FMO DATABASE

FMODB ID: 851QY

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:

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	140
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1092241.27466
FMO2-HF: Nuclear repulsion	1038597.500867
FMO2-HF: Total energy	-53643.773793
FMO2-MP2: Total energy	-53799.247218

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.
0.08	3.373	0.299	-1.219	-2.374	0.002

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 : 0.038 / 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	A	6	ALA	0	-0.043	-0.022	2.600	-1.510	0.779	0.153	-0.970	-1.472	0.002
4	A	7	ARG	1	0.895	0.933	2.995	-0.912	-0.164	0.147	-0.190	-0.705	0.000
5	A	8	LEU	0	0.045	0.037	4.256	0.774	1.030	-0.001	-0.059	-0.197	0.000
6	A	9	ALA	0	0.026	0.015	5.792	0.672	0.672	0.000	0.000	0.000	0.000
7	A	10	SER	0	-0.013	-0.015	7.726	0.302	0.302	0.000	0.000	0.000	0.000
8	A	11	ASP	-1	-0.869	-0.940	7.764	0.145	0.145	0.000	0.000	0.000	0.000
9	A	12	LEU	0	0.008	0.015	9.567	0.145	0.145	0.000	0.000	0.000	0.000
10	A	13	SER	0	0.035	0.019	11.325	0.124	0.124	0.000	0.000	0.000	0.000
11	A	14	LEU	0	-0.010	-0.003	12.972	0.079	0.079	0.000	0.000	0.000	0.000
12	A	15	ALA	0	-0.005	-0.008	13.757	0.051	0.051	0.000	0.000	0.000	0.000
13	A	16	VAL	0	0.062	0.032	15.214	0.042	0.042	0.000	0.000	0.000	0.000
14	A	17	MET	0	0.007	0.021	17.409	0.034	0.034	0.000	0.000	0.000	0.000
15	A	18	ARG	1	0.906	0.948	16.981	0.095	0.095	0.000	0.000	0.000	0.000
16	A	19	LEU	0	0.028	0.018	19.524	0.018	0.018	0.000	0.000	0.000	0.000
17	A	20	SER	0	0.006	-0.020	21.142	0.016	0.016	0.000	0.000	0.000	0.000
18	A	21	ARG	1	0.921	0.969	22.966	0.071	0.071	0.000	0.000	0.000	0.000
19	A	22	GLN	0	-0.032	-0.022	24.263	0.014	0.014	0.000	0.000	0.000	0.000
20	A	23	LEU	0	0.032	0.011	23.910	0.007	0.007	0.000	0.000	0.000	0.000
21	A	24	ARG	1	0.949	0.982	25.040	0.093	0.093	0.000	0.000	0.000	0.000
22	A	25	PHE	0	-0.046	-0.047	28.137	0.003	0.003	0.000	0.000	0.000	0.000
23	A	26	ARG	1	0.882	0.971	28.968	0.037	0.037	0.000	0.000	0.000	0.000
24	A	27	ASN	0	0.023	0.026	31.306	0.002	0.002	0.000	0.000	0.000	0.000
25	A	28	PRO	0	0.053	0.033	34.141	0.001	0.001	0.000	0.000	0.000	0.000
26	A	29	SER	0	-0.008	-0.011	37.792	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	30	SER	0	-0.003	0.000	38.881	0.001	0.001	0.000	0.000	0.000	0.000
28	A	31	PRO	0	0.011	0.010	41.405	0.000	0.000	0.000	0.000	0.000	0.000
29	A	32	VAL	0	0.038	0.024	38.056	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	33	SER	0	-0.004	-0.004	37.045	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	34	LEU	0	0.024	-0.018	30.237	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	35	SER	0	-0.011	0.000	33.662	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	36	GLN	0	0.091	0.044	34.715	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	37	LEU	0	0.027	0.022	33.271	0.000	0.000	0.000	0.000	0.000	0.000
35	A	38	SER	0	-0.102	-0.075	31.642	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	39	ALA	0	0.068	0.035	33.284	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	40	LEU	0	-0.005	0.000	36.068	0.001	0.001	0.000	0.000	0.000	0.000
38	A	41	THR	0	-0.045	-0.050	31.931	0.002	0.002	0.000	0.000	0.000	0.000
39	A	42	THR	0	-0.024	-0.023	32.628	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	43	LEU	0	-0.015	-0.013	34.232	0.001	0.001	0.000	0.000	0.000	0.000
41	A	44	ALA	0	-0.071	-0.039	37.019	0.002	0.002	0.000	0.000	0.000	0.000
42	A	45	ASN	0	-0.074	-0.044	32.047	0.005	0.005	0.000	0.000	0.000	0.000
43	A	46	GLU	-1	-0.830	-0.897	31.340	-0.075	-0.075	0.000	0.000	0.000	0.000
44	A	47	GLY	0	-0.001	0.016	35.663	0.002	0.002	0.000	0.000	0.000	0.000
45	A	48	ALA	0	-0.012	-0.013	39.406	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	49	MET	0	0.008	0.005	35.651	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	50	THR	0	0.027	0.036	41.585	0.001	0.001	0.000	0.000	0.000	0.000
48	A	51	PRO	0	0.043	0.014	41.345	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	52	GLY	0	-0.038	-0.016	40.542	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	53	ALA	0	0.026	0.014	38.312	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	54	LEU	0	0.081	0.035	36.192	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	55	ALA	0	-0.044	-0.024	35.800	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	56	ILE	0	-0.038	-0.019	33.395	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	57	ARG	1	0.841	0.912	29.019	0.077	0.077	0.000	0.000	0.000	0.000
55	A	58	GLU	-1	-0.793	-0.842	31.065	-0.078	-0.078	0.000	0.000	0.000	0.000
56	A	59	ARG	1	0.906	0.969	24.283	0.112	0.112	0.000	0.000	0.000	0.000
57	A	60	VAL	0	-0.006	0.012	31.289	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	61	ARG	1	0.949	0.964	33.389	0.063	0.063	0.000	0.000	0.000	0.000
59	A	62	PRO	0	0.095	0.027	36.695	0.001	0.001	0.000	0.000	0.000	0.000
60	A	63	PRO	0	0.035	0.030	39.670	0.001	0.001	0.000	0.000	0.000	0.000
61	A	64	SER	0	-0.034	0.001	36.973	0.003	0.003	0.000	0.000	0.000	0.000
62	A	65	MET	0	0.068	0.035	36.594	0.002	0.002	0.000	0.000	0.000	0.000
63	A	66	THR	0	-0.017	-0.030	39.900	0.002	0.002	0.000	0.000	0.000	0.000
64	A	67	ARG	1	0.948	0.968	42.612	0.040	0.040	0.000	0.000	0.000	0.000
65	A	68	VAL	0	-0.012	0.016	38.147	0.001	0.001	0.000	0.000	0.000	0.000
66	A	69	ILE	0	0.031	0.008	41.504	0.001	0.001	0.000	0.000	0.000	0.000
67	A	70	ALA	0	0.000	-0.002	43.517	0.001	0.001	0.000	0.000	0.000	0.000
68	A	71	SER	0	0.006	0.000	43.534	0.001	0.001	0.000	0.000	0.000	0.000
69	A	72	LEU	0	-0.014	-0.008	39.961	0.001	0.001	0.000	0.000	0.000	0.000
70	A	73	ALA	0	-0.019	-0.008	44.486	0.001	0.001	0.000	0.000	0.000	0.000
71	A	74	ASP	-1	-0.912	-0.946	47.839	-0.027	-0.027	0.000	0.000	0.000	0.000
72	A	75	MET	0	-0.121	-0.055	43.147	0.001	0.001	0.000	0.000	0.000	0.000
73	A	76	GLY	0	0.019	0.024	47.926	0.001	0.001	0.000	0.000	0.000	0.000
74	A	77	PHE	0	-0.053	-0.019	43.119	0.000	0.000	0.000	0.000	0.000	0.000
75	A	78	VAL	0	0.015	-0.002	42.834	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	79	ASP	-1	-0.843	-0.916	45.648	-0.030	-0.030	0.000	0.000	0.000	0.000
77	A	80	ARG	1	0.903	0.952	47.998	0.030	0.030	0.000	0.000	0.000	0.000
78	A	81	ALA	0	0.042	0.001	47.305	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	82	PRO	0	-0.057	-0.002	46.829	0.001	0.001	0.000	0.000	0.000	0.000
80	A	83	HIS	0	0.116	0.061	47.995	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	84	PRO	0	-0.011	-0.011	45.154	0.000	0.000	0.000	0.000	0.000	0.000
82	A	85	ILE	0	-0.085	-0.045	46.815	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	86	ASP	-1	-0.876	-0.954	49.495	-0.026	-0.026	0.000	0.000	0.000	0.000
84	A	87	GLY	0	0.001	-0.005	50.722	0.001	0.001	0.000	0.000	0.000	0.000
85	A	88	ARG	1	0.943	0.977	46.098	0.033	0.033	0.000	0.000	0.000	0.000
86	A	89	GLN	0	-0.031	-0.020	46.478	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	90	VAL	0	-0.024	-0.005	48.425	0.001	0.001	0.000	0.000	0.000	0.000
88	A	91	LEU	0	-0.026	-0.018	43.934	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	92	VAL	0	-0.039	-0.025	43.362	0.002	0.002	0.000	0.000	0.000	0.000
90	A	93	SER	0	0.042	0.005	43.303	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	94	VAL	0	-0.012	0.014	40.250	0.001	0.001	0.000	0.000	0.000	0.000
92	A	95	SER	0	-0.008	-0.029	43.499	0.001	0.001	0.000	0.000	0.000	0.000
93	A	96	GLU	-1	-0.891	-0.969	44.856	-0.029	-0.029	0.000	0.000	0.000	0.000
94	A	97	SER	0	0.010	0.012	45.196	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	98	GLY	0	0.037	0.013	42.771	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	99	ALA	0	0.027	0.007	40.500	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	100	GLU	-1	-0.875	-0.936	40.116	-0.030	-0.030	0.000	0.000	0.000	0.000
98	A	101	LEU	0	-0.007	0.008	39.244	0.000	0.000	0.000	0.000	0.000	0.000
99	A	102	VAL	0	0.010	0.007	35.128	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	103	LYS	1	0.918	0.956	35.766	0.030	0.030	0.000	0.000	0.000	0.000
101	A	104	ALA	0	-0.006	0.000	36.635	0.000	0.000	0.000	0.000	0.000	0.000
102	A	105	ALA	0	-0.004	-0.012	34.147	0.000	0.000	0.000	0.000	0.000	0.000
103	A	106	ARG	1	0.906	0.960	31.505	0.044	0.044	0.000	0.000	0.000	0.000
104	A	107	ARG	1	0.898	0.940	32.124	0.028	0.028	0.000	0.000	0.000	0.000
105	A	108	ALA	0	0.087	0.056	33.608	0.001	0.001	0.000	0.000	0.000	0.000
106	A	109	ARG	1	0.866	0.928	28.316	0.061	0.061	0.000	0.000	0.000	0.000
107	A	110	GLN	0	-0.031	-0.022	28.732	0.003	0.003	0.000	0.000	0.000	0.000
108	A	111	GLU	-1	-0.903	-0.947	29.793	-0.023	-0.023	0.000	0.000	0.000	0.000
109	A	112	TRP	0	0.062	0.026	25.218	0.001	0.001	0.000	0.000	0.000	0.000
110	A	113	LEU	0	-0.012	-0.016	23.206	0.003	0.003	0.000	0.000	0.000	0.000
111	A	114	ALA	0	0.000	-0.003	26.699	0.004	0.004	0.000	0.000	0.000	0.000
112	A	115	GLU	-1	-0.931	-0.961	28.904	-0.009	-0.009	0.000	0.000	0.000	0.000
113	A	116	ARG	1	0.900	0.953	25.024	0.009	0.009	0.000	0.000	0.000	0.000
114	A	117	LEU	0	0.014	0.022	22.387	0.007	0.007	0.000	0.000	0.000	0.000
115	A	118	ALA	0	-0.025	0.001	25.230	0.006	0.006	0.000	0.000	0.000	0.000
116	A	119	THR	0	-0.115	-0.068	25.432	0.006	0.006	0.000	0.000	0.000	0.000
117	A	120	LEU	0	0.021	0.032	20.385	0.005	0.005	0.000	0.000	0.000	0.000
118	A	121	ASN	0	0.017	0.012	21.162	-0.009	-0.009	0.000	0.000	0.000	0.000
119	A	122	ARG	1	0.959	0.942	23.198	-0.020	-0.020	0.000	0.000	0.000	0.000
120	A	123	SER	0	0.067	0.044	19.895	-0.006	-0.006	0.000	0.000	0.000	0.000
121	A	124	GLU	-1	-0.841	-0.920	18.269	0.061	0.061	0.000	0.000	0.000	0.000
122	A	125	ARG	1	0.856	0.904	18.936	-0.023	-0.023	0.000	0.000	0.000	0.000
123	A	126	ASP	-1	-0.905	-0.946	20.340	-0.013	-0.013	0.000	0.000	0.000	0.000
124	A	127	ILE	0	-0.002	-0.002	14.335	-0.017	-0.017	0.000	0.000	0.000	0.000
125	A	128	LEU	0	-0.023	-0.022	16.622	-0.032	-0.032	0.000	0.000	0.000	0.000
126	A	129	ARG	1	0.908	0.966	18.379	0.015	0.015	0.000	0.000	0.000	0.000
127	A	130	SER	0	0.030	0.013	16.883	-0.005	-0.005	0.000	0.000	0.000	0.000
128	A	131	ALA	0	-0.011	-0.009	15.011	-0.022	-0.022	0.000	0.000	0.000	0.000
129	A	132	ALA	0	-0.039	-0.016	16.263	-0.025	-0.025	0.000	0.000	0.000	0.000
130	A	133	ASP	-1	-0.882	-0.933	19.543	-0.103	-0.103	0.000	0.000	0.000	0.000
131	A	134	LEU	0	-0.021	-0.016	13.524	-0.012	-0.012	0.000	0.000	0.000	0.000
132	A	135	MET	0	-0.061	-0.040	15.366	-0.026	-0.026	0.000	0.000	0.000	0.000
133	A	136	LEU	0	0.027	0.016	17.231	-0.002	-0.002	0.000	0.000	0.000	0.000
134	A	137	ALA	0	0.027	0.020	18.255	0.005	0.005	0.000	0.000	0.000	0.000
135	A	138	LEU	0	-0.103	-0.044	13.420	-0.011	-0.011	0.000	0.000	0.000	0.000
136	A	139	VAL	0	-0.092	-0.040	17.580	-0.004	-0.004	0.000	0.000	0.000	0.000
137	A	140	ASP	-1	-0.973	-0.982	20.815	-0.098	-0.098	0.000	0.000	0.000	0.000
138	A	141	GLU	-1	-0.980	-0.978	22.805	-0.103	-0.103	0.000	0.000	0.000	0.000
139	A	142	SER	0	-0.038	-0.025	22.480	0.001	0.001	0.000	0.000	0.000	0.000
140	A	143	PRO	0	-0.014	-0.001	24.934	0.006	0.006	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:SER)