Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: R92V8

Calculation Name: 5J3N-B-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: GYS

PDB ID: 5J3N

Chain ID: B

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 230
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2991066.156407
FMO2-HF: Nuclear repulsion 2899850.910807
FMO2-HF: Total energy -91215.245599
FMO2-MP2: Total energy -91483.258671


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(B:7:HIS)


Summations of interaction energy for fragment #1(B:7:HIS)
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.
-35.828-21.7494.638-7.378-11.336-0.037
Interaction energy analysis for fragmet #1(B:7:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.036 / q_NPA : -0.022
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].
3B9LYS10.8920.9223.740-1.3860.347-0.012-0.879-0.8420.002
4B10GLY00.0130.0146.434-0.148-0.1480.0000.0000.0000.000
5B11GLU-1-0.899-0.9682.442-24.477-18.0701.567-4.105-3.869-0.050
6B12GLU-1-0.906-0.9565.130-1.413-1.293-0.0010.000-0.1180.000
7B13LEU0-0.078-0.0367.7870.1970.1970.0000.0000.0000.000
8B14PHE0-0.002-0.0169.6250.1440.1440.0000.0000.0000.000
9B15THR0-0.051-0.0259.0630.0180.0180.0000.0000.0000.000
10B16GLY0-0.0040.00511.5130.0520.0520.0000.0000.0000.000
11B17VAL0-0.042-0.01515.267-0.037-0.0370.0000.0000.0000.000
12B18VAL0-0.0020.01214.8420.0360.0360.0000.0000.0000.000
13B19PRO00.0250.02018.1370.0000.0000.0000.0000.0000.000
14B20ILE0-0.027-0.02719.158-0.006-0.0060.0000.0000.0000.000
15B21LEU00.0030.00522.1780.0240.0240.0000.0000.0000.000
16B22VAL0-0.025-0.01223.720-0.007-0.0070.0000.0000.0000.000
17B23GLU-1-0.900-0.93525.894-0.130-0.1300.0000.0000.0000.000
18B24LEU0-0.025-0.01628.0090.0010.0010.0000.0000.0000.000
19B25ASP-1-0.860-0.90330.230-0.074-0.0740.0000.0000.0000.000
20B26GLY0-0.001-0.01332.8790.0030.0030.0000.0000.0000.000
21B27ASP-1-0.961-0.97734.840-0.035-0.0350.0000.0000.0000.000
22B28VAL00.0430.02036.3790.0030.0030.0000.0000.0000.000
23B29ASN00.005-0.01538.8120.0000.0000.0000.0000.0000.000
24B30GLY0-0.0130.00441.6070.0010.0010.0000.0000.0000.000
25B31HIS0-0.033-0.01141.600-0.002-0.0020.0000.0000.0000.000
26B32LYS10.9400.95939.4180.0340.0340.0000.0000.0000.000
27B33PHE0-0.061-0.03333.899-0.003-0.0030.0000.0000.0000.000
28B34SER00.0500.00534.9410.0040.0040.0000.0000.0000.000
29B35VAL0-0.080-0.04031.033-0.002-0.0020.0000.0000.0000.000
30B36SER00.0130.00230.9220.0020.0020.0000.0000.0000.000
31B37GLY0-0.012-0.01428.3480.0000.0000.0000.0000.0000.000
32B38GLU-1-0.953-0.95526.384-0.206-0.2060.0000.0000.0000.000
33B39GLY0-0.004-0.01625.3740.0040.0040.0000.0000.0000.000
34B40GLU-1-0.945-0.96721.360-0.433-0.4330.0000.0000.0000.000
35B41GLY00.0410.00418.1070.0170.0170.0000.0000.0000.000
36B42ASP-1-0.850-0.92015.467-1.033-1.0330.0000.0000.0000.000
37B43ALA00.0210.00111.4820.0060.0060.0000.0000.0000.000
38B44THR0-0.042-0.00311.911-0.289-0.2890.0000.0000.0000.000
39B45TYR0-0.113-0.07412.935-0.025-0.0250.0000.0000.0000.000
40B46GLY0-0.0180.00714.7100.0730.0730.0000.0000.0000.000
41B47LYS10.9070.97815.7350.6060.6060.0000.0000.0000.000
42B48LEU00.0530.02818.186-0.027-0.0270.0000.0000.0000.000
43B49THR0-0.037-0.02121.1410.0200.0200.0000.0000.0000.000
44B50LEU00.0300.01422.4320.0010.0010.0000.0000.0000.000
45B51LYS10.8210.90526.4490.1920.1920.0000.0000.0000.000
46B52PHE00.0330.01325.6780.0020.0020.0000.0000.0000.000
47B53ILE0-0.023-0.03631.3560.0070.0070.0000.0000.0000.000
48B54CYS0-0.0150.01034.5610.0040.0040.0000.0000.0000.000
49B55THR0-0.042-0.03035.6040.0060.0060.0000.0000.0000.000
50B56THR00.0200.00938.2550.0040.0040.0000.0000.0000.000
51B57GLY0-0.0090.00440.8050.0060.0060.0000.0000.0000.000
52B58LYS10.8990.95441.2620.0740.0740.0000.0000.0000.000
53B59LEU00.0220.01135.2350.0050.0050.0000.0000.0000.000
54B60PRO0-0.035-0.01338.3740.0000.0000.0000.0000.0000.000
55B61VAL00.0090.01135.2650.0050.0050.0000.0000.0000.000
56B62PRO00.0470.02036.566-0.006-0.0060.0000.0000.0000.000
57B63TRP00.003-0.00632.374-0.005-0.0050.0000.0000.0000.000
58B64PRO00.0620.02631.616-0.008-0.0080.0000.0000.0000.000
59B65THR0-0.081-0.04230.728-0.004-0.0040.0000.0000.0000.000
60B66LEU00.0300.01129.8980.0060.0060.0000.0000.0000.000
61B67VAL00.0210.03025.716-0.009-0.0090.0000.0000.0000.000
62B68THR0-0.060-0.05024.185-0.019-0.0190.0000.0000.0000.000
63B69THR0-0.0020.00323.603-0.006-0.0060.0000.0000.0000.000
64B70PHE00.0430.02624.439-0.002-0.0020.0000.0000.0000.000
65B72GYS1-0.042-0.03620.2780.2590.2590.0000.0000.0000.000
66B74VAL-10.0800.04917.586-0.282-0.2820.0000.0000.0000.000
67B75GLN00.018-0.00714.935-0.050-0.0500.0000.0000.0000.000
68B76CYS00.0220.03211.624-0.054-0.0540.0000.0000.0000.000
69B77PHE00.0260.00111.581-0.241-0.2410.0000.0000.0000.000
70B78SER0-0.029-0.02111.7960.0210.0210.0000.0000.0000.000
71B79ARG10.9931.00511.2861.0771.0770.0000.0000.0000.000
72B80TYR0-0.014-0.0317.3740.1570.1570.0000.0000.0000.000
73B81PRO0-0.013-0.0077.930-0.553-0.5530.0000.0000.0000.000
74B82ASP-1-0.827-0.9365.351-3.924-3.9240.0000.0000.0000.000
75B83HIS0-0.116-0.0613.859-2.468-2.2860.000-0.061-0.1210.000
76B84MET0-0.072-0.0315.9960.9700.9700.0000.0000.0000.000
77B85LYS10.9901.0152.7215.3196.4481.734-0.749-2.1130.004
78B86ARG10.9110.9732.923-5.721-2.0620.648-1.373-2.9330.007
79B87HIS0-0.007-0.0113.875-1.046-0.7370.0510.060-0.4200.002
80B88ASP-1-0.766-0.8815.250-2.047-2.0470.0000.0000.0000.000
81B89PHE00.0130.0106.432-0.282-0.2820.0000.0000.0000.000
82B90PHE00.0270.0348.709-0.053-0.0530.0000.0000.0000.000
83B91LYS10.8020.8956.8401.8901.8900.0000.0000.0000.000
84B92SER0-0.060-0.0475.9910.2460.2460.0000.0000.0000.000
85B93ALA00.0020.0057.4330.2430.2430.0000.0000.0000.000
86B94MET0-0.0510.04310.2670.1260.1260.0000.0000.0000.000
87B95PRO0-0.007-0.02811.0760.0130.0130.0000.0000.0000.000
88B96GLU-1-0.833-0.92113.9780.0870.0870.0000.0000.0000.000
89B97GLY00.0550.00114.578-0.001-0.0010.0000.0000.0000.000
90B98TYR0-0.030-0.02713.4320.0440.0440.0000.0000.0000.000
91B99VAL00.0040.01216.796-0.028-0.0280.0000.0000.0000.000
92B100GLN00.0410.00818.6650.0040.0040.0000.0000.0000.000
93B101GLU-1-0.957-0.98420.6720.0370.0370.0000.0000.0000.000
94B102ARG10.7960.85520.9570.1520.1520.0000.0000.0000.000
95B103THR0-0.056-0.01625.7580.0080.0080.0000.0000.0000.000
96B104ILE0-0.0040.00827.424-0.001-0.0010.0000.0000.0000.000
97B105PHE0-0.009-0.02030.0840.0040.0040.0000.0000.0000.000
98B106PHE0-0.007-0.00532.516-0.008-0.0080.0000.0000.0000.000
99B107LYS10.9560.97835.5060.0420.0420.0000.0000.0000.000
100B108ASP-1-0.917-0.95537.649-0.042-0.0420.0000.0000.0000.000
101B109ASP-1-0.821-0.91239.114-0.054-0.0540.0000.0000.0000.000
102B110GLY00.0460.04138.7530.0050.0050.0000.0000.0000.000
103B111ASN0-0.049-0.02333.672-0.001-0.0010.0000.0000.0000.000
104B112TYR00.048-0.00531.1220.0040.0040.0000.0000.0000.000
105B113LYS10.8890.93330.2890.0140.0140.0000.0000.0000.000
106B114THR00.003-0.00226.084-0.008-0.0080.0000.0000.0000.000
107B115ARG10.9430.98124.9200.0040.0040.0000.0000.0000.000
108B116ALA00.0220.01422.761-0.004-0.0040.0000.0000.0000.000
109B117GLU-1-0.935-0.96421.246-0.016-0.0160.0000.0000.0000.000
110B118VAL0-0.0010.00916.564-0.018-0.0180.0000.0000.0000.000
111B119LYS10.9480.96916.9780.1030.1030.0000.0000.0000.000
112B120PHE00.0310.01813.503-0.017-0.0170.0000.0000.0000.000
113B121GLU-1-0.855-0.92818.380-0.081-0.0810.0000.0000.0000.000
114B122GLY0-0.013-0.00621.321-0.007-0.0070.0000.0000.0000.000
115B123ASP-1-0.923-0.97518.934-0.281-0.2810.0000.0000.0000.000
116B124THR0-0.0100.00219.302-0.056-0.0560.0000.0000.0000.000
117B125LEU0-0.0260.00415.8580.0240.0240.0000.0000.0000.000
118B126VAL0-0.017-0.01919.0210.0100.0100.0000.0000.0000.000
119B127ASN00.0170.00820.6100.0210.0210.0000.0000.0000.000
120B128ARG10.8250.91222.3880.1320.1320.0000.0000.0000.000
121B129ILE0-0.008-0.01525.1320.0120.0120.0000.0000.0000.000
122B130GLU-1-0.943-0.95327.215-0.019-0.0190.0000.0000.0000.000
123B131LEU0-0.011-0.02229.5510.0010.0010.0000.0000.0000.000
124B132LYS10.9450.96231.6020.0140.0140.0000.0000.0000.000
125B133GLY0-0.010-0.00734.1420.0000.0000.0000.0000.0000.000
126B134ILE0-0.041-0.00936.4820.0020.0020.0000.0000.0000.000
127B135ASP-1-0.914-0.96739.243-0.017-0.0170.0000.0000.0000.000
128B136PHE0-0.017-0.01035.770-0.001-0.0010.0000.0000.0000.000
129B137LYS10.8760.93141.8660.0420.0420.0000.0000.0000.000
130B138ASP-1-0.902-0.95444.480-0.043-0.0430.0000.0000.0000.000
131B139ASP-1-0.916-0.96246.774-0.059-0.0590.0000.0000.0000.000
132B140GLY0-0.027-0.01843.469-0.001-0.0010.0000.0000.0000.000
133B141ASN0-0.005-0.02840.234-0.003-0.0030.0000.0000.0000.000
134B142ILE00.0170.01136.878-0.006-0.0060.0000.0000.0000.000
135B143LEU0-0.008-0.01139.771-0.003-0.0030.0000.0000.0000.000
136B144GLY00.0300.02742.5870.0000.0000.0000.0000.0000.000
137B145HIS0-0.150-0.06840.499-0.005-0.0050.0000.0000.0000.000
138B146LYS10.9260.98142.0990.0620.0620.0000.0000.0000.000
139B147LEU0-0.075-0.02135.992-0.001-0.0010.0000.0000.0000.000
140B148GLU-1-0.813-0.90237.717-0.142-0.1420.0000.0000.0000.000
141B149TYR0-0.096-0.05734.522-0.004-0.0040.0000.0000.0000.000
142B150ASN00.014-0.00333.741-0.020-0.0200.0000.0000.0000.000
143B151TYR0-0.063-0.05326.6420.0100.0100.0000.0000.0000.000
144B152ASN0-0.0160.01829.986-0.012-0.0120.0000.0000.0000.000
145B153GLU-1-0.895-0.94225.223-0.327-0.3270.0000.0000.0000.000
146B154HIS00.018-0.00424.3110.0430.0430.0000.0000.0000.000
147B155LEU0-0.022-0.00121.063-0.037-0.0370.0000.0000.0000.000
148B156VAL0-0.031-0.01018.2810.0370.0370.0000.0000.0000.000
149B157TYR00.007-0.00618.343-0.020-0.0200.0000.0000.0000.000
150B158ILE00.0510.02913.1350.0250.0250.0000.0000.0000.000
151B159MET0-0.042-0.02715.9670.0350.0350.0000.0000.0000.000
152B160ALA00.0120.00413.223-0.012-0.0120.0000.0000.0000.000
153B161ASP-1-0.877-0.95314.7970.2150.2150.0000.0000.0000.000
154B162LYS10.9620.96912.825-0.879-0.8790.0000.0000.0000.000
155B163GLN00.0160.01616.624-0.012-0.0120.0000.0000.0000.000
156B164LYS10.8900.94118.974-0.211-0.2110.0000.0000.0000.000
157B165ASN00.0040.01313.4210.0580.0580.0000.0000.0000.000
158B166GLY00.0890.03813.565-0.020-0.0200.0000.0000.0000.000
159B167THR0-0.037-0.00612.4810.0690.0690.0000.0000.0000.000
160B168LYS10.8900.95915.387-0.134-0.1340.0000.0000.0000.000
161B169ALA00.0180.00417.580-0.001-0.0010.0000.0000.0000.000
162B170ILE0-0.027-0.01019.8220.0080.0080.0000.0000.0000.000
163B171PHE0-0.029-0.01721.902-0.016-0.0160.0000.0000.0000.000
164B172GLN0-0.016-0.01724.8150.0010.0010.0000.0000.0000.000
165B173VAL0-0.043-0.00626.819-0.012-0.0120.0000.0000.0000.000
166B174HIS00.0060.00129.1150.0140.0140.0000.0000.0000.000
167B175HIS00.0060.00530.760-0.016-0.0160.0000.0000.0000.000
168B176ASN00.0460.02334.2490.0100.0100.0000.0000.0000.000
169B177ILE0-0.046-0.02037.184-0.001-0.0010.0000.0000.0000.000
170B178GLU-1-0.932-0.98740.501-0.118-0.1180.0000.0000.0000.000
171B179ASP-1-0.961-0.97942.640-0.078-0.0780.0000.0000.0000.000
172B180GLY0-0.0140.00243.4220.0050.0050.0000.0000.0000.000
173B181GLY0-0.034-0.01241.6530.0040.0040.0000.0000.0000.000
174B182VAL0-0.003-0.00835.471-0.007-0.0070.0000.0000.0000.000
175B183GLN0-0.039-0.00836.0060.0110.0110.0000.0000.0000.000
176B184LEU0-0.026-0.01533.346-0.007-0.0070.0000.0000.0000.000
177B185ALA00.0730.02631.0090.0070.0070.0000.0000.0000.000
178B186ASP-1-0.881-0.90529.345-0.064-0.0640.0000.0000.0000.000
179B187HIS0-0.0100.00025.095-0.005-0.0050.0000.0000.0000.000
180B188TYR0-0.025-0.01724.8750.0140.0140.0000.0000.0000.000
181B189GLN00.002-0.01418.258-0.014-0.0140.0000.0000.0000.000
182B190GLN0-0.042-0.02519.7730.0260.0260.0000.0000.0000.000
183B191ASN00.0210.02815.876-0.023-0.0230.0000.0000.0000.000
184B192THR00.0170.00616.5980.0490.0490.0000.0000.0000.000
185B193PRO00.0330.02613.598-0.057-0.0570.0000.0000.0000.000
186B194ILE0-0.058-0.02015.7030.0270.0270.0000.0000.0000.000
187B195GLY0-0.0060.00116.2450.0160.0160.0000.0000.0000.000
188B196ASP-1-0.902-0.95316.7310.2980.2980.0000.0000.0000.000
189B197GLY0-0.071-0.02813.0400.0750.0750.0000.0000.0000.000
190B198PRO0-0.043-0.0169.1200.0010.0010.0000.0000.0000.000
191B199VAL00.0250.0108.164-0.134-0.1340.0000.0000.0000.000
192B200LEU0-0.039-0.0162.502-0.1640.3760.651-0.271-0.920-0.002
193B201LEU0-0.034-0.0276.718-0.381-0.3810.0000.0000.0000.000
194B202PRO0-0.042-0.0039.0400.3080.3080.0000.0000.0000.000
195B203ASP-1-0.908-0.9519.9750.9860.9860.0000.0000.0000.000
196B204ASN0-0.033-0.02612.378-0.074-0.0740.0000.0000.0000.000
197B205HIS0-0.046-0.01311.278-0.128-0.1280.0000.0000.0000.000
198B206TYR00.0100.00115.1130.0390.0390.0000.0000.0000.000
199B207LEU00.007-0.00113.146-0.081-0.0810.0000.0000.0000.000
200B208HIS0-0.063-0.05316.8400.0480.0480.0000.0000.0000.000
201B209THR0-0.038-0.01918.997-0.071-0.0710.0000.0000.0000.000
202B210GLN00.001-0.00221.2260.0440.0440.0000.0000.0000.000
203B211SER0-0.031-0.06823.690-0.030-0.0300.0000.0000.0000.000
204B212ALA00.0180.01726.1000.0200.0200.0000.0000.0000.000
205B213LEU00.000-0.00129.223-0.007-0.0070.0000.0000.0000.000
206B214SER0-0.013-0.01531.6330.0080.0080.0000.0000.0000.000
207B215LYS10.9000.96534.2870.1530.1530.0000.0000.0000.000
208B216ASP-1-0.760-0.88635.490-0.182-0.1820.0000.0000.0000.000
209B217PRO0-0.0090.00337.1590.0100.0100.0000.0000.0000.000
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