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: 6YK6Z

Calculation Name: 4MKR-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4MKR

Chain ID: B

ChEMBL ID:

UniProt ID: A0A096

Base Structure: X-ray

Registration Date: 2023-09-23

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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2844910.016349
FMO2-HF: Nuclear repulsion 2753349.353712
FMO2-HF: Total energy -91560.662637
FMO2-MP2: Total energy -91828.904192


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:49:VAL)


Summations of interaction energy for fragment #1(B:49:VAL)
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.
-2.627-6.88230.467-8.491-17.722-0.03
Interaction energy analysis for fragmet #1(B:49:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : 0.017
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].
3B51LEU0-0.001-0.0132.0852.941-1.12012.119-2.556-5.502-0.003
4B52LYS10.9710.9913.6400.1630.2330.0180.010-0.0990.000
5B53ASN00.0300.0127.1920.1010.1010.0000.0000.0000.000
6B54LEU0-0.055-0.0178.9390.0400.0400.0000.0000.0000.000
7B55TYR00.001-0.02211.8080.0130.0130.0000.0000.0000.000
8B56LEU00.0440.03912.114-0.017-0.0170.0000.0000.0000.000
9B57SER00.008-0.02214.8180.0320.0320.0000.0000.0000.000
10B58CYS0-0.073-0.02617.162-0.030-0.0300.0000.0000.0000.000
11B59ASP-1-0.870-0.93618.092-0.073-0.0730.0000.0000.0000.000
12B60PRO0-0.031-0.01220.938-0.010-0.0100.0000.0000.0000.000
13B86GLY00.0350.01512.3850.0100.0100.0000.0000.0000.000
14B87PHE0-0.022-0.01311.758-0.042-0.0420.0000.0000.0000.000
15B88GLY00.0530.00711.129-0.010-0.0100.0000.0000.0000.000
16B89VAL0-0.060-0.0209.5150.0520.0520.0000.0000.0000.000
17B90GLY00.0490.0176.571-0.124-0.1240.0000.0000.0000.000
18B91LYS10.8570.9366.6550.0450.0450.0000.0000.0000.000
19B92VAL00.0380.0202.120-0.709-0.9052.761-0.536-2.0290.002
20B93VAL0-0.048-0.0203.651-0.0680.0780.0010.013-0.1610.000
21B94ASP-1-0.901-0.9362.307-1.697-0.9613.089-1.765-2.059-0.015
22B102THR00.0510.0246.1140.0270.0270.0000.0000.0000.000
23B103GLY0-0.140-0.0786.948-0.105-0.1050.0000.0000.0000.000
24B104ASP-1-0.868-0.9276.0591.1041.1040.0000.0000.0000.000
25B105TYR0-0.011-0.0196.574-0.027-0.0270.0000.0000.0000.000
26B106VAL0-0.013-0.0173.913-0.0740.0990.000-0.026-0.1480.000
27B107TRP00.0180.0027.098-0.157-0.1570.0000.0000.0000.000
28B108GLY00.0570.0297.8450.1150.1150.0000.0000.0000.000
29B109LEU0-0.061-0.0128.517-0.043-0.0430.0000.0000.0000.000
30B110ILE0-0.019-0.0016.181-0.139-0.1390.0000.0000.0000.000
31B111GLY00.0340.0158.5250.0880.0880.0000.0000.0000.000
32B112TRP0-0.012-0.02311.0550.0310.0310.0000.0000.0000.000
33B113GLU-1-0.905-0.96612.231-0.484-0.4840.0000.0000.0000.000
34B114GLU-1-0.945-0.96011.801-0.368-0.3680.0000.0000.0000.000
35B115TYR0-0.014-0.0277.6680.0670.0670.0000.0000.0000.000
36B116SER0-0.041-0.0125.9580.0860.0860.0000.0000.0000.000
37B117LEU00.0220.0174.170-1.008-0.838-0.001-0.066-0.1020.000
38B118ILE0-0.002-0.0122.0491.963-0.3557.792-1.771-3.703-0.002
39B119THR00.0100.0102.786-4.240-2.1420.340-1.118-1.320-0.013
40B120LYS10.9740.9815.4740.5590.5590.0000.0000.0000.000
41B121PRO00.0610.0232.789-0.867-0.2650.241-0.171-0.6720.001
42B122GLN0-0.024-0.0284.4230.1750.280-0.001-0.006-0.0970.000
43B123GLY0-0.0010.0196.968-0.045-0.0450.0000.0000.0000.000
44B124LEU0-0.0220.0012.2160.748-1.0324.108-0.499-1.8300.000
45B125PHE0-0.024-0.0086.2850.1950.1950.0000.0000.0000.000
46B126LYS10.9130.9486.300-1.059-1.0590.0000.0000.0000.000
47B127ILE0-0.032-0.0139.675-0.075-0.0750.0000.0000.0000.000
48B128HIS10.8320.91011.904-0.400-0.4000.0000.0000.0000.000
49B129HIS10.8500.91214.535-0.199-0.1990.0000.0000.0000.000
50B130THR00.015-0.00213.430-0.006-0.0060.0000.0000.0000.000
51B131GLU-1-0.819-0.88216.0460.1480.1480.0000.0000.0000.000
52B132ILE0-0.066-0.01317.616-0.022-0.0220.0000.0000.0000.000
53B133PRO00.0360.00818.0300.0050.0050.0000.0000.0000.000
54B134LEU00.0420.00012.133-0.003-0.0030.0000.0000.0000.000
55B135SER00.0210.02014.6820.0020.0020.0000.0000.0000.000
56B136TYR00.0400.00116.819-0.015-0.0150.0000.0000.0000.000
57B137TYR00.0010.01213.1890.0050.0050.0000.0000.0000.000
58B138THR0-0.0160.00314.235-0.004-0.0040.0000.0000.0000.000
59B139GLY00.0450.01316.031-0.014-0.0140.0000.0000.0000.000
60B140ILE0-0.014-0.01019.2720.0100.0100.0000.0000.0000.000
61B141LEU00.010-0.01217.0700.0050.0050.0000.0000.0000.000
62B142GLY00.0390.02815.5950.0230.0230.0000.0000.0000.000
63B143MET00.0230.03215.5600.0160.0160.0000.0000.0000.000
64B144VAL00.0250.03417.1930.0060.0060.0000.0000.0000.000
65B145GLY0-0.005-0.02020.1510.0020.0020.0000.0000.0000.000
66B146LEU00.0170.01616.9240.0020.0020.0000.0000.0000.000
67B147THR00.004-0.03320.434-0.001-0.0010.0000.0000.0000.000
68B148ALA0-0.052-0.02822.520-0.001-0.0010.0000.0000.0000.000
69B149TYR00.0040.00823.1000.0000.0000.0000.0000.0000.000
70B150VAL00.0390.01422.0150.0010.0010.0000.0000.0000.000
71B151GLY00.0660.03225.048-0.002-0.0020.0000.0000.0000.000
72B152PHE0-0.046-0.03327.604-0.003-0.0030.0000.0000.0000.000
73B153TYR0-0.029-0.03927.220-0.002-0.0020.0000.0000.0000.000
74B154ASP-1-0.918-0.93827.3190.0610.0610.0000.0000.0000.000
75B155ILE00.0300.02827.657-0.004-0.0040.0000.0000.0000.000
76B156CYS0-0.071-0.03730.808-0.006-0.0060.0000.0000.0000.000
77B157SER0-0.052-0.01733.052-0.003-0.0030.0000.0000.0000.000
78B158PRO00.0010.01833.453-0.003-0.0030.0000.0000.0000.000
79B159LYS10.9640.97036.369-0.029-0.0290.0000.0000.0000.000
80B160LYS10.9070.93538.529-0.042-0.0420.0000.0000.0000.000
81B161GLY0-0.010-0.00440.596-0.001-0.0010.0000.0000.0000.000
82B162GLU-1-0.856-0.92739.7870.0240.0240.0000.0000.0000.000
83B163ARG10.8310.92341.336-0.016-0.0160.0000.0000.0000.000
84B164VAL00.0200.00235.709-0.001-0.0010.0000.0000.0000.000
85B165PHE00.004-0.00238.557-0.002-0.0020.0000.0000.0000.000
86B166VAL00.0090.01132.6630.0010.0010.0000.0000.0000.000
87B167SER00.0380.00934.755-0.002-0.0020.0000.0000.0000.000
88B168ALA00.0230.00831.4240.0000.0000.0000.0000.0000.000
89B169ALA00.0170.02431.588-0.001-0.0010.0000.0000.0000.000
90B170ALA0-0.015-0.00231.9870.0020.0020.0000.0000.0000.000
91B171GLY0-0.0130.00028.878-0.003-0.0030.0000.0000.0000.000
92B172ALA00.005-0.00524.0320.0060.0060.0000.0000.0000.000
93B173VAL00.0640.02423.8550.0070.0070.0000.0000.0000.000
94B174GLY00.0520.02626.1810.0070.0070.0000.0000.0000.000
95B175GLN00.000-0.00628.5260.0100.0100.0000.0000.0000.000
96B176ILE0-0.0150.00223.9770.0040.0040.0000.0000.0000.000
97B177VAL00.0020.01328.1740.0060.0060.0000.0000.0000.000
98B178GLY00.0310.01230.0070.0040.0040.0000.0000.0000.000
99B179GLN0-0.013-0.00229.6320.0020.0020.0000.0000.0000.000
100B180PHE00.013-0.00124.9530.0040.0040.0000.0000.0000.000
101B181ALA00.0220.01831.1630.0030.0030.0000.0000.0000.000
102B182LYS10.8250.90134.494-0.017-0.0170.0000.0000.0000.000
103B183GLN0-0.016-0.01930.5070.0040.0040.0000.0000.0000.000
104B184PHE00.0120.02933.6540.0030.0030.0000.0000.0000.000
105B185GLY0-0.041-0.02835.8940.0010.0010.0000.0000.0000.000
106B186CYS0-0.076-0.01637.8850.0000.0000.0000.0000.0000.000
107B187TYR0-0.0210.00039.773-0.001-0.0010.0000.0000.0000.000
108B188VAL0-0.014-0.01536.3780.0000.0000.0000.0000.0000.000
109B189VAL00.0270.01539.595-0.002-0.0020.0000.0000.0000.000
110B190GLY0-0.006-0.00437.3840.0000.0000.0000.0000.0000.000
111B191SER0-0.0180.00437.017-0.002-0.0020.0000.0000.0000.000
112B192ALA0-0.012-0.02136.153-0.002-0.0020.0000.0000.0000.000
113B193GLY00.0400.01436.6160.0010.0010.0000.0000.0000.000
114B194SER0-0.007-0.01937.908-0.001-0.0010.0000.0000.0000.000
115B195ASP-1-0.761-0.88239.508-0.019-0.0190.0000.0000.0000.000
116B196GLU-1-0.788-0.86735.780-0.028-0.0280.0000.0000.0000.000
117B197LYS10.8040.87232.8750.0330.0330.0000.0000.0000.000
118B198VAL00.0130.01236.9330.0030.0030.0000.0000.0000.000
119B199ASN00.026-0.00239.6270.0020.0020.0000.0000.0000.000
120B200LEU0-0.0070.01333.2580.0020.0020.0000.0000.0000.000
121B201LEU0-0.051-0.03533.8410.0030.0030.0000.0000.0000.000
122B202LYS10.8120.91236.9880.0010.0010.0000.0000.0000.000
123B203THR0-0.0010.00238.7600.0010.0010.0000.0000.0000.000
124B204LYS10.9270.96531.2250.0080.0080.0000.0000.0000.000
125B205PHE0-0.059-0.04829.6170.0020.0020.0000.0000.0000.000
126B206GLY00.0250.02734.3940.0020.0020.0000.0000.0000.000
127B207PHE0-0.005-0.00833.9950.0020.0020.0000.0000.0000.000
128B208ASP-1-0.771-0.84738.7230.0130.0130.0000.0000.0000.000
129B209GLU-1-0.861-0.93241.827-0.001-0.0010.0000.0000.0000.000
130B210ALA00.000-0.01239.8140.0000.0000.0000.0000.0000.000
131B211PHE0-0.0020.01541.272-0.001-0.0010.0000.0000.0000.000
132B212ASN00.0500.00240.993-0.003-0.0030.0000.0000.0000.000
133B213TYR00.007-0.00237.0810.0000.0000.0000.0000.0000.000
134B214LYS10.9660.98939.0220.0360.0360.0000.0000.0000.000
135B215LYS10.8200.92544.3040.0200.0200.0000.0000.0000.000
136B216GLU-1-0.814-0.90145.961-0.009-0.0090.0000.0000.0000.000
137B217PRO0-0.0150.01247.8590.0000.0000.0000.0000.0000.000
138B218ASP-1-0.834-0.92149.840-0.011-0.0110.0000.0000.0000.000
139B219LEU00.0730.01542.9110.0020.0020.0000.0000.0000.000
140B220THR00.0470.02446.6430.0010.0010.0000.0000.0000.000
141B221LYS10.9350.97248.4360.0110.0110.0000.0000.0000.000
142B222ALA0-0.047-0.02146.5990.0010.0010.0000.0000.0000.000
143B223LEU00.002-0.00442.3400.0010.0010.0000.0000.0000.000
144B224LYS10.9270.96646.4080.0000.0000.0000.0000.0000.000
145B225ARG10.7790.86648.5670.0090.0090.0000.0000.0000.000
146B226TYR0-0.0010.01445.4480.0000.0000.0000.0000.0000.000
147B227PHE00.0040.00441.5620.0020.0020.0000.0000.0000.000
148B228PRO00.0400.02747.6660.0000.0000.0000.0000.0000.000
149B229GLU-1-0.912-0.96749.5280.0120.0120.0000.0000.0000.000
150B230GLY0-0.0010.01047.8110.0010.0010.0000.0000.0000.000
151B231ILE00.003-0.01741.2100.0010.0010.0000.0000.0000.000
152B232ASP-1-0.762-0.86041.4280.0170.0170.0000.0000.0000.000
153B233ILE00.0010.01635.5370.0010.0010.0000.0000.0000.000
154B234TYR0-0.048-0.05036.511-0.002-0.0020.0000.0000.0000.000
155B235PHE00.0180.00927.4660.0010.0010.0000.0000.0000.000
156B236GLU-1-0.726-0.85132.772-0.018-0.0180.0000.0000.0000.000
157B237ASN0-0.020-0.03929.146-0.001-0.0010.0000.0000.0000.000
158B238VAL0-0.036-0.02831.427-0.006-0.0060.0000.0000.0000.000
159B239GLY00.0410.02334.246-0.004-0.0040.0000.0000.0000.000
160B240GLY00.0390.01336.7060.0000.0000.0000.0000.0000.000
161B241PRO00.1020.04040.0010.0030.0030.0000.0000.0000.000
162B242MET0-0.0470.00038.6900.0030.0030.0000.0000.0000.000
163B243LEU0-0.0050.00937.8290.0030.0030.0000.0000.0000.000
164B244GLU-1-0.843-0.92040.483-0.013-0.0130.0000.0000.0000.000
165B245ALA0-0.0080.01543.8130.0020.0020.0000.0000.0000.000
166B246VAL0-0.002-0.02139.7880.0020.0020.0000.0000.0000.000
167B247LEU0-0.022-0.00841.7740.0020.0020.0000.0000.0000.000
168B248HIS00.0340.01444.6120.0030.0030.0000.0000.0000.000
169B249ASN0-0.110-0.04845.8900.0020.0020.0000.0000.0000.000
170B250MET0-0.0270.01939.9260.0020.0020.0000.0000.0000.000
171B251ARG10.7870.88145.077-0.014-0.0140.0000.0000.0000.000
172B252ILE00.000-0.01745.4990.0000.0000.0000.0000.0000.000
173B253LYS10.9110.95942.351-0.022-0.0220.0000.0000.0000.000
174B254GLY00.0410.04341.7290.0020.0020.0000.0000.0000.000
175B255ARG10.7680.85636.638-0.024-0.0240.0000.0000.0000.000
176B256ILE00.0130.00435.257-0.001-0.0010.0000.0000.0000.000
177B257ALA00.0450.03430.5130.0010.0010.0000.0000.0000.000
178B258ALA0-0.039-0.04031.598-0.003-0.0030.0000.0000.0000.000
179B259CYS00.0140.00626.5510.0010.0010.0000.0000.0000.000
180B260GLY0-0.012-0.00626.945-0.007-0.0070.0000.0000.0000.000
181B261MET0-0.041-0.03629.1270.0060.0060.0000.0000.0000.000
182B262ILE0-0.0420.00031.360-0.005-0.0050.0000.0000.0000.000
183B263SER0-0.024-0.04333.348-0.002-0.0020.0000.0000.0000.000
184B264GLN00.0020.01936.2160.0040.0040.0000.0000.0000.000
185B265TYR0-0.0140.01334.841-0.004-0.0040.0000.0000.0000.000
186B266ASN0-0.012-0.03632.179-0.003-0.0030.0000.0000.0000.000
187B267LEU00.0120.00632.3400.0020.0020.0000.0000.0000.000
188B268GLU-1-0.872-0.92936.340-0.045-0.0450.0000.0000.0000.000
189B269LYS10.8930.97038.8880.0340.0340.0000.0000.0000.000
190B270PRO0-0.025-0.02336.5130.0000.0000.0000.0000.0000.000
191B271GLU-1-0.864-0.92639.096-0.027-0.0270.0000.0000.0000.000
192B272GLY0-0.051-0.01840.6790.0010.0010.0000.0000.0000.000
193B273VAL0-0.024-0.01140.7010.0010.0010.0000.0000.0000.000
194B274HIS0-0.033-0.03343.7110.0000.0000.0000.0000.0000.000
195B275ASN00.031-0.00645.3940.0010.0010.0000.0000.0000.000
196B276LEU00.0650.00941.0810.0020.0020.0000.0000.0000.000
197B277PHE00.0470.04445.1500.0020.0020.0000.0000.0000.000
198B278LEU0-0.013-0.00547.0020.0020.0020.0000.0000.0000.000
199B279ILE0-0.011-0.00741.0510.0020.0020.0000.0000.0000.000
200B280VAL00.0060.00445.1630.0020.0020.0000.0000.0000.000
201B281GLY00.0180.00847.7730.0020.0020.0000.0000.0000.000
202B282LYS10.8140.89546.613-0.002-0.0020.0000.0000.0000.000
203B283ARG10.8610.94245.394-0.010-0.0100.0000.0000.0000.000
204B284ILE0-0.0190.00440.6690.0020.0020.0000.0000.0000.000
205B285ARG10.8430.92933.555-0.029-0.0290.0000.0000.0000.000
206B286LEU0-0.027-0.01935.5710.0000.0000.0000.0000.0000.000
207B287GLU-1-0.844-0.91930.9490.0250.0250.0000.0000.0000.000
208B288GLY0-0.0070.01030.311-0.001-0.0010.0000.0000.0000.000
209B289PHE0-0.012-0.00724.5110.0050.0050.0000.0000.0000.000
210B290LEU00.0950.03921.633-0.009-0.0090.0000.0000.0000.000
211B291VAL0-0.012-0.01018.1760.0100.0100.0000.0000.0000.000
212B292PHE0-0.024-0.02815.2100.0140.0140.0000.0000.0000.000
213B293ASP-1-0.896-0.92217.5550.0390.0390.0000.0000.0000.000
214B294HIS0-0.052-0.03519.2570.0190.0190.0000.0000.0000.000
215B295TYR0-0.007-0.01413.5630.0100.0100.0000.0000.0000.000
216B296GLY0-0.006-0.00215.6750.0300.0300.0000.0000.0000.000
217B297SER00.0270.01317.4540.0130.0130.0000.0000.0000.000
218B298TYR0-0.036-0.00813.636-0.021-0.0210.0000.0000.0000.000
219B299PRO0-0.012-0.01415.320-0.003-0.0030.0000.0000.0000.000
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