FMO DATABASE

FMODB ID: 9G3V2

Calculation Name: 2AP6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2AP6

Chain ID: A

ChEMBL ID:

UniProt ID: A9CGA4

Base Structure: X-ray

Registration Date: 2023-06-20

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	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	104
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-829342.447269
FMO2-HF: Nuclear repulsion	786877.922421
FMO2-HF: Total energy	-42464.524848
FMO2-MP2: Total energy	-42588.727865

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:1:MET)

Summations of interaction energy for fragment #1(A:1: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.
-24.37	-17.336	16.672	-6.31	-17.397	-0.06

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.045 / 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	A	3	TYR	0	0.054	0.030	2.335	-5.041	-1.042	1.451	-1.995	-3.454	-0.007
4	A	4	GLU	-1	-0.775	-0.857	5.482	0.343	0.343	0.000	0.000	0.000	0.000
5	A	5	ILE	0	-0.002	-0.006	8.666	-0.214	-0.214	0.000	0.000	0.000	0.000
6	A	6	ARG	1	0.786	0.870	11.624	0.588	0.588	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.065	0.031	14.715	-0.078	-0.078	0.000	0.000	0.000	0.000
8	A	8	TYR	0	-0.018	-0.011	17.473	0.041	0.041	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.929	0.959	21.261	0.145	0.145	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.022	-0.021	23.087	0.017	0.017	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.931	0.970	26.678	0.172	0.172	0.000	0.000	0.000	0.000
12	A	12	ASN	0	-0.018	-0.023	30.058	-0.022	-0.022	0.000	0.000	0.000	0.000
13	A	13	GLY	0	0.047	0.017	31.085	0.013	0.013	0.000	0.000	0.000	0.000
14	A	14	ALA	0	-0.018	-0.009	28.510	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	15	ILE	0	0.031	0.026	24.620	-0.007	-0.007	0.000	0.000	0.000	0.000
16	A	16	PRO	0	0.024	0.010	25.764	-0.021	-0.021	0.000	0.000	0.000	0.000
17	A	17	ALA	0	0.012	0.007	27.317	-0.011	-0.011	0.000	0.000	0.000	0.000
18	A	18	TYR	0	0.018	-0.018	18.836	0.010	0.010	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.011	-0.011	20.994	-0.021	-0.021	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.883	0.950	22.981	0.256	0.256	0.000	0.000	0.000	0.000
21	A	21	VAL	0	0.037	0.021	24.241	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	22	VAL	0	-0.016	-0.003	18.560	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.971	-0.973	20.310	-0.510	-0.510	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.838	-0.905	21.363	-0.327	-0.327	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.877	-0.928	22.985	-0.233	-0.233	0.000	0.000	0.000	0.000
26	A	26	GLY	0	-0.025	-0.004	19.724	0.015	0.015	0.000	0.000	0.000	0.000
27	A	27	ILE	0	0.007	-0.019	14.105	-0.042	-0.042	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.753	-0.861	15.048	-0.882	-0.882	0.000	0.000	0.000	0.000
29	A	29	ILE	0	-0.019	0.000	15.717	-0.036	-0.036	0.000	0.000	0.000	0.000
30	A	30	GLN	0	0.002	-0.002	12.643	0.031	0.031	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.829	0.892	11.081	0.906	0.906	0.000	0.000	0.000	0.000
32	A	32	SER	0	-0.078	-0.025	10.924	-0.098	-0.098	0.000	0.000	0.000	0.000
33	A	33	HIS	1	0.797	0.873	12.411	0.417	0.417	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.019	-0.030	8.674	0.124	0.124	0.000	0.000	0.000	0.000
35	A	35	GLY	0	-0.011	0.007	6.411	-0.129	-0.129	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.895	-0.941	2.579	-16.112	-13.392	2.408	-2.358	-2.770	-0.033
37	A	37	LEU	0	-0.041	-0.016	5.855	-0.086	-0.086	0.000	0.000	0.000	0.000
38	A	38	VAL	0	-0.038	-0.037	6.138	-0.130	-0.130	0.000	0.000	0.000	0.000
39	A	39	GLY	0	0.012	0.002	8.636	0.217	0.217	0.000	0.000	0.000	0.000
40	A	40	TYR	0	0.010	0.002	12.313	0.031	0.031	0.000	0.000	0.000	0.000
41	A	41	PHE	0	-0.008	-0.003	13.825	0.023	0.023	0.000	0.000	0.000	0.000
42	A	42	PHE	0	0.022	0.006	18.338	0.014	0.014	0.000	0.000	0.000	0.000
43	A	43	SER	0	-0.036	-0.011	21.798	0.002	0.002	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.917	-0.956	24.186	-0.304	-0.304	0.000	0.000	0.000	0.000
45	A	45	ILE	0	0.010	-0.001	25.971	0.030	0.030	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.002	0.003	25.782	-0.018	-0.018	0.000	0.000	0.000	0.000
47	A	47	PRO	0	-0.026	-0.008	23.561	0.023	0.023	0.000	0.000	0.000	0.000
48	A	48	ILE	0	0.043	0.015	25.830	-0.022	-0.022	0.000	0.000	0.000	0.000
49	A	49	ASN	0	-0.048	-0.025	27.207	0.006	0.006	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.896	-0.948	21.141	-0.351	-0.351	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.004	0.004	18.296	-0.027	-0.027	0.000	0.000	0.000	0.000
52	A	52	VAL	0	0.012	0.001	14.842	0.015	0.015	0.000	0.000	0.000	0.000
53	A	53	HIS	0	0.021	0.030	13.021	-0.133	-0.133	0.000	0.000	0.000	0.000
54	A	54	ILE	0	-0.039	-0.023	7.742	0.079	0.079	0.000	0.000	0.000	0.000
55	A	55	TRP	0	0.026	0.001	6.913	-0.150	-0.150	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.030	0.028	2.431	0.016	0.191	1.967	-0.619	-1.523	0.002
57	A	57	PHE	0	0.000	-0.017	2.947	-2.510	-0.832	0.512	-0.528	-1.662	-0.004
58	A	58	SER	0	0.040	0.003	2.733	0.844	1.430	8.157	-4.489	-4.256	-0.004
59	A	59	SER	0	0.010	-0.009	3.403	3.738	-0.254	-0.063	4.900	-0.846	-0.003
60	A	60	LEU	0	0.019	-0.010	5.643	-0.972	-0.972	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.854	-0.917	8.384	1.127	1.127	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.799	-0.868	6.200	1.056	1.056	0.000	0.000	0.000	0.000
63	A	63	ARG	1	0.806	0.895	8.026	-0.597	-0.597	0.000	0.000	0.000	0.000
64	A	64	ALA	0	-0.030	-0.018	9.257	-0.318	-0.318	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.808	-0.880	12.034	0.372	0.372	0.000	0.000	0.000	0.000
66	A	66	ARG	1	0.835	0.898	6.592	0.209	0.209	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.899	0.942	11.262	0.104	0.104	0.000	0.000	0.000	0.000
68	A	68	ALA	0	-0.002	0.018	13.537	-0.042	-0.042	0.000	0.000	0.000	0.000
69	A	69	ARG	1	0.840	0.888	11.623	-0.223	-0.223	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.048	-0.010	13.714	-0.037	-0.037	0.000	0.000	0.000	0.000
71	A	71	MET	0	-0.056	-0.033	16.265	-0.030	-0.030	0.000	0.000	0.000	0.000
72	A	72	ALA	0	0.017	0.024	19.089	0.014	0.014	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.766	-0.831	19.018	-0.256	-0.256	0.000	0.000	0.000	0.000
74	A	74	PRO	0	0.071	0.029	21.011	-0.012	-0.012	0.000	0.000	0.000	0.000
75	A	75	ARG	1	0.885	0.920	18.795	0.300	0.300	0.000	0.000	0.000	0.000
76	A	76	TRP	0	0.017	0.001	17.216	-0.037	-0.037	0.000	0.000	0.000	0.000
77	A	77	LEU	0	-0.017	-0.011	21.198	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	78	SER	0	-0.038	-0.027	24.142	0.013	0.013	0.000	0.000	0.000	0.000
79	A	79	PHE	0	0.002	0.009	20.056	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	80	LEU	0	0.025	0.012	20.106	0.003	0.003	0.000	0.000	0.000	0.000
81	A	81	PRO	0	-0.027	-0.025	23.774	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.782	0.878	25.826	0.229	0.229	0.000	0.000	0.000	0.000
83	A	83	ILE	0	0.011	-0.004	20.749	-0.010	-0.010	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.780	0.866	25.235	0.129	0.129	0.000	0.000	0.000	0.000
85	A	85	ASP	-1	-0.793	-0.860	26.122	-0.129	-0.129	0.000	0.000	0.000	0.000
86	A	86	LEU	0	-0.054	-0.012	26.138	0.003	0.003	0.000	0.000	0.000	0.000
87	A	87	ILE	0	-0.025	-0.008	21.614	-0.014	-0.014	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.856	-0.907	25.589	-0.140	-0.140	0.000	0.000	0.000	0.000
89	A	89	VAL	0	-0.017	-0.011	24.287	0.021	0.021	0.000	0.000	0.000	0.000
90	A	90	ALA	0	-0.014	-0.009	20.271	-0.036	-0.036	0.000	0.000	0.000	0.000
91	A	91	GLU	-1	-0.844	-0.897	18.527	-0.183	-0.183	0.000	0.000	0.000	0.000
92	A	92	ASN	0	-0.017	-0.011	13.700	-0.078	-0.078	0.000	0.000	0.000	0.000
93	A	93	LYS	1	0.889	0.941	13.175	0.447	0.447	0.000	0.000	0.000	0.000
94	A	94	ILE	0	0.010	0.012	7.943	-0.152	-0.152	0.000	0.000	0.000	0.000
95	A	95	MET	0	-0.017	-0.010	8.314	0.164	0.164	0.000	0.000	0.000	0.000
96	A	96	LYS	1	0.962	0.975	5.067	-3.026	-3.026	0.000	0.000	0.000	0.000
97	A	97	PRO	0	0.006	0.039	3.010	-0.436	0.247	0.053	-0.168	-0.568	0.000
98	A	98	ALA	0	0.021	0.011	6.149	0.427	0.427	0.000	0.000	0.000	0.000
99	A	99	ARG	1	0.987	0.961	8.283	-0.377	-0.377	0.000	0.000	0.000	0.000
100	A	100	PHE	0	-0.013	-0.007	9.536	-0.022	-0.022	0.000	0.000	0.000	0.000
101	A	101	SER	0	-0.057	-0.024	7.102	0.089	0.089	0.000	0.000	0.000	0.000
102	A	102	PRO	0	0.029	0.005	8.479	-0.048	-0.048	0.000	0.000	0.000	0.000
103	A	103	LEU	0	0.000	0.023	5.734	-0.169	-0.169	0.000	0.000	0.000	0.000
104	A	104	MET	0	0.065	0.033	2.611	-2.306	-1.121	2.187	-1.053	-2.318	-0.011

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