FMO DATABASE

FMODB ID: QVNYY

Calculation Name: 1AF5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1AF5

Chain ID: A

ChEMBL ID:

UniProt ID: P05725

Base Structure: X-ray

Registration Date: 2023-09-22

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	126
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1098181.84992
FMO2-HF: Nuclear repulsion	1048409.423049
FMO2-HF: Total energy	-49772.426871
FMO2-MP2: Total energy	-49921.675057

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:4:LYS)

Summations of interaction energy for fragment #1(A:4:LYS)

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.
-40.1	-35.426	20.284	-10.038	-14.921	-0.108

Interaction energy analysis for fragmet #1(A:4:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.939 / q_NPA : 0.989

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	6	ASN	0	0.005	0.008	1.784	-36.217	-36.372	10.178	-5.164	-4.860	-0.046
4	A	7	LYS	1	0.940	0.958	5.031	45.801	45.918	-0.001	-0.007	-0.109	0.000
5	A	8	GLU	-1	-0.844	-0.912	7.644	-24.455	-24.455	0.000	0.000	0.000	0.000
6	A	9	PHE	0	0.018	-0.007	3.719	1.048	1.260	0.000	-0.023	-0.189	0.000
7	A	10	LEU	0	-0.041	-0.010	3.292	-1.278	-1.006	0.011	-0.059	-0.224	0.000
8	A	11	LEU	0	0.028	0.027	7.290	2.210	2.210	0.000	0.000	0.000	0.000
9	A	12	TYR	0	-0.014	-0.001	10.078	2.273	2.273	0.000	0.000	0.000	0.000
10	A	13	LEU	0	-0.019	-0.010	5.136	1.169	1.169	0.000	0.000	0.000	0.000
11	A	14	ALA	0	0.036	0.019	9.119	1.000	1.000	0.000	0.000	0.000	0.000
12	A	15	GLY	0	0.016	0.015	10.773	1.773	1.773	0.000	0.000	0.000	0.000
13	A	16	PHE	0	-0.023	-0.020	11.597	1.303	1.303	0.000	0.000	0.000	0.000
14	A	17	VAL	0	-0.001	-0.004	9.406	1.182	1.182	0.000	0.000	0.000	0.000
15	A	18	ASP	-1	-0.741	-0.866	12.589	-18.192	-18.192	0.000	0.000	0.000	0.000
16	A	19	GLY	0	-0.008	0.010	15.713	1.350	1.350	0.000	0.000	0.000	0.000
17	A	20	ASP	-1	-0.904	-0.951	16.010	-17.171	-17.171	0.000	0.000	0.000	0.000
18	A	21	GLY	0	0.064	0.009	13.462	-1.767	-1.767	0.000	0.000	0.000	0.000
19	A	22	SER	0	-0.062	-0.019	13.848	1.737	1.737	0.000	0.000	0.000	0.000
20	A	23	ILE	0	0.013	0.006	11.430	-1.245	-1.245	0.000	0.000	0.000	0.000
21	A	24	ILE	0	-0.006	0.005	14.154	1.259	1.259	0.000	0.000	0.000	0.000
22	A	25	ALA	0	0.037	0.008	16.110	-1.038	-1.038	0.000	0.000	0.000	0.000
23	A	26	GLN	0	-0.001	-0.005	18.727	0.645	0.645	0.000	0.000	0.000	0.000
24	A	27	ILE	0	0.052	0.037	21.662	-0.427	-0.427	0.000	0.000	0.000	0.000
25	A	28	LYS	1	0.883	0.928	19.610	15.240	15.240	0.000	0.000	0.000	0.000
26	A	29	PRO	0	-0.024	0.002	25.543	0.135	0.135	0.000	0.000	0.000	0.000
27	A	30	ASN	0	0.044	0.004	27.019	-0.093	-0.093	0.000	0.000	0.000	0.000
28	A	31	GLN	0	0.018	0.006	28.857	0.526	0.526	0.000	0.000	0.000	0.000
29	A	32	SER	0	-0.002	0.003	32.159	0.326	0.326	0.000	0.000	0.000	0.000
30	A	33	TYR	0	0.051	0.013	32.191	-0.321	-0.321	0.000	0.000	0.000	0.000
31	A	34	LYS	1	0.987	0.984	32.825	8.988	8.988	0.000	0.000	0.000	0.000
32	A	35	PHE	0	-0.002	0.014	32.245	-0.281	-0.281	0.000	0.000	0.000	0.000
33	A	36	LYS	1	0.838	0.921	30.887	9.400	9.400	0.000	0.000	0.000	0.000
34	A	37	HIS	0	0.069	0.035	27.856	-0.223	-0.223	0.000	0.000	0.000	0.000
35	A	38	GLN	0	-0.014	-0.011	20.476	0.164	0.164	0.000	0.000	0.000	0.000
36	A	39	LEU	0	0.004	0.014	19.664	0.280	0.280	0.000	0.000	0.000	0.000
37	A	40	SER	0	0.000	-0.004	17.607	0.045	0.045	0.000	0.000	0.000	0.000
38	A	41	LEU	0	-0.012	0.004	14.250	0.325	0.325	0.000	0.000	0.000	0.000
39	A	42	THR	0	-0.017	-0.039	12.903	-0.894	-0.894	0.000	0.000	0.000	0.000
40	A	43	PHE	0	0.018	0.020	7.564	0.629	0.629	0.000	0.000	0.000	0.000
41	A	44	GLN	0	0.003	-0.006	11.075	-0.182	-0.182	0.000	0.000	0.000	0.000
42	A	45	VAL	0	0.008	0.010	11.013	-0.046	-0.046	0.000	0.000	0.000	0.000
43	A	46	THR	0	-0.059	-0.038	13.873	0.548	0.548	0.000	0.000	0.000	0.000
44	A	47	GLN	0	0.077	0.039	16.881	0.776	0.776	0.000	0.000	0.000	0.000
45	A	48	LYS	1	0.947	0.974	19.280	12.114	12.114	0.000	0.000	0.000	0.000
46	A	49	THR	0	0.072	0.022	21.317	-0.723	-0.723	0.000	0.000	0.000	0.000
47	A	50	GLN	0	-0.001	-0.004	22.288	-0.200	-0.200	0.000	0.000	0.000	0.000
48	A	51	ARG	1	0.866	0.930	19.217	15.271	15.271	0.000	0.000	0.000	0.000
49	A	52	ARG	1	1.007	1.010	16.306	16.131	16.131	0.000	0.000	0.000	0.000
50	A	53	TRP	0	0.044	0.014	16.336	-1.221	-1.221	0.000	0.000	0.000	0.000
51	A	54	PHE	0	0.007	0.015	12.256	-0.982	-0.982	0.000	0.000	0.000	0.000
52	A	55	LEU	0	-0.006	-0.006	12.719	-1.576	-1.576	0.000	0.000	0.000	0.000
53	A	56	GLY	0	-0.017	-0.011	11.716	-1.373	-1.373	0.000	0.000	0.000	0.000
54	A	57	LYS	1	0.938	0.961	10.637	23.904	23.904	0.000	0.000	0.000	0.000
55	A	58	LEU	0	-0.020	-0.003	8.384	-2.666	-2.666	0.000	0.000	0.000	0.000
56	A	59	VAL	0	-0.021	-0.014	6.710	-5.301	-5.301	0.000	0.000	0.000	0.000
57	A	60	ASP	-1	-0.916	-0.947	6.790	-29.104	-29.104	0.000	0.000	0.000	0.000
58	A	61	GLU	-1	-0.911	-0.950	5.888	-33.194	-33.194	0.000	0.000	0.000	0.000
59	A	62	ILE	0	-0.097	-0.048	2.188	-15.777	-15.429	2.532	-0.784	-2.097	-0.006
60	A	63	GLY	0	0.019	0.012	2.368	-18.472	-18.981	6.103	-2.056	-3.537	-0.038
61	A	64	VAL	0	-0.016	-0.013	3.255	5.810	6.284	0.027	-0.092	-0.409	0.000
62	A	65	GLY	0	0.021	0.028	5.687	-2.932	-2.932	0.000	0.000	0.000	0.000
63	A	66	TYR	0	-0.037	-0.015	8.400	1.749	1.749	0.000	0.000	0.000	0.000
64	A	67	VAL	0	0.000	-0.010	11.770	-0.596	-0.596	0.000	0.000	0.000	0.000
65	A	68	ARG	1	0.836	0.904	14.459	17.110	17.110	0.000	0.000	0.000	0.000
66	A	69	ASP	-1	-0.871	-0.932	17.694	-13.286	-13.286	0.000	0.000	0.000	0.000
67	A	70	ARG	1	0.828	0.884	19.516	14.845	14.845	0.000	0.000	0.000	0.000
68	A	71	GLY	0	0.069	0.049	23.591	0.402	0.402	0.000	0.000	0.000	0.000
69	A	72	SER	0	-0.007	-0.002	25.116	-0.215	-0.215	0.000	0.000	0.000	0.000
70	A	73	VAL	0	-0.102	-0.052	20.948	-0.126	-0.126	0.000	0.000	0.000	0.000
71	A	74	SER	0	0.047	0.022	18.416	0.219	0.219	0.000	0.000	0.000	0.000
72	A	75	ASP	-1	-0.756	-0.857	15.659	-17.107	-17.107	0.000	0.000	0.000	0.000
73	A	76	TYR	0	-0.010	0.003	5.967	0.322	0.322	0.000	0.000	0.000	0.000
74	A	77	ILE	0	-0.005	-0.016	11.684	0.237	0.237	0.000	0.000	0.000	0.000
75	A	78	LEU	0	-0.005	-0.001	5.335	-0.145	-0.145	0.000	0.000	0.000	0.000
76	A	79	SER	0	-0.025	-0.020	8.757	0.851	0.851	0.000	0.000	0.000	0.000
77	A	80	GLU	-1	-0.775	-0.872	11.467	-19.647	-19.647	0.000	0.000	0.000	0.000
78	A	81	ILE	0	0.071	0.024	10.626	-2.434	-2.434	0.000	0.000	0.000	0.000
79	A	82	LYS	1	0.933	0.983	9.768	19.332	19.332	0.000	0.000	0.000	0.000
80	A	83	PRO	0	0.028	0.012	5.267	-1.110	-1.110	0.000	0.000	0.000	0.000
81	A	84	LEU	0	0.014	0.004	5.264	-6.546	-6.546	0.000	0.000	0.000	0.000
82	A	85	HIS	0	0.040	0.026	7.514	-2.665	-2.665	0.000	0.000	0.000	0.000
83	A	86	ASN	0	0.005	0.017	2.501	-14.873	-12.873	1.229	-1.182	-2.047	-0.017
84	A	87	PHE	0	0.026	0.021	2.634	-8.742	-7.749	0.197	-0.260	-0.930	-0.001
85	A	88	LEU	0	0.041	0.009	4.100	2.095	2.180	-0.001	-0.012	-0.072	0.000
86	A	89	THR	0	-0.027	-0.026	7.570	3.475	3.475	0.000	0.000	0.000	0.000
87	A	90	GLN	0	-0.063	-0.042	3.423	6.019	6.856	0.009	-0.399	-0.447	0.000
88	A	91	LEU	0	0.027	0.018	5.929	1.391	1.391	0.000	0.000	0.000	0.000
89	A	92	GLN	0	-0.017	-0.007	8.003	4.295	4.295	0.000	0.000	0.000	0.000
90	A	93	PRO	0	0.010	0.005	9.806	2.069	2.069	0.000	0.000	0.000	0.000
91	A	94	PHE	0	-0.036	-0.024	8.621	1.838	1.838	0.000	0.000	0.000	0.000
92	A	95	LEU	0	0.012	-0.006	12.951	0.793	0.793	0.000	0.000	0.000	0.000
93	A	96	LYS	1	0.938	0.970	14.791	17.083	17.083	0.000	0.000	0.000	0.000
94	A	97	LEU	0	-0.025	0.009	17.188	0.775	0.775	0.000	0.000	0.000	0.000
95	A	98	LYS	1	0.776	0.860	15.141	19.054	19.054	0.000	0.000	0.000	0.000
96	A	99	GLN	0	-0.053	-0.036	11.881	-1.007	-1.007	0.000	0.000	0.000	0.000
97	A	100	LYS	1	0.951	0.996	14.754	14.248	14.248	0.000	0.000	0.000	0.000
98	A	101	GLN	0	0.081	0.025	16.513	0.389	0.389	0.000	0.000	0.000	0.000
99	A	102	ALA	0	-0.003	0.012	11.731	-0.520	-0.520	0.000	0.000	0.000	0.000
100	A	103	ASN	0	0.002	0.001	13.689	-0.759	-0.759	0.000	0.000	0.000	0.000
101	A	104	LEU	0	-0.013	0.000	15.613	0.223	0.223	0.000	0.000	0.000	0.000
102	A	105	VAL	0	0.022	0.003	12.959	0.393	0.393	0.000	0.000	0.000	0.000
103	A	106	LEU	0	-0.041	-0.033	10.301	-0.373	-0.373	0.000	0.000	0.000	0.000
104	A	107	LYS	1	0.828	0.944	14.142	14.704	14.704	0.000	0.000	0.000	0.000
105	A	108	ILE	0	-0.019	-0.008	17.436	0.662	0.662	0.000	0.000	0.000	0.000
106	A	109	ILE	0	-0.089	-0.037	11.141	-0.225	-0.225	0.000	0.000	0.000	0.000
107	A	110	GLU	-1	-0.893	-0.934	15.078	-18.275	-18.275	0.000	0.000	0.000	0.000
108	A	111	GLN	0	-0.086	-0.057	17.298	1.336	1.336	0.000	0.000	0.000	0.000
109	A	112	LEU	0	0.011	0.016	18.111	0.588	0.588	0.000	0.000	0.000	0.000
110	A	113	PRO	0	-0.029	-0.004	22.146	0.279	0.279	0.000	0.000	0.000	0.000
111	A	123	LEU	0	0.005	-0.023	29.788	0.068	0.068	0.000	0.000	0.000	0.000
112	A	124	GLU	-1	-0.815	-0.871	26.139	-11.593	-11.593	0.000	0.000	0.000	0.000
113	A	125	VAL	0	0.002	0.005	24.241	-0.565	-0.565	0.000	0.000	0.000	0.000
114	A	126	CYS	0	-0.104	-0.071	23.486	0.535	0.535	0.000	0.000	0.000	0.000
115	A	127	THR	0	0.017	-0.010	24.504	-0.182	-0.182	0.000	0.000	0.000	0.000
116	A	128	TRP	0	0.069	0.013	21.492	0.023	0.023	0.000	0.000	0.000	0.000
117	A	129	VAL	0	-0.011	-0.005	21.657	-0.479	-0.479	0.000	0.000	0.000	0.000
118	A	130	ASP	-1	-0.832	-0.900	23.140	-11.791	-11.791	0.000	0.000	0.000	0.000
119	A	131	GLN	0	-0.007	-0.002	23.874	-0.273	-0.273	0.000	0.000	0.000	0.000
120	A	132	ILE	0	-0.046	-0.019	18.615	-0.326	-0.326	0.000	0.000	0.000	0.000
121	A	133	ALA	0	0.069	0.048	22.394	-0.157	-0.157	0.000	0.000	0.000	0.000
122	A	134	ALA	0	-0.100	-0.057	21.305	0.219	0.219	0.000	0.000	0.000	0.000
123	A	135	LEU	0	-0.042	-0.038	23.314	-0.177	-0.177	0.000	0.000	0.000	0.000
124	A	136	ASN	0	-0.066	-0.020	21.887	0.192	0.192	0.000	0.000	0.000	0.000
125	A	137	ASP	-1	-0.876	-0.941	26.213	-9.780	-9.780	0.000	0.000	0.000	0.000
126	A	138	SER	0	-0.125	-0.063	29.109	0.050	0.050	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:LYS)