FMO DATABASE

FMODB ID: M351Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-829037.945255
FMO2-HF: Nuclear repulsion	786573.130213
FMO2-HF: Total energy	-42464.815042
FMO2-MP2: Total energy	-42588.991884

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.
-25.011	-15.401	12.691	-6.595	-15.704	-0.056

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 : -0.042 / q_NPA : -0.005

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	3	TYR	0	0.043	0.007	2.341	-5.691	-1.384	1.305	-2.124	-3.487	-0.009
4	A	4	GLU	-1	-0.778	-0.860	5.341	0.207	0.277	-0.001	-0.003	-0.066	0.000
5	A	5	ILE	0	0.012	0.004	8.764	-0.240	-0.240	0.000	0.000	0.000	0.000
6	A	6	ARG	1	0.792	0.872	11.727	0.673	0.673	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.051	0.025	14.902	-0.068	-0.068	0.000	0.000	0.000	0.000
8	A	8	TYR	0	0.016	0.008	17.877	0.038	0.038	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.895	0.944	21.504	0.167	0.167	0.000	0.000	0.000	0.000
10	A	10	LEU	0	0.010	-0.004	23.291	0.017	0.017	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.881	0.934	26.653	0.189	0.189	0.000	0.000	0.000	0.000
12	A	12	ASN	0	-0.019	-0.009	30.345	-0.021	-0.021	0.000	0.000	0.000	0.000
13	A	13	GLY	0	0.044	0.020	31.496	0.015	0.015	0.000	0.000	0.000	0.000
14	A	14	ALA	0	-0.007	-0.008	28.772	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	15	ILE	0	0.021	0.024	25.244	-0.009	-0.009	0.000	0.000	0.000	0.000
16	A	16	PRO	0	0.028	0.008	26.171	-0.022	-0.022	0.000	0.000	0.000	0.000
17	A	17	ALA	0	0.019	0.012	27.565	-0.012	-0.012	0.000	0.000	0.000	0.000
18	A	18	TYR	0	0.025	-0.009	19.154	0.009	0.009	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.004	-0.002	21.407	-0.024	-0.024	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.843	0.912	23.321	0.281	0.281	0.000	0.000	0.000	0.000
21	A	21	VAL	0	0.026	0.016	24.612	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	22	VAL	0	-0.021	-0.024	18.822	-0.013	-0.013	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.984	-0.983	20.502	-0.503	-0.503	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.826	-0.887	22.056	-0.321	-0.321	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.853	-0.904	23.082	-0.255	-0.255	0.000	0.000	0.000	0.000
26	A	26	GLY	0	-0.008	0.003	20.015	-0.010	-0.010	0.000	0.000	0.000	0.000
27	A	27	ILE	0	0.015	-0.013	14.504	-0.050	-0.050	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.743	-0.861	15.236	-0.912	-0.912	0.000	0.000	0.000	0.000
29	A	29	ILE	0	-0.033	-0.001	16.073	-0.024	-0.024	0.000	0.000	0.000	0.000
30	A	30	GLN	0	0.007	0.016	12.652	0.045	0.045	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.844	0.896	11.288	0.907	0.907	0.000	0.000	0.000	0.000
32	A	32	SER	0	-0.081	-0.037	11.392	-0.076	-0.076	0.000	0.000	0.000	0.000
33	A	33	HIS	1	0.795	0.872	12.514	0.519	0.519	0.000	0.000	0.000	0.000
34	A	34	LEU	0	0.019	0.004	8.575	0.102	0.102	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.004	0.019	7.026	-0.350	-0.350	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.918	-0.964	2.539	-15.645	-13.085	2.670	-2.380	-2.850	-0.033
37	A	37	LEU	0	-0.022	-0.012	6.150	-0.073	-0.073	0.000	0.000	0.000	0.000
38	A	38	VAL	0	-0.042	-0.024	6.249	-0.120	-0.120	0.000	0.000	0.000	0.000
39	A	39	GLY	0	0.003	-0.003	8.800	0.219	0.219	0.000	0.000	0.000	0.000
40	A	40	TYR	0	0.009	-0.002	12.499	0.027	0.027	0.000	0.000	0.000	0.000
41	A	41	PHE	0	-0.003	0.008	13.861	0.022	0.022	0.000	0.000	0.000	0.000
42	A	42	PHE	0	0.017	0.000	18.673	0.013	0.013	0.000	0.000	0.000	0.000
43	A	43	SER	0	-0.050	-0.011	22.166	0.003	0.003	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.906	-0.947	24.781	-0.309	-0.309	0.000	0.000	0.000	0.000
45	A	45	ILE	0	0.017	-0.001	26.356	0.030	0.030	0.000	0.000	0.000	0.000
46	A	46	GLY	0	-0.010	-0.005	25.689	-0.024	-0.024	0.000	0.000	0.000	0.000
47	A	47	PRO	0	-0.010	0.000	23.853	0.026	0.026	0.000	0.000	0.000	0.000
48	A	48	ILE	0	0.027	0.006	26.487	-0.020	-0.020	0.000	0.000	0.000	0.000
49	A	49	ASN	0	-0.028	-0.018	27.591	0.012	0.012	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.903	-0.954	21.357	-0.382	-0.382	0.000	0.000	0.000	0.000
51	A	51	ILE	0	0.001	0.001	18.709	-0.019	-0.019	0.000	0.000	0.000	0.000
52	A	52	VAL	0	-0.012	-0.005	15.234	0.010	0.010	0.000	0.000	0.000	0.000
53	A	53	HIS	0	0.015	0.010	13.608	-0.122	-0.122	0.000	0.000	0.000	0.000
54	A	54	ILE	0	-0.019	-0.009	8.304	0.068	0.068	0.000	0.000	0.000	0.000
55	A	55	TRP	0	0.026	0.001	7.238	-0.066	-0.066	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.006	0.017	2.378	-0.185	0.163	1.184	-0.407	-1.125	0.002
57	A	57	PHE	0	0.019	-0.007	2.897	-2.255	-0.814	0.652	-0.412	-1.681	-0.002
58	A	58	SER	0	0.015	-0.017	2.883	1.558	2.587	5.583	-3.046	-3.566	-0.004
59	A	59	SER	0	0.003	-0.010	3.692	2.260	0.088	-0.034	2.774	-0.568	-0.001
60	A	60	LEU	0	0.003	-0.013	5.840	-0.991	-0.991	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.844	-0.912	8.694	1.227	1.227	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.772	-0.840	5.696	0.723	0.723	0.000	0.000	0.000	0.000
63	A	63	ARG	1	0.828	0.912	7.729	-0.423	-0.423	0.000	0.000	0.000	0.000
64	A	64	ALA	0	-0.005	-0.004	8.945	-0.282	-0.282	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.808	-0.884	12.003	0.292	0.292	0.000	0.000	0.000	0.000
66	A	66	ARG	1	0.778	0.860	4.687	1.257	1.318	-0.001	0.000	-0.059	0.000
67	A	67	ARG	1	0.876	0.930	11.252	0.257	0.257	0.000	0.000	0.000	0.000
68	A	68	ALA	0	-0.012	0.006	13.501	-0.029	-0.029	0.000	0.000	0.000	0.000
69	A	69	ARG	1	0.834	0.881	11.479	-0.128	-0.128	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.041	-0.012	13.661	-0.036	-0.036	0.000	0.000	0.000	0.000
71	A	71	MET	0	-0.046	-0.022	16.173	-0.020	-0.020	0.000	0.000	0.000	0.000
72	A	72	ALA	0	0.015	0.017	19.156	0.014	0.014	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.766	-0.829	19.112	-0.286	-0.286	0.000	0.000	0.000	0.000
74	A	74	PRO	0	0.054	0.017	21.140	-0.010	-0.010	0.000	0.000	0.000	0.000
75	A	75	ARG	1	0.871	0.922	18.427	0.350	0.350	0.000	0.000	0.000	0.000
76	A	76	TRP	0	0.024	0.003	17.257	-0.030	-0.030	0.000	0.000	0.000	0.000
77	A	77	LEU	0	-0.013	-0.011	21.355	0.000	0.000	0.000	0.000	0.000	0.000
78	A	78	SER	0	-0.037	-0.028	24.247	0.016	0.016	0.000	0.000	0.000	0.000
79	A	79	PHE	0	-0.005	0.012	20.209	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	80	LEU	0	0.021	0.004	20.124	0.006	0.006	0.000	0.000	0.000	0.000
81	A	81	PRO	0	-0.029	-0.025	23.814	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.786	0.878	26.173	0.246	0.246	0.000	0.000	0.000	0.000
83	A	83	ILE	0	0.015	0.002	20.809	-0.012	-0.012	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.792	0.867	25.261	0.151	0.151	0.000	0.000	0.000	0.000
85	A	85	ASP	-1	-0.793	-0.854	26.230	-0.152	-0.152	0.000	0.000	0.000	0.000
86	A	86	LEU	0	-0.051	-0.017	26.459	0.006	0.006	0.000	0.000	0.000	0.000
87	A	87	ILE	0	-0.027	-0.006	22.093	-0.019	-0.019	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.823	-0.885	26.083	-0.158	-0.158	0.000	0.000	0.000	0.000
89	A	89	VAL	0	-0.025	-0.020	24.370	0.021	0.021	0.000	0.000	0.000	0.000
90	A	90	ALA	0	-0.001	-0.002	20.580	-0.035	-0.035	0.000	0.000	0.000	0.000
91	A	91	GLU	-1	-0.822	-0.882	17.763	-0.294	-0.294	0.000	0.000	0.000	0.000
92	A	92	ASN	0	0.011	-0.008	13.983	-0.078	-0.078	0.000	0.000	0.000	0.000
93	A	93	LYS	1	0.820	0.912	13.429	0.529	0.529	0.000	0.000	0.000	0.000
94	A	94	ILE	0	0.000	-0.001	8.298	-0.150	-0.150	0.000	0.000	0.000	0.000
95	A	95	MET	0	-0.005	-0.003	8.337	0.170	0.170	0.000	0.000	0.000	0.000
96	A	96	LYS	1	0.949	0.972	4.728	-3.631	-3.536	-0.001	-0.036	-0.058	0.000
97	A	97	PRO	0	0.012	0.039	3.172	-0.316	0.358	0.034	-0.158	-0.550	0.000
98	A	98	ALA	0	0.032	0.017	6.068	0.509	0.509	0.000	0.000	0.000	0.000
99	A	99	ARG	1	0.955	0.948	8.565	-0.432	-0.432	0.000	0.000	0.000	0.000
100	A	100	PHE	0	0.020	0.016	9.731	0.023	0.023	0.000	0.000	0.000	0.000
101	A	101	SER	0	-0.054	-0.031	7.344	0.105	0.105	0.000	0.000	0.000	0.000
102	A	102	PRO	0	0.027	-0.001	8.682	-0.051	-0.051	0.000	0.000	0.000	0.000
103	A	103	LEU	0	-0.002	0.025	6.105	-0.159	-0.159	0.000	0.000	0.000	0.000
104	A	104	MET	0	0.055	0.040	2.615	-2.772	-1.575	1.300	-0.803	-1.694	-0.009

Top

Graph

Manual

About

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