FMO DATABASE

FMODB ID: ZVN6N

Calculation Name: 1AF5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

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:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	126
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1101211.035304
FMO2-HF: Nuclear repulsion	1051441.417932
FMO2-HF: Total energy	-49769.617372
FMO2-MP2: Total energy	-49919.340666

3D Structure Molmil

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.
-31.417	-31.766	27.114	-11.424	-15.339	-0.101

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 : 0.913 / q_NPA : 0.951

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	6	ASN	0	0.000	0.000	1.703	-29.846	-39.713	23.536	-6.751	-6.919	-0.055
4	A	7	LYS	1	0.921	0.954	4.912	50.020	50.200	-0.001	-0.016	-0.163	0.000
5	A	8	GLU	-1	-0.869	-0.912	7.491	-22.740	-22.740	0.000	0.000	0.000	0.000
6	A	9	PHE	0	0.050	0.011	3.660	-0.030	0.299	0.003	-0.048	-0.284	0.000
7	A	10	LEU	0	-0.036	-0.006	2.614	-1.195	-0.629	0.150	-0.195	-0.520	-0.002
8	A	11	LEU	0	0.029	0.020	6.328	1.808	1.808	0.000	0.000	0.000	0.000
9	A	12	TYR	0	-0.007	-0.003	9.564	2.550	2.550	0.000	0.000	0.000	0.000
10	A	13	LEU	0	-0.027	-0.017	5.120	1.684	1.684	0.000	0.000	0.000	0.000
11	A	14	ALA	0	0.049	0.025	8.669	0.817	0.817	0.000	0.000	0.000	0.000
12	A	15	GLY	0	0.012	0.017	10.229	2.041	2.041	0.000	0.000	0.000	0.000
13	A	16	PHE	0	-0.017	-0.024	11.637	1.138	1.138	0.000	0.000	0.000	0.000
14	A	17	VAL	0	-0.023	0.006	9.162	0.898	0.898	0.000	0.000	0.000	0.000
15	A	18	ASP	-1	-0.779	-0.917	12.323	-19.169	-19.169	0.000	0.000	0.000	0.000
16	A	19	GLY	0	-0.060	-0.016	15.047	1.529	1.529	0.000	0.000	0.000	0.000
17	A	20	ASP	-1	-0.984	-1.001	15.617	-16.187	-16.187	0.000	0.000	0.000	0.000
18	A	21	GLY	0	0.071	0.005	13.202	-1.530	-1.530	0.000	0.000	0.000	0.000
19	A	22	SER	0	-0.117	-0.036	14.047	1.297	1.297	0.000	0.000	0.000	0.000
20	A	23	ILE	0	-0.008	0.007	11.726	-1.618	-1.618	0.000	0.000	0.000	0.000
21	A	24	ILE	0	0.032	0.013	14.025	0.928	0.928	0.000	0.000	0.000	0.000
22	A	25	ALA	0	0.061	0.025	16.027	-1.051	-1.051	0.000	0.000	0.000	0.000
23	A	26	GLN	0	-0.038	-0.020	18.322	0.316	0.316	0.000	0.000	0.000	0.000
24	A	27	ILE	0	0.062	0.033	21.429	-0.488	-0.488	0.000	0.000	0.000	0.000
25	A	28	LYS	1	0.932	0.953	20.958	14.885	14.885	0.000	0.000	0.000	0.000
26	A	29	PRO	0	-0.029	-0.013	25.621	0.101	0.101	0.000	0.000	0.000	0.000
27	A	30	ASN	0	0.077	0.006	27.313	-0.031	-0.031	0.000	0.000	0.000	0.000
28	A	31	GLN	0	0.020	0.004	29.419	0.571	0.571	0.000	0.000	0.000	0.000
29	A	32	SER	0	-0.004	-0.021	32.260	0.388	0.388	0.000	0.000	0.000	0.000
30	A	33	TYR	0	0.034	0.013	32.798	-0.224	-0.224	0.000	0.000	0.000	0.000
31	A	34	LYS	1	1.035	1.019	32.916	8.923	8.923	0.000	0.000	0.000	0.000
32	A	35	PHE	0	-0.009	-0.006	32.398	-0.241	-0.241	0.000	0.000	0.000	0.000
33	A	36	LYS	1	0.768	0.925	30.909	9.451	9.451	0.000	0.000	0.000	0.000
34	A	37	HIS	0	0.087	0.040	28.151	-0.273	-0.273	0.000	0.000	0.000	0.000
35	A	38	GLN	0	0.011	0.007	21.273	0.103	0.103	0.000	0.000	0.000	0.000
36	A	39	LEU	0	0.009	0.034	20.028	0.142	0.142	0.000	0.000	0.000	0.000
37	A	40	SER	0	-0.036	-0.014	18.321	0.056	0.056	0.000	0.000	0.000	0.000
38	A	41	LEU	0	0.003	0.013	14.281	0.343	0.343	0.000	0.000	0.000	0.000
39	A	42	THR	0	-0.041	-0.034	13.439	-0.765	-0.765	0.000	0.000	0.000	0.000
40	A	43	PHE	0	0.032	0.027	8.085	-0.131	-0.131	0.000	0.000	0.000	0.000
41	A	44	GLN	0	0.005	-0.019	11.601	0.056	0.056	0.000	0.000	0.000	0.000
42	A	45	VAL	0	0.037	0.015	11.560	-0.236	-0.236	0.000	0.000	0.000	0.000
43	A	46	THR	0	-0.050	-0.022	13.752	0.311	0.311	0.000	0.000	0.000	0.000
44	A	47	GLN	0	0.049	0.028	16.095	0.859	0.859	0.000	0.000	0.000	0.000
45	A	48	LYS	1	0.967	0.971	18.580	12.625	12.625	0.000	0.000	0.000	0.000
46	A	49	THR	0	0.069	0.038	20.862	-0.762	-0.762	0.000	0.000	0.000	0.000
47	A	50	GLN	0	-0.033	-0.019	22.214	0.201	0.201	0.000	0.000	0.000	0.000
48	A	51	ARG	1	0.914	0.959	18.726	15.267	15.267	0.000	0.000	0.000	0.000
49	A	52	ARG	1	1.071	1.040	15.363	16.840	16.840	0.000	0.000	0.000	0.000
50	A	53	TRP	0	0.096	0.032	15.668	-1.664	-1.664	0.000	0.000	0.000	0.000
51	A	54	PHE	0	0.013	0.011	12.368	-0.793	-0.793	0.000	0.000	0.000	0.000
52	A	55	LEU	0	0.004	0.010	12.207	-1.563	-1.563	0.000	0.000	0.000	0.000
53	A	56	GLY	0	-0.057	-0.036	11.752	-1.153	-1.153	0.000	0.000	0.000	0.000
54	A	57	LYS	1	0.912	0.986	10.368	21.802	21.802	0.000	0.000	0.000	0.000
55	A	58	LEU	0	0.020	0.017	8.098	-2.177	-2.177	0.000	0.000	0.000	0.000
56	A	59	VAL	0	-0.034	-0.025	6.464	-5.181	-5.181	0.000	0.000	0.000	0.000
57	A	60	ASP	-1	-0.897	-0.925	7.026	-28.132	-28.132	0.000	0.000	0.000	0.000
58	A	61	GLU	-1	-0.999	-1.006	5.943	-33.760	-33.760	0.000	0.000	0.000	0.000
59	A	62	ILE	0	-0.092	-0.060	2.206	-12.774	-11.962	1.778	-0.840	-1.749	-0.006
60	A	63	GLY	0	0.010	0.016	2.737	-14.606	-11.935	0.735	-1.441	-1.965	-0.022
61	A	64	VAL	0	-0.031	-0.011	4.060	7.259	7.472	0.000	-0.024	-0.189	0.000
62	A	65	GLY	0	0.033	0.014	6.161	-2.170	-2.170	0.000	0.000	0.000	0.000
63	A	66	TYR	0	-0.030	-0.008	9.120	2.210	2.210	0.000	0.000	0.000	0.000
64	A	67	VAL	0	0.020	0.006	12.408	-0.363	-0.363	0.000	0.000	0.000	0.000
65	A	68	ARG	1	0.854	0.927	14.678	17.182	17.182	0.000	0.000	0.000	0.000
66	A	69	ASP	-1	-0.917	-0.943	17.869	-13.058	-13.058	0.000	0.000	0.000	0.000
67	A	70	ARG	1	0.874	0.921	20.070	14.897	14.897	0.000	0.000	0.000	0.000
68	A	71	GLY	0	0.079	0.052	23.396	0.310	0.310	0.000	0.000	0.000	0.000
69	A	72	SER	0	-0.029	-0.022	24.954	-0.356	-0.356	0.000	0.000	0.000	0.000
70	A	73	VAL	0	-0.071	-0.035	20.385	-0.183	-0.183	0.000	0.000	0.000	0.000
71	A	74	SER	0	0.032	0.014	18.488	0.307	0.307	0.000	0.000	0.000	0.000
72	A	75	ASP	-1	-0.789	-0.930	15.773	-17.063	-17.063	0.000	0.000	0.000	0.000
73	A	76	TYR	0	-0.013	0.011	6.228	-0.164	-0.164	0.000	0.000	0.000	0.000
74	A	77	ILE	0	-0.004	-0.009	12.179	-0.040	-0.040	0.000	0.000	0.000	0.000
75	A	78	LEU	0	-0.015	-0.003	6.364	0.386	0.386	0.000	0.000	0.000	0.000
76	A	79	SER	0	-0.023	-0.034	9.473	1.721	1.721	0.000	0.000	0.000	0.000
77	A	80	GLU	-1	-0.843	-0.946	11.327	-20.603	-20.603	0.000	0.000	0.000	0.000
78	A	81	ILE	0	0.090	0.031	11.075	-2.075	-2.075	0.000	0.000	0.000	0.000
79	A	82	LYS	1	0.940	0.997	10.070	19.480	19.480	0.000	0.000	0.000	0.000
80	A	83	PRO	0	0.006	-0.006	5.603	-1.827	-1.827	0.000	0.000	0.000	0.000
81	A	84	LEU	0	0.011	-0.004	5.667	-6.925	-6.925	0.000	0.000	0.000	0.000
82	A	85	HIS	0	0.035	0.026	7.601	-1.331	-1.331	0.000	0.000	0.000	0.000
83	A	86	ASN	0	-0.020	0.021	3.120	-13.043	-11.328	0.126	-0.769	-1.073	-0.006
84	A	87	PHE	0	0.031	0.010	2.515	-9.420	-8.344	0.708	-0.442	-1.341	-0.004
85	A	88	LEU	0	0.037	0.021	3.704	2.155	2.279	0.001	-0.018	-0.106	0.000
86	A	89	THR	0	-0.002	-0.013	7.219	3.030	3.030	0.000	0.000	0.000	0.000
87	A	90	GLN	0	-0.019	-0.035	3.111	-4.924	-3.092	0.078	-0.880	-1.030	-0.006
88	A	91	LEU	0	-0.037	0.004	5.884	2.260	2.260	0.000	0.000	0.000	0.000
89	A	92	GLN	0	0.024	-0.001	6.944	3.904	3.904	0.000	0.000	0.000	0.000
90	A	93	PRO	0	0.086	0.041	9.274	2.529	2.529	0.000	0.000	0.000	0.000
91	A	94	PHE	0	-0.067	-0.042	8.047	1.994	1.994	0.000	0.000	0.000	0.000
92	A	95	LEU	0	-0.066	-0.090	11.942	0.644	0.644	0.000	0.000	0.000	0.000
93	A	96	LYS	1	0.982	0.990	13.955	17.662	17.662	0.000	0.000	0.000	0.000
94	A	97	LEU	0	-0.032	0.005	16.766	0.977	0.977	0.000	0.000	0.000	0.000
95	A	98	LYS	1	0.932	0.969	14.678	18.149	18.149	0.000	0.000	0.000	0.000
96	A	99	GLN	0	-0.017	0.040	11.492	-1.628	-1.628	0.000	0.000	0.000	0.000
97	A	100	LYS	1	0.904	0.974	14.564	15.192	15.192	0.000	0.000	0.000	0.000
98	A	101	GLN	0	0.057	-0.014	15.933	0.017	0.017	0.000	0.000	0.000	0.000
99	A	102	ALA	0	0.029	0.052	11.756	-0.525	-0.525	0.000	0.000	0.000	0.000
100	A	103	ASN	0	0.030	0.000	13.180	-1.082	-1.082	0.000	0.000	0.000	0.000
101	A	104	LEU	0	-0.026	0.003	15.057	0.022	0.022	0.000	0.000	0.000	0.000
102	A	105	VAL	0	-0.013	0.003	12.887	0.588	0.588	0.000	0.000	0.000	0.000
103	A	106	LEU	0	0.002	-0.034	9.770	-0.259	-0.259	0.000	0.000	0.000	0.000
104	A	107	LYS	1	0.935	0.987	13.522	15.460	15.460	0.000	0.000	0.000	0.000
105	A	108	ILE	0	0.019	0.018	17.248	0.604	0.604	0.000	0.000	0.000	0.000
106	A	109	ILE	0	-0.161	-0.052	11.629	0.164	0.164	0.000	0.000	0.000	0.000
107	A	110	GLU	-1	-0.946	-0.992	14.379	-21.066	-21.066	0.000	0.000	0.000	0.000
108	A	111	GLN	0	-0.030	-0.021	17.624	1.430	1.430	0.000	0.000	0.000	0.000
109	A	112	LEU	0	0.023	0.021	18.354	0.457	0.457	0.000	0.000	0.000	0.000
110	A	113	PRO	0	-0.045	-0.005	22.470	0.308	0.308	0.000	0.000	0.000	0.000
111	A	123	LEU	0	0.015	-0.023	29.198	0.095	0.095	0.000	0.000	0.000	0.000
112	A	124	GLU	-1	-0.884	-0.920	26.140	-11.688	-11.688	0.000	0.000	0.000	0.000
113	A	125	VAL	0	-0.009	0.003	24.548	-0.555	-0.555	0.000	0.000	0.000	0.000
114	A	126	CYS	0	-0.071	-0.059	23.733	0.382	0.382	0.000	0.000	0.000	0.000
115	A	127	THR	0	0.005	0.011	24.630	0.221	0.221	0.000	0.000	0.000	0.000
116	A	128	TRP	0	0.029	-0.001	21.190	-0.088	-0.088	0.000	0.000	0.000	0.000
117	A	129	VAL	0	0.026	-0.002	20.906	-0.240	-0.240	0.000	0.000	0.000	0.000
118	A	130	ASP	-1	-0.866	-0.913	22.629	-11.669	-11.669	0.000	0.000	0.000	0.000
119	A	131	GLN	0	-0.006	-0.008	23.755	-0.305	-0.305	0.000	0.000	0.000	0.000
120	A	132	ILE	0	-0.127	-0.049	18.062	-0.341	-0.341	0.000	0.000	0.000	0.000
121	A	133	ALA	0	0.067	0.029	22.143	-0.254	-0.254	0.000	0.000	0.000	0.000
122	A	134	ALA	0	-0.117	-0.047	21.165	0.132	0.132	0.000	0.000	0.000	0.000
123	A	135	LEU	0	-0.037	-0.045	23.280	-0.148	-0.148	0.000	0.000	0.000	0.000
124	A	136	ASN	0	-0.020	0.014	22.243	0.245	0.245	0.000	0.000	0.000	0.000
125	A	137	ASP	-1	-0.898	-0.956	26.655	-10.175	-10.175	0.000	0.000	0.000	0.000
126	A	138	SER	0	-0.068	-0.022	28.531	0.148	0.148	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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