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: 8N9GY

Calculation Name: 1ZCJ-A-Xray372

Preferred Name: Enoyl-CoA hydratase

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1ZCJ

Chain ID: A

ChEMBL ID: CHEMBL3232

UniProt ID: P07896

Base Structure: X-ray

Registration Date: 2023-09-27

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 459
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -8647784.116858
FMO2-HF: Nuclear repulsion 8471432.787814
FMO2-HF: Total energy -176351.329044
FMO2-MP2: Total energy -176870.282254


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:261:SER)


Summations of interaction energy for fragment #1(A:261:SER)
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.
-24.416-21.58810.67-5.742-7.7550.043
Interaction energy analysis for fragmet #1(A:261:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.066 / q_NPA : 0.032
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].
3A263GLN00.0700.0322.718-2.620-0.2550.873-1.263-1.9750.008
4A264ALA0-0.007-0.0081.913-9.164-10.8969.035-3.450-3.8530.026
5A265LYS10.9400.9672.756-10.880-8.8170.763-1.019-1.8070.009
6A266ALA00.0460.0275.213-0.639-0.507-0.001-0.010-0.1200.000
7A267LEU0-0.0220.0005.732-0.485-0.4850.0000.0000.0000.000
8A268GLN00.0110.0157.398-0.304-0.3040.0000.0000.0000.000
9A269TYR0-0.108-0.1049.013-0.102-0.1020.0000.0000.0000.000
10A270ALA00.027-0.00111.005-0.109-0.1090.0000.0000.0000.000
11A271PHE0-0.068-0.03310.472-0.085-0.0850.0000.0000.0000.000
12A272PHE00.0210.00012.652-0.039-0.0390.0000.0000.0000.000
13A273ALA00.0630.05315.050-0.014-0.0140.0000.0000.0000.000
14A274GLU-1-0.833-0.91616.4360.0920.0920.0000.0000.0000.000
15A275LYS10.9280.95518.382-0.104-0.1040.0000.0000.0000.000
16A276SER0-0.051-0.03618.394-0.012-0.0120.0000.0000.0000.000
17A277ALA00.0660.04420.308-0.005-0.0050.0000.0000.0000.000
18A278ASN0-0.033-0.02123.285-0.017-0.0170.0000.0000.0000.000
19A279LYS10.8740.94619.389-0.257-0.2570.0000.0000.0000.000
20A280TRP00.0590.04125.1460.0160.0160.0000.0000.0000.000
21A281SER00.017-0.01927.801-0.001-0.0010.0000.0000.0000.000
22A282THR00.0090.00930.1200.0050.0050.0000.0000.0000.000
23A283PRO00.0860.03832.4160.0000.0000.0000.0000.0000.000
24A284SER0-0.034-0.01033.8490.0010.0010.0000.0000.0000.000
25A285GLY00.0540.03233.891-0.004-0.0040.0000.0000.0000.000
26A286ALA0-0.0240.00134.722-0.003-0.0030.0000.0000.0000.000
27A287SER00.015-0.00629.9280.0110.0110.0000.0000.0000.000
28A288TRP0-0.026-0.00625.202-0.005-0.0050.0000.0000.0000.000
29A289LYS10.9110.94527.089-0.170-0.1700.0000.0000.0000.000
30A290THR00.0250.00430.848-0.004-0.0040.0000.0000.0000.000
31A291ALA0-0.0420.01133.843-0.007-0.0070.0000.0000.0000.000
32A292SER00.003-0.00334.463-0.001-0.0010.0000.0000.0000.000
33A293ALA0-0.032-0.02834.9740.0000.0000.0000.0000.0000.000
34A294GLN00.0220.00536.913-0.005-0.0050.0000.0000.0000.000
35A295PRO0-0.035-0.02739.2780.0010.0010.0000.0000.0000.000
36A296VAL00.0180.01739.1990.0000.0000.0000.0000.0000.000
37A297SER0-0.093-0.04440.166-0.002-0.0020.0000.0000.0000.000
38A298SER0-0.003-0.00142.616-0.003-0.0030.0000.0000.0000.000
39A299VAL00.021-0.00839.7780.0030.0030.0000.0000.0000.000
40A300GLY00.0220.00943.159-0.003-0.0030.0000.0000.0000.000
41A301VAL0-0.035-0.01440.5970.0030.0030.0000.0000.0000.000
42A302LEU00.0380.02743.395-0.003-0.0030.0000.0000.0000.000
43A303GLY00.0290.01944.3740.0030.0030.0000.0000.0000.000
44A304LEU0-0.049-0.04242.9860.0010.0010.0000.0000.0000.000
45A305GLY00.1000.03342.536-0.003-0.0030.0000.0000.0000.000
46A306THR0-0.041-0.04336.796-0.002-0.0020.0000.0000.0000.000
47A307MET00.0090.01334.553-0.001-0.0010.0000.0000.0000.000
48A308GLY00.1050.05537.6040.0000.0000.0000.0000.0000.000
49A309ARG10.8990.96639.535-0.020-0.0200.0000.0000.0000.000
50A310GLY00.0170.01635.492-0.003-0.0030.0000.0000.0000.000
51A311ILE00.0160.01535.605-0.001-0.0010.0000.0000.0000.000
52A312ALA00.0250.00336.860-0.001-0.0010.0000.0000.0000.000
53A313ILE0-0.021-0.01635.397-0.002-0.0020.0000.0000.0000.000
54A314SER0-0.017-0.03433.525-0.002-0.0020.0000.0000.0000.000
55A315PHE00.0240.00535.025-0.001-0.0010.0000.0000.0000.000
56A316ALA0-0.005-0.00337.643-0.002-0.0020.0000.0000.0000.000
57A317ARG10.7300.80431.802-0.010-0.0100.0000.0000.0000.000
58A318VAL0-0.033-0.00633.441-0.004-0.0040.0000.0000.0000.000
59A319GLY0-0.050-0.01336.6260.0010.0010.0000.0000.0000.000
60A320ILE0-0.018-0.00437.1380.0010.0010.0000.0000.0000.000
61A321SER0-0.036-0.03240.949-0.003-0.0030.0000.0000.0000.000
62A322VAL0-0.019-0.00841.0040.0030.0030.0000.0000.0000.000
63A323VAL0-0.033-0.00944.245-0.003-0.0030.0000.0000.0000.000
64A324ALA00.0070.00744.3700.0030.0030.0000.0000.0000.000
65A325VAL00.000-0.02246.013-0.002-0.0020.0000.0000.0000.000
66A326GLU-1-0.817-0.89947.0390.0270.0270.0000.0000.0000.000
67A327SER00.0240.01149.077-0.001-0.0010.0000.0000.0000.000
68A328ASP-1-0.845-0.92350.4580.0170.0170.0000.0000.0000.000
69A329PRO00.0380.01851.371-0.001-0.0010.0000.0000.0000.000
70A330LYS11.0061.01150.143-0.012-0.0120.0000.0000.0000.000
71A331GLN0-0.0090.00045.370-0.003-0.0030.0000.0000.0000.000
72A332LEU0-0.010-0.00647.536-0.001-0.0010.0000.0000.0000.000
73A333ASP-1-0.958-0.97748.6270.0040.0040.0000.0000.0000.000
74A334ALA00.0230.00346.256-0.002-0.0020.0000.0000.0000.000
75A335ALA0-0.032-0.03344.218-0.001-0.0010.0000.0000.0000.000
76A336LYS10.9340.97244.314-0.009-0.0090.0000.0000.0000.000
77A337LYS10.9850.99745.705-0.001-0.0010.0000.0000.0000.000
78A338ILE0-0.0080.00340.115-0.002-0.0020.0000.0000.0000.000
79A339ILE0-0.0300.00540.653-0.001-0.0010.0000.0000.0000.000
80A340THR0-0.0040.00141.059-0.002-0.0020.0000.0000.0000.000
81A341PHE00.0350.02939.346-0.003-0.0030.0000.0000.0000.000
82A342THR0-0.062-0.05736.191-0.003-0.0030.0000.0000.0000.000
83A343LEU00.013-0.00237.713-0.003-0.0030.0000.0000.0000.000
84A344GLU-1-0.898-0.94439.245-0.014-0.0140.0000.0000.0000.000
85A345LYS10.9130.97233.9810.0190.0190.0000.0000.0000.000
86A346GLU-1-0.842-0.90533.789-0.009-0.0090.0000.0000.0000.000
87A347ALA00.0320.02835.958-0.004-0.0040.0000.0000.0000.000
88A348SER0-0.017-0.01738.620-0.005-0.0050.0000.0000.0000.000
89A349ARG10.9140.95831.0730.0510.0510.0000.0000.0000.000
90A350ALA00.0220.00834.379-0.005-0.0050.0000.0000.0000.000
91A351HIS00.0270.01935.394-0.004-0.0040.0000.0000.0000.000
92A352GLN0-0.068-0.03036.331-0.005-0.0050.0000.0000.0000.000
93A353ASN0-0.063-0.03730.612-0.009-0.0090.0000.0000.0000.000
94A354GLY00.0120.02234.164-0.004-0.0040.0000.0000.0000.000
95A355GLN0-0.074-0.04432.4600.0000.0000.0000.0000.0000.000
96A356ALA00.0080.00635.9430.0030.0030.0000.0000.0000.000
97A357SER00.026-0.00337.1790.0020.0020.0000.0000.0000.000
98A358ALA0-0.025-0.00239.1860.0000.0000.0000.0000.0000.000
99A359LYS10.9790.98641.3760.0080.0080.0000.0000.0000.000
100A360PRO00.0370.02040.9900.0020.0020.0000.0000.0000.000
101A361LYS10.9280.98442.861-0.005-0.0050.0000.0000.0000.000
102A362LEU00.0200.01743.1060.0030.0030.0000.0000.0000.000
103A363ARG10.8390.91745.784-0.017-0.0170.0000.0000.0000.000
104A364PHE00.0350.00444.9770.0020.0020.0000.0000.0000.000
105A365SER00.0060.00349.663-0.001-0.0010.0000.0000.0000.000
106A366SER00.0350.02751.0740.0010.0010.0000.0000.0000.000
107A367SER00.002-0.01253.5540.0020.0020.0000.0000.0000.000
108A368THR00.034-0.07150.989-0.001-0.0010.0000.0000.0000.000
109A369LYS11.0131.00952.578-0.018-0.0180.0000.0000.0000.000
110A370GLU-1-0.895-0.92152.5450.0150.0150.0000.0000.0000.000
111A371LEU0-0.027-0.02247.907-0.001-0.0010.0000.0000.0000.000
112A372SER00.0210.01950.4350.0020.0020.0000.0000.0000.000
113A373THR00.001-0.00651.3660.0010.0010.0000.0000.0000.000
114A374VAL0-0.010-0.00545.8540.0000.0000.0000.0000.0000.000
115A375ASP-1-0.776-0.87443.6620.0300.0300.0000.0000.0000.000
116A376LEU0-0.025-0.00738.9160.0030.0030.0000.0000.0000.000
117A377VAL00.0060.00943.373-0.003-0.0030.0000.0000.0000.000
118A378VAL0-0.003-0.00238.2240.0040.0040.0000.0000.0000.000
119A379GLU-1-0.705-0.82341.3220.0460.0460.0000.0000.0000.000
120A380ALA0-0.052-0.03840.0090.0050.0050.0000.0000.0000.000
121A381VAL0-0.035-0.02041.751-0.003-0.0030.0000.0000.0000.000
122A382PHE0-0.003-0.00843.5520.0030.0030.0000.0000.0000.000
123A383GLU-1-0.735-0.87140.4530.0650.0650.0000.0000.0000.000
124A384ASP-1-0.818-0.90243.4620.0430.0430.0000.0000.0000.000
125A385MET00.0460.03044.539-0.002-0.0020.0000.0000.0000.000
126A386ASN00.0300.04547.342-0.001-0.0010.0000.0000.0000.000
127A387LEU00.0350.00347.843-0.001-0.0010.0000.0000.0000.000
128A388LYS10.8000.90642.241-0.051-0.0510.0000.0000.0000.000
129A389LYS10.9750.99147.493-0.052-0.0520.0000.0000.0000.000
130A390LYS10.8700.92249.952-0.036-0.0360.0000.0000.0000.000
131A391VAL00.0130.00847.859-0.001-0.0010.0000.0000.0000.000
132A392PHE0-0.012-0.03643.311-0.001-0.0010.0000.0000.0000.000
133A393ALA00.0270.03549.2150.0000.0000.0000.0000.0000.000
134A394GLU-1-0.850-0.86452.6370.0280.0280.0000.0000.0000.000
135A395LEU0-0.026-0.04247.100-0.001-0.0010.0000.0000.0000.000
136A396SER0-0.059-0.02750.4860.0000.0000.0000.0000.0000.000
137A397ALA00.0270.03151.773-0.001-0.0010.0000.0000.0000.000
138A398LEU0-0.065-0.03453.673-0.002-0.0020.0000.0000.0000.000
139A399CYS0-0.076-0.02749.584-0.001-0.0010.0000.0000.0000.000
140A400LYS10.8890.97847.788-0.027-0.0270.0000.0000.0000.000
141A401PRO00.0840.03150.4050.0020.0020.0000.0000.0000.000
142A402GLY0-0.006-0.00647.622-0.001-0.0010.0000.0000.0000.000
143A403ALA0-0.049-0.01245.8300.0020.0020.0000.0000.0000.000
144A404PHE00.014-0.00541.5970.0020.0020.0000.0000.0000.000
145A405LEU0-0.0050.00843.508-0.003-0.0030.0000.0000.0000.000
146A406CYS0-0.010-0.00238.9270.0040.0040.0000.0000.0000.000
147A407THR0-0.018-0.00940.093-0.003-0.0030.0000.0000.0000.000
148A408ASN00.0330.01035.8860.0080.0080.0000.0000.0000.000
149A409THR0-0.076-0.03937.4550.0020.0020.0000.0000.0000.000
150A410SER00.0220.00535.2790.0030.0030.0000.0000.0000.000
151A411ALA0-0.091-0.04835.8910.0060.0060.0000.0000.0000.000
152A412LEU0-0.053-0.01838.460-0.001-0.0010.0000.0000.0000.000
153A413ASN00.0780.06039.7860.0060.0060.0000.0000.0000.000
154A414VAL00.0640.01238.789-0.005-0.0050.0000.0000.0000.000
155A415ASP-1-0.805-0.89741.6240.0790.0790.0000.0000.0000.000
156A416ASP-1-0.908-0.95743.7040.0610.0610.0000.0000.0000.000
157A417ILE0-0.038-0.01942.640-0.004-0.0040.0000.0000.0000.000
158A418ALA00.0090.00844.081-0.003-0.0030.0000.0000.0000.000
159A419SER0-0.073-0.00746.104-0.003-0.0030.0000.0000.0000.000
160A420SER0-0.028-0.01749.058-0.002-0.0020.0000.0000.0000.000
161A421THR0-0.059-0.06147.821-0.002-0.0020.0000.0000.0000.000
162A422ASP-1-0.864-0.92750.6220.0400.0400.0000.0000.0000.000
163A423ARG10.7870.84647.480-0.039-0.0390.0000.0000.0000.000
164A424PRO00.0560.04446.2820.0020.0020.0000.0000.0000.000
165A425GLN00.0430.00743.8180.0040.0040.0000.0000.0000.000
166A426LEU0-0.0570.01342.6210.0040.0040.0000.0000.0000.000
167A427VAL00.0140.02842.872-0.002-0.0020.0000.0000.0000.000
168A428ILE0-0.0370.00335.5310.0050.0050.0000.0000.0000.000
169A429GLY00.0520.04237.476-0.005-0.0050.0000.0000.0000.000
170A430THR0-0.050-0.05734.5200.0040.0040.0000.0000.0000.000
171A431HIS0-0.0220.01130.884-0.014-0.0140.0000.0000.0000.000
172A432PHE00.015-0.03731.5240.0060.0060.0000.0000.0000.000
173A433PHE00.0440.02627.468-0.001-0.0010.0000.0000.0000.000
174A434SER0-0.0120.00630.269-0.010-0.0100.0000.0000.0000.000
175A435PRO00.019-0.00429.2270.0040.0040.0000.0000.0000.000
176A436ALA00.0980.04930.753-0.001-0.0010.0000.0000.0000.000
177A437HIS00.0040.02732.3220.0060.0060.0000.0000.0000.000
178A438VAL0-0.051-0.01627.146-0.006-0.0060.0000.0000.0000.000
179A439MET0-0.027-0.00225.196-0.002-0.0020.0000.0000.0000.000
180A440ARG10.9050.94520.026-0.075-0.0750.0000.0000.0000.000
181A441LEU0-0.0360.03924.0500.0030.0030.0000.0000.0000.000
182A442LEU0-0.028-0.01326.468-0.010-0.0100.0000.0000.0000.000
183A443GLU-1-0.697-0.83728.3930.1430.1430.0000.0000.0000.000
184A444VAL0-0.003-0.01330.111-0.012-0.0120.0000.0000.0000.000
185A445ILE0-0.0140.00132.1460.0080.0080.0000.0000.0000.000
186A446PRO0-0.014-0.01033.618-0.008-0.0080.0000.0000.0000.000
187A447SER00.0600.03336.7880.0030.0030.0000.0000.0000.000
188A448ARG10.8850.92339.469-0.073-0.0730.0000.0000.0000.000
189A449TYR0-0.022-0.02641.2230.0000.0000.0000.0000.0000.000
190A450SER0-0.061-0.02738.775-0.001-0.0010.0000.0000.0000.000
191A451SER00.0450.03039.8200.0040.0040.0000.0000.0000.000
192A452PRO00.0650.00036.6870.0020.0020.0000.0000.0000.000
193A453THR00.0340.02636.6270.0030.0030.0000.0000.0000.000
194A454THR00.002-0.02038.117-0.003-0.0030.0000.0000.0000.000
195A455ILE00.0120.01532.9150.0000.0000.0000.0000.0000.000
196A456ALA00.001-0.00133.3270.0020.0020.0000.0000.0000.000
197A457THR00.016-0.00434.002-0.003-0.0030.0000.0000.0000.000
198A458VAL00.0480.03633.450-0.004-0.0040.0000.0000.0000.000
199A459MET0-0.0560.02927.596-0.003-0.0030.0000.0000.0000.000
200A460SER0-0.073-0.04230.685-0.003-0.0030.0000.0000.0000.000
201A461LEU00.0100.00132.464-0.005-0.0050.0000.0000.0000.000
202A462SER00.010-0.03329.878-0.004-0.0040.0000.0000.0000.000
203A463LYS10.9480.98126.711-0.077-0.0770.0000.0000.0000.000
204A464LYS10.8840.95329.363-0.045-0.0450.0000.0000.0000.000
205A465ILE0-0.0060.00931.734-0.007-0.0070.0000.0000.0000.000
206A466GLY0-0.038-0.00928.224-0.003-0.0030.0000.0000.0000.000
207A467LYS10.7570.86527.244-0.046-0.0460.0000.0000.0000.000
208A468ILE0-0.080-0.04721.9540.0020.0020.0000.0000.0000.000
209A469GLY00.0430.02125.9030.0010.0010.0000.0000.0000.000
210A470VAL0-0.029-0.03124.3960.0110.0110.0000.0000.0000.000
211A471VAL0-0.015-0.00727.068-0.007-0.0070.0000.0000.0000.000
212A472VAL0-0.051-0.02827.7050.0150.0150.0000.0000.0000.000
213A473GLY0-0.004-0.02530.251-0.010-0.0100.0000.0000.0000.000
214A474ASN00.018-0.02633.036-0.001-0.0010.0000.0000.0000.000
215A475CYS00.0040.02833.1510.0010.0010.0000.0000.0000.000
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