FMO DATABASE

FMODB ID: Z661N

Calculation Name: 4YO3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YO3

Chain ID: A

ChEMBL ID:

UniProt ID: D3GUX1

Base Structure: X-ray

Registration Date: 2023-06-21

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	157
LigandCharge	DAR=1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1583071.372503
FMO2-HF: Nuclear repulsion	1520505.884022
FMO2-HF: Total energy	-62565.488481
FMO2-MP2: Total energy	-62748.979725

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:221:SER)

Summations of interaction energy for fragment #1(A:221: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.
-9.125	-5.447	7.333	-5.227	-5.782	-0.006

Interaction energy analysis for fragmet #1(A:221:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : -0.012

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	223	ILE	0	-0.003	0.011	3.890	1.118	2.752	-0.015	-0.890	-0.730	0.001
4	A	224	THR	0	-0.004	0.001	5.373	0.130	0.130	0.000	0.000	0.000	0.000
5	A	225	SER	0	0.010	-0.001	2.077	-4.361	-5.544	5.376	-2.165	-2.029	-0.015
6	A	226	GLY	0	0.081	0.055	3.831	-1.218	-1.014	0.001	-0.094	-0.110	-0.001
7	A	227	GLN	0	-0.007	-0.030	6.633	-0.001	-0.001	0.000	0.000	0.000	0.000
8	A	228	GLU	-1	-0.849	-0.915	2.278	-1.857	-0.433	1.809	-1.331	-1.901	0.000
9	A	229	LEU	0	0.006	0.022	4.388	0.767	0.882	-0.001	-0.017	-0.097	0.000
10	A	230	LEU	0	-0.002	-0.008	5.622	0.495	0.495	0.000	0.000	0.000	0.000
11	A	231	SER	0	-0.081	-0.070	6.137	0.195	0.195	0.000	0.000	0.000	0.000
12	A	232	GLN	0	0.061	0.029	2.793	-4.222	-2.738	0.163	-0.730	-0.915	0.009
13	A	233	ALA	0	-0.003	0.003	7.240	-0.082	-0.082	0.000	0.000	0.000	0.000
14	A	234	ARG	1	0.933	0.959	10.147	0.070	0.070	0.000	0.000	0.000	0.000
15	A	235	VAL	0	-0.007	0.007	9.120	-0.042	-0.042	0.000	0.000	0.000	0.000
16	A	236	LEU	0	0.001	0.016	10.930	-0.024	-0.024	0.000	0.000	0.000	0.000
17	A	237	ALA	0	0.004	-0.009	12.801	-0.029	-0.029	0.000	0.000	0.000	0.000
18	A	238	LYS	1	0.792	0.863	15.146	-0.171	-0.171	0.000	0.000	0.000	0.000
19	A	239	TYR	0	0.033	0.028	15.599	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	240	LEU	0	0.001	-0.010	16.995	-0.016	-0.016	0.000	0.000	0.000	0.000
21	A	241	ARG	1	0.797	0.884	19.491	0.001	0.001	0.000	0.000	0.000	0.000
22	A	242	ASP	-1	-0.840	-0.885	20.297	0.130	0.130	0.000	0.000	0.000	0.000
23	A	243	GLN	0	-0.079	-0.031	20.740	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	244	PRO	0	0.029	0.019	23.905	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	245	GLU	-1	-0.930	-0.976	26.941	-0.012	-0.012	0.000	0.000	0.000	0.000
26	A	246	GLY	0	0.019	0.023	23.736	-0.013	-0.013	0.000	0.000	0.000	0.000
27	A	247	TRP	0	-0.028	-0.038	22.773	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	248	LEU	0	0.054	0.024	22.888	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	249	ALA	0	0.008	0.014	20.818	-0.015	-0.015	0.000	0.000	0.000	0.000
30	A	250	ALA	0	0.031	0.014	18.641	-0.024	-0.024	0.000	0.000	0.000	0.000
31	A	251	HIS	0	0.016	0.004	18.453	-0.019	-0.019	0.000	0.000	0.000	0.000
32	A	252	ARG	1	0.803	0.837	19.803	0.127	0.127	0.000	0.000	0.000	0.000
33	A	253	LEU	0	0.011	0.033	13.207	-0.032	-0.032	0.000	0.000	0.000	0.000
34	A	254	MET	0	-0.010	-0.005	12.533	-0.051	-0.051	0.000	0.000	0.000	0.000
35	A	255	LYS	1	0.858	0.924	16.414	0.123	0.123	0.000	0.000	0.000	0.000
36	A	256	SER	0	0.043	0.023	17.240	-0.030	-0.030	0.000	0.000	0.000	0.000
37	A	257	VAL	0	-0.034	-0.008	10.931	-0.049	-0.049	0.000	0.000	0.000	0.000
38	A	258	ARG	1	0.778	0.893	13.510	0.214	0.214	0.000	0.000	0.000	0.000
39	A	259	HIS	0	0.026	0.003	15.857	0.022	0.022	0.000	0.000	0.000	0.000
40	A	260	ASP	-1	-0.843	-0.899	18.002	-0.281	-0.281	0.000	0.000	0.000	0.000
41	A	261	THR	0	-0.069	-0.040	12.809	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	262	LEU	0	-0.057	-0.019	15.999	-0.010	-0.010	0.000	0.000	0.000	0.000
43	A	263	HIS	0	0.049	0.024	17.118	0.062	0.062	0.000	0.000	0.000	0.000
44	A	264	GLN	0	-0.042	-0.014	20.887	0.023	0.023	0.000	0.000	0.000	0.000
45	A	265	LEU	0	0.057	0.005	22.573	0.000	0.000	0.000	0.000	0.000	0.000
46	A	266	PRO	0	-0.005	0.024	24.029	0.008	0.008	0.000	0.000	0.000	0.000
47	A	267	PRO	0	-0.026	-0.026	19.996	0.001	0.001	0.000	0.000	0.000	0.000
48	A	268	LEU	0	-0.036	-0.018	22.366	0.001	0.001	0.000	0.000	0.000	0.000
49	A	269	SER	0	0.031	0.005	25.126	0.002	0.002	0.000	0.000	0.000	0.000
50	A	270	ALA	0	-0.037	-0.008	28.605	0.001	0.001	0.000	0.000	0.000	0.000
51	A	271	ASP	-1	-0.888	-0.945	30.698	-0.068	-0.068	0.000	0.000	0.000	0.000
52	A	272	GLY	0	-0.032	-0.011	33.725	0.005	0.005	0.000	0.000	0.000	0.000
53	A	273	ARG	1	0.835	0.927	30.473	0.054	0.054	0.000	0.000	0.000	0.000
54	A	274	THR	0	0.019	0.005	25.648	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	275	ARG	1	0.961	0.982	20.283	0.180	0.180	0.000	0.000	0.000	0.000
56	A	276	ILE	0	-0.032	-0.013	20.647	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	277	ALA	0	0.032	0.002	22.627	0.012	0.012	0.000	0.000	0.000	0.000
58	A	278	PRO	0	-0.014	0.003	23.952	-0.007	-0.007	0.000	0.000	0.000	0.000
59	A	279	PRO	0	-0.006	-0.007	24.416	0.002	0.002	0.000	0.000	0.000	0.000
60	A	280	GLY	0	0.013	0.016	24.913	0.005	0.005	0.000	0.000	0.000	0.000
61	A	281	PRO	0	-0.042	-0.036	27.261	0.001	0.001	0.000	0.000	0.000	0.000
62	A	282	ASP	-1	-0.871	-0.945	27.430	0.009	0.009	0.000	0.000	0.000	0.000
63	A	283	ARG	1	0.907	0.920	22.308	-0.011	-0.011	0.000	0.000	0.000	0.000
64	A	284	ARG	1	0.904	0.967	27.988	0.044	0.044	0.000	0.000	0.000	0.000
65	A	285	ALA	0	0.001	0.004	30.013	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	286	SER	0	-0.046	-0.040	29.689	0.004	0.004	0.000	0.000	0.000	0.000
67	A	287	LEU	0	0.026	0.018	27.189	0.002	0.002	0.000	0.000	0.000	0.000
68	A	288	LYS	1	0.947	0.969	31.491	0.036	0.036	0.000	0.000	0.000	0.000
69	A	289	ARG	1	0.928	0.982	32.248	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	290	LEU	0	0.036	0.015	30.777	0.001	0.001	0.000	0.000	0.000	0.000
71	A	291	TYR	0	0.001	0.001	34.808	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	292	LEU	0	-0.008	0.006	36.221	0.000	0.000	0.000	0.000	0.000	0.000
73	A	293	GLN	0	-0.045	-0.035	37.035	0.000	0.000	0.000	0.000	0.000	0.000
74	A	294	GLN	0	-0.014	-0.005	38.183	0.001	0.001	0.000	0.000	0.000	0.000
75	A	295	ASN	0	0.006	0.022	34.142	0.000	0.000	0.000	0.000	0.000	0.000
76	A	296	TRP	0	0.050	0.003	33.832	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	297	LEU	0	0.025	0.006	30.893	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	298	SER	0	0.005	-0.005	29.772	0.001	0.001	0.000	0.000	0.000	0.000
79	A	299	LEU	0	-0.016	-0.005	28.773	0.000	0.000	0.000	0.000	0.000	0.000
80	A	300	LEU	0	-0.008	0.000	27.271	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	301	GLU	-1	-0.862	-0.913	25.189	0.022	0.022	0.000	0.000	0.000	0.000
82	A	302	GLN	0	0.014	0.013	24.000	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	303	CYS	0	-0.044	-0.030	24.289	-0.006	-0.006	0.000	0.000	0.000	0.000
84	A	304	ASP	-1	-0.743	-0.854	20.757	-0.066	-0.066	0.000	0.000	0.000	0.000
85	A	305	ASP	-1	-0.837	-0.890	19.466	0.026	0.026	0.000	0.000	0.000	0.000
86	A	306	MET	0	-0.055	-0.019	19.506	-0.007	-0.007	0.000	0.000	0.000	0.000
87	A	307	PHE	0	-0.030	-0.007	17.810	-0.011	-0.011	0.000	0.000	0.000	0.000
88	A	308	ALA	0	0.031	0.021	15.247	-0.035	-0.035	0.000	0.000	0.000	0.000
89	A	309	DAR	1	0.914	0.963	15.290	0.008	0.008	0.000	0.000	0.000	0.000
90	A	310	GLY	0	0.033	0.004	17.216	0.020	0.020	0.000	0.000	0.000	0.000
91	A	311	ALA	0	0.042	0.026	17.246	-0.035	-0.035	0.000	0.000	0.000	0.000
92	A	312	SER	0	-0.046	-0.026	17.014	0.000	0.000	0.000	0.000	0.000	0.000
93	A	313	HIS	0	-0.019	-0.038	18.031	-0.008	-0.008	0.000	0.000	0.000	0.000
94	A	314	LEU	0	0.080	0.059	21.035	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	315	TRP	0	-0.042	-0.015	23.793	0.011	0.011	0.000	0.000	0.000	0.000
96	A	316	LEU	0	0.064	0.014	25.956	0.000	0.000	0.000	0.000	0.000	0.000
97	A	317	ASP	-1	-0.751	-0.862	27.871	-0.063	-0.063	0.000	0.000	0.000	0.000
98	A	318	LEU	0	-0.101	-0.039	23.367	0.007	0.007	0.000	0.000	0.000	0.000
99	A	319	GLN	0	0.027	0.017	24.556	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	320	TRP	0	0.072	0.049	27.947	0.005	0.005	0.000	0.000	0.000	0.000
101	A	321	TYR	0	0.006	-0.005	29.685	0.007	0.007	0.000	0.000	0.000	0.000
102	A	322	ILE	0	-0.016	-0.011	24.961	0.006	0.006	0.000	0.000	0.000	0.000
103	A	323	HIS	0	-0.015	-0.003	29.488	0.002	0.002	0.000	0.000	0.000	0.000
104	A	324	GLN	0	0.050	0.021	32.177	0.001	0.001	0.000	0.000	0.000	0.000
105	A	325	ALA	0	-0.009	-0.005	31.577	0.004	0.004	0.000	0.000	0.000	0.000
106	A	326	LEU	0	-0.056	-0.043	28.986	0.004	0.004	0.000	0.000	0.000	0.000
107	A	327	LEU	0	0.019	0.019	33.294	0.002	0.002	0.000	0.000	0.000	0.000
108	A	328	GLN	0	-0.006	-0.003	36.862	0.002	0.002	0.000	0.000	0.000	0.000
109	A	329	THR	0	-0.096	-0.021	33.092	0.004	0.004	0.000	0.000	0.000	0.000
110	A	330	GLY	0	0.033	0.015	36.487	0.003	0.003	0.000	0.000	0.000	0.000
111	A	331	LYS	1	0.863	0.938	32.058	0.018	0.018	0.000	0.000	0.000	0.000
112	A	332	GLU	-1	-0.853	-0.939	34.150	-0.044	-0.044	0.000	0.000	0.000	0.000
113	A	333	ASN	0	-0.024	-0.016	32.879	-0.006	-0.006	0.000	0.000	0.000	0.000
114	A	334	TYR	0	0.011	-0.012	28.808	-0.008	-0.008	0.000	0.000	0.000	0.000
115	A	335	ALA	0	0.053	0.024	30.440	-0.008	-0.008	0.000	0.000	0.000	0.000
116	A	336	ALA	0	0.011	0.012	32.453	-0.005	-0.005	0.000	0.000	0.000	0.000
117	A	337	ILE	0	-0.010	-0.006	27.266	-0.007	-0.007	0.000	0.000	0.000	0.000
118	A	338	ILE	0	-0.026	-0.006	26.657	-0.010	-0.010	0.000	0.000	0.000	0.000
119	A	339	GLN	0	0.063	0.036	28.557	-0.008	-0.008	0.000	0.000	0.000	0.000
120	A	340	TYR	0	-0.009	-0.006	29.901	-0.005	-0.005	0.000	0.000	0.000	0.000
121	A	341	ASP	-1	-0.806	-0.870	24.756	-0.159	-0.159	0.000	0.000	0.000	0.000
122	A	342	LEU	0	-0.038	-0.015	26.106	-0.015	-0.015	0.000	0.000	0.000	0.000
123	A	343	LYS	1	0.878	0.928	27.756	0.093	0.093	0.000	0.000	0.000	0.000
124	A	344	GLY	0	0.022	0.008	27.196	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	345	LEU	0	-0.026	-0.015	22.738	-0.011	-0.011	0.000	0.000	0.000	0.000
126	A	346	LEU	0	0.001	-0.009	25.732	-0.007	-0.007	0.000	0.000	0.000	0.000
127	A	347	LEU	0	-0.050	0.003	29.011	0.005	0.005	0.000	0.000	0.000	0.000
128	A	348	ARG	1	0.808	0.878	21.223	0.268	0.268	0.000	0.000	0.000	0.000
129	A	349	LEU	0	-0.063	-0.029	22.537	-0.003	-0.003	0.000	0.000	0.000	0.000
130	A	350	PRO	0	0.038	0.013	27.205	0.007	0.007	0.000	0.000	0.000	0.000
131	A	351	GLY	0	0.011	-0.001	30.915	0.006	0.006	0.000	0.000	0.000	0.000
132	A	352	LEU	0	-0.009	-0.003	24.849	0.004	0.004	0.000	0.000	0.000	0.000
133	A	353	GLU	-1	-0.890	-0.969	28.644	-0.094	-0.094	0.000	0.000	0.000	0.000
134	A	354	THR	0	-0.012	-0.004	31.217	0.007	0.007	0.000	0.000	0.000	0.000
135	A	355	LEU	0	-0.032	0.015	27.607	0.004	0.004	0.000	0.000	0.000	0.000
136	A	356	ALA	0	0.022	0.011	30.432	0.005	0.005	0.000	0.000	0.000	0.000
137	A	357	PHE	0	-0.020	0.001	24.307	-0.007	-0.007	0.000	0.000	0.000	0.000
138	A	358	ASN	0	0.024	-0.001	25.168	0.004	0.004	0.000	0.000	0.000	0.000
139	A	359	ASP	-1	-0.825	-0.937	28.957	-0.054	-0.054	0.000	0.000	0.000	0.000
140	A	360	GLY	0	-0.008	-0.005	31.573	0.005	0.005	0.000	0.000	0.000	0.000
141	A	361	MET	0	-0.055	-0.002	31.059	0.002	0.002	0.000	0.000	0.000	0.000
142	A	362	PRO	0	0.057	0.025	31.062	-0.007	-0.007	0.000	0.000	0.000	0.000
143	A	363	PHE	0	-0.044	-0.039	25.764	0.000	0.000	0.000	0.000	0.000	0.000
144	A	364	ALA	0	0.033	0.005	29.498	-0.001	-0.001	0.000	0.000	0.000	0.000
145	A	365	ASP	-1	-0.882	-0.933	32.346	-0.050	-0.050	0.000	0.000	0.000	0.000
146	A	366	ASP	-1	-0.877	-0.944	35.609	-0.051	-0.051	0.000	0.000	0.000	0.000
147	A	367	VAL	0	-0.049	-0.023	36.723	-0.001	-0.001	0.000	0.000	0.000	0.000
148	A	368	THR	0	-0.079	-0.055	33.029	-0.003	-0.003	0.000	0.000	0.000	0.000
149	A	369	LEU	0	0.041	0.008	34.855	-0.004	-0.004	0.000	0.000	0.000	0.000
150	A	370	SER	0	-0.008	0.020	36.084	-0.001	-0.001	0.000	0.000	0.000	0.000
151	A	371	TRP	0	-0.026	-0.032	30.520	-0.002	-0.002	0.000	0.000	0.000	0.000
152	A	372	ILE	0	0.012	0.000	31.513	-0.002	-0.002	0.000	0.000	0.000	0.000
153	A	373	GLN	0	0.012	0.002	35.256	0.001	0.001	0.000	0.000	0.000	0.000
154	A	374	GLN	0	-0.037	-0.018	38.114	0.001	0.001	0.000	0.000	0.000	0.000
155	A	375	GLN	0	-0.043	-0.008	37.316	0.002	0.002	0.000	0.000	0.000	0.000
156	A	376	VAL	0	-0.014	0.007	32.228	-0.002	-0.002	0.000	0.000	0.000	0.000
157	A	377	MET	0	-0.031	0.006	33.987	-0.008	-0.008	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:221:SER)