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: QY6MY

Calculation Name: 4ZF4-A-Xray372

Preferred Name:

Target Type:

Ligand Name: [(4z)-2-[(1r,2r)-1-amino-2-hydroxypropyl]-4-(3-chloro-4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1h-imidazol-1-yl]acetic acid

ligand 3-letter code: 4NT

PDB ID: 4ZF4

Chain ID: A

ChEMBL ID:

UniProt ID: P42212

Base Structure: X-ray

Registration Date: 2023-09-19

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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2918177.363215
FMO2-HF: Nuclear repulsion 2828803.252748
FMO2-HF: Total energy -89374.110468
FMO2-MP2: Total energy -89637.306813


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:1:GLY)


Summations of interaction energy for fragment #1(A:1: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.
-4.46-0.472.971-2.858-4.101-0.003
Interaction energy analysis for fragmet #1(A:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : -0.001
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].
3A3LEU00.0260.0213.8080.6571.542-0.004-0.371-0.5090.001
4A4PRO0-0.014-0.0046.3300.0960.0960.0000.0000.0000.000
5A5VAL00.0150.0118.6450.1110.1110.0000.0000.0000.000
6A6PRO00.0330.02010.483-0.198-0.1980.0000.0000.0000.000
7A7TRP00.0190.0006.9930.2550.2550.0000.0000.0000.000
8A8PRO00.0600.02512.4380.0560.0560.0000.0000.0000.000
9A9THR0-0.072-0.03514.3630.0650.0650.0000.0000.0000.000
10A10LEU00.014-0.00110.5950.0550.0550.0000.0000.0000.000
11A11VAL00.0250.03014.9360.0190.0190.0000.0000.0000.000
12A12THR0-0.045-0.04417.1830.0170.0170.0000.0000.0000.000
13A13THR0-0.035-0.00616.3380.0360.0360.0000.0000.0000.000
14A14LEU00.0060.00712.3110.0200.0200.0000.0000.0000.000
15A154NT10.0040.14816.5030.2150.2150.0000.0000.0000.000
16A18VAL-1-0.063-0.14620.744-0.137-0.1370.0000.0000.0000.000
17A19GLN0-0.004-0.05023.2920.0070.0070.0000.0000.0000.000
18A20CYS00.0070.01026.5240.0050.0050.0000.0000.0000.000
19A21PHE00.011-0.00824.1200.0040.0040.0000.0000.0000.000
20A22SER0-0.029-0.01627.847-0.007-0.0070.0000.0000.0000.000
21A23ARG10.9710.98729.8840.0910.0910.0000.0000.0000.000
22A24TYR0-0.004-0.03832.463-0.001-0.0010.0000.0000.0000.000
23A25PRO0-0.028-0.02136.0230.0010.0010.0000.0000.0000.000
24A26ASP-1-0.804-0.90739.182-0.053-0.0530.0000.0000.0000.000
25A27HIS0-0.080-0.04141.9880.0020.0020.0000.0000.0000.000
26A28MET0-0.061-0.03437.8470.0010.0010.0000.0000.0000.000
27A29LYS10.9430.97938.1430.0560.0560.0000.0000.0000.000
28A30ARG10.9250.96639.4160.0340.0340.0000.0000.0000.000
29A31HIS0-0.015-0.00238.8930.0020.0020.0000.0000.0000.000
30A32ASP-1-0.763-0.88233.433-0.069-0.0690.0000.0000.0000.000
31A33PHE00.0250.01030.9400.0020.0020.0000.0000.0000.000
32A34PHE0-0.022-0.00128.7680.0020.0020.0000.0000.0000.000
33A35LYS10.8540.92531.2160.0790.0790.0000.0000.0000.000
34A36SER0-0.052-0.02032.7090.0040.0040.0000.0000.0000.000
35A37ALA00.0070.01331.6480.0030.0030.0000.0000.0000.000
36A38MET0-0.0930.01427.4450.0040.0040.0000.0000.0000.000
37A39PRO00.0380.00030.9790.0020.0020.0000.0000.0000.000
38A40GLU-1-0.915-0.97929.838-0.017-0.0170.0000.0000.0000.000
39A41GLY00.0520.00728.4510.0020.0020.0000.0000.0000.000
40A42TYR0-0.016-0.01825.7060.0050.0050.0000.0000.0000.000
41A43VAL0-0.022-0.00425.482-0.001-0.0010.0000.0000.0000.000
42A44GLN00.0220.01022.6380.0020.0020.0000.0000.0000.000
43A45GLU-1-0.923-0.96923.7400.0020.0020.0000.0000.0000.000
44A46ARG10.8200.87921.6360.0950.0950.0000.0000.0000.000
45A47THR0-0.071-0.03323.6250.0160.0160.0000.0000.0000.000
46A48ILE0-0.0090.00719.756-0.003-0.0030.0000.0000.0000.000
47A49SER0-0.023-0.02522.5390.0100.0100.0000.0000.0000.000
48A50PHE0-0.020-0.00718.540-0.013-0.0130.0000.0000.0000.000
49A51LYS10.9110.95323.5590.0580.0580.0000.0000.0000.000
50A52ASP-1-0.895-0.94625.502-0.047-0.0470.0000.0000.0000.000
51A53ASP-1-0.799-0.90020.727-0.059-0.0590.0000.0000.0000.000
52A54GLY00.0640.05221.0110.0080.0080.0000.0000.0000.000
53A55LYS10.8940.94021.434-0.024-0.0240.0000.0000.0000.000
54A56TYR00.0480.00815.0510.0360.0360.0000.0000.0000.000
55A57LYS10.8870.94719.762-0.025-0.0250.0000.0000.0000.000
56A58THR0-0.022-0.01218.0890.0110.0110.0000.0000.0000.000
57A59ARG10.9740.98020.100-0.021-0.0210.0000.0000.0000.000
58A60ALA00.0250.02520.3090.0100.0100.0000.0000.0000.000
59A61VAL0-0.022-0.01421.3380.0060.0060.0000.0000.0000.000
60A62VAL00.0220.01822.131-0.006-0.0060.0000.0000.0000.000
61A63LYS10.9600.97824.0900.0240.0240.0000.0000.0000.000
62A64PHE00.0370.02624.840-0.007-0.0070.0000.0000.0000.000
63A65GLU-1-0.914-0.93622.402-0.016-0.0160.0000.0000.0000.000
64A66GLY0-0.021-0.01425.793-0.006-0.0060.0000.0000.0000.000
65A67ASP-1-0.886-0.94926.367-0.078-0.0780.0000.0000.0000.000
66A68THR0-0.022-0.00421.363-0.011-0.0110.0000.0000.0000.000
67A69LEU0-0.042-0.01023.0110.0110.0110.0000.0000.0000.000
68A70VAL00.000-0.01519.297-0.018-0.0180.0000.0000.0000.000
69A71ASN00.019-0.00218.5130.0320.0320.0000.0000.0000.000
70A72ARG10.8020.89017.1980.0070.0070.0000.0000.0000.000
71A73ILE0-0.026-0.02715.5840.0080.0080.0000.0000.0000.000
72A74GLU-1-0.882-0.93015.6640.1730.1730.0000.0000.0000.000
73A75LEU0-0.069-0.04914.068-0.027-0.0270.0000.0000.0000.000
74A76LYS10.9100.95315.673-0.026-0.0260.0000.0000.0000.000
75A77GLY00.006-0.00416.868-0.035-0.0350.0000.0000.0000.000
76A78THR0-0.044-0.02217.8350.0310.0310.0000.0000.0000.000
77A79ASP-1-0.943-0.99120.2700.0010.0010.0000.0000.0000.000
78A80PHE0-0.0130.00817.701-0.015-0.0150.0000.0000.0000.000
79A81LYS10.9220.97019.7360.0440.0440.0000.0000.0000.000
80A82GLU-1-0.858-0.95214.7840.0830.0830.0000.0000.0000.000
81A83ASP-1-0.940-0.95816.431-0.043-0.0430.0000.0000.0000.000
82A84GLY00.0220.00518.977-0.013-0.0130.0000.0000.0000.000
83A85ASN00.016-0.02618.103-0.022-0.0220.0000.0000.0000.000
84A86ILE0-0.019-0.00115.031-0.041-0.0410.0000.0000.0000.000
85A87LEU0-0.0090.00212.834-0.060-0.0600.0000.0000.0000.000
86A88GLY00.0020.01413.330-0.007-0.0070.0000.0000.0000.000
87A89HIS0-0.153-0.0759.496-0.028-0.0280.0000.0000.0000.000
88A90LYS10.9731.01614.4770.1030.1030.0000.0000.0000.000
89A91LEU0-0.064-0.02616.8900.0250.0250.0000.0000.0000.000
90A92GLU-1-0.879-0.94817.306-0.241-0.2410.0000.0000.0000.000
91A93TYR0-0.062-0.05213.459-0.065-0.0650.0000.0000.0000.000
92A94ASN0-0.042-0.01817.9390.0070.0070.0000.0000.0000.000
93A95PHE00.032-0.00919.708-0.010-0.0100.0000.0000.0000.000
94A96ASN0-0.066-0.02322.0990.0090.0090.0000.0000.0000.000
95A97SER00.0160.01625.572-0.004-0.0040.0000.0000.0000.000
96A98ASP-1-0.758-0.80425.450-0.137-0.1370.0000.0000.0000.000
97A99ASN0-0.0010.00028.761-0.002-0.0020.0000.0000.0000.000
98A100VAL0-0.036-0.02027.4860.0030.0030.0000.0000.0000.000
99A101TYR00.0180.00730.5810.0020.0020.0000.0000.0000.000
100A102ILE00.0050.00731.3800.0020.0020.0000.0000.0000.000
101A103THR0-0.040-0.02334.4310.0040.0040.0000.0000.0000.000
102A104ALA00.0630.03036.0450.0000.0000.0000.0000.0000.000
103A105ASP-1-0.794-0.90835.976-0.017-0.0170.0000.0000.0000.000
104A106LYS11.0090.98438.1700.0240.0240.0000.0000.0000.000
105A107GLN0-0.0070.00140.0410.0000.0000.0000.0000.0000.000
106A108LYS10.8210.92532.9690.0130.0130.0000.0000.0000.000
107A109ASN00.0240.02436.390-0.001-0.0010.0000.0000.0000.000
108A110GLY00.0820.02634.528-0.002-0.0020.0000.0000.0000.000
109A111ILE0-0.066-0.00830.6910.0000.0000.0000.0000.0000.000
110A112LYS10.8080.88832.0720.0250.0250.0000.0000.0000.000
111A113ALA0-0.0040.00229.396-0.003-0.0030.0000.0000.0000.000
112A114ASN00.006-0.00430.1750.0040.0040.0000.0000.0000.000
113A115PHE00.003-0.00424.703-0.003-0.0030.0000.0000.0000.000
114A116THR0-0.028-0.02027.7440.0020.0020.0000.0000.0000.000
115A117VAL00.0110.02922.225-0.001-0.0010.0000.0000.0000.000
116A118ARG10.9410.96525.5200.1250.1250.0000.0000.0000.000
117A119HIS00.0380.01819.640-0.020-0.0200.0000.0000.0000.000
118A120ASN00.0120.00322.8150.0340.0340.0000.0000.0000.000
119A121VAL00.0110.01921.677-0.030-0.0300.0000.0000.0000.000
120A122GLU-1-0.897-0.95019.158-0.207-0.2070.0000.0000.0000.000
121A123ASP-1-0.901-0.91722.583-0.103-0.1030.0000.0000.0000.000
122A124GLY0-0.015-0.00725.6300.0130.0130.0000.0000.0000.000
123A125SER0-0.107-0.06726.2010.0070.0070.0000.0000.0000.000
124A126VAL0-0.014-0.02625.994-0.011-0.0110.0000.0000.0000.000
125A127GLN0-0.002-0.00421.3320.0100.0100.0000.0000.0000.000
126A128LEU0-0.042-0.02624.136-0.010-0.0100.0000.0000.0000.000
127A129ALA00.0450.01322.1710.0030.0030.0000.0000.0000.000
128A130ASP-1-0.907-0.94424.178-0.065-0.0650.0000.0000.0000.000
129A131HIS00.0120.02222.486-0.007-0.0070.0000.0000.0000.000
130A132TYR00.004-0.00126.4070.0040.0040.0000.0000.0000.000
131A133GLN0-0.011-0.03926.648-0.007-0.0070.0000.0000.0000.000
132A134GLN0-0.060-0.01227.9240.0030.0030.0000.0000.0000.000
133A135ASN00.0240.01126.9550.0000.0000.0000.0000.0000.000
134A136THR00.003-0.00829.9050.0030.0030.0000.0000.0000.000
135A137PRO00.0290.01630.684-0.001-0.0010.0000.0000.0000.000
136A138ILE0-0.088-0.03027.4770.0050.0050.0000.0000.0000.000
137A139GLY00.0310.02332.0630.0040.0040.0000.0000.0000.000
138A140ASP-1-0.961-0.98435.121-0.007-0.0070.0000.0000.0000.000
139A141GLY0-0.0400.00038.2230.0000.0000.0000.0000.0000.000
140A142PRO0-0.047-0.03139.309-0.001-0.0010.0000.0000.0000.000
141A143VAL00.0330.02335.749-0.002-0.0020.0000.0000.0000.000
142A144LEU0-0.074-0.03537.8630.0020.0020.0000.0000.0000.000
143A145LEU0-0.042-0.02837.802-0.002-0.0020.0000.0000.0000.000
144A146PRO0-0.062-0.00936.3200.0010.0010.0000.0000.0000.000
145A147ASP-1-0.879-0.95139.612-0.032-0.0320.0000.0000.0000.000
146A148ASN0-0.047-0.04339.146-0.002-0.0020.0000.0000.0000.000
147A149HIS0-0.0100.02735.621-0.004-0.0040.0000.0000.0000.000
148A150TYR0-0.009-0.00633.9860.0020.0020.0000.0000.0000.000
149A151LEU0-0.0150.00629.1680.0000.0000.0000.0000.0000.000
150A152SER00.001-0.00631.0270.0000.0000.0000.0000.0000.000
151A153THR0-0.015-0.02426.052-0.001-0.0010.0000.0000.0000.000
152A154GLN0-0.013-0.01827.1100.0090.0090.0000.0000.0000.000
153A155THR00.0380.00520.6670.0050.0050.0000.0000.0000.000
154A156VAL0-0.0080.00421.4120.0030.0030.0000.0000.0000.000
155A157LEU0-0.0030.00216.180-0.014-0.0140.0000.0000.0000.000
156A158SER0-0.022-0.02417.0330.0180.0180.0000.0000.0000.000
157A159LYS10.8880.94610.8660.8500.8500.0000.0000.0000.000
158A160ASP-1-0.747-0.88513.707-0.382-0.3820.0000.0000.0000.000
159A161PRO0-0.039-0.01614.231-0.058-0.0580.0000.0000.0000.000
160A162ASN0-0.042-0.02315.4010.0210.0210.0000.0000.0000.000
161A163GLU-1-0.776-0.8469.366-0.873-0.8730.0000.0000.0000.000
162A164LYS10.9520.9598.5990.2480.2480.0000.0000.0000.000
163A165ARG10.8380.9195.3070.9650.9650.0000.0000.0000.000
164A166ASP-1-0.772-0.8834.552-2.432-2.249-0.001-0.029-0.1520.000
165A167HIS00.0120.0016.038-0.001-0.0010.0000.0000.0000.000
166A168MET0-0.0220.0118.7020.1050.1050.0000.0000.0000.000
167A169VAL00.0140.01912.1530.0330.0330.0000.0000.0000.000
168A170LEU0-0.0060.00515.3960.0100.0100.0000.0000.0000.000
169A171LEU0-0.007-0.00217.8990.0220.0220.0000.0000.0000.000
170A172GLU-1-0.823-0.91021.432-0.204-0.2040.0000.0000.0000.000
171A173PHE00.0110.00523.7440.0070.0070.0000.0000.0000.000
172A174VAL00.0290.01426.3020.0010.0010.0000.0000.0000.000
173A175THR0-0.041-0.01029.1250.0060.0060.0000.0000.0000.000
174A176ALA0-0.0180.00432.8470.0000.0000.0000.0000.0000.000
175A177ALA0-0.003-0.02434.8130.0020.0020.0000.0000.0000.000
176A178GLY00.0270.00237.8030.0010.0010.0000.0000.0000.000
177A179ILE0-0.0050.01740.3090.0030.0030.0000.0000.0000.000
178A194ALA00.0290.01840.7320.0010.0010.0000.0000.0000.000
179A195SER0-0.058-0.04337.9200.0020.0020.0000.0000.0000.000
180A196GLN00.0470.01039.329-0.002-0.0020.0000.0000.0000.000
181A197GLY00.0600.04335.240-0.002-0.0020.0000.0000.0000.000
182A198GLU-1-0.876-0.95334.435-0.055-0.0550.0000.0000.0000.000
183A199GLU-1-0.885-0.95835.298-0.051-0.0510.0000.0000.0000.000
184A200LEU0-0.086-0.03632.046-0.001-0.0010.0000.0000.0000.000
185A201PHE0-0.023-0.02827.824-0.005-0.0050.0000.0000.0000.000
186A202THR0-0.033-0.00232.290-0.005-0.0050.0000.0000.0000.000
187A203GLY0-0.0050.00632.9120.0000.0000.0000.0000.0000.000
188A204VAL0-0.025-0.00727.087-0.002-0.0020.0000.0000.0000.000
189A205VAL0-0.021-0.01125.6430.0060.0060.0000.0000.0000.000
190A206PRO00.0440.03522.983-0.015-0.0150.0000.0000.0000.000
191A207ILE0-0.013-0.01419.1320.0110.0110.0000.0000.0000.000
192A208LEU0-0.038-0.01015.273-0.022-0.0220.0000.0000.0000.000
193A209VAL0-0.052-0.02614.3790.0200.0200.0000.0000.0000.000
194A210GLU-1-0.849-0.92712.949-0.078-0.0780.0000.0000.0000.000
195A211LEU0-0.025-0.01111.0790.0160.0160.0000.0000.0000.000
196A212ASP-1-0.813-0.89410.8220.2890.2890.0000.0000.0000.000
197A213GLY0-0.009-0.02610.849-0.082-0.0820.0000.0000.0000.000
198A214ASP-1-0.877-0.91711.5110.4640.4640.0000.0000.0000.000
199A215VAL00.0250.01112.645-0.077-0.0770.0000.0000.0000.000
200A216ASN0-0.019-0.01913.5280.0130.0130.0000.0000.0000.000
201A217GLY00.0010.01514.4750.0090.0090.0000.0000.0000.000
202A218HIS0-0.053-0.0279.3750.1950.1950.0000.0000.0000.000
203A219LYS10.8380.8929.837-0.589-0.5890.0000.0000.0000.000
204A220PHE0-0.024-0.0216.3270.3810.3810.0000.0000.0000.000
205A221SER00.0360.0336.106-0.133-0.1330.0000.0000.0000.000
206A222VAL0-0.063-0.0336.201-0.368-0.3680.0000.0000.0000.000
207A223ARG10.8880.9638.4980.3580.3580.0000.0000.0000.000
208A224GLY0-0.020-0.02110.589-0.162-0.1620.0000.0000.0000.000
209A225GLU-1-0.860-0.92413.320-0.193-0.1930.0000.0000.0000.000
210A226GLY00.010-0.01916.231-0.041-0.0410.0000.0000.0000.000
211A227GLU-1-0.948-0.97119.359-0.133-0.1330.0000.0000.0000.000
212A228GLY00.010-0.00822.845-0.013-0.0130.0000.0000.0000.000
213A229ASP-1-0.840-0.92625.330-0.094-0.0940.0000.0000.0000.000
214A230ALA00.0320.00728.889-0.001-0.0010.0000.0000.0000.000
215A231THR0-0.0210.00830.6530.0060.0060.0000.0000.0000.000
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