FMO DATABASE

FMODB ID: KRNL3

Calculation Name: 6UFA-A-Xray303

Preferred Name:

Target Type:

Ligand Name: d-histidine

ligand 3-letter code: DHI

PDB ID: 6UFA

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2021-08-02

Reference: C. Watanabe, T. Honma et. al., Interaction energy analysis of high resolution X-ray structure dataset on FMODB, To be pubulished.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	BaseStructure_original
Restraint	BaseStructure_original
Protonation	MOE:AddH
Complement	MOE:AddH
Water	All crystal waters in PDB.
Procedure	Manual calculation

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Manual
Number of fragment	60
LigandCharge	Null
Software	ABINIT-MP

Total energy (hartree)

FMO2-HF: Electronic energy	-127317.204244
FMO2-HF: Nuclear repulsion	113039.990633
FMO2-HF: Total energy	-14277.213611
FMO2-MP2: Total energy	-14313.567646

3D Structure

Snapshot

Ligand structure

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/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:1:LYS)

Summations of interaction energy for fragment #1(A:1:LYS)

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.
-9469.762	-9339.668	-91.084	22.224	-61.237	6.643

Interaction energy analysis for fragmet #1(A:1:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.869 / q_NPA : 0.832

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

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Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

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].
3	A	3	DGN	0	-0.046	0.006	2.166	-15.067	-9.462	6.037	-5.424	-6.217	0.061
4	A	4	DGL	-1	-0.837	-0.942	3.826	-25.850	-25.644	0.004	0.008	-0.218	0.001
5	A	5	AIB	0	0.002	0.008	6.913	-0.392	-0.392	0.000	0.000	0.000	0.000
6	A	6	HIS	0	0.007	-0.014	4.689	-0.102	-0.012	-0.002	-0.017	-0.071	0.000
7	A	7	DLY	1	0.923	0.868	5.651	22.002	21.994	-0.002	0.000	0.010	0.000
8	A	6	HIS	2	1.479	2.278	1.542	190.526	75.813	18.260	102.458	-6.004	0.093
9	A	8	DLE	0	0.008	0.018	8.030	0.814	0.814	0.000	0.000	0.000	0.000
10	A	9	GLN	0	0.000	0.002	7.630	-1.124	-1.124	0.000	0.000	0.000	0.000
11	A	10	GLU	-1	-0.791	-0.882	9.157	-15.059	-15.059	0.000	0.000	0.000	0.000
12	A	11	AIB	0	0.012	0.006	10.577	-0.179	-0.179	0.000	0.000	0.000	0.000
13	A	12	DHI	0	0.004	-0.017	7.120	-0.081	-0.081	0.000	0.000	0.000	0.000
14	A	13	LYS	1	0.945	0.879	7.517	14.049	14.049	0.000	0.000	0.000	0.000
15	A	14	LEU	0	0.020	0.023	9.560	0.128	0.128	0.000	0.000	0.000	0.000
16	A	15	DGN	0	-0.004	-0.001	4.888	2.399	2.518	-0.002	-0.002	-0.115	0.000
17	A	16	DGL	-1	-0.846	-0.946	8.072	-22.163	-22.163	0.000	0.000	0.000	0.000
18	A	17	AIB	0	-0.011	-0.008	5.174	-0.791	-0.791	0.000	0.000	0.000	0.000
19	A	18	HIS	0	0.017	-0.010	4.369	-1.948	-1.887	0.000	0.013	-0.075	0.000
20	A	19	DLY	1	0.885	0.842	5.819	20.516	20.513	-0.002	0.001	0.004	0.000
21	A	20	DLE	0	0.013	0.020	6.802	1.838	1.838	0.000	0.000	0.000	0.000
22	A	21	GLN	0	-0.028	0.013	4.985	-1.272	-1.162	-0.001	-0.005	-0.103	0.000
23	A	22	GLU	-1	-0.793	-0.898	1.993	-125.448	-121.391	4.910	-4.398	-4.569	-0.069
24	A	23	AIB	0	-0.030	-0.007	1.962	-21.036	-17.748	6.519	-4.720	-5.087	-0.052
26	A	201	HOH	0	-0.032	-0.040	14.002	-0.148	-0.148	0.000	0.000	0.000	0.000
27	A	202	HOH	0	-0.051	-0.045	2.933	3.443	3.871	0.008	-0.231	-0.206	-0.001
28	A	203	HOH	0	-0.030	-0.029	12.982	0.278	0.278	0.000	0.000	0.000	0.000
29	A	204	HOH	0	-0.018	-0.019	13.310	0.254	0.254	0.000	0.000	0.000	0.000
30	A	205	HOH	0	0.034	0.014	2.508	3.127	4.418	0.964	-0.959	-1.296	-0.008
31	A	206	HOH	0	0.035	0.013	9.691	-0.467	-0.467	0.000	0.000	0.000	0.000
32	A	207	HOH	0	0.002	-0.005	6.161	-0.161	-0.161	0.000	0.000	0.000	0.000
33	A	208	HOH	0	-0.015	-0.029	7.047	-0.080	-0.080	0.000	0.000	0.000	0.000
34	A	209	HOH	0	0.032	0.020	7.014	-0.244	-0.244	0.000	0.000	0.000	0.000
35	A	210	HOH	0	-0.053	-0.042	5.201	2.951	2.951	0.000	0.000	0.000	0.000
36	A	211	HOH	0	-0.021	-0.034	3.464	3.044	3.285	0.003	-0.106	-0.139	0.000
37	A	212	HOH	0	0.032	0.014	1.928	-19.347	-21.099	6.058	-2.046	-2.261	-0.029
38	A	213	HOH	0	0.024	0.007	15.681	-0.031	-0.031	0.000	0.000	0.000	0.000
39	A	214	HOH	0	-0.011	-0.015	4.361	-2.485	-2.429	-0.001	-0.004	-0.052	0.000
40	A	215	HOH	0	-0.036	-0.031	9.316	0.363	0.363	0.000	0.000	0.000	0.000
41	A	216	HOH	0	0.014	0.005	12.958	-0.283	-0.283	0.000	0.000	0.000	0.000
42	A	217	HOH	0	0.033	0.031	8.387	-0.872	-0.872	0.000	0.000	0.000	0.000
43	A	218	HOH	0	0.033	0.010	7.281	0.415	0.415	0.000	0.000	0.000	0.000
44	A	219	HOH	0	0.013	0.009	7.374	0.123	0.123	0.000	0.000	0.000	0.000
45	A	220	HOH	0	0.006	-0.003	6.538	-0.760	-0.760	0.000	0.000	0.000	0.000
46	A	221	HOH	0	0.040	0.023	7.360	-0.404	-0.404	0.000	0.000	0.000	0.000
47	A	222	HOH	0	0.019	0.007	16.277	-0.366	-0.366	0.000	0.000	0.000	0.000
48	A	223	HOH	0	0.033	0.020	13.296	-0.272	-0.272	0.000	0.000	0.000	0.000
49	A	224	HOH	0	0.016	0.017	6.288	0.961	0.961	0.000	0.000	0.000	0.000
50	A	225	HOH	0	0.008	0.001	2.673	-14.188	-12.988	0.787	-0.881	-1.106	-0.012
51	A	226	HOH	0	0.049	0.039	11.238	-1.142	-1.142	0.000	0.000	0.000	0.000
52	A	227	HOH	0	0.024	0.008	10.281	-0.105	-0.105	0.000	0.000	0.000	0.000
53	A	228	HOH	0	-0.026	-0.020	14.196	0.085	0.085	0.000	0.000	0.000	0.000
54	A	229	HOH	0	-0.056	-0.051	8.931	-0.380	-0.380	0.000	0.000	0.000	0.000
55	A	230	HOH	0	-0.005	-0.007	15.014	-0.134	-0.134	0.000	0.000	0.000	0.000
56	A	231	HOH	0	0.052	0.039	2.437	-2.304	-1.435	0.986	-0.717	-1.138	-0.011
57	A	232	HOH	0	0.025	0.010	10.506	-0.514	-0.514	0.000	0.000	0.000	0.000
58	A	233	HOH	0	0.005	0.001	6.971	1.454	1.454	0.000	0.000	0.000	0.000
59	A	234	HOH	0	0.018	0.022	8.588	-0.986	-0.986	0.000	0.000	0.000	0.000
60	A	235	HOH	0	-0.013	-0.009	7.021	-0.070	-0.070	0.000	0.000	0.000	0.000

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Overview

Highlights

Manual

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:LYS)