FMO DATABASE

FMODB ID: 72KYK

Calculation Name: 4XP8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4XP8

Chain ID: A

ChEMBL ID:

UniProt ID: C7BUG6

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	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	87
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-600279.889156
FMO2-HF: Nuclear repulsion	565626.048711
FMO2-HF: Total energy	-34653.840445
FMO2-MP2: Total energy	-34753.66218

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:18:MET)

Summations of interaction energy for fragment #1(A:18:MET)

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.
-6.784	-1.273	9.729	-4.64	-10.599	-0.013

Interaction energy analysis for fragmet #1(A:18:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : 0.003

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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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	20	CYS	0	0.010	-0.019	3.505	-2.566	0.068	0.010	-1.468	-1.176	0.005
4	A	21	PHE	0	0.017	0.019	6.108	0.783	0.783	0.000	0.000	0.000	0.000
5	A	22	GLU	-1	-0.839	-0.909	2.318	-3.466	-2.850	3.363	-1.031	-2.948	-0.005
6	A	23	ILE	0	-0.044	-0.020	2.344	-1.908	-0.104	3.508	-1.596	-3.716	-0.014
7	A	24	THR	0	-0.006	-0.009	3.360	1.293	1.313	0.012	0.235	-0.267	0.000
8	A	25	GLY	0	0.021	-0.002	5.632	0.425	0.425	0.000	0.000	0.000	0.000
9	A	26	LYS	1	0.924	0.950	2.284	-4.355	-4.055	2.836	-0.740	-2.396	0.001
10	A	27	ALA	0	-0.048	-0.016	4.335	0.397	0.534	0.000	-0.040	-0.096	0.000
11	A	28	TYR	0	-0.013	-0.009	7.313	0.128	0.128	0.000	0.000	0.000	0.000
12	A	29	ASN	0	-0.062	-0.023	8.192	0.111	0.111	0.000	0.000	0.000	0.000
13	A	30	ILE	0	-0.019	0.008	8.834	0.008	0.008	0.000	0.000	0.000	0.000
14	A	31	ASP	-1	-0.815	-0.913	8.190	-0.680	-0.680	0.000	0.000	0.000	0.000
15	A	32	PRO	0	0.046	0.014	5.050	-0.023	-0.023	0.000	0.000	0.000	0.000
16	A	33	LEU	0	-0.015	0.005	7.851	-0.075	-0.075	0.000	0.000	0.000	0.000
17	A	34	ILE	0	0.006	0.007	10.903	0.025	0.025	0.000	0.000	0.000	0.000
18	A	35	LEU	0	-0.015	-0.002	8.058	0.011	0.011	0.000	0.000	0.000	0.000
19	A	36	LYS	1	0.802	0.869	5.889	2.410	2.410	0.000	0.000	0.000	0.000
20	A	37	ALA	0	0.010	0.004	12.256	0.067	0.067	0.000	0.000	0.000	0.000
21	A	38	ILE	0	-0.006	0.000	14.619	0.063	0.063	0.000	0.000	0.000	0.000
22	A	39	ALA	0	0.065	0.026	14.214	0.042	0.042	0.000	0.000	0.000	0.000
23	A	40	TRP	0	-0.013	0.018	16.137	0.050	0.050	0.000	0.000	0.000	0.000
24	A	41	ASN	0	-0.017	-0.015	17.791	0.053	0.053	0.000	0.000	0.000	0.000
25	A	42	GLU	-1	-0.952	-0.984	19.602	-0.332	-0.332	0.000	0.000	0.000	0.000
26	A	43	SER	0	-0.051	-0.051	18.143	0.017	0.017	0.000	0.000	0.000	0.000
27	A	44	LYS	1	0.766	0.896	19.378	0.430	0.430	0.000	0.000	0.000	0.000
28	A	45	ASN	0	-0.006	-0.016	13.230	0.056	0.056	0.000	0.000	0.000	0.000
29	A	46	LYS	1	0.900	0.970	16.332	0.424	0.424	0.000	0.000	0.000	0.000
30	A	47	ASN	0	0.042	0.023	16.553	0.045	0.045	0.000	0.000	0.000	0.000
31	A	48	GLY	0	0.046	0.025	18.672	0.034	0.034	0.000	0.000	0.000	0.000
32	A	49	ILE	0	-0.059	-0.031	21.855	0.047	0.047	0.000	0.000	0.000	0.000
33	A	50	LYS	1	0.858	0.914	23.256	0.255	0.255	0.000	0.000	0.000	0.000
34	A	51	SER	0	-0.014	-0.007	25.956	0.006	0.006	0.000	0.000	0.000	0.000
35	A	52	LYS	1	0.964	0.981	27.825	0.216	0.216	0.000	0.000	0.000	0.000
36	A	53	ILE	0	0.001	0.014	30.830	-0.008	-0.008	0.000	0.000	0.000	0.000
37	A	54	ASN	0	-0.034	-0.008	28.338	0.003	0.003	0.000	0.000	0.000	0.000
38	A	55	LYS	1	0.963	0.954	32.737	0.142	0.142	0.000	0.000	0.000	0.000
39	A	56	ASN	0	0.029	0.046	31.238	0.001	0.001	0.000	0.000	0.000	0.000
40	A	57	GLY	0	0.028	0.019	35.175	0.004	0.004	0.000	0.000	0.000	0.000
41	A	58	THR	0	-0.030	-0.018	29.480	-0.010	-0.010	0.000	0.000	0.000	0.000
42	A	59	TYR	0	-0.046	-0.060	27.363	0.012	0.012	0.000	0.000	0.000	0.000
43	A	60	ASN	0	0.031	0.027	23.923	0.023	0.023	0.000	0.000	0.000	0.000
44	A	61	ILE	0	0.020	0.009	21.541	0.008	0.008	0.000	0.000	0.000	0.000
45	A	62	GLY	0	0.070	0.048	19.270	-0.023	-0.023	0.000	0.000	0.000	0.000
46	A	63	ILE	0	-0.021	0.006	13.407	0.033	0.033	0.000	0.000	0.000	0.000
47	A	64	MET	0	-0.007	0.024	13.159	-0.024	-0.024	0.000	0.000	0.000	0.000
48	A	65	GLN	0	-0.043	-0.027	17.236	0.104	0.104	0.000	0.000	0.000	0.000
49	A	66	ILE	0	0.019	0.025	16.843	0.054	0.054	0.000	0.000	0.000	0.000
50	A	67	ASN	0	-0.010	-0.012	20.928	0.029	0.029	0.000	0.000	0.000	0.000
51	A	68	SER	0	0.061	0.017	24.472	0.006	0.006	0.000	0.000	0.000	0.000
52	A	69	SER	0	-0.060	-0.038	26.688	0.011	0.011	0.000	0.000	0.000	0.000
53	A	70	HIS	1	0.869	0.915	22.274	0.239	0.239	0.000	0.000	0.000	0.000
54	A	71	LEU	0	0.049	0.033	24.252	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	72	ASP	-1	-0.800	-0.891	25.841	-0.124	-0.124	0.000	0.000	0.000	0.000
56	A	73	LEU	0	-0.014	0.008	21.629	0.007	0.007	0.000	0.000	0.000	0.000
57	A	74	LEU	0	0.023	0.003	19.289	0.009	0.009	0.000	0.000	0.000	0.000
58	A	75	SER	0	0.000	0.005	22.693	0.003	0.003	0.000	0.000	0.000	0.000
59	A	76	LYS	1	0.794	0.882	25.527	0.125	0.125	0.000	0.000	0.000	0.000
60	A	77	PHE	0	-0.045	-0.018	20.123	0.024	0.024	0.000	0.000	0.000	0.000
61	A	78	ASN	0	-0.058	-0.027	20.893	0.003	0.003	0.000	0.000	0.000	0.000
62	A	79	ILE	0	-0.004	0.015	17.557	-0.035	-0.035	0.000	0.000	0.000	0.000
63	A	80	SER	0	-0.032	-0.052	21.474	0.029	0.029	0.000	0.000	0.000	0.000
64	A	81	GLU	-1	-0.749	-0.870	22.390	-0.299	-0.299	0.000	0.000	0.000	0.000
65	A	82	ASP	-1	-0.844	-0.913	23.009	-0.420	-0.420	0.000	0.000	0.000	0.000
66	A	83	ASP	-1	-0.801	-0.865	18.910	-0.430	-0.430	0.000	0.000	0.000	0.000
67	A	84	LEU	0	-0.022	-0.011	18.134	-0.071	-0.071	0.000	0.000	0.000	0.000
68	A	85	LEU	0	-0.032	-0.005	19.096	-0.043	-0.043	0.000	0.000	0.000	0.000
69	A	86	ASN	0	-0.014	-0.045	19.842	-0.056	-0.056	0.000	0.000	0.000	0.000
70	A	87	ASP	-1	-0.822	-0.895	13.941	-1.075	-1.075	0.000	0.000	0.000	0.000
71	A	88	ALA	0	-0.003	-0.015	12.931	0.016	0.016	0.000	0.000	0.000	0.000
72	A	90	ILE	0	0.059	0.044	11.157	0.054	0.054	0.000	0.000	0.000	0.000
73	A	91	ASN	0	-0.052	-0.026	13.995	0.026	0.026	0.000	0.000	0.000	0.000
74	A	92	ILE	0	0.008	-0.010	9.313	0.083	0.083	0.000	0.000	0.000	0.000
75	A	93	SER	0	-0.009	-0.018	10.036	0.144	0.144	0.000	0.000	0.000	0.000
76	A	94	VAL	0	0.014	0.002	11.264	0.152	0.152	0.000	0.000	0.000	0.000
77	A	95	ALA	0	-0.010	-0.011	13.899	0.080	0.080	0.000	0.000	0.000	0.000
78	A	96	GLY	0	0.015	-0.003	11.433	0.059	0.059	0.000	0.000	0.000	0.000
79	A	97	TYR	0	-0.021	-0.004	12.452	0.091	0.091	0.000	0.000	0.000	0.000
80	A	98	ILE	0	-0.037	-0.024	14.758	0.057	0.057	0.000	0.000	0.000	0.000
81	A	99	LEU	0	-0.023	-0.009	14.263	0.043	0.043	0.000	0.000	0.000	0.000
82	A	100	ALA	0	-0.018	0.014	13.607	0.031	0.031	0.000	0.000	0.000	0.000
83	A	101	SER	0	-0.037	-0.023	15.644	0.057	0.057	0.000	0.000	0.000	0.000
84	A	102	ASN	0	-0.010	-0.014	19.359	-0.015	-0.015	0.000	0.000	0.000	0.000
85	A	103	ILE	0	-0.022	-0.004	20.897	0.004	0.004	0.000	0.000	0.000	0.000
86	A	104	LYS	1	0.937	0.962	22.515	0.092	0.092	0.000	0.000	0.000	0.000
87	A	105	TYR	0	0.003	0.005	17.402	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:18:MET)