Manual

About

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: G5G71

Calculation Name: 3QPA-A-Xray372

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: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
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 195
LigandCharge MIR=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2091500.138447
FMO2-HF: Nuclear repulsion 2019062.891566
FMO2-HF: Total energy -72437.246881
FMO2-MP2: Total energy -72648.256439


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.
2.833-0.8654.1162.232-2.651-0.009
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 : 0 / q_Mulliken : 0.040 / q_NPA : 0.023
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].
3A18THR00.0600.0232.5414.6690.3583.6632.529-1.881-0.007
4A19THR0-0.022-0.0083.554-0.490-0.4980.0380.013-0.0440.000
5A20ARG10.6560.7736.4970.9590.9590.0000.0000.0000.000
6A21ASP-1-0.740-0.8689.0240.1360.1360.0000.0000.0000.000
7A22ASP-1-0.795-0.87311.807-0.713-0.7130.0000.0000.0000.000
8A23LEU00.0200.03814.4350.0190.0190.0000.0000.0000.000
9A24ILE0-0.0110.01015.7670.0250.0250.0000.0000.0000.000
10A25ASN0-0.098-0.07315.0460.0380.0380.0000.0000.0000.000
11A26GLY00.0190.03618.106-0.018-0.0180.0000.0000.0000.000
12A27ASN00.0230.00019.6330.0490.0490.0000.0000.0000.000
13A28SER00.0690.01323.000-0.015-0.0150.0000.0000.0000.000
14A29ALA0-0.029-0.01025.6630.0010.0010.0000.0000.0000.000
15A30SER0-0.059-0.04323.115-0.001-0.0010.0000.0000.0000.000
16A31CYS0-0.036-0.00822.758-0.030-0.0300.0000.0000.0000.000
17A32ALA00.0000.03319.202-0.005-0.0050.0000.0000.0000.000
18A33ASP-1-0.820-0.89821.229-0.235-0.2350.0000.0000.0000.000
19A34VAL0-0.023-0.00218.0730.0210.0210.0000.0000.0000.000
20A35ILE00.004-0.00417.397-0.033-0.0330.0000.0000.0000.000
21A36PHE0-0.001-0.00510.5980.0310.0310.0000.0000.0000.000
22A37ILE0-0.008-0.00414.215-0.015-0.0150.0000.0000.0000.000
23A38TYR00.0000.0079.587-0.035-0.0350.0000.0000.0000.000
24A39ALA00.0160.00412.5310.0560.0560.0000.0000.0000.000
25A40ARG10.8220.9209.936-0.619-0.6190.0000.0000.0000.000
26A41GLY00.0300.02811.544-0.072-0.0720.0000.0000.0000.000
27A42SER00.010-0.04813.6350.0610.0610.0000.0000.0000.000
28A43THR0-0.083-0.04214.8540.0150.0150.0000.0000.0000.000
29A44GLU-1-0.769-0.8429.4661.0641.0640.0000.0000.0000.000
30A45THR00.011-0.0027.592-0.035-0.0350.0000.0000.0000.000
31A46GLY0-0.0070.0027.5760.1080.1080.0000.0000.0000.000
32A47ASN00.000-0.0228.040-0.182-0.1820.0000.0000.0000.000
33A48LEU00.0000.0075.541-0.170-0.1700.0000.0000.0000.000
34A49GLY0-0.0240.0036.807-0.185-0.1850.0000.0000.0000.000
35A50THR0-0.063-0.0674.7660.3720.472-0.001-0.005-0.0940.000
36A51LEU00.0020.0016.146-0.468-0.4680.0000.0000.0000.000
37A52GLY00.0740.0377.601-0.347-0.3470.0000.0000.0000.000
38A53PRO0-0.020-0.0172.690-0.877-0.3750.417-0.302-0.618-0.002
39A54SER0-0.0200.0055.036-0.419-0.400-0.001-0.003-0.0140.000
40A55ILE00.0150.0227.3470.1440.1440.0000.0000.0000.000
41A56ALA0-0.002-0.0037.2960.0560.0560.0000.0000.0000.000
42A57SER00.0190.0037.1660.3150.3150.0000.0000.0000.000
43A58ASN0-0.025-0.0109.2720.3180.3180.0000.0000.0000.000
44A59LEU00.0040.00612.2770.1420.1420.0000.0000.0000.000
45A60GLU-1-0.801-0.8959.428-1.626-1.6260.0000.0000.0000.000
46A61SER0-0.055-0.03012.6050.0880.0880.0000.0000.0000.000
47A62ALA0-0.058-0.02115.0970.0970.0970.0000.0000.0000.000
48A63PHE0-0.005-0.00917.2530.0860.0860.0000.0000.0000.000
49A64GLY00.0550.04617.5260.0500.0500.0000.0000.0000.000
50A65LYS10.7980.88312.4250.7060.7060.0000.0000.0000.000
51A66ASP-1-0.864-0.93315.341-0.559-0.5590.0000.0000.0000.000
52A67GLY00.0500.04818.1400.0560.0560.0000.0000.0000.000
53A68VAL0-0.053-0.03714.3640.0250.0250.0000.0000.0000.000
54A69TRP0-0.0060.00515.029-0.023-0.0230.0000.0000.0000.000
55A70ILE0-0.002-0.0048.8690.0030.0030.0000.0000.0000.000
56A71GLN0-0.038-0.03712.009-0.020-0.0200.0000.0000.0000.000
57A72GLY00.0390.02310.455-0.008-0.0080.0000.0000.0000.000
58A73VAL0-0.025-0.01911.3300.0220.0220.0000.0000.0000.000
59A74GLY00.022-0.00213.4440.0890.0890.0000.0000.0000.000
60A75GLY00.0570.02814.5040.0030.0030.0000.0000.0000.000
61A76ALA0-0.032-0.01717.8950.0430.0430.0000.0000.0000.000
62A77TYR0-0.054-0.04414.3030.0020.0020.0000.0000.0000.000
63A78ARG10.9020.93116.175-0.240-0.2400.0000.0000.0000.000
64A79ALA0-0.0150.02215.0630.0600.0600.0000.0000.0000.000
65A80THR00.031-0.01117.0780.0590.0590.0000.0000.0000.000
66A81LEU00.0230.01419.321-0.033-0.0330.0000.0000.0000.000
67A82GLY00.0250.01520.720-0.025-0.0250.0000.0000.0000.000
68A83ASP-1-0.801-0.87221.9620.2040.2040.0000.0000.0000.000
69A84ASN0-0.020-0.02120.209-0.040-0.0400.0000.0000.0000.000
70A85ALA0-0.001-0.00623.964-0.019-0.0190.0000.0000.0000.000
71A86LEU0-0.0190.01225.661-0.015-0.0150.0000.0000.0000.000
72A87PRO00.012-0.00427.743-0.001-0.0010.0000.0000.0000.000
73A88ARG10.7840.83126.720-0.041-0.0410.0000.0000.0000.000
74A89GLY0-0.044-0.02124.111-0.005-0.0050.0000.0000.0000.000
75A90THR00.014-0.01620.6890.0180.0180.0000.0000.0000.000
76A91SER00.020-0.00522.966-0.022-0.0220.0000.0000.0000.000
77A92SER00.015-0.01523.9080.0000.0000.0000.0000.0000.000
78A93ALA0-0.020-0.00123.841-0.012-0.0120.0000.0000.0000.000
79A94ALA00.0290.01619.654-0.004-0.0040.0000.0000.0000.000
80A95ILE00.0380.01520.799-0.012-0.0120.0000.0000.0000.000
81A96ARG10.9640.98523.181-0.081-0.0810.0000.0000.0000.000
82A97GLU-1-0.874-0.92017.9440.0990.0990.0000.0000.0000.000
83A98MET00.0050.01116.613-0.011-0.0110.0000.0000.0000.000
84A99LEU0-0.0060.00319.868-0.027-0.0270.0000.0000.0000.000
85A100GLY00.0230.01822.941-0.015-0.0150.0000.0000.0000.000
86A101LEU0-0.041-0.01816.065-0.018-0.0180.0000.0000.0000.000
87A102PHE00.0610.00720.040-0.026-0.0260.0000.0000.0000.000
88A103GLN00.0020.00222.247-0.008-0.0080.0000.0000.0000.000
89A104GLN00.0230.00620.067-0.020-0.0200.0000.0000.0000.000
90A105ALA0-0.0020.00220.543-0.011-0.0110.0000.0000.0000.000
91A106ASN00.0170.01222.352-0.014-0.0140.0000.0000.0000.000
92A107THR0-0.046-0.03625.9730.0030.0030.0000.0000.0000.000
93A108LYS10.7570.87520.6180.1360.1360.0000.0000.0000.000
94A110PRO00.0250.02725.713-0.007-0.0070.0000.0000.0000.000
95A111ASP-1-0.855-0.91828.238-0.129-0.1290.0000.0000.0000.000
96A112ALA0-0.0010.01822.473-0.013-0.0130.0000.0000.0000.000
97A113THR0-0.039-0.00622.7510.0180.0180.0000.0000.0000.000
98A114LEU0-0.006-0.00120.688-0.031-0.0310.0000.0000.0000.000
99A115ILE0-0.004-0.00716.3700.0020.0020.0000.0000.0000.000
100A116ALA00.0060.00716.832-0.009-0.0090.0000.0000.0000.000
101A117GLY00.0420.00115.537-0.028-0.0280.0000.0000.0000.000
102A118GLY00.0160.00913.7820.0180.0180.0000.0000.0000.000
103A119TYR0-0.064-0.03312.103-0.025-0.0250.0000.0000.0000.000
104A120MIR-1-0.819-0.83714.8000.4010.4010.0000.0000.0000.000
105A121GLN00.040-0.00517.644-0.052-0.0520.0000.0000.0000.000
106A122GLY00.0520.02415.380-0.028-0.0280.0000.0000.0000.000
107A123ALA0-0.051-0.02116.451-0.048-0.0480.0000.0000.0000.000
108A124ALA00.002-0.00318.438-0.026-0.0260.0000.0000.0000.000
109A125LEU0-0.0170.00317.103-0.017-0.0170.0000.0000.0000.000
110A126ALA00.0350.01617.799-0.019-0.0190.0000.0000.0000.000
111A127ALA0-0.014-0.00619.835-0.017-0.0170.0000.0000.0000.000
112A128ALA00.0180.00323.269-0.009-0.0090.0000.0000.0000.000
113A129SER0-0.009-0.03321.622-0.001-0.0010.0000.0000.0000.000
114A130ILE0-0.008-0.00421.018-0.010-0.0100.0000.0000.0000.000
115A131GLU-1-0.883-0.91424.7910.0180.0180.0000.0000.0000.000
116A132ASP-1-0.780-0.87227.2040.0270.0270.0000.0000.0000.000
117A133LEU0-0.107-0.01824.408-0.001-0.0010.0000.0000.0000.000
118A134ASP-1-0.799-0.91528.075-0.046-0.0460.0000.0000.0000.000
119A135SER00.0050.00029.553-0.005-0.0050.0000.0000.0000.000
120A136ALA00.0290.03030.602-0.008-0.0080.0000.0000.0000.000
121A137ILE0-0.036-0.01125.307-0.011-0.0110.0000.0000.0000.000
122A138ARG10.8680.91326.0490.0270.0270.0000.0000.0000.000
123A139ASP-1-0.872-0.94526.591-0.079-0.0790.0000.0000.0000.000
124A140LYS10.8140.90226.3350.1060.1060.0000.0000.0000.000
125A141ILE0-0.031-0.00121.203-0.022-0.0220.0000.0000.0000.000
126A142ALA00.0220.03223.3740.0160.0160.0000.0000.0000.000
127A143GLY00.012-0.00221.8550.0070.0070.0000.0000.0000.000
128A144THR0-0.008-0.01619.212-0.014-0.0140.0000.0000.0000.000
129A145VAL0-0.034-0.00315.3120.0090.0090.0000.0000.0000.000
130A146LEU0-0.032-0.00316.9390.0150.0150.0000.0000.0000.000
131A147PHE00.0530.02213.2320.0020.0020.0000.0000.0000.000
132A148GLY00.0400.01017.0060.0400.0400.0000.0000.0000.000
133A149TYR0-0.015-0.03319.1720.0300.0300.0000.0000.0000.000
134A150THR00.0340.01520.702-0.020-0.0200.0000.0000.0000.000
135A151LYS10.8520.94923.074-0.107-0.1070.0000.0000.0000.000
136A152ASN00.0010.00324.445-0.023-0.0230.0000.0000.0000.000
137A153LEU00.0260.02926.250-0.011-0.0110.0000.0000.0000.000
138A154GLN0-0.013-0.01327.503-0.014-0.0140.0000.0000.0000.000
139A155ASN00.007-0.00726.584-0.002-0.0020.0000.0000.0000.000
140A156ARG10.8590.92329.807-0.033-0.0330.0000.0000.0000.000
141A157GLY00.0260.02427.146-0.007-0.0070.0000.0000.0000.000
142A158ARG10.8490.91927.1640.0230.0230.0000.0000.0000.000
143A159ILE00.0350.04022.2680.0140.0140.0000.0000.0000.000
144A160PRO00.0320.00626.554-0.008-0.0080.0000.0000.0000.000
145A161ASN0-0.044-0.03228.741-0.004-0.0040.0000.0000.0000.000
146A162TYR00.0120.01423.716-0.006-0.0060.0000.0000.0000.000
147A163PRO00.0140.02428.3430.0080.0080.0000.0000.0000.000
148A164ALA00.018-0.01128.073-0.005-0.0050.0000.0000.0000.000
149A165ASP-1-0.806-0.90027.800-0.113-0.1130.0000.0000.0000.000
150A166ARG10.8160.92524.9930.1010.1010.0000.0000.0000.000
151A167THR0-0.026-0.02123.441-0.006-0.0060.0000.0000.0000.000
152A168LYS10.8520.95220.5930.2120.2120.0000.0000.0000.000
153A169VAL0-0.018-0.01720.386-0.006-0.0060.0000.0000.0000.000
154A170PHE00.0060.00518.088-0.012-0.0120.0000.0000.0000.000
155A171CYS0-0.057-0.03019.7520.0210.0210.0000.0000.0000.000
156A172ASN00.0320.02818.370-0.024-0.0240.0000.0000.0000.000
157A173THR00.0230.00122.1870.0120.0120.0000.0000.0000.000
158A174GLY00.0480.02124.9210.0070.0070.0000.0000.0000.000
159A175ASP-1-0.769-0.84720.4650.1850.1850.0000.0000.0000.000
160A176LEU00.0450.01023.463-0.012-0.0120.0000.0000.0000.000
161A177VAL0-0.0140.00621.310-0.008-0.0080.0000.0000.0000.000
162A179THR0-0.031-0.01825.119-0.016-0.0160.0000.0000.0000.000
163A180GLY00.0120.00527.637-0.003-0.0030.0000.0000.0000.000
164A181SER0-0.0210.00027.3640.0070.0070.0000.0000.0000.000
165A182LEU00.030-0.00524.2570.0030.0030.0000.0000.0000.000
166A183ILE0-0.029-0.00924.5830.0220.0220.0000.0000.0000.000
167A184VAL00.0180.01019.362-0.012-0.0120.0000.0000.0000.000
168A185ALA00.0290.01822.3930.0000.0000.0000.0000.0000.000
169A186ALA00.0400.00820.0780.0080.0080.0000.0000.0000.000
170A187PRO00.0400.01118.9850.0190.0190.0000.0000.0000.000
171A188HIS10.7880.87417.600-0.279-0.2790.0000.0000.0000.000
172A189LEU00.0090.00414.8930.0260.0260.0000.0000.0000.000
173A190ALA0-0.036-0.00714.1360.0190.0190.0000.0000.0000.000
174A191TYR0-0.035-0.03413.865-0.054-0.0540.0000.0000.0000.000
175A192GLY00.0020.00710.612-0.056-0.0560.0000.0000.0000.000
176A193PRO0-0.016-0.02411.121-0.146-0.1460.0000.0000.0000.000
177A194ASP-1-0.807-0.91713.743-0.167-0.1670.0000.0000.0000.000
178A195ALA0-0.017-0.01810.230-0.048-0.0480.0000.0000.0000.000
179A196ARG10.9450.9668.4440.2870.2870.0000.0000.0000.000
180A197GLY00.0410.03111.421-0.052-0.0520.0000.0000.0000.000
181A198PRO00.0230.02615.207-0.012-0.0120.0000.0000.0000.000
182A199ALA00.0170.01214.4780.0300.0300.0000.0000.0000.000
183A200PRO00.003-0.00512.4680.0170.0170.0000.0000.0000.000
184A201GLU-1-0.907-0.95015.300-0.241-0.2410.0000.0000.0000.000
185A202PHE00.0070.00418.5420.0160.0160.0000.0000.0000.000
186A203LEU0-0.0120.00114.9300.0160.0160.0000.0000.0000.000
187A204ILE0-0.008-0.01216.0810.0130.0130.0000.0000.0000.000
188A205GLU-1-0.933-0.96919.891-0.173-0.1730.0000.0000.0000.000
189A206LYS10.8190.89122.4670.1660.1660.0000.0000.0000.000
190A207VAL00.0120.00520.0290.0200.0200.0000.0000.0000.000
191A208ARG10.9020.94321.1910.3810.3810.0000.0000.0000.000
192A209ALA0-0.052-0.01825.4310.0150.0150.0000.0000.0000.000
193A210VAL0-0.063-0.03226.0660.0160.0160.0000.0000.0000.000
194A211ARG10.7750.86324.1940.2290.2290.0000.0000.0000.000
195A212GLY0-0.034-0.00126.975-0.009-0.0090.0000.0000.0000.000