FMO DATABASE

FMODB ID: N9RLQ

Calculation Name: 4YIF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YIF

Chain ID: A

ChEMBL ID:

UniProt ID: P9WMF1

Base Structure: X-ray

Registration Date: 2023-09-20

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	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	140
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1092153.433437
FMO2-HF: Nuclear repulsion	1038509.042298
FMO2-HF: Total energy	-53644.391139
FMO2-MP2: Total energy	-53799.818986

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:SER)

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

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.
-4.714	-1.035	0.267	-1.531	-2.416	0.008

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.024 / q_NPA : -0.004

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	ALA	0	-0.024	-0.012	3.037	-2.400	0.286	0.134	-1.280	-1.541	0.008
4	A	7	ARG	1	0.866	0.900	2.978	-3.290	-2.526	0.134	-0.194	-0.704	0.000
5	A	8	LEU	0	0.033	0.033	4.313	0.115	0.344	-0.001	-0.057	-0.171	0.000
6	A	9	ALA	0	0.029	0.016	5.800	0.589	0.589	0.000	0.000	0.000	0.000
7	A	10	SER	0	-0.007	-0.011	7.718	0.160	0.160	0.000	0.000	0.000	0.000
8	A	11	ASP	-1	-0.847	-0.914	7.877	0.396	0.396	0.000	0.000	0.000	0.000
9	A	12	LEU	0	0.016	0.016	9.443	0.091	0.091	0.000	0.000	0.000	0.000
10	A	13	SER	0	0.028	0.018	11.227	0.088	0.088	0.000	0.000	0.000	0.000
11	A	14	LEU	0	-0.013	-0.006	12.977	0.037	0.037	0.000	0.000	0.000	0.000
12	A	15	ALA	0	-0.005	-0.006	13.419	0.028	0.028	0.000	0.000	0.000	0.000
13	A	16	VAL	0	0.063	0.032	15.177	0.030	0.030	0.000	0.000	0.000	0.000
14	A	17	MET	0	0.005	0.006	17.245	0.020	0.020	0.000	0.000	0.000	0.000
15	A	18	ARG	1	0.903	0.946	16.579	-0.109	-0.109	0.000	0.000	0.000	0.000
16	A	19	LEU	0	0.022	0.015	19.256	0.012	0.012	0.000	0.000	0.000	0.000
17	A	20	SER	0	0.018	0.000	20.959	0.012	0.012	0.000	0.000	0.000	0.000
18	A	21	ARG	1	0.926	0.967	22.742	-0.027	-0.027	0.000	0.000	0.000	0.000
19	A	22	GLN	0	0.020	0.011	23.975	0.001	0.001	0.000	0.000	0.000	0.000
20	A	23	LEU	0	0.031	0.015	23.580	0.003	0.003	0.000	0.000	0.000	0.000
21	A	24	ARG	1	0.938	0.976	24.642	0.041	0.041	0.000	0.000	0.000	0.000
22	A	25	PHE	0	-0.056	-0.046	28.228	0.004	0.004	0.000	0.000	0.000	0.000
23	A	26	ARG	1	0.864	0.951	28.481	0.014	0.014	0.000	0.000	0.000	0.000
24	A	27	ASN	0	0.019	0.025	31.464	-0.008	-0.008	0.000	0.000	0.000	0.000
25	A	28	PRO	0	0.048	0.028	33.976	0.004	0.004	0.000	0.000	0.000	0.000
26	A	29	SER	0	-0.010	-0.009	37.606	0.000	0.000	0.000	0.000	0.000	0.000
27	A	30	SER	0	-0.005	-0.006	38.568	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	31	PRO	0	-0.013	0.003	41.263	0.002	0.002	0.000	0.000	0.000	0.000
29	A	32	VAL	0	0.040	0.027	38.070	0.000	0.000	0.000	0.000	0.000	0.000
30	A	33	SER	0	0.010	0.002	37.104	0.000	0.000	0.000	0.000	0.000	0.000
31	A	34	LEU	0	0.028	-0.014	30.311	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	35	SER	0	-0.006	0.000	33.660	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	36	GLN	0	0.068	0.032	34.713	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	37	LEU	0	0.029	0.020	33.551	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	38	SER	0	-0.082	-0.048	31.560	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	39	ALA	0	0.060	0.030	33.369	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	40	LEU	0	-0.012	-0.002	36.214	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	41	THR	0	-0.037	-0.044	31.995	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	42	THR	0	-0.023	-0.025	32.713	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	43	LEU	0	-0.033	-0.011	34.455	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	44	ALA	0	-0.065	-0.037	37.144	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	45	ASN	0	-0.075	-0.045	32.268	0.001	0.001	0.000	0.000	0.000	0.000
43	A	46	GLU	-1	-0.815	-0.872	31.644	-0.089	-0.089	0.000	0.000	0.000	0.000
44	A	47	GLY	0	0.002	0.017	35.991	0.000	0.000	0.000	0.000	0.000	0.000
45	A	48	ALA	0	-0.016	-0.020	39.722	0.002	0.002	0.000	0.000	0.000	0.000
46	A	49	MET	0	0.010	0.012	35.705	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	50	THR	0	0.028	0.037	41.930	0.002	0.002	0.000	0.000	0.000	0.000
48	A	51	PRO	0	0.034	0.009	41.650	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	52	GLY	0	-0.035	-0.016	40.702	0.000	0.000	0.000	0.000	0.000	0.000
50	A	53	ALA	0	0.022	0.012	38.503	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	54	LEU	0	0.084	0.037	36.456	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	55	ALA	0	-0.039	-0.022	36.018	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	56	ILE	0	-0.043	-0.021	33.794	0.001	0.001	0.000	0.000	0.000	0.000
54	A	57	ARG	1	0.786	0.870	28.499	0.095	0.095	0.000	0.000	0.000	0.000
55	A	58	GLU	-1	-0.792	-0.867	31.328	-0.053	-0.053	0.000	0.000	0.000	0.000
56	A	59	ARG	1	0.902	0.966	24.603	0.076	0.076	0.000	0.000	0.000	0.000
57	A	60	VAL	0	-0.011	0.008	31.542	0.008	0.008	0.000	0.000	0.000	0.000
58	A	61	ARG	1	0.961	0.971	34.067	0.003	0.003	0.000	0.000	0.000	0.000
59	A	62	PRO	0	0.089	0.023	37.070	0.001	0.001	0.000	0.000	0.000	0.000
60	A	63	PRO	0	0.008	0.016	40.183	0.000	0.000	0.000	0.000	0.000	0.000
61	A	64	SER	0	0.023	0.016	37.730	0.001	0.001	0.000	0.000	0.000	0.000
62	A	65	MET	0	0.020	0.020	36.898	0.001	0.001	0.000	0.000	0.000	0.000
63	A	66	THR	0	-0.021	-0.023	39.962	0.000	0.000	0.000	0.000	0.000	0.000
64	A	67	ARG	1	0.958	0.978	42.501	0.001	0.001	0.000	0.000	0.000	0.000
65	A	68	VAL	0	-0.012	0.020	38.101	0.001	0.001	0.000	0.000	0.000	0.000
66	A	69	ILE	0	0.035	0.008	41.499	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	70	ALA	0	0.000	-0.001	43.653	0.000	0.000	0.000	0.000	0.000	0.000
68	A	71	SER	0	0.013	-0.005	43.520	0.001	0.001	0.000	0.000	0.000	0.000
69	A	72	LEU	0	-0.016	-0.011	39.998	0.000	0.000	0.000	0.000	0.000	0.000
70	A	73	ALA	0	-0.027	-0.008	44.554	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	74	ASP	-1	-0.906	-0.944	47.941	-0.009	-0.009	0.000	0.000	0.000	0.000
72	A	75	MET	0	-0.116	-0.050	43.390	0.000	0.000	0.000	0.000	0.000	0.000
73	A	76	GLY	0	0.020	0.025	47.937	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	77	PHE	0	-0.059	-0.027	43.201	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	78	VAL	0	0.021	0.000	42.938	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	79	ASP	-1	-0.811	-0.877	45.796	-0.028	-0.028	0.000	0.000	0.000	0.000
77	A	80	ARG	1	0.861	0.929	48.191	0.029	0.029	0.000	0.000	0.000	0.000
78	A	81	ALA	0	0.050	0.007	47.496	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	82	PRO	0	-0.054	-0.005	47.171	0.002	0.002	0.000	0.000	0.000	0.000
80	A	83	HIS	0	0.116	0.067	48.113	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	84	PRO	0	-0.007	-0.006	45.461	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	85	ILE	0	-0.090	-0.056	47.186	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	86	ASP	-1	-0.866	-0.949	49.893	-0.013	-0.013	0.000	0.000	0.000	0.000
84	A	87	GLY	0	0.008	-0.001	50.974	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	88	ARG	1	0.921	0.970	46.344	0.017	0.017	0.000	0.000	0.000	0.000
86	A	89	GLN	0	-0.017	-0.014	46.684	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	90	VAL	0	-0.021	-0.005	48.701	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	91	LEU	0	-0.015	-0.012	44.372	0.000	0.000	0.000	0.000	0.000	0.000
89	A	92	VAL	0	-0.032	-0.022	43.611	0.002	0.002	0.000	0.000	0.000	0.000
90	A	93	SER	0	0.039	-0.022	43.561	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	94	VAL	0	-0.019	0.008	40.358	0.003	0.003	0.000	0.000	0.000	0.000
92	A	95	SER	0	-0.011	-0.023	43.683	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	96	GLU	-1	-0.843	-0.948	44.994	-0.040	-0.040	0.000	0.000	0.000	0.000
94	A	97	SER	0	0.003	0.006	45.284	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	98	GLY	0	0.029	0.008	42.831	0.000	0.000	0.000	0.000	0.000	0.000
96	A	99	ALA	0	0.051	0.023	40.626	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	100	GLU	-1	-0.795	-0.885	40.202	-0.042	-0.042	0.000	0.000	0.000	0.000
98	A	101	LEU	0	-0.002	0.009	39.150	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	102	VAL	0	0.017	0.010	35.159	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	103	LYS	1	0.816	0.911	35.799	0.038	0.038	0.000	0.000	0.000	0.000
101	A	104	ALA	0	-0.010	-0.009	36.635	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	105	ALA	0	-0.007	-0.015	34.244	0.000	0.000	0.000	0.000	0.000	0.000
103	A	106	ARG	1	0.887	0.943	31.540	0.077	0.077	0.000	0.000	0.000	0.000
104	A	107	ARG	1	0.839	0.909	32.082	0.036	0.036	0.000	0.000	0.000	0.000
105	A	108	ALA	0	0.074	0.047	33.497	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	109	ARG	1	0.876	0.935	28.357	0.061	0.061	0.000	0.000	0.000	0.000
107	A	110	GLN	0	0.002	-0.003	28.636	0.001	0.001	0.000	0.000	0.000	0.000
108	A	111	GLU	-1	-0.895	-0.944	29.655	-0.046	-0.046	0.000	0.000	0.000	0.000
109	A	112	TRP	0	0.040	0.016	25.170	0.001	0.001	0.000	0.000	0.000	0.000
110	A	113	LEU	0	-0.008	-0.014	22.960	0.002	0.002	0.000	0.000	0.000	0.000
111	A	114	ALA	0	0.003	-0.002	26.463	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	115	GLU	-1	-0.868	-0.931	28.684	-0.021	-0.021	0.000	0.000	0.000	0.000
113	A	116	ARG	1	0.853	0.927	24.746	0.022	0.022	0.000	0.000	0.000	0.000
114	A	117	LEU	0	0.022	0.021	22.183	0.001	0.001	0.000	0.000	0.000	0.000
115	A	118	ALA	0	-0.025	0.006	24.962	-0.004	-0.004	0.000	0.000	0.000	0.000
116	A	119	THR	0	-0.105	-0.060	25.129	0.008	0.008	0.000	0.000	0.000	0.000
117	A	120	LEU	0	0.012	0.031	20.223	0.005	0.005	0.000	0.000	0.000	0.000
118	A	121	ASN	0	-0.002	-0.025	20.746	-0.010	-0.010	0.000	0.000	0.000	0.000
119	A	122	ARG	1	0.956	0.953	22.955	0.068	0.068	0.000	0.000	0.000	0.000
120	A	123	SER	0	0.071	0.041	19.760	-0.008	-0.008	0.000	0.000	0.000	0.000
121	A	124	GLU	-1	-0.833	-0.902	17.859	-0.082	-0.082	0.000	0.000	0.000	0.000
122	A	125	ARG	1	0.858	0.907	18.783	0.055	0.055	0.000	0.000	0.000	0.000
123	A	126	ASP	-1	-0.828	-0.891	20.492	-0.178	-0.178	0.000	0.000	0.000	0.000
124	A	127	ILE	0	0.005	0.007	14.111	-0.029	-0.029	0.000	0.000	0.000	0.000
125	A	128	LEU	0	-0.020	-0.020	16.518	-0.042	-0.042	0.000	0.000	0.000	0.000
126	A	129	ARG	1	0.820	0.898	18.357	0.173	0.173	0.000	0.000	0.000	0.000
127	A	130	SER	0	0.028	0.011	16.914	0.001	0.001	0.000	0.000	0.000	0.000
128	A	131	ALA	0	-0.011	-0.009	15.097	-0.030	-0.030	0.000	0.000	0.000	0.000
129	A	132	ALA	0	-0.035	-0.015	16.444	-0.010	-0.010	0.000	0.000	0.000	0.000
130	A	133	ASP	-1	-0.884	-0.935	19.721	-0.247	-0.247	0.000	0.000	0.000	0.000
131	A	134	LEU	0	-0.017	-0.013	13.999	-0.012	-0.012	0.000	0.000	0.000	0.000
132	A	135	MET	0	-0.061	-0.038	15.550	-0.007	-0.007	0.000	0.000	0.000	0.000
133	A	136	LEU	0	0.023	0.014	17.538	0.021	0.021	0.000	0.000	0.000	0.000
134	A	137	ALA	0	0.008	0.010	18.820	0.018	0.018	0.000	0.000	0.000	0.000
135	A	138	LEU	0	-0.080	-0.031	13.620	-0.005	-0.005	0.000	0.000	0.000	0.000
136	A	139	VAL	0	-0.101	-0.049	18.065	0.020	0.020	0.000	0.000	0.000	0.000
137	A	140	ASP	-1	-0.956	-0.971	21.251	-0.173	-0.173	0.000	0.000	0.000	0.000
138	A	141	GLU	-1	-0.934	-0.960	23.265	-0.119	-0.119	0.000	0.000	0.000	0.000
139	A	142	SER	0	-0.046	-0.024	23.169	-0.008	-0.008	0.000	0.000	0.000	0.000
140	A	143	PRO	0	-0.010	-0.002	25.411	0.010	0.010	0.000	0.000	0.000	0.000

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