FMO DATABASE

FMODB ID: MVLRZ

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	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	87
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-598991.012518
FMO2-HF: Nuclear repulsion	564337.285966
FMO2-HF: Total energy	-34653.726552
FMO2-MP2: Total energy	-34753.5567

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.
-6.033	-0.567	9.463	-4.418	-10.513	-0.018

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 : -0.003 / q_NPA : 0.001

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	20	CYS	0	0.022	-0.023	3.197	-3.195	-0.369	0.075	-1.543	-1.357	0.002
4	A	21	PHE	0	0.016	0.010	5.840	0.783	0.783	0.000	0.000	0.000	0.000
5	A	22	GLU	-1	-0.835	-0.913	2.245	-3.112	-2.580	3.479	-1.161	-2.850	-0.005
6	A	23	ILE	0	-0.040	-0.022	2.206	-2.090	-0.357	4.566	-1.946	-4.354	-0.015
7	A	24	THR	0	-0.027	-0.015	3.156	1.681	1.337	0.033	0.613	-0.304	-0.001
8	A	25	GLY	0	0.012	-0.006	5.761	0.425	0.425	0.000	0.000	0.000	0.000
9	A	26	LYS	1	0.939	0.970	2.389	-3.351	-2.711	1.311	-0.370	-1.581	0.001
10	A	27	ALA	0	-0.055	-0.014	4.665	0.355	0.434	-0.001	-0.011	-0.067	0.000
11	A	28	TYR	0	0.007	-0.006	7.371	0.148	0.148	0.000	0.000	0.000	0.000
12	A	29	ASN	0	-0.070	-0.020	8.563	0.075	0.075	0.000	0.000	0.000	0.000
13	A	30	ILE	0	-0.017	-0.002	8.833	0.014	0.014	0.000	0.000	0.000	0.000
14	A	31	ASP	-1	-0.836	-0.917	8.470	-0.650	-0.650	0.000	0.000	0.000	0.000
15	A	32	PRO	0	0.065	0.016	5.329	-0.024	-0.024	0.000	0.000	0.000	0.000
16	A	33	LEU	0	0.000	0.001	8.135	-0.083	-0.083	0.000	0.000	0.000	0.000
17	A	34	ILE	0	0.000	0.007	11.281	0.043	0.043	0.000	0.000	0.000	0.000
18	A	35	LEU	0	0.012	0.008	8.293	0.024	0.024	0.000	0.000	0.000	0.000
19	A	36	LYS	1	0.791	0.882	6.358	2.234	2.234	0.000	0.000	0.000	0.000
20	A	37	ALA	0	0.016	0.010	12.655	0.064	0.064	0.000	0.000	0.000	0.000
21	A	38	ILE	0	-0.027	-0.015	14.961	0.057	0.057	0.000	0.000	0.000	0.000
22	A	39	ALA	0	0.056	0.015	14.276	0.045	0.045	0.000	0.000	0.000	0.000
23	A	40	TRP	0	-0.004	0.018	16.229	0.051	0.051	0.000	0.000	0.000	0.000
24	A	41	ASN	0	-0.017	-0.021	17.992	0.056	0.056	0.000	0.000	0.000	0.000
25	A	42	GLU	-1	-0.977	-0.980	19.609	-0.335	-0.335	0.000	0.000	0.000	0.000
26	A	43	SER	0	-0.041	-0.043	18.375	0.017	0.017	0.000	0.000	0.000	0.000
27	A	44	LYS	1	0.778	0.891	19.513	0.430	0.430	0.000	0.000	0.000	0.000
28	A	45	ASN	0	-0.012	-0.014	13.146	0.060	0.060	0.000	0.000	0.000	0.000
29	A	46	LYS	1	0.935	0.992	16.588	0.459	0.459	0.000	0.000	0.000	0.000
30	A	47	ASN	0	0.027	-0.005	16.576	0.022	0.022	0.000	0.000	0.000	0.000
31	A	48	GLY	0	0.045	0.019	18.647	0.040	0.040	0.000	0.000	0.000	0.000
32	A	49	ILE	0	-0.054	-0.022	21.827	0.047	0.047	0.000	0.000	0.000	0.000
33	A	50	LYS	1	0.872	0.930	23.458	0.266	0.266	0.000	0.000	0.000	0.000
34	A	51	SER	0	-0.018	-0.003	26.169	0.008	0.008	0.000	0.000	0.000	0.000
35	A	52	LYS	1	0.967	0.975	27.687	0.221	0.221	0.000	0.000	0.000	0.000
36	A	53	ILE	0	-0.010	0.010	30.566	-0.009	-0.009	0.000	0.000	0.000	0.000
37	A	54	ASN	0	-0.048	-0.028	28.218	0.006	0.006	0.000	0.000	0.000	0.000
38	A	55	LYS	1	0.997	0.981	32.504	0.148	0.148	0.000	0.000	0.000	0.000
39	A	56	ASN	0	0.012	0.033	31.277	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	57	GLY	0	0.031	0.022	34.849	0.006	0.006	0.000	0.000	0.000	0.000
41	A	58	THR	0	-0.029	-0.017	29.566	-0.010	-0.010	0.000	0.000	0.000	0.000
42	A	59	TYR	0	-0.045	-0.077	27.388	0.011	0.011	0.000	0.000	0.000	0.000
43	A	60	ASN	0	0.050	0.040	24.031	0.015	0.015	0.000	0.000	0.000	0.000
44	A	61	ILE	0	0.014	0.009	21.657	0.002	0.002	0.000	0.000	0.000	0.000
45	A	62	GLY	0	0.067	0.048	19.399	-0.025	-0.025	0.000	0.000	0.000	0.000
46	A	63	ILE	0	-0.011	0.022	13.594	0.032	0.032	0.000	0.000	0.000	0.000
47	A	64	MET	0	0.001	0.024	13.366	-0.021	-0.021	0.000	0.000	0.000	0.000
48	A	65	GLN	0	-0.050	-0.030	17.323	0.100	0.100	0.000	0.000	0.000	0.000
49	A	66	ILE	0	0.031	0.030	16.823	0.051	0.051	0.000	0.000	0.000	0.000
50	A	67	ASN	0	-0.014	-0.010	21.062	0.030	0.030	0.000	0.000	0.000	0.000
51	A	68	SER	0	0.063	0.012	24.445	0.003	0.003	0.000	0.000	0.000	0.000
52	A	69	SER	0	-0.049	-0.036	26.779	0.009	0.009	0.000	0.000	0.000	0.000
53	A	70	HIS	1	0.850	0.917	22.609	0.257	0.257	0.000	0.000	0.000	0.000
54	A	71	LEU	0	0.040	0.028	24.045	0.000	0.000	0.000	0.000	0.000	0.000
55	A	72	ASP	-1	-0.807	-0.892	25.571	-0.132	-0.132	0.000	0.000	0.000	0.000
56	A	73	LEU	0	-0.025	-0.013	21.656	0.008	0.008	0.000	0.000	0.000	0.000
57	A	74	LEU	0	0.023	-0.004	19.403	0.009	0.009	0.000	0.000	0.000	0.000
58	A	75	SER	0	0.002	0.006	22.746	0.002	0.002	0.000	0.000	0.000	0.000
59	A	76	LYS	1	0.811	0.913	25.171	0.134	0.134	0.000	0.000	0.000	0.000
60	A	77	PHE	0	-0.038	-0.016	20.090	0.021	0.021	0.000	0.000	0.000	0.000
61	A	78	ASN	0	-0.056	-0.026	20.842	0.004	0.004	0.000	0.000	0.000	0.000
62	A	79	ILE	0	-0.007	0.012	17.383	-0.034	-0.034	0.000	0.000	0.000	0.000
63	A	80	SER	0	-0.039	-0.053	21.219	0.028	0.028	0.000	0.000	0.000	0.000
64	A	81	GLU	-1	-0.759	-0.875	22.184	-0.309	-0.309	0.000	0.000	0.000	0.000
65	A	82	ASP	-1	-0.866	-0.932	22.925	-0.424	-0.424	0.000	0.000	0.000	0.000
66	A	83	ASP	-1	-0.777	-0.853	18.708	-0.449	-0.449	0.000	0.000	0.000	0.000
67	A	84	LEU	0	-0.021	-0.009	18.217	-0.073	-0.073	0.000	0.000	0.000	0.000
68	A	85	LEU	0	-0.046	-0.008	18.925	-0.047	-0.047	0.000	0.000	0.000	0.000
69	A	86	ASN	0	-0.010	-0.036	19.851	-0.052	-0.052	0.000	0.000	0.000	0.000
70	A	87	ASP	-1	-0.840	-0.908	13.959	-1.073	-1.073	0.000	0.000	0.000	0.000
71	A	88	ALA	0	0.000	-0.003	12.945	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	90	ILE	0	0.064	0.049	11.064	0.042	0.042	0.000	0.000	0.000	0.000
73	A	91	ASN	0	-0.062	-0.035	13.819	0.028	0.028	0.000	0.000	0.000	0.000
74	A	92	ILE	0	0.006	-0.015	9.170	0.088	0.088	0.000	0.000	0.000	0.000
75	A	93	SER	0	-0.018	-0.020	10.097	0.131	0.131	0.000	0.000	0.000	0.000
76	A	94	VAL	0	0.005	0.002	11.406	0.145	0.145	0.000	0.000	0.000	0.000
77	A	95	ALA	0	-0.004	-0.008	13.940	0.084	0.084	0.000	0.000	0.000	0.000
78	A	96	GLY	0	0.016	0.008	11.633	0.060	0.060	0.000	0.000	0.000	0.000
79	A	97	TYR	0	-0.008	0.004	12.636	0.090	0.090	0.000	0.000	0.000	0.000
80	A	98	ILE	0	-0.044	-0.027	14.937	0.060	0.060	0.000	0.000	0.000	0.000
81	A	99	LEU	0	-0.052	-0.023	14.514	0.043	0.043	0.000	0.000	0.000	0.000
82	A	100	ALA	0	0.009	0.012	13.786	0.035	0.035	0.000	0.000	0.000	0.000
83	A	101	SER	0	-0.039	0.003	15.912	0.053	0.053	0.000	0.000	0.000	0.000
84	A	102	ASN	0	-0.020	-0.027	19.261	-0.012	-0.012	0.000	0.000	0.000	0.000
85	A	103	ILE	0	-0.026	-0.005	21.283	0.009	0.009	0.000	0.000	0.000	0.000
86	A	104	LYS	1	0.934	0.964	22.781	0.104	0.104	0.000	0.000	0.000	0.000
87	A	105	TYR	0	0.033	0.012	17.675	0.007	0.007	0.000	0.000	0.000	0.000

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