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: ZVKYN

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 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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2846811.965851
FMO2-HF: Nuclear repulsion 2755250.447467
FMO2-HF: Total energy -91561.518384
FMO2-MP2: Total energy -91829.832107


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.
-9.924-5.43118.333-6.932-15.894-0.023
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 : 0.026 / q_NPA : 0.014
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].
3B51LEU00.004-0.0092.168-0.5570.7245.510-1.892-4.900-0.002
4B52LYS10.8590.9293.6230.2260.2970.0180.020-0.1090.000
5B53ASN00.0110.0127.2530.1130.1130.0000.0000.0000.000
6B54LEU0-0.045-0.0148.9810.0070.0070.0000.0000.0000.000
7B55TYR00.006-0.01211.865-0.011-0.0110.0000.0000.0000.000
8B56LEU00.0410.03912.1310.0130.0130.0000.0000.0000.000
9B57SER00.025-0.01514.9350.0110.0110.0000.0000.0000.000
10B58CYS0-0.058-0.02617.283-0.027-0.0270.0000.0000.0000.000
11B59ASP-1-0.899-0.94918.1310.0390.0390.0000.0000.0000.000
12B60PRO0-0.018-0.00521.125-0.008-0.0080.0000.0000.0000.000
13B86GLY00.0520.03312.5980.0010.0010.0000.0000.0000.000
14B87PHE0-0.021-0.02311.918-0.007-0.0070.0000.0000.0000.000
15B88GLY00.0530.01111.296-0.045-0.0450.0000.0000.0000.000
16B89VAL0-0.058-0.0229.5580.0870.0870.0000.0000.0000.000
17B90GLY00.0520.0186.607-0.147-0.1470.0000.0000.0000.000
18B91LYS10.8630.9396.4950.1660.1660.0000.0000.0000.000
19B92VAL00.0350.0202.107-0.484-1.0363.394-0.661-2.1810.003
20B93VAL0-0.044-0.0203.504-0.144-0.0070.0040.060-0.2010.000
21B94ASP-1-0.889-0.9302.453-3.994-2.3822.179-1.650-2.141-0.016
22B102THR00.002-0.0015.884-0.043-0.0430.0000.0000.0000.000
23B103GLY0-0.126-0.0696.747-0.056-0.0560.0000.0000.0000.000
24B104ASP-1-0.838-0.9175.8520.9590.9590.0000.0000.0000.000
25B105TYR0-0.004-0.0136.390-0.013-0.0130.0000.0000.0000.000
26B106VAL0-0.017-0.0213.859-0.0820.1010.001-0.028-0.1560.000
27B107TRP00.0270.0107.107-0.176-0.1760.0000.0000.0000.000
28B108GLY00.0530.0297.9850.1700.1700.0000.0000.0000.000
29B109LEU0-0.066-0.0168.783-0.091-0.0910.0000.0000.0000.000
30B110ILE0-0.0090.0006.209-0.036-0.0360.0000.0000.0000.000
31B111GLY00.0250.0128.6500.0400.0400.0000.0000.0000.000
32B112TRP0-0.014-0.02611.1070.0300.0300.0000.0000.0000.000
33B113GLU-1-0.901-0.96012.517-0.390-0.3900.0000.0000.0000.000
34B114GLU-1-0.890-0.93211.906-0.348-0.3480.0000.0000.0000.000
35B115TYR00.021-0.0127.6250.0610.0610.0000.0000.0000.000
36B116SER0-0.037-0.0146.0490.1300.1300.0000.0000.0000.000
37B117LEU00.0170.0164.330-0.864-0.717-0.001-0.059-0.0870.000
38B118ILE0-0.005-0.0142.1090.4930.7103.493-1.117-2.5930.002
39B119THR00.0130.0132.754-3.525-1.6430.302-1.010-1.174-0.012
40B120LYS10.9690.9755.4330.2510.2510.0000.0000.0000.000
41B121PRO00.0620.0282.674-0.841-0.2310.221-0.173-0.6580.001
42B122GLN0-0.023-0.0254.5130.0960.198-0.001-0.008-0.0930.000
43B123GLY0-0.0010.0177.215-0.123-0.1230.0000.0000.0000.000
44B124LEU0-0.0160.0042.3960.369-0.8283.213-0.414-1.6010.001
45B125PHE0-0.0030.0136.2590.1520.1520.0000.0000.0000.000
46B126LYS10.8800.9136.224-1.415-1.4150.0000.0000.0000.000
47B127ILE0-0.0040.0119.698-0.076-0.0760.0000.0000.0000.000
48B128HIS10.8520.92411.885-0.498-0.4980.0000.0000.0000.000
49B129HIS10.8190.88314.486-0.251-0.2510.0000.0000.0000.000
50B130THR00.0100.00113.251-0.001-0.0010.0000.0000.0000.000
51B131GLU-1-0.835-0.89015.9340.1750.1750.0000.0000.0000.000
52B132ILE0-0.050-0.00917.768-0.025-0.0250.0000.0000.0000.000
53B133PRO00.0250.00417.9500.0070.0070.0000.0000.0000.000
54B134LEU00.0420.00412.1280.0040.0040.0000.0000.0000.000
55B135SER00.0080.00914.6720.0170.0170.0000.0000.0000.000
56B136TYR00.038-0.00216.809-0.007-0.0070.0000.0000.0000.000
57B137TYR0-0.031-0.02913.306-0.012-0.0120.0000.0000.0000.000
58B138THR0-0.0120.00614.2100.0190.0190.0000.0000.0000.000
59B139GLY00.0320.01316.117-0.016-0.0160.0000.0000.0000.000
60B140ILE0-0.021-0.01219.2640.0150.0150.0000.0000.0000.000
61B141LEU0-0.009-0.01517.0910.0000.0000.0000.0000.0000.000
62B142GLY00.0470.02915.4060.0360.0360.0000.0000.0000.000
63B143MET00.0220.03115.6210.0000.0000.0000.0000.0000.000
64B144VAL00.0150.02217.205-0.006-0.0060.0000.0000.0000.000
65B145GLY00.006-0.01120.104-0.007-0.0070.0000.0000.0000.000
66B146LEU00.0120.01116.826-0.005-0.0050.0000.0000.0000.000
67B147THR00.011-0.02520.334-0.006-0.0060.0000.0000.0000.000
68B148ALA0-0.054-0.02922.457-0.007-0.0070.0000.0000.0000.000
69B149TYR00.0110.01022.971-0.007-0.0070.0000.0000.0000.000
70B150VAL00.0360.01422.066-0.005-0.0050.0000.0000.0000.000
71B151GLY00.0680.03325.021-0.007-0.0070.0000.0000.0000.000
72B152PHE0-0.057-0.03627.577-0.009-0.0090.0000.0000.0000.000
73B153TYR0-0.020-0.03427.061-0.004-0.0040.0000.0000.0000.000
74B154ASP-1-0.910-0.93927.2670.1180.1180.0000.0000.0000.000
75B155ILE00.0240.02427.580-0.008-0.0080.0000.0000.0000.000
76B156CYS0-0.058-0.02130.829-0.009-0.0090.0000.0000.0000.000
77B157SER0-0.033-0.00233.047-0.007-0.0070.0000.0000.0000.000
78B158PRO0-0.0010.01833.371-0.005-0.0050.0000.0000.0000.000
79B159LYS10.9530.96936.318-0.055-0.0550.0000.0000.0000.000
80B160LYS10.9070.92838.281-0.068-0.0680.0000.0000.0000.000
81B161GLY00.0000.00340.492-0.002-0.0020.0000.0000.0000.000
82B162GLU-1-0.838-0.89339.5890.0530.0530.0000.0000.0000.000
83B163ARG10.7660.86841.227-0.037-0.0370.0000.0000.0000.000
84B164VAL00.004-0.00735.5750.0000.0000.0000.0000.0000.000
85B165PHE0-0.005-0.00338.484-0.003-0.0030.0000.0000.0000.000
86B166VAL00.0100.01232.6350.0020.0020.0000.0000.0000.000
87B167SER00.0360.01635.018-0.003-0.0030.0000.0000.0000.000
88B168ALA00.0260.00531.7340.0020.0020.0000.0000.0000.000
89B169ALA00.0150.02531.7960.0010.0010.0000.0000.0000.000
90B170ALA0-0.0120.00032.1820.0030.0030.0000.0000.0000.000
91B171GLY0-0.0080.00829.059-0.002-0.0020.0000.0000.0000.000
92B172ALA00.004-0.00424.1940.0050.0050.0000.0000.0000.000
93B173VAL00.0710.02623.9750.0050.0050.0000.0000.0000.000
94B174GLY00.0550.02726.3300.0050.0050.0000.0000.0000.000
95B175GLN0-0.020-0.01828.6530.0080.0080.0000.0000.0000.000
96B176ILE0-0.010-0.00123.7800.0020.0020.0000.0000.0000.000
97B177VAL00.0060.01628.0810.0040.0040.0000.0000.0000.000
98B178GLY00.0330.01229.8680.0010.0010.0000.0000.0000.000
99B179GLN0-0.018-0.00529.7780.0020.0020.0000.0000.0000.000
100B180PHE00.0190.00924.6890.0030.0030.0000.0000.0000.000
101B181ALA00.0130.00830.9990.0010.0010.0000.0000.0000.000
102B182LYS10.8300.89434.351-0.044-0.0440.0000.0000.0000.000
103B183GLN0-0.015-0.01230.2900.0040.0040.0000.0000.0000.000
104B184PHE0-0.0050.01433.7460.0010.0010.0000.0000.0000.000
105B185GLY0-0.033-0.02335.749-0.001-0.0010.0000.0000.0000.000
106B186CYS0-0.081-0.01637.696-0.001-0.0010.0000.0000.0000.000
107B187TYR0-0.035-0.02239.639-0.001-0.0010.0000.0000.0000.000
108B188VAL0-0.014-0.01636.1290.0010.0010.0000.0000.0000.000
109B189VAL00.0240.01639.491-0.003-0.0030.0000.0000.0000.000
110B190GLY0-0.005-0.00237.5240.0020.0020.0000.0000.0000.000
111B191SER0-0.0200.00337.225-0.004-0.0040.0000.0000.0000.000
112B192ALA0-0.004-0.01436.3590.0010.0010.0000.0000.0000.000
113B193GLY00.0560.02336.793-0.001-0.0010.0000.0000.0000.000
114B194SER00.004-0.00738.129-0.003-0.0030.0000.0000.0000.000
115B195ASP-1-0.718-0.84039.6660.0040.0040.0000.0000.0000.000
116B196GLU-1-0.778-0.86135.9750.0050.0050.0000.0000.0000.000
117B197LYS10.8040.87333.051-0.003-0.0030.0000.0000.0000.000
118B198VAL00.0000.00737.0830.0030.0030.0000.0000.0000.000
119B199ASN00.0350.00739.7940.0030.0030.0000.0000.0000.000
120B200LEU00.0050.02833.3290.0020.0020.0000.0000.0000.000
121B201LEU0-0.053-0.03933.8900.0030.0030.0000.0000.0000.000
122B202LYS10.7940.89237.083-0.021-0.0210.0000.0000.0000.000
123B203THR00.002-0.01238.8340.0000.0000.0000.0000.0000.000
124B204LYS10.9260.96631.223-0.024-0.0240.0000.0000.0000.000
125B205PHE0-0.046-0.04029.8470.0030.0030.0000.0000.0000.000
126B206GLY00.0310.03034.4550.0040.0040.0000.0000.0000.000
127B207PHE0-0.015-0.01133.7430.0020.0020.0000.0000.0000.000
128B208ASP-1-0.766-0.84338.7210.0370.0370.0000.0000.0000.000
129B209GLU-1-0.835-0.91541.8110.0190.0190.0000.0000.0000.000
130B210ALA0-0.009-0.01039.9490.0020.0020.0000.0000.0000.000
131B211PHE0-0.0060.01041.479-0.002-0.0020.0000.0000.0000.000
132B212ASN00.002-0.02241.1890.0000.0000.0000.0000.0000.000
133B213TYR00.023-0.00937.790-0.001-0.0010.0000.0000.0000.000
134B214LYS10.9210.96038.8490.0050.0050.0000.0000.0000.000
135B215LYS10.8080.90744.496-0.003-0.0030.0000.0000.0000.000
136B216GLU-1-0.762-0.88346.2200.0120.0120.0000.0000.0000.000
137B217PRO0-0.0040.02048.0740.0000.0000.0000.0000.0000.000
138B218ASP-1-0.805-0.91350.0470.0110.0110.0000.0000.0000.000
139B219LEU00.0550.01743.2020.0020.0020.0000.0000.0000.000
140B220THR00.0520.02546.8820.0020.0020.0000.0000.0000.000
141B221LYS10.8630.92948.683-0.009-0.0090.0000.0000.0000.000
142B222ALA0-0.077-0.03246.8110.0010.0010.0000.0000.0000.000
143B223LEU00.002-0.00242.5130.0010.0010.0000.0000.0000.000
144B224LYS10.9110.95046.561-0.020-0.0200.0000.0000.0000.000
145B225ARG10.7740.87148.423-0.013-0.0130.0000.0000.0000.000
146B226TYR00.0160.02345.4630.0000.0000.0000.0000.0000.000
147B227PHE00.0220.02541.3800.0020.0020.0000.0000.0000.000
148B228PRO00.0530.03747.6160.0000.0000.0000.0000.0000.000
149B229GLU-1-0.845-0.91449.1860.0310.0310.0000.0000.0000.000
150B230GLY00.0030.00847.7460.0010.0010.0000.0000.0000.000
151B231ILE0-0.007-0.01841.2190.0010.0010.0000.0000.0000.000
152B232ASP-1-0.742-0.84341.3530.0410.0410.0000.0000.0000.000
153B233ILE00.0110.01935.5400.0020.0020.0000.0000.0000.000
154B234TYR0-0.041-0.04437.013-0.003-0.0030.0000.0000.0000.000
155B235PHE00.0210.00527.3820.0020.0020.0000.0000.0000.000
156B236GLU-1-0.736-0.86432.8170.0220.0220.0000.0000.0000.000
157B237ASN0-0.022-0.03429.3510.0060.0060.0000.0000.0000.000
158B238VAL0-0.043-0.03431.677-0.005-0.0050.0000.0000.0000.000
159B239GLY00.0540.02834.492-0.003-0.0030.0000.0000.0000.000
160B240GLY00.0380.01636.966-0.001-0.0010.0000.0000.0000.000
161B241PRO00.1030.04140.2580.0030.0030.0000.0000.0000.000
162B242MET0-0.0410.00038.9180.0020.0020.0000.0000.0000.000
163B243LEU00.0090.01337.8630.0020.0020.0000.0000.0000.000
164B244GLU-1-0.815-0.88840.7480.0120.0120.0000.0000.0000.000
165B245ALA0-0.0150.00344.0600.0010.0010.0000.0000.0000.000
166B246VAL00.013-0.01439.9870.0010.0010.0000.0000.0000.000
167B247LEU0-0.019-0.00542.1140.0010.0010.0000.0000.0000.000
168B248HIS00.0540.02944.7020.0020.0020.0000.0000.0000.000
169B249ASN0-0.100-0.04745.9070.0000.0000.0000.0000.0000.000
170B250MET0-0.0420.01539.9030.0010.0010.0000.0000.0000.000
171B251ARG10.7940.88645.055-0.038-0.0380.0000.0000.0000.000
172B252ILE0-0.009-0.02845.4970.0010.0010.0000.0000.0000.000
173B253LYS10.9070.95642.258-0.048-0.0480.0000.0000.0000.000
174B254GLY00.0530.04341.7170.0030.0030.0000.0000.0000.000
175B255ARG10.7330.81836.627-0.057-0.0570.0000.0000.0000.000
176B256ILE00.006-0.00335.347-0.001-0.0010.0000.0000.0000.000
177B257ALA00.0480.03930.5200.0010.0010.0000.0000.0000.000
178B258ALA0-0.047-0.04531.690-0.003-0.0030.0000.0000.0000.000
179B259CYS00.0040.00626.3650.0060.0060.0000.0000.0000.000
180B260GLY00.0040.00127.217-0.001-0.0010.0000.0000.0000.000
181B261MET0-0.047-0.03429.3910.0020.0020.0000.0000.0000.000
182B262ILE0-0.0310.00131.544-0.004-0.0040.0000.0000.0000.000
183B263SER0-0.030-0.04333.586-0.002-0.0020.0000.0000.0000.000
184B264GLN00.0040.02136.5060.0030.0030.0000.0000.0000.000
185B265TYR0-0.0260.00235.255-0.002-0.0020.0000.0000.0000.000
186B266ASN00.000-0.03832.704-0.005-0.0050.0000.0000.0000.000
187B267LEU00.0220.02032.6640.0010.0010.0000.0000.0000.000
188B268GLU-1-0.875-0.93236.658-0.015-0.0150.0000.0000.0000.000
189B269LYS10.8980.96839.1470.0040.0040.0000.0000.0000.000
190B270PRO0-0.025-0.01936.695-0.001-0.0010.0000.0000.0000.000
191B271GLU-1-0.879-0.93839.3440.0010.0010.0000.0000.0000.000
192B272GLY0-0.047-0.01540.9400.0020.0020.0000.0000.0000.000
193B273VAL0-0.044-0.02140.8970.0010.0010.0000.0000.0000.000
194B274HIS0-0.041-0.04943.984-0.001-0.0010.0000.0000.0000.000
195B275ASN00.015-0.01445.836-0.001-0.0010.0000.0000.0000.000
196B276LEU00.0490.00941.4730.0020.0020.0000.0000.0000.000
197B277PHE00.0500.04345.3070.0020.0020.0000.0000.0000.000
198B278LEU0-0.009-0.00247.0990.0010.0010.0000.0000.0000.000
199B279ILE0-0.016-0.01141.2510.0010.0010.0000.0000.0000.000
200B280VAL00.0030.00545.2280.0020.0020.0000.0000.0000.000
201B281GLY00.0260.01247.8590.0010.0010.0000.0000.0000.000
202B282LYS10.7910.88946.587-0.026-0.0260.0000.0000.0000.000
203B283ARG10.8550.92745.467-0.031-0.0310.0000.0000.0000.000
204B284ILE0-0.0180.00640.6420.0020.0020.0000.0000.0000.000
205B285ARG10.8040.89433.511-0.070-0.0700.0000.0000.0000.000
206B286LEU0-0.030-0.01935.6340.0000.0000.0000.0000.0000.000
207B287GLU-1-0.827-0.90331.2290.0710.0710.0000.0000.0000.000
208B288GLY00.0070.01830.3980.0000.0000.0000.0000.0000.000
209B289PHE0-0.023-0.01024.5220.0050.0050.0000.0000.0000.000
210B290LEU00.0660.03721.249-0.008-0.0080.0000.0000.0000.000
211B291VAL00.015-0.00318.3810.0120.0120.0000.0000.0000.000
212B292PHE0-0.011-0.02115.2350.0240.0240.0000.0000.0000.000
213B293ASP-1-0.884-0.92817.6960.1420.1420.0000.0000.0000.000
214B294HIS0-0.044-0.03119.3190.0080.0080.0000.0000.0000.000
215B295TYR0-0.024-0.02013.9990.0170.0170.0000.0000.0000.000
216B296GLY0-0.004-0.00215.7080.0350.0350.0000.0000.0000.000
217B297SER00.0250.01817.5320.0040.0040.0000.0000.0000.000
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