
Interaction energy analysis for fragmet #262(A:1271:ZYR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.014 / q_NPA : -0.021
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].
1A9TRP10.7490.85510.252-0.548-0.5480.0000.0000.0000.000
2A10ASP-1-0.761-0.86114.4110.3830.3830.0000.0000.0000.000
3A11LEU0-0.017-0.02111.4360.1400.1400.0000.0000.0000.000
4A12VAL00.0100.01210.050-0.137-0.1370.0000.0000.0000.000
5A13GLN00.0090.0037.216-0.514-0.5140.0000.0000.0000.000
6A14THR00.0170.0086.2980.6810.6810.0000.0000.0000.000
7A15LEU0-0.091-0.0472.047-2.045-0.5784.443-1.103-4.8060.010
8A16GLY00.0770.0352.465-6.082-4.9363.021-1.142-3.025-0.015
9A17GLU-1-0.897-0.9423.422-1.067-0.9540.0240.106-0.2430.000
10A18GLY00.0260.0206.798-0.204-0.2040.0000.0000.0000.000
11A19ALA0-0.021-0.0219.3070.2520.2520.0000.0000.0000.000
12A20TYR0-0.086-0.06211.045-0.029-0.0290.0000.0000.0000.000
13A21GLY00.035-0.00110.354-0.060-0.0600.0000.0000.0000.000
14A22GLU-1-0.881-0.9137.5400.4780.4780.0000.0000.0000.000
15A23VAL0-0.078-0.0493.056-1.5720.1041.561-0.634-2.6030.004
16A24GLN0-0.012-0.0065.692-0.898-0.8980.0000.0000.0000.000
17A25LEU00.0030.0115.5590.5430.5430.0000.0000.0000.000
18A26ALA0-0.024-0.0157.005-0.643-0.6430.0000.0000.0000.000
19A27VAL00.0680.0319.2110.1510.1510.0000.0000.0000.000
20A28ASN0-0.057-0.01911.884-0.163-0.1630.0000.0000.0000.000
21A29ARG10.9260.96414.405-0.355-0.3550.0000.0000.0000.000
22A30VAL0-0.047-0.01817.552-0.038-0.0380.0000.0000.0000.000
23A31THR00.005-0.00914.9650.0040.0040.0000.0000.0000.000
24A32GLU-1-0.914-0.96714.9500.5500.5500.0000.0000.0000.000
25A33GLU-1-0.986-0.98811.1080.4960.4960.0000.0000.0000.000
26A34ALA0-0.001-0.0038.072-0.044-0.0440.0000.0000.0000.000
27A35VAL0-0.050-0.0345.485-0.205-0.2050.0000.0000.0000.000
28A36ALA00.0420.0292.740-0.1070.5822.566-0.983-2.2720.005
29A37VAL0-0.028-0.0174.592-1.254-1.0910.000-0.032-0.1310.000
30A38LYS10.9500.9915.420-3.066-3.0660.0000.0000.0000.000
31A39ILE00.003-0.0037.220-0.500-0.5000.0000.0000.0000.000
32A40VAL00.0410.05110.721-0.067-0.0670.0000.0000.0000.000
33A41ASP-1-0.830-0.94812.9960.1840.1840.0000.0000.0000.000
34A42MET0-0.058-0.02916.648-0.039-0.0390.0000.0000.0000.000
35A43LYS10.8660.92219.248-0.242-0.2420.0000.0000.0000.000
36A44ARG10.9410.98317.954-0.027-0.0270.0000.0000.0000.000
37A45ALA0-0.0300.00118.700-0.029-0.0290.0000.0000.0000.000
38A46VAL00.0580.02920.528-0.005-0.0050.0000.0000.0000.000
39A47ASP-1-0.871-0.93222.2930.0660.0660.0000.0000.0000.000
40A48CYS0-0.058-0.03319.1790.0020.0020.0000.0000.0000.000
41A49PRO00.0390.00818.6370.0360.0360.0000.0000.0000.000
42A50GLU-1-0.965-0.96418.8210.1630.1630.0000.0000.0000.000
43A51ASN0-0.090-0.05515.072-0.017-0.0170.0000.0000.0000.000
44A52ILE00.0940.03511.9580.0120.0120.0000.0000.0000.000
45A53LYS10.9530.96514.219-0.164-0.1640.0000.0000.0000.000
46A54LYS10.9430.97216.210-0.184-0.1840.0000.0000.0000.000
47A55GLU-1-0.812-0.9038.5451.3911.3910.0000.0000.0000.000
48A56ILE0-0.009-0.00211.582-0.013-0.0130.0000.0000.0000.000
49A57CYS0-0.099-0.04512.669-0.071-0.0710.0000.0000.0000.000
50A58ILE00.0580.00412.325-0.045-0.0450.0000.0000.0000.000
51A59ASN00.013-0.0018.031-0.212-0.2120.0000.0000.0000.000
52A60LYS10.8740.95911.076-0.152-0.1520.0000.0000.0000.000
53A61MET0-0.072-0.03413.697-0.017-0.0170.0000.0000.0000.000
54A62LEU0-0.0400.00310.351-0.007-0.0070.0000.0000.0000.000
55A63ASN0-0.057-0.05012.316-0.081-0.0810.0000.0000.0000.000
56A64HIS00.0470.02612.0550.0300.0300.0000.0000.0000.000
57A65GLU-1-0.920-0.94711.333-0.008-0.0080.0000.0000.0000.000
58A66ASN00.007-0.00811.3970.0330.0330.0000.0000.0000.000
59A67VAL0-0.056-0.0168.7910.0570.0570.0000.0000.0000.000
60A68VAL00.0150.0162.536-1.035-0.3090.529-0.317-0.9380.000
61A69LYS10.9300.9605.7220.3950.3950.0000.0000.0000.000
62A70PHE00.0220.0215.436-0.830-0.8300.0000.0000.0000.000
63A71TYR00.0000.0026.0530.1330.1330.0000.0000.0000.000
64A72GLY0-0.051-0.0259.2640.1330.1330.0000.0000.0000.000
65A73HIS0-0.020-0.0099.9230.0100.0100.0000.0000.0000.000
66A74ARG10.9220.96312.200-0.277-0.2770.0000.0000.0000.000
67A75ARG10.9270.97314.446-0.173-0.1730.0000.0000.0000.000
68A76GLU-1-0.828-0.83917.1290.2760.2760.0000.0000.0000.000
69A77GLY00.0410.01119.289-0.032-0.0320.0000.0000.0000.000
70A78ASN0-0.070-0.03420.3920.0240.0240.0000.0000.0000.000
71A79ILE0-0.0010.00415.812-0.025-0.0250.0000.0000.0000.000
72A80GLN0-0.021-0.01012.976-0.050-0.0500.0000.0000.0000.000
73A81TYR0-0.004-0.05911.1430.0960.0960.0000.0000.0000.000
74A82LEU0-0.018-0.0197.568-0.218-0.2180.0000.0000.0000.000
75A83PHE0-0.030-0.0066.7730.3480.3480.0000.0000.0000.000
76A84LEU00.012-0.0102.248-1.134-0.3481.988-0.833-1.9410.002
77A85GLU-1-0.763-0.8853.712-2.982-0.4040.015-1.210-1.382-0.005
78A86TYR00.0000.0181.576-18.564-33.77933.566-12.929-5.422-0.056
79A87CYS0-0.047-0.0301.737-7.907-16.35617.712-4.818-4.4450.046
80A88SER00.016-0.0033.034-0.7080.9590.177-0.248-1.596-0.004
81A89GLY00.0150.0215.596-1.174-1.1740.0000.0000.0000.000
82A90GLY00.0140.0052.370-1.768-1.5521.866-0.973-1.1090.001
83A91GLU-1-0.864-0.9523.404-8.511-6.9490.088-0.092-1.558-0.007
84A92LEU00.004-0.0054.4400.3520.4370.000-0.014-0.0710.000
85A93PHE0-0.019-0.0077.5280.3980.3980.0000.0000.0000.000
86A94ASP-1-0.874-0.9336.078-3.014-3.0140.0000.0000.0000.000
87A95ARG10.6910.8268.3250.4350.4350.0000.0000.0000.000
88A96ILE0-0.072-0.02811.3330.1940.1940.0000.0000.0000.000
89A97GLU-1-0.915-0.94213.782-0.458-0.4580.0000.0000.0000.000
90A98PRO00.005-0.01415.4800.0500.0500.0000.0000.0000.000
91A99ASP-1-0.965-0.99317.905-0.270-0.2700.0000.0000.0000.000
92A100ILE0-0.042-0.01219.8580.0500.0500.0000.0000.0000.000
93A101GLY0-0.028-0.01517.6170.0310.0310.0000.0000.0000.000
94A102MET0-0.043-0.01613.246-0.008-0.0080.0000.0000.0000.000
95A103PRO00.0200.01117.9710.0230.0230.0000.0000.0000.000
96A104GLU-1-0.828-0.92319.723-0.115-0.1150.0000.0000.0000.000
97A105PRO00.014-0.01021.2760.0000.0000.0000.0000.0000.000
98A106ASP-1-0.871-0.92916.213-0.062-0.0620.0000.0000.0000.000
99A107ALA00.0320.00916.9330.0030.0030.0000.0000.0000.000
100A108GLN0-0.087-0.06517.9920.0120.0120.0000.0000.0000.000
101A109ARG10.8950.95414.261-0.157-0.1570.0000.0000.0000.000
102A110PHE00.020-0.00512.1570.0210.0210.0000.0000.0000.000
103A111PHE00.0310.00515.5190.0140.0140.0000.0000.0000.000
104A112HIS0-0.055-0.03717.9290.0160.0160.0000.0000.0000.000
105A113GLN00.0230.01914.0430.0220.0220.0000.0000.0000.000
106A114LEU00.0340.02513.7780.0170.0170.0000.0000.0000.000
107A115MET0-0.021-0.01916.0290.0170.0170.0000.0000.0000.000
108A116ALA0-0.064-0.01217.3610.0070.0070.0000.0000.0000.000
109A117GLY00.0690.02814.2930.0030.0030.0000.0000.0000.000
110A118VAL00.008-0.00515.0590.0090.0090.0000.0000.0000.000
111A119VAL0-0.039-0.02917.2230.0050.0050.0000.0000.0000.000
112A120TYR00.0240.03414.060-0.001-0.0010.0000.0000.0000.000
113A121LEU0-0.0040.00512.7420.0040.0040.0000.0000.0000.000
114A122HIS0-0.027-0.02216.8350.0020.0020.0000.0000.0000.000
115A123GLY00.0140.01320.322-0.002-0.0020.0000.0000.0000.000
116A124ILE0-0.084-0.03716.0490.0000.0000.0000.0000.0000.000
117A125GLY0-0.030-0.01619.9930.0090.0090.0000.0000.0000.000
118A126ILE00.002-0.01014.8700.0090.0090.0000.0000.0000.000
119A127THR0-0.042-0.02617.944-0.012-0.0120.0000.0000.0000.000
120A128HIS00.018-0.0049.678-0.126-0.1260.0000.0000.0000.000
121A129ARG10.8030.87314.611-0.046-0.0460.0000.0000.0000.000
122A130ASP-1-0.825-0.92311.899-0.239-0.2390.0000.0000.0000.000
123A131ILE00.0230.01411.996-0.021-0.0210.0000.0000.0000.000
124A132LYS10.9170.9559.5290.6680.6680.0000.0000.0000.000
125A133PRO00.001-0.0029.7470.0650.0650.0000.0000.0000.000
126A134GLU-1-0.790-0.8916.176-1.336-1.3360.0000.0000.0000.000
127A135ASN0-0.116-0.0444.916-0.796-0.541-0.001-0.006-0.2480.000
128A136LEU0-0.086-0.0467.0880.6370.6370.0000.0000.0000.000
129A137LEU00.0310.0112.643-3.740-1.9075.837-1.250-6.4210.002
130A138LEU0-0.0060.0095.3980.0160.0160.0000.0000.0000.000
131A139ASP-1-0.793-0.8795.8052.2122.2120.0000.0000.0000.000
132A140GLU-1-0.866-0.9507.6301.2981.2980.0000.0000.0000.000
133A141ARG10.8370.92310.200-0.695-0.6950.0000.0000.0000.000
134A142ASP-1-0.749-0.85510.5620.1450.1450.0000.0000.0000.000
135A143ASN0-0.157-0.09511.151-0.301-0.3010.0000.0000.0000.000
136A144LEU00.0250.0219.7400.2090.2090.0000.0000.0000.000
137A145LYS10.7710.8786.724-0.366-0.3660.0000.0000.0000.000
138A146ILE0-0.010-0.0098.1530.0520.0520.0000.0000.0000.000
139A147SER00.0260.0063.720-0.5810.1490.053-0.239-0.5440.002
140A148ASP-1-0.843-0.9065.5630.9200.9200.0000.0000.0000.000
141A149PHE00.045-0.0037.164-0.569-0.5690.0000.0000.0000.000
142A150GLY0-0.0050.0139.995-0.177-0.1770.0000.0000.0000.000
143A151LEU00.016-0.00311.823-0.134-0.1340.0000.0000.0000.000
144A152ALA00.0210.04413.392-0.089-0.0890.0000.0000.0000.000
145A153THR0-0.119-0.07515.0830.0050.0050.0000.0000.0000.000
146A154VAL0-0.0150.00418.563-0.010-0.0100.0000.0000.0000.000
147A155PHE0-0.029-0.00420.798-0.006-0.0060.0000.0000.0000.000
148A156ARG10.8800.94423.171-0.036-0.0360.0000.0000.0000.000
149A157TYR00.0170.00123.5430.0050.0050.0000.0000.0000.000
150A158ASN00.0010.00326.136-0.004-0.0040.0000.0000.0000.000
151A159ASN00.001-0.00527.992-0.002-0.0020.0000.0000.0000.000
152A160ARG10.9330.97829.130-0.021-0.0210.0000.0000.0000.000
153A161GLU-1-0.855-0.92327.5490.0090.0090.0000.0000.0000.000
154A162ARG10.8540.91925.864-0.052-0.0520.0000.0000.0000.000
155A163LEU00.0190.02526.7940.0020.0020.0000.0000.0000.000
156A164LEU0-0.034-0.01022.2460.0100.0100.0000.0000.0000.000
157A165ASN00.023-0.00725.875-0.004-0.0040.0000.0000.0000.000
158A166LYS10.9020.96520.555-0.081-0.0810.0000.0000.0000.000
159A167MET00.0270.02222.928-0.002-0.0020.0000.0000.0000.000
160A168CYS0-0.067-0.03017.4690.0230.0230.0000.0000.0000.000
161A169GLY00.0820.05115.941-0.009-0.0090.0000.0000.0000.000
162A170THR0-0.007-0.00413.995-0.045-0.0450.0000.0000.0000.000
163A171LEU00.008-0.01116.4000.0070.0070.0000.0000.0000.000
164A172PRO00.0660.03817.0210.0290.0290.0000.0000.0000.000
165A173TYR00.0420.00413.3430.0300.0300.0000.0000.0000.000
166A174VAL0-0.030-0.00517.9300.0440.0440.0000.0000.0000.000
167A175ALA00.0110.00220.502-0.003-0.0030.0000.0000.0000.000
168A176PRO00.0480.02023.7070.0060.0060.0000.0000.0000.000
169A177GLU-1-0.802-0.89726.477-0.073-0.0730.0000.0000.0000.000
170A178LEU0-0.049-0.01121.7350.0100.0100.0000.0000.0000.000
171A179LEU00.0170.00324.4430.0040.0040.0000.0000.0000.000
172A180LYS10.8650.94827.6710.1030.1030.0000.0000.0000.000
173A181ARG10.8900.95730.1070.0550.0550.0000.0000.0000.000
174A182ARG10.9690.98029.9600.0150.0150.0000.0000.0000.000
175A183GLU-1-0.933-0.98229.4490.0030.0030.0000.0000.0000.000
176A184PHE0-0.017-0.00623.764-0.006-0.0060.0000.0000.0000.000
177A185HIS0-0.010-0.01927.3730.0050.0050.0000.0000.0000.000
178A186ALA00.0420.00122.004-0.007-0.0070.0000.0000.0000.000
179A187GLU-1-0.874-0.93922.614-0.004-0.0040.0000.0000.0000.000
180A188PRO00.017-0.00523.069-0.009-0.0090.0000.0000.0000.000
181A189VAL00.0170.02720.394-0.017-0.0170.0000.0000.0000.000
182A190ASP-1-0.707-0.85218.133-0.013-0.0130.0000.0000.0000.000
183A191VAL0-0.039-0.00719.440-0.020-0.0200.0000.0000.0000.000
184A192TRP00.004-0.00721.009-0.003-0.0030.0000.0000.0000.000
185A193SER00.0030.01216.852-0.017-0.0170.0000.0000.0000.000
186A194CYS0-0.017-0.00117.240-0.036-0.0360.0000.0000.0000.000
187A195GLY00.0210.01718.301-0.018-0.0180.0000.0000.0000.000
188A196ILE0-0.018-0.00417.496-0.011-0.0110.0000.0000.0000.000
189A197VAL00.0440.01613.745-0.042-0.0420.0000.0000.0000.000
190A198LEU0-0.049-0.01616.364-0.027-0.0270.0000.0000.0000.000
191A199THR0-0.021-0.03218.9570.0090.0090.0000.0000.0000.000
192A200ALA00.0070.00715.7400.0000.0000.0000.0000.0000.000
193A201MET0-0.042-0.01514.564-0.014-0.0140.0000.0000.0000.000
194A202LEU0-0.023-0.01416.9520.0210.0210.0000.0000.0000.000
195A203ALA00.0020.01120.0520.0220.0220.0000.0000.0000.000
196A204GLY00.0540.03817.5260.0020.0020.0000.0000.0000.000
197A205GLU-1-0.870-0.93318.582-0.335-0.3350.0000.0000.0000.000
198A206LEU0-0.025-0.02015.5620.0260.0260.0000.0000.0000.000
199A207PRO0-0.003-0.00319.7480.0180.0180.0000.0000.0000.000
200A208TRP00.0230.00222.2270.0300.0300.0000.0000.0000.000
201A209ASP-1-0.850-0.91621.623-0.309-0.3090.0000.0000.0000.000
202A210GLN0-0.049-0.04421.523-0.020-0.0200.0000.0000.0000.000
203A211PRO0-0.0160.02222.9920.0110.0110.0000.0000.0000.000
204A212SER0-0.059-0.03826.0050.0210.0210.0000.0000.0000.000
205A213ASP-1-0.809-0.93129.185-0.109-0.1090.0000.0000.0000.000
206A214SER0-0.111-0.04030.437-0.002-0.0020.0000.0000.0000.000
207A215CYS0-0.0070.01227.513-0.008-0.0080.0000.0000.0000.000
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