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: 1NKVZ

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 OptHSide
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 -2087528.812866
FMO2-HF: Nuclear repulsion 2015091.637341
FMO2-HF: Total energy -72437.175525
FMO2-MP2: Total energy -72648.164648


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.
7.966-2.4718.0545.259-2.877-0.009
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 : 0.026 / q_NPA : 0.026
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].
3A18THR00.0490.0212.3429.829-1.2577.6695.437-2.020-0.007
4A19THR0-0.027-0.0053.333-0.666-0.7760.0760.116-0.0820.000
5A20ARG10.6830.7996.1790.8610.8610.0000.0000.0000.000
6A21ASP-1-0.794-0.8948.6560.2990.2990.0000.0000.0000.000
7A22ASP-1-0.774-0.86711.447-0.612-0.6120.0000.0000.0000.000
8A23LEU00.0230.03413.9800.0070.0070.0000.0000.0000.000
9A24ILE0-0.028-0.00415.5000.0150.0150.0000.0000.0000.000
10A25ASN0-0.111-0.06814.7910.0290.0290.0000.0000.0000.000
11A26GLY00.0190.03417.720-0.029-0.0290.0000.0000.0000.000
12A27ASN00.013-0.00819.3070.0420.0420.0000.0000.0000.000
13A28SER00.0540.00522.519-0.013-0.0130.0000.0000.0000.000
14A29ALA0-0.038-0.01125.0980.0030.0030.0000.0000.0000.000
15A30SER0-0.054-0.03423.074-0.001-0.0010.0000.0000.0000.000
16A31CYS0-0.060-0.01822.532-0.026-0.0260.0000.0000.0000.000
17A32ALA00.0000.02418.693-0.010-0.0100.0000.0000.0000.000
18A33ASP-1-0.824-0.89620.755-0.226-0.2260.0000.0000.0000.000
19A34VAL0-0.030-0.01318.0390.0220.0220.0000.0000.0000.000
20A35ILE0-0.011-0.00817.069-0.033-0.0330.0000.0000.0000.000
21A36PHE00.012-0.00410.7050.0240.0240.0000.0000.0000.000
22A37ILE0-0.0060.00013.922-0.007-0.0070.0000.0000.0000.000
23A38TYR00.0000.0009.803-0.059-0.0590.0000.0000.0000.000
24A39ALA00.0150.00912.2990.0760.0760.0000.0000.0000.000
25A40ARG10.8320.92510.085-0.758-0.7580.0000.0000.0000.000
26A41GLY00.0410.02911.824-0.087-0.0870.0000.0000.0000.000
27A42SER00.011-0.05813.6410.0760.0760.0000.0000.0000.000
28A43THR0-0.073-0.03614.9730.0160.0160.0000.0000.0000.000
29A44GLU-1-0.765-0.8329.6341.0641.0640.0000.0000.0000.000
30A45THR00.001-0.0147.3210.0360.0360.0000.0000.0000.000
31A46GLY00.0040.0026.9860.1390.1390.0000.0000.0000.000
32A47ASN00.015-0.0127.705-0.189-0.1890.0000.0000.0000.000
33A48LEU00.0000.0095.301-0.263-0.2630.0000.0000.0000.000
34A49GLY0-0.036-0.0106.905-0.247-0.2470.0000.0000.0000.000
35A50THR0-0.054-0.0615.4080.4190.4190.0000.0000.0000.000
36A51LEU0-0.010-0.0046.369-0.374-0.3740.0000.0000.0000.000
37A52GLY00.0480.0277.620-0.356-0.3560.0000.0000.0000.000
38A53PRO0-0.003-0.0112.895-1.134-0.4030.310-0.290-0.752-0.002
39A54SER0-0.010-0.0035.058-0.303-0.275-0.001-0.004-0.0230.000
40A55ILE00.0180.0236.8680.1720.1720.0000.0000.0000.000
41A56ALA00.005-0.0017.3120.0710.0710.0000.0000.0000.000
42A57SER00.0130.0107.0550.3200.3200.0000.0000.0000.000
43A58ASN0-0.023-0.0189.1820.3300.3300.0000.0000.0000.000
44A59LEU00.0020.00512.1090.1530.1530.0000.0000.0000.000
45A60GLU-1-0.818-0.9099.659-1.517-1.5170.0000.0000.0000.000
46A61SER0-0.052-0.02312.9360.1030.1030.0000.0000.0000.000
47A62ALA0-0.061-0.01515.3390.0890.0890.0000.0000.0000.000
48A63PHE0-0.006-0.02317.1710.0730.0730.0000.0000.0000.000
49A64GLY00.0680.05517.5880.0550.0550.0000.0000.0000.000
50A65LYS10.8560.92111.7560.6940.6940.0000.0000.0000.000
51A66ASP-1-0.934-0.98415.425-0.453-0.4530.0000.0000.0000.000
52A67GLY00.0420.04318.2960.0510.0510.0000.0000.0000.000
53A68VAL0-0.054-0.03213.9850.0240.0240.0000.0000.0000.000
54A69TRP0-0.010-0.00114.487-0.025-0.0250.0000.0000.0000.000
55A70ILE0-0.004-0.0038.5160.0140.0140.0000.0000.0000.000
56A71GLN0-0.032-0.03211.488-0.004-0.0040.0000.0000.0000.000
57A72GLY00.0430.02410.259-0.002-0.0020.0000.0000.0000.000
58A73VAL0-0.018-0.00611.1330.0100.0100.0000.0000.0000.000
59A74GLY00.016-0.00813.5700.0980.0980.0000.0000.0000.000
60A75GLY00.0520.03514.099-0.030-0.0300.0000.0000.0000.000
61A76ALA0-0.027-0.02817.4260.0490.0490.0000.0000.0000.000
62A77TYR0-0.039-0.02914.403-0.006-0.0060.0000.0000.0000.000
63A78ARG10.8750.92215.876-0.289-0.2890.0000.0000.0000.000
64A79ALA0-0.0180.02214.8200.0520.0520.0000.0000.0000.000
65A80THR00.0590.02716.7660.0610.0610.0000.0000.0000.000
66A81LEU00.0570.03119.762-0.036-0.0360.0000.0000.0000.000
67A82GLY00.0330.01321.015-0.027-0.0270.0000.0000.0000.000
68A83ASP-1-0.829-0.91622.0860.2210.2210.0000.0000.0000.000
69A84ASN0-0.064-0.04520.182-0.036-0.0360.0000.0000.0000.000
70A85ALA0-0.019-0.01223.904-0.020-0.0200.0000.0000.0000.000
71A86LEU0-0.0110.01925.627-0.016-0.0160.0000.0000.0000.000
72A87PRO00.0270.00928.142-0.002-0.0020.0000.0000.0000.000
73A88ARG10.7660.81326.836-0.061-0.0610.0000.0000.0000.000
74A89GLY0-0.062-0.03024.651-0.004-0.0040.0000.0000.0000.000
75A90THR00.032-0.00320.7900.0190.0190.0000.0000.0000.000
76A91SER0-0.013-0.01222.720-0.020-0.0200.0000.0000.0000.000
77A92SER00.028-0.00224.161-0.004-0.0040.0000.0000.0000.000
78A93ALA0-0.019-0.00523.772-0.009-0.0090.0000.0000.0000.000
79A94ALA00.0230.01319.833-0.001-0.0010.0000.0000.0000.000
80A95ILE00.0600.02420.861-0.008-0.0080.0000.0000.0000.000
81A96ARG10.9490.98223.244-0.116-0.1160.0000.0000.0000.000
82A97GLU-1-0.870-0.92217.9490.1640.1640.0000.0000.0000.000
83A98MET00.0050.01016.665-0.008-0.0080.0000.0000.0000.000
84A99LEU0-0.013-0.00319.877-0.027-0.0270.0000.0000.0000.000
85A100GLY00.0160.01522.854-0.017-0.0170.0000.0000.0000.000
86A101LEU0-0.030-0.01516.004-0.017-0.0170.0000.0000.0000.000
87A102PHE00.0650.01220.026-0.025-0.0250.0000.0000.0000.000
88A103GLN00.0050.00622.026-0.011-0.0110.0000.0000.0000.000
89A104GLN00.0250.00219.884-0.023-0.0230.0000.0000.0000.000
90A105ALA00.0120.00920.387-0.013-0.0130.0000.0000.0000.000
91A106ASN00.0020.00422.205-0.017-0.0170.0000.0000.0000.000
92A107THR0-0.040-0.02825.7870.0000.0000.0000.0000.0000.000
93A108LYS10.8140.90820.3410.0680.0680.0000.0000.0000.000
94A110PRO00.0250.02325.230-0.008-0.0080.0000.0000.0000.000
95A111ASP-1-0.866-0.91927.697-0.111-0.1110.0000.0000.0000.000
96A112ALA0-0.0230.00422.134-0.015-0.0150.0000.0000.0000.000
97A113THR0-0.030-0.00322.7530.0180.0180.0000.0000.0000.000
98A114LEU0-0.015-0.00820.455-0.026-0.0260.0000.0000.0000.000
99A115ILE0-0.003-0.00316.320-0.002-0.0020.0000.0000.0000.000
100A116ALA00.0040.00516.700-0.001-0.0010.0000.0000.0000.000
101A117GLY00.0320.00115.218-0.033-0.0330.0000.0000.0000.000
102A118GLY00.0100.00814.2390.0320.0320.0000.0000.0000.000
103A119TYR0-0.053-0.02612.350-0.037-0.0370.0000.0000.0000.000
104A120MIR-1-0.791-0.82214.9910.4320.4320.0000.0000.0000.000
105A121GLN00.022-0.01117.637-0.051-0.0510.0000.0000.0000.000
106A122GLY00.0440.02215.497-0.025-0.0250.0000.0000.0000.000
107A123ALA0-0.045-0.02316.563-0.049-0.0490.0000.0000.0000.000
108A124ALA0-0.007-0.00118.740-0.025-0.0250.0000.0000.0000.000
109A125LEU0-0.026-0.00517.180-0.017-0.0170.0000.0000.0000.000
110A126ALA00.0430.01318.040-0.019-0.0190.0000.0000.0000.000
111A127ALA0-0.023-0.01120.025-0.017-0.0170.0000.0000.0000.000
112A128ALA00.0100.00623.451-0.009-0.0090.0000.0000.0000.000
113A129SER00.010-0.02721.728-0.002-0.0020.0000.0000.0000.000
114A130ILE0-0.009-0.00621.072-0.009-0.0090.0000.0000.0000.000
115A131GLU-1-0.897-0.91924.8630.0260.0260.0000.0000.0000.000
116A132ASP-1-0.789-0.87327.2730.0440.0440.0000.0000.0000.000
117A133LEU0-0.107-0.02924.316-0.001-0.0010.0000.0000.0000.000
118A134ASP-1-0.819-0.91427.965-0.029-0.0290.0000.0000.0000.000
119A135SER00.035-0.00129.634-0.004-0.0040.0000.0000.0000.000
120A136ALA00.0290.02930.828-0.008-0.0080.0000.0000.0000.000
121A137ILE0-0.042-0.02125.288-0.010-0.0100.0000.0000.0000.000
122A138ARG10.8530.91726.1310.0110.0110.0000.0000.0000.000
123A139ASP-1-0.890-0.94726.730-0.069-0.0690.0000.0000.0000.000
124A140LYS10.8160.91025.9620.0840.0840.0000.0000.0000.000
125A141ILE0-0.053-0.00821.187-0.021-0.0210.0000.0000.0000.000
126A142ALA00.0180.01523.1410.0140.0140.0000.0000.0000.000
127A143GLY00.0180.00221.9260.0030.0030.0000.0000.0000.000
128A144THR0-0.013-0.01719.303-0.010-0.0100.0000.0000.0000.000
129A145VAL0-0.032-0.00215.3150.0090.0090.0000.0000.0000.000
130A146LEU0-0.031-0.00617.2720.0210.0210.0000.0000.0000.000
131A147PHE00.0460.02213.377-0.012-0.0120.0000.0000.0000.000
132A148GLY00.0310.01217.1540.0460.0460.0000.0000.0000.000
133A149TYR0-0.023-0.03819.1720.0330.0330.0000.0000.0000.000
134A150THR00.0720.02720.892-0.018-0.0180.0000.0000.0000.000
135A151LYS10.8870.96923.385-0.109-0.1090.0000.0000.0000.000
136A152ASN0-0.004-0.00124.704-0.023-0.0230.0000.0000.0000.000
137A153LEU00.0350.02626.549-0.010-0.0100.0000.0000.0000.000
138A154GLN0-0.019-0.02028.030-0.014-0.0140.0000.0000.0000.000
139A155ASN00.0260.01027.032-0.001-0.0010.0000.0000.0000.000
140A156ARG10.8610.92130.271-0.035-0.0350.0000.0000.0000.000
141A157GLY00.0210.01927.288-0.008-0.0080.0000.0000.0000.000
142A158ARG10.8390.91627.1530.0190.0190.0000.0000.0000.000
143A159ILE00.0350.03622.5120.0140.0140.0000.0000.0000.000
144A160PRO00.0250.00426.892-0.010-0.0100.0000.0000.0000.000
145A161ASN0-0.031-0.01129.180-0.003-0.0030.0000.0000.0000.000
146A162TYR00.0330.00923.858-0.005-0.0050.0000.0000.0000.000
147A163PRO00.0130.03128.5090.0060.0060.0000.0000.0000.000
148A164ALA00.026-0.00528.207-0.005-0.0050.0000.0000.0000.000
149A165ASP-1-0.804-0.89427.753-0.110-0.1100.0000.0000.0000.000
150A166ARG10.8560.94725.3330.0920.0920.0000.0000.0000.000
151A167THR0-0.038-0.02723.664-0.005-0.0050.0000.0000.0000.000
152A168LYS10.9230.98620.2050.1720.1720.0000.0000.0000.000
153A169VAL0-0.020-0.01420.594-0.002-0.0020.0000.0000.0000.000
154A170PHE0-0.0050.00517.953-0.013-0.0130.0000.0000.0000.000
155A171CYS0-0.064-0.03019.6410.0240.0240.0000.0000.0000.000
156A172ASN00.0150.01718.151-0.033-0.0330.0000.0000.0000.000
157A173THR00.0410.00522.2010.0130.0130.0000.0000.0000.000
158A174GLY00.0180.00424.5720.0050.0050.0000.0000.0000.000
159A175ASP-1-0.761-0.84520.3440.1690.1690.0000.0000.0000.000
160A176LEU00.0400.00623.364-0.012-0.0120.0000.0000.0000.000
161A177VAL0-0.020-0.00421.201-0.005-0.0050.0000.0000.0000.000
162A179THR0-0.016-0.01425.294-0.014-0.0140.0000.0000.0000.000
163A180GLY00.0100.00528.121-0.003-0.0030.0000.0000.0000.000
164A181SER0-0.0290.00427.7090.0070.0070.0000.0000.0000.000
165A182LEU00.0310.00324.4340.0030.0030.0000.0000.0000.000
166A183ILE0-0.024-0.00624.7310.0230.0230.0000.0000.0000.000
167A184VAL00.0220.01319.298-0.011-0.0110.0000.0000.0000.000
168A185ALA00.0280.01422.3640.0010.0010.0000.0000.0000.000
169A186ALA00.0510.01020.2020.0100.0100.0000.0000.0000.000
170A187PRO00.0360.01719.1370.0140.0140.0000.0000.0000.000
171A188HIS10.7940.87717.644-0.271-0.2710.0000.0000.0000.000
172A189LEU0-0.013-0.00515.0420.0230.0230.0000.0000.0000.000
173A190ALA0-0.035-0.00714.3840.0160.0160.0000.0000.0000.000
174A191TYR00.019-0.01413.694-0.052-0.0520.0000.0000.0000.000
175A192GLY00.0060.01110.610-0.061-0.0610.0000.0000.0000.000
176A193PRO0-0.013-0.02611.488-0.139-0.1390.0000.0000.0000.000
177A194ASP-1-0.794-0.91413.988-0.194-0.1940.0000.0000.0000.000
178A195ALA0-0.044-0.0289.907-0.043-0.0430.0000.0000.0000.000
179A196ARG10.9350.9578.9570.3880.3880.0000.0000.0000.000
180A197GLY00.0390.03411.476-0.054-0.0540.0000.0000.0000.000
181A198PRO00.0280.02515.191-0.009-0.0090.0000.0000.0000.000
182A199ALA0-0.011-0.01114.1530.0260.0260.0000.0000.0000.000
183A200PRO00.008-0.00112.4350.0240.0240.0000.0000.0000.000
184A201GLU-1-0.937-0.95515.149-0.274-0.2740.0000.0000.0000.000
185A202PHE00.002-0.00518.4110.0240.0240.0000.0000.0000.000
186A203LEU0-0.020-0.00915.1340.0180.0180.0000.0000.0000.000
187A204ILE0-0.009-0.01015.9840.0190.0190.0000.0000.0000.000
188A205GLU-1-0.936-0.96419.807-0.172-0.1720.0000.0000.0000.000
189A206LYS10.8170.89122.5390.1680.1680.0000.0000.0000.000
190A207VAL0-0.002-0.00520.2210.0210.0210.0000.0000.0000.000
191A208ARG10.9080.95621.0920.3810.3810.0000.0000.0000.000
192A209ALA0-0.051-0.00925.3880.0150.0150.0000.0000.0000.000
193A210VAL0-0.048-0.02526.2820.0140.0140.0000.0000.0000.000
194A211ARG10.7990.87024.0860.2170.2170.0000.0000.0000.000
195A212GLY0-0.0210.00226.921-0.006-0.0060.0000.0000.0000.000