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: N1M1Q

Calculation Name: 4PKX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4PKX

Chain ID: A

ChEMBL ID:

UniProt ID: O01260

Base Structure: X-ray

Registration Date: 2023-06-20

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 OptH
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 251
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3257290.090408
FMO2-HF: Nuclear repulsion 3158170.301848
FMO2-HF: Total energy -99119.78856
FMO2-MP2: Total energy -99412.117852


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:14:GLU)


Summations of interaction energy for fragment #1(A:14:GLU)
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.
-16.514-3.27914.05-10.726-16.5580.06
Interaction energy analysis for fragmet #1(A:14:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.912 / q_NPA : -0.960
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].
3A16VAL00.0850.0523.7720.3783.371-0.023-1.377-1.5930.006
4A17THR0-0.074-0.0395.687-3.239-3.2390.0000.0000.0000.000
5A18LEU00.0070.0249.446-0.064-0.0640.0000.0000.0000.000
6A19ARG10.8260.90312.398-19.909-19.9090.0000.0000.0000.000
7A20ILE00.0390.03516.001-0.058-0.0580.0000.0000.0000.000
8A21SER00.005-0.01019.370-0.257-0.2570.0000.0000.0000.000
9A22ILE00.0120.02122.458-0.169-0.1690.0000.0000.0000.000
10A23GLU-1-0.911-0.98924.24111.82811.8280.0000.0000.0000.000
11A24GLY0-0.055-0.02224.337-0.493-0.4930.0000.0000.0000.000
12A25TYR0-0.065-0.03925.349-0.398-0.3980.0000.0000.0000.000
13A26PRO0-0.0040.00122.5960.4290.4290.0000.0000.0000.000
14A27PRO0-0.012-0.00518.495-0.375-0.3750.0000.0000.0000.000
15A28LEU0-0.057-0.01721.133-0.380-0.3800.0000.0000.0000.000
16A29TYR0-0.045-0.05615.248-0.035-0.0350.0000.0000.0000.000
17A30GLU-1-0.814-0.90815.05616.60416.6040.0000.0000.0000.000
18A31ARG10.9040.96012.561-18.077-18.0770.0000.0000.0000.000
19A32GLU-1-0.923-0.9657.77025.82225.8220.0000.0000.0000.000
20A33ALA0-0.022-0.0076.690-1.526-1.5260.0000.0000.0000.000
21A34GLN0-0.0070.0023.9373.0383.236-0.001-0.047-0.1500.000
22A35GLY0-0.030-0.0214.7112.8612.906-0.001-0.014-0.0300.000
23A36SER0-0.044-0.0525.741-1.196-1.1960.0000.0000.0000.000
24A37ASN0-0.033-0.0186.505-0.147-0.1470.0000.0000.0000.000
25A38HIS00.0400.0347.8163.3713.3710.0000.0000.0000.000
26A39ASP-1-0.797-0.8855.98432.66232.6620.0000.0000.0000.000
27A40ASN0-0.096-0.0598.479-3.885-3.8850.0000.0000.0000.000
28A41ALA0-0.034-0.0239.4611.1431.1430.0000.0000.0000.000
29A42GLU-1-0.866-0.9508.47922.84322.8430.0000.0000.0000.000
30A43LEU00.0220.0232.1231.0950.7682.254-0.466-1.461-0.002
31A44GLY00.0260.0366.160-0.479-0.4790.0000.0000.0000.000
32A45MET00.0150.0267.8121.7621.7620.0000.0000.0000.000
33A46ILE0-0.0260.0169.342-3.129-3.1290.0000.0000.0000.000
34A47LYS10.9580.96812.464-18.136-18.1360.0000.0000.0000.000
35A48PRO00.0920.02915.628-0.271-0.2710.0000.0000.0000.000
36A49ASP-1-0.860-0.93118.28313.95213.9520.0000.0000.0000.000
37A50GLN0-0.064-0.03214.7370.4290.4290.0000.0000.0000.000
38A51LEU00.0560.02715.403-0.336-0.3360.0000.0000.0000.000
39A52ALA00.0370.01717.631-0.551-0.5510.0000.0000.0000.000
40A53SER0-0.037-0.03621.227-0.957-0.9570.0000.0000.0000.000
41A54LEU00.0370.03616.337-0.673-0.6730.0000.0000.0000.000
42A55ASN00.0720.02420.324-0.173-0.1730.0000.0000.0000.000
43A56GLN0-0.046-0.02722.039-0.230-0.2300.0000.0000.0000.000
44A57ALA0-0.0270.00123.083-0.490-0.4900.0000.0000.0000.000
45A58LEU00.0200.01319.800-0.419-0.4190.0000.0000.0000.000
46A59THR0-0.032-0.01524.430-0.463-0.4630.0000.0000.0000.000
47A60ASP-1-0.938-0.98127.15210.46910.4690.0000.0000.0000.000
48A61SER0-0.065-0.03627.126-0.318-0.3180.0000.0000.0000.000
49A62TYR0-0.039-0.00229.239-0.297-0.2970.0000.0000.0000.000
50A63THR00.0460.01332.062-0.224-0.2240.0000.0000.0000.000
51A64THR00.020-0.01535.669-0.034-0.0340.0000.0000.0000.000
52A65ARG10.9320.96938.246-7.383-7.3830.0000.0000.0000.000
53A66ASP-1-0.853-0.92235.8978.7908.7900.0000.0000.0000.000
54A67THR00.0630.02035.7530.2280.2280.0000.0000.0000.000
55A68ASN00.0140.00333.4680.3270.3270.0000.0000.0000.000
56A69SER00.0140.01031.3520.3690.3690.0000.0000.0000.000
57A70ILE0-0.0030.00230.5230.3980.3980.0000.0000.0000.000
58A71LEU0-0.031-0.01830.3480.3560.3560.0000.0000.0000.000
59A72ARG10.8020.89827.513-9.809-9.8090.0000.0000.0000.000
60A73SER00.0580.03325.9720.5410.5410.0000.0000.0000.000
61A74ARG10.8770.94625.747-10.390-10.3900.0000.0000.0000.000
62A75MET0-0.005-0.00224.4780.4320.4320.0000.0000.0000.000
63A76SER00.0210.02621.6700.8680.8680.0000.0000.0000.000
64A77VAL0-0.015-0.00120.8880.7280.7280.0000.0000.0000.000
65A78SER0-0.086-0.05321.4960.5840.5840.0000.0000.0000.000
66A79TYR0-0.0050.00414.4520.4010.4010.0000.0000.0000.000
67A80LEU00.0190.00415.7781.0141.0140.0000.0000.0000.000
68A81LYS10.9080.95316.730-12.897-12.8970.0000.0000.0000.000
69A82GLY0-0.034-0.00617.317-0.211-0.2110.0000.0000.0000.000
70A83TYR0-0.062-0.02911.1380.0560.0560.0000.0000.0000.000
71A84THR0-0.0020.00412.264-1.017-1.0170.0000.0000.0000.000
72A85TYR0-0.017-0.03112.0151.1661.1660.0000.0000.0000.000
73A86GLU-1-0.930-0.9749.04628.50528.5050.0000.0000.0000.000
74A87ASP-1-0.814-0.8567.56738.33538.3350.0000.0000.0000.000
75A88ILE0-0.042-0.0268.568-0.829-0.8290.0000.0000.0000.000
76A89LEU00.0130.0152.728-6.205-4.4711.040-1.083-1.6910.013
77A90ILE0-0.052-0.0397.154-3.754-3.7540.0000.0000.0000.000
78A91VAL00.0430.0235.7280.5840.5840.0000.0000.0000.000
79A92ARG10.8300.8937.915-23.919-23.9190.0000.0000.0000.000
80A93PHE00.0230.0078.9400.1580.1580.0000.0000.0000.000
81A94ARG10.8830.94512.054-19.389-19.3890.0000.0000.0000.000
82A95PRO00.0580.04714.9410.1320.1320.0000.0000.0000.000
83A96GLU-1-0.739-0.84418.05313.70813.7080.0000.0000.0000.000
84A97SER00.0260.02917.8231.1061.1060.0000.0000.0000.000
85A98GLU-1-0.960-0.98913.88917.96017.9600.0000.0000.0000.000
86A99ILE00.0080.00817.654-0.407-0.4070.0000.0000.0000.000
87A100TYR0-0.060-0.04320.724-0.059-0.0590.0000.0000.0000.000
88A101TRP00.0190.02824.453-0.120-0.1200.0000.0000.0000.000
89A102PRO0-0.078-0.04326.603-0.255-0.2550.0000.0000.0000.000
90A103ILE00.0520.00024.010-0.372-0.3720.0000.0000.0000.000
91A104SER0-0.055-0.06628.1820.0010.0010.0000.0000.0000.000
92A105GLN0-0.0190.00127.4030.2150.2150.0000.0000.0000.000
93A106ASP-1-0.738-0.84825.48511.43311.4330.0000.0000.0000.000
94A107SER0-0.015-0.03127.629-0.098-0.0980.0000.0000.0000.000
95A108ARG10.9610.98930.691-9.021-9.0210.0000.0000.0000.000
96A109ASN00.011-0.01031.927-0.117-0.1170.0000.0000.0000.000
97A110ALA00.0350.02632.457-0.163-0.1630.0000.0000.0000.000
98A111MET00.0070.01428.013-0.030-0.0300.0000.0000.0000.000
99A112ILE0-0.018-0.01032.317-0.131-0.1310.0000.0000.0000.000
100A113ASP-1-0.798-0.87335.2027.5787.5780.0000.0000.0000.000
101A114LYS10.9491.01631.136-9.774-9.7740.0000.0000.0000.000
102A115LEU0-0.018-0.00532.021-0.084-0.0840.0000.0000.0000.000
103A116SER00.0070.00435.775-0.193-0.1930.0000.0000.0000.000
104A117ARG10.8720.93338.332-7.786-7.7860.0000.0000.0000.000
105A118ASN0-0.077-0.08136.0010.1770.1770.0000.0000.0000.000
106A119THR00.0360.01732.2770.0070.0070.0000.0000.0000.000
107A120SER0-0.036-0.02731.1940.0550.0550.0000.0000.0000.000
108A121VAL00.0240.03025.666-0.170-0.1700.0000.0000.0000.000
109A122ASN00.0230.01424.7170.1390.1390.0000.0000.0000.000
110A123PHE00.0170.01118.8270.0620.0620.0000.0000.0000.000
111A124GLU-1-0.771-0.88817.19714.48114.4810.0000.0000.0000.000
112A125VAL0-0.042-0.01913.2740.1330.1330.0000.0000.0000.000
113A126SER00.0670.02310.749-0.071-0.0710.0000.0000.0000.000
114A127LEU0-0.102-0.0548.569-1.280-1.2800.0000.0000.0000.000
115A128GLU-1-0.855-0.9284.80648.57248.736-0.001-0.005-0.1580.000
116A129PHE0-0.055-0.0484.087-7.203-6.7890.000-0.069-0.3440.000
117A130THR00.0800.0362.576-6.846-0.9752.381-3.867-4.3840.013
118A131ARG10.9290.9592.174-92.074-90.2788.402-3.735-6.4630.030
119A132PRO0-0.021-0.0114.482-0.804-0.6950.000-0.026-0.0830.000
120A133TYR0-0.026-0.0268.254-0.979-0.9790.0000.0000.0000.000
121A134ASP-1-0.875-0.9409.98223.94323.9430.0000.0000.0000.000
122A135PRO00.0050.02113.354-1.376-1.3760.0000.0000.0000.000
123A136ASN0-0.046-0.03914.7210.9870.9870.0000.0000.0000.000
124A137GLU-1-0.894-0.93814.74919.05919.0590.0000.0000.0000.000
125A138ASN0-0.073-0.0158.6441.8611.8610.0000.0000.0000.000
126A139ALA00.0040.00710.553-2.341-2.3410.0000.0000.0000.000
127A140ALA0-0.041-0.02111.6140.3120.3120.0000.0000.0000.000
128A141LEU00.0640.0237.7402.3552.3550.0000.0000.0000.000
129A142LYS10.8890.9567.245-18.739-18.7390.0000.0000.0000.000
130A143HIS10.8660.9377.527-34.326-34.3260.0000.0000.0000.000
131A144SER00.006-0.0159.6271.3051.3050.0000.0000.0000.000
132A145LYS10.9380.98812.314-17.406-17.4060.0000.0000.0000.000
133A146SER00.0050.01115.0940.3420.3420.0000.0000.0000.000
134A147TRP0-0.018-0.01913.649-0.248-0.2480.0000.0000.0000.000
135A148LEU00.0330.02120.295-0.190-0.1900.0000.0000.0000.000
136A149VAL00.0290.00723.751-0.215-0.2150.0000.0000.0000.000
137A150PRO0-0.031-0.02126.275-0.216-0.2160.0000.0000.0000.000
138A151ILE0-0.0050.00529.011-0.112-0.1120.0000.0000.0000.000
139A152SER00.0340.01731.606-0.293-0.2930.0000.0000.0000.000
140A153LEU00.0350.01035.0570.0080.0080.0000.0000.0000.000
141A154ASP-1-0.853-0.92438.1057.5147.5140.0000.0000.0000.000
142A155MET00.0460.00638.3650.2220.2220.0000.0000.0000.000
143A156THR0-0.0220.00639.999-0.007-0.0070.0000.0000.0000.000
144A157ILE0-0.014-0.02533.0200.0830.0830.0000.0000.0000.000
145A158ARG10.7840.87734.575-8.444-8.4440.0000.0000.0000.000
146A159ALA00.0170.02636.1890.0910.0910.0000.0000.0000.000
147A160LYS10.9440.96335.495-8.463-8.4630.0000.0000.0000.000
148A161ILE00.0520.03130.5820.0930.0930.0000.0000.0000.000
149A162GLN0-0.032-0.02632.8570.0120.0120.0000.0000.0000.000
150A163SER0-0.073-0.04435.0230.0240.0240.0000.0000.0000.000
151A164ALA00.0780.04931.362-0.040-0.0400.0000.0000.0000.000
152A165LEU0-0.0030.00329.0180.1100.1100.0000.0000.0000.000
153A166ARG10.8950.93032.117-7.857-7.8570.0000.0000.0000.000
154A167GLY0-0.041-0.01233.166-0.173-0.1730.0000.0000.0000.000
155A168ASP-1-0.921-0.95034.1837.8127.8120.0000.0000.0000.000
156A169PRO00.0450.01734.1410.2510.2510.0000.0000.0000.000
157A170GLY00.0380.03233.804-0.194-0.1940.0000.0000.0000.000
158A171HIS10.7770.88433.572-8.411-8.4110.0000.0000.0000.000
159A172PRO00.0370.02529.4750.1480.1480.0000.0000.0000.000
160A173ILE0-0.039-0.01327.162-0.294-0.2940.0000.0000.0000.000
161A174LEU0-0.0110.00127.0270.3520.3520.0000.0000.0000.000
162A175ILE0-0.027-0.01623.395-0.312-0.3120.0000.0000.0000.000
163A176PRO00.0320.02224.5840.5550.5550.0000.0000.0000.000
164A177GLN0-0.032-0.02923.885-0.132-0.1320.0000.0000.0000.000
165A178SER0-0.030-0.02421.7890.2150.2150.0000.0000.0000.000
166A179ILE00.0110.00914.7810.6240.6240.0000.0000.0000.000
167A180PRO0-0.0280.01514.658-0.681-0.6810.0000.0000.0000.000
168A181ALA00.0540.01815.1580.9620.9620.0000.0000.0000.000
169A182PHE0-0.041-0.01813.3640.9150.9150.0000.0000.0000.000
170A183ILE0-0.004-0.0119.440-1.799-1.7990.0000.0000.0000.000
171A184GLN00.0060.01110.6210.4340.4340.0000.0000.0000.000
172A185VAL00.0180.0005.923-2.311-2.3110.0000.0000.0000.000
173A186PRO00.0160.0328.7851.1451.1450.0000.0000.0000.000
174A187ASN00.0370.00010.1163.6203.6200.0000.0000.0000.000
175A188GLN0-0.022-0.02011.636-0.088-0.0880.0000.0000.0000.000
176A189GLY0-0.0010.00114.318-0.260-0.2600.0000.0000.0000.000
177A190GLU-1-0.929-0.95012.59119.15719.1570.0000.0000.0000.000
178A191LEU0-0.0110.0028.8410.0230.0230.0000.0000.0000.000
179A192THR00.0010.00212.537-2.110-2.1100.0000.0000.0000.000
180A193LEU0-0.010-0.02013.9280.8120.8120.0000.0000.0000.000
181A194PRO00.0900.06614.564-0.597-0.5970.0000.0000.0000.000
182A195THR0-0.034-0.03417.074-0.754-0.7540.0000.0000.0000.000
183A196SER00.0210.00920.764-0.765-0.7650.0000.0000.0000.000
184A197ILE00.0640.03517.168-0.579-0.5790.0000.0000.0000.000
185A198GLY00.002-0.00120.495-0.394-0.3940.0000.0000.0000.000
186A199ASN0-0.038-0.03921.803-0.707-0.7070.0000.0000.0000.000
187A200THR0-0.025-0.01923.615-0.614-0.6140.0000.0000.0000.000
188A201ILE0-0.046-0.01720.433-0.350-0.3500.0000.0000.0000.000
189A202ILE0-0.111-0.04024.916-0.383-0.3830.0000.0000.0000.000
190A203ASN0-0.085-0.04727.472-0.057-0.0570.0000.0000.0000.000
191A204ASP-1-0.740-0.84727.81110.18610.1860.0000.0000.0000.000
192A220ALA00.0460.05221.6210.1150.1150.0000.0000.0000.000
193A221ARG10.8930.92422.818-12.275-12.2750.0000.0000.0000.000
194A222ALA00.004-0.01524.2570.1720.1720.0000.0000.0000.000
195A223TRP00.0260.01016.948-0.335-0.3350.0000.0000.0000.000
196A224PHE0-0.043-0.01718.9680.5790.5790.0000.0000.0000.000
197A225ASP-1-0.772-0.87319.00614.84514.8450.0000.0000.0000.000
198A226SER0-0.018-0.00321.598-0.119-0.1190.0000.0000.0000.000
199A227LEU00.0100.00118.6100.1750.1750.0000.0000.0000.000
200A228THR00.0090.00022.749-0.770-0.7700.0000.0000.0000.000
201A229LEU0-0.033-0.00521.5810.3040.3040.0000.0000.0000.000
202A230ASN00.0550.01025.116-0.891-0.8910.0000.0000.0000.000
203A231LEU0-0.023-0.00626.3090.3380.3380.0000.0000.0000.000
204A232GLU-1-0.870-0.95426.6329.8899.8890.0000.0000.0000.000
205A233GLN0-0.066-0.03428.5150.1740.1740.0000.0000.0000.000
206A234GLY0-0.016-0.00429.5710.2210.2210.0000.0000.0000.000
207A235LYS10.8690.93725.949-10.509-10.5090.0000.0000.0000.000
208A236SER00.0280.01531.616-0.019-0.0190.0000.0000.0000.000
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