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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: XYK2X

Calculation Name: 3QPA-A-Xray13

Preferred Name: Cutinase 1

Target Type: SINGLE PROTEIN

Ligand Name: monoethylphosphorylserine

ligand 3-letter code: MIR

PDB ID: 3QPA

Chain ID: A

ChEMBL ID: CHEMBL2176862

UniProt ID: P00590

Base Structure: X-ray

Registration Date: 2017-11-21

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. 1.20171117
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 195
LigandCharge MIR=-1
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -2086168.534685
FMO2-HF: Nuclear repulsion 2013731.839831
FMO2-HF: Total energy -72436.694854
FMO2-MP2: Total energy -72647.690978


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:16:GLY)


Summations of interaction energy for fragment #1(A:16:GLY)
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.
-0.53899999999999-8.0178.1362.398-3.056-0.024
Interaction energy analysis for fragmet #1(A:16:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.845 / q_NPA : 0.928
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].
3A18THR00.0430.0132.2283.910-4.4997.7772.817-2.185-0.017
4A19THR00.0130.0193.3115.7275.7450.076-0.005-0.089-0.002
5A20ARG10.6500.8076.17131.23831.2380.0000.0000.0000.000
6A21ASP-1-0.797-0.9008.625-21.930-21.9300.0000.0000.0000.000
7A22ASP-1-0.771-0.86812.008-24.050-24.0500.0000.0000.0000.000
8A23LEU00.0020.01913.9501.0941.0940.0000.0000.0000.000
9A24ILE0-0.071-0.03415.5671.2541.2540.0000.0000.0000.000
10A25ASN0-0.077-0.04314.6021.7021.7020.0000.0000.0000.000
11A26GLY00.0210.03217.686-0.130-0.1300.0000.0000.0000.000
12A27ASN00.000-0.00819.2761.0081.0080.0000.0000.0000.000
13A28SER00.0440.00022.489-0.073-0.0730.0000.0000.0000.000
14A29ALA0-0.038-0.01225.0700.3480.3480.0000.0000.0000.000
15A30SER0-0.050-0.02923.1370.3750.3750.0000.0000.0000.000
16109CYS0-0.054-0.02122.507-0.554-0.5540.0000.0000.0000.000
17A32ALA0-0.0020.02618.6760.0810.0810.0000.0000.0000.000
18A33ASP-1-0.875-0.93620.737-12.829-12.8290.0000.0000.0000.000
19A34VAL0-0.036-0.01517.8250.3050.3050.0000.0000.0000.000
20A35ILE0-0.005-0.00717.022-0.891-0.8910.0000.0000.0000.000
21A36PHE00.005-0.00710.7920.1260.1260.0000.0000.0000.000
22A37ILE0-0.0050.00013.912-1.173-1.1730.0000.0000.0000.000
23A38TYR0-0.013-0.0019.839-0.210-0.2100.0000.0000.0000.000
24A39ALA00.0200.00912.295-0.880-0.8800.0000.0000.0000.000
25A40ARG10.8350.93310.12223.24723.2470.0000.0000.0000.000
26A41GLY00.0480.03011.8322.1452.1450.0000.0000.0000.000
27A42SER00.016-0.04113.651-0.335-0.3350.0000.0000.0000.000
28A43THR0-0.070-0.02914.943-0.163-0.1630.0000.0000.0000.000
29A44GLU-1-0.774-0.8589.661-31.061-31.0610.0000.0000.0000.000
30A45THR00.003-0.0106.923-0.038-0.0380.0000.0000.0000.000
31A46GLY0-0.014-0.0106.968-2.580-2.5800.0000.0000.0000.000
32A47ASN00.0350.0007.670-0.330-0.3300.0000.0000.0000.000
33A48LEU0-0.0080.0085.2070.9660.9660.0000.0000.0000.000
34A49GLY0-0.023-0.0046.9320.5940.5940.0000.0000.0000.000
35A50THR0-0.067-0.0585.430-8.412-8.4120.0000.0000.0000.000
36A51LEU00.0010.0026.324-3.369-3.3690.0000.0000.0000.000
37A52GLY00.0590.0327.6490.0600.0600.0000.0000.0000.000
38A53PRO0-0.046-0.0362.844-3.107-2.2090.284-0.410-0.772-0.005
39A54SER0-0.0070.0005.0562.3122.327-0.001-0.004-0.0100.000
40A55ILE00.0290.0286.8803.2723.2720.0000.0000.0000.000
41A56ALA00.002-0.0037.3361.9301.9300.0000.0000.0000.000
42A57SER0-0.0170.0017.4093.1783.1780.0000.0000.0000.000
43A58ASN00.002-0.0129.2243.8513.8510.0000.0000.0000.000
44A59LEU00.0010.00712.1312.0112.0110.0000.0000.0000.000
45A60GLU-1-0.815-0.9129.839-31.533-31.5330.0000.0000.0000.000
46A61SER0-0.055-0.02413.0781.5521.5520.0000.0000.0000.000
47A62ALA0-0.062-0.01515.3881.2641.2640.0000.0000.0000.000
48A63PHE00.007-0.01317.0401.0201.0200.0000.0000.0000.000
49A64GLY00.0700.05417.5670.8420.8420.0000.0000.0000.000
50A65LYS10.8950.92911.00823.69523.6950.0000.0000.0000.000
51A66ASP-1-0.910-0.96815.425-17.587-17.5870.0000.0000.0000.000
52A67GLY00.0350.04018.2610.7100.7100.0000.0000.0000.000
53A68VAL0-0.063-0.03414.0220.1720.1720.0000.0000.0000.000
54A69TRP0-0.0050.00614.465-0.769-0.7690.0000.0000.0000.000
55A70ILE0-0.035-0.0308.500-0.344-0.3440.0000.0000.0000.000
56A71GLN0-0.021-0.02111.465-0.173-0.1730.0000.0000.0000.000
57A72GLY00.0250.01010.2420.2410.2410.0000.0000.0000.000
58A73VAL0-0.012-0.00711.1181.4911.4910.0000.0000.0000.000
59A74GLY00.001-0.01613.558-0.884-0.8840.0000.0000.0000.000
60A75GLY00.0450.03114.0790.9420.9420.0000.0000.0000.000
61A76ALA0-0.046-0.03717.403-0.184-0.1840.0000.0000.0000.000
62A77TYR0-0.043-0.02814.4401.0881.0880.0000.0000.0000.000
63A78ARG10.9040.93715.86614.77614.7760.0000.0000.0000.000
64A79ALA0-0.0090.03214.769-0.416-0.4160.0000.0000.0000.000
65A80THR00.0520.02316.767-0.658-0.6580.0000.0000.0000.000
66A81LEU00.0650.02919.7660.4180.4180.0000.0000.0000.000
67A82GLY00.0260.01221.0250.3290.3290.0000.0000.0000.000
68A83ASP-1-0.845-0.93922.139-12.664-12.6640.0000.0000.0000.000
69A84ASN0-0.079-0.05220.3060.0380.0380.0000.0000.0000.000
70A85ALA0-0.022-0.01523.9140.2940.2940.0000.0000.0000.000
71A86LEU0-0.0220.01225.7120.5460.5460.0000.0000.0000.000
72A87PRO00.0070.00228.150-0.222-0.2220.0000.0000.0000.000
73A88ARG10.7680.83826.87910.95910.9590.0000.0000.0000.000
74A89GLY0-0.044-0.01224.674-0.378-0.3780.0000.0000.0000.000
75A90THR00.026-0.00620.788-0.742-0.7420.0000.0000.0000.000
76A91SER00.0130.02322.4590.6850.6850.0000.0000.0000.000
77A92SER00.0510.00324.157-0.254-0.2540.0000.0000.0000.000
78A93ALA0-0.022-0.00423.724-0.023-0.0230.0000.0000.0000.000
79A94ALA00.0100.00119.786-0.315-0.3150.0000.0000.0000.000
80A95ILE00.0580.02320.852-0.429-0.4290.0000.0000.0000.000
81A96ARG10.9460.98223.23811.51711.5170.0000.0000.0000.000
82A97GLU-1-0.879-0.93317.917-15.582-15.5820.0000.0000.0000.000
83A98MET00.0010.00816.658-0.266-0.2660.0000.0000.0000.000
84A99LEU0-0.0010.00219.866-0.032-0.0320.0000.0000.0000.000
85A100GLY00.0140.01422.8410.2370.2370.0000.0000.0000.000
86A101LEU0-0.025-0.01415.989-0.031-0.0310.0000.0000.0000.000
87A102PHE00.0600.01220.048-0.056-0.0560.0000.0000.0000.000
88A103GLN0-0.0010.00122.0120.2920.2920.0000.0000.0000.000
89A104GLN00.019-0.00320.2780.1040.1040.0000.0000.0000.000
90A105ALA00.0150.00820.3840.1550.1550.0000.0000.0000.000
91A106ASN0-0.0030.00622.1860.3310.3310.0000.0000.0000.000
92A107THR0-0.024-0.01225.7800.4890.4890.0000.0000.0000.000
93A108LYS10.8570.93720.54514.56614.5660.0000.0000.0000.000
94A110PRO00.0040.00525.209-0.252-0.2520.0000.0000.0000.000
95A111ASP-1-0.880-0.93527.674-10.244-10.2440.0000.0000.0000.000
96A112ALA0-0.038-0.00622.113-0.161-0.1610.0000.0000.0000.000
97A113THR0-0.039-0.00822.9010.3740.3740.0000.0000.0000.000
98A114LEU0-0.012-0.00620.448-0.815-0.8150.0000.0000.0000.000
99A115ILE00.0040.00316.3000.2560.2560.0000.0000.0000.000
100A116ALA00.0060.00516.704-0.650-0.6500.0000.0000.0000.000
101A117GLY00.030-0.00215.2320.0430.0430.0000.0000.0000.000
102A118GLY00.0100.00614.253-0.333-0.3330.0000.0000.0000.000
103A119TYR0-0.074-0.03712.3910.6440.6440.0000.0000.0000.000
104A120MIR-1-0.790-0.83815.010-17.978-17.9780.0000.0000.0000.000
105A121GLN00.028-0.00117.6660.8890.8890.0000.0000.0000.000
106A122GLY00.0380.02015.5060.6270.6270.0000.0000.0000.000
107A123ALA0-0.047-0.02416.5720.2650.2650.0000.0000.0000.000
108A124ALA0-0.0060.00018.7540.6870.6870.0000.0000.0000.000
109A125LEU0-0.034-0.00817.1750.5710.5710.0000.0000.0000.000
110A126ALA00.0450.00718.0790.5090.5090.0000.0000.0000.000
111A127ALA0-0.017-0.00820.0290.5680.5680.0000.0000.0000.000
112A128ALA00.0110.00323.4580.5240.5240.0000.0000.0000.000
113A129SER00.004-0.02021.7010.4570.4570.0000.0000.0000.000
114A130ILE0-0.007-0.00421.0680.3770.3770.0000.0000.0000.000
115A131GLU-1-0.913-0.94024.863-10.087-10.0870.0000.0000.0000.000
116A132ASP-1-0.781-0.88327.373-10.445-10.4450.0000.0000.0000.000
117A133LEU0-0.114-0.02824.3130.2390.2390.0000.0000.0000.000
118A134ASP-1-0.838-0.92127.959-9.352-9.3520.0000.0000.0000.000
119A135SER00.042-0.00229.627-0.260-0.2600.0000.0000.0000.000
120A136ALA00.0400.03630.824-0.163-0.1630.0000.0000.0000.000
121A137ILE0-0.037-0.01925.289-0.275-0.2750.0000.0000.0000.000
122A138ARG10.8590.91926.12910.11210.1120.0000.0000.0000.000
123A139ASP-1-0.901-0.95226.730-10.358-10.3580.0000.0000.0000.000
124A140LYS10.8320.91825.94811.31611.3160.0000.0000.0000.000
125A141ILE0-0.061-0.01321.223-0.541-0.5410.0000.0000.0000.000
126A142ALA00.0180.01523.1370.3630.3630.0000.0000.0000.000
127A143GLY00.0150.00221.9370.3530.3530.0000.0000.0000.000
128A144THR0-0.014-0.01619.306-0.801-0.8010.0000.0000.0000.000
129A145VAL0-0.034-0.00315.3100.4880.4880.0000.0000.0000.000
130A146LEU0-0.024-0.00517.288-0.719-0.7190.0000.0000.0000.000
131A147PHE00.0420.02113.4140.1630.1630.0000.0000.0000.000
132A148GLY00.0200.00717.116-0.266-0.2660.0000.0000.0000.000
133A149TYR0-0.012-0.03719.126-0.040-0.0400.0000.0000.0000.000
134A150THR00.0730.02921.0050.7230.7230.0000.0000.0000.000
135A151LYS10.9410.98423.40611.99211.9920.0000.0000.0000.000
136A152ASN00.0060.00924.6780.2720.2720.0000.0000.0000.000
137A153LEU00.0260.02026.5050.3820.3820.0000.0000.0000.000
138A154GLN0-0.015-0.02128.8180.1880.1880.0000.0000.0000.000
139A155ASN00.0350.02027.0130.6680.6680.0000.0000.0000.000
140A156ARG10.8590.91930.2889.3009.3000.0000.0000.0000.000
141A157GLY00.0190.01527.2500.1280.1280.0000.0000.0000.000
142A158ARG10.8460.93327.12210.00910.0090.0000.0000.0000.000
143A159ILE00.0340.03522.602-0.239-0.2390.0000.0000.0000.000
144A160PRO00.0240.00726.9030.2570.2570.0000.0000.0000.000
145A161ASN0-0.022-0.00629.1870.0240.0240.0000.0000.0000.000
146A162TYR00.012-0.00523.919-0.100-0.1000.0000.0000.0000.000
147A163PRO00.0210.02228.5440.1230.1230.0000.0000.0000.000
148A164ALA00.016-0.00928.220-0.398-0.3980.0000.0000.0000.000
149A165ASP-1-0.830-0.90127.737-11.270-11.2700.0000.0000.0000.000
150A166ARG10.9060.97225.35710.98910.9890.0000.0000.0000.000
151A167THR0-0.034-0.02523.647-0.689-0.6890.0000.0000.0000.000
152A168LYS10.9390.98820.46814.38714.3870.0000.0000.0000.000
153A169VAL0-0.027-0.01520.571-0.811-0.8110.0000.0000.0000.000
154A170PHE0-0.0100.00317.8240.3400.3400.0000.0000.0000.000
155178CYS0-0.065-0.03319.606-0.609-0.6090.0000.0000.0000.000
156A172ASN00.0020.00618.1260.8610.8610.0000.0000.0000.000
157A173THR00.0380.00222.1670.2520.2520.0000.0000.0000.000
158A174GLY00.0220.00724.535-0.244-0.2440.0000.0000.0000.000
159A175ASP-1-0.758-0.84520.292-15.567-15.5670.0000.0000.0000.000
160A176LEU00.033-0.00323.3180.3050.3050.0000.0000.0000.000
161A177VAL0-0.0050.00321.0970.3870.3870.0000.0000.0000.000
162A179THR0-0.057-0.03725.2470.4740.4740.0000.0000.0000.000
163A180GLY00.0320.01428.0730.4030.4030.0000.0000.0000.000
164A181SER0-0.0220.01227.7300.1750.1750.0000.0000.0000.000
165A182LEU00.0380.00124.199-0.379-0.3790.0000.0000.0000.000
166A183ILE0-0.038-0.01224.494-0.393-0.3930.0000.0000.0000.000
167A184VAL00.0230.01419.045-0.211-0.2110.0000.0000.0000.000
168A185ALA00.0280.01522.2050.3120.3120.0000.0000.0000.000
169A186ALA00.0470.00820.107-0.619-0.6190.0000.0000.0000.000
170A187PRO00.0410.01919.093-0.925-0.9250.0000.0000.0000.000
171A188HIS10.7830.86917.80916.47616.4760.0000.0000.0000.000
172A189LEU0-0.0040.00514.871-0.913-0.9130.0000.0000.0000.000
173A190ALA0-0.035-0.00714.343-1.336-1.3360.0000.0000.0000.000
174A191TYR00.027-0.00113.6360.8030.8030.0000.0000.0000.000
175A192GLY0-0.0020.00410.589-0.934-0.9340.0000.0000.0000.000
176A193PRO0-0.018-0.03411.468-1.044-1.0440.0000.0000.0000.000
177A194ASP-1-0.775-0.90113.983-17.719-17.7190.0000.0000.0000.000
178A195ALA0-0.049-0.0309.8920.1840.1840.0000.0000.0000.000
179A196ARG10.9220.9539.31426.56526.5650.0000.0000.0000.000
180A197GLY00.0420.03511.4870.2750.2750.0000.0000.0000.000
181A198PRO00.0360.02315.2040.1450.1450.0000.0000.0000.000
182A199ALA0-0.012-0.00814.1470.6830.6830.0000.0000.0000.000
183A200PRO0-0.002-0.00612.5320.6390.6390.0000.0000.0000.000
184A201GLU-1-0.941-0.95515.159-14.306-14.3060.0000.0000.0000.000
185A202PHE00.0090.00118.4260.6380.6380.0000.0000.0000.000
186A203LEU0-0.031-0.01915.1550.5120.5120.0000.0000.0000.000
187A204ILE0-0.009-0.00616.0140.5950.5950.0000.0000.0000.000
188A205GLU-1-0.945-0.96319.825-12.129-12.1290.0000.0000.0000.000
189A206LYS10.8330.89822.55412.55912.5590.0000.0000.0000.000
190A207VAL0-0.012-0.00920.1950.4780.4780.0000.0000.0000.000
191A208ARG10.9530.97421.10214.86714.8670.0000.0000.0000.000
192A209ALA0-0.058-0.00825.4090.4880.4880.0000.0000.0000.000
193A210VAL0-0.072-0.04226.3490.4290.4290.0000.0000.0000.000
194A211ARG10.8530.92124.01212.81812.8180.0000.0000.0000.000
195A212GLY-1-0.927-0.94926.949-11.724-11.7240.0000.0000.0000.000