FMO DATABASE

FMODB ID: 1N1NZ

Calculation Name: 4YME-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YME

Chain ID: A

ChEMBL ID:

UniProt ID: Q9ABX9

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	156
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1348462.500212
FMO2-HF: Nuclear repulsion	1290546.856122
FMO2-HF: Total energy	-57915.64409
FMO2-MP2: Total energy	-58082.742937

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:372:ALA)

Summations of interaction energy for fragment #1(A:372: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.
-2.994	1.254	-0.012	-2.164	-2.072	-0.001

Interaction energy analysis for fragmet #1(A:372:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : -0.010

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	374	HIS	0	-0.016	0.000	3.110	-3.386	-0.033	-0.016	-1.803	-1.534	-0.002
4	A	375	ASP	-1	-0.769	-0.832	4.019	-1.397	-1.175	0.000	-0.066	-0.156	0.000
5	A	376	GLY	0	-0.026	-0.011	6.221	0.263	0.263	0.000	0.000	0.000	0.000
6	A	377	LEU	0	-0.054	-0.015	6.975	0.124	0.124	0.000	0.000	0.000	0.000
7	A	378	THR	0	0.015	-0.040	10.072	0.064	0.064	0.000	0.000	0.000	0.000
8	A	379	GLY	0	0.007	0.012	8.456	0.050	0.050	0.000	0.000	0.000	0.000
9	A	380	LEU	0	-0.039	0.007	9.452	0.112	0.112	0.000	0.000	0.000	0.000
10	A	381	LEU	0	0.001	0.008	8.085	0.036	0.036	0.000	0.000	0.000	0.000
11	A	382	ASN	0	-0.010	-0.015	3.620	0.160	0.702	0.005	-0.280	-0.267	0.001
12	A	383	ARG	1	1.023	1.002	7.989	0.458	0.458	0.000	0.000	0.000	0.000
13	A	384	ASN	0	-0.025	-0.011	4.313	0.552	0.683	-0.001	-0.015	-0.115	0.000
14	A	385	SER	0	0.004	-0.022	6.442	0.171	0.171	0.000	0.000	0.000	0.000
15	A	386	LEU	0	0.016	0.009	8.136	0.196	0.196	0.000	0.000	0.000	0.000
16	A	387	GLN	0	-0.025	-0.015	11.283	0.050	0.050	0.000	0.000	0.000	0.000
17	A	388	MET	0	0.006	0.003	6.193	0.102	0.102	0.000	0.000	0.000	0.000
18	A	389	ARG	1	0.893	0.952	10.925	0.035	0.035	0.000	0.000	0.000	0.000
19	A	390	LEU	0	-0.014	0.005	13.311	0.042	0.042	0.000	0.000	0.000	0.000
20	A	391	ALA	0	0.019	0.003	15.072	0.026	0.026	0.000	0.000	0.000	0.000
21	A	392	ALA	0	0.007	0.007	15.191	0.022	0.022	0.000	0.000	0.000	0.000
22	A	393	ALA	0	-0.026	-0.017	17.021	0.022	0.022	0.000	0.000	0.000	0.000
23	A	394	ILE	0	0.018	0.007	19.270	0.011	0.011	0.000	0.000	0.000	0.000
24	A	395	ASP	-1	-0.909	-0.944	19.756	-0.064	-0.064	0.000	0.000	0.000	0.000
25	A	396	ARG	1	0.724	0.820	20.936	-0.007	-0.007	0.000	0.000	0.000	0.000
26	A	397	VAL	0	-0.019	-0.008	22.896	0.007	0.007	0.000	0.000	0.000	0.000
27	A	398	GLU	-1	-0.792	-0.849	25.042	-0.040	-0.040	0.000	0.000	0.000	0.000
28	A	399	ALA	0	-0.076	-0.032	26.271	0.004	0.004	0.000	0.000	0.000	0.000
29	A	400	SER	0	-0.092	-0.082	26.377	0.002	0.002	0.000	0.000	0.000	0.000
30	A	401	GLY	0	-0.011	-0.002	28.699	0.003	0.003	0.000	0.000	0.000	0.000
31	A	402	GLU	-1	-0.862	-0.870	25.533	0.011	0.011	0.000	0.000	0.000	0.000
32	A	403	SER	0	-0.003	0.001	27.992	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	404	LEU	0	-0.002	-0.007	20.775	0.003	0.003	0.000	0.000	0.000	0.000
34	A	405	ALA	0	0.004	0.009	23.820	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	406	VAL	0	-0.027	-0.020	19.423	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	407	ILE	0	0.014	0.007	21.202	0.003	0.003	0.000	0.000	0.000	0.000
37	A	408	CYS	0	-0.017	0.005	20.477	-0.013	-0.013	0.000	0.000	0.000	0.000
38	A	409	ILE	0	0.017	-0.005	20.368	0.015	0.015	0.000	0.000	0.000	0.000
39	A	410	ASP	-1	-0.769	-0.859	20.472	-0.102	-0.102	0.000	0.000	0.000	0.000
40	A	411	LEU	0	-0.016	-0.019	20.502	0.012	0.012	0.000	0.000	0.000	0.000
41	A	412	ASP	-1	-0.868	-0.931	23.879	-0.050	-0.050	0.000	0.000	0.000	0.000
42	A	413	HIS	0	-0.072	-0.048	26.633	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	414	PHE	0	0.032	0.023	19.023	0.001	0.001	0.000	0.000	0.000	0.000
44	A	415	LYS	1	0.812	0.881	24.275	0.065	0.065	0.000	0.000	0.000	0.000
45	A	416	GLU	-1	-0.869	-0.939	25.990	-0.031	-0.031	0.000	0.000	0.000	0.000
46	A	417	ALA	0	0.090	0.041	24.950	0.003	0.003	0.000	0.000	0.000	0.000
47	A	418	ASN	0	-0.068	-0.048	21.678	0.003	0.003	0.000	0.000	0.000	0.000
48	A	419	ASP	-1	-0.898	-0.915	25.342	-0.058	-0.058	0.000	0.000	0.000	0.000
49	A	420	GLN	0	-0.085	-0.034	28.822	0.001	0.001	0.000	0.000	0.000	0.000
50	A	421	HIS	0	-0.056	-0.029	27.581	0.003	0.003	0.000	0.000	0.000	0.000
51	A	422	GLY	0	0.018	0.025	26.017	0.003	0.003	0.000	0.000	0.000	0.000
52	A	423	HIS	0	0.013	-0.014	19.096	0.003	0.003	0.000	0.000	0.000	0.000
53	A	424	LEU	0	-0.023	-0.010	19.715	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	425	ALA	0	0.022	0.024	21.468	0.007	0.007	0.000	0.000	0.000	0.000
55	A	426	GLY	0	0.057	0.023	21.394	0.004	0.004	0.000	0.000	0.000	0.000
56	A	427	ASP	-1	-0.892	-0.970	16.888	-0.086	-0.086	0.000	0.000	0.000	0.000
57	A	428	ALA	0	-0.026	-0.008	17.912	0.010	0.010	0.000	0.000	0.000	0.000
58	A	429	LEU	0	0.037	0.022	20.372	0.009	0.009	0.000	0.000	0.000	0.000
59	A	430	LEU	0	-0.059	-0.003	15.360	0.002	0.002	0.000	0.000	0.000	0.000
60	A	431	VAL	0	-0.004	-0.010	14.942	0.010	0.010	0.000	0.000	0.000	0.000
61	A	432	GLU	-1	-0.743	-0.819	16.830	0.059	0.059	0.000	0.000	0.000	0.000
62	A	433	THR	0	0.012	-0.009	18.409	0.007	0.007	0.000	0.000	0.000	0.000
63	A	434	ALA	0	-0.005	-0.003	14.379	0.004	0.004	0.000	0.000	0.000	0.000
64	A	435	ARG	1	0.839	0.899	16.397	-0.040	-0.040	0.000	0.000	0.000	0.000
65	A	436	ARG	1	0.728	0.842	18.376	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	437	LEU	0	0.041	0.030	17.067	0.004	0.004	0.000	0.000	0.000	0.000
67	A	438	GLN	0	-0.022	-0.019	13.045	-0.010	-0.010	0.000	0.000	0.000	0.000
68	A	439	SER	0	-0.127	-0.069	17.767	0.008	0.008	0.000	0.000	0.000	0.000
69	A	440	ALA	0	0.019	0.003	21.241	0.001	0.001	0.000	0.000	0.000	0.000
70	A	441	VAL	0	-0.063	-0.011	18.292	-0.010	-0.010	0.000	0.000	0.000	0.000
71	A	442	GLN	0	-0.049	-0.018	18.876	0.033	0.033	0.000	0.000	0.000	0.000
72	A	443	ALA	0	0.011	0.021	17.702	-0.014	-0.014	0.000	0.000	0.000	0.000
73	A	444	PRO	0	-0.057	-0.043	19.114	0.002	0.002	0.000	0.000	0.000	0.000
74	A	445	SER	0	0.048	0.026	18.735	-0.018	-0.018	0.000	0.000	0.000	0.000
75	A	446	PHE	0	-0.043	-0.041	14.211	0.031	0.031	0.000	0.000	0.000	0.000
76	A	447	ALA	0	0.052	0.028	14.606	-0.025	-0.025	0.000	0.000	0.000	0.000
77	A	448	ALA	0	-0.015	-0.008	11.668	0.020	0.020	0.000	0.000	0.000	0.000
78	A	449	ARG	1	0.843	0.899	10.548	0.275	0.275	0.000	0.000	0.000	0.000
79	A	450	LEU	0	-0.060	-0.039	11.010	-0.117	-0.117	0.000	0.000	0.000	0.000
80	A	451	GLY	0	-0.038	-0.028	11.851	-0.089	-0.089	0.000	0.000	0.000	0.000
81	A	452	GLY	0	0.003	0.011	13.866	0.030	0.030	0.000	0.000	0.000	0.000
82	A	453	ASP	-1	-0.815	-0.933	16.055	-0.114	-0.114	0.000	0.000	0.000	0.000
83	A	454	GLU	-1	-0.869	-0.912	16.836	-0.201	-0.201	0.000	0.000	0.000	0.000
84	A	455	PHE	0	-0.026	-0.035	14.974	-0.037	-0.037	0.000	0.000	0.000	0.000
85	A	456	ILE	0	0.001	-0.006	15.728	0.000	0.000	0.000	0.000	0.000	0.000
86	A	457	VAL	0	-0.017	-0.011	16.381	0.009	0.009	0.000	0.000	0.000	0.000
87	A	458	VAL	0	-0.015	-0.006	16.874	-0.009	-0.009	0.000	0.000	0.000	0.000
88	A	459	GLN	0	-0.005	-0.020	19.307	0.014	0.014	0.000	0.000	0.000	0.000
89	A	460	ILE	0	-0.012	-0.004	19.680	-0.007	-0.007	0.000	0.000	0.000	0.000
90	A	461	ALA	0	-0.022	-0.010	23.592	0.011	0.011	0.000	0.000	0.000	0.000
91	A	462	GLY	0	0.055	0.029	27.140	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	463	GLY	0	-0.031	-0.024	30.710	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	464	ASP	-1	-0.845	-0.926	33.638	-0.018	-0.018	0.000	0.000	0.000	0.000
94	A	465	GLN	0	0.062	0.020	28.682	0.001	0.001	0.000	0.000	0.000	0.000
95	A	466	PRO	0	0.029	0.008	30.809	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	467	ALA	0	-0.002	0.006	32.527	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	468	VAL	0	-0.036	-0.016	28.945	0.001	0.001	0.000	0.000	0.000	0.000
98	A	469	ALA	0	0.054	0.039	27.840	0.002	0.002	0.000	0.000	0.000	0.000
99	A	470	ALA	0	-0.020	-0.009	28.749	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	471	GLU	-1	-0.842	-0.886	30.424	0.006	0.006	0.000	0.000	0.000	0.000
101	A	472	LEU	0	-0.003	0.003	23.394	0.004	0.004	0.000	0.000	0.000	0.000
102	A	473	ALA	0	0.016	0.000	26.799	0.001	0.001	0.000	0.000	0.000	0.000
103	A	474	GLY	0	0.013	0.009	27.840	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	475	ARG	1	0.803	0.856	26.475	-0.010	-0.010	0.000	0.000	0.000	0.000
105	A	476	LEU	0	-0.021	-0.018	22.329	0.003	0.003	0.000	0.000	0.000	0.000
106	A	477	ILE	0	0.025	0.011	25.850	0.000	0.000	0.000	0.000	0.000	0.000
107	A	478	GLU	-1	-0.949	-0.961	28.141	0.000	0.000	0.000	0.000	0.000	0.000
108	A	479	MET	0	-0.068	-0.033	24.304	0.005	0.005	0.000	0.000	0.000	0.000
109	A	480	LEU	0	-0.029	-0.020	21.807	0.005	0.005	0.000	0.000	0.000	0.000
110	A	481	ALA	0	0.050	0.040	25.775	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	482	ALA	0	-0.057	-0.015	28.674	0.000	0.000	0.000	0.000	0.000	0.000
112	A	483	PRO	0	0.064	0.029	27.769	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	484	VAL	0	0.003	-0.005	23.323	0.006	0.006	0.000	0.000	0.000	0.000
114	A	485	PRO	0	-0.012	0.007	26.484	-0.003	-0.003	0.000	0.000	0.000	0.000
115	A	486	PHE	0	0.011	-0.018	23.277	0.002	0.002	0.000	0.000	0.000	0.000
116	A	487	ASP	-1	-0.916	-0.946	27.109	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	488	GLY	0	-0.042	-0.018	29.016	-0.002	-0.002	0.000	0.000	0.000	0.000
118	A	489	GLN	0	-0.054	-0.033	30.774	-0.004	-0.004	0.000	0.000	0.000	0.000
119	A	490	GLU	-1	-0.951	-0.979	29.971	0.009	0.009	0.000	0.000	0.000	0.000
120	A	491	LEU	0	-0.006	0.008	25.191	-0.003	-0.003	0.000	0.000	0.000	0.000
121	A	492	ALA	0	0.029	0.008	28.435	0.004	0.004	0.000	0.000	0.000	0.000
122	A	493	MET	0	-0.017	-0.001	22.541	-0.006	-0.006	0.000	0.000	0.000	0.000
123	A	494	GLY	0	-0.015	0.014	27.121	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	495	SER	0	-0.016	-0.008	24.685	-0.003	-0.003	0.000	0.000	0.000	0.000
125	A	496	SER	0	-0.002	0.011	25.789	0.006	0.006	0.000	0.000	0.000	0.000
126	A	497	LEU	0	-0.026	-0.035	24.975	-0.006	-0.006	0.000	0.000	0.000	0.000
127	A	498	GLY	0	0.013	0.021	25.111	0.005	0.005	0.000	0.000	0.000	0.000
128	A	499	VAL	0	-0.058	-0.039	24.925	-0.006	-0.006	0.000	0.000	0.000	0.000
129	A	500	SER	0	0.028	0.023	24.403	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	501	LEU	0	-0.056	-0.040	25.452	0.001	0.001	0.000	0.000	0.000	0.000
131	A	502	TYR	0	-0.022	-0.008	24.447	-0.007	-0.007	0.000	0.000	0.000	0.000
132	A	503	PRO	0	-0.021	-0.017	26.802	0.006	0.006	0.000	0.000	0.000	0.000
133	A	504	ASP	-1	-0.922	-0.979	28.497	-0.046	-0.046	0.000	0.000	0.000	0.000
134	A	505	ASP	-1	-0.818	-0.891	27.422	-0.064	-0.064	0.000	0.000	0.000	0.000
135	A	506	GLY	0	-0.039	-0.036	25.447	-0.010	-0.010	0.000	0.000	0.000	0.000
136	A	507	ARG	1	0.827	0.892	25.343	0.057	0.057	0.000	0.000	0.000	0.000
137	A	508	THR	0	-0.014	-0.017	20.718	0.005	0.005	0.000	0.000	0.000	0.000
138	A	509	ALA	0	0.086	0.036	16.667	0.005	0.005	0.000	0.000	0.000	0.000
139	A	510	GLU	-1	-0.843	-0.916	16.824	-0.211	-0.211	0.000	0.000	0.000	0.000
140	A	511	ALA	0	-0.042	-0.013	19.384	0.005	0.005	0.000	0.000	0.000	0.000
141	A	512	LEU	0	0.029	0.010	21.148	0.005	0.005	0.000	0.000	0.000	0.000
142	A	513	MET	0	-0.025	-0.010	15.937	0.003	0.003	0.000	0.000	0.000	0.000
143	A	514	ALA	0	-0.013	0.002	19.933	0.004	0.004	0.000	0.000	0.000	0.000
144	A	515	ASN	0	-0.045	-0.014	22.381	0.010	0.010	0.000	0.000	0.000	0.000
145	A	516	ALA	0	0.068	0.032	21.887	0.008	0.008	0.000	0.000	0.000	0.000
146	A	517	ASP	-1	-0.916	-0.960	21.393	-0.132	-0.132	0.000	0.000	0.000	0.000
147	A	518	MET	0	-0.039	-0.018	23.357	0.010	0.010	0.000	0.000	0.000	0.000
148	A	519	ALA	0	-0.022	-0.015	26.701	0.008	0.008	0.000	0.000	0.000	0.000
149	A	520	LEU	0	0.000	0.008	22.970	0.009	0.009	0.000	0.000	0.000	0.000
150	A	521	TYR	0	-0.079	-0.062	26.646	0.007	0.007	0.000	0.000	0.000	0.000
151	A	522	ARG	1	0.891	0.935	28.565	0.067	0.067	0.000	0.000	0.000	0.000
152	A	523	ALA	0	0.033	0.026	29.275	0.005	0.005	0.000	0.000	0.000	0.000
153	A	524	LYS	1	0.800	0.886	25.761	0.082	0.082	0.000	0.000	0.000	0.000
154	A	525	GLU	-1	-0.954	-0.948	31.037	-0.054	-0.054	0.000	0.000	0.000	0.000
155	A	526	SER	0	-0.060	-0.037	34.174	0.003	0.003	0.000	0.000	0.000	0.000
156	A	527	GLY	0	-0.051	-0.007	33.980	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:372:ALA)