FMO DATABASE

FMODB ID: 6N4YZ

Calculation Name: 4K59-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4K59

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H2

Base Structure: X-ray

Registration Date: 2023-06-22

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	66
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-342811.343304
FMO2-HF: Nuclear repulsion	317710.881638
FMO2-HF: Total energy	-25100.461667
FMO2-MP2: Total energy	-25174.751436

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:3:ALA)

Summations of interaction energy for fragment #1(A:3:ALA)

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.
-14.317	-13.641	16.29	-5.929	-11.037	-0.049

Interaction energy analysis for fragmet #1(A:3:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.031 / q_NPA : -0.016

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 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	5	GLY	0	-0.007	0.010	3.630	-1.485	-0.066	-0.018	-0.653	-0.748	0.001
4	A	6	PHE	0	0.031	0.002	5.062	1.070	1.095	-0.001	-0.009	-0.015	0.000
5	A	7	LEU	0	0.003	0.007	7.431	-0.229	-0.229	0.000	0.000	0.000	0.000
6	A	8	ILE	0	0.011	0.009	10.260	0.036	0.036	0.000	0.000	0.000	0.000
7	A	9	LEU	0	-0.022	-0.005	12.789	-0.032	-0.032	0.000	0.000	0.000	0.000
8	A	10	SER	0	-0.031	-0.004	15.980	-0.018	-0.018	0.000	0.000	0.000	0.000
9	A	11	ARG	1	0.729	0.833	17.670	-0.225	-0.225	0.000	0.000	0.000	0.000
10	A	12	ARG	1	0.912	0.963	20.495	-0.143	-0.143	0.000	0.000	0.000	0.000
11	A	13	GLU	-1	-0.890	-0.953	23.300	0.091	0.091	0.000	0.000	0.000	0.000
12	A	14	GLY	0	-0.026	-0.009	24.550	-0.002	-0.002	0.000	0.000	0.000	0.000
13	A	15	GLU	-1	-0.879	-0.933	21.973	0.176	0.176	0.000	0.000	0.000	0.000
14	A	16	GLY	0	0.024	0.011	19.136	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	17	ILE	0	-0.052	-0.035	13.175	0.014	0.014	0.000	0.000	0.000	0.000
16	A	18	THR	0	0.026	0.020	15.584	-0.011	-0.011	0.000	0.000	0.000	0.000
17	A	19	LEU	0	-0.040	-0.025	9.319	0.075	0.075	0.000	0.000	0.000	0.000
18	A	20	SER	0	-0.013	-0.006	11.881	-0.108	-0.108	0.000	0.000	0.000	0.000
19	A	21	LEU	0	0.023	0.010	10.521	0.164	0.164	0.000	0.000	0.000	0.000
20	A	22	LYS	1	0.861	0.924	9.811	-0.975	-0.975	0.000	0.000	0.000	0.000
21	A	23	ALA	0	0.016	0.006	13.455	-0.014	-0.014	0.000	0.000	0.000	0.000
22	A	24	ASP	-1	-0.909	-0.951	15.528	0.333	0.333	0.000	0.000	0.000	0.000
23	A	25	TYR	0	-0.073	-0.036	9.554	0.029	0.029	0.000	0.000	0.000	0.000
24	A	26	PRO	0	0.037	0.022	12.763	-0.018	-0.018	0.000	0.000	0.000	0.000
25	A	27	ALA	0	0.046	0.008	13.656	0.050	0.050	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.829	-0.917	13.335	0.241	0.241	0.000	0.000	0.000	0.000
27	A	29	GLU	-1	-0.921	-0.968	10.473	0.255	0.255	0.000	0.000	0.000	0.000
28	A	30	LEU	0	-0.018	0.008	8.441	0.110	0.110	0.000	0.000	0.000	0.000
29	A	31	ILE	0	-0.002	0.003	8.340	0.087	0.087	0.000	0.000	0.000	0.000
30	A	32	ARG	1	0.890	0.921	9.705	-0.180	-0.180	0.000	0.000	0.000	0.000
31	A	33	GLN	0	0.047	0.022	4.715	0.104	0.165	-0.001	-0.005	-0.055	0.000
32	A	34	LEU	0	-0.003	-0.012	5.257	-0.092	-0.092	0.000	0.000	0.000	0.000
33	A	35	ARG	1	0.892	0.950	6.476	-0.326	-0.326	0.000	0.000	0.000	0.000
34	A	36	GLU	-1	-1.006	-0.977	6.492	-0.043	-0.043	0.000	0.000	0.000	0.000
35	A	37	GLY	0	-0.044	-0.015	2.920	-0.630	-0.318	0.108	-0.160	-0.261	0.000
36	A	38	GLY	0	0.015	0.013	3.767	-0.009	0.343	0.009	-0.140	-0.221	-0.001
37	A	39	ILE	0	-0.006	-0.014	3.262	-0.818	0.212	0.048	-0.455	-0.623	-0.004
38	A	40	ARG	1	0.852	0.932	3.939	-0.320	-0.148	-0.001	-0.017	-0.153	0.000
39	A	41	ILE	0	0.055	0.021	5.713	0.467	0.467	0.000	0.000	0.000	0.000
40	A	42	LEU	0	-0.017	-0.009	9.155	-0.201	-0.201	0.000	0.000	0.000	0.000
41	A	43	VAL	0	0.020	0.016	11.221	0.076	0.076	0.000	0.000	0.000	0.000
42	A	44	THR	0	-0.069	-0.034	12.555	-0.043	-0.043	0.000	0.000	0.000	0.000
43	A	45	ASP	-1	-0.864	-0.921	14.981	-0.071	-0.071	0.000	0.000	0.000	0.000
44	A	46	ILE	0	-0.025	-0.025	18.689	0.030	0.030	0.000	0.000	0.000	0.000
45	A	47	ILE	0	-0.011	-0.003	21.594	-0.013	-0.013	0.000	0.000	0.000	0.000
46	A	48	GLY	0	0.025	0.010	24.278	0.011	0.011	0.000	0.000	0.000	0.000
47	A	49	ASN	0	0.008	0.005	26.411	-0.006	-0.006	0.000	0.000	0.000	0.000
48	A	50	GLN	0	-0.023	-0.014	21.545	0.012	0.012	0.000	0.000	0.000	0.000
49	A	51	ALA	0	0.055	0.028	19.221	-0.018	-0.018	0.000	0.000	0.000	0.000
50	A	52	ARG	1	0.920	0.957	16.494	-0.022	-0.022	0.000	0.000	0.000	0.000
51	A	53	VAL	0	0.024	0.007	12.622	-0.038	-0.038	0.000	0.000	0.000	0.000
52	A	54	GLY	0	0.005	0.003	10.147	0.041	0.041	0.000	0.000	0.000	0.000
53	A	55	ILE	0	-0.017	-0.024	7.203	-0.056	-0.056	0.000	0.000	0.000	0.000
54	A	56	GLU	-1	-0.902	-0.951	2.089	-11.524	-10.245	6.711	-4.416	-3.575	-0.039
55	A	57	ALA	0	0.045	0.009	2.812	-0.236	0.603	0.446	-0.073	-1.211	0.002
56	A	58	PRO	0	0.077	0.016	2.357	0.098	-2.581	8.827	-2.203	-3.945	-0.007
57	A	59	ARG	1	0.978	0.971	2.999	0.402	-1.732	0.162	2.202	-0.230	-0.001
58	A	60	GLY	0	0.010	0.018	6.411	-0.311	-0.311	0.000	0.000	0.000	0.000
59	A	61	VAL	0	-0.021	0.003	6.307	-0.270	-0.270	0.000	0.000	0.000	0.000
60	A	62	LEU	0	-0.054	-0.022	8.134	0.081	0.081	0.000	0.000	0.000	0.000
61	A	63	ILE	0	0.007	-0.003	7.250	-0.032	-0.032	0.000	0.000	0.000	0.000
62	A	64	VAL	0	-0.006	-0.004	11.475	-0.068	-0.068	0.000	0.000	0.000	0.000
63	A	65	ARG	1	0.919	0.964	15.261	-0.319	-0.319	0.000	0.000	0.000	0.000
64	A	66	ASP	-1	-0.774	-0.897	17.807	0.311	0.311	0.000	0.000	0.000	0.000
65	A	67	GLU	-1	-0.839	-0.892	20.605	0.237	0.237	0.000	0.000	0.000	0.000
66	A	68	LEU	0	-0.083	-0.024	19.245	-0.010	-0.010	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:ALA)