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: J2Q49

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 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 459
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -8585125.180635
FMO2-HF: Nuclear repulsion 8408768.981015
FMO2-HF: Total energy -176356.19962
FMO2-MP2: Total energy -176874.070133


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.
-33.916-32.48812.597-7.027-6.9990.061
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 : 0.080 / q_NPA : 0.045
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].
3A263GLN00.0850.0383.344-2.492-0.5630.038-0.833-1.1340.004
4A264ALA00.0050.0012.291-4.684-2.7711.540-1.520-1.9330.008
5A265LYS10.9180.9401.974-26.737-29.15111.019-4.674-3.9320.049
6A266ALA00.0210.0235.515-0.106-0.1060.0000.0000.0000.000
7A267LEU0-0.015-0.0086.640-0.199-0.1990.0000.0000.0000.000
8A268GLN00.0050.0047.801-0.133-0.1330.0000.0000.0000.000
9A269TYR0-0.080-0.0669.3860.0040.0040.0000.0000.0000.000
10A270ALA00.0320.00611.338-0.051-0.0510.0000.0000.0000.000
11A271PHE0-0.060-0.02511.554-0.038-0.0380.0000.0000.0000.000
12A272PHE0-0.019-0.01613.144-0.008-0.0080.0000.0000.0000.000
13A273ALA00.0780.05315.4170.0120.0120.0000.0000.0000.000
14A274GLU-1-0.771-0.84916.8020.0270.0270.0000.0000.0000.000
15A275LYS10.8400.89918.711-0.035-0.0350.0000.0000.0000.000
16A276SER0-0.031-0.03918.7660.0000.0000.0000.0000.0000.000
17A277ALA00.0310.01620.6830.0000.0000.0000.0000.0000.000
18A278ASN0-0.017-0.00923.693-0.023-0.0230.0000.0000.0000.000
19A279LYS10.8610.94219.159-0.287-0.2870.0000.0000.0000.000
20A280TRP00.0430.02625.1540.0210.0210.0000.0000.0000.000
21A281SER00.027-0.00827.8380.0000.0000.0000.0000.0000.000
22A282THR00.0250.02830.3930.0020.0020.0000.0000.0000.000
23A283PRO00.0730.02732.5080.0000.0000.0000.0000.0000.000
24A284SER0-0.029-0.01034.194-0.003-0.0030.0000.0000.0000.000
25A285GLY00.0450.02934.322-0.004-0.0040.0000.0000.0000.000
26A286ALA0-0.038-0.00934.690-0.001-0.0010.0000.0000.0000.000
27A287SER00.001-0.03629.8900.0110.0110.0000.0000.0000.000
28A288TRP0-0.026-0.00225.224-0.008-0.0080.0000.0000.0000.000
29A289LYS10.9280.96327.968-0.174-0.1740.0000.0000.0000.000
30A290THR00.0130.00531.341-0.004-0.0040.0000.0000.0000.000
31A291ALA0-0.0140.01434.277-0.006-0.0060.0000.0000.0000.000
32A292SER00.0250.01934.9130.0000.0000.0000.0000.0000.000
33A293ALA0-0.044-0.03835.6280.0000.0000.0000.0000.0000.000
34A294GLN00.0420.01637.578-0.005-0.0050.0000.0000.0000.000
35A295PRO0-0.019-0.01639.6290.0000.0000.0000.0000.0000.000
36A296VAL0-0.017-0.00639.6270.0010.0010.0000.0000.0000.000
37A297SER0-0.087-0.04340.675-0.003-0.0030.0000.0000.0000.000
38A298SER0-0.014-0.01643.296-0.004-0.0040.0000.0000.0000.000
39A299VAL00.010-0.00440.4950.0030.0030.0000.0000.0000.000
40A300GLY00.0320.01243.886-0.003-0.0030.0000.0000.0000.000
41A301VAL0-0.052-0.03041.5840.0030.0030.0000.0000.0000.000
42A302LEU00.0340.02944.259-0.003-0.0030.0000.0000.0000.000
43A303GLY00.0470.02545.6480.0040.0040.0000.0000.0000.000
44A304LEU0-0.061-0.04643.967-0.001-0.0010.0000.0000.0000.000
45A305GLY00.0830.03943.453-0.003-0.0030.0000.0000.0000.000
46A306THR0-0.049-0.04637.521-0.002-0.0020.0000.0000.0000.000
47A307MET0-0.0040.01734.321-0.004-0.0040.0000.0000.0000.000
48A308GLY00.1140.04838.402-0.001-0.0010.0000.0000.0000.000
49A309ARG10.8640.92740.382-0.009-0.0090.0000.0000.0000.000
50A310GLY00.0400.01436.407-0.003-0.0030.0000.0000.0000.000
51A311ILE00.0000.01136.326-0.003-0.0030.0000.0000.0000.000
52A312ALA00.0270.00837.654-0.002-0.0020.0000.0000.0000.000
53A313ILE0-0.017-0.01236.345-0.002-0.0020.0000.0000.0000.000
54A314SER0-0.024-0.02934.220-0.004-0.0040.0000.0000.0000.000
55A315PHE00.0250.00135.765-0.001-0.0010.0000.0000.0000.000
56A316ALA00.0230.01238.281-0.002-0.0020.0000.0000.0000.000
57A317ARG10.7680.83432.2180.0170.0170.0000.0000.0000.000
58A318VAL0-0.034-0.00433.889-0.005-0.0050.0000.0000.0000.000
59A319GLY0-0.0070.00937.1560.0010.0010.0000.0000.0000.000
60A320ILE0-0.014-0.00437.4840.0020.0020.0000.0000.0000.000
61A321SER0-0.048-0.05141.417-0.003-0.0030.0000.0000.0000.000
62A322VAL0-0.0120.00541.7760.0030.0030.0000.0000.0000.000
63A323VAL0-0.011-0.00844.785-0.002-0.0020.0000.0000.0000.000
64A324ALA00.0180.02045.2730.0030.0030.0000.0000.0000.000
65A325VAL0-0.019-0.02446.823-0.002-0.0020.0000.0000.0000.000
66A326GLU-1-0.820-0.92247.7940.0200.0200.0000.0000.0000.000
67A327SER00.0250.00550.136-0.001-0.0010.0000.0000.0000.000
68A328ASP-1-0.806-0.88451.5450.0100.0100.0000.0000.0000.000
69A329PRO00.036-0.00252.482-0.001-0.0010.0000.0000.0000.000
70A330LYS10.9600.98951.162-0.006-0.0060.0000.0000.0000.000
71A331GLN0-0.004-0.00746.031-0.003-0.0030.0000.0000.0000.000
72A332LEU00.0020.00648.394-0.002-0.0020.0000.0000.0000.000
73A333ASP-1-0.850-0.90549.887-0.006-0.0060.0000.0000.0000.000
74A334ALA00.0100.00147.119-0.002-0.0020.0000.0000.0000.000
75A335ALA0-0.027-0.01545.254-0.002-0.0020.0000.0000.0000.000
76A336LYS10.9470.98545.575-0.002-0.0020.0000.0000.0000.000
77A337LYS10.8690.93846.9900.0050.0050.0000.0000.0000.000
78A338ILE0-0.001-0.00141.294-0.002-0.0020.0000.0000.0000.000
79A339ILE0-0.030-0.00341.747-0.002-0.0020.0000.0000.0000.000
80A340THR0-0.016-0.01842.171-0.002-0.0020.0000.0000.0000.000
81A341PHE00.0580.03840.976-0.003-0.0030.0000.0000.0000.000
82A342THR0-0.077-0.05437.326-0.005-0.0050.0000.0000.0000.000
83A343LEU00.0010.00138.737-0.004-0.0040.0000.0000.0000.000
84A344GLU-1-0.882-0.94040.260-0.029-0.0290.0000.0000.0000.000
85A345LYS10.9270.98935.7650.0380.0380.0000.0000.0000.000
86A346GLU-1-0.844-0.90534.741-0.033-0.0330.0000.0000.0000.000
87A347ALA00.0290.01636.705-0.006-0.0060.0000.0000.0000.000
88A348SER0-0.023-0.03239.303-0.005-0.0050.0000.0000.0000.000
89A349ARG10.8420.91033.2260.0760.0760.0000.0000.0000.000
90A350ALA00.0070.00334.930-0.007-0.0070.0000.0000.0000.000
91A351HIS00.0280.01535.952-0.004-0.0040.0000.0000.0000.000
92A352GLN00.0130.01337.202-0.005-0.0050.0000.0000.0000.000
93A353ASN0-0.077-0.04330.970-0.009-0.0090.0000.0000.0000.000
94A354GLY00.0360.04234.512-0.006-0.0060.0000.0000.0000.000
95A355GLN0-0.066-0.04232.918-0.002-0.0020.0000.0000.0000.000
96A356ALA00.0320.01036.4080.0030.0030.0000.0000.0000.000
97A357SER0-0.0110.00138.5010.0030.0030.0000.0000.0000.000
98A358ALA0-0.0020.00539.4280.0020.0020.0000.0000.0000.000
99A359LYS10.9730.97841.8810.0190.0190.0000.0000.0000.000
100A360PRO00.0250.01241.3980.0020.0020.0000.0000.0000.000
101A361LYS10.8740.94943.2940.0060.0060.0000.0000.0000.000
102A362LEU0-0.0040.00043.9920.0030.0030.0000.0000.0000.000
103A363ARG10.8170.91546.633-0.008-0.0080.0000.0000.0000.000
104A364PHE00.0500.00646.0600.0020.0020.0000.0000.0000.000
105A365SER00.0050.00050.574-0.001-0.0010.0000.0000.0000.000
106A366SER00.0460.01852.0200.0000.0000.0000.0000.0000.000
107A367SER0-0.056-0.01454.4150.0020.0020.0000.0000.0000.000
108A368THR00.050-0.02952.165-0.001-0.0010.0000.0000.0000.000
109A369LYS11.0131.00953.232-0.014-0.0140.0000.0000.0000.000
110A370GLU-1-0.835-0.89052.7230.0090.0090.0000.0000.0000.000
111A371LEU0-0.0170.00048.316-0.001-0.0010.0000.0000.0000.000
112A372SER00.0460.01950.8760.0010.0010.0000.0000.0000.000
113A373THR00.0020.00152.1270.0010.0010.0000.0000.0000.000
114A374VAL0-0.0040.01246.539-0.001-0.0010.0000.0000.0000.000
115A375ASP-1-0.737-0.84144.1090.0200.0200.0000.0000.0000.000
116A376LEU0-0.030-0.01039.5250.0040.0040.0000.0000.0000.000
117A377VAL00.0220.01343.884-0.004-0.0040.0000.0000.0000.000
118A378VAL0-0.028-0.01138.9830.0040.0040.0000.0000.0000.000
119A379GLU-1-0.741-0.83542.0550.0390.0390.0000.0000.0000.000
120A380ALA0-0.021-0.02340.9690.0040.0040.0000.0000.0000.000
121A381VAL0-0.015-0.00142.530-0.003-0.0030.0000.0000.0000.000
122A382PHE0-0.004-0.01444.1620.0030.0030.0000.0000.0000.000
123A383GLU-1-0.736-0.84240.2250.0580.0580.0000.0000.0000.000
124A384ASP-1-0.789-0.88744.3270.0410.0410.0000.0000.0000.000
125A385MET00.0400.04745.173-0.002-0.0020.0000.0000.0000.000
126A386ASN0-0.011-0.01748.137-0.001-0.0010.0000.0000.0000.000
127A387LEU0-0.019-0.01148.609-0.001-0.0010.0000.0000.0000.000
128A388LYS10.7810.88942.809-0.045-0.0450.0000.0000.0000.000
129A389LYS10.8490.89448.126-0.052-0.0520.0000.0000.0000.000
130A390LYS10.8900.94850.631-0.034-0.0340.0000.0000.0000.000
131A391VAL00.0330.01548.518-0.001-0.0010.0000.0000.0000.000
132A392PHE00.002-0.01543.806-0.001-0.0010.0000.0000.0000.000
133A393ALA00.0480.04549.8340.0000.0000.0000.0000.0000.000
134A394GLU-1-0.893-0.91853.4010.0220.0220.0000.0000.0000.000
135A395LEU0-0.010-0.03047.619-0.002-0.0020.0000.0000.0000.000
136A396SER0-0.033-0.03051.3440.0000.0000.0000.0000.0000.000
137A397ALA0-0.0230.00052.627-0.001-0.0010.0000.0000.0000.000
138A398LEU0-0.054-0.02254.187-0.002-0.0020.0000.0000.0000.000
139A399CYS0-0.097-0.03750.071-0.002-0.0020.0000.0000.0000.000
140A400LYS10.8650.91848.303-0.019-0.0190.0000.0000.0000.000
141A401PRO00.0560.01251.0440.0020.0020.0000.0000.0000.000
142A402GLY0-0.0070.00048.141-0.001-0.0010.0000.0000.0000.000
143A403ALA0-0.033-0.00246.4490.0010.0010.0000.0000.0000.000
144A404PHE00.013-0.00642.2910.0020.0020.0000.0000.0000.000
145A405LEU00.0040.00144.022-0.003-0.0030.0000.0000.0000.000
146A406CYS0-0.019-0.00539.2660.0050.0050.0000.0000.0000.000
147A407THR0-0.005-0.01240.443-0.002-0.0020.0000.0000.0000.000
148A408ASN0-0.017-0.01436.6890.0050.0050.0000.0000.0000.000
149A409THR0-0.022-0.03139.020-0.001-0.0010.0000.0000.0000.000
150A410SER0-0.070-0.06135.8390.0040.0040.0000.0000.0000.000
151A411ALA0-0.039-0.02936.1150.0070.0070.0000.0000.0000.000
152A412LEU0-0.047-0.01238.7530.0010.0010.0000.0000.0000.000
153A413ASN00.0550.01740.6510.0060.0060.0000.0000.0000.000
154A414VAL00.0600.02339.047-0.005-0.0050.0000.0000.0000.000
155A415ASP-1-0.792-0.90141.9230.0790.0790.0000.0000.0000.000
156A416ASP-1-0.816-0.87144.1550.0570.0570.0000.0000.0000.000
157A417ILE00.0050.01843.168-0.004-0.0040.0000.0000.0000.000
158A418ALA00.0110.00244.313-0.003-0.0030.0000.0000.0000.000
159A419SER0-0.067-0.04546.385-0.003-0.0030.0000.0000.0000.000
160A420SER0-0.050-0.02249.378-0.002-0.0020.0000.0000.0000.000
161A421THR0-0.043-0.03748.407-0.002-0.0020.0000.0000.0000.000
162A422ASP-1-0.773-0.86251.2660.0370.0370.0000.0000.0000.000
163A423ARG10.7500.85947.840-0.033-0.0330.0000.0000.0000.000
164A424PRO00.0480.02646.8170.0020.0020.0000.0000.0000.000
165A425GLN00.0300.01144.3470.0040.0040.0000.0000.0000.000
166A426LEU0-0.0310.00943.0840.0030.0030.0000.0000.0000.000
167A427VAL00.0280.04043.202-0.002-0.0020.0000.0000.0000.000
168A428ILE0-0.0350.00135.8870.0050.0050.0000.0000.0000.000
169A429GLY00.0410.02837.804-0.005-0.0050.0000.0000.0000.000
170A430THR0-0.039-0.03934.9510.0030.0030.0000.0000.0000.000
171A431HIS00.0100.02031.674-0.014-0.0140.0000.0000.0000.000
172A432PHE00.028-0.01732.3010.0040.0040.0000.0000.0000.000
173A433PHE00.0230.02927.794-0.001-0.0010.0000.0000.0000.000
174A434SER0-0.007-0.01031.004-0.011-0.0110.0000.0000.0000.000
175A435PRO00.0030.00030.3070.0020.0020.0000.0000.0000.000
176A436ALA00.0740.03131.893-0.003-0.0030.0000.0000.0000.000
177A437HIS00.0190.03333.2070.0050.0050.0000.0000.0000.000
178A438VAL0-0.056-0.02028.009-0.006-0.0060.0000.0000.0000.000
179A439MET0-0.0330.00125.688-0.007-0.0070.0000.0000.0000.000
180A440ARG10.8810.91320.712-0.012-0.0120.0000.0000.0000.000
181A441LEU0-0.0310.02824.9860.0050.0050.0000.0000.0000.000
182A442LEU00.002-0.00427.299-0.008-0.0080.0000.0000.0000.000
183A443GLU-1-0.723-0.84728.9640.1290.1290.0000.0000.0000.000
184A444VAL0-0.030-0.02530.565-0.011-0.0110.0000.0000.0000.000
185A445ILE00.0000.00632.4390.0090.0090.0000.0000.0000.000
186A446PRO0-0.030-0.02233.986-0.008-0.0080.0000.0000.0000.000
187A447SER00.0470.01537.0480.0030.0030.0000.0000.0000.000
188A448ARG10.8840.93939.889-0.075-0.0750.0000.0000.0000.000
189A449TYR0-0.003-0.00941.6460.0000.0000.0000.0000.0000.000
190A450SER0-0.053-0.02439.145-0.001-0.0010.0000.0000.0000.000
191A451SER00.0310.01439.7580.0050.0050.0000.0000.0000.000
192A452PRO00.0550.00037.0600.0010.0010.0000.0000.0000.000
193A453THR00.0350.02736.9290.0020.0020.0000.0000.0000.000
194A454THR0-0.016-0.01138.637-0.004-0.0040.0000.0000.0000.000
195A455ILE0-0.0060.00833.231-0.002-0.0020.0000.0000.0000.000
196A456ALA00.0150.00933.7530.0000.0000.0000.0000.0000.000
197A457THR0-0.008-0.01934.475-0.005-0.0050.0000.0000.0000.000
198A458VAL00.0510.03633.675-0.005-0.0050.0000.0000.0000.000
199A459MET0-0.0570.00927.779-0.005-0.0050.0000.0000.0000.000
200A460SER0-0.021-0.01631.075-0.007-0.0070.0000.0000.0000.000
201A461LEU0-0.0250.00233.080-0.008-0.0080.0000.0000.0000.000
202A462SER00.005-0.02730.371-0.005-0.0050.0000.0000.0000.000
203A463LYS10.9110.95926.878-0.057-0.0570.0000.0000.0000.000
204A464LYS10.8730.93529.950-0.034-0.0340.0000.0000.0000.000
205A465ILE00.0000.01532.247-0.007-0.0070.0000.0000.0000.000
206A466GLY0-0.0160.00028.767-0.004-0.0040.0000.0000.0000.000
207A467LYS10.7610.88227.788-0.019-0.0190.0000.0000.0000.000
208A468ILE0-0.070-0.03622.5330.0030.0030.0000.0000.0000.000
209A469GLY00.0650.03326.5540.0030.0030.0000.0000.0000.000
210A470VAL0-0.049-0.04424.8880.0090.0090.0000.0000.0000.000
211A471VAL0-0.016-0.00327.478-0.004-0.0040.0000.0000.0000.000
212A472VAL0-0.040-0.01428.0800.0160.0160.0000.0000.0000.000
213A473GLY00.009-0.00830.569-0.010-0.0100.0000.0000.0000.000
214A474ASN0-0.025-0.04033.573-0.001-0.0010.0000.0000.0000.000
215A475CYS00.0240.03933.8550.0020.0020.0000.0000.0000.000
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