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: K9583

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 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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2918623.5815
FMO2-HF: Nuclear repulsion 2829248.512972
FMO2-HF: Total energy -89375.068528
FMO2-MP2: Total energy -89638.300377


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.
-2.05-0.0180000000000015.344-3.486-3.8860
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 : 0.057 / q_NPA : 0.028
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].
3A3LEU00.0400.0283.808-1.1730.505-0.009-0.900-0.7680.004
4A4PRO00.0090.0116.2240.5580.5580.0000.0000.0000.000
5A5VAL00.0080.0108.6270.3700.3700.0000.0000.0000.000
6A6PRO00.0290.02110.421-0.260-0.2600.0000.0000.0000.000
7A7TRP00.031-0.0127.1270.2390.2390.0000.0000.0000.000
8A8PRO00.0640.02912.7170.0600.0600.0000.0000.0000.000
9A9THR0-0.061-0.02814.2700.0790.0790.0000.0000.0000.000
10A10LEU00.0130.00110.5150.0580.0580.0000.0000.0000.000
11A11VAL00.0150.02614.9570.0380.0380.0000.0000.0000.000
12A12THR0-0.042-0.03917.4330.0240.0240.0000.0000.0000.000
13A13THR0-0.036-0.01116.2840.0640.0640.0000.0000.0000.000
14A14LEU00.0070.01012.4480.0300.0300.0000.0000.0000.000
15A154NT10.0410.17416.6910.4560.4560.0000.0000.0000.000
16A18VAL-1-0.064-0.14721.070-0.327-0.3270.0000.0000.0000.000
17A19GLN0-0.006-0.05523.5700.0180.0180.0000.0000.0000.000
18A20CYS00.0030.01726.7950.0130.0130.0000.0000.0000.000
19A21PHE00.029-0.00124.4620.0160.0160.0000.0000.0000.000
20A22SER0-0.036-0.02928.128-0.004-0.0040.0000.0000.0000.000
21A23ARG10.9340.96530.1940.1520.1520.0000.0000.0000.000
22A24TYR0-0.007-0.03332.740-0.003-0.0030.0000.0000.0000.000
23A25PRO0-0.012-0.01036.3330.0060.0060.0000.0000.0000.000
24A26ASP-1-0.810-0.91739.475-0.094-0.0940.0000.0000.0000.000
25A27HIS0-0.066-0.03042.3490.0030.0030.0000.0000.0000.000
26A28MET0-0.075-0.03838.3820.0010.0010.0000.0000.0000.000
27A29LYS10.9390.98038.6080.0990.0990.0000.0000.0000.000
28A30ARG10.9250.96339.7160.0780.0780.0000.0000.0000.000
29A31HIS0-0.013-0.00739.0800.0000.0000.0000.0000.0000.000
30A32ASP-1-0.759-0.86733.705-0.153-0.1530.0000.0000.0000.000
31A33PHE00.0310.01230.9680.0020.0020.0000.0000.0000.000
32A34PHE0-0.0140.00328.5720.0020.0020.0000.0000.0000.000
33A35LYS10.8320.90231.3920.1530.1530.0000.0000.0000.000
34A36SER0-0.055-0.02632.9740.0080.0080.0000.0000.0000.000
35A37ALA00.0050.01231.7590.0060.0060.0000.0000.0000.000
36A38MET0-0.0850.01727.3590.0030.0030.0000.0000.0000.000
37A39PRO00.0360.00131.1780.0060.0060.0000.0000.0000.000
38A40GLU-1-0.923-0.98329.966-0.087-0.0870.0000.0000.0000.000
39A41GLY00.0590.01028.478-0.006-0.0060.0000.0000.0000.000
40A42TYR0-0.016-0.01525.5690.0150.0150.0000.0000.0000.000
41A43VAL0-0.027-0.00625.238-0.012-0.0120.0000.0000.0000.000
42A44GLN00.0190.01122.7130.0270.0270.0000.0000.0000.000
43A45GLU-1-0.848-0.92223.462-0.187-0.1870.0000.0000.0000.000
44A46ARG10.8160.86621.7350.3300.3300.0000.0000.0000.000
45A47THR0-0.064-0.02523.1540.0000.0000.0000.0000.0000.000
46A48ILE0-0.016-0.00119.5150.0150.0150.0000.0000.0000.000
47A49SER0-0.010-0.01622.056-0.010-0.0100.0000.0000.0000.000
48A50PHE0-0.017-0.00618.3300.0040.0040.0000.0000.0000.000
49A51LYS10.8340.90123.1400.2310.2310.0000.0000.0000.000
50A52ASP-1-0.860-0.92725.435-0.213-0.2130.0000.0000.0000.000
51A53ASP-1-0.777-0.88120.627-0.368-0.3680.0000.0000.0000.000
52A54GLY00.0480.04620.7470.0220.0220.0000.0000.0000.000
53A55LYS10.7760.86620.9130.2210.2210.0000.0000.0000.000
54A56TYR00.032-0.00214.731-0.004-0.0040.0000.0000.0000.000
55A57LYS10.9030.95519.1790.2420.2420.0000.0000.0000.000
56A58THR0-0.006-0.01117.527-0.007-0.0070.0000.0000.0000.000
57A59ARG10.9250.96519.6470.2000.2000.0000.0000.0000.000
58A60ALA00.0230.02319.960-0.017-0.0170.0000.0000.0000.000
59A61VAL0-0.021-0.01121.1560.0300.0300.0000.0000.0000.000
60A62VAL00.0180.01422.086-0.013-0.0130.0000.0000.0000.000
61A63LYS10.9540.97824.1280.1260.1260.0000.0000.0000.000
62A64PHE00.0380.02325.041-0.013-0.0130.0000.0000.0000.000
63A65GLU-1-0.915-0.93022.716-0.115-0.1150.0000.0000.0000.000
64A66GLY0-0.013-0.01225.931-0.001-0.0010.0000.0000.0000.000
65A67ASP-1-0.881-0.94526.321-0.104-0.1040.0000.0000.0000.000
66A68THR0-0.027-0.01221.493-0.013-0.0130.0000.0000.0000.000
67A69LEU0-0.042-0.00723.2330.0050.0050.0000.0000.0000.000
68A70VAL00.005-0.01519.571-0.026-0.0260.0000.0000.0000.000
69A71ASN00.0310.00618.8340.0310.0310.0000.0000.0000.000
70A72ARG10.8010.89417.1360.1260.1260.0000.0000.0000.000
71A73ILE0-0.032-0.03015.4840.0260.0260.0000.0000.0000.000
72A74GLU-1-0.817-0.88015.290-0.295-0.2950.0000.0000.0000.000
73A75LEU0-0.032-0.03613.2280.0370.0370.0000.0000.0000.000
74A76LYS10.8050.89114.9200.3050.3050.0000.0000.0000.000
75A77GLY00.000-0.00815.9980.0110.0110.0000.0000.0000.000
76A78THR0-0.026-0.01817.1690.0300.0300.0000.0000.0000.000
77A79ASP-1-0.847-0.92219.799-0.211-0.2110.0000.0000.0000.000
78A80PHE0-0.0180.00717.678-0.010-0.0100.0000.0000.0000.000
79A81LYS10.8670.93219.7180.2500.2500.0000.0000.0000.000
80A82GLU-1-0.813-0.91014.941-0.400-0.4000.0000.0000.0000.000
81A83ASP-1-0.919-0.95116.419-0.270-0.2700.0000.0000.0000.000
82A84GLY00.0360.01718.9660.0140.0140.0000.0000.0000.000
83A85ASN00.001-0.03318.090-0.038-0.0380.0000.0000.0000.000
84A86ILE0-0.0010.00515.017-0.055-0.0550.0000.0000.0000.000
85A87LEU0-0.010-0.00212.776-0.113-0.1130.0000.0000.0000.000
86A88GLY00.0140.01713.318-0.032-0.0320.0000.0000.0000.000
87A89HIS0-0.160-0.0889.5400.0250.0250.0000.0000.0000.000
88A90LYS10.9531.00114.4740.3390.3390.0000.0000.0000.000
89A91LEU0-0.069-0.02716.8940.0460.0460.0000.0000.0000.000
90A92GLU-1-0.818-0.89617.306-0.368-0.3680.0000.0000.0000.000
91A93TYR0-0.075-0.06113.490-0.100-0.1000.0000.0000.0000.000
92A94ASN0-0.089-0.05917.9930.0310.0310.0000.0000.0000.000
93A95PHE00.023-0.01019.677-0.037-0.0370.0000.0000.0000.000
94A96ASN0-0.041-0.00922.4270.0460.0460.0000.0000.0000.000
95A97SER00.0260.02025.930-0.006-0.0060.0000.0000.0000.000
96A98ASP-1-0.774-0.85225.671-0.301-0.3010.0000.0000.0000.000
97A99ASN0-0.0060.00029.0160.0080.0080.0000.0000.0000.000
98A100VAL0-0.033-0.01827.601-0.002-0.0020.0000.0000.0000.000
99A101TYR00.0170.00830.7000.0100.0100.0000.0000.0000.000
100A102ILE00.0100.00631.330-0.005-0.0050.0000.0000.0000.000
101A103THR0-0.039-0.02434.4430.0110.0110.0000.0000.0000.000
102A104ALA00.0600.02835.944-0.005-0.0050.0000.0000.0000.000
103A105ASP-1-0.861-0.92935.777-0.115-0.1150.0000.0000.0000.000
104A106LYS11.0120.98537.9520.0910.0910.0000.0000.0000.000
105A107GLN0-0.0110.00139.6060.0040.0040.0000.0000.0000.000
106A108LYS10.8510.93132.5990.1310.1310.0000.0000.0000.000
107A109ASN00.0130.01636.136-0.003-0.0030.0000.0000.0000.000
108A110GLY00.0900.02734.356-0.002-0.0020.0000.0000.0000.000
109A111ILE0-0.071-0.01130.9410.0060.0060.0000.0000.0000.000
110A112LYS10.8490.90831.8950.1310.1310.0000.0000.0000.000
111A113ALA0-0.010-0.00429.3760.0040.0040.0000.0000.0000.000
112A114ASN0-0.008-0.01030.012-0.010-0.0100.0000.0000.0000.000
113A115PHE00.0140.00224.4920.0040.0040.0000.0000.0000.000
114A116THR0-0.027-0.02427.633-0.007-0.0070.0000.0000.0000.000
115A117VAL00.0080.02722.3760.0060.0060.0000.0000.0000.000
116A118ARG10.9000.94625.4720.2460.2460.0000.0000.0000.000
117A119HIS00.0130.00419.569-0.025-0.0250.0000.0000.0000.000
118A120ASN00.0300.01722.8630.0310.0310.0000.0000.0000.000
119A121VAL00.0100.01421.703-0.050-0.0500.0000.0000.0000.000
120A122GLU-1-0.905-0.95719.323-0.349-0.3490.0000.0000.0000.000
121A123ASP-1-0.884-0.91622.583-0.222-0.2220.0000.0000.0000.000
122A124GLY0-0.023-0.00925.6280.0230.0230.0000.0000.0000.000
123A125SER0-0.109-0.06426.1070.0070.0070.0000.0000.0000.000
124A126VAL0-0.010-0.02325.979-0.015-0.0150.0000.0000.0000.000
125A127GLN00.0030.00621.2720.0090.0090.0000.0000.0000.000
126A128LEU0-0.030-0.02224.043-0.016-0.0160.0000.0000.0000.000
127A129ALA00.0400.01122.025-0.012-0.0120.0000.0000.0000.000
128A130ASP-1-0.840-0.89523.959-0.209-0.2090.0000.0000.0000.000
129A131HIS00.0090.01622.320-0.040-0.0400.0000.0000.0000.000
130A132TYR0-0.0050.00326.1760.0230.0230.0000.0000.0000.000
131A133GLN00.014-0.01226.479-0.030-0.0300.0000.0000.0000.000
132A134GLN0-0.053-0.02127.6480.0280.0280.0000.0000.0000.000
133A135ASN00.0090.00526.990-0.017-0.0170.0000.0000.0000.000
134A136THR00.0110.00129.6960.0100.0100.0000.0000.0000.000
135A137PRO00.0430.02030.494-0.010-0.0100.0000.0000.0000.000
136A138ILE0-0.095-0.03727.2540.0030.0030.0000.0000.0000.000
137A139GLY00.0330.02531.8890.0070.0070.0000.0000.0000.000
138A140ASP-1-0.976-0.99035.013-0.067-0.0670.0000.0000.0000.000
139A141GLY0-0.0260.00538.1670.0030.0030.0000.0000.0000.000
140A142PRO0-0.052-0.03239.267-0.003-0.0030.0000.0000.0000.000
141A143VAL00.0280.01835.714-0.003-0.0030.0000.0000.0000.000
142A144LEU0-0.070-0.02837.9510.0050.0050.0000.0000.0000.000
143A145LEU0-0.036-0.02637.865-0.007-0.0070.0000.0000.0000.000
144A146PRO0-0.060-0.01036.3750.0040.0040.0000.0000.0000.000
145A147ASP-1-0.894-0.95439.684-0.090-0.0900.0000.0000.0000.000
146A148ASN0-0.035-0.04139.169-0.007-0.0070.0000.0000.0000.000
147A149HIS00.0040.03535.566-0.003-0.0030.0000.0000.0000.000
148A150TYR0-0.004-0.00634.195-0.001-0.0010.0000.0000.0000.000
149A151LEU0-0.0150.00929.5240.0050.0050.0000.0000.0000.000
150A152SER0-0.007-0.01031.299-0.005-0.0050.0000.0000.0000.000
151A153THR0-0.013-0.02426.4770.0050.0050.0000.0000.0000.000
152A154GLN0-0.017-0.01427.4120.0130.0130.0000.0000.0000.000
153A155THR00.0520.01021.0560.0100.0100.0000.0000.0000.000
154A156VAL0-0.021-0.00621.7980.0050.0050.0000.0000.0000.000
155A157LEU00.0020.00516.629-0.021-0.0210.0000.0000.0000.000
156A158SER0-0.019-0.02117.1660.0430.0430.0000.0000.0000.000
157A159LYS10.8980.94310.6141.0701.0700.0000.0000.0000.000
158A160ASP-1-0.740-0.86013.592-0.240-0.2400.0000.0000.0000.000
159A161PRO0-0.025-0.01614.089-0.033-0.0330.0000.0000.0000.000
160A162ASN0-0.068-0.03515.3960.0660.0660.0000.0000.0000.000
161A163GLU-1-0.786-0.8429.267-0.349-0.3490.0000.0000.0000.000
162A164LYS10.9530.9668.808-0.438-0.4380.0000.0000.0000.000
163A165ARG10.8380.9025.1000.3950.3950.0000.0000.0000.000
164A166ASP-1-0.783-0.8824.595-3.163-3.008-0.001-0.025-0.1280.000
165A167HIS00.0110.0016.100-0.143-0.1430.0000.0000.0000.000
166A168MET0-0.0190.0228.7960.0960.0960.0000.0000.0000.000
167A169VAL00.0150.01612.3190.0370.0370.0000.0000.0000.000
168A170LEU0-0.0060.00415.5040.0000.0000.0000.0000.0000.000
169A171LEU0-0.0080.00418.0900.0340.0340.0000.0000.0000.000
170A172GLU-1-0.845-0.91421.815-0.375-0.3750.0000.0000.0000.000
171A173PHE00.0190.01923.9920.0170.0170.0000.0000.0000.000
172A174VAL00.0270.01326.585-0.004-0.0040.0000.0000.0000.000
173A175THR0-0.032-0.00129.4320.0150.0150.0000.0000.0000.000
174A176ALA0-0.0030.01133.160-0.005-0.0050.0000.0000.0000.000
175A177ALA0-0.001-0.02235.1610.0080.0080.0000.0000.0000.000
176A178GLY00.0330.00438.148-0.002-0.0020.0000.0000.0000.000
177A179ILE0-0.0170.00640.5720.0040.0040.0000.0000.0000.000
178A194ALA00.0010.00341.1680.0020.0020.0000.0000.0000.000
179A195SER0-0.052-0.04138.294-0.001-0.0010.0000.0000.0000.000
180A196GLN00.0300.00339.5750.0010.0010.0000.0000.0000.000
181A197GLY00.0610.03935.5040.0000.0000.0000.0000.0000.000
182A198GLU-1-0.830-0.92634.691-0.103-0.1030.0000.0000.0000.000
183A199GLU-1-0.879-0.95135.537-0.086-0.0860.0000.0000.0000.000
184A200LEU0-0.095-0.03832.2870.0020.0020.0000.0000.0000.000
185A201PHE0-0.024-0.03127.959-0.007-0.0070.0000.0000.0000.000
186A202THR0-0.029-0.00132.500-0.005-0.0050.0000.0000.0000.000
187A203GLY0-0.0100.00433.0450.0020.0020.0000.0000.0000.000
188A204VAL0-0.043-0.01827.072-0.008-0.0080.0000.0000.0000.000
189A205VAL0-0.016-0.00926.1300.0090.0090.0000.0000.0000.000
190A206PRO00.0250.03022.973-0.024-0.0240.0000.0000.0000.000
191A207ILE0-0.005-0.01019.2540.0000.0000.0000.0000.0000.000
192A208LEU0-0.045-0.01115.561-0.011-0.0110.0000.0000.0000.000
193A209VAL0-0.046-0.02314.8840.0040.0040.0000.0000.0000.000
194A210GLU-1-0.826-0.92113.067-0.272-0.2720.0000.0000.0000.000
195A211LEU0-0.023-0.01210.8950.0530.0530.0000.0000.0000.000
196A212ASP-1-0.809-0.88210.536-0.540-0.5400.0000.0000.0000.000
197A213GLY0-0.009-0.01910.1600.0680.0680.0000.0000.0000.000
198A214ASP-1-0.867-0.90510.600-0.305-0.3050.0000.0000.0000.000
199A215VAL00.0090.00411.9990.0620.0620.0000.0000.0000.000
200A216ASN0-0.039-0.04213.360-0.024-0.0240.0000.0000.0000.000
201A217GLY00.0040.01614.2940.0370.0370.0000.0000.0000.000
202A218HIS0-0.070-0.0389.4040.0380.0380.0000.0000.0000.000
203A219LYS10.8450.8929.0960.0210.0210.0000.0000.0000.000
204A220PHE0-0.024-0.0305.662-0.207-0.2070.0000.0000.0000.000
205A221SER00.0270.0105.5300.5330.5330.0000.0000.0000.000
206A222VAL0-0.073-0.0356.117-0.831-0.8310.0000.0000.0000.000
207A223ARG10.8360.9248.6470.5700.5700.0000.0000.0000.000
208A224GLY0-0.010-0.01710.754-0.148-0.1480.0000.0000.0000.000
209A225GLU-1-0.841-0.90213.501-0.151-0.1510.0000.0000.0000.000
210A226GLY00.018-0.01216.325-0.039-0.0390.0000.0000.0000.000
211A227GLU-1-0.932-0.96519.450-0.160-0.1600.0000.0000.0000.000
212A228GLY00.022-0.00422.970-0.023-0.0230.0000.0000.0000.000
213A229ASP-1-0.847-0.93125.512-0.128-0.1280.0000.0000.0000.000
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