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: R8658

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 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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2851558.82593
FMO2-HF: Nuclear repulsion 2759996.624072
FMO2-HF: Total energy -91562.201859
FMO2-MP2: Total energy -91830.506485


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.
-16.281-5.86112.963-7.947-15.437-0.043
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 : 0.021 / 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].
3B51LEU00.0180.0002.366-1.6631.4441.908-1.500-3.5150.001
4B52LYS10.8180.9004.0840.5590.6500.001-0.026-0.0660.000
5B53ASN0-0.0010.0037.784-0.028-0.0280.0000.0000.0000.000
6B54LEU0-0.045-0.0229.8700.0480.0480.0000.0000.0000.000
7B55TYR00.004-0.01112.5810.0450.0450.0000.0000.0000.000
8B56LEU00.0240.02212.569-0.021-0.0210.0000.0000.0000.000
9B57SER00.020-0.00415.4540.0270.0270.0000.0000.0000.000
10B58CYS0-0.038-0.03017.916-0.026-0.0260.0000.0000.0000.000
11B59ASP-1-0.878-0.93818.187-0.071-0.0710.0000.0000.0000.000
12B60PRO0-0.019-0.00221.091-0.009-0.0090.0000.0000.0000.000
13B86GLY00.0580.03413.1060.0120.0120.0000.0000.0000.000
14B87PHE0-0.039-0.03112.367-0.036-0.0360.0000.0000.0000.000
15B88GLY00.024-0.00211.764-0.017-0.0170.0000.0000.0000.000
16B89VAL0-0.041-0.01710.4400.0630.0630.0000.0000.0000.000
17B90GLY00.0610.0227.766-0.102-0.1020.0000.0000.0000.000
18B91LYS10.8420.9297.0460.5210.5210.0000.0000.0000.000
19B92VAL00.0220.0152.227-0.908-0.8462.281-0.571-1.7720.003
20B93VAL0-0.085-0.0343.9060.0690.2370.000-0.026-0.1430.000
21B94ASP-1-0.879-0.9312.670-5.829-2.3621.440-2.115-2.793-0.026
22B102THR0-0.012-0.0075.918-0.048-0.0480.0000.0000.0000.000
23B103GLY0-0.045-0.0436.769-0.032-0.0320.0000.0000.0000.000
24B104ASP-1-0.867-0.9255.8500.4800.4800.0000.0000.0000.000
25B105TYR00.0140.0036.803-0.099-0.0990.0000.0000.0000.000
26B106VAL0-0.008-0.0144.8900.1270.1270.0000.0000.0000.000
27B107TRP00.0340.0158.036-0.156-0.1560.0000.0000.0000.000
28B108GLY00.0340.0148.4820.1440.1440.0000.0000.0000.000
29B109LEU0-0.053-0.0089.479-0.066-0.0660.0000.0000.0000.000
30B110ILE0-0.016-0.0056.650-0.072-0.0720.0000.0000.0000.000
31B111GLY00.0050.0078.8570.0710.0710.0000.0000.0000.000
32B112TRP00.014-0.00410.9320.0290.0290.0000.0000.0000.000
33B113GLU-1-0.882-0.95312.690-0.499-0.4990.0000.0000.0000.000
34B114GLU-1-0.843-0.89212.616-0.525-0.5250.0000.0000.0000.000
35B115TYR0-0.013-0.0258.0280.0270.0270.0000.0000.0000.000
36B116SER0-0.003-0.0116.3760.1410.1410.0000.0000.0000.000
37B117LEU00.0000.0143.593-1.028-0.7190.002-0.116-0.1950.000
38B118ILE00.001-0.0072.3920.0551.3521.307-0.736-1.8680.002
39B119THR00.0300.0102.145-5.266-4.0693.591-2.244-2.545-0.027
40B120LYS10.9580.9754.5970.2910.414-0.001-0.005-0.1170.000
41B121PRO00.0550.0272.414-1.508-0.7880.720-0.317-1.1230.003
42B122GLN0-0.027-0.0264.229-0.0220.0960.000-0.020-0.0970.000
43B123GLY00.0010.0187.369-0.100-0.1000.0000.0000.0000.000
44B124LEU0-0.0140.0072.400-0.226-0.4651.714-0.271-1.2030.001
45B125PHE00.0080.0166.3520.2300.2300.0000.0000.0000.000
46B126LYS10.8900.9216.040-1.265-1.2650.0000.0000.0000.000
47B127ILE0-0.033-0.0039.646-0.036-0.0360.0000.0000.0000.000
48B128HIS10.8780.93212.250-0.324-0.3240.0000.0000.0000.000
49B129HIS10.7860.87914.900-0.130-0.1300.0000.0000.0000.000
50B130THR00.024-0.00413.830-0.003-0.0030.0000.0000.0000.000
51B131GLU-1-0.842-0.89816.6750.0620.0620.0000.0000.0000.000
52B132ILE0-0.038-0.00218.740-0.013-0.0130.0000.0000.0000.000
53B133PRO0-0.006-0.01918.623-0.003-0.0030.0000.0000.0000.000
54B134LEU00.0760.03513.1420.0000.0000.0000.0000.0000.000
55B135SER00.0070.00615.5310.0030.0030.0000.0000.0000.000
56B136TYR00.014-0.00717.681-0.002-0.0020.0000.0000.0000.000
57B137TYR0-0.023-0.03813.722-0.003-0.0030.0000.0000.0000.000
58B138THR0-0.017-0.00414.4060.0110.0110.0000.0000.0000.000
59B139GLY00.0230.00316.052-0.006-0.0060.0000.0000.0000.000
60B140ILE0-0.033-0.01419.2920.0150.0150.0000.0000.0000.000
61B141LEU0-0.012-0.01717.6300.0090.0090.0000.0000.0000.000
62B142GLY00.0670.03915.5330.0240.0240.0000.0000.0000.000
63B143MET0-0.0150.01815.6720.0110.0110.0000.0000.0000.000
64B144VAL00.0130.01817.2630.0070.0070.0000.0000.0000.000
65B145GLY00.014-0.00820.1360.0010.0010.0000.0000.0000.000
66B146LEU00.0160.01616.9890.0020.0020.0000.0000.0000.000
67B147THR00.008-0.02220.4920.0040.0040.0000.0000.0000.000
68B148ALA0-0.035-0.02322.6030.0000.0000.0000.0000.0000.000
69B149TYR0-0.056-0.04322.952-0.005-0.0050.0000.0000.0000.000
70B150VAL00.0340.01522.621-0.001-0.0010.0000.0000.0000.000
71B151GLY00.0620.02925.412-0.003-0.0030.0000.0000.0000.000
72B152PHE0-0.026-0.02427.700-0.005-0.0050.0000.0000.0000.000
73B153TYR0-0.025-0.03327.435-0.001-0.0010.0000.0000.0000.000
74B154ASP-1-0.896-0.92127.8540.0870.0870.0000.0000.0000.000
75B155ILE00.0420.02327.782-0.006-0.0060.0000.0000.0000.000
76B156CYS0-0.060-0.01930.913-0.007-0.0070.0000.0000.0000.000
77B157SER0-0.029-0.00832.962-0.004-0.0040.0000.0000.0000.000
78B158PRO0-0.0360.01533.350-0.004-0.0040.0000.0000.0000.000
79B159LYS10.9680.97836.294-0.036-0.0360.0000.0000.0000.000
80B160LYS10.9110.94138.446-0.040-0.0400.0000.0000.0000.000
81B161GLY00.0100.00440.5450.0000.0000.0000.0000.0000.000
82B162GLU-1-0.830-0.88939.8620.0320.0320.0000.0000.0000.000
83B163ARG10.7270.83041.495-0.019-0.0190.0000.0000.0000.000
84B164VAL00.0390.01335.6130.0000.0000.0000.0000.0000.000
85B165PHE0-0.011-0.00638.504-0.003-0.0030.0000.0000.0000.000
86B166VAL00.0090.00632.8310.0020.0020.0000.0000.0000.000
87B167SER00.0130.00035.166-0.003-0.0030.0000.0000.0000.000
88B168ALA00.0340.01032.4410.0000.0000.0000.0000.0000.000
89B169ALA00.0100.01832.228-0.002-0.0020.0000.0000.0000.000
90B170ALA0-0.013-0.00532.3170.0000.0000.0000.0000.0000.000
91B171GLY00.0120.01929.253-0.005-0.0050.0000.0000.0000.000
92B172ALA0-0.007-0.00924.5350.0060.0060.0000.0000.0000.000
93B173VAL00.0800.03423.9740.0050.0050.0000.0000.0000.000
94B174GLY00.0370.02026.2980.0060.0060.0000.0000.0000.000
95B175GLN0-0.008-0.01228.6570.0060.0060.0000.0000.0000.000
96B176ILE0-0.0090.00523.7110.0020.0020.0000.0000.0000.000
97B177VAL00.0240.02528.0100.0060.0060.0000.0000.0000.000
98B178GLY00.0200.01029.9940.0030.0030.0000.0000.0000.000
99B179GLN0-0.009-0.01329.7510.0010.0010.0000.0000.0000.000
100B180PHE00.0150.00924.6750.0030.0030.0000.0000.0000.000
101B181ALA00.0300.01330.9520.0030.0030.0000.0000.0000.000
102B182LYS10.8200.89534.258-0.013-0.0130.0000.0000.0000.000
103B183GLN0-0.013-0.01330.1660.0050.0050.0000.0000.0000.000
104B184PHE0-0.0080.00633.6460.0020.0020.0000.0000.0000.000
105B185GLY0-0.0130.00135.6190.0010.0010.0000.0000.0000.000
106B186CYS0-0.064-0.01437.8570.0010.0010.0000.0000.0000.000
107B187TYR0-0.050-0.02739.689-0.002-0.0020.0000.0000.0000.000
108B188VAL0-0.025-0.01936.1330.0010.0010.0000.0000.0000.000
109B189VAL00.0140.01239.409-0.003-0.0030.0000.0000.0000.000
110B190GLY0-0.003-0.00337.6160.0010.0010.0000.0000.0000.000
111B191SER0-0.035-0.01437.367-0.002-0.0020.0000.0000.0000.000
112B192ALA0-0.004-0.00936.792-0.002-0.0020.0000.0000.0000.000
113B193GLY00.0680.03237.4690.0010.0010.0000.0000.0000.000
114B194SER0-0.004-0.01438.215-0.002-0.0020.0000.0000.0000.000
115B195ASP-1-0.727-0.84139.720-0.022-0.0220.0000.0000.0000.000
116B196GLU-1-0.798-0.86736.140-0.037-0.0370.0000.0000.0000.000
117B197LYS10.8130.87833.0600.0410.0410.0000.0000.0000.000
118B198VAL00.0090.01337.2320.0030.0030.0000.0000.0000.000
119B199ASN00.0390.01040.0530.0030.0030.0000.0000.0000.000
120B200LEU0-0.0120.02133.7880.0020.0020.0000.0000.0000.000
121B201LEU0-0.044-0.03433.9090.0020.0020.0000.0000.0000.000
122B202LYS10.7890.88737.1300.0050.0050.0000.0000.0000.000
123B203THR00.000-0.02039.0860.0000.0000.0000.0000.0000.000
124B204LYS10.9380.97932.4270.0290.0290.0000.0000.0000.000
125B205PHE0-0.046-0.03730.3940.0000.0000.0000.0000.0000.000
126B206GLY00.0250.02334.7170.0030.0030.0000.0000.0000.000
127B207PHE0-0.010-0.00733.7900.0030.0030.0000.0000.0000.000
128B208ASP-1-0.781-0.85338.7660.0100.0100.0000.0000.0000.000
129B209GLU-1-0.813-0.91041.823-0.005-0.0050.0000.0000.0000.000
130B210ALA0-0.0140.00340.2550.0000.0000.0000.0000.0000.000
131B211PHE00.0120.00741.609-0.001-0.0010.0000.0000.0000.000
132B212ASN0-0.001-0.02941.510-0.002-0.0020.0000.0000.0000.000
133B213TYR00.0590.00938.248-0.001-0.0010.0000.0000.0000.000
134B214LYS10.8740.93738.9510.0350.0350.0000.0000.0000.000
135B215LYS10.8270.90244.6650.0220.0220.0000.0000.0000.000
136B216GLU-1-0.767-0.86946.552-0.007-0.0070.0000.0000.0000.000
137B217PRO0-0.0160.00248.2020.0000.0000.0000.0000.0000.000
138B218ASP-1-0.728-0.85649.978-0.004-0.0040.0000.0000.0000.000
139B219LEU00.0460.01843.3270.0010.0010.0000.0000.0000.000
140B220THR0-0.021-0.01947.0710.0020.0020.0000.0000.0000.000
141B221LYS10.8700.91949.0510.0080.0080.0000.0000.0000.000
142B222ALA0-0.081-0.02246.8540.0000.0000.0000.0000.0000.000
143B223LEU0-0.009-0.00642.6720.0010.0010.0000.0000.0000.000
144B224LYS10.9220.95446.702-0.005-0.0050.0000.0000.0000.000
145B225ARG10.7850.88248.2170.0070.0070.0000.0000.0000.000
146B226TYR0-0.0030.01645.5080.0000.0000.0000.0000.0000.000
147B227PHE00.0330.02541.6670.0020.0020.0000.0000.0000.000
148B228PRO00.0470.03547.8630.0000.0000.0000.0000.0000.000
149B229GLU-1-0.839-0.91449.0730.0160.0160.0000.0000.0000.000
150B230GLY00.0170.01947.9580.0010.0010.0000.0000.0000.000
151B231ILE0-0.031-0.02241.3650.0000.0000.0000.0000.0000.000
152B232ASP-1-0.767-0.85941.7660.0220.0220.0000.0000.0000.000
153B233ILE0-0.011-0.00535.8710.0020.0020.0000.0000.0000.000
154B234TYR0-0.037-0.05437.135-0.003-0.0030.0000.0000.0000.000
155B235PHE00.0360.01927.3190.0020.0020.0000.0000.0000.000
156B236GLU-1-0.728-0.84132.742-0.007-0.0070.0000.0000.0000.000
157B237ASN0-0.018-0.02529.5630.0020.0020.0000.0000.0000.000
158B238VAL0-0.045-0.03631.970-0.006-0.0060.0000.0000.0000.000
159B239GLY00.0560.02735.113-0.002-0.0020.0000.0000.0000.000
160B240GLY00.0690.03037.474-0.001-0.0010.0000.0000.0000.000
161B241PRO00.0740.02340.8640.0030.0030.0000.0000.0000.000
162B242MET0-0.0400.00339.0910.0020.0020.0000.0000.0000.000
163B243LEU00.0190.02038.1890.0020.0020.0000.0000.0000.000
164B244GLU-1-0.815-0.88540.994-0.001-0.0010.0000.0000.0000.000
165B245ALA00.0240.01944.5290.0020.0020.0000.0000.0000.000
166B246VAL00.0180.00240.3640.0010.0010.0000.0000.0000.000
167B247LEU0-0.012-0.00342.3200.0020.0020.0000.0000.0000.000
168B248HIS00.0220.02244.9050.0030.0030.0000.0000.0000.000
169B249ASN0-0.087-0.06245.9330.0010.0010.0000.0000.0000.000
170B250MET0-0.0670.01939.8350.0010.0010.0000.0000.0000.000
171B251ARG10.8490.90945.304-0.019-0.0190.0000.0000.0000.000
172B252ILE0-0.005-0.02145.8880.0010.0010.0000.0000.0000.000
173B253LYS10.8960.95442.378-0.034-0.0340.0000.0000.0000.000
174B254GLY00.0480.03142.0990.0020.0020.0000.0000.0000.000
175B255ARG10.7090.80137.032-0.035-0.0350.0000.0000.0000.000
176B256ILE0-0.009-0.01735.690-0.002-0.0020.0000.0000.0000.000
177B257ALA00.0590.03830.7450.0020.0020.0000.0000.0000.000
178B258ALA0-0.020-0.02631.807-0.004-0.0040.0000.0000.0000.000
179B259CYS0-0.0130.00026.5030.0050.0050.0000.0000.0000.000
180B260GLY0-0.004-0.00127.359-0.005-0.0050.0000.0000.0000.000
181B261MET0-0.056-0.02429.8040.0040.0040.0000.0000.0000.000
182B262ILE0-0.025-0.01231.800-0.004-0.0040.0000.0000.0000.000
183B263SER0-0.039-0.04134.0670.0010.0010.0000.0000.0000.000
184B264GLN00.0140.02436.8760.0020.0020.0000.0000.0000.000
185B265TYR0-0.0200.00335.671-0.005-0.0050.0000.0000.0000.000
186B266ASN0-0.016-0.03433.380-0.003-0.0030.0000.0000.0000.000
187B267LEU00.0250.02033.0950.0020.0020.0000.0000.0000.000
188B268GLU-1-0.876-0.93237.100-0.030-0.0300.0000.0000.0000.000
189B269LYS10.9190.96739.4870.0160.0160.0000.0000.0000.000
190B270PRO0-0.038-0.02636.799-0.001-0.0010.0000.0000.0000.000
191B271GLU-1-0.868-0.93439.346-0.016-0.0160.0000.0000.0000.000
192B272GLY0-0.042-0.01741.3690.0020.0020.0000.0000.0000.000
193B273VAL0-0.036-0.03040.5890.0000.0000.0000.0000.0000.000
194B274HIS0-0.004-0.02043.9670.0010.0010.0000.0000.0000.000
195B275ASN0-0.061-0.05546.1840.0020.0020.0000.0000.0000.000
196B276LEU00.0180.01141.4860.0020.0020.0000.0000.0000.000
197B277PHE00.0250.01545.3820.0020.0020.0000.0000.0000.000
198B278LEU0-0.0050.00147.2420.0020.0020.0000.0000.0000.000
199B279ILE00.0000.00341.4410.0010.0010.0000.0000.0000.000
200B280VAL00.0270.02045.2720.0020.0020.0000.0000.0000.000
201B281GLY00.0260.01747.7270.0010.0010.0000.0000.0000.000
202B282LYS10.7910.88146.760-0.011-0.0110.0000.0000.0000.000
203B283ARG10.8630.92745.756-0.020-0.0200.0000.0000.0000.000
204B284ILE0-0.031-0.00140.9030.0020.0020.0000.0000.0000.000
205B285ARG10.7790.88233.692-0.047-0.0470.0000.0000.0000.000
206B286LEU0-0.018-0.01436.070-0.001-0.0010.0000.0000.0000.000
207B287GLU-1-0.842-0.91031.6700.0520.0520.0000.0000.0000.000
208B288GLY00.0070.00730.314-0.004-0.0040.0000.0000.0000.000
209B289PHE0-0.0260.00524.3660.0050.0050.0000.0000.0000.000
210B290LEU00.0400.02420.935-0.012-0.0120.0000.0000.0000.000
211B291VAL0-0.007-0.00118.1520.0140.0140.0000.0000.0000.000
212B292PHE00.024-0.01114.9690.0190.0190.0000.0000.0000.000
213B293ASP-1-0.842-0.92817.7270.1120.1120.0000.0000.0000.000
214B294HIS0-0.034-0.03119.5940.0130.0130.0000.0000.0000.000
215B295TYR0-0.040-0.01614.2960.0050.0050.0000.0000.0000.000
216B296GLY0-0.018-0.00415.8770.0300.0300.0000.0000.0000.000
217B297SER00.0250.01517.7000.0100.0100.0000.0000.0000.000
218B298TYR0-0.050-0.03913.422-0.024-0.0240.0000.0000.0000.000
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