FMO DATABASE

FMODB ID: MVK2Z

Calculation Name: 5CUL-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5CUL

Chain ID: B

ChEMBL ID:

UniProt ID: Q9I337

Base Structure: X-ray

Registration Date: 2023-09-20

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	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	79
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-499824.009541
FMO2-HF: Nuclear repulsion	469460.572304
FMO2-HF: Total energy	-30363.437238
FMO2-MP2: Total energy	-30455.018967

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(B:48:PRO)

Summations of interaction energy for fragment #1(B:48:PRO)

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.
-0.289	4.229	0.307	-1.734	-3.089	-0.003

Interaction energy analysis for fragmet #1(B:48:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : -0.002

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	B	50	HIS	0	0.022	0.023	3.797	-0.059	1.531	-0.010	-0.735	-0.846	0.001
4	B	51	VAL	0	0.007	-0.002	2.858	-0.686	0.003	0.141	-0.178	-0.651	0.000
5	B	52	ALA	0	-0.014	-0.006	5.447	0.098	0.098	0.000	0.000	0.000	0.000
6	B	53	ILE	0	-0.013	0.000	7.632	0.096	0.096	0.000	0.000	0.000	0.000
7	B	54	GLY	0	-0.004	0.021	10.897	-0.022	-0.022	0.000	0.000	0.000	0.000
8	B	55	ILE	0	0.002	-0.014	14.655	0.020	0.020	0.000	0.000	0.000	0.000
9	B	56	ARG	1	0.892	0.942	17.217	0.057	0.057	0.000	0.000	0.000	0.000
10	B	57	TYR	0	0.026	-0.007	20.973	0.005	0.005	0.000	0.000	0.000	0.000
11	B	58	ARG	1	0.877	0.923	23.644	0.052	0.052	0.000	0.000	0.000	0.000
12	B	59	ARG	1	0.974	0.984	27.305	0.073	0.073	0.000	0.000	0.000	0.000
13	B	60	GLY	0	0.031	0.018	29.794	0.002	0.002	0.000	0.000	0.000	0.000
14	B	61	GLU	-1	-0.807	-0.853	26.536	-0.049	-0.049	0.000	0.000	0.000	0.000
15	B	62	THR	0	-0.003	-0.001	24.437	0.002	0.002	0.000	0.000	0.000	0.000
16	B	63	PRO	0	-0.004	0.008	26.867	-0.005	-0.005	0.000	0.000	0.000	0.000
17	B	64	LEU	0	0.008	-0.005	22.796	-0.005	-0.005	0.000	0.000	0.000	0.000
18	B	65	PRO	0	0.000	-0.009	19.455	0.005	0.005	0.000	0.000	0.000	0.000
19	B	66	LEU	0	-0.002	0.017	19.634	0.004	0.004	0.000	0.000	0.000	0.000
20	B	67	VAL	0	-0.002	0.000	13.362	-0.020	-0.020	0.000	0.000	0.000	0.000
21	B	68	THR	0	0.022	0.000	16.444	0.016	0.016	0.000	0.000	0.000	0.000
22	B	69	LEU	0	-0.005	0.005	12.361	0.018	0.018	0.000	0.000	0.000	0.000
23	B	70	LYS	1	0.843	0.908	9.217	-0.128	-0.128	0.000	0.000	0.000	0.000
24	B	71	HIS	0	0.040	0.022	8.771	0.120	0.120	0.000	0.000	0.000	0.000
25	B	72	THR	0	0.010	-0.025	3.485	-0.627	-0.223	0.018	-0.092	-0.330	0.000
26	B	73	ASP	-1	-0.835	-0.903	3.565	-0.485	0.580	0.031	-0.553	-0.542	-0.004
27	B	74	ALA	0	0.046	0.015	5.915	-0.087	-0.087	0.000	0.000	0.000	0.000
28	B	75	LEU	0	0.034	0.026	9.052	-0.043	-0.043	0.000	0.000	0.000	0.000
29	B	76	ALA	0	-0.016	-0.003	7.484	-0.029	-0.029	0.000	0.000	0.000	0.000
30	B	77	LEU	0	-0.025	-0.012	9.445	-0.006	-0.006	0.000	0.000	0.000	0.000
31	B	78	ARG	1	0.788	0.857	11.536	0.135	0.135	0.000	0.000	0.000	0.000
32	B	79	VAL	0	0.008	0.000	12.199	0.011	0.011	0.000	0.000	0.000	0.000
33	B	80	ARG	1	0.871	0.920	8.978	0.861	0.861	0.000	0.000	0.000	0.000
34	B	81	ARG	1	0.850	0.927	14.306	0.164	0.164	0.000	0.000	0.000	0.000
35	B	82	ILE	0	0.021	0.011	17.108	0.020	0.020	0.000	0.000	0.000	0.000
36	B	83	ALA	0	-0.014	-0.005	16.783	0.011	0.011	0.000	0.000	0.000	0.000
37	B	84	GLU	-1	-0.864	-0.921	18.631	-0.184	-0.184	0.000	0.000	0.000	0.000
38	B	85	GLU	-1	-0.841	-0.886	20.668	-0.101	-0.101	0.000	0.000	0.000	0.000
39	B	86	GLU	-1	-0.935	-0.961	21.746	-0.070	-0.070	0.000	0.000	0.000	0.000
40	B	87	GLY	0	-0.035	-0.002	23.096	0.005	0.005	0.000	0.000	0.000	0.000
41	B	88	ILE	0	-0.052	-0.025	18.484	0.001	0.001	0.000	0.000	0.000	0.000
42	B	89	PRO	0	0.013	-0.012	19.240	-0.025	-0.025	0.000	0.000	0.000	0.000
43	B	90	VAL	0	0.001	0.011	13.599	-0.022	-0.022	0.000	0.000	0.000	0.000
44	B	91	LEU	0	-0.006	0.004	15.742	-0.029	-0.029	0.000	0.000	0.000	0.000
45	B	92	GLN	0	-0.023	-0.006	11.167	-0.108	-0.108	0.000	0.000	0.000	0.000
46	B	93	ARG	1	0.822	0.872	11.439	0.366	0.366	0.000	0.000	0.000	0.000
47	B	94	ILE	0	0.047	0.024	6.937	0.030	0.030	0.000	0.000	0.000	0.000
48	B	95	PRO	0	-0.027	-0.023	8.118	-0.051	-0.051	0.000	0.000	0.000	0.000
49	B	96	LEU	0	0.063	0.041	9.632	0.022	0.022	0.000	0.000	0.000	0.000
50	B	97	ALA	0	0.009	0.012	7.338	0.046	0.046	0.000	0.000	0.000	0.000
51	B	98	ARG	1	0.968	0.975	4.235	0.759	1.013	0.000	-0.034	-0.220	0.000
52	B	99	ALA	0	0.029	0.022	6.352	0.135	0.135	0.000	0.000	0.000	0.000
53	B	100	LEU	0	0.021	0.002	9.447	0.076	0.076	0.000	0.000	0.000	0.000
54	B	101	LEU	0	-0.004	-0.006	3.083	-0.477	0.039	0.127	-0.142	-0.500	0.000
55	B	102	ARG	1	0.768	0.859	7.434	0.102	0.102	0.000	0.000	0.000	0.000
56	B	103	ASP	-1	-0.780	-0.856	8.723	0.028	0.028	0.000	0.000	0.000	0.000
57	B	104	GLY	0	0.016	0.011	11.971	0.006	0.006	0.000	0.000	0.000	0.000
58	B	105	ASN	0	-0.047	-0.027	12.586	0.054	0.054	0.000	0.000	0.000	0.000
59	B	106	VAL	0	0.023	0.006	14.107	-0.020	-0.020	0.000	0.000	0.000	0.000
60	B	107	ASP	-1	-0.895	-0.941	16.568	0.009	0.009	0.000	0.000	0.000	0.000
61	B	108	GLN	0	-0.041	-0.015	18.695	0.011	0.011	0.000	0.000	0.000	0.000
62	B	109	TYR	0	-0.015	-0.025	18.955	-0.012	-0.012	0.000	0.000	0.000	0.000
63	B	110	ILE	0	-0.032	-0.009	16.173	0.006	0.006	0.000	0.000	0.000	0.000
64	B	111	PRO	0	0.045	0.018	14.794	0.006	0.006	0.000	0.000	0.000	0.000
65	B	112	ALA	0	0.050	0.017	18.089	-0.016	-0.016	0.000	0.000	0.000	0.000
66	B	113	ASP	-1	-0.895	-0.947	16.818	-0.071	-0.071	0.000	0.000	0.000	0.000
67	B	114	LEU	0	-0.041	-0.026	13.066	-0.026	-0.026	0.000	0.000	0.000	0.000
68	B	115	ILE	0	0.006	0.025	17.177	-0.018	-0.018	0.000	0.000	0.000	0.000
69	B	116	GLN	0	0.019	0.006	20.396	-0.007	-0.007	0.000	0.000	0.000	0.000
70	B	117	ALA	0	0.019	0.005	16.012	-0.006	-0.006	0.000	0.000	0.000	0.000
71	B	118	THR	0	0.017	-0.021	16.718	-0.022	-0.022	0.000	0.000	0.000	0.000
72	B	119	ALA	0	0.015	0.007	17.912	0.000	0.000	0.000	0.000	0.000	0.000
73	B	120	GLU	-1	-0.877	-0.908	18.842	-0.247	-0.247	0.000	0.000	0.000	0.000
74	B	121	VAL	0	0.013	0.000	15.581	-0.005	-0.005	0.000	0.000	0.000	0.000
75	B	122	LEU	0	-0.018	-0.011	18.919	0.004	0.004	0.000	0.000	0.000	0.000
76	B	123	ARG	1	0.949	0.976	22.025	0.152	0.152	0.000	0.000	0.000	0.000
77	B	124	TRP	0	-0.048	-0.017	21.122	-0.003	-0.003	0.000	0.000	0.000	0.000
78	B	125	LEU	0	-0.042	-0.022	20.382	-0.004	-0.004	0.000	0.000	0.000	0.000
79	B	126	GLU	-1	-0.987	-0.973	24.431	-0.102	-0.102	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:48:PRO)