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: QY6JY

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 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 230
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2994830.697425
FMO2-HF: Nuclear repulsion 2903614.469205
FMO2-HF: Total energy -91216.22822
FMO2-MP2: Total energy -91484.36384


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.
-44.045-28.3186.783-8.944-13.566-0.066
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 : -0.061 / q_NPA : -0.031
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].
3B9LYS10.8950.9213.687-1.2390.485-0.011-0.868-0.8460.002
4B10GLY00.0150.0156.377-0.109-0.1090.0000.0000.0000.000
5B11GLU-1-0.844-0.9502.318-31.424-23.5653.510-5.684-5.684-0.079
6B12GLU-1-0.902-0.9525.632-1.876-1.8760.0000.0000.0000.000
7B13LEU0-0.082-0.0367.7660.2700.2700.0000.0000.0000.000
8B14PHE00.003-0.0189.6110.1910.1910.0000.0000.0000.000
9B15THR0-0.045-0.0199.1530.0400.0400.0000.0000.0000.000
10B16GLY00.0010.00711.5190.0790.0790.0000.0000.0000.000
11B17VAL0-0.036-0.01515.270-0.039-0.0390.0000.0000.0000.000
12B18VAL0-0.0050.01014.8300.0400.0400.0000.0000.0000.000
13B19PRO00.0030.01018.1240.0080.0080.0000.0000.0000.000
14B20ILE0-0.015-0.02119.105-0.012-0.0120.0000.0000.0000.000
15B21LEU0-0.006-0.00122.1460.0330.0330.0000.0000.0000.000
16B22VAL0-0.018-0.01223.592-0.010-0.0100.0000.0000.0000.000
17B23GLU-1-0.876-0.91525.839-0.173-0.1730.0000.0000.0000.000
18B24LEU0-0.025-0.01627.9390.0000.0000.0000.0000.0000.000
19B25ASP-1-0.866-0.91030.160-0.105-0.1050.0000.0000.0000.000
20B26GLY00.001-0.01132.7990.0030.0030.0000.0000.0000.000
21B27ASP-1-0.932-0.97034.763-0.054-0.0540.0000.0000.0000.000
22B28VAL00.0320.01836.1920.0030.0030.0000.0000.0000.000
23B29ASN00.007-0.01238.7340.0010.0010.0000.0000.0000.000
24B30GLY0-0.0130.00441.5310.0020.0020.0000.0000.0000.000
25B31HIS0-0.034-0.01141.606-0.002-0.0020.0000.0000.0000.000
26B32LYS10.9080.95339.3430.0520.0520.0000.0000.0000.000
27B33PHE0-0.046-0.03133.789-0.003-0.0030.0000.0000.0000.000
28B34SER00.0430.00634.8790.0040.0040.0000.0000.0000.000
29B35VAL0-0.075-0.04331.149-0.001-0.0010.0000.0000.0000.000
30B36SER00.009-0.00130.8480.0030.0030.0000.0000.0000.000
31B37GLY0-0.008-0.01128.3000.0020.0020.0000.0000.0000.000
32B38GLU-1-0.965-0.96126.361-0.258-0.2580.0000.0000.0000.000
33B39GLY00.007-0.01225.3460.0080.0080.0000.0000.0000.000
34B40GLU-1-0.918-0.95621.398-0.566-0.5660.0000.0000.0000.000
35B41GLY00.0610.01218.0980.0270.0270.0000.0000.0000.000
36B42ASP-1-0.830-0.90615.095-1.236-1.2360.0000.0000.0000.000
37B43ALA00.0200.00411.2770.0150.0150.0000.0000.0000.000
38B44THR0-0.031-0.00211.780-0.313-0.3130.0000.0000.0000.000
39B45TYR0-0.101-0.07312.792-0.020-0.0200.0000.0000.0000.000
40B46GLY0-0.0260.00914.5510.0920.0920.0000.0000.0000.000
41B47LYS10.8820.96915.6210.7110.7110.0000.0000.0000.000
42B48LEU00.0330.01518.256-0.035-0.0350.0000.0000.0000.000
43B49THR0-0.036-0.02821.0930.0270.0270.0000.0000.0000.000
44B50LEU00.0220.02122.399-0.003-0.0030.0000.0000.0000.000
45B51LYS10.8230.90526.4290.2320.2320.0000.0000.0000.000
46B52PHE00.0260.00725.6300.0000.0000.0000.0000.0000.000
47B53ILE0-0.029-0.03831.3190.0100.0100.0000.0000.0000.000
48B54CYS0-0.0200.00234.5130.0030.0030.0000.0000.0000.000
49B55THR0-0.022-0.01635.6150.0070.0070.0000.0000.0000.000
50B56THR00.0230.01238.2030.0050.0050.0000.0000.0000.000
51B57GLY0-0.0130.00340.7470.0080.0080.0000.0000.0000.000
52B58LYS10.8560.94041.2130.0970.0970.0000.0000.0000.000
53B59LEU00.0240.01735.1670.0050.0050.0000.0000.0000.000
54B60PRO0-0.024-0.00938.4530.0010.0010.0000.0000.0000.000
55B61VAL00.0200.01835.2560.0070.0070.0000.0000.0000.000
56B62PRO00.0380.02036.492-0.007-0.0070.0000.0000.0000.000
57B63TRP00.024-0.00732.308-0.006-0.0060.0000.0000.0000.000
58B64PRO00.0690.03331.567-0.010-0.0100.0000.0000.0000.000
59B65THR0-0.082-0.03930.682-0.005-0.0050.0000.0000.0000.000
60B66LEU00.0240.00829.8370.0060.0060.0000.0000.0000.000
61B67VAL00.0240.03225.755-0.013-0.0130.0000.0000.0000.000
62B68THR0-0.060-0.05224.133-0.025-0.0250.0000.0000.0000.000
63B69THR0-0.0120.00423.542-0.004-0.0040.0000.0000.0000.000
64B70PHE00.0280.01524.373-0.004-0.0040.0000.0000.0000.000
65B72GYS1-0.048-0.02620.2170.2920.2920.0000.0000.0000.000
66B74VAL-10.0810.04617.526-0.355-0.3550.0000.0000.0000.000
67B75GLN00.014-0.00714.981-0.050-0.0500.0000.0000.0000.000
68B76CYS00.0070.02911.577-0.082-0.0820.0000.0000.0000.000
69B77PHE00.0450.01111.550-0.287-0.2870.0000.0000.0000.000
70B78SER0-0.035-0.02911.7620.0440.0440.0000.0000.0000.000
71B79ARG10.9470.97611.2121.1041.1040.0000.0000.0000.000
72B80TYR0-0.008-0.0357.4290.2260.2260.0000.0000.0000.000
73B81PRO00.0000.0007.978-0.645-0.6450.0000.0000.0000.000
74B82ASP-1-0.787-0.9044.959-4.904-4.9040.0000.0000.0000.000
75B83HIS0-0.118-0.0643.733-2.604-2.3700.002-0.097-0.139-0.001
76B84MET0-0.071-0.0316.0311.1291.1290.0000.0000.0000.000
77B85LYS10.9200.9702.6796.5087.7861.868-0.789-2.3580.004
78B86ARG10.8700.9512.921-6.245-2.4960.782-1.399-3.1310.007
79B87HIS0-0.032-0.0203.748-1.435-1.2000.0790.159-0.4730.003
80B88ASP-1-0.764-0.8725.202-2.348-2.3480.0000.0000.0000.000
81B89PHE00.0080.0036.344-0.373-0.3730.0000.0000.0000.000
82B90PHE00.0230.0168.746-0.073-0.0730.0000.0000.0000.000
83B91LYS10.8160.9056.7532.2752.2750.0000.0000.0000.000
84B92SER0-0.050-0.0305.8250.2720.2720.0000.0000.0000.000
85B93ALA00.0010.0037.3330.2640.2640.0000.0000.0000.000
86B94MET0-0.0530.04310.1740.1640.1640.0000.0000.0000.000
87B95PRO0-0.004-0.02611.022-0.027-0.0270.0000.0000.0000.000
88B96GLU-1-0.838-0.92113.676-0.077-0.0770.0000.0000.0000.000
89B97GLY00.056-0.00114.4870.0130.0130.0000.0000.0000.000
90B98TYR0-0.030-0.02713.3830.0460.0460.0000.0000.0000.000
91B99VAL00.0060.01716.695-0.026-0.0260.0000.0000.0000.000
92B100GLN00.0390.01018.307-0.007-0.0070.0000.0000.0000.000
93B101GLU-1-0.896-0.94220.578-0.007-0.0070.0000.0000.0000.000
94B102ARG10.7950.84620.7680.2020.2020.0000.0000.0000.000
95B103THR0-0.053-0.00925.7040.0080.0080.0000.0000.0000.000
96B104ILE0-0.0060.00227.174-0.001-0.0010.0000.0000.0000.000
97B105PHE0-0.013-0.02030.0090.0050.0050.0000.0000.0000.000
98B106PHE0-0.0030.00032.386-0.007-0.0070.0000.0000.0000.000
99B107LYS10.8290.90535.4390.0510.0510.0000.0000.0000.000
100B108ASP-1-0.828-0.89737.586-0.048-0.0480.0000.0000.0000.000
101B109ASP-1-0.768-0.89839.038-0.067-0.0670.0000.0000.0000.000
102B110GLY00.0510.05338.6770.0060.0060.0000.0000.0000.000
103B111ASN0-0.058-0.01733.768-0.002-0.0020.0000.0000.0000.000
104B112TYR00.058-0.00331.0500.0040.0040.0000.0000.0000.000
105B113LYS10.8770.92330.1990.0310.0310.0000.0000.0000.000
106B114THR00.0110.00425.965-0.007-0.0070.0000.0000.0000.000
107B115ARG10.8730.93224.3650.0480.0480.0000.0000.0000.000
108B116ALA00.0090.01222.710-0.003-0.0030.0000.0000.0000.000
109B117GLU-1-0.875-0.92221.148-0.076-0.0760.0000.0000.0000.000
110B118VAL0-0.0040.00116.872-0.018-0.0180.0000.0000.0000.000
111B119LYS10.9050.94116.9020.1550.1550.0000.0000.0000.000
112B120PHE00.0280.01713.451-0.014-0.0140.0000.0000.0000.000
113B121GLU-1-0.830-0.88418.338-0.140-0.1400.0000.0000.0000.000
114B122GLY0-0.013-0.00521.313-0.003-0.0030.0000.0000.0000.000
115B123ASP-1-0.911-0.96118.905-0.383-0.3830.0000.0000.0000.000
116B124THR0-0.021-0.01319.275-0.063-0.0630.0000.0000.0000.000
117B125LEU0-0.0270.00815.9120.0260.0260.0000.0000.0000.000
118B126VAL0-0.009-0.02218.9740.0200.0200.0000.0000.0000.000
119B127ASN00.0230.00920.5410.0200.0200.0000.0000.0000.000
120B128ARG10.7930.86822.3200.2030.2030.0000.0000.0000.000
121B129ILE00.000-0.01224.9070.0130.0130.0000.0000.0000.000
122B130GLU-1-0.852-0.89927.135-0.047-0.0470.0000.0000.0000.000
123B131LEU0-0.015-0.02629.4640.0010.0010.0000.0000.0000.000
124B132LYS10.8460.91031.5190.0470.0470.0000.0000.0000.000
125B133GLY00.003-0.00434.0560.0000.0000.0000.0000.0000.000
126B134ILE0-0.053-0.01136.4000.0020.0020.0000.0000.0000.000
127B135ASP-1-0.878-0.96239.161-0.029-0.0290.0000.0000.0000.000
128B136PHE0-0.027-0.00935.754-0.001-0.0010.0000.0000.0000.000
129B137LYS10.8630.92141.7910.0510.0510.0000.0000.0000.000
130B138ASP-1-0.902-0.95444.413-0.055-0.0550.0000.0000.0000.000
131B139ASP-1-0.892-0.93846.711-0.069-0.0690.0000.0000.0000.000
132B140GLY00.0110.00743.4050.0000.0000.0000.0000.0000.000
133B141ASN0-0.009-0.02640.121-0.003-0.0030.0000.0000.0000.000
134B142ILE00.0160.01236.949-0.007-0.0070.0000.0000.0000.000
135B143LEU0-0.007-0.00839.712-0.004-0.0040.0000.0000.0000.000
136B144GLY00.0300.02342.5250.0000.0000.0000.0000.0000.000
137B145HIS0-0.179-0.09840.287-0.006-0.0060.0000.0000.0000.000
138B146LYS10.8740.93342.0480.0710.0710.0000.0000.0000.000
139B147LEU0-0.071-0.01635.926-0.001-0.0010.0000.0000.0000.000
140B148GLU-1-0.765-0.85237.385-0.164-0.1640.0000.0000.0000.000
141B149TYR0-0.085-0.05634.614-0.005-0.0050.0000.0000.0000.000
142B150ASN0-0.018-0.03433.861-0.023-0.0230.0000.0000.0000.000
143B151TYR0-0.058-0.04526.4450.0100.0100.0000.0000.0000.000
144B152ASN0-0.0310.00129.969-0.011-0.0110.0000.0000.0000.000
145B153GLU-1-0.843-0.90924.992-0.372-0.3720.0000.0000.0000.000
146B154HIS00.0150.00724.3910.0510.0510.0000.0000.0000.000
147B155LEU0-0.0240.00220.884-0.040-0.0400.0000.0000.0000.000
148B156VAL0-0.028-0.00818.5270.0380.0380.0000.0000.0000.000
149B157TYR00.007-0.00418.300-0.019-0.0190.0000.0000.0000.000
150B158ILE00.0440.02513.1910.0220.0220.0000.0000.0000.000
151B159MET0-0.043-0.02615.9770.0510.0510.0000.0000.0000.000
152B160ALA00.010-0.00113.143-0.021-0.0210.0000.0000.0000.000
153B161ASP-1-0.841-0.92114.8030.2210.2210.0000.0000.0000.000
154B162LYS10.9540.96212.434-0.979-0.9790.0000.0000.0000.000
155B163GLN00.0190.02616.620-0.017-0.0170.0000.0000.0000.000
156B164LYS10.8720.92718.835-0.208-0.2080.0000.0000.0000.000
157B165ASN00.0040.00913.4010.0560.0560.0000.0000.0000.000
158B166GLY00.0970.04013.583-0.036-0.0360.0000.0000.0000.000
159B167THR0-0.044-0.00912.4440.0840.0840.0000.0000.0000.000
160B168LYS10.8770.94315.409-0.121-0.1210.0000.0000.0000.000
161B169ALA00.0130.00717.6040.0030.0030.0000.0000.0000.000
162B170ILE0-0.028-0.01119.8490.0050.0050.0000.0000.0000.000
163B171PHE0-0.018-0.01422.121-0.014-0.0140.0000.0000.0000.000
164B172GLN0-0.013-0.02624.795-0.001-0.0010.0000.0000.0000.000
165B173VAL0-0.040-0.00326.739-0.012-0.0120.0000.0000.0000.000
166B174HIS0-0.006-0.01229.0700.0150.0150.0000.0000.0000.000
167B175HIS00.0040.00530.666-0.019-0.0190.0000.0000.0000.000
168B176ASN00.0290.00934.2110.0120.0120.0000.0000.0000.000
169B177ILE0-0.051-0.02737.153-0.003-0.0030.0000.0000.0000.000
170B178GLU-1-0.919-0.97940.465-0.133-0.1330.0000.0000.0000.000
171B179ASP-1-0.972-0.98442.610-0.086-0.0860.0000.0000.0000.000
172B180GLY0-0.0020.00843.3960.0060.0060.0000.0000.0000.000
173B181GLY0-0.035-0.01341.6220.0040.0040.0000.0000.0000.000
174B182VAL0-0.008-0.01635.348-0.007-0.0070.0000.0000.0000.000
175B183GLN0-0.043-0.00235.9490.0120.0120.0000.0000.0000.000
176B184LEU0-0.023-0.01133.302-0.008-0.0080.0000.0000.0000.000
177B185ALA00.0760.02231.0160.0060.0060.0000.0000.0000.000
178B186ASP-1-0.880-0.89929.275-0.074-0.0740.0000.0000.0000.000
179B187HIS00.0120.01724.999-0.010-0.0100.0000.0000.0000.000
180B188TYR0-0.017-0.01824.8910.0180.0180.0000.0000.0000.000
181B189GLN00.0220.00118.173-0.007-0.0070.0000.0000.0000.000
182B190GLN0-0.073-0.04819.7650.0300.0300.0000.0000.0000.000
183B191ASN00.0120.01515.872-0.023-0.0230.0000.0000.0000.000
184B192THR00.015-0.00116.6270.0530.0530.0000.0000.0000.000
185B193PRO00.0200.02413.671-0.064-0.0640.0000.0000.0000.000
186B194ILE0-0.045-0.01615.7330.0380.0380.0000.0000.0000.000
187B195GLY0-0.0020.00016.2700.0220.0220.0000.0000.0000.000
188B196ASP-1-0.913-0.95916.7510.2380.2380.0000.0000.0000.000
189B197GLY0-0.060-0.02013.0380.0800.0800.0000.0000.0000.000
190B198PRO0-0.048-0.0219.1380.0050.0050.0000.0000.0000.000
191B199VAL00.0170.0088.173-0.173-0.1730.0000.0000.0000.000
192B200LEU0-0.039-0.0112.599-0.2260.4220.553-0.266-0.935-0.002
193B201LEU0-0.035-0.0356.727-0.359-0.3590.0000.0000.0000.000
194B202PRO0-0.0400.0039.0380.3510.3510.0000.0000.0000.000
195B203ASP-1-0.845-0.9319.9801.3231.3230.0000.0000.0000.000
196B204ASN0-0.024-0.02812.373-0.086-0.0860.0000.0000.0000.000
197B205HIS0-0.0350.00911.040-0.153-0.1530.0000.0000.0000.000
198B206TYR00.0210.00615.0420.0340.0340.0000.0000.0000.000
199B207LEU00.0060.00313.035-0.077-0.0770.0000.0000.0000.000
200B208HIS0-0.052-0.04316.8180.0690.0690.0000.0000.0000.000
201B209THR0-0.035-0.02319.003-0.084-0.0840.0000.0000.0000.000
202B210GLN0-0.047-0.02921.2120.0390.0390.0000.0000.0000.000
203B211SER0-0.022-0.05323.620-0.030-0.0300.0000.0000.0000.000
204B212ALA00.0090.01126.0890.0240.0240.0000.0000.0000.000
205B213LEU00.0010.00229.168-0.010-0.0100.0000.0000.0000.000
206B214SER0-0.015-0.01831.6180.0090.0090.0000.0000.0000.000
207B215LYS10.8930.94534.2680.1750.1750.0000.0000.0000.000
208B216ASP-1-0.738-0.87235.507-0.212-0.2120.0000.0000.0000.000
209B217PRO00.0010.00137.1370.0120.0120.0000.0000.0000.000
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