FMO DATABASE

FMODB ID: N1M7Q

Calculation Name: 4Y66-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4Y66

Chain ID: F

ChEMBL ID:

UniProt ID: E2RTU1

Base Structure: X-ray

Registration Date: 2023-06-20

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	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	167
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1125006.633882
FMO2-HF: Nuclear repulsion	1058150.571458
FMO2-HF: Total energy	-66856.062424
FMO2-MP2: Total energy	-67048.488106

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(F:3:ALA)

Summations of interaction energy for fragment #1(F:3: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.
-4.811	-1.924	0.044	-1.215	-1.716	0.003

Interaction energy analysis for fragmet #1(F:3:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : 0.003

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	F	5	TYR	0	-0.089	-0.075	3.627	-2.023	-0.014	0.001	-0.956	-1.054	0.003
4	F	6	LYS	1	0.993	0.996	3.435	-1.160	-0.454	0.044	-0.229	-0.521	0.000
5	F	7	GLU	-1	-0.894	-0.949	4.709	-1.835	-1.663	-0.001	-0.030	-0.141	0.000
6	F	8	ALA	0	-0.012	-0.004	6.977	0.172	0.172	0.000	0.000	0.000	0.000
7	F	9	PHE	0	-0.001	-0.002	8.066	-0.043	-0.043	0.000	0.000	0.000	0.000
8	F	10	ALA	0	0.013	0.005	8.728	-0.044	-0.044	0.000	0.000	0.000	0.000
9	F	11	ALA	0	0.020	0.019	10.505	-0.007	-0.007	0.000	0.000	0.000	0.000
10	F	12	VAL	0	-0.013	-0.020	12.519	0.002	0.002	0.000	0.000	0.000	0.000
11	F	13	LYS	1	0.821	0.896	12.477	-0.043	-0.043	0.000	0.000	0.000	0.000
12	F	14	GLU	-1	-0.833	-0.887	14.870	-0.023	-0.023	0.000	0.000	0.000	0.000
13	F	15	LEU	0	-0.024	-0.014	16.717	-0.002	-0.002	0.000	0.000	0.000	0.000
14	F	16	MET	0	-0.019	-0.003	18.340	-0.007	-0.007	0.000	0.000	0.000	0.000
15	F	17	GLN	0	-0.008	-0.021	17.663	0.011	0.011	0.000	0.000	0.000	0.000
16	F	18	THR	0	-0.009	0.002	20.502	-0.008	-0.008	0.000	0.000	0.000	0.000
17	F	19	SER	0	-0.076	-0.040	22.333	-0.007	-0.007	0.000	0.000	0.000	0.000
18	F	20	ASN	0	0.011	0.030	23.867	0.007	0.007	0.000	0.000	0.000	0.000
19	F	21	LYS	1	0.898	0.944	24.644	-0.040	-0.040	0.000	0.000	0.000	0.000
20	F	22	PRO	0	0.027	0.014	25.069	0.009	0.009	0.000	0.000	0.000	0.000
21	F	23	GLN	0	-0.003	-0.016	21.648	-0.004	-0.004	0.000	0.000	0.000	0.000
22	F	24	ASN	0	-0.008	-0.008	23.115	0.012	0.012	0.000	0.000	0.000	0.000
23	F	25	VAL	0	0.022	0.009	18.018	-0.007	-0.007	0.000	0.000	0.000	0.000
24	F	26	GLN	0	0.054	0.033	19.537	0.018	0.018	0.000	0.000	0.000	0.000
25	F	27	THR	0	0.030	0.013	21.642	-0.009	-0.009	0.000	0.000	0.000	0.000
26	F	28	ALA	0	0.055	0.037	17.893	-0.015	-0.015	0.000	0.000	0.000	0.000
27	F	29	ILE	0	0.004	0.015	15.872	-0.011	-0.011	0.000	0.000	0.000	0.000
28	F	30	ASN	0	0.015	0.011	17.908	-0.026	-0.026	0.000	0.000	0.000	0.000
29	F	31	ASN	0	0.003	-0.001	20.771	-0.017	-0.017	0.000	0.000	0.000	0.000
30	F	32	THR	0	-0.007	-0.008	15.082	-0.013	-0.013	0.000	0.000	0.000	0.000
31	F	33	GLY	0	-0.006	0.001	16.306	-0.036	-0.036	0.000	0.000	0.000	0.000
32	F	34	SER	0	-0.029	-0.026	18.101	-0.012	-0.012	0.000	0.000	0.000	0.000
33	F	35	LYS	1	0.899	0.956	13.141	0.132	0.132	0.000	0.000	0.000	0.000
34	F	36	TYR	0	0.023	0.014	9.643	0.035	0.035	0.000	0.000	0.000	0.000
35	F	37	GLY	0	0.062	0.036	12.264	-0.014	-0.014	0.000	0.000	0.000	0.000
36	F	38	LYS	1	0.932	0.950	14.062	-0.135	-0.135	0.000	0.000	0.000	0.000
37	F	39	THR	0	0.025	0.001	13.934	0.006	0.006	0.000	0.000	0.000	0.000
38	F	40	THR	0	0.025	0.014	9.057	-0.006	-0.006	0.000	0.000	0.000	0.000
39	F	41	VAL	0	0.070	0.028	11.772	0.058	0.058	0.000	0.000	0.000	0.000
40	F	42	GLN	0	0.005	0.010	14.150	0.017	0.017	0.000	0.000	0.000	0.000
41	F	43	LYS	1	0.798	0.897	12.051	-0.476	-0.476	0.000	0.000	0.000	0.000
42	F	44	ALA	0	0.084	0.048	11.215	-0.010	-0.010	0.000	0.000	0.000	0.000
43	F	45	LEU	0	-0.016	-0.009	12.800	-0.058	-0.058	0.000	0.000	0.000	0.000
44	F	46	ASP	-1	-0.772	-0.872	16.612	0.286	0.286	0.000	0.000	0.000	0.000
45	F	47	GLU	-1	-0.863	-0.893	10.677	0.931	0.931	0.000	0.000	0.000	0.000
46	F	48	LEU	0	0.005	-0.008	14.458	-0.040	-0.040	0.000	0.000	0.000	0.000
47	F	49	VAL	0	-0.052	-0.019	16.526	-0.036	-0.036	0.000	0.000	0.000	0.000
48	F	50	ALA	0	-0.035	-0.008	16.936	-0.023	-0.023	0.000	0.000	0.000	0.000
49	F	51	GLN	0	-0.035	-0.019	14.495	0.010	0.010	0.000	0.000	0.000	0.000
50	F	52	ASN	0	-0.002	-0.010	18.349	-0.026	-0.026	0.000	0.000	0.000	0.000
51	F	53	LEU	0	0.049	0.036	16.675	-0.020	-0.020	0.000	0.000	0.000	0.000
52	F	54	CYS	0	-0.100	-0.033	19.678	-0.015	-0.015	0.000	0.000	0.000	0.000
53	F	55	ILE	0	0.046	0.033	21.384	0.009	0.009	0.000	0.000	0.000	0.000
54	F	56	TYR	0	-0.006	-0.026	23.424	0.007	0.007	0.000	0.000	0.000	0.000
55	F	57	THR	0	-0.012	-0.003	25.483	-0.011	-0.011	0.000	0.000	0.000	0.000
56	F	58	GLU	-1	-0.867	-0.941	26.729	0.157	0.157	0.000	0.000	0.000	0.000
57	F	59	ILE	0	0.037	0.019	29.602	-0.005	-0.005	0.000	0.000	0.000	0.000
58	F	60	GLY	0	0.058	0.022	32.709	0.001	0.001	0.000	0.000	0.000	0.000
59	F	61	LYS	1	0.854	0.921	29.941	-0.125	-0.125	0.000	0.000	0.000	0.000
60	F	62	THR	0	-0.026	0.005	31.140	0.002	0.002	0.000	0.000	0.000	0.000
61	F	63	GLY	0	0.008	-0.002	27.604	0.004	0.004	0.000	0.000	0.000	0.000
62	F	64	LYS	1	0.835	0.934	21.361	-0.240	-0.240	0.000	0.000	0.000	0.000
63	F	65	LEU	0	-0.037	-0.013	25.544	-0.001	-0.001	0.000	0.000	0.000	0.000
64	F	66	TYR	0	-0.013	-0.048	19.955	-0.004	-0.004	0.000	0.000	0.000	0.000
65	F	67	LEU	0	0.003	0.000	23.670	-0.014	-0.014	0.000	0.000	0.000	0.000
66	F	68	TRP	0	0.090	0.043	18.132	0.022	0.022	0.000	0.000	0.000	0.000
67	F	69	ASN	0	0.000	0.001	22.974	-0.018	-0.018	0.000	0.000	0.000	0.000
68	F	70	GLN	0	0.032	-0.016	24.920	0.000	0.000	0.000	0.000	0.000	0.000
69	F	71	ASN	0	-0.059	-0.029	28.069	-0.012	-0.012	0.000	0.000	0.000	0.000
70	F	72	LEU	0	-0.037	-0.010	23.109	-0.001	-0.001	0.000	0.000	0.000	0.000
71	F	73	LEU	0	-0.049	-0.011	26.422	-0.005	-0.005	0.000	0.000	0.000	0.000
72	F	74	GLU	-1	-0.842	-0.916	29.229	0.028	0.028	0.000	0.000	0.000	0.000
73	F	75	VAL	0	-0.024	-0.014	32.435	-0.002	-0.002	0.000	0.000	0.000	0.000
74	F	76	LEU	0	-0.036	-0.011	34.998	-0.002	-0.002	0.000	0.000	0.000	0.000
75	F	77	SER	0	0.032	0.020	37.568	-0.001	-0.001	0.000	0.000	0.000	0.000
76	F	78	ASP	-1	-0.849	-0.936	41.081	0.022	0.022	0.000	0.000	0.000	0.000
77	F	79	ALA	0	-0.006	-0.004	43.982	-0.002	-0.002	0.000	0.000	0.000	0.000
78	F	80	GLN	0	-0.039	-0.027	36.738	-0.004	-0.004	0.000	0.000	0.000	0.000
79	F	81	LEU	0	-0.002	-0.002	39.042	-0.002	-0.002	0.000	0.000	0.000	0.000
80	F	82	MET	0	-0.035	-0.014	41.448	-0.001	-0.001	0.000	0.000	0.000	0.000
81	F	83	GLU	-1	-0.847	-0.894	41.010	0.003	0.003	0.000	0.000	0.000	0.000
82	F	84	VAL	0	0.029	0.010	37.328	-0.002	-0.002	0.000	0.000	0.000	0.000
83	F	85	ASN	0	-0.069	-0.060	40.160	-0.002	-0.002	0.000	0.000	0.000	0.000
84	F	86	ALA	0	-0.023	0.001	42.741	-0.001	-0.001	0.000	0.000	0.000	0.000
85	F	87	GLN	0	-0.045	-0.038	38.595	-0.002	-0.002	0.000	0.000	0.000	0.000
86	F	88	ILE	0	-0.003	-0.009	37.764	-0.002	-0.002	0.000	0.000	0.000	0.000
87	F	89	ASN	0	-0.004	-0.011	41.172	-0.001	-0.001	0.000	0.000	0.000	0.000
88	F	90	ASP	-1	-0.829	-0.886	44.044	-0.006	-0.006	0.000	0.000	0.000	0.000
89	F	91	LEU	0	0.008	0.003	38.184	-0.001	-0.001	0.000	0.000	0.000	0.000
90	F	92	LYS	1	0.864	0.930	42.065	-0.007	-0.007	0.000	0.000	0.000	0.000
91	F	93	ALA	0	0.022	0.019	43.554	-0.001	-0.001	0.000	0.000	0.000	0.000
92	F	94	GLN	0	-0.061	-0.058	43.428	-0.003	-0.003	0.000	0.000	0.000	0.000
93	F	95	VAL	0	0.055	0.026	39.786	-0.002	-0.002	0.000	0.000	0.000	0.000
94	F	96	GLU	-1	-0.858	-0.901	42.836	-0.009	-0.009	0.000	0.000	0.000	0.000
95	F	97	LYS	1	0.846	0.928	45.789	0.010	0.010	0.000	0.000	0.000	0.000
96	F	98	LEU	0	0.016	-0.003	41.499	-0.001	-0.001	0.000	0.000	0.000	0.000
97	F	99	THR	0	-0.031	-0.013	43.046	-0.002	-0.002	0.000	0.000	0.000	0.000
98	F	100	GLN	0	-0.010	-0.024	44.541	-0.001	-0.001	0.000	0.000	0.000	0.000
99	F	101	GLN	0	-0.019	0.010	46.948	0.000	0.000	0.000	0.000	0.000	0.000
100	F	102	GLY	0	0.027	0.010	44.590	-0.001	-0.001	0.000	0.000	0.000	0.000
101	F	103	GLU	-1	-0.845	-0.888	45.261	-0.016	-0.016	0.000	0.000	0.000	0.000
102	F	104	THR	0	-0.017	-0.016	47.590	0.000	0.000	0.000	0.000	0.000	0.000
103	F	105	LEU	0	-0.010	0.008	45.610	0.000	0.000	0.000	0.000	0.000	0.000
104	F	106	ARG	1	0.851	0.891	43.993	0.017	0.017	0.000	0.000	0.000	0.000
105	F	107	ILE	0	-0.033	-0.019	47.443	0.000	0.000	0.000	0.000	0.000	0.000
106	F	108	THR	0	-0.040	-0.037	50.995	0.000	0.000	0.000	0.000	0.000	0.000
107	F	109	GLN	0	-0.083	-0.054	44.969	0.000	0.000	0.000	0.000	0.000	0.000
108	F	110	ARG	1	0.911	0.954	49.336	0.015	0.015	0.000	0.000	0.000	0.000
109	F	111	ASN	0	-0.028	-0.018	50.656	0.000	0.000	0.000	0.000	0.000	0.000
110	F	112	LEU	0	-0.025	-0.002	52.654	0.001	0.001	0.000	0.000	0.000	0.000
111	F	113	GLU	-1	-0.863	-0.924	47.677	-0.025	-0.025	0.000	0.000	0.000	0.000
112	F	114	ALA	0	-0.031	-0.008	51.770	0.000	0.000	0.000	0.000	0.000	0.000
113	F	115	ALA	0	-0.030	-0.002	54.318	0.000	0.000	0.000	0.000	0.000	0.000
114	F	116	PRO	0	0.022	0.020	55.396	-0.001	-0.001	0.000	0.000	0.000	0.000
115	F	117	ILE	0	0.015	-0.003	52.538	0.001	0.001	0.000	0.000	0.000	0.000
116	F	118	THR	0	0.036	0.003	56.773	0.000	0.000	0.000	0.000	0.000	0.000
117	F	119	GLU	-1	-0.848	-0.914	58.721	-0.020	-0.020	0.000	0.000	0.000	0.000
118	F	120	VAL	0	0.014	0.008	56.172	0.000	0.000	0.000	0.000	0.000	0.000
119	F	121	LEU	0	0.025	0.012	59.616	0.001	0.001	0.000	0.000	0.000	0.000
120	F	122	LYS	1	0.827	0.903	61.983	0.019	0.019	0.000	0.000	0.000	0.000
121	F	123	GLN	0	-0.010	-0.005	60.638	0.000	0.000	0.000	0.000	0.000	0.000
122	F	124	GLU	-1	-0.923	-0.949	60.613	-0.017	-0.017	0.000	0.000	0.000	0.000
123	F	125	VAL	0	-0.008	-0.016	63.782	0.001	0.001	0.000	0.000	0.000	0.000
124	F	126	ASP	-1	-0.848	-0.912	67.077	-0.015	-0.015	0.000	0.000	0.000	0.000
125	F	127	GLU	-1	-0.889	-0.951	63.492	-0.018	-0.018	0.000	0.000	0.000	0.000
126	F	128	LEU	0	-0.020	0.011	67.005	0.000	0.000	0.000	0.000	0.000	0.000
127	F	129	ARG	1	0.812	0.887	68.731	0.015	0.015	0.000	0.000	0.000	0.000
128	F	130	GLN	0	-0.010	-0.002	71.088	0.000	0.000	0.000	0.000	0.000	0.000
129	F	131	GLN	0	-0.045	-0.036	66.644	0.001	0.001	0.000	0.000	0.000	0.000
130	F	132	VAL	0	0.034	0.021	72.145	0.000	0.000	0.000	0.000	0.000	0.000
131	F	133	SER	0	-0.024	0.003	74.524	0.000	0.000	0.000	0.000	0.000	0.000
132	F	134	ALA	0	0.005	-0.003	74.479	0.000	0.000	0.000	0.000	0.000	0.000
133	F	135	ASN	0	-0.047	-0.027	73.398	0.000	0.000	0.000	0.000	0.000	0.000
134	F	136	ASP	-1	-0.751	-0.865	77.149	-0.010	-0.010	0.000	0.000	0.000	0.000
135	F	137	GLU	-1	-0.792	-0.884	79.947	-0.010	-0.010	0.000	0.000	0.000	0.000
136	F	138	LYS	1	0.760	0.863	78.973	0.011	0.011	0.000	0.000	0.000	0.000
137	F	139	LEU	0	-0.007	0.005	80.299	0.000	0.000	0.000	0.000	0.000	0.000
138	F	140	ARG	1	0.765	0.845	81.997	0.010	0.010	0.000	0.000	0.000	0.000
139	F	141	LEU	0	-0.079	-0.016	83.306	0.000	0.000	0.000	0.000	0.000	0.000
140	F	142	VAL	0	-0.031	-0.002	84.294	0.000	0.000	0.000	0.000	0.000	0.000
141	F	153	ASP	-1	-0.775	-0.873	95.643	-0.005	-0.005	0.000	0.000	0.000	0.000
142	F	154	MET	0	0.028	0.008	92.530	0.000	0.000	0.000	0.000	0.000	0.000
143	F	155	LEU	0	-0.023	0.000	95.764	0.000	0.000	0.000	0.000	0.000	0.000
144	F	156	THR	0	-0.004	-0.043	98.157	0.000	0.000	0.000	0.000	0.000	0.000
145	F	157	LEU	0	-0.032	-0.003	96.476	0.000	0.000	0.000	0.000	0.000	0.000
146	F	158	GLN	0	0.018	-0.008	97.612	0.000	0.000	0.000	0.000	0.000	0.000
147	F	159	LYS	1	0.747	0.857	99.730	0.004	0.004	0.000	0.000	0.000	0.000
148	F	160	ASN	0	-0.026	-0.014	103.026	0.000	0.000	0.000	0.000	0.000	0.000
149	F	161	TYR	0	-0.018	-0.025	100.547	0.000	0.000	0.000	0.000	0.000	0.000
150	F	162	LYS	1	0.889	0.943	101.732	0.004	0.004	0.000	0.000	0.000	0.000
151	F	163	ASP	-1	-0.813	-0.891	104.418	-0.004	-0.004	0.000	0.000	0.000	0.000
152	F	164	ALA	0	-0.034	0.003	106.825	0.000	0.000	0.000	0.000	0.000	0.000
153	F	165	MET	0	-0.059	-0.019	104.941	0.000	0.000	0.000	0.000	0.000	0.000
154	F	205	MET	0	0.067	0.021	109.734	0.000	0.000	0.000	0.000	0.000	0.000
155	F	206	THR	0	0.012	0.013	106.936	0.000	0.000	0.000	0.000	0.000	0.000
156	F	207	THR	0	0.089	0.048	105.076	0.000	0.000	0.000	0.000	0.000	0.000
157	F	208	TYR	0	0.005	-0.005	104.565	0.000	0.000	0.000	0.000	0.000	0.000
158	F	209	THR	0	-0.060	-0.039	104.291	0.000	0.000	0.000	0.000	0.000	0.000
159	F	210	GLU	-1	-0.931	-0.979	100.862	-0.004	-0.004	0.000	0.000	0.000	0.000
160	F	211	MET	0	0.039	0.016	99.952	0.000	0.000	0.000	0.000	0.000	0.000
161	F	212	LYS	1	0.898	0.954	99.846	0.004	0.004	0.000	0.000	0.000	0.000
162	F	213	LYS	1	0.904	0.954	97.725	0.004	0.004	0.000	0.000	0.000	0.000
163	F	214	ALA	0	-0.005	0.006	95.523	0.000	0.000	0.000	0.000	0.000	0.000
164	F	215	LEU	0	0.007	0.020	95.418	0.000	0.000	0.000	0.000	0.000	0.000
165	F	216	PRO	0	0.072	0.034	94.955	0.000	0.000	0.000	0.000	0.000	0.000
166	F	217	PRO	0	0.004	0.019	98.222	0.000	0.000	0.000	0.000	0.000	0.000
167	F	218	VAL	0	0.000	0.003	97.475	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:3:ALA)