FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: 72JYK

Calculation Name: 5MQH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5MQH

Chain ID: A

ChEMBL ID:

UniProt ID: P37475

Base Structure: X-ray

Registration Date: 2023-06-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 231
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2733987.966773
FMO2-HF: Nuclear repulsion 2643571.623775
FMO2-HF: Total energy -90416.342998
FMO2-MP2: Total energy -90676.050399


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:587:HIS)


Summations of interaction energy for fragment #1(A:587: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.
1.8623.647-0.012-0.769-1.0030.001
Interaction energy analysis for fragmet #1(A:587:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : -0.012
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].
3A589HIS00.0220.0133.8380.9792.694-0.011-0.762-0.9410.001
4A590SER00.0160.0025.9730.1870.1870.0000.0000.0000.000
5A591TYR0-0.054-0.0058.6990.1940.1940.0000.0000.0000.000
6A592ARG10.8910.95510.2770.8030.8030.0000.0000.0000.000
7A593VAL0-0.0010.00712.8450.1110.1110.0000.0000.0000.000
8A594SER0-0.042-0.01416.052-0.006-0.0060.0000.0000.0000.000
9A595THR00.0280.00318.7160.0220.0220.0000.0000.0000.000
10A596GLY00.0060.00921.4080.0000.0000.0000.0000.0000.000
11A597ALA0-0.014-0.01424.757-0.003-0.0030.0000.0000.0000.000
12A598ALA00.0140.03027.4260.0040.0040.0000.0000.0000.000
13A599HIS00.0320.00728.819-0.007-0.0070.0000.0000.0000.000
14A600ALA0-0.034-0.01033.1890.0040.0040.0000.0000.0000.000
15A601ALA00.0350.01936.8980.0000.0000.0000.0000.0000.000
16A602LYS10.9510.96239.2530.0540.0540.0000.0000.0000.000
17A603GLY0-0.063-0.03442.8560.0020.0020.0000.0000.0000.000
18A604GLY0-0.030-0.00342.2750.0020.0020.0000.0000.0000.000
19A605GLY0-0.023-0.00142.0710.0020.0020.0000.0000.0000.000
20A606LEU0-0.025-0.04138.818-0.003-0.0030.0000.0000.0000.000
21A607VAL0-0.054-0.02535.868-0.001-0.0010.0000.0000.0000.000
22A608SER0-0.0080.00434.3210.0010.0010.0000.0000.0000.000
23A609GLY0-0.072-0.04535.6870.0040.0040.0000.0000.0000.000
24A610ASP-1-0.767-0.86932.833-0.089-0.0890.0000.0000.0000.000
25A611SER0-0.100-0.04929.2990.0000.0000.0000.0000.0000.000
26A612TYR00.023-0.01225.116-0.013-0.0130.0000.0000.0000.000
27A613SER0-0.065-0.02022.6220.0130.0130.0000.0000.0000.000
28A614MET00.018-0.00419.694-0.021-0.0210.0000.0000.0000.000
29A615MET0-0.029-0.00517.0530.0170.0170.0000.0000.0000.000
30A616GLU-1-0.929-0.97710.365-0.647-0.6470.0000.0000.0000.000
31A617LEU0-0.0270.01112.546-0.045-0.0450.0000.0000.0000.000
32A618GLY0-0.010-0.01011.296-0.057-0.0570.0000.0000.0000.000
33A619ALA0-0.015-0.0186.012-0.028-0.0280.0000.0000.0000.000
34A620ARG10.9550.9586.5930.5440.5440.0000.0000.0000.000
35A621LYS10.8790.9738.2330.4500.4500.0000.0000.0000.000
36A622TYR00.0660.04911.791-0.021-0.0210.0000.0000.0000.000
37A623ALA0-0.0030.01014.3540.0150.0150.0000.0000.0000.000
38A624ILE0-0.002-0.01117.8910.0050.0050.0000.0000.0000.000
39A625ALA00.001-0.00421.2680.0080.0080.0000.0000.0000.000
40A626ILE00.0140.00624.5580.0000.0000.0000.0000.0000.000
41A627SER00.019-0.01928.169-0.003-0.0030.0000.0000.0000.000
42A628ASP-1-0.835-0.89230.961-0.070-0.0700.0000.0000.0000.000
43A629GLY00.0330.00434.6710.0020.0020.0000.0000.0000.000
44A630MET0-0.0500.09330.8020.0020.0020.0000.0000.0000.000
45A631GLY00.0310.01634.0760.0070.0070.0000.0000.0000.000
46A632ASN0-0.029-0.01336.1710.0010.0010.0000.0000.0000.000
47A633GLY00.0560.00736.9540.0040.0040.0000.0000.0000.000
48A634ALA0-0.025-0.01034.147-0.002-0.0020.0000.0000.0000.000
49A635ARG10.9991.00733.053-0.015-0.0150.0000.0000.0000.000
50A636ALA00.020-0.00533.4860.0020.0020.0000.0000.0000.000
51A637HIS00.1260.05430.016-0.003-0.0030.0000.0000.0000.000
52A638PHE0-0.085-0.02727.1170.0000.0000.0000.0000.0000.000
53A639GLU-1-0.958-0.98428.924-0.003-0.0030.0000.0000.0000.000
54A640SER00.037-0.07729.4250.0000.0000.0000.0000.0000.000
55A641ASN00.0070.00124.422-0.012-0.0120.0000.0000.0000.000
56A642GLU-1-0.990-0.97824.8350.0150.0150.0000.0000.0000.000
57A643THR0-0.019-0.01825.896-0.006-0.0060.0000.0000.0000.000
58A644ILE00.0770.03223.024-0.006-0.0060.0000.0000.0000.000
59A645LYS10.9700.99420.288-0.051-0.0510.0000.0000.0000.000
60A646LEU0-0.087-0.03822.056-0.007-0.0070.0000.0000.0000.000
61A647LEU00.019-0.00323.860-0.009-0.0090.0000.0000.0000.000
62A648GLU-1-0.877-0.94819.225-0.144-0.1440.0000.0000.0000.000
63A649LYS10.8860.94117.1980.0200.0200.0000.0000.0000.000
64A650ILE0-0.0200.00020.561-0.007-0.0070.0000.0000.0000.000
65A651LEU00.0420.05020.786-0.006-0.0060.0000.0000.0000.000
66A652GLU-1-0.923-0.97116.221-0.337-0.3370.0000.0000.0000.000
67A653SER0-0.136-0.09317.549-0.008-0.0080.0000.0000.0000.000
68A654GLY0-0.036-0.01819.9460.0060.0060.0000.0000.0000.000
69A655ILE0-0.075-0.01920.4160.0130.0130.0000.0000.0000.000
70A656ASP-1-0.828-0.93624.097-0.103-0.1030.0000.0000.0000.000
71A657GLU-1-0.841-0.93925.358-0.144-0.1440.0000.0000.0000.000
72A658LYS10.9360.97127.6000.0840.0840.0000.0000.0000.000
73A659ILE0-0.036-0.02028.7660.0070.0070.0000.0000.0000.000
74A660ALA00.0460.03026.0230.0080.0080.0000.0000.0000.000
75A661ILE00.0650.04427.9540.0060.0060.0000.0000.0000.000
76A662LYS10.9680.98330.8070.0520.0520.0000.0000.0000.000
77A663THR0-0.098-0.05528.4080.0100.0100.0000.0000.0000.000
78A664ILE00.0240.00926.3960.0070.0070.0000.0000.0000.000
79A665ASN00.0260.00930.4660.0050.0050.0000.0000.0000.000
80A666SER0-0.047-0.02333.4650.0060.0060.0000.0000.0000.000
81A667ILE0-0.102-0.05228.1740.0060.0060.0000.0000.0000.000
82A668LEU00.0030.00431.4460.0040.0040.0000.0000.0000.000
83A669SER00.0650.02433.9960.0020.0020.0000.0000.0000.000
84A670LEU0-0.083-0.02834.1740.0050.0050.0000.0000.0000.000
85A671ARG10.8750.93330.4310.0090.0090.0000.0000.0000.000
86A672THR00.0220.02235.232-0.004-0.0040.0000.0000.0000.000
87A673THR0-0.091-0.05137.6380.0040.0040.0000.0000.0000.000
88A674ASP-1-0.829-0.92340.968-0.028-0.0280.0000.0000.0000.000
89A675GLU-1-1.001-0.98643.538-0.024-0.0240.0000.0000.0000.000
90A676ILE0-0.065-0.02238.0810.0000.0000.0000.0000.0000.000
91A677TYR0-0.013-0.00739.760-0.001-0.0010.0000.0000.0000.000
92A678SER0-0.047-0.01434.697-0.003-0.0030.0000.0000.0000.000
93A679THR0-0.0070.00432.993-0.001-0.0010.0000.0000.0000.000
94A680LEU0-0.022-0.03926.8640.0020.0020.0000.0000.0000.000
95A681ASP-1-0.893-0.92427.989-0.135-0.1350.0000.0000.0000.000
96A682LEU0-0.043-0.03421.399-0.004-0.0040.0000.0000.0000.000
97A683SER00.008-0.03321.5000.0060.0060.0000.0000.0000.000
98A684ILE0-0.024-0.00715.852-0.014-0.0140.0000.0000.0000.000
99A685ILE00.009-0.00513.850-0.001-0.0010.0000.0000.0000.000
100A686ASP-1-0.872-0.93210.283-0.913-0.9130.0000.0000.0000.000
101A687LEU00.001-0.0228.806-0.017-0.0170.0000.0000.0000.000
102A688GLN0-0.081-0.0574.3510.2650.335-0.001-0.007-0.0620.000
103A689ASP-1-0.829-0.9248.492-0.449-0.4490.0000.0000.0000.000
104A690ALA00.0000.02112.0750.0740.0740.0000.0000.0000.000
105A691SER0-0.059-0.02814.1960.0850.0850.0000.0000.0000.000
106A692CYS0-0.002-0.01315.797-0.053-0.0530.0000.0000.0000.000
107A693LYS10.9550.99618.1920.2930.2930.0000.0000.0000.000
108A694PHE00.016-0.01520.613-0.020-0.0200.0000.0000.0000.000
109A695LEU0-0.028-0.02023.7240.0100.0100.0000.0000.0000.000
110A696LYS10.9220.97226.4020.1110.1110.0000.0000.0000.000
111A697VAL00.0400.03229.8420.0060.0060.0000.0000.0000.000
112A698GLY00.1180.05932.8470.0010.0010.0000.0000.0000.000
113A699SER0-0.023-0.02435.592-0.002-0.0020.0000.0000.0000.000
114A700THR0-0.015-0.00133.3660.0020.0020.0000.0000.0000.000
115A701PRO0-0.060-0.00632.639-0.006-0.0060.0000.0000.0000.000
116A702SER00.0810.04027.336-0.008-0.0080.0000.0000.0000.000
117A703PHE0-0.020-0.03528.5280.0080.0080.0000.0000.0000.000
118A704ILE00.0450.03323.952-0.016-0.0160.0000.0000.0000.000
119A705LYS10.8710.94526.3520.2180.2180.0000.0000.0000.000
120A706ARG10.8120.89222.5170.2550.2550.0000.0000.0000.000
121A707GLY0-0.021-0.01126.9570.0160.0160.0000.0000.0000.000
122A708ASP-1-0.860-0.93829.271-0.169-0.1690.0000.0000.0000.000
123A709GLN0-0.124-0.06130.5080.0140.0140.0000.0000.0000.000
124A710VAL00.001-0.01430.518-0.009-0.0090.0000.0000.0000.000
125A711MET0-0.054-0.01927.3590.0160.0160.0000.0000.0000.000
126A712LYS10.8900.94829.9730.1040.1040.0000.0000.0000.000
127A713VAL0-0.028-0.00826.3890.0030.0030.0000.0000.0000.000
128A714GLN0-0.042-0.03029.4090.0090.0090.0000.0000.0000.000
129A715ALA00.0280.03330.375-0.005-0.0050.0000.0000.0000.000
130A716SER0-0.049-0.03031.9130.0040.0040.0000.0000.0000.000
131A717ASN00.0150.01634.7960.0020.0020.0000.0000.0000.000
132A718LEU00.010-0.00434.303-0.001-0.0010.0000.0000.0000.000
133A719PRO0-0.029-0.01636.7440.0020.0020.0000.0000.0000.000
134A720ILE00.0800.03640.1260.0010.0010.0000.0000.0000.000
135A721GLY0-0.021-0.01243.3390.0010.0010.0000.0000.0000.000
136A722ILE0-0.080-0.03437.3800.0030.0030.0000.0000.0000.000
137A723ILE00.0010.00040.281-0.002-0.0020.0000.0000.0000.000
138A724ASN0-0.034-0.01834.7760.0000.0000.0000.0000.0000.000
139A725GLU-1-0.927-0.96238.108-0.040-0.0400.0000.0000.0000.000
140A726PHE00.0470.03135.2950.0000.0000.0000.0000.0000.000
141A727ASP-1-0.960-0.98135.934-0.071-0.0710.0000.0000.0000.000
142A728VAL0-0.015-0.00930.375-0.007-0.0070.0000.0000.0000.000
143A729GLU-1-0.924-0.97330.710-0.113-0.1130.0000.0000.0000.000
144A730VAL00.007-0.01125.102-0.005-0.0050.0000.0000.0000.000
145A731VAL00.0060.02425.7640.0060.0060.0000.0000.0000.000
146A732SER00.000-0.00821.499-0.021-0.0210.0000.0000.0000.000
147A733GLU-1-0.943-0.96321.639-0.188-0.1880.0000.0000.0000.000
148A734GLN0-0.108-0.04516.1700.0010.0010.0000.0000.0000.000
149A735LEU0-0.019-0.01317.7120.0260.0260.0000.0000.0000.000
150A736LYS10.9260.94918.2360.2670.2670.0000.0000.0000.000
151A737ALA00.0340.01517.067-0.003-0.0030.0000.0000.0000.000
152A738GLY0-0.056-0.02718.6880.0430.0430.0000.0000.0000.000
153A739ASP-1-0.779-0.86720.945-0.294-0.2940.0000.0000.0000.000
154A740LEU0-0.007-0.01221.865-0.026-0.0260.0000.0000.0000.000
155A741LEU00.0230.02121.1350.0180.0180.0000.0000.0000.000
156A742ILE0-0.021-0.02024.343-0.007-0.0070.0000.0000.0000.000
157A743MET0-0.0030.03024.602-0.004-0.0040.0000.0000.0000.000
158A744MET00.004-0.02328.4170.0000.0000.0000.0000.0000.000
159A745SER00.0600.04531.600-0.002-0.0020.0000.0000.0000.000
160A746ASP-1-0.812-0.92433.759-0.088-0.0880.0000.0000.0000.000
161A747GLY00.0880.05337.1130.0010.0010.0000.0000.0000.000
162A748ILE0-0.084-0.06034.4990.0020.0020.0000.0000.0000.000
163A749PHE0-0.059-0.03836.246-0.003-0.0030.0000.0000.0000.000
164A750GLU-1-0.920-0.96737.925-0.075-0.0750.0000.0000.0000.000
165A751GLY00.0160.02740.6460.0050.0050.0000.0000.0000.000
166A752PRO0-0.071-0.02440.9430.0040.0040.0000.0000.0000.000
167A753LYS10.9610.97643.9720.0630.0630.0000.0000.0000.000
168A754HIS0-0.067-0.04047.779-0.001-0.0010.0000.0000.0000.000
169A755VAL0-0.0040.00244.014-0.001-0.0010.0000.0000.0000.000
170A756GLU-1-0.917-0.94346.668-0.068-0.0680.0000.0000.0000.000
171A757ASN0-0.008-0.01742.471-0.004-0.0040.0000.0000.0000.000
172A758HIS00.1010.04740.504-0.004-0.0040.0000.0000.0000.000
173A759ASP-1-0.833-0.90437.406-0.120-0.1200.0000.0000.0000.000
174A760LEU0-0.027-0.03037.990-0.007-0.0070.0000.0000.0000.000
175A761TRP00.0140.00438.918-0.004-0.0040.0000.0000.0000.000
176A762MET00.0700.04035.552-0.007-0.0070.0000.0000.0000.000
177A763LYS10.9370.97634.8470.1230.1230.0000.0000.0000.000
178A764ARG10.8800.94336.3510.0920.0920.0000.0000.0000.000
179A765LYS10.9480.98337.6050.1010.1010.0000.0000.0000.000
180A766MET00.0320.03132.283-0.008-0.0080.0000.0000.0000.000
181A767LYS10.9030.93933.8890.1310.1310.0000.0000.0000.000
182A768GLY0-0.038-0.00835.506-0.002-0.0020.0000.0000.0000.000
183A769LEU0-0.0080.01331.7170.0030.0030.0000.0000.0000.000
184A770LYS10.9030.94333.7550.1390.1390.0000.0000.0000.000
185A771THR0-0.0150.00329.964-0.016-0.0160.0000.0000.0000.000
186A772ASN00.0500.01025.3220.0220.0220.0000.0000.0000.000
187A773ASP-1-0.863-0.93925.374-0.314-0.3140.0000.0000.0000.000
188A774PRO0-0.013-0.01722.3960.0220.0220.0000.0000.0000.000
189A775GLN00.0300.00525.6770.0010.0010.0000.0000.0000.000
190A776GLU-1-0.888-0.92427.312-0.186-0.1860.0000.0000.0000.000
191A777ILE0-0.055-0.03227.6480.0180.0180.0000.0000.0000.000
192A778ALA0-0.0040.00028.7350.0130.0130.0000.0000.0000.000
193A779ASP-1-0.838-0.92730.741-0.146-0.1460.0000.0000.0000.000
194A780LEU0-0.061-0.03133.2910.0120.0120.0000.0000.0000.000
195A781LEU0-0.037-0.02332.1340.0110.0110.0000.0000.0000.000
196A782MET00.0450.02834.6490.0110.0110.0000.0000.0000.000
197A783GLU-1-0.850-0.91536.875-0.092-0.0920.0000.0000.0000.000
198A784GLU-1-0.890-0.93638.670-0.106-0.1060.0000.0000.0000.000
199A785VAL00.0190.00638.7490.0060.0060.0000.0000.0000.000
200A786ILE00.0300.04839.3420.0070.0070.0000.0000.0000.000
201A787ARG10.7920.88242.1990.1030.1030.0000.0000.0000.000
202A788THR0-0.117-0.08744.0640.0050.0050.0000.0000.0000.000
203A789ARG10.8310.91143.8850.0740.0740.0000.0000.0000.000
204A790SER0-0.069-0.04447.8290.0040.0040.0000.0000.0000.000
205A791GLY0-0.011-0.00245.5910.0030.0030.0000.0000.0000.000
206A792GLN0-0.049-0.01945.6840.0000.0000.0000.0000.0000.000
207A793ILE00.011-0.00140.907-0.003-0.0030.0000.0000.0000.000
208A794GLU-1-0.907-0.94744.541-0.050-0.0500.0000.0000.0000.000
209A795ASP-1-0.881-0.94040.792-0.060-0.0600.0000.0000.0000.000
210A796ASP-1-0.794-0.87937.041-0.066-0.0660.0000.0000.0000.000
211A797MET0-0.055-0.01736.824-0.004-0.0040.0000.0000.0000.000
212A798THR00.031-0.00530.471-0.002-0.0020.0000.0000.0000.000
213A799VAL0-0.020-0.00630.087-0.001-0.0010.0000.0000.0000.000
214A800VAL00.0040.00424.634-0.004-0.0040.0000.0000.0000.000
215A801VAL0-0.022-0.00225.262-0.001-0.0010.0000.0000.0000.000
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