FMO DATABASE

FMODB ID: VQ3Q1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1348138.254239
FMO2-HF: Nuclear repulsion	1290223.226932
FMO2-HF: Total energy	-57915.027307
FMO2-MP2: Total energy	-58082.151352

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.
-2.895	1.362	-0.014	-2.184	-2.058	0

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 : 0.018 / 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	374	HIS	0	0.011	0.024	3.198	-3.573	-0.179	-0.019	-1.846	-1.528	-0.001
4	A	375	ASP	-1	-0.782	-0.848	4.074	-1.126	-0.926	-0.001	-0.052	-0.147	0.000
5	A	376	GLY	0	-0.027	-0.015	6.185	0.240	0.240	0.000	0.000	0.000	0.000
6	A	377	LEU	0	-0.044	-0.014	6.996	0.096	0.096	0.000	0.000	0.000	0.000
7	A	378	THR	0	0.010	-0.035	10.132	0.055	0.055	0.000	0.000	0.000	0.000
8	A	379	GLY	0	0.002	0.006	8.525	0.034	0.034	0.000	0.000	0.000	0.000
9	A	380	LEU	0	-0.038	0.001	9.520	0.091	0.091	0.000	0.000	0.000	0.000
10	A	381	LEU	0	-0.022	-0.004	8.150	0.090	0.090	0.000	0.000	0.000	0.000
11	A	382	ASN	0	0.016	-0.002	3.552	0.131	0.634	0.007	-0.257	-0.252	0.001
12	A	383	ARG	1	1.038	1.008	8.026	0.410	0.410	0.000	0.000	0.000	0.000
13	A	384	ASN	0	-0.029	-0.017	4.059	0.589	0.749	-0.001	-0.029	-0.131	0.000
14	A	385	SER	0	0.008	-0.024	6.507	0.161	0.161	0.000	0.000	0.000	0.000
15	A	386	LEU	0	0.016	0.010	8.054	0.180	0.180	0.000	0.000	0.000	0.000
16	A	387	GLN	0	-0.037	-0.024	11.203	0.034	0.034	0.000	0.000	0.000	0.000
17	A	388	MET	0	-0.005	0.000	6.252	0.091	0.091	0.000	0.000	0.000	0.000
18	A	389	ARG	1	0.912	0.953	10.885	0.029	0.029	0.000	0.000	0.000	0.000
19	A	390	LEU	0	-0.008	0.009	13.234	0.040	0.040	0.000	0.000	0.000	0.000
20	A	391	ALA	0	0.018	0.001	15.054	0.024	0.024	0.000	0.000	0.000	0.000
21	A	392	ALA	0	0.004	0.005	15.174	0.022	0.022	0.000	0.000	0.000	0.000
22	A	393	ALA	0	-0.026	-0.015	16.948	0.022	0.022	0.000	0.000	0.000	0.000
23	A	394	ILE	0	0.013	0.006	19.194	0.011	0.011	0.000	0.000	0.000	0.000
24	A	395	ASP	-1	-0.897	-0.938	20.062	-0.068	-0.068	0.000	0.000	0.000	0.000
25	A	396	ARG	1	0.722	0.827	20.636	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	397	VAL	0	-0.027	-0.014	22.827	0.006	0.006	0.000	0.000	0.000	0.000
27	A	398	GLU	-1	-0.888	-0.897	24.966	-0.036	-0.036	0.000	0.000	0.000	0.000
28	A	399	ALA	0	-0.055	-0.023	26.199	0.004	0.004	0.000	0.000	0.000	0.000
29	A	400	SER	0	-0.102	-0.077	26.349	0.002	0.002	0.000	0.000	0.000	0.000
30	A	401	GLY	0	-0.001	0.001	28.631	0.003	0.003	0.000	0.000	0.000	0.000
31	A	402	GLU	-1	-0.867	-0.886	25.416	0.010	0.010	0.000	0.000	0.000	0.000
32	A	403	SER	0	-0.010	0.003	27.916	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	404	LEU	0	0.013	0.002	20.777	0.003	0.003	0.000	0.000	0.000	0.000
34	A	405	ALA	0	0.018	0.017	23.832	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	406	VAL	0	-0.036	-0.026	19.533	0.000	0.000	0.000	0.000	0.000	0.000
36	A	407	ILE	0	0.013	0.005	21.213	0.002	0.002	0.000	0.000	0.000	0.000
37	A	408	CYS	0	-0.022	0.006	20.494	-0.008	-0.008	0.000	0.000	0.000	0.000
38	A	409	ILE	0	0.016	-0.004	20.140	0.013	0.013	0.000	0.000	0.000	0.000
39	A	410	ASP	-1	-0.778	-0.879	20.522	-0.080	-0.080	0.000	0.000	0.000	0.000
40	A	411	LEU	0	-0.035	-0.026	20.567	0.011	0.011	0.000	0.000	0.000	0.000
41	A	412	ASP	-1	-0.850	-0.917	23.921	-0.036	-0.036	0.000	0.000	0.000	0.000
42	A	413	HIS	0	-0.078	-0.051	26.696	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	414	PHE	0	0.013	0.013	18.984	0.001	0.001	0.000	0.000	0.000	0.000
44	A	415	LYS	1	0.825	0.892	24.300	0.049	0.049	0.000	0.000	0.000	0.000
45	A	416	GLU	-1	-0.872	-0.941	26.003	-0.018	-0.018	0.000	0.000	0.000	0.000
46	A	417	ALA	0	0.081	0.040	24.915	0.002	0.002	0.000	0.000	0.000	0.000
47	A	418	ASN	0	-0.032	-0.028	21.488	0.006	0.006	0.000	0.000	0.000	0.000
48	A	419	ASP	-1	-0.888	-0.921	25.348	-0.042	-0.042	0.000	0.000	0.000	0.000
49	A	420	GLN	0	-0.098	-0.041	28.824	0.000	0.000	0.000	0.000	0.000	0.000
50	A	421	HIS	0	-0.054	-0.028	27.493	0.002	0.002	0.000	0.000	0.000	0.000
51	A	422	GLY	0	0.021	0.023	26.014	0.003	0.003	0.000	0.000	0.000	0.000
52	A	423	HIS	0	0.015	-0.011	19.102	0.001	0.001	0.000	0.000	0.000	0.000
53	A	424	LEU	0	-0.018	-0.012	19.624	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	425	ALA	0	0.025	0.030	21.482	0.008	0.008	0.000	0.000	0.000	0.000
55	A	426	GLY	0	0.064	0.024	21.394	0.004	0.004	0.000	0.000	0.000	0.000
56	A	427	ASP	-1	-0.912	-0.977	17.215	-0.047	-0.047	0.000	0.000	0.000	0.000
57	A	428	ALA	0	-0.030	-0.005	17.941	0.012	0.012	0.000	0.000	0.000	0.000
58	A	429	LEU	0	0.027	0.016	20.411	0.009	0.009	0.000	0.000	0.000	0.000
59	A	430	LEU	0	-0.056	-0.008	15.463	0.003	0.003	0.000	0.000	0.000	0.000
60	A	431	VAL	0	-0.003	-0.004	15.003	0.013	0.013	0.000	0.000	0.000	0.000
61	A	432	GLU	-1	-0.748	-0.832	16.876	0.080	0.080	0.000	0.000	0.000	0.000
62	A	433	THR	0	0.018	-0.005	18.472	0.005	0.005	0.000	0.000	0.000	0.000
63	A	434	ALA	0	0.001	-0.002	14.472	0.004	0.004	0.000	0.000	0.000	0.000
64	A	435	ARG	1	0.831	0.903	16.462	-0.059	-0.059	0.000	0.000	0.000	0.000
65	A	436	ARG	1	0.734	0.847	18.444	-0.023	-0.023	0.000	0.000	0.000	0.000
66	A	437	LEU	0	0.047	0.035	17.101	0.002	0.002	0.000	0.000	0.000	0.000
67	A	438	GLN	0	-0.030	-0.024	13.528	-0.013	-0.013	0.000	0.000	0.000	0.000
68	A	439	SER	0	-0.139	-0.071	17.849	0.004	0.004	0.000	0.000	0.000	0.000
69	A	440	ALA	0	0.026	0.004	21.339	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	441	VAL	0	-0.072	-0.014	18.336	-0.012	-0.012	0.000	0.000	0.000	0.000
71	A	442	GLN	0	-0.031	-0.008	18.964	0.032	0.032	0.000	0.000	0.000	0.000
72	A	443	ALA	0	0.009	0.021	17.645	-0.015	-0.015	0.000	0.000	0.000	0.000
73	A	444	PRO	0	-0.061	-0.045	19.075	0.001	0.001	0.000	0.000	0.000	0.000
74	A	445	SER	0	0.045	0.026	18.680	-0.018	-0.018	0.000	0.000	0.000	0.000
75	A	446	PHE	0	-0.066	-0.047	14.097	0.030	0.030	0.000	0.000	0.000	0.000
76	A	447	ALA	0	0.067	0.030	14.696	-0.026	-0.026	0.000	0.000	0.000	0.000
77	A	448	ALA	0	-0.021	-0.008	11.669	0.029	0.029	0.000	0.000	0.000	0.000
78	A	449	ARG	1	0.837	0.906	10.639	0.195	0.195	0.000	0.000	0.000	0.000
79	A	450	LEU	0	-0.056	-0.042	11.054	-0.100	-0.100	0.000	0.000	0.000	0.000
80	A	451	GLY	0	-0.041	-0.027	11.849	-0.079	-0.079	0.000	0.000	0.000	0.000
81	A	452	GLY	0	-0.011	0.003	13.883	0.025	0.025	0.000	0.000	0.000	0.000
82	A	453	ASP	-1	-0.814	-0.927	16.081	-0.083	-0.083	0.000	0.000	0.000	0.000
83	A	454	GLU	-1	-0.873	-0.914	17.091	-0.143	-0.143	0.000	0.000	0.000	0.000
84	A	455	PHE	0	-0.037	-0.038	15.034	-0.028	-0.028	0.000	0.000	0.000	0.000
85	A	456	ILE	0	-0.007	-0.005	15.728	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	457	VAL	0	-0.018	-0.011	16.452	0.013	0.013	0.000	0.000	0.000	0.000
87	A	458	VAL	0	-0.019	-0.008	16.941	-0.012	-0.012	0.000	0.000	0.000	0.000
88	A	459	GLN	0	-0.003	-0.017	19.307	0.014	0.014	0.000	0.000	0.000	0.000
89	A	460	ILE	0	-0.010	-0.006	19.758	-0.007	-0.007	0.000	0.000	0.000	0.000
90	A	461	ALA	0	-0.021	-0.012	23.549	0.011	0.011	0.000	0.000	0.000	0.000
91	A	462	GLY	0	0.044	0.023	27.083	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	463	GLY	0	-0.033	-0.029	30.651	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	464	ASP	-1	-0.863	-0.936	33.638	-0.013	-0.013	0.000	0.000	0.000	0.000
94	A	465	GLN	0	0.072	0.026	28.637	0.000	0.000	0.000	0.000	0.000	0.000
95	A	466	PRO	0	0.024	0.010	30.809	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	467	ALA	0	0.009	0.013	32.527	0.000	0.000	0.000	0.000	0.000	0.000
97	A	468	VAL	0	-0.037	-0.012	29.113	0.002	0.002	0.000	0.000	0.000	0.000
98	A	469	ALA	0	0.052	0.033	27.840	0.003	0.003	0.000	0.000	0.000	0.000
99	A	470	ALA	0	-0.018	-0.004	28.785	0.000	0.000	0.000	0.000	0.000	0.000
100	A	471	GLU	-1	-0.852	-0.905	30.554	0.015	0.015	0.000	0.000	0.000	0.000
101	A	472	LEU	0	-0.013	-0.003	23.503	0.004	0.004	0.000	0.000	0.000	0.000
102	A	473	ALA	0	0.019	0.004	26.873	0.002	0.002	0.000	0.000	0.000	0.000
103	A	474	GLY	0	0.009	0.006	27.913	0.000	0.000	0.000	0.000	0.000	0.000
104	A	475	ARG	1	0.819	0.876	26.452	-0.019	-0.019	0.000	0.000	0.000	0.000
105	A	476	LEU	0	-0.010	-0.010	22.642	0.004	0.004	0.000	0.000	0.000	0.000
106	A	477	ILE	0	0.021	0.010	25.923	0.001	0.001	0.000	0.000	0.000	0.000
107	A	478	GLU	-1	-0.946	-0.959	28.208	0.010	0.010	0.000	0.000	0.000	0.000
108	A	479	MET	0	-0.069	-0.037	24.440	0.005	0.005	0.000	0.000	0.000	0.000
109	A	480	LEU	0	-0.047	-0.030	21.914	0.005	0.005	0.000	0.000	0.000	0.000
110	A	481	ALA	0	0.068	0.049	25.839	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	482	ALA	0	-0.049	-0.013	28.700	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	483	PRO	0	0.074	0.027	27.824	0.000	0.000	0.000	0.000	0.000	0.000
113	A	484	VAL	0	-0.008	-0.005	23.437	0.006	0.006	0.000	0.000	0.000	0.000
114	A	485	PRO	0	-0.009	0.007	26.402	-0.004	-0.004	0.000	0.000	0.000	0.000
115	A	486	PHE	0	0.000	-0.022	23.369	0.004	0.004	0.000	0.000	0.000	0.000
116	A	487	ASP	-1	-0.934	-0.952	27.136	0.010	0.010	0.000	0.000	0.000	0.000
117	A	488	GLY	0	-0.047	-0.025	29.035	-0.002	-0.002	0.000	0.000	0.000	0.000
118	A	489	GLN	0	-0.022	-0.016	30.808	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	490	GLU	-1	-0.971	-0.985	30.007	0.020	0.020	0.000	0.000	0.000	0.000
120	A	491	LEU	0	-0.008	0.006	25.116	-0.004	-0.004	0.000	0.000	0.000	0.000
121	A	492	ALA	0	0.025	0.004	28.475	0.004	0.004	0.000	0.000	0.000	0.000
122	A	493	MET	0	-0.025	-0.004	22.761	-0.004	-0.004	0.000	0.000	0.000	0.000
123	A	494	GLY	0	-0.013	0.008	27.175	-0.003	-0.003	0.000	0.000	0.000	0.000
124	A	495	SER	0	-0.016	-0.010	24.790	-0.003	-0.003	0.000	0.000	0.000	0.000
125	A	496	SER	0	0.027	0.029	25.849	0.004	0.004	0.000	0.000	0.000	0.000
126	A	497	LEU	0	-0.027	-0.036	25.082	-0.004	-0.004	0.000	0.000	0.000	0.000
127	A	498	GLY	0	-0.006	0.011	25.169	0.004	0.004	0.000	0.000	0.000	0.000
128	A	499	VAL	0	-0.054	-0.036	24.917	-0.004	-0.004	0.000	0.000	0.000	0.000
129	A	500	SER	0	0.018	0.015	24.399	-0.002	-0.002	0.000	0.000	0.000	0.000
130	A	501	LEU	0	-0.064	-0.046	25.452	0.002	0.002	0.000	0.000	0.000	0.000
131	A	502	TYR	0	-0.054	-0.027	24.588	-0.008	-0.008	0.000	0.000	0.000	0.000
132	A	503	PRO	0	-0.030	-0.033	26.716	0.006	0.006	0.000	0.000	0.000	0.000
133	A	504	ASP	-1	-0.936	-0.982	28.411	-0.042	-0.042	0.000	0.000	0.000	0.000
134	A	505	ASP	-1	-0.844	-0.895	27.481	-0.055	-0.055	0.000	0.000	0.000	0.000
135	A	506	GLY	0	-0.045	-0.039	25.359	-0.009	-0.009	0.000	0.000	0.000	0.000
136	A	507	ARG	1	0.960	0.961	25.257	0.057	0.057	0.000	0.000	0.000	0.000
137	A	508	THR	0	0.018	0.012	20.656	0.002	0.002	0.000	0.000	0.000	0.000
138	A	509	ALA	0	0.097	0.040	16.615	0.006	0.006	0.000	0.000	0.000	0.000
139	A	510	GLU	-1	-0.871	-0.942	16.162	-0.221	-0.221	0.000	0.000	0.000	0.000
140	A	511	ALA	0	-0.042	-0.015	19.297	0.006	0.006	0.000	0.000	0.000	0.000
141	A	512	LEU	0	0.022	0.010	21.023	0.005	0.005	0.000	0.000	0.000	0.000
142	A	513	MET	0	-0.024	-0.006	15.746	0.006	0.006	0.000	0.000	0.000	0.000
143	A	514	ALA	0	-0.001	0.005	19.920	0.005	0.005	0.000	0.000	0.000	0.000
144	A	515	ASN	0	0.009	0.012	22.367	0.011	0.011	0.000	0.000	0.000	0.000
145	A	516	ALA	0	0.056	0.023	21.885	0.008	0.008	0.000	0.000	0.000	0.000
146	A	517	ASP	-1	-0.894	-0.955	21.449	-0.116	-0.116	0.000	0.000	0.000	0.000
147	A	518	MET	0	-0.054	-0.026	23.348	0.010	0.010	0.000	0.000	0.000	0.000
148	A	519	ALA	0	-0.026	-0.016	26.686	0.008	0.008	0.000	0.000	0.000	0.000
149	A	520	LEU	0	0.027	0.022	23.101	0.008	0.008	0.000	0.000	0.000	0.000
150	A	521	TYR	0	-0.014	-0.006	26.639	0.007	0.007	0.000	0.000	0.000	0.000
151	A	522	ARG	1	0.893	0.935	28.558	0.058	0.058	0.000	0.000	0.000	0.000
152	A	523	ALA	0	0.026	0.025	29.312	0.005	0.005	0.000	0.000	0.000	0.000
153	A	524	LYS	1	0.839	0.917	25.661	0.071	0.071	0.000	0.000	0.000	0.000
154	A	525	GLU	-1	-1.022	-1.000	31.078	-0.044	-0.044	0.000	0.000	0.000	0.000
155	A	526	SER	0	-0.122	-0.068	34.169	0.004	0.004	0.000	0.000	0.000	0.000
156	A	527	GLY	0	-0.014	0.006	34.030	0.003	0.003	0.000	0.000	0.000	0.000

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