FMO DATABASE

FMODB ID: 2J9YR

Calculation Name: 2YZ1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YZ1

Chain ID: A

ChEMBL ID:

UniProt ID: P97797

Base Structure: X-ray

Registration Date: 2023-09-19

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	OptH
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	113
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-849191.987367
FMO2-HF: Nuclear repulsion	805485.540864
FMO2-HF: Total energy	-43706.446502
FMO2-MP2: Total energy	-43834.122693

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:7:GLU)

Summations of interaction energy for fragment #1(A:7:GLU)

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.
-79.536	-74.072	7.88	-6.075	-7.27	0.057

Interaction energy analysis for fragmet #1(A:7:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.884 / q_NPA : -0.945

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	9	LYS	1	0.909	0.948	1.957	-79.474	-75.030	7.883	-5.614	-6.714	0.056
4	A	10	VAL	0	0.021	0.007	4.417	-5.065	-4.981	-0.001	-0.026	-0.057	0.000
5	A	11	THR	0	0.005	-0.001	8.195	1.418	1.418	0.000	0.000	0.000	0.000
6	A	12	GLN	0	0.020	-0.006	10.017	-0.609	-0.609	0.000	0.000	0.000	0.000
7	A	13	PRO	0	-0.056	-0.033	13.739	0.353	0.353	0.000	0.000	0.000	0.000
8	A	14	GLU	-1	-0.876	-0.923	13.852	20.423	20.423	0.000	0.000	0.000	0.000
9	A	15	LYS	1	0.937	0.953	17.032	-15.007	-15.007	0.000	0.000	0.000	0.000
10	A	16	SER	0	-0.026	-0.032	20.669	0.303	0.303	0.000	0.000	0.000	0.000
11	A	17	VAL	0	-0.077	-0.041	23.702	-0.153	-0.153	0.000	0.000	0.000	0.000
12	A	18	SER	0	0.013	0.006	25.565	-0.147	-0.147	0.000	0.000	0.000	0.000
13	A	19	VAL	0	-0.016	-0.009	29.285	-0.059	-0.059	0.000	0.000	0.000	0.000
14	A	20	ALA	0	0.056	0.033	31.244	-0.087	-0.087	0.000	0.000	0.000	0.000
15	A	21	ALA	0	0.050	0.010	34.333	0.144	0.144	0.000	0.000	0.000	0.000
16	A	22	GLY	0	-0.039	-0.012	35.258	-0.250	-0.250	0.000	0.000	0.000	0.000
17	A	23	ASP	-1	-0.883	-0.927	33.012	8.788	8.788	0.000	0.000	0.000	0.000
18	A	24	SER	0	-0.032	-0.022	30.326	0.134	0.134	0.000	0.000	0.000	0.000
19	A	25	THR	0	-0.021	-0.005	25.398	0.093	0.093	0.000	0.000	0.000	0.000
20	A	26	VAL	0	-0.047	-0.022	21.740	-0.054	-0.054	0.000	0.000	0.000	0.000
21	A	27	LEU	0	-0.006	0.012	19.973	0.215	0.215	0.000	0.000	0.000	0.000
22	A	28	ASN	0	0.022	-0.003	16.694	-0.055	-0.055	0.000	0.000	0.000	0.000
23	A	29	CYS	0	-0.048	-0.019	13.354	0.336	0.336	0.000	0.000	0.000	0.000
24	A	30	THR	0	-0.050	-0.009	11.470	-0.444	-0.444	0.000	0.000	0.000	0.000
25	A	31	LEU	0	0.018	0.015	8.536	1.605	1.605	0.000	0.000	0.000	0.000
26	A	32	THR	0	-0.007	-0.017	3.828	-2.692	-1.931	-0.001	-0.413	-0.348	0.001
27	A	33	SER	0	0.020	-0.008	4.952	-2.415	-2.415	0.000	0.000	0.000	0.000
28	A	34	LEU	0	-0.006	-0.008	6.877	-0.395	-0.395	0.000	0.000	0.000	0.000
29	A	35	LEU	0	-0.048	0.013	8.187	-1.953	-1.953	0.000	0.000	0.000	0.000
30	A	36	PRO	0	0.067	0.015	7.795	3.151	3.151	0.000	0.000	0.000	0.000
31	A	37	VAL	0	0.048	0.011	10.688	0.344	0.344	0.000	0.000	0.000	0.000
32	A	38	GLY	0	0.012	0.001	14.011	-0.138	-0.138	0.000	0.000	0.000	0.000
33	A	39	PRO	0	-0.008	0.015	15.223	0.685	0.685	0.000	0.000	0.000	0.000
34	A	40	ILE	0	0.007	0.018	13.480	1.479	1.479	0.000	0.000	0.000	0.000
35	A	41	LYS	1	0.805	0.892	16.086	-17.216	-17.216	0.000	0.000	0.000	0.000
36	A	42	TRP	0	0.007	-0.006	17.381	1.085	1.085	0.000	0.000	0.000	0.000
37	A	43	TYR	0	0.000	0.000	18.319	-0.988	-0.988	0.000	0.000	0.000	0.000
38	A	44	ARG	1	0.920	0.970	20.713	-10.944	-10.944	0.000	0.000	0.000	0.000
39	A	45	GLY	0	-0.005	0.004	22.659	-0.373	-0.373	0.000	0.000	0.000	0.000
40	A	46	VAL	0	0.021	0.004	21.321	0.720	0.720	0.000	0.000	0.000	0.000
41	A	47	GLY	0	0.015	0.005	21.697	-0.583	-0.583	0.000	0.000	0.000	0.000
42	A	48	GLN	0	0.022	-0.006	21.483	0.776	0.776	0.000	0.000	0.000	0.000
43	A	49	SER	0	-0.032	-0.013	23.672	-0.063	-0.063	0.000	0.000	0.000	0.000
44	A	50	ARG	1	0.850	0.951	16.256	-18.301	-18.301	0.000	0.000	0.000	0.000
45	A	51	LEU	0	0.036	0.014	23.769	-0.067	-0.067	0.000	0.000	0.000	0.000
46	A	52	LEU	0	-0.030	-0.019	22.241	0.487	0.487	0.000	0.000	0.000	0.000
47	A	53	ILE	0	-0.038	-0.007	23.177	-0.535	-0.535	0.000	0.000	0.000	0.000
48	A	54	TYR	0	0.016	0.000	21.625	-0.641	-0.641	0.000	0.000	0.000	0.000
49	A	55	SER	0	0.018	0.010	21.148	0.923	0.923	0.000	0.000	0.000	0.000
50	A	56	PHE	0	-0.038	-0.020	18.400	-0.661	-0.661	0.000	0.000	0.000	0.000
51	A	57	THR	0	0.014	-0.011	19.212	0.943	0.943	0.000	0.000	0.000	0.000
52	A	58	GLY	0	0.012	0.016	19.763	0.601	0.601	0.000	0.000	0.000	0.000
53	A	59	GLU	-1	-0.800	-0.908	18.462	14.769	14.769	0.000	0.000	0.000	0.000
54	A	60	HIS	0	0.006	0.000	21.235	0.730	0.730	0.000	0.000	0.000	0.000
55	A	61	PHE	0	0.027	0.022	16.577	-0.332	-0.332	0.000	0.000	0.000	0.000
56	A	62	PRO	0	0.014	0.003	20.063	0.015	0.015	0.000	0.000	0.000	0.000
57	A	63	ARG	1	0.896	0.950	21.465	-11.151	-11.151	0.000	0.000	0.000	0.000
58	A	64	VAL	0	-0.047	-0.018	22.810	-0.592	-0.592	0.000	0.000	0.000	0.000
59	A	65	THR	0	-0.023	-0.028	19.240	0.381	0.381	0.000	0.000	0.000	0.000
60	A	66	ASN	0	0.013	0.011	19.077	0.581	0.581	0.000	0.000	0.000	0.000
61	A	67	VAL	0	-0.010	-0.005	20.923	-0.456	-0.456	0.000	0.000	0.000	0.000
62	A	68	SER	0	-0.014	-0.008	18.164	0.667	0.667	0.000	0.000	0.000	0.000
63	A	69	ASP	-1	-0.842	-0.895	19.406	13.052	13.052	0.000	0.000	0.000	0.000
64	A	70	ALA	0	-0.019	-0.016	20.153	0.405	0.405	0.000	0.000	0.000	0.000
65	A	71	THR	0	-0.052	-0.057	22.544	-0.383	-0.383	0.000	0.000	0.000	0.000
66	A	72	LYS	1	0.846	0.960	16.852	-16.978	-16.978	0.000	0.000	0.000	0.000
67	A	73	ARG	1	0.984	0.986	21.154	-13.181	-13.181	0.000	0.000	0.000	0.000
68	A	74	ASN	0	0.030	0.002	14.607	0.815	0.815	0.000	0.000	0.000	0.000
69	A	75	ASN	0	0.047	0.013	13.476	0.300	0.300	0.000	0.000	0.000	0.000
70	A	76	MET	0	-0.025	0.018	8.806	0.064	0.064	0.000	0.000	0.000	0.000
71	A	77	ASP	-1	-0.868	-0.923	12.981	17.138	17.138	0.000	0.000	0.000	0.000
72	A	78	PHE	0	0.001	-0.023	13.222	-0.588	-0.588	0.000	0.000	0.000	0.000
73	A	79	SER	0	0.010	-0.021	16.806	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	80	ILE	0	-0.023	0.010	19.078	-0.536	-0.536	0.000	0.000	0.000	0.000
75	A	81	ARG	1	0.947	0.963	22.279	-10.942	-10.942	0.000	0.000	0.000	0.000
76	A	82	ILE	0	0.011	0.018	24.749	-0.070	-0.070	0.000	0.000	0.000	0.000
77	A	83	SER	0	0.005	-0.024	27.804	0.011	0.011	0.000	0.000	0.000	0.000
78	A	84	ASN	0	-0.103	-0.048	31.357	-0.041	-0.041	0.000	0.000	0.000	0.000
79	A	85	VAL	0	0.012	0.017	29.440	-0.011	-0.011	0.000	0.000	0.000	0.000
80	A	86	THR	0	0.028	0.018	32.200	-0.373	-0.373	0.000	0.000	0.000	0.000
81	A	87	PRO	0	0.056	-0.001	32.665	0.341	0.341	0.000	0.000	0.000	0.000
82	A	88	GLU	-1	-0.898	-0.947	32.742	9.150	9.150	0.000	0.000	0.000	0.000
83	A	89	ASP	-1	-0.917	-0.955	28.898	10.791	10.791	0.000	0.000	0.000	0.000
84	A	90	ALA	0	-0.016	0.015	27.881	0.549	0.549	0.000	0.000	0.000	0.000
85	A	91	GLY	0	0.005	-0.006	25.959	-0.032	-0.032	0.000	0.000	0.000	0.000
86	A	92	THR	0	-0.001	0.003	19.476	-0.074	-0.074	0.000	0.000	0.000	0.000
87	A	93	TYR	0	-0.009	-0.028	20.425	-0.014	-0.014	0.000	0.000	0.000	0.000
88	A	94	TYR	0	-0.021	0.004	15.159	0.169	0.169	0.000	0.000	0.000	0.000
89	A	96	VAL	0	0.026	0.006	13.105	1.857	1.857	0.000	0.000	0.000	0.000
90	A	97	LYS	1	0.818	0.911	10.004	-26.573	-26.573	0.000	0.000	0.000	0.000
91	A	98	PHE	0	0.043	-0.004	12.543	0.746	0.746	0.000	0.000	0.000	0.000
92	A	99	GLN	0	-0.022	-0.007	12.723	1.473	1.473	0.000	0.000	0.000	0.000
93	A	100	LYS	1	0.942	0.971	14.454	-15.721	-15.721	0.000	0.000	0.000	0.000
94	A	101	GLY	0	0.009	0.015	17.619	0.419	0.419	0.000	0.000	0.000	0.000
95	A	102	PRO	0	-0.014	-0.030	18.953	-0.483	-0.483	0.000	0.000	0.000	0.000
96	A	103	SER	0	-0.031	-0.021	22.233	-0.804	-0.804	0.000	0.000	0.000	0.000
97	A	104	GLU	-1	-0.926	-0.933	22.461	14.558	14.558	0.000	0.000	0.000	0.000
98	A	105	PRO	0	-0.022	-0.015	22.226	-0.453	-0.453	0.000	0.000	0.000	0.000
99	A	106	ASP	-1	-0.793	-0.895	18.418	16.347	16.347	0.000	0.000	0.000	0.000
100	A	107	THR	0	-0.043	-0.019	14.898	-0.410	-0.410	0.000	0.000	0.000	0.000
101	A	108	GLU	-1	-0.843	-0.912	12.624	23.518	23.518	0.000	0.000	0.000	0.000
102	A	109	ILE	0	-0.060	-0.044	9.075	0.124	0.124	0.000	0.000	0.000	0.000
103	A	110	GLN	0	-0.026	-0.008	4.336	-2.285	-2.110	-0.001	-0.022	-0.151	0.000
104	A	111	SER	0	0.039	0.007	8.769	-4.475	-4.475	0.000	0.000	0.000	0.000
105	A	112	GLY	0	-0.029	-0.005	9.423	2.747	2.747	0.000	0.000	0.000	0.000
106	A	113	GLY	0	0.016	0.010	11.528	-0.535	-0.535	0.000	0.000	0.000	0.000
107	A	114	GLY	0	-0.021	-0.008	13.112	-1.173	-1.173	0.000	0.000	0.000	0.000
108	A	115	THR	0	-0.054	-0.032	16.619	0.244	0.244	0.000	0.000	0.000	0.000
109	A	116	GLU	-1	-0.884	-0.892	19.269	12.120	12.120	0.000	0.000	0.000	0.000
110	A	117	VAL	0	-0.019	-0.004	22.873	-0.078	-0.078	0.000	0.000	0.000	0.000
111	A	118	TYR	0	0.030	0.008	25.802	-0.206	-0.206	0.000	0.000	0.000	0.000
112	A	119	VAL	0	0.002	-0.002	29.098	-0.053	-0.053	0.000	0.000	0.000	0.000
113	A	120	LEU	0	-0.043	-0.016	32.217	-0.246	-0.246	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:GLU)