FMO DATABASE

FMODB ID: 94G82

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

Total energy (hartree)

FMO2-HF: Electronic energy	-558937.723712
FMO2-HF: Nuclear repulsion	524113.480702
FMO2-HF: Total energy	-34824.24301
FMO2-MP2: Total energy	-34920.673605

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.
-42.476	-31.063	22.13	-10.192	-23.352	-0.049

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 : -0.037 / q_NPA : 0.009

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	-0.910	-1.003	2.300	-1.764	4.293	4.024	-3.941	-6.139	0.007
4	A	30	ALA	0	-0.018	0.002	3.873	-0.006	-0.939	0.021	1.398	-0.486	0.000
5	A	31	ASN	0	0.006	-0.021	6.159	0.230	0.230	0.000	0.000	0.000	0.000
6	A	32	TYR	0	0.030	0.018	3.332	-2.328	-0.423	3.185	-1.085	-4.005	-0.007
7	A	33	GLY	0	0.056	0.021	5.321	-1.077	-1.022	-0.002	-0.023	-0.031	0.000
8	A	34	ALA	0	-0.078	-0.028	8.233	-0.405	-0.405	0.000	0.000	0.000	0.000
9	A	35	LEU	0	0.061	0.033	6.681	-0.277	-0.277	0.000	0.000	0.000	0.000
10	A	36	LEU	0	0.013	0.011	6.713	-0.419	-0.419	0.000	0.000	0.000	0.000
11	A	37	ARG	1	0.892	0.939	9.789	-0.341	-0.341	0.000	0.000	0.000	0.000
12	A	38	GLU	-1	-0.927	-0.977	12.820	0.015	0.015	0.000	0.000	0.000	0.000
13	A	39	LEU	0	-0.028	0.002	11.848	-0.062	-0.062	0.000	0.000	0.000	0.000
14	A	40	CYS	0	-0.032	0.006	10.424	-0.502	-0.502	0.000	0.000	0.000	0.000
15	A	41	LEU	0	-0.037	-0.014	13.490	0.020	0.020	0.000	0.000	0.000	0.000
16	A	42	THR	0	0.009	-0.005	15.630	-0.013	-0.013	0.000	0.000	0.000	0.000
17	A	43	GLN	0	0.005	0.019	17.390	0.020	0.020	0.000	0.000	0.000	0.000
18	A	44	PHE	0	0.006	-0.007	17.389	0.024	0.024	0.000	0.000	0.000	0.000
19	A	45	GLN	0	-0.055	-0.039	19.247	0.031	0.031	0.000	0.000	0.000	0.000
20	A	46	VAL	0	0.022	0.030	21.725	0.023	0.023	0.000	0.000	0.000	0.000
21	A	47	ASP	-1	-0.814	-0.888	21.828	-0.393	-0.393	0.000	0.000	0.000	0.000
22	A	48	MET	0	-0.032	-0.026	21.912	0.014	0.014	0.000	0.000	0.000	0.000
23	A	49	GLU	-1	-0.980	-0.972	24.719	-0.106	-0.106	0.000	0.000	0.000	0.000
24	A	50	ALA	0	-0.059	-0.030	27.265	0.013	0.013	0.000	0.000	0.000	0.000
25	A	51	VAL	0	-0.073	-0.018	26.655	0.007	0.007	0.000	0.000	0.000	0.000
26	A	52	GLY	0	0.055	0.025	29.123	0.012	0.012	0.000	0.000	0.000	0.000
27	A	53	GLU	-1	-0.891	-0.957	28.831	-0.067	-0.067	0.000	0.000	0.000	0.000
28	A	54	THR	0	-0.057	-0.039	29.748	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	55	LEU	0	-0.054	-0.030	31.036	0.003	0.003	0.000	0.000	0.000	0.000
30	A	56	TRP	0	0.027	0.000	25.807	-0.009	-0.009	0.000	0.000	0.000	0.000
31	A	57	CYS	0	-0.042	-0.006	26.204	-0.015	-0.015	0.000	0.000	0.000	0.000
32	A	58	ASP	-1	-0.834	-0.887	28.163	-0.172	-0.172	0.000	0.000	0.000	0.000
33	A	59	TRP	0	0.065	0.024	22.023	-0.022	-0.022	0.000	0.000	0.000	0.000
34	A	60	GLY	0	-0.017	0.003	26.390	-0.027	-0.027	0.000	0.000	0.000	0.000
35	A	61	ARG	1	0.824	0.894	28.327	0.152	0.152	0.000	0.000	0.000	0.000
36	A	62	THR	0	0.006	0.004	23.653	-0.021	-0.021	0.000	0.000	0.000	0.000
37	A	63	ILE	0	-0.017	-0.002	21.261	-0.032	-0.032	0.000	0.000	0.000	0.000
38	A	64	ARG	1	0.828	0.902	21.038	0.406	0.406	0.000	0.000	0.000	0.000
39	A	65	SER	0	0.021	-0.010	20.108	-0.048	-0.048	0.000	0.000	0.000	0.000
40	A	66	TYR	0	-0.038	-0.034	16.837	-0.058	-0.058	0.000	0.000	0.000	0.000
41	A	67	ARG	1	0.797	0.870	16.061	0.789	0.789	0.000	0.000	0.000	0.000
42	A	68	GLU	-1	-0.824	-0.909	15.545	-0.771	-0.771	0.000	0.000	0.000	0.000
43	A	69	LEU	0	-0.037	-0.007	13.661	-0.127	-0.127	0.000	0.000	0.000	0.000
44	A	70	ALA	0	0.003	-0.001	11.870	-0.111	-0.111	0.000	0.000	0.000	0.000
45	A	71	ASP	-1	-0.737	-0.845	10.572	-1.370	-1.370	0.000	0.000	0.000	0.000
46	A	73	THR	0	-0.022	-0.023	7.852	-0.286	-0.286	0.000	0.000	0.000	0.000
47	A	74	TRP	0	-0.009	0.002	6.036	-0.865	-0.865	0.000	0.000	0.000	0.000
48	A	75	HIS	0	-0.023	-0.028	6.224	-1.055	-1.055	0.000	0.000	0.000	0.000
49	A	76	MET	0	-0.048	-0.034	6.408	-1.197	-1.197	0.000	0.000	0.000	0.000
50	A	77	ALA	0	-0.007	0.001	2.311	-1.563	0.107	1.504	-1.087	-2.088	-0.004
51	A	78	GLU	-1	-0.846	-0.909	1.845	-19.668	-23.752	9.845	-2.119	-3.643	-0.043
52	A	79	LYS	1	0.895	0.947	3.316	-0.725	-1.199	0.158	0.906	-0.589	-0.006
53	A	80	LEU	0	-0.055	-0.035	2.492	-2.473	0.215	3.150	-1.976	-3.862	-0.003
56	A	84	TRP	0	0.001	0.031	3.319	-6.563	-2.862	0.078	-1.990	-1.789	0.009
57	A	85	PRO	0	0.009	-0.008	5.929	0.426	0.426	0.000	0.000	0.000	0.000
58	A	86	ASN	0	0.009	-0.025	3.052	0.677	1.505	0.167	-0.275	-0.720	-0.002
59	A	87	ALA	0	0.098	0.040	5.861	-0.149	-0.149	0.000	0.000	0.000	0.000
60	A	88	GLU	-1	-0.848	-0.880	5.986	0.914	0.914	0.000	0.000	0.000	0.000
61	A	89	VAL	0	0.034	0.002	6.253	-0.207	-0.207	0.000	0.000	0.000	0.000
62	A	90	ASP	-1	-0.880	-0.939	7.897	0.059	0.059	0.000	0.000	0.000	0.000
63	A	91	ARG	1	0.805	0.870	10.494	-0.878	-0.878	0.000	0.000	0.000	0.000
64	A	92	PHE	0	-0.034	-0.021	10.519	-0.059	-0.059	0.000	0.000	0.000	0.000
65	A	93	PHE	0	0.066	0.011	10.896	-0.046	-0.046	0.000	0.000	0.000	0.000
66	A	94	LEU	0	-0.023	0.010	14.011	-0.014	-0.014	0.000	0.000	0.000	0.000
67	A	95	ALA	0	-0.023	-0.014	15.567	-0.017	-0.017	0.000	0.000	0.000	0.000
68	A	96	VAL	0	-0.016	-0.004	15.363	-0.015	-0.015	0.000	0.000	0.000	0.000
69	A	97	HIS	0	0.031	0.025	17.707	-0.056	-0.056	0.000	0.000	0.000	0.000
70	A	98	GLY	0	0.014	0.018	19.840	0.001	0.001	0.000	0.000	0.000	0.000
71	A	99	ARG	1	0.877	0.938	20.806	0.041	0.041	0.000	0.000	0.000	0.000
72	A	100	TYR	0	0.026	0.001	20.241	0.006	0.006	0.000	0.000	0.000	0.000
73	A	101	PHE	0	-0.003	-0.002	19.678	-0.011	-0.011	0.000	0.000	0.000	0.000
74	A	102	ARG	1	0.909	0.966	24.013	0.038	0.038	0.000	0.000	0.000	0.000
75	A	103	SER	0	-0.018	-0.026	26.368	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	105	PRO	0	0.021	0.006	28.790	0.004	0.004	0.000	0.000	0.000	0.000
77	A	106	ILE	0	0.007	0.016	28.684	-0.013	-0.013	0.000	0.000	0.000	0.000
78	A	107	SER	0	-0.015	-0.004	31.304	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)