FMO DATABASE

FMODB ID: G5351

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1350141.320062
FMO2-HF: Nuclear repulsion	1292225.348477
FMO2-HF: Total energy	-57915.971585
FMO2-MP2: Total energy	-58083.016993

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.
-2.5	1.259	-0.024	-1.934	-1.802	-0.002

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 : 0.013 / 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	-0.006	0.010	3.338	-2.790	0.199	-0.023	-1.612	-1.355	-0.003
4	A	375	ASP	-1	-0.757	-0.815	4.309	-1.244	-1.138	-0.001	-0.023	-0.081	0.000
5	A	376	GLY	0	-0.038	-0.020	6.198	0.251	0.251	0.000	0.000	0.000	0.000
6	A	377	LEU	0	-0.038	-0.007	7.159	0.082	0.082	0.000	0.000	0.000	0.000
7	A	378	THR	0	0.005	-0.039	9.940	0.050	0.050	0.000	0.000	0.000	0.000
8	A	379	GLY	0	-0.003	0.004	8.762	0.039	0.039	0.000	0.000	0.000	0.000
9	A	380	LEU	0	-0.025	0.017	9.770	0.081	0.081	0.000	0.000	0.000	0.000
10	A	381	LEU	0	0.003	0.002	8.194	0.108	0.108	0.000	0.000	0.000	0.000
11	A	382	ASN	0	-0.026	-0.032	3.785	0.030	0.534	0.001	-0.276	-0.230	0.001
12	A	383	ARG	1	0.844	0.881	8.138	0.391	0.391	0.000	0.000	0.000	0.000
13	A	384	ASN	0	-0.031	-0.004	4.201	0.570	0.730	-0.001	-0.023	-0.136	0.000
14	A	385	SER	0	0.004	-0.027	6.082	0.139	0.139	0.000	0.000	0.000	0.000
15	A	386	LEU	0	-0.002	0.002	7.697	0.230	0.230	0.000	0.000	0.000	0.000
16	A	387	GLN	0	-0.018	-0.009	10.881	0.056	0.056	0.000	0.000	0.000	0.000
17	A	388	MET	0	0.011	0.007	5.691	0.103	0.103	0.000	0.000	0.000	0.000
18	A	389	ARG	1	0.891	0.953	10.221	0.000	0.000	0.000	0.000	0.000	0.000
19	A	390	LEU	0	-0.014	0.007	12.885	0.043	0.043	0.000	0.000	0.000	0.000
20	A	391	ALA	0	0.015	0.003	14.642	0.025	0.025	0.000	0.000	0.000	0.000
21	A	392	ALA	0	0.023	0.011	14.802	0.023	0.023	0.000	0.000	0.000	0.000
22	A	393	ALA	0	-0.029	-0.017	16.597	0.023	0.023	0.000	0.000	0.000	0.000
23	A	394	ILE	0	0.006	0.006	18.876	0.011	0.011	0.000	0.000	0.000	0.000
24	A	395	ASP	-1	-0.930	-0.961	18.838	-0.064	-0.064	0.000	0.000	0.000	0.000
25	A	396	ARG	1	0.715	0.821	20.350	-0.016	-0.016	0.000	0.000	0.000	0.000
26	A	397	VAL	0	0.003	-0.001	22.352	0.006	0.006	0.000	0.000	0.000	0.000
27	A	398	GLU	-1	-0.805	-0.855	24.780	-0.037	-0.037	0.000	0.000	0.000	0.000
28	A	399	ALA	0	-0.056	-0.022	25.778	0.003	0.003	0.000	0.000	0.000	0.000
29	A	400	SER	0	-0.076	-0.075	25.748	0.002	0.002	0.000	0.000	0.000	0.000
30	A	401	GLY	0	-0.020	-0.005	28.163	0.003	0.003	0.000	0.000	0.000	0.000
31	A	402	GLU	-1	-0.825	-0.841	24.952	0.018	0.018	0.000	0.000	0.000	0.000
32	A	403	SER	0	-0.019	-0.009	27.597	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	404	LEU	0	-0.012	-0.010	20.576	0.004	0.004	0.000	0.000	0.000	0.000
34	A	405	ALA	0	-0.008	0.005	23.621	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	406	VAL	0	-0.024	-0.015	19.043	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	407	ILE	0	0.005	-0.001	20.862	0.003	0.003	0.000	0.000	0.000	0.000
37	A	408	CYS	0	-0.027	0.006	20.283	-0.011	-0.011	0.000	0.000	0.000	0.000
38	A	409	ILE	0	0.014	-0.007	20.267	0.016	0.016	0.000	0.000	0.000	0.000
39	A	410	ASP	-1	-0.774	-0.855	20.236	-0.096	-0.096	0.000	0.000	0.000	0.000
40	A	411	LEU	0	0.005	-0.019	20.351	0.013	0.013	0.000	0.000	0.000	0.000
41	A	412	ASP	-1	-0.862	-0.914	23.837	-0.047	-0.047	0.000	0.000	0.000	0.000
42	A	413	HIS	0	-0.040	-0.028	26.754	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	414	PHE	0	0.024	0.021	19.029	0.001	0.001	0.000	0.000	0.000	0.000
44	A	415	LYS	1	0.815	0.887	24.271	0.064	0.064	0.000	0.000	0.000	0.000
45	A	416	GLU	-1	-0.875	-0.926	25.949	-0.026	-0.026	0.000	0.000	0.000	0.000
46	A	417	ALA	0	0.087	0.038	25.124	0.002	0.002	0.000	0.000	0.000	0.000
47	A	418	ASN	0	-0.071	-0.056	21.532	0.000	0.000	0.000	0.000	0.000	0.000
48	A	419	ASP	-1	-0.897	-0.920	25.253	-0.057	-0.057	0.000	0.000	0.000	0.000
49	A	420	GLN	0	-0.113	-0.064	28.708	0.002	0.002	0.000	0.000	0.000	0.000
50	A	421	HIS	0	-0.050	-0.014	27.763	0.003	0.003	0.000	0.000	0.000	0.000
51	A	422	GLY	0	0.007	0.019	26.002	0.003	0.003	0.000	0.000	0.000	0.000
52	A	423	HIS	0	0.011	-0.011	19.166	0.002	0.002	0.000	0.000	0.000	0.000
53	A	424	LEU	0	-0.025	-0.009	19.759	0.000	0.000	0.000	0.000	0.000	0.000
54	A	425	ALA	0	0.028	0.026	21.610	0.008	0.008	0.000	0.000	0.000	0.000
55	A	426	GLY	0	0.050	0.019	21.467	0.003	0.003	0.000	0.000	0.000	0.000
56	A	427	ASP	-1	-0.883	-0.973	17.014	-0.070	-0.070	0.000	0.000	0.000	0.000
57	A	428	ALA	0	-0.036	-0.015	18.111	0.012	0.012	0.000	0.000	0.000	0.000
58	A	429	LEU	0	0.049	0.027	20.590	0.010	0.010	0.000	0.000	0.000	0.000
59	A	430	LEU	0	-0.065	-0.004	15.558	0.002	0.002	0.000	0.000	0.000	0.000
60	A	431	VAL	0	0.005	-0.006	15.205	0.012	0.012	0.000	0.000	0.000	0.000
61	A	432	GLU	-1	-0.752	-0.822	16.975	0.071	0.071	0.000	0.000	0.000	0.000
62	A	433	THR	0	0.022	-0.003	18.475	0.008	0.008	0.000	0.000	0.000	0.000
63	A	434	ALA	0	-0.009	-0.007	14.542	0.004	0.004	0.000	0.000	0.000	0.000
64	A	435	ARG	1	0.837	0.897	16.489	-0.052	-0.052	0.000	0.000	0.000	0.000
65	A	436	ARG	1	0.715	0.822	18.592	-0.013	-0.013	0.000	0.000	0.000	0.000
66	A	437	LEU	0	0.053	0.033	17.087	0.004	0.004	0.000	0.000	0.000	0.000
67	A	438	GLN	0	-0.044	-0.030	13.055	-0.011	-0.011	0.000	0.000	0.000	0.000
68	A	439	SER	0	-0.106	-0.055	17.825	0.008	0.008	0.000	0.000	0.000	0.000
69	A	440	ALA	0	-0.003	-0.007	21.099	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	441	VAL	0	-0.061	-0.013	18.489	-0.012	-0.012	0.000	0.000	0.000	0.000
71	A	442	GLN	0	-0.038	-0.010	18.595	0.035	0.035	0.000	0.000	0.000	0.000
72	A	443	ALA	0	0.005	0.003	17.697	-0.015	-0.015	0.000	0.000	0.000	0.000
73	A	444	PRO	0	-0.059	-0.035	19.143	0.001	0.001	0.000	0.000	0.000	0.000
74	A	445	SER	0	0.030	0.025	18.563	-0.016	-0.016	0.000	0.000	0.000	0.000
75	A	446	PHE	0	-0.023	-0.034	14.128	0.034	0.034	0.000	0.000	0.000	0.000
76	A	447	ALA	0	0.058	0.029	14.753	-0.029	-0.029	0.000	0.000	0.000	0.000
77	A	448	ALA	0	-0.018	-0.012	11.621	0.030	0.030	0.000	0.000	0.000	0.000
78	A	449	ARG	1	0.840	0.898	10.710	0.233	0.233	0.000	0.000	0.000	0.000
79	A	450	LEU	0	-0.056	-0.035	10.833	-0.119	-0.119	0.000	0.000	0.000	0.000
80	A	451	GLY	0	-0.007	-0.010	12.151	-0.081	-0.081	0.000	0.000	0.000	0.000
81	A	452	GLY	0	-0.011	-0.002	14.023	0.029	0.029	0.000	0.000	0.000	0.000
82	A	453	ASP	-1	-0.780	-0.900	16.195	-0.105	-0.105	0.000	0.000	0.000	0.000
83	A	454	GLU	-1	-0.780	-0.857	16.051	-0.250	-0.250	0.000	0.000	0.000	0.000
84	A	455	PHE	0	0.004	-0.022	14.889	-0.031	-0.031	0.000	0.000	0.000	0.000
85	A	456	ILE	0	-0.011	-0.007	15.492	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	457	VAL	0	-0.012	-0.003	16.426	0.017	0.017	0.000	0.000	0.000	0.000
87	A	458	VAL	0	-0.002	0.003	16.445	-0.015	-0.015	0.000	0.000	0.000	0.000
88	A	459	GLN	0	-0.004	-0.025	18.958	0.016	0.016	0.000	0.000	0.000	0.000
89	A	460	ILE	0	0.000	-0.006	19.024	-0.009	-0.009	0.000	0.000	0.000	0.000
90	A	461	ALA	0	-0.016	-0.013	23.135	0.012	0.012	0.000	0.000	0.000	0.000
91	A	462	GLY	0	0.064	0.034	26.738	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	463	GLY	0	-0.042	-0.022	30.340	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	464	ASP	-1	-0.853	-0.936	33.222	-0.016	-0.016	0.000	0.000	0.000	0.000
94	A	465	GLN	0	0.054	0.021	28.407	0.003	0.003	0.000	0.000	0.000	0.000
95	A	466	PRO	0	0.032	0.007	30.600	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	467	ALA	0	-0.007	0.002	32.186	0.000	0.000	0.000	0.000	0.000	0.000
97	A	468	VAL	0	-0.036	-0.018	28.737	0.002	0.002	0.000	0.000	0.000	0.000
98	A	469	ALA	0	0.052	0.042	27.734	0.002	0.002	0.000	0.000	0.000	0.000
99	A	470	ALA	0	-0.014	-0.009	28.564	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	471	GLU	-1	-0.850	-0.884	30.196	0.012	0.012	0.000	0.000	0.000	0.000
101	A	472	LEU	0	-0.007	0.004	23.256	0.003	0.003	0.000	0.000	0.000	0.000
102	A	473	ALA	0	0.025	0.007	26.735	0.001	0.001	0.000	0.000	0.000	0.000
103	A	474	GLY	0	0.009	0.005	27.758	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	475	ARG	1	0.803	0.853	26.186	-0.017	-0.017	0.000	0.000	0.000	0.000
105	A	476	LEU	0	-0.028	-0.021	22.226	0.004	0.004	0.000	0.000	0.000	0.000
106	A	477	ILE	0	0.040	0.022	25.743	0.000	0.000	0.000	0.000	0.000	0.000
107	A	478	GLU	-1	-0.949	-0.966	28.160	0.005	0.005	0.000	0.000	0.000	0.000
108	A	479	MET	0	-0.081	-0.037	24.168	0.005	0.005	0.000	0.000	0.000	0.000
109	A	480	LEU	0	-0.004	-0.002	21.854	0.006	0.006	0.000	0.000	0.000	0.000
110	A	481	ALA	0	0.022	0.024	25.798	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	482	ALA	0	-0.013	0.001	28.840	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	483	PRO	0	0.053	0.038	27.935	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	484	VAL	0	0.024	0.009	23.717	0.006	0.006	0.000	0.000	0.000	0.000
114	A	485	PRO	0	0.001	0.010	27.003	-0.004	-0.004	0.000	0.000	0.000	0.000
115	A	486	PHE	0	0.006	-0.016	23.462	0.004	0.004	0.000	0.000	0.000	0.000
116	A	487	ASP	-1	-0.914	-0.952	27.470	0.003	0.003	0.000	0.000	0.000	0.000
117	A	488	GLY	0	-0.039	-0.010	29.487	-0.002	-0.002	0.000	0.000	0.000	0.000
118	A	489	GLN	0	-0.068	-0.040	31.200	-0.004	-0.004	0.000	0.000	0.000	0.000
119	A	490	GLU	-1	-0.942	-0.984	30.184	0.015	0.015	0.000	0.000	0.000	0.000
120	A	491	LEU	0	-0.033	0.001	25.446	-0.004	-0.004	0.000	0.000	0.000	0.000
121	A	492	ALA	0	0.020	0.004	28.866	0.003	0.003	0.000	0.000	0.000	0.000
122	A	493	MET	0	-0.015	0.000	22.982	-0.005	-0.005	0.000	0.000	0.000	0.000
123	A	494	GLY	0	-0.006	0.017	27.142	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	495	SER	0	-0.021	-0.028	24.315	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	496	SER	0	-0.006	0.001	26.112	0.005	0.005	0.000	0.000	0.000	0.000
126	A	497	LEU	0	-0.036	-0.034	24.837	-0.005	-0.005	0.000	0.000	0.000	0.000
127	A	498	GLY	0	0.012	0.014	24.917	0.004	0.004	0.000	0.000	0.000	0.000
128	A	499	VAL	0	-0.056	-0.039	24.798	-0.003	-0.003	0.000	0.000	0.000	0.000
129	A	500	SER	0	0.011	0.015	24.357	-0.003	-0.003	0.000	0.000	0.000	0.000
130	A	501	LEU	0	-0.035	-0.033	25.204	0.001	0.001	0.000	0.000	0.000	0.000
131	A	502	TYR	0	0.000	0.004	23.991	-0.008	-0.008	0.000	0.000	0.000	0.000
132	A	503	PRO	0	-0.030	-0.021	26.326	0.007	0.007	0.000	0.000	0.000	0.000
133	A	504	ASP	-1	-0.923	-0.977	27.967	-0.045	-0.045	0.000	0.000	0.000	0.000
134	A	505	ASP	-1	-0.810	-0.891	27.098	-0.062	-0.062	0.000	0.000	0.000	0.000
135	A	506	GLY	0	-0.022	-0.023	25.025	-0.010	-0.010	0.000	0.000	0.000	0.000
136	A	507	ARG	1	0.802	0.876	24.812	0.057	0.057	0.000	0.000	0.000	0.000
137	A	508	THR	0	-0.015	-0.026	20.108	0.007	0.007	0.000	0.000	0.000	0.000
138	A	509	ALA	0	0.070	0.027	16.061	0.006	0.006	0.000	0.000	0.000	0.000
139	A	510	GLU	-1	-0.825	-0.903	16.454	-0.215	-0.215	0.000	0.000	0.000	0.000
140	A	511	ALA	0	-0.033	-0.006	18.917	0.006	0.006	0.000	0.000	0.000	0.000
141	A	512	LEU	0	0.022	0.012	20.694	0.006	0.006	0.000	0.000	0.000	0.000
142	A	513	MET	0	-0.014	0.000	15.501	0.007	0.007	0.000	0.000	0.000	0.000
143	A	514	ALA	0	-0.001	0.000	19.824	0.006	0.006	0.000	0.000	0.000	0.000
144	A	515	ASN	0	-0.086	-0.043	22.276	0.010	0.010	0.000	0.000	0.000	0.000
145	A	516	ALA	0	0.062	0.030	21.732	0.006	0.006	0.000	0.000	0.000	0.000
146	A	517	ASP	-1	-0.910	-0.963	21.267	-0.131	-0.131	0.000	0.000	0.000	0.000
147	A	518	MET	0	-0.030	-0.008	23.264	0.010	0.010	0.000	0.000	0.000	0.000
148	A	519	ALA	0	-0.022	-0.016	26.662	0.008	0.008	0.000	0.000	0.000	0.000
149	A	520	LEU	0	0.001	0.016	22.702	0.009	0.009	0.000	0.000	0.000	0.000
150	A	521	TYR	0	-0.070	-0.073	26.479	0.006	0.006	0.000	0.000	0.000	0.000
151	A	522	ARG	1	0.882	0.929	28.280	0.067	0.067	0.000	0.000	0.000	0.000
152	A	523	ALA	0	0.043	0.030	29.263	0.005	0.005	0.000	0.000	0.000	0.000
153	A	524	LYS	1	0.770	0.869	26.093	0.074	0.074	0.000	0.000	0.000	0.000
154	A	525	GLU	-1	-0.931	-0.924	31.135	-0.053	-0.053	0.000	0.000	0.000	0.000
155	A	526	SER	0	-0.086	-0.056	34.304	0.003	0.003	0.000	0.000	0.000	0.000
156	A	527	GLY	0	-0.032	0.012	33.775	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)