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: 6N3ZZ

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:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
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
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2737108.7378
FMO2-HF: Nuclear repulsion 2646689.754733
FMO2-HF: Total energy -90418.983067
FMO2-MP2: Total energy -90678.599234


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.
-1.1750.529-0.01-0.75-0.9440.001
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 : -0.007 / q_NPA : -0.024
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].
3A589HIS00.0170.0183.8300.0321.655-0.010-0.726-0.8870.001
4A590SER00.024-0.0045.9060.7140.7140.0000.0000.0000.000
5A591TYR0-0.056-0.0208.5600.3720.3720.0000.0000.0000.000
6A592ARG10.8300.90110.3290.9610.9610.0000.0000.0000.000
7A593VAL00.0400.02512.5610.1940.1940.0000.0000.0000.000
8A594SER0-0.057-0.01415.234-0.029-0.0290.0000.0000.0000.000
9A595THR00.015-0.01518.0830.0390.0390.0000.0000.0000.000
10A596GLY00.0210.01120.7430.0090.0090.0000.0000.0000.000
11A597ALA0-0.025-0.01624.253-0.010-0.0100.0000.0000.0000.000
12A598ALA00.0200.03526.9510.0130.0130.0000.0000.0000.000
13A599HIS00.0500.02828.936-0.017-0.0170.0000.0000.0000.000
14A600ALA0-0.024-0.01032.6320.0090.0090.0000.0000.0000.000
15A601ALA00.0180.01436.276-0.004-0.0040.0000.0000.0000.000
16A602LYS10.8450.88438.6390.1430.1430.0000.0000.0000.000
17A603GLY0-0.047-0.02642.1970.0040.0040.0000.0000.0000.000
18A604GLY0-0.032-0.00641.6760.0050.0050.0000.0000.0000.000
19A605GLY0-0.038-0.01241.2700.0030.0030.0000.0000.0000.000
20A606LEU0-0.025-0.03337.969-0.007-0.0070.0000.0000.0000.000
21A607VAL0-0.058-0.02934.740-0.007-0.0070.0000.0000.0000.000
22A608SER0-0.0180.00533.4230.0080.0080.0000.0000.0000.000
23A609GLY0-0.056-0.03035.0320.0020.0020.0000.0000.0000.000
24A610ASP-1-0.776-0.85332.989-0.253-0.2530.0000.0000.0000.000
25A611SER0-0.057-0.03229.390-0.003-0.0030.0000.0000.0000.000
26A612TYR00.011-0.02424.911-0.019-0.0190.0000.0000.0000.000
27A613SER0-0.035-0.01021.9340.0010.0010.0000.0000.0000.000
28A614MET00.0170.00319.281-0.023-0.0230.0000.0000.0000.000
29A615MET0-0.022-0.00716.3040.0220.0220.0000.0000.0000.000
30A616GLU-1-0.902-0.95810.281-1.996-1.9960.0000.0000.0000.000
31A617LEU0-0.042-0.00512.264-0.129-0.1290.0000.0000.0000.000
32A618GLY0-0.017-0.00811.7130.0020.0020.0000.0000.0000.000
33A619ALA0-0.003-0.0016.879-0.195-0.1950.0000.0000.0000.000
34A620ARG10.8240.8616.9040.4070.4070.0000.0000.0000.000
35A621LYS10.8340.9258.6201.1451.1450.0000.0000.0000.000
36A622TYR00.0210.00612.042-0.128-0.1280.0000.0000.0000.000
37A623ALA0-0.0090.01714.7740.0840.0840.0000.0000.0000.000
38A624ILE0-0.010-0.01818.233-0.027-0.0270.0000.0000.0000.000
39A625ALA00.0190.00821.4450.0230.0230.0000.0000.0000.000
40A626ILE0-0.0060.00024.907-0.005-0.0050.0000.0000.0000.000
41A627SER00.007-0.00228.429-0.001-0.0010.0000.0000.0000.000
42A628ASP-1-0.809-0.88131.333-0.182-0.1820.0000.0000.0000.000
43A629GLY00.012-0.00334.8890.0010.0010.0000.0000.0000.000
44A630MET0-0.080-0.01331.0310.0020.0020.0000.0000.0000.000
45A631GLY00.0470.02834.1830.0110.0110.0000.0000.0000.000
46A632ASN0-0.015-0.01235.595-0.009-0.0090.0000.0000.0000.000
47A633GLY00.0550.00735.7540.0110.0110.0000.0000.0000.000
48A634ALA0-0.020-0.01132.600-0.008-0.0080.0000.0000.0000.000
49A635ARG10.8750.92631.8180.0800.0800.0000.0000.0000.000
50A636ALA00.0510.04332.547-0.003-0.0030.0000.0000.0000.000
51A637HIS00.0820.03929.122-0.020-0.0200.0000.0000.0000.000
52A638PHE0-0.063-0.01626.805-0.015-0.0150.0000.0000.0000.000
53A639GLU-1-0.854-0.93328.310-0.121-0.1210.0000.0000.0000.000
54A640SER00.0610.01329.8870.0000.0000.0000.0000.0000.000
55A641ASN00.0160.00324.498-0.033-0.0330.0000.0000.0000.000
56A642GLU-1-0.891-0.92825.129-0.195-0.1950.0000.0000.0000.000
57A643THR00.017-0.00126.7820.0020.0020.0000.0000.0000.000
58A644ILE00.0420.02423.161-0.009-0.0090.0000.0000.0000.000
59A645LYS10.8480.91521.2480.1860.1860.0000.0000.0000.000
60A646LEU0-0.064-0.02522.455-0.012-0.0120.0000.0000.0000.000
61A647LEU00.0310.01824.654-0.005-0.0050.0000.0000.0000.000
62A648GLU-1-0.861-0.94719.570-0.535-0.5350.0000.0000.0000.000
63A649LYS10.8500.92117.2130.3300.3300.0000.0000.0000.000
64A650ILE00.0080.01121.1290.0060.0060.0000.0000.0000.000
65A651LEU00.0400.04321.0680.0020.0020.0000.0000.0000.000
66A652GLU-1-0.854-0.92416.501-0.684-0.6840.0000.0000.0000.000
67A653SER0-0.090-0.05417.9540.0010.0010.0000.0000.0000.000
68A654GLY0-0.022-0.01020.2870.0170.0170.0000.0000.0000.000
69A655ILE0-0.054-0.01320.7950.0270.0270.0000.0000.0000.000
70A656ASP-1-0.753-0.87524.641-0.218-0.2180.0000.0000.0000.000
71A657GLU-1-0.826-0.90025.765-0.295-0.2950.0000.0000.0000.000
72A658LYS10.8750.92328.0390.2140.2140.0000.0000.0000.000
73A659ILE0-0.019-0.01529.3830.0100.0100.0000.0000.0000.000
74A660ALA00.0220.02626.6300.0080.0080.0000.0000.0000.000
75A661ILE00.0700.04128.5220.0060.0060.0000.0000.0000.000
76A662LYS10.9200.96931.4990.1510.1510.0000.0000.0000.000
77A663THR0-0.089-0.05329.5670.0190.0190.0000.0000.0000.000
78A664ILE00.0300.01426.8810.0060.0060.0000.0000.0000.000
79A665ASN00.005-0.01730.8480.0100.0100.0000.0000.0000.000
80A666SER0-0.033-0.02033.7470.0100.0100.0000.0000.0000.000
81A667ILE0-0.077-0.04928.7830.0100.0100.0000.0000.0000.000
82A668LEU0-0.0260.00931.556-0.002-0.0020.0000.0000.0000.000
83A669SER00.0400.00434.6540.0030.0030.0000.0000.0000.000
84A670LEU0-0.073-0.02834.2340.0100.0100.0000.0000.0000.000
85A671ARG10.8100.89130.3140.1490.1490.0000.0000.0000.000
86A672THR0-0.0010.00335.739-0.011-0.0110.0000.0000.0000.000
87A673THR0-0.081-0.04837.9920.0070.0070.0000.0000.0000.000
88A674ASP-1-0.835-0.91541.535-0.101-0.1010.0000.0000.0000.000
89A675GLU-1-0.895-0.93244.088-0.098-0.0980.0000.0000.0000.000
90A676ILE0-0.104-0.04138.428-0.003-0.0030.0000.0000.0000.000
91A677TYR0-0.061-0.05039.759-0.006-0.0060.0000.0000.0000.000
92A678SER0-0.044-0.01435.251-0.003-0.0030.0000.0000.0000.000
93A679THR0-0.017-0.01333.5900.0020.0020.0000.0000.0000.000
94A680LEU0-0.071-0.04727.185-0.008-0.0080.0000.0000.0000.000
95A681ASP-1-0.803-0.87328.612-0.297-0.2970.0000.0000.0000.000
96A682LEU0-0.025-0.02922.106-0.018-0.0180.0000.0000.0000.000
97A683SER00.023-0.01721.8940.0230.0230.0000.0000.0000.000
98A684ILE0-0.026-0.01916.473-0.046-0.0460.0000.0000.0000.000
99A685ILE00.0410.02014.5820.0280.0280.0000.0000.0000.000
100A686ASP-1-0.751-0.85510.600-1.611-1.6110.0000.0000.0000.000
101A687LEU0-0.002-0.0108.9530.0300.0300.0000.0000.0000.000
102A688GLN0-0.038-0.0283.8040.4460.5270.000-0.024-0.0570.000
103A689ASP-1-0.814-0.8748.675-0.770-0.7700.0000.0000.0000.000
104A690ALA0-0.0050.01712.2570.1410.1410.0000.0000.0000.000
105A691SER0-0.038-0.03214.6090.1120.1120.0000.0000.0000.000
106A692CYS0-0.039-0.02716.256-0.110-0.1100.0000.0000.0000.000
107A693LYS10.8060.90418.3640.5940.5940.0000.0000.0000.000
108A694PHE00.0370.00521.105-0.042-0.0420.0000.0000.0000.000
109A695LEU0-0.020-0.01124.2940.0220.0220.0000.0000.0000.000
110A696LYS10.8130.90926.9500.2270.2270.0000.0000.0000.000
111A697VAL00.0140.01430.3490.0130.0130.0000.0000.0000.000
112A698GLY00.1360.06733.413-0.001-0.0010.0000.0000.0000.000
113A699SER0-0.012-0.00436.231-0.006-0.0060.0000.0000.0000.000
114A700THR0-0.011-0.00133.7840.0070.0070.0000.0000.0000.000
115A701PRO0-0.040-0.00133.330-0.007-0.0070.0000.0000.0000.000
116A702SER00.049-0.00327.917-0.016-0.0160.0000.0000.0000.000
117A703PHE0-0.037-0.04428.7680.0190.0190.0000.0000.0000.000
118A704ILE00.0390.02424.121-0.036-0.0360.0000.0000.0000.000
119A705LYS10.8420.93427.1300.3400.3400.0000.0000.0000.000
120A706ARG10.8120.86422.6430.4050.4050.0000.0000.0000.000
121A707GLY00.0150.01127.3090.0270.0270.0000.0000.0000.000
122A708ASP-1-0.855-0.92429.328-0.264-0.2640.0000.0000.0000.000
123A709GLN0-0.076-0.02929.8850.0070.0070.0000.0000.0000.000
124A710VAL00.001-0.01430.803-0.016-0.0160.0000.0000.0000.000
125A711MET0-0.043-0.01227.7400.0300.0300.0000.0000.0000.000
126A712LYS10.8830.94030.1260.1990.1990.0000.0000.0000.000
127A713VAL0-0.029-0.00826.2200.0100.0100.0000.0000.0000.000
128A714GLN0-0.008-0.01829.4630.0090.0090.0000.0000.0000.000
129A715ALA00.0040.01731.252-0.001-0.0010.0000.0000.0000.000
130A716SER0-0.043-0.02732.5120.0080.0080.0000.0000.0000.000
131A717ASN0-0.013-0.00135.2770.0000.0000.0000.0000.0000.000
132A718LEU00.0320.01535.1600.0010.0010.0000.0000.0000.000
133A719PRO0-0.018-0.01037.4790.0050.0050.0000.0000.0000.000
134A720ILE00.0490.01240.8410.0020.0020.0000.0000.0000.000
135A721GLY0-0.005-0.00144.0100.0050.0050.0000.0000.0000.000
136A722ILE0-0.075-0.03437.6330.0030.0030.0000.0000.0000.000
137A723ILE0-0.006-0.00240.525-0.004-0.0040.0000.0000.0000.000
138A724ASN0-0.029-0.02235.631-0.006-0.0060.0000.0000.0000.000
139A725GLU-1-0.877-0.90338.797-0.122-0.1220.0000.0000.0000.000
140A726PHE00.002-0.00735.7550.0010.0010.0000.0000.0000.000
141A727ASP-1-0.907-0.97036.414-0.173-0.1730.0000.0000.0000.000
142A728VAL0-0.0360.00231.125-0.012-0.0120.0000.0000.0000.000
143A729GLU-1-0.811-0.89231.226-0.239-0.2390.0000.0000.0000.000
144A730VAL0-0.025-0.03625.687-0.014-0.0140.0000.0000.0000.000
145A731VAL0-0.0060.00726.1650.0180.0180.0000.0000.0000.000
146A732SER0-0.026-0.03822.186-0.048-0.0480.0000.0000.0000.000
147A733GLU-1-0.907-0.94921.870-0.343-0.3430.0000.0000.0000.000
148A734GLN0-0.113-0.06016.385-0.023-0.0230.0000.0000.0000.000
149A735LEU0-0.0020.00618.0860.0490.0490.0000.0000.0000.000
150A736LYS10.9220.94718.4980.4290.4290.0000.0000.0000.000
151A737ALA00.0120.00616.696-0.008-0.0080.0000.0000.0000.000
152A738GLY0-0.036-0.01818.5170.0680.0680.0000.0000.0000.000
153A739ASP-1-0.763-0.84621.214-0.465-0.4650.0000.0000.0000.000
154A740LEU0-0.010-0.01822.112-0.052-0.0520.0000.0000.0000.000
155A741LEU0-0.0020.01621.5320.0440.0440.0000.0000.0000.000
156A742ILE0-0.027-0.02524.433-0.011-0.0110.0000.0000.0000.000
157A743MET0-0.0080.03424.982-0.008-0.0080.0000.0000.0000.000
158A744MET0-0.008-0.02328.4220.0060.0060.0000.0000.0000.000
159A745SER00.0580.02031.429-0.002-0.0020.0000.0000.0000.000
160A746ASP-1-0.778-0.89633.768-0.206-0.2060.0000.0000.0000.000
161A747GLY00.0250.02137.2550.0070.0070.0000.0000.0000.000
162A748ILE0-0.069-0.04034.0690.0080.0080.0000.0000.0000.000
163A749PHE0-0.028-0.02936.2520.0020.0020.0000.0000.0000.000
164A750GLU-1-0.915-0.97537.857-0.163-0.1630.0000.0000.0000.000
165A751GLY00.0290.03440.3590.0090.0090.0000.0000.0000.000
166A752PRO0-0.086-0.04840.4870.0100.0100.0000.0000.0000.000
167A753LYS10.8760.93143.5890.1300.1300.0000.0000.0000.000
168A754HIS0-0.049-0.03847.366-0.003-0.0030.0000.0000.0000.000
169A755VAL00.0170.01144.069-0.001-0.0010.0000.0000.0000.000
170A756GLU-1-0.895-0.93847.195-0.128-0.1280.0000.0000.0000.000
171A757ASN0-0.034-0.02542.879-0.009-0.0090.0000.0000.0000.000
172A758HIS00.0970.05540.614-0.006-0.0060.0000.0000.0000.000
173A759ASP-1-0.774-0.86137.896-0.222-0.2220.0000.0000.0000.000
174A760LEU0-0.055-0.03538.489-0.009-0.0090.0000.0000.0000.000
175A761TRP00.0340.01139.022-0.003-0.0030.0000.0000.0000.000
176A762MET00.0520.03235.915-0.006-0.0060.0000.0000.0000.000
177A763LYS10.8670.92434.9170.2060.2060.0000.0000.0000.000
178A764ARG10.8710.93436.7120.1640.1640.0000.0000.0000.000
179A765LYS10.8110.91037.4700.1840.1840.0000.0000.0000.000
180A766MET00.0210.01332.272-0.006-0.0060.0000.0000.0000.000
181A767LYS10.8690.91633.8510.2160.2160.0000.0000.0000.000
182A768GLY0-0.0080.01835.9510.0040.0040.0000.0000.0000.000
183A769LEU0-0.0080.01831.2830.0090.0090.0000.0000.0000.000
184A770LYS10.8680.90933.7210.2130.2130.0000.0000.0000.000
185A771THR0-0.027-0.02429.606-0.014-0.0140.0000.0000.0000.000
186A772ASN0-0.003-0.02224.7050.0230.0230.0000.0000.0000.000
187A773ASP-1-0.821-0.91724.620-0.509-0.5090.0000.0000.0000.000
188A774PRO0-0.022-0.02321.8160.0320.0320.0000.0000.0000.000
189A775GLN00.002-0.00725.121-0.014-0.0140.0000.0000.0000.000
190A776GLU-1-0.873-0.90627.040-0.280-0.2800.0000.0000.0000.000
191A777ILE0-0.045-0.02727.2630.0270.0270.0000.0000.0000.000
192A778ALA00.0120.01228.1600.0210.0210.0000.0000.0000.000
193A779ASP-1-0.811-0.90830.225-0.273-0.2730.0000.0000.0000.000
194A780LEU0-0.060-0.03132.8690.0230.0230.0000.0000.0000.000
195A781LEU0-0.049-0.02931.5950.0180.0180.0000.0000.0000.000
196A782MET00.0330.03233.8960.0190.0190.0000.0000.0000.000
197A783GLU-1-0.815-0.87436.152-0.162-0.1620.0000.0000.0000.000
198A784GLU-1-0.796-0.88638.211-0.173-0.1730.0000.0000.0000.000
199A785VAL0-0.020-0.00338.1800.0120.0120.0000.0000.0000.000
200A786ILE00.0210.02639.0300.0130.0130.0000.0000.0000.000
201A787ARG10.7390.82241.2990.1820.1820.0000.0000.0000.000
202A788THR0-0.085-0.04843.6970.0090.0090.0000.0000.0000.000
203A789ARG10.7420.85142.8710.1560.1560.0000.0000.0000.000
204A790SER0-0.054-0.03347.2440.0060.0060.0000.0000.0000.000
205A791GLY00.0090.01445.2050.0050.0050.0000.0000.0000.000
206A792GLN0-0.066-0.03045.309-0.007-0.0070.0000.0000.0000.000
207A793ILE00.0550.02640.582-0.004-0.0040.0000.0000.0000.000
208A794GLU-1-0.718-0.82444.278-0.123-0.1230.0000.0000.0000.000
209A795ASP-1-0.841-0.90441.035-0.140-0.1400.0000.0000.0000.000
210A796ASP-1-0.747-0.86636.625-0.177-0.1770.0000.0000.0000.000
211A797MET0-0.066-0.03236.3730.0010.0010.0000.0000.0000.000
212A798THR00.039-0.00229.818-0.005-0.0050.0000.0000.0000.000
213A799VAL0-0.044-0.01629.8420.0000.0000.0000.0000.0000.000
214A800VAL00.0210.01324.631-0.008-0.0080.0000.0000.0000.000
215A801VAL0-0.040-0.00924.8570.0070.0070.0000.0000.0000.000
216A802VAL00.0370.00119.266-0.042-0.0420.0000.0000.0000.000
217A803ARG10.7800.88519.1520.7100.7100.0000.0000.0000.000
218A804ILE00.0040.01915.010-0.100-0.1000.0000.0000.0000.000
219A805ASP-1-0.804-0.87915.596-0.756-0.7560.0000.0000.0000.000
220A806HIS00.0690.01113.776-0.215-0.2150.0000.0000.0000.000
221A807ASN0-0.038-0.0137.7220.5580.5580.0000.0000.0000.000
222A808THR0-0.013-0.01110.954-0.148-0.1480.0000.0000.0000.000
223A809PRO00.0410.03610.751-0.135-0.1350.0000.0000.0000.000
224A810LYS10.9780.96012.2451.1051.1050.0000.0000.0000.000
225A811TRP00.0150.01711.1370.0610.0610.0000.0000.0000.000
226A812ALA0-0.031-0.01215.6210.0820.0820.0000.0000.0000.000
227A813SER0-0.0020.01117.3940.0010.0010.0000.0000.0000.000
228A814ILE00.003-0.00820.735-0.010-0.0100.0000.0000.0000.000
229A815PRO0-0.0090.00921.3950.0340.0340.0000.0000.0000.000
230A816VAL00.013-0.00524.262-0.011-0.0110.0000.0000.0000.000
231A817PRO0-0.0040.00728.0080.0150.0150.0000.0000.0000.000