FMO DATABASE

FMODB ID: G5J51

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1179714.985768
FMO2-HF: Nuclear repulsion	1125964.620814
FMO2-HF: Total energy	-53750.364954
FMO2-MP2: Total energy	-53901.10686

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.
-7.526	-3.424	5.797	-4.269	-5.628	-0.028

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 : -0.028 / q_NPA : -0.013

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	-0.014	0.000	3.848	-0.819	1.297	-0.024	-1.155	-0.936	0.000
4	A	3	PHE	0	0.023	0.018	6.730	-0.290	-0.290	0.000	0.000	0.000	0.000
5	A	4	SER	0	0.010	0.010	9.940	0.115	0.115	0.000	0.000	0.000	0.000
6	A	5	ARG	1	0.872	0.895	13.393	-0.146	-0.146	0.000	0.000	0.000	0.000
7	A	6	CYS	0	-0.073	-0.022	15.926	-0.020	-0.020	0.000	0.000	0.000	0.000
8	A	7	GLU	-1	-0.816	-0.892	11.147	-0.107	-0.107	0.000	0.000	0.000	0.000
9	A	8	LEU	0	-0.020	-0.014	11.387	-0.048	-0.048	0.000	0.000	0.000	0.000
10	A	9	ALA	0	0.028	0.013	14.113	-0.030	-0.030	0.000	0.000	0.000	0.000
11	A	10	LYS	1	0.835	0.907	17.237	0.094	0.094	0.000	0.000	0.000	0.000
12	A	11	GLU	-1	-0.923	-0.975	12.478	-0.318	-0.318	0.000	0.000	0.000	0.000
13	A	12	MET	0	-0.050	-0.028	14.233	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	13	HIS	0	-0.044	-0.021	17.560	0.012	0.012	0.000	0.000	0.000	0.000
15	A	14	ASP	-1	-0.806	-0.883	17.981	-0.120	-0.120	0.000	0.000	0.000	0.000
16	A	15	PHE	0	-0.034	-0.011	13.775	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	16	GLY	0	-0.041	-0.011	19.277	0.003	0.003	0.000	0.000	0.000	0.000
18	A	17	LEU	0	-0.020	-0.030	17.997	0.006	0.006	0.000	0.000	0.000	0.000
19	A	18	ASP	-1	-0.856	-0.926	22.132	-0.019	-0.019	0.000	0.000	0.000	0.000
20	A	19	GLY	0	0.017	0.005	24.707	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	20	TYR	0	-0.044	-0.017	23.828	0.001	0.001	0.000	0.000	0.000	0.000
22	A	21	ARG	1	0.785	0.866	25.946	0.053	0.053	0.000	0.000	0.000	0.000
23	A	22	GLY	0	0.004	0.016	28.227	0.004	0.004	0.000	0.000	0.000	0.000
24	A	23	TYR	0	-0.012	0.021	24.417	0.005	0.005	0.000	0.000	0.000	0.000
25	A	24	ASN	0	0.009	-0.001	25.548	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	25	LEU	0	-0.006	-0.011	19.934	0.001	0.001	0.000	0.000	0.000	0.000
27	A	26	ALA	0	0.042	0.019	20.751	0.002	0.002	0.000	0.000	0.000	0.000
28	A	27	ASP	-1	-0.859	-0.925	21.292	0.014	0.014	0.000	0.000	0.000	0.000
29	A	28	TRP	0	0.030	-0.002	18.105	0.001	0.001	0.000	0.000	0.000	0.000
30	A	29	VAL	0	0.000	0.000	16.589	0.005	0.005	0.000	0.000	0.000	0.000
31	A	30	CYS	0	-0.057	0.002	16.702	0.039	0.039	0.000	0.000	0.000	0.000
32	A	31	LEU	0	-0.005	-0.009	16.620	0.022	0.022	0.000	0.000	0.000	0.000
33	A	32	ALA	0	-0.007	-0.002	12.629	0.011	0.011	0.000	0.000	0.000	0.000
34	A	33	TYR	0	-0.048	-0.006	13.136	0.068	0.068	0.000	0.000	0.000	0.000
35	A	34	TYR	0	0.013	-0.020	14.629	0.052	0.052	0.000	0.000	0.000	0.000
36	A	35	THR	0	-0.062	-0.016	13.179	0.004	0.004	0.000	0.000	0.000	0.000
37	A	36	SER	0	-0.016	-0.029	9.235	0.041	0.041	0.000	0.000	0.000	0.000
38	A	37	GLY	0	0.014	0.023	9.841	0.177	0.177	0.000	0.000	0.000	0.000
39	A	38	PHE	0	-0.059	-0.037	9.903	0.099	0.099	0.000	0.000	0.000	0.000
40	A	39	ASN	0	0.010	0.002	4.351	0.589	0.661	-0.001	-0.009	-0.062	0.000
41	A	40	THR	0	0.028	-0.001	3.664	-0.345	-0.031	0.004	-0.145	-0.173	-0.001
42	A	41	ASN	0	-0.033	-0.032	1.992	-4.353	-3.010	2.659	-1.695	-2.308	-0.013
43	A	42	ALA	0	0.002	0.023	4.153	0.188	0.312	0.000	-0.034	-0.089	0.000
44	A	43	VAL	0	-0.028	-0.025	7.435	-0.251	-0.251	0.000	0.000	0.000	0.000
45	A	44	ASP	-1	-0.892	-0.932	10.320	0.197	0.197	0.000	0.000	0.000	0.000
46	A	45	HIS	0	-0.029	-0.017	12.477	-0.066	-0.066	0.000	0.000	0.000	0.000
47	A	46	GLU	-1	-0.745	-0.829	16.851	0.016	0.016	0.000	0.000	0.000	0.000
48	A	47	ALA	0	-0.009	-0.011	20.079	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	48	ASP	-1	-0.865	-0.917	22.832	-0.025	-0.025	0.000	0.000	0.000	0.000
50	A	49	GLY	0	-0.020	-0.012	21.134	-0.008	-0.008	0.000	0.000	0.000	0.000
51	A	50	SER	0	-0.135	-0.075	19.982	-0.017	-0.017	0.000	0.000	0.000	0.000
52	A	51	THR	0	0.020	0.007	14.340	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	52	ASN	0	-0.073	-0.050	14.658	-0.042	-0.042	0.000	0.000	0.000	0.000
54	A	53	ASN	0	0.005	-0.024	10.913	-0.024	-0.024	0.000	0.000	0.000	0.000
55	A	54	GLY	0	0.071	0.049	7.786	-0.021	-0.021	0.000	0.000	0.000	0.000
56	A	55	ILE	0	0.006	0.012	8.438	0.162	0.162	0.000	0.000	0.000	0.000
57	A	56	PHE	0	0.029	0.014	9.724	0.085	0.085	0.000	0.000	0.000	0.000
58	A	57	GLN	0	-0.063	-0.035	10.376	0.040	0.040	0.000	0.000	0.000	0.000
59	A	58	ILE	0	0.008	0.005	13.443	0.021	0.021	0.000	0.000	0.000	0.000
60	A	59	SER	0	0.091	0.049	15.108	-0.023	-0.023	0.000	0.000	0.000	0.000
61	A	60	SER	0	0.025	-0.029	17.206	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	61	ARG	1	0.799	0.903	18.729	0.029	0.029	0.000	0.000	0.000	0.000
63	A	62	ARG	1	0.758	0.859	21.353	0.070	0.070	0.000	0.000	0.000	0.000
64	A	63	TRP	0	0.058	0.024	18.990	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	64	CYS	0	-0.001	0.023	14.005	-0.036	-0.036	0.000	0.000	0.000	0.000
66	A	65	ARG	1	0.931	0.971	18.211	0.177	0.177	0.000	0.000	0.000	0.000
67	A	66	THR	0	0.098	0.035	16.366	-0.033	-0.033	0.000	0.000	0.000	0.000
68	A	67	LEU	0	-0.043	-0.032	18.898	0.017	0.017	0.000	0.000	0.000	0.000
69	A	68	ALA	0	0.011	0.004	21.615	0.003	0.003	0.000	0.000	0.000	0.000
70	A	69	SER	0	0.029	0.020	21.226	0.013	0.013	0.000	0.000	0.000	0.000
71	A	70	ASN	0	-0.068	-0.025	22.849	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	71	GLY	0	0.098	0.036	24.553	0.009	0.009	0.000	0.000	0.000	0.000
73	A	72	PRO	0	-0.071	-0.028	25.377	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	73	ASN	0	0.003	0.014	20.544	-0.017	-0.017	0.000	0.000	0.000	0.000
75	A	74	LEU	0	0.040	0.016	22.730	-0.007	-0.007	0.000	0.000	0.000	0.000
76	A	75	CYS	0	-0.191	-0.087	16.350	0.044	0.044	0.000	0.000	0.000	0.000
77	A	76	ARG	1	0.852	0.924	19.893	0.131	0.131	0.000	0.000	0.000	0.000
78	A	77	ILE	0	0.052	0.032	13.988	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	78	TYR	0	0.008	0.011	14.893	0.046	0.046	0.000	0.000	0.000	0.000
80	A	80	THR	0	0.063	0.033	9.813	-0.025	-0.025	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.916	-0.968	9.224	-0.632	-0.632	0.000	0.000	0.000	0.000
82	A	82	LEU	0	-0.072	-0.028	10.184	-0.034	-0.034	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.049	-0.020	6.116	0.062	0.062	0.000	0.000	0.000	0.000
84	A	84	ASN	0	-0.015	0.001	4.568	-1.035	-0.940	-0.001	-0.004	-0.089	0.000
85	A	85	ASN	0	0.019	-0.008	2.295	-1.696	-1.690	3.161	-1.219	-1.947	-0.014
86	A	86	ASP	-1	-0.836	-0.892	4.930	-0.246	-0.214	-0.001	-0.008	-0.024	0.000
87	A	87	LEU	0	0.048	0.009	8.639	-0.028	-0.028	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.858	0.914	10.626	0.555	0.555	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.858	-0.926	12.251	-0.382	-0.382	0.000	0.000	0.000	0.000
90	A	90	SER	0	0.008	-0.002	10.828	0.072	0.072	0.000	0.000	0.000	0.000
91	A	91	ILE	0	-0.008	0.011	13.338	0.062	0.062	0.000	0.000	0.000	0.000
92	A	92	VAL	0	0.013	0.001	15.826	0.039	0.039	0.000	0.000	0.000	0.000
93	A	94	ALA	0	0.073	0.026	16.734	0.026	0.026	0.000	0.000	0.000	0.000
94	A	95	MET	0	0.014	0.008	18.642	0.017	0.017	0.000	0.000	0.000	0.000
95	A	96	LYS	1	0.910	0.963	20.445	0.179	0.179	0.000	0.000	0.000	0.000
96	A	97	ILE	0	-0.010	-0.003	18.753	0.012	0.012	0.000	0.000	0.000	0.000
97	A	98	VAL	0	0.008	0.015	21.840	0.012	0.012	0.000	0.000	0.000	0.000
98	A	99	GLN	0	-0.034	-0.017	24.365	0.004	0.004	0.000	0.000	0.000	0.000
99	A	100	GLU	-1	-0.788	-0.873	26.215	-0.054	-0.054	0.000	0.000	0.000	0.000
100	A	101	PRO	0	-0.050	-0.051	28.388	0.003	0.003	0.000	0.000	0.000	0.000
101	A	102	LEU	0	-0.003	0.007	27.464	0.003	0.003	0.000	0.000	0.000	0.000
102	A	103	GLY	0	-0.006	0.021	26.291	0.005	0.005	0.000	0.000	0.000	0.000
103	A	104	LEU	0	0.043	0.000	20.906	-0.004	-0.004	0.000	0.000	0.000	0.000
104	A	105	GLY	0	0.003	0.014	23.435	0.008	0.008	0.000	0.000	0.000	0.000
105	A	106	TYR	0	-0.045	-0.019	21.724	0.002	0.002	0.000	0.000	0.000	0.000
106	A	107	TRP	0	0.038	0.019	16.794	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	108	GLU	-1	-0.857	-0.929	19.591	0.038	0.038	0.000	0.000	0.000	0.000
108	A	109	ALA	0	0.001	-0.001	18.725	0.005	0.005	0.000	0.000	0.000	0.000
109	A	110	TRP	0	0.056	0.009	20.625	0.006	0.006	0.000	0.000	0.000	0.000
110	A	111	ARG	1	0.845	0.922	22.163	-0.013	-0.013	0.000	0.000	0.000	0.000
111	A	112	HIS	0	-0.035	-0.031	23.830	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	113	HIS	0	-0.028	-0.008	21.001	0.005	0.005	0.000	0.000	0.000	0.000
113	A	115	GLN	0	0.048	0.030	24.306	-0.004	-0.004	0.000	0.000	0.000	0.000
114	A	116	GLY	0	-0.049	-0.034	27.360	0.006	0.006	0.000	0.000	0.000	0.000
115	A	117	ARG	1	0.838	0.926	26.400	-0.063	-0.063	0.000	0.000	0.000	0.000
116	A	118	ASP	-1	-0.843	-0.900	28.962	0.028	0.028	0.000	0.000	0.000	0.000
117	A	119	LEU	0	-0.026	-0.010	23.486	0.009	0.009	0.000	0.000	0.000	0.000
118	A	120	SER	0	0.005	-0.020	24.766	0.004	0.004	0.000	0.000	0.000	0.000
119	A	121	ASP	-1	-0.833	-0.914	25.036	0.067	0.067	0.000	0.000	0.000	0.000
120	A	122	TRP	0	-0.057	-0.042	17.735	0.013	0.013	0.000	0.000	0.000	0.000
121	A	123	VAL	0	-0.033	-0.025	20.811	0.004	0.004	0.000	0.000	0.000	0.000
122	A	124	ASP	-1	-0.830	-0.900	22.995	0.036	0.036	0.000	0.000	0.000	0.000
123	A	125	GLY	0	-0.055	-0.030	24.048	0.011	0.011	0.000	0.000	0.000	0.000
124	A	127	ASP	-1	-0.897	-0.956	22.276	-0.009	-0.009	0.000	0.000	0.000	0.000
125	A	128	PHE	0	-0.022	-0.018	20.482	-0.005	-0.005	0.000	0.000	0.000	0.000
126	A	129	LEU	0	-0.032	0.010	23.558	-0.007	-0.007	0.000	0.000	0.000	0.000

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