FMO DATABASE

FMODB ID: 89R9Y

Calculation Name: 4YF2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YF2

Chain ID: A

ChEMBL ID:

UniProt ID: Q9D9X8

Base Structure: X-ray

Registration Date: 2023-09-23

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	-1181820.529415
FMO2-HF: Nuclear repulsion	1128069.932265
FMO2-HF: Total energy	-53750.59715
FMO2-MP2: Total energy	-53901.46515

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:0:ALA)

Summations of interaction energy for fragment #1(A:0:ALA)

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.
-8.941	-5.265	9.76	-6.462	-6.973	-0.038

Interaction energy analysis for fragmet #1(A:0:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.008

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	2	VAL	0	0.005	0.018	3.894	-0.179	1.550	-0.016	-0.955	-0.758	0.001
4	A	3	PHE	0	0.034	0.013	6.806	-0.310	-0.310	0.000	0.000	0.000	0.000
5	A	4	SER	0	-0.018	-0.022	9.740	0.137	0.137	0.000	0.000	0.000	0.000
6	A	5	ARG	1	0.845	0.903	13.310	-0.108	-0.108	0.000	0.000	0.000	0.000
7	A	6	CYS	0	-0.088	-0.039	16.029	-0.020	-0.020	0.000	0.000	0.000	0.000
8	A	7	GLU	-1	-0.779	-0.854	11.503	-0.221	-0.221	0.000	0.000	0.000	0.000
9	A	8	LEU	0	0.008	-0.004	11.171	-0.047	-0.047	0.000	0.000	0.000	0.000
10	A	9	ALA	0	0.044	0.018	14.019	-0.022	-0.022	0.000	0.000	0.000	0.000
11	A	10	LYS	1	0.820	0.898	16.974	0.147	0.147	0.000	0.000	0.000	0.000
12	A	11	GLU	-1	-0.888	-0.949	12.183	-0.451	-0.451	0.000	0.000	0.000	0.000
13	A	12	MET	0	-0.075	-0.037	14.060	0.009	0.009	0.000	0.000	0.000	0.000
14	A	13	HIS	0	-0.018	-0.014	17.619	0.021	0.021	0.000	0.000	0.000	0.000
15	A	14	ASP	-1	-0.799	-0.863	18.079	-0.163	-0.163	0.000	0.000	0.000	0.000
16	A	15	PHE	0	-0.072	-0.049	13.289	-0.005	-0.005	0.000	0.000	0.000	0.000
17	A	16	GLY	0	-0.017	0.003	18.867	0.006	0.006	0.000	0.000	0.000	0.000
18	A	17	LEU	0	-0.035	-0.036	17.639	0.009	0.009	0.000	0.000	0.000	0.000
19	A	18	ASP	-1	-0.872	-0.926	21.799	-0.047	-0.047	0.000	0.000	0.000	0.000
20	A	19	GLY	0	0.052	0.026	24.298	0.001	0.001	0.000	0.000	0.000	0.000
21	A	20	TYR	0	-0.065	-0.036	23.444	0.004	0.004	0.000	0.000	0.000	0.000
22	A	21	ARG	1	0.808	0.882	25.516	0.070	0.070	0.000	0.000	0.000	0.000
23	A	22	GLY	0	-0.004	0.008	27.776	0.006	0.006	0.000	0.000	0.000	0.000
24	A	23	TYR	0	-0.031	0.003	23.925	0.006	0.006	0.000	0.000	0.000	0.000
25	A	24	ASN	0	0.045	0.016	24.848	-0.009	-0.009	0.000	0.000	0.000	0.000
26	A	25	LEU	0	-0.006	-0.012	19.934	0.000	0.000	0.000	0.000	0.000	0.000
27	A	26	ALA	0	0.012	0.003	20.573	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	27	ASP	-1	-0.834	-0.912	21.217	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	28	TRP	0	-0.009	-0.014	17.862	0.003	0.003	0.000	0.000	0.000	0.000
30	A	29	VAL	0	0.028	0.011	16.298	0.000	0.000	0.000	0.000	0.000	0.000
31	A	30	CYS	0	-0.055	0.008	16.454	0.039	0.039	0.000	0.000	0.000	0.000
32	A	31	LEU	0	-0.001	-0.010	16.157	0.027	0.027	0.000	0.000	0.000	0.000
33	A	32	ALA	0	0.008	0.006	12.328	0.019	0.019	0.000	0.000	0.000	0.000
34	A	33	TYR	0	-0.039	-0.006	12.647	0.081	0.081	0.000	0.000	0.000	0.000
35	A	34	TYR	0	0.009	-0.020	14.428	0.059	0.059	0.000	0.000	0.000	0.000
36	A	35	THR	0	-0.048	-0.019	12.714	0.005	0.005	0.000	0.000	0.000	0.000
37	A	36	SER	0	-0.043	-0.034	8.814	0.040	0.040	0.000	0.000	0.000	0.000
38	A	37	GLY	0	0.003	0.012	9.642	0.212	0.212	0.000	0.000	0.000	0.000
39	A	38	PHE	0	-0.043	-0.028	9.869	0.099	0.099	0.000	0.000	0.000	0.000
40	A	39	ASN	0	0.003	0.002	4.254	0.582	0.678	-0.001	-0.013	-0.082	0.000
41	A	40	THR	0	0.009	-0.015	3.174	-1.055	0.011	0.061	-0.570	-0.557	-0.004
42	A	41	ASN	0	-0.010	-0.020	1.805	-4.403	-5.003	7.788	-3.595	-3.593	-0.023
43	A	42	ALA	0	-0.008	0.016	3.858	0.307	0.514	0.002	-0.078	-0.131	0.000
44	A	43	VAL	0	-0.043	-0.033	7.155	-0.328	-0.328	0.000	0.000	0.000	0.000
45	A	44	ASP	-1	-0.875	-0.920	10.035	0.269	0.269	0.000	0.000	0.000	0.000
46	A	45	HIS	0	-0.040	-0.038	11.924	-0.096	-0.096	0.000	0.000	0.000	0.000
47	A	46	GLU	-1	-0.763	-0.818	16.615	0.026	0.026	0.000	0.000	0.000	0.000
48	A	47	ALA	0	-0.008	-0.016	20.102	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	48	ASP	-1	-0.844	-0.901	22.748	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	49	GLY	0	-0.034	-0.015	20.860	-0.009	-0.009	0.000	0.000	0.000	0.000
51	A	50	SER	0	-0.129	-0.074	19.846	-0.017	-0.017	0.000	0.000	0.000	0.000
52	A	51	THR	0	0.014	0.002	14.283	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	52	ASN	0	-0.022	-0.026	14.524	-0.058	-0.058	0.000	0.000	0.000	0.000
54	A	53	ASN	0	-0.015	-0.025	10.674	0.009	0.009	0.000	0.000	0.000	0.000
55	A	54	GLY	0	0.075	0.048	7.478	-0.026	-0.026	0.000	0.000	0.000	0.000
56	A	55	ILE	0	0.000	0.014	8.093	0.193	0.193	0.000	0.000	0.000	0.000
57	A	56	PHE	0	0.005	0.007	9.222	0.101	0.101	0.000	0.000	0.000	0.000
58	A	57	GLN	0	-0.033	-0.025	10.271	0.049	0.049	0.000	0.000	0.000	0.000
59	A	58	ILE	0	0.002	0.007	13.051	0.021	0.021	0.000	0.000	0.000	0.000
60	A	59	SER	0	0.071	0.033	14.835	-0.018	-0.018	0.000	0.000	0.000	0.000
61	A	60	SER	0	0.019	-0.032	17.162	-0.008	-0.008	0.000	0.000	0.000	0.000
62	A	61	ARG	1	0.792	0.884	18.566	0.015	0.015	0.000	0.000	0.000	0.000
63	A	62	ARG	1	0.733	0.847	21.111	0.080	0.080	0.000	0.000	0.000	0.000
64	A	63	TRP	0	0.033	0.013	18.601	-0.008	-0.008	0.000	0.000	0.000	0.000
65	A	64	CYS	0	-0.026	0.011	13.473	-0.049	-0.049	0.000	0.000	0.000	0.000
66	A	65	ARG	1	0.933	0.970	17.778	0.184	0.184	0.000	0.000	0.000	0.000
67	A	66	THR	0	0.093	0.035	15.860	-0.036	-0.036	0.000	0.000	0.000	0.000
68	A	67	LEU	0	-0.033	-0.027	18.499	0.010	0.010	0.000	0.000	0.000	0.000
69	A	68	ALA	0	0.024	0.018	21.012	0.007	0.007	0.000	0.000	0.000	0.000
70	A	69	SER	0	0.056	0.023	20.478	0.010	0.010	0.000	0.000	0.000	0.000
71	A	70	ASN	0	-0.076	-0.022	22.002	-0.011	-0.011	0.000	0.000	0.000	0.000
72	A	71	GLY	0	0.088	0.032	24.022	0.010	0.010	0.000	0.000	0.000	0.000
73	A	72	PRO	0	-0.075	-0.035	24.807	-0.009	-0.009	0.000	0.000	0.000	0.000
74	A	73	ASN	0	-0.001	0.007	19.988	-0.018	-0.018	0.000	0.000	0.000	0.000
75	A	74	LEU	0	0.061	0.036	22.287	-0.011	-0.011	0.000	0.000	0.000	0.000
76	A	75	CYS	0	-0.152	-0.081	15.772	0.051	0.051	0.000	0.000	0.000	0.000
77	A	76	ARG	1	0.873	0.937	19.683	0.149	0.149	0.000	0.000	0.000	0.000
78	A	77	ILE	0	0.033	0.030	13.507	0.001	0.001	0.000	0.000	0.000	0.000
79	A	78	TYR	0	0.011	0.010	14.364	0.059	0.059	0.000	0.000	0.000	0.000
80	A	80	THR	0	0.054	0.015	9.245	-0.017	-0.017	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.875	-0.941	8.767	-0.688	-0.688	0.000	0.000	0.000	0.000
82	A	82	LEU	0	-0.055	-0.033	9.099	-0.115	-0.115	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.029	-0.001	5.634	0.086	0.086	0.000	0.000	0.000	0.000
84	A	84	ASN	0	0.005	0.011	4.247	-1.412	-1.263	-0.001	-0.020	-0.128	0.000
85	A	85	ASN	0	0.013	-0.016	2.527	-2.545	-1.558	1.928	-1.222	-1.693	-0.012
86	A	86	ASP	-1	-0.855	-0.906	4.807	-0.297	-0.255	-0.001	-0.009	-0.031	0.000
87	A	87	LEU	0	0.043	0.012	8.465	-0.010	-0.010	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.822	0.889	10.078	0.642	0.642	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.849	-0.907	11.911	-0.470	-0.470	0.000	0.000	0.000	0.000
90	A	90	SER	0	0.014	-0.006	10.197	0.114	0.114	0.000	0.000	0.000	0.000
91	A	91	ILE	0	-0.006	0.011	12.824	0.076	0.076	0.000	0.000	0.000	0.000
92	A	92	VAL	0	0.017	0.002	15.329	0.049	0.049	0.000	0.000	0.000	0.000
93	A	94	ALA	0	0.070	0.029	16.145	0.034	0.034	0.000	0.000	0.000	0.000
94	A	95	MET	0	-0.011	-0.004	18.058	0.021	0.021	0.000	0.000	0.000	0.000
95	A	96	LYS	1	0.855	0.936	20.403	0.209	0.209	0.000	0.000	0.000	0.000
96	A	97	ILE	0	0.001	0.009	18.145	0.015	0.015	0.000	0.000	0.000	0.000
97	A	98	VAL	0	-0.003	0.013	21.560	0.016	0.016	0.000	0.000	0.000	0.000
98	A	99	GLN	0	-0.008	-0.004	24.036	0.002	0.002	0.000	0.000	0.000	0.000
99	A	100	GLU	-1	-0.786	-0.868	25.652	-0.063	-0.063	0.000	0.000	0.000	0.000
100	A	101	PRO	0	-0.058	-0.048	27.849	0.002	0.002	0.000	0.000	0.000	0.000
101	A	102	LEU	0	-0.019	0.001	26.974	0.004	0.004	0.000	0.000	0.000	0.000
102	A	103	GLY	0	0.015	0.026	26.002	0.005	0.005	0.000	0.000	0.000	0.000
103	A	104	LEU	0	0.042	0.011	20.451	-0.003	-0.003	0.000	0.000	0.000	0.000
104	A	105	GLY	0	0.018	0.019	23.090	0.009	0.009	0.000	0.000	0.000	0.000
105	A	106	TYR	0	-0.032	-0.011	21.575	0.004	0.004	0.000	0.000	0.000	0.000
106	A	107	TRP	0	0.017	0.010	16.446	0.000	0.000	0.000	0.000	0.000	0.000
107	A	108	GLU	-1	-0.862	-0.931	19.320	0.033	0.033	0.000	0.000	0.000	0.000
108	A	109	ALA	0	0.004	-0.003	18.174	0.006	0.006	0.000	0.000	0.000	0.000
109	A	110	TRP	0	0.029	-0.002	20.122	0.007	0.007	0.000	0.000	0.000	0.000
110	A	111	ARG	1	0.830	0.906	21.908	-0.007	-0.007	0.000	0.000	0.000	0.000
111	A	112	HIS	0	-0.020	-0.011	23.497	-0.004	-0.004	0.000	0.000	0.000	0.000
112	A	113	HIS	0	-0.028	-0.009	20.664	0.002	0.002	0.000	0.000	0.000	0.000
113	A	115	GLN	0	0.028	0.013	24.034	-0.004	-0.004	0.000	0.000	0.000	0.000
114	A	116	GLY	0	-0.035	-0.023	27.251	0.007	0.007	0.000	0.000	0.000	0.000
115	A	117	ARG	1	0.823	0.917	26.394	-0.055	-0.055	0.000	0.000	0.000	0.000
116	A	118	ASP	-1	-0.808	-0.877	29.336	0.010	0.010	0.000	0.000	0.000	0.000
117	A	119	LEU	0	-0.035	-0.030	23.558	0.008	0.008	0.000	0.000	0.000	0.000
118	A	120	SER	0	0.017	-0.011	24.607	0.002	0.002	0.000	0.000	0.000	0.000
119	A	121	ASP	-1	-0.874	-0.931	24.787	0.047	0.047	0.000	0.000	0.000	0.000
120	A	122	TRP	0	-0.036	-0.032	17.772	0.010	0.010	0.000	0.000	0.000	0.000
121	A	123	VAL	0	-0.025	-0.030	20.434	-0.003	-0.003	0.000	0.000	0.000	0.000
122	A	124	ASP	-1	-0.837	-0.911	22.709	0.012	0.012	0.000	0.000	0.000	0.000
123	A	125	GLY	0	-0.021	-0.013	24.200	0.008	0.008	0.000	0.000	0.000	0.000
124	A	127	ASP	-1	-0.924	-0.972	22.488	-0.051	-0.051	0.000	0.000	0.000	0.000
125	A	128	PHE	0	-0.002	0.007	20.293	-0.004	-0.004	0.000	0.000	0.000	0.000
126	A	129	LEU	0	-0.053	-0.005	23.994	-0.003	-0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:ALA)