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: N2NZQ

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 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 459
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -8640760.580921
FMO2-HF: Nuclear repulsion 8464406.519932
FMO2-HF: Total energy -176354.060989
FMO2-MP2: Total energy -176872.751574


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.
-24.185-17.5195.663-5.05-7.2760.039
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 : 0.070 / q_NPA : 0.027
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].
3A263GLN00.0640.0292.634-4.223-1.6940.758-1.311-1.9760.010
4A264ALA00.000-0.0022.349-7.644-5.4923.184-2.282-3.0530.016
5A265LYS10.9390.9672.514-11.572-9.7181.722-1.448-2.1270.013
6A266ALA00.0470.0355.240-0.377-0.246-0.001-0.009-0.1200.000
7A267LEU0-0.016-0.0056.278-0.314-0.3140.0000.0000.0000.000
8A268GLN00.0170.0187.443-0.188-0.1880.0000.0000.0000.000
9A269TYR0-0.089-0.0809.033-0.035-0.0350.0000.0000.0000.000
10A270ALA00.0320.00611.028-0.069-0.0690.0000.0000.0000.000
11A271PHE0-0.076-0.03810.984-0.051-0.0510.0000.0000.0000.000
12A272PHE00.006-0.00612.590-0.017-0.0170.0000.0000.0000.000
13A273ALA00.0680.05715.076-0.001-0.0010.0000.0000.0000.000
14A274GLU-1-0.761-0.85416.4590.0400.0400.0000.0000.0000.000
15A275LYS10.8620.90418.497-0.046-0.0460.0000.0000.0000.000
16A276SER0-0.051-0.03918.407-0.004-0.0040.0000.0000.0000.000
17A277ALA00.0510.02320.333-0.001-0.0010.0000.0000.0000.000
18A278ASN0-0.036-0.02623.267-0.024-0.0240.0000.0000.0000.000
19A279LYS10.9020.96519.125-0.227-0.2270.0000.0000.0000.000
20A280TRP00.0510.03325.1720.0160.0160.0000.0000.0000.000
21A281SER00.017-0.01327.829-0.001-0.0010.0000.0000.0000.000
22A282THR00.0150.01630.1500.0040.0040.0000.0000.0000.000
23A283PRO00.0920.03932.5080.0000.0000.0000.0000.0000.000
24A284SER0-0.059-0.02033.883-0.002-0.0020.0000.0000.0000.000
25A285GLY00.0550.02633.923-0.003-0.0030.0000.0000.0000.000
26A286ALA0-0.034-0.00434.752-0.003-0.0030.0000.0000.0000.000
27A287SER00.022-0.01430.0270.0100.0100.0000.0000.0000.000
28A288TRP0-0.0150.00325.198-0.007-0.0070.0000.0000.0000.000
29A289LYS10.9200.95727.557-0.148-0.1480.0000.0000.0000.000
30A290THR00.019-0.00230.873-0.003-0.0030.0000.0000.0000.000
31A291ALA0-0.0480.01333.861-0.006-0.0060.0000.0000.0000.000
32A292SER00.0460.01434.4850.0000.0000.0000.0000.0000.000
33A293ALA0-0.069-0.04334.9620.0000.0000.0000.0000.0000.000
34A294GLN00.0290.00836.933-0.004-0.0040.0000.0000.0000.000
35A295PRO0-0.023-0.01939.2960.0000.0000.0000.0000.0000.000
36A296VAL0-0.0010.00439.1810.0010.0010.0000.0000.0000.000
37A297SER0-0.082-0.03540.180-0.003-0.0030.0000.0000.0000.000
38A298SER0-0.022-0.03242.630-0.003-0.0030.0000.0000.0000.000
39A299VAL00.004-0.01739.7560.0030.0030.0000.0000.0000.000
40A300GLY00.0250.00343.175-0.003-0.0030.0000.0000.0000.000
41A301VAL0-0.042-0.01641.0610.0030.0030.0000.0000.0000.000
42A302LEU00.0390.02843.831-0.003-0.0030.0000.0000.0000.000
43A303GLY00.0250.02344.7910.0030.0030.0000.0000.0000.000
44A304LEU0-0.057-0.04143.3990.0000.0000.0000.0000.0000.000
45A305GLY00.0960.04242.905-0.003-0.0030.0000.0000.0000.000
46A306THR0-0.042-0.04237.457-0.002-0.0020.0000.0000.0000.000
47A307MET00.0230.02634.063-0.002-0.0020.0000.0000.0000.000
48A308GLY00.1110.04938.0150.0000.0000.0000.0000.0000.000
49A309ARG10.8690.93540.044-0.014-0.0140.0000.0000.0000.000
50A310GLY00.0220.01835.982-0.003-0.0030.0000.0000.0000.000
51A311ILE00.0040.00136.105-0.002-0.0020.0000.0000.0000.000
52A312ALA00.0210.00637.311-0.002-0.0020.0000.0000.0000.000
53A313ILE0-0.021-0.01936.039-0.002-0.0020.0000.0000.0000.000
54A314SER0-0.011-0.02034.006-0.003-0.0030.0000.0000.0000.000
55A315PHE00.0270.00435.485-0.001-0.0010.0000.0000.0000.000
56A316ALA0-0.006-0.00537.890-0.002-0.0020.0000.0000.0000.000
57A317ARG10.7530.82332.1460.0060.0060.0000.0000.0000.000
58A318VAL0-0.030-0.00633.444-0.004-0.0040.0000.0000.0000.000
59A319GLY0-0.031-0.00136.7370.0010.0010.0000.0000.0000.000
60A320ILE00.0040.00737.2050.0010.0010.0000.0000.0000.000
61A321SER0-0.030-0.03040.960-0.002-0.0020.0000.0000.0000.000
62A322VAL0-0.015-0.00241.3720.0030.0030.0000.0000.0000.000
63A323VAL0-0.026-0.00944.456-0.002-0.0020.0000.0000.0000.000
64A324ALA00.0040.00644.8800.0030.0030.0000.0000.0000.000
65A325VAL00.000-0.02146.483-0.002-0.0020.0000.0000.0000.000
66A326GLU-1-0.826-0.91647.3310.0220.0220.0000.0000.0000.000
67A327SER00.0380.02449.492-0.001-0.0010.0000.0000.0000.000
68A328ASP-1-0.829-0.91650.8290.0120.0120.0000.0000.0000.000
69A329PRO00.0510.02151.807-0.001-0.0010.0000.0000.0000.000
70A330LYS10.9791.00050.557-0.009-0.0090.0000.0000.0000.000
71A331GLN00.0100.00445.695-0.003-0.0030.0000.0000.0000.000
72A332LEU00.0060.00848.029-0.001-0.0010.0000.0000.0000.000
73A333ASP-1-0.876-0.91849.164-0.002-0.0020.0000.0000.0000.000
74A334ALA00.005-0.00446.815-0.002-0.0020.0000.0000.0000.000
75A335ALA0-0.017-0.02244.739-0.002-0.0020.0000.0000.0000.000
76A336LYS10.9400.98144.872-0.005-0.0050.0000.0000.0000.000
77A337LYS10.8810.93246.2790.0010.0010.0000.0000.0000.000
78A338ILE0-0.0120.00140.649-0.002-0.0020.0000.0000.0000.000
79A339ILE0-0.025-0.00241.228-0.002-0.0020.0000.0000.0000.000
80A340THR0-0.018-0.01741.652-0.002-0.0020.0000.0000.0000.000
81A341PHE00.0400.03039.921-0.003-0.0030.0000.0000.0000.000
82A342THR0-0.054-0.03836.661-0.004-0.0040.0000.0000.0000.000
83A343LEU00.005-0.00538.309-0.003-0.0030.0000.0000.0000.000
84A344GLU-1-0.884-0.93939.866-0.021-0.0210.0000.0000.0000.000
85A345LYS10.9180.97734.8680.0270.0270.0000.0000.0000.000
86A346GLU-1-0.854-0.91034.378-0.021-0.0210.0000.0000.0000.000
87A347ALA00.0320.02736.546-0.005-0.0050.0000.0000.0000.000
88A348SER0-0.012-0.02039.166-0.004-0.0040.0000.0000.0000.000
89A349ARG10.8600.92932.4380.0610.0610.0000.0000.0000.000
90A350ALA00.0230.00434.854-0.006-0.0060.0000.0000.0000.000
91A351HIS00.0310.02435.878-0.004-0.0040.0000.0000.0000.000
92A352GLN0-0.028-0.00736.701-0.005-0.0050.0000.0000.0000.000
93A353ASN0-0.079-0.05230.990-0.009-0.0090.0000.0000.0000.000
94A354GLY00.0200.02734.511-0.005-0.0050.0000.0000.0000.000
95A355GLN0-0.068-0.03432.781-0.001-0.0010.0000.0000.0000.000
96A356ALA00.0080.00536.1610.0030.0030.0000.0000.0000.000
97A357SER00.003-0.00637.4800.0020.0020.0000.0000.0000.000
98A358ALA0-0.0040.00139.4600.0010.0010.0000.0000.0000.000
99A359LYS10.9890.99041.6700.0150.0150.0000.0000.0000.000
100A360PRO00.0240.01241.2370.0020.0020.0000.0000.0000.000
101A361LYS10.8810.95743.0810.0030.0030.0000.0000.0000.000
102A362LEU00.0130.01143.7430.0020.0020.0000.0000.0000.000
103A363ARG10.8270.91346.179-0.010-0.0100.0000.0000.0000.000
104A364PHE00.0390.00545.7280.0020.0020.0000.0000.0000.000
105A365SER00.0110.00150.192-0.001-0.0010.0000.0000.0000.000
106A366SER00.0330.02451.5260.0010.0010.0000.0000.0000.000
107A367SER0-0.010-0.01553.9910.0020.0020.0000.0000.0000.000
108A368THR00.058-0.02351.302-0.001-0.0010.0000.0000.0000.000
109A369LYS11.0241.01552.893-0.014-0.0140.0000.0000.0000.000
110A370GLU-1-0.869-0.90652.9490.0100.0100.0000.0000.0000.000
111A371LEU0-0.037-0.01547.919-0.001-0.0010.0000.0000.0000.000
112A372SER00.0340.01850.4540.0010.0010.0000.0000.0000.000
113A373THR0-0.002-0.00451.3830.0010.0010.0000.0000.0000.000
114A374VAL0-0.0150.00445.9270.0000.0000.0000.0000.0000.000
115A375ASP-1-0.759-0.84943.5920.0200.0200.0000.0000.0000.000
116A376LEU0-0.021-0.00538.9860.0030.0030.0000.0000.0000.000
117A377VAL00.0180.01343.393-0.003-0.0030.0000.0000.0000.000
118A378VAL0-0.012-0.00438.4050.0040.0040.0000.0000.0000.000
119A379GLU-1-0.714-0.82041.5570.0390.0390.0000.0000.0000.000
120A380ALA0-0.041-0.03840.3990.0040.0040.0000.0000.0000.000
121A381VAL0-0.020-0.01142.146-0.003-0.0030.0000.0000.0000.000
122A382PHE00.008-0.00643.9070.0030.0030.0000.0000.0000.000
123A383GLU-1-0.729-0.83239.8600.0570.0570.0000.0000.0000.000
124A384ASP-1-0.757-0.88243.7780.0390.0390.0000.0000.0000.000
125A385MET00.0200.03544.847-0.002-0.0020.0000.0000.0000.000
126A386ASN00.0070.00147.658-0.002-0.0020.0000.0000.0000.000
127A387LEU0-0.006-0.00248.334-0.001-0.0010.0000.0000.0000.000
128A388LYS10.7900.90942.284-0.045-0.0450.0000.0000.0000.000
129A389LYS10.8690.92247.858-0.048-0.0480.0000.0000.0000.000
130A390LYS10.9050.94950.272-0.032-0.0320.0000.0000.0000.000
131A391VAL00.0100.00548.263-0.001-0.0010.0000.0000.0000.000
132A392PHE00.010-0.02543.436-0.001-0.0010.0000.0000.0000.000
133A393ALA00.0240.04949.3620.0000.0000.0000.0000.0000.000
134A394GLU-1-0.883-0.91352.8490.0220.0220.0000.0000.0000.000
135A395LEU0-0.024-0.03947.134-0.002-0.0020.0000.0000.0000.000
136A396SER0-0.049-0.04450.5750.0000.0000.0000.0000.0000.000
137A397ALA00.0070.02051.797-0.001-0.0010.0000.0000.0000.000
138A398LEU0-0.059-0.03153.700-0.002-0.0020.0000.0000.0000.000
139A399CYS0-0.080-0.03449.597-0.001-0.0010.0000.0000.0000.000
140A400LYS10.8810.95147.791-0.019-0.0190.0000.0000.0000.000
141A401PRO00.0700.02650.4260.0020.0020.0000.0000.0000.000
142A402GLY0-0.008-0.00647.644-0.001-0.0010.0000.0000.0000.000
143A403ALA0-0.050-0.01145.8510.0010.0010.0000.0000.0000.000
144A404PHE00.014-0.01341.5970.0020.0020.0000.0000.0000.000
145A405LEU0-0.0040.00943.539-0.003-0.0030.0000.0000.0000.000
146A406CYS0-0.013-0.01238.8420.0040.0040.0000.0000.0000.000
147A407THR0-0.012-0.00840.304-0.002-0.0020.0000.0000.0000.000
148A408ASN00.007-0.01636.3560.0060.0060.0000.0000.0000.000
149A409THR0-0.090-0.05637.8210.0020.0020.0000.0000.0000.000
150A410SER0-0.022-0.03735.5250.0040.0040.0000.0000.0000.000
151A411ALA0-0.051-0.03636.1810.0060.0060.0000.0000.0000.000
152A412LEU0-0.053-0.02138.7400.0000.0000.0000.0000.0000.000
153A413ASN00.0670.03140.1050.0060.0060.0000.0000.0000.000
154A414VAL00.0730.01838.741-0.005-0.0050.0000.0000.0000.000
155A415ASP-1-0.811-0.91041.5420.0710.0710.0000.0000.0000.000
156A416ASP-1-0.820-0.88743.7350.0530.0530.0000.0000.0000.000
157A417ILE0-0.007-0.00142.925-0.003-0.0030.0000.0000.0000.000
158A418ALA00.0150.01144.064-0.003-0.0030.0000.0000.0000.000
159A419SER0-0.078-0.02146.133-0.003-0.0030.0000.0000.0000.000
160A420SER0-0.029-0.01649.077-0.002-0.0020.0000.0000.0000.000
161A421THR0-0.057-0.04347.853-0.002-0.0020.0000.0000.0000.000
162A422ASP-1-0.844-0.91450.6490.0340.0340.0000.0000.0000.000
163A423ARG10.7980.85847.687-0.032-0.0320.0000.0000.0000.000
164A424PRO00.0440.03646.2900.0020.0020.0000.0000.0000.000
165A425GLN00.0520.01643.8510.0030.0030.0000.0000.0000.000
166A426LEU0-0.0610.01242.6470.0030.0030.0000.0000.0000.000
167A427VAL00.0230.03642.853-0.002-0.0020.0000.0000.0000.000
168A428ILE0-0.036-0.00335.5170.0040.0040.0000.0000.0000.000
169A429GLY00.0490.04037.551-0.005-0.0050.0000.0000.0000.000
170A430THR0-0.053-0.05034.6240.0030.0030.0000.0000.0000.000
171A431HIS0-0.0300.00731.472-0.012-0.0120.0000.0000.0000.000
172A432PHE00.035-0.01331.9160.0050.0050.0000.0000.0000.000
173A433PHE00.0330.03027.487-0.001-0.0010.0000.0000.0000.000
174A434SER0-0.0140.00230.642-0.010-0.0100.0000.0000.0000.000
175A435PRO00.028-0.00529.7660.0040.0040.0000.0000.0000.000
176A436ALA00.0840.04731.233-0.002-0.0020.0000.0000.0000.000
177A437HIS00.0170.02832.7960.0040.0040.0000.0000.0000.000
178A438VAL0-0.069-0.03127.554-0.007-0.0070.0000.0000.0000.000
179A439MET0-0.031-0.00525.177-0.005-0.0050.0000.0000.0000.000
180A440ARG10.8850.92420.709-0.034-0.0340.0000.0000.0000.000
181A441LEU0-0.0410.04024.2850.0030.0030.0000.0000.0000.000
182A442LEU0-0.015-0.00926.902-0.008-0.0080.0000.0000.0000.000
183A443GLU-1-0.709-0.84728.6580.1260.1260.0000.0000.0000.000
184A444VAL0-0.007-0.01730.306-0.010-0.0100.0000.0000.0000.000
185A445ILE0-0.0090.00732.1740.0070.0070.0000.0000.0000.000
186A446PRO0-0.007-0.00333.625-0.007-0.0070.0000.0000.0000.000
187A447SER00.0380.01636.8170.0030.0030.0000.0000.0000.000
188A448ARG10.8650.92639.499-0.067-0.0670.0000.0000.0000.000
189A449TYR00.005-0.01241.2540.0000.0000.0000.0000.0000.000
190A450SER0-0.047-0.01438.772-0.001-0.0010.0000.0000.0000.000
191A451SER00.0540.03139.8490.0040.0040.0000.0000.0000.000
192A452PRO00.059-0.00536.5890.0010.0010.0000.0000.0000.000
193A453THR00.0290.03236.6520.0010.0010.0000.0000.0000.000
194A454THR00.011-0.01338.140-0.003-0.0030.0000.0000.0000.000
195A455ILE00.0030.00832.953-0.001-0.0010.0000.0000.0000.000
196A456ALA00.0070.00333.3500.0000.0000.0000.0000.0000.000
197A457THR00.011-0.01234.023-0.004-0.0040.0000.0000.0000.000
198A458VAL00.0410.03133.364-0.004-0.0040.0000.0000.0000.000
199A459MET0-0.0670.01427.231-0.003-0.0030.0000.0000.0000.000
200A460SER0-0.044-0.03030.704-0.005-0.0050.0000.0000.0000.000
201A461LEU0-0.014-0.00532.480-0.006-0.0060.0000.0000.0000.000
202A462SER00.020-0.01929.852-0.004-0.0040.0000.0000.0000.000
203A463LYS10.9130.96826.494-0.057-0.0570.0000.0000.0000.000
204A464LYS10.8830.95029.378-0.032-0.0320.0000.0000.0000.000
205A465ILE0-0.0120.00731.764-0.006-0.0060.0000.0000.0000.000
206A466GLY0-0.040-0.01028.235-0.003-0.0030.0000.0000.0000.000
207A467LYS10.7610.87327.486-0.027-0.0270.0000.0000.0000.000
208A468ILE0-0.091-0.05322.0890.0020.0020.0000.0000.0000.000
209A469GLY00.0420.02625.9220.0030.0030.0000.0000.0000.000
210A470VAL0-0.028-0.03424.4450.0080.0080.0000.0000.0000.000
211A471VAL0-0.011-0.00327.094-0.005-0.0050.0000.0000.0000.000
212A472VAL0-0.049-0.02727.7120.0130.0130.0000.0000.0000.000
213A473GLY00.001-0.01730.281-0.010-0.0100.0000.0000.0000.000
214A474ASN0-0.011-0.03033.068-0.001-0.0010.0000.0000.0000.000
215A475CYS00.0110.02533.4070.0020.0020.0000.0000.0000.000
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