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: J3129

Calculation Name: 4KRD-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4KRD

Chain ID: B

ChEMBL ID:

UniProt ID: P53124

Base Structure: X-ray

Registration Date: 2023-06-20

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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2225356.540972
FMO2-HF: Nuclear repulsion 2148804.297549
FMO2-HF: Total energy -76552.243423
FMO2-MP2: Total energy -76773.769492


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:243:SER)


Summations of interaction energy for fragment #1(B:243:SER)
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.
-11.791-6.4410.366-2.787-2.929-0.007
Interaction energy analysis for fragmet #1(B:243:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.063 / q_NPA : 0.021
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].
3B245ASN0-0.006-0.0272.653-6.893-3.6810.292-1.944-1.559-0.013
4B246PRO00.0690.0304.3040.2050.365-0.001-0.010-0.1490.000
5B247LEU00.0140.0135.4850.4720.4720.0000.0000.0000.000
6B248LEU0-0.062-0.0406.9470.0790.0790.0000.0000.0000.000
7B249HIS10.8220.8983.048-3.469-2.5340.038-0.359-0.6150.003
8B250GLY00.0460.0267.897-0.096-0.0960.0000.0000.0000.000
9B251ILE0-0.0350.00110.399-0.056-0.0560.0000.0000.0000.000
10B252PRO00.0630.03411.192-0.006-0.0060.0000.0000.0000.000
11B253VAL0-0.028-0.0379.614-0.068-0.0680.0000.0000.0000.000
12B254ASP-1-0.899-0.95311.647-0.118-0.1180.0000.0000.0000.000
13B255VAL0-0.063-0.01214.5930.0100.0100.0000.0000.0000.000
14B256GLU-1-0.833-0.91516.661-0.149-0.1490.0000.0000.0000.000
15B257VAL0-0.074-0.04819.619-0.006-0.0060.0000.0000.0000.000
16B258PRO0-0.013-0.01619.4730.0170.0170.0000.0000.0000.000
17B259HIS00.0200.02622.4850.0000.0000.0000.0000.0000.000
18B260ILE0-0.050-0.02322.6590.0080.0080.0000.0000.0000.000
19B261SER00.0620.03126.589-0.005-0.0050.0000.0000.0000.000
20B262VAL00.0580.01328.545-0.004-0.0040.0000.0000.0000.000
21B263ASP-1-0.881-0.93729.677-0.052-0.0520.0000.0000.0000.000
22B264GLU-1-0.782-0.86925.805-0.057-0.0570.0000.0000.0000.000
23B265ALA0-0.007-0.00925.232-0.002-0.0020.0000.0000.0000.000
24B266LEU0-0.030-0.01625.674-0.004-0.0040.0000.0000.0000.000
25B267ALA0-0.019-0.00628.0570.0010.0010.0000.0000.0000.000
26B268ASN00.013-0.02023.0340.0100.0100.0000.0000.0000.000
27B269PHE00.0100.02822.757-0.001-0.0010.0000.0000.0000.000
28B270LYS10.8390.91224.5440.0360.0360.0000.0000.0000.000
29B271GLU-1-0.866-0.94125.654-0.026-0.0260.0000.0000.0000.000
30B272THR00.0490.01319.8400.0060.0060.0000.0000.0000.000
31B273ILE0-0.027-0.01422.9210.0040.0040.0000.0000.0000.000
32B274GLU-1-0.881-0.94124.802-0.023-0.0230.0000.0000.0000.000
33B275LEU00.0010.00323.1130.0070.0070.0000.0000.0000.000
34B276LEU00.0430.02718.9060.0080.0080.0000.0000.0000.000
35B277LEU0-0.055-0.00822.9720.0070.0070.0000.0000.0000.000
36B278LYS10.9390.97326.4480.0190.0190.0000.0000.0000.000
37B279LEU00.0330.01220.2770.0060.0060.0000.0000.0000.000
38B280SER0-0.064-0.04223.9840.0050.0050.0000.0000.0000.000
39B281GLY0-0.023-0.00925.1530.0020.0020.0000.0000.0000.000
40B282ASN0-0.0070.00825.8310.0030.0030.0000.0000.0000.000
41B283ARG10.9170.96618.312-0.043-0.0430.0000.0000.0000.000
42B284LYS10.8910.93425.123-0.017-0.0170.0000.0000.0000.000
43B285CYS0-0.044-0.00820.7240.0090.0090.0000.0000.0000.000
44B286THR00.0600.03118.1790.0000.0000.0000.0000.0000.000
45B287GLY0-0.047-0.00520.4500.0010.0010.0000.0000.0000.000
46B288PHE00.000-0.00818.6860.0020.0020.0000.0000.0000.000
47B289ASN00.0180.00615.3180.0240.0240.0000.0000.0000.000
48B290THR0-0.015-0.02618.6100.0080.0080.0000.0000.0000.000
49B291ARG10.8440.89321.463-0.010-0.0100.0000.0000.0000.000
50B292VAL00.0900.04922.459-0.003-0.0030.0000.0000.0000.000
51B293GLU-1-0.696-0.82117.476-0.043-0.0430.0000.0000.0000.000
52B294LYS10.9730.99722.1980.0030.0030.0000.0000.0000.000
53B295LYS10.8410.91824.8520.0320.0320.0000.0000.0000.000
54B296GLU-1-0.792-0.87223.864-0.054-0.0540.0000.0000.0000.000
55B297TYR00.034-0.00922.445-0.004-0.0040.0000.0000.0000.000
56B298SER0-0.083-0.04725.0840.0020.0020.0000.0000.0000.000
57B299ASN0-0.050-0.04028.0120.0080.0080.0000.0000.0000.000
58B300PHE00.0270.00423.4470.0000.0000.0000.0000.0000.000
59B301TYR0-0.0250.00028.7760.0020.0020.0000.0000.0000.000
60B302MET0-0.077-0.03231.470-0.001-0.0010.0000.0000.0000.000
61B303LYS10.9780.98134.4800.0180.0180.0000.0000.0000.000
62B304SER00.0420.03037.7040.0010.0010.0000.0000.0000.000
63B305LYS10.9540.97335.4230.0230.0230.0000.0000.0000.000
64B306PRO0-0.028-0.02034.9990.0000.0000.0000.0000.0000.000
65B307THR00.0320.01738.1100.0010.0010.0000.0000.0000.000
66B308LEU00.0040.01837.6840.0010.0010.0000.0000.0000.000
67B309SER0-0.007-0.03236.360-0.002-0.0020.0000.0000.0000.000
68B310SER00.051-0.00330.786-0.002-0.0020.0000.0000.0000.000
69B311ALA00.0610.03432.654-0.004-0.0040.0000.0000.0000.000
70B312ASP-1-0.782-0.85833.841-0.033-0.0330.0000.0000.0000.000
71B313PHE0-0.048-0.02131.696-0.001-0.0010.0000.0000.0000.000
72B314LEU00.0190.00028.529-0.002-0.0020.0000.0000.0000.000
73B315LYS10.9300.96632.5480.0320.0320.0000.0000.0000.000
74B316ARG10.8990.95435.5850.0410.0410.0000.0000.0000.000
75B317ILE0-0.039-0.03530.8610.0000.0000.0000.0000.0000.000
76B318GLN00.0670.04931.874-0.006-0.0060.0000.0000.0000.000
77B319ASP-1-0.899-0.93933.972-0.044-0.0440.0000.0000.0000.000
78B320LYS10.8670.93736.9990.0420.0420.0000.0000.0000.000
79B321CYS0-0.096-0.04332.9340.0010.0010.0000.0000.0000.000
80B322GLU-1-0.924-0.94134.373-0.057-0.0570.0000.0000.0000.000
81B323TYR0-0.045-0.04228.819-0.004-0.0040.0000.0000.0000.000
82B324GLN00.1180.05127.6600.0080.0080.0000.0000.0000.000
83B325PRO00.0450.00826.022-0.004-0.0040.0000.0000.0000.000
84B326THR00.0290.00521.856-0.001-0.0010.0000.0000.0000.000
85B327VAL00.0330.03422.312-0.016-0.0160.0000.0000.0000.000
86B328TYR00.017-0.00723.239-0.009-0.0090.0000.0000.0000.000
87B329LEU00.0080.03320.008-0.003-0.0030.0000.0000.0000.000
88B330VAL00.0310.01218.064-0.021-0.0210.0000.0000.0000.000
89B331ALA0-0.017-0.00518.653-0.015-0.0150.0000.0000.0000.000
90B332THR0-0.022-0.04119.1870.0070.0070.0000.0000.0000.000
91B333PHE00.0650.02710.297-0.027-0.0270.0000.0000.0000.000
92B334LEU0-0.058-0.02015.212-0.029-0.0290.0000.0000.0000.000
93B335ILE0-0.025-0.01716.9010.0040.0040.0000.0000.0000.000
94B336ASP-1-0.801-0.91214.564-0.156-0.1560.0000.0000.0000.000
95B337THR0-0.0380.00111.145-0.042-0.0420.0000.0000.0000.000
96B338LEU00.0060.00813.3660.0030.0030.0000.0000.0000.000
97B339PHE0-0.029-0.03516.1570.0210.0210.0000.0000.0000.000
98B340LEU00.0260.03513.9640.0390.0390.0000.0000.0000.000
99B341THR0-0.019-0.0199.634-0.118-0.1180.0000.0000.0000.000
100B342ARG10.7500.8468.606-0.036-0.0360.0000.0000.0000.000
101B343ASP-1-0.826-0.8999.4550.2760.2760.0000.0000.0000.000
102B344GLY00.003-0.01210.0170.0910.0910.0000.0000.0000.000
103B345ASN0-0.042-0.01710.7710.1500.1500.0000.0000.0000.000
104B346ASN0-0.023-0.0188.6820.0870.0870.0000.0000.0000.000
105B347ILE00.0590.03911.050-0.076-0.0760.0000.0000.0000.000
106B348LEU00.0110.01512.891-0.016-0.0160.0000.0000.0000.000
107B349GLN0-0.021-0.01013.960-0.015-0.0150.0000.0000.0000.000
108B350LEU0-0.019-0.01215.157-0.032-0.0320.0000.0000.0000.000
109B351LYS10.8510.92512.6380.2150.2150.0000.0000.0000.000
110B352LEU0-0.025-0.02616.9940.0130.0130.0000.0000.0000.000
111B353ASN0-0.052-0.03820.3300.0010.0010.0000.0000.0000.000
112B354LEU00.0270.02823.257-0.004-0.0040.0000.0000.0000.000
113B355GLN0-0.034-0.04424.9140.0100.0100.0000.0000.0000.000
114B356GLU-1-0.786-0.92428.740-0.035-0.0350.0000.0000.0000.000
115B357LYS10.8230.90431.0720.0160.0160.0000.0000.0000.000
116B358GLU-1-0.792-0.86626.683-0.037-0.0370.0000.0000.0000.000
117B359VAL00.0450.03527.547-0.007-0.0070.0000.0000.0000.000
118B360HIS10.9020.95828.5030.0400.0400.0000.0000.0000.000
119B361ARG10.8870.92729.6950.0380.0380.0000.0000.0000.000
120B362MET00.0260.03722.878-0.009-0.0090.0000.0000.0000.000
121B363ILE00.0150.01325.239-0.010-0.0100.0000.0000.0000.000
122B364ILE0-0.036-0.01927.022-0.005-0.0050.0000.0000.0000.000
123B365ALA0-0.007-0.00424.884-0.003-0.0030.0000.0000.0000.000
124B366ALA00.0280.01122.160-0.009-0.0090.0000.0000.0000.000
125B367VAL00.0230.01023.188-0.011-0.0110.0000.0000.0000.000
126B368ARG10.8090.90725.7930.0800.0800.0000.0000.0000.000
127B369LEU00.001-0.00919.958-0.001-0.0010.0000.0000.0000.000
128B370SER0-0.008-0.02621.460-0.016-0.0160.0000.0000.0000.000
129B371THR0-0.007-0.01522.498-0.003-0.0030.0000.0000.0000.000
130B372LYS10.8440.90823.8940.0970.0970.0000.0000.0000.000
131B373LEU0-0.062-0.02317.358-0.007-0.0070.0000.0000.0000.000
132B374LEU0-0.070-0.02820.088-0.018-0.0180.0000.0000.0000.000
133B375GLU-1-0.930-0.96122.312-0.118-0.1180.0000.0000.0000.000
134B376ASP-1-0.905-0.93825.787-0.127-0.1270.0000.0000.0000.000
135B377PHE0-0.059-0.02927.3010.0080.0080.0000.0000.0000.000
136B378VAL00.0000.00827.308-0.001-0.0010.0000.0000.0000.000
137B379HIS00.0830.05230.5120.0020.0020.0000.0000.0000.000
138B380SER00.0650.03132.697-0.002-0.0020.0000.0000.0000.000
139B381HIS00.0510.00930.917-0.002-0.0020.0000.0000.0000.000
140B382GLU-1-0.839-0.88834.517-0.041-0.0410.0000.0000.0000.000
141B383TYR0-0.029-0.03236.2550.0030.0030.0000.0000.0000.000
142B384PHE00.0990.03829.5030.0030.0030.0000.0000.0000.000
143B385SER0-0.025-0.03534.9160.0010.0010.0000.0000.0000.000
144B386LYS10.8950.94236.2270.0420.0420.0000.0000.0000.000
145B387VAL00.0120.02635.2930.0030.0030.0000.0000.0000.000
146B388CYS0-0.029-0.00333.1220.0010.0010.0000.0000.0000.000
147B389GLY0-0.0160.00435.6030.0020.0020.0000.0000.0000.000
148B390ILE0-0.057-0.01832.9480.0020.0020.0000.0000.0000.000
149B391SER00.0260.00437.471-0.001-0.0010.0000.0000.0000.000
150B392LYS10.9570.95236.0130.0410.0410.0000.0000.0000.000
151B393ARG10.9580.98334.7440.0340.0340.0000.0000.0000.000
152B394LEU0-0.023-0.01532.714-0.001-0.0010.0000.0000.0000.000
153B395LEU00.0780.03730.432-0.002-0.0020.0000.0000.0000.000
154B396THR00.0120.01029.953-0.004-0.0040.0000.0000.0000.000
155B397LYS10.9170.96029.0460.0360.0360.0000.0000.0000.000
156B398LEU0-0.004-0.00127.773-0.001-0.0010.0000.0000.0000.000
157B399GLU-1-0.816-0.89225.521-0.094-0.0940.0000.0000.0000.000
158B400VAL00.0170.01024.006-0.010-0.0100.0000.0000.0000.000
159B401SER0-0.001-0.01023.5600.0000.0000.0000.0000.0000.000
160B402LEU0-0.0150.01519.7920.0010.0010.0000.0000.0000.000
161B403LEU00.0400.01618.442-0.013-0.0130.0000.0000.0000.000
162B404ILE0-0.008-0.02218.681-0.009-0.0090.0000.0000.0000.000
163B405CYS0-0.097-0.05118.5320.0070.0070.0000.0000.0000.000
164B406VAL00.0120.01015.068-0.003-0.0030.0000.0000.0000.000
165B407CYS0-0.051-0.00213.924-0.038-0.0380.0000.0000.0000.000
166B408ASN0-0.0150.00112.649-0.031-0.0310.0000.0000.0000.000
167B409THR0-0.039-0.0259.642-0.021-0.0210.0000.0000.0000.000
168B410LYS10.8870.9303.299-3.000-1.9570.037-0.474-0.6060.003
169B411LEU00.0680.0179.051-0.081-0.0810.0000.0000.0000.000
170B412MET0-0.0350.0029.7080.0430.0430.0000.0000.0000.000
171B413VAL00.1090.05511.931-0.076-0.0760.0000.0000.0000.000
172B414SER0-0.001-0.00612.192-0.050-0.0500.0000.0000.0000.000
173B415ASN00.1180.05014.277-0.003-0.0030.0000.0000.0000.000
174B416ARG10.8300.8946.7730.2390.2390.0000.0000.0000.000
175B417LYS10.8040.9249.4360.8580.8580.0000.0000.0000.000
176B418LEU00.0110.01113.4420.0420.0420.0000.0000.0000.000
177B419ALA00.0310.02415.2580.0300.0300.0000.0000.0000.000
178B420ALA00.000-0.01312.4580.0310.0310.0000.0000.0000.000
179B421SER0-0.049-0.01414.4950.0360.0360.0000.0000.0000.000
180B422LYS10.8760.92617.3040.0760.0760.0000.0000.0000.000
181B423LEU0-0.033-0.02515.2230.0210.0210.0000.0000.0000.000
182B424LEU00.0230.00612.4170.0220.0220.0000.0000.0000.000
183B425LEU0-0.0150.01716.5070.0190.0190.0000.0000.0000.000
184B426ASN00.004-0.00520.0710.0120.0120.0000.0000.0000.000
185B427GLU-1-0.758-0.83214.9210.0720.0720.0000.0000.0000.000
186B428LEU0-0.0070.00518.4130.0110.0110.0000.0000.0000.000
187B429ARG10.8420.89620.6450.0320.0320.0000.0000.0000.000
188B430SER0-0.098-0.05021.4130.0080.0080.0000.0000.0000.000
189B431PHE0-0.032-0.01718.0830.0070.0070.0000.0000.0000.000
190B432CYS0-0.057-0.00823.977-0.003-0.0030.0000.0000.0000.000