FMO DATABASE

FMODB ID: MV3NZ

Calculation Name: 2YX8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YX8

Chain ID: A

ChEMBL ID:

UniProt ID: O60894

Base Structure: X-ray

Registration Date: 2023-06-21

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	78
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-560136.364461
FMO2-HF: Nuclear repulsion	525311.919293
FMO2-HF: Total energy	-34824.445167
FMO2-MP2: Total energy	-34920.835923

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:27:CYS)

Summations of interaction energy for fragment #1(A:27:CYS)

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.
-36.66	-26.067	21.381	-10.32	-21.654	-0.057

Interaction energy analysis for fragmet #1(A:27:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : 0.012

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	29	GLU	-1	-0.897	-0.963	2.247	-2.381	2.466	6.154	-4.267	-6.734	-0.008
4	A	30	ALA	0	0.009	0.003	3.899	-0.384	-1.194	0.036	1.214	-0.441	0.000
5	A	31	ASN	0	0.000	-0.008	6.600	-0.286	-0.286	0.000	0.000	0.000	0.000
6	A	32	TYR	0	0.002	-0.006	3.280	-2.314	-0.311	1.820	-0.820	-3.003	-0.005
7	A	33	GLY	0	0.048	0.013	5.361	-1.092	-1.061	-0.002	-0.024	-0.005	0.000
8	A	34	ALA	0	-0.083	-0.029	8.328	-0.381	-0.381	0.000	0.000	0.000	0.000
9	A	35	LEU	0	0.070	0.034	6.868	-0.225	-0.225	0.000	0.000	0.000	0.000
10	A	36	LEU	0	0.004	-0.001	6.797	-0.376	-0.376	0.000	0.000	0.000	0.000
11	A	37	ARG	1	0.884	0.934	9.985	-0.244	-0.244	0.000	0.000	0.000	0.000
12	A	38	GLU	-1	-0.923	-0.963	12.619	-0.070	-0.070	0.000	0.000	0.000	0.000
13	A	39	LEU	0	-0.030	0.003	12.292	-0.039	-0.039	0.000	0.000	0.000	0.000
14	A	40	CYS	0	-0.035	0.001	10.409	-0.473	-0.473	0.000	0.000	0.000	0.000
15	A	41	LEU	0	-0.033	-0.011	13.541	0.029	0.029	0.000	0.000	0.000	0.000
16	A	42	THR	0	-0.001	-0.010	15.888	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	43	GLN	0	0.003	0.015	17.323	0.024	0.024	0.000	0.000	0.000	0.000
18	A	44	PHE	0	0.017	0.000	17.443	0.037	0.037	0.000	0.000	0.000	0.000
19	A	45	GLN	0	-0.060	-0.040	19.239	0.031	0.031	0.000	0.000	0.000	0.000
20	A	46	VAL	0	0.002	0.007	21.704	0.024	0.024	0.000	0.000	0.000	0.000
21	A	47	ASP	-1	-0.769	-0.852	21.617	-0.395	-0.395	0.000	0.000	0.000	0.000
22	A	48	MET	0	-0.037	-0.015	21.924	0.015	0.015	0.000	0.000	0.000	0.000
23	A	49	GLU	-1	-0.958	-0.968	24.750	-0.117	-0.117	0.000	0.000	0.000	0.000
24	A	50	ALA	0	-0.053	-0.022	27.247	0.014	0.014	0.000	0.000	0.000	0.000
25	A	51	VAL	0	-0.063	-0.017	26.872	0.005	0.005	0.000	0.000	0.000	0.000
26	A	52	GLY	0	0.042	0.020	29.045	0.014	0.014	0.000	0.000	0.000	0.000
27	A	53	GLU	-1	-0.837	-0.932	28.847	-0.072	-0.072	0.000	0.000	0.000	0.000
28	A	54	THR	0	-0.074	-0.050	29.892	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	55	LEU	0	-0.041	-0.023	31.082	0.004	0.004	0.000	0.000	0.000	0.000
30	A	56	TRP	0	0.017	0.014	25.695	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	57	CYS	0	-0.030	0.009	26.257	-0.016	-0.016	0.000	0.000	0.000	0.000
32	A	58	ASP	-1	-0.841	-0.892	28.140	-0.162	-0.162	0.000	0.000	0.000	0.000
33	A	59	TRP	0	0.038	0.006	22.164	-0.022	-0.022	0.000	0.000	0.000	0.000
34	A	60	GLY	0	-0.015	-0.002	26.370	-0.025	-0.025	0.000	0.000	0.000	0.000
35	A	61	ARG	1	0.831	0.907	28.388	0.145	0.145	0.000	0.000	0.000	0.000
36	A	62	THR	0	0.010	0.005	23.667	-0.022	-0.022	0.000	0.000	0.000	0.000
37	A	63	ILE	0	-0.029	-0.010	21.109	-0.033	-0.033	0.000	0.000	0.000	0.000
38	A	64	ARG	1	0.798	0.873	20.889	0.384	0.384	0.000	0.000	0.000	0.000
39	A	65	SER	0	0.033	0.000	19.798	-0.045	-0.045	0.000	0.000	0.000	0.000
40	A	66	TYR	0	-0.042	-0.037	16.752	-0.054	-0.054	0.000	0.000	0.000	0.000
41	A	67	ARG	1	0.801	0.875	15.918	0.741	0.741	0.000	0.000	0.000	0.000
42	A	68	GLU	-1	-0.817	-0.915	15.326	-0.693	-0.693	0.000	0.000	0.000	0.000
43	A	69	LEU	0	-0.045	-0.008	13.614	-0.127	-0.127	0.000	0.000	0.000	0.000
44	A	70	ALA	0	-0.003	0.003	11.927	-0.121	-0.121	0.000	0.000	0.000	0.000
45	A	71	ASP	-1	-0.743	-0.840	10.500	-1.303	-1.303	0.000	0.000	0.000	0.000
46	A	73	THR	0	-0.014	-0.033	7.937	-0.318	-0.318	0.000	0.000	0.000	0.000
47	A	74	TRP	0	-0.011	0.004	5.986	-0.789	-0.789	0.000	0.000	0.000	0.000
48	A	75	HIS	0	-0.033	-0.032	5.947	-1.118	-1.118	0.000	0.000	0.000	0.000
49	A	76	MET	0	-0.033	-0.030	6.465	-0.846	-0.846	0.000	0.000	0.000	0.000
50	A	77	ALA	0	-0.010	0.001	2.203	-1.566	-0.298	2.616	-1.557	-2.328	-0.005
51	A	78	GLU	-1	-0.820	-0.903	1.906	-18.279	-21.018	7.730	-1.359	-3.632	-0.038
52	A	79	LYS	1	0.861	0.926	3.899	0.345	0.740	0.018	-0.142	-0.271	-0.001
53	A	80	LEU	0	-0.036	-0.020	2.847	0.408	2.678	2.919	-1.753	-3.436	-0.003
56	A	84	TRP	0	0.022	0.027	3.323	-5.520	-2.796	0.051	-1.435	-1.339	0.004
57	A	85	PRO	0	0.002	0.001	6.091	0.430	0.430	0.000	0.000	0.000	0.000
58	A	86	ASN	0	-0.007	-0.023	3.310	0.811	1.415	0.039	-0.177	-0.465	-0.001
59	A	87	ALA	0	0.089	0.040	6.176	-0.136	-0.136	0.000	0.000	0.000	0.000
60	A	88	GLU	-1	-0.841	-0.867	6.407	0.730	0.730	0.000	0.000	0.000	0.000
61	A	89	VAL	0	0.023	0.001	6.416	-0.154	-0.154	0.000	0.000	0.000	0.000
62	A	90	ASP	-1	-0.855	-0.934	8.103	0.100	0.100	0.000	0.000	0.000	0.000
63	A	91	ARG	1	0.793	0.861	10.821	-0.698	-0.698	0.000	0.000	0.000	0.000
64	A	92	PHE	0	-0.025	-0.016	10.638	-0.043	-0.043	0.000	0.000	0.000	0.000
65	A	93	PHE	0	0.057	0.012	11.190	-0.033	-0.033	0.000	0.000	0.000	0.000
66	A	94	LEU	0	-0.022	0.009	14.098	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	95	ALA	0	-0.022	-0.014	15.852	-0.013	-0.013	0.000	0.000	0.000	0.000
68	A	96	VAL	0	-0.011	-0.002	15.723	-0.011	-0.011	0.000	0.000	0.000	0.000
69	A	97	HIS	0	0.031	0.022	17.916	-0.049	-0.049	0.000	0.000	0.000	0.000
70	A	98	GLY	0	0.009	0.014	20.083	0.001	0.001	0.000	0.000	0.000	0.000
71	A	99	ARG	1	0.902	0.942	21.375	0.069	0.069	0.000	0.000	0.000	0.000
72	A	100	TYR	0	0.023	0.002	20.621	0.004	0.004	0.000	0.000	0.000	0.000
73	A	101	PHE	0	0.008	-0.007	19.678	-0.014	-0.014	0.000	0.000	0.000	0.000
74	A	102	ARG	1	0.831	0.922	24.044	0.054	0.054	0.000	0.000	0.000	0.000
75	A	103	SER	0	-0.013	-0.023	26.231	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	105	PRO	0	0.008	0.002	28.771	0.005	0.005	0.000	0.000	0.000	0.000
77	A	106	ILE	0	0.012	0.012	28.536	-0.012	-0.012	0.000	0.000	0.000	0.000
78	A	107	SER	0	-0.013	0.001	31.325	0.006	0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:27:CYS)