FMO DATABASE

FMODB ID: KKRQ3

Calculation Name: 1YO5-C-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1YO5

Chain ID: C

ChEMBL ID:

UniProt ID: O95238

Base Structure: X-ray

Registration Date: 2025-07-11

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	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	167
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-708155.293149
FMO2-HF: Nuclear repulsion	671609.059329
FMO2-HF: Total energy	-36546.23382
FMO2-MP2: Total energy	-36655.963548

3D Structure Molmil

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(C:247:GLN)

Summations of interaction energy for fragment #1(C:247:GLN)

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.
3.642	5.144	-0.006	-0.904	-0.59	0.005

Interaction energy analysis for fragmet #1(C:247:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.210 / q_NPA : 0.043

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].
4	C	249	ILE	0	0.151	0.042	3.891	-1.989	-0.523	-0.005	-0.899	-0.561	0.005
5	C	249	ILE	0	-0.099	0.106	7.371	0.122	0.122	0.000	0.000	0.000	0.000
6	C	250	HIS	0	0.166	-0.105	6.517	0.595	0.595	0.000	0.000	0.000	0.000
7	C	250	HIS	0	-0.106	0.089	4.973	0.724	0.760	-0.001	-0.005	-0.029	0.000
8	C	251	LEU	0	0.091	-0.082	8.403	0.022	0.022	0.000	0.000	0.000	0.000
9	C	251	LEU	0	-0.103	0.105	12.793	0.020	0.020	0.000	0.000	0.000	0.000
10	C	252	TRP	0	0.101	-0.107	12.174	0.060	0.060	0.000	0.000	0.000	0.000
11	C	252	TRP	0	-0.032	0.101	9.757	0.027	0.027	0.000	0.000	0.000	0.000
12	C	253	GLN	0	0.040	-0.113	10.160	0.200	0.200	0.000	0.000	0.000	0.000
13	C	253	GLN	0	-0.032	0.116	6.804	-0.331	-0.331	0.000	0.000	0.000	0.000
14	C	254	PHE	0	0.151	-0.048	11.483	0.067	0.067	0.000	0.000	0.000	0.000
15	C	254	PHE	0	-0.099	0.087	11.602	0.001	0.001	0.000	0.000	0.000	0.000
16	C	255	LEU	0	0.061	-0.110	12.943	0.065	0.065	0.000	0.000	0.000	0.000
17	C	255	LEU	0	-0.069	0.092	15.822	0.017	0.017	0.000	0.000	0.000	0.000
18	C	256	LYS	0	0.087	-0.104	15.160	0.095	0.095	0.000	0.000	0.000	0.000
19	C	256	LYS	1	0.813	1.057	14.835	0.557	0.557	0.000	0.000	0.000	0.000
20	C	257	GLU	0	0.104	-0.091	14.850	0.084	0.084	0.000	0.000	0.000	0.000
21	C	257	GLU	-1	-0.866	-0.746	13.674	-0.844	-0.844	0.000	0.000	0.000	0.000
22	C	258	LEU	0	0.000	-0.121	15.990	0.048	0.048	0.000	0.000	0.000	0.000
23	C	258	LEU	0	-0.073	0.077	17.051	0.015	0.015	0.000	0.000	0.000	0.000
24	C	259	LEU	0	0.089	-0.097	18.900	0.048	0.048	0.000	0.000	0.000	0.000
25	C	259	LEU	0	-0.094	0.108	19.530	0.000	0.000	0.000	0.000	0.000	0.000
26	C	260	LEU	0	0.091	-0.093	19.267	0.059	0.059	0.000	0.000	0.000	0.000
27	C	260	LEU	0	-0.087	0.112	17.642	-0.013	-0.013	0.000	0.000	0.000	0.000
28	C	261	LYS	0	-0.026	-0.113	20.567	0.033	0.033	0.000	0.000	0.000	0.000
29	C	261	LYS	1	0.814	1.026	16.552	0.575	0.575	0.000	0.000	0.000	0.000
30	C	262	PRO	0	0.095	-0.093	22.373	0.011	0.011	0.000	0.000	0.000	0.000
31	C	263	HIS	0	0.117	0.025	25.430	0.017	0.017	0.000	0.000	0.000	0.000
32	C	263	HIS	0	-0.026	0.128	26.006	-0.003	-0.003	0.000	0.000	0.000	0.000
33	C	264	SER	0	0.066	-0.081	23.219	0.028	0.028	0.000	0.000	0.000	0.000
34	C	264	SER	0	-0.021	0.084	22.637	-0.012	-0.012	0.000	0.000	0.000	0.000
35	C	265	TYR	0	-0.051	-0.126	22.597	0.023	0.023	0.000	0.000	0.000	0.000
36	C	265	TYR	0	-0.053	0.120	18.272	0.006	0.006	0.000	0.000	0.000	0.000
37	C	266	GLY	0	0.096	-0.077	24.072	0.000	0.000	0.000	0.000	0.000	0.000
38	C	267	ARG	0	-0.023	-0.033	26.881	0.009	0.009	0.000	0.000	0.000	0.000
39	C	267	ARG	1	0.835	1.046	27.766	0.223	0.223	0.000	0.000	0.000	0.000
40	C	268	PHE	0	0.080	-0.088	24.615	0.020	0.020	0.000	0.000	0.000	0.000
41	C	268	PHE	0	-0.053	0.088	23.690	-0.003	-0.003	0.000	0.000	0.000	0.000
42	C	269	ILE	0	0.087	-0.083	22.711	0.011	0.011	0.000	0.000	0.000	0.000
43	C	269	ILE	0	-0.084	0.086	20.194	-0.007	-0.007	0.000	0.000	0.000	0.000
44	C	270	ARG	0	0.045	-0.095	24.223	-0.015	-0.015	0.000	0.000	0.000	0.000
45	C	270	ARG	1	0.823	1.026	27.161	0.201	0.201	0.000	0.000	0.000	0.000
46	C	271	TRP	0	0.101	-0.105	25.740	-0.004	-0.004	0.000	0.000	0.000	0.000
47	C	271	TRP	0	-0.093	0.079	20.699	-0.002	-0.002	0.000	0.000	0.000	0.000
48	C	272	LEU	0	-0.018	-0.123	26.448	0.010	0.010	0.000	0.000	0.000	0.000
49	C	272	LEU	0	-0.060	0.097	28.607	0.002	0.002	0.000	0.000	0.000	0.000
50	C	273	ASN	0	0.157	-0.049	28.168	0.013	0.013	0.000	0.000	0.000	0.000
51	C	273	ASN	0	-0.083	0.087	29.559	-0.009	-0.009	0.000	0.000	0.000	0.000
52	C	274	LYS	0	0.129	-0.065	25.644	-0.009	-0.009	0.000	0.000	0.000	0.000
53	C	274	LYS	1	0.876	1.062	23.604	0.321	0.321	0.000	0.000	0.000	0.000
54	C	275	GLU	0	0.098	-0.084	25.373	-0.029	-0.029	0.000	0.000	0.000	0.000
55	C	275	GLU	-1	-0.870	-0.769	29.213	-0.189	-0.189	0.000	0.000	0.000	0.000
56	C	276	LYS	0	0.063	-0.090	26.744	-0.011	-0.011	0.000	0.000	0.000	0.000
57	C	276	LYS	1	0.743	0.990	28.327	0.181	0.181	0.000	0.000	0.000	0.000
58	C	277	GLY	0	0.081	-0.078	23.331	-0.004	-0.004	0.000	0.000	0.000	0.000
59	C	278	ILE	0	0.108	-0.007	23.285	-0.030	-0.030	0.000	0.000	0.000	0.000
60	C	278	ILE	0	-0.073	0.110	27.160	0.003	0.003	0.000	0.000	0.000	0.000
61	C	279	PHE	0	0.050	-0.086	23.592	0.012	0.012	0.000	0.000	0.000	0.000
62	C	279	PHE	0	-0.067	0.090	19.913	-0.013	-0.013	0.000	0.000	0.000	0.000
63	C	280	LYS	0	0.098	-0.100	25.030	0.005	0.005	0.000	0.000	0.000	0.000
64	C	280	LYS	1	0.803	1.020	27.827	0.181	0.181	0.000	0.000	0.000	0.000
65	C	281	ILE	0	0.095	-0.083	24.412	-0.013	-0.013	0.000	0.000	0.000	0.000
66	C	281	ILE	0	-0.144	0.073	21.136	-0.003	-0.003	0.000	0.000	0.000	0.000
67	C	282	GLU	0	0.027	-0.144	25.234	0.015	0.015	0.000	0.000	0.000	0.000
68	C	282	GLU	-1	-0.809	-0.727	28.146	-0.185	-0.185	0.000	0.000	0.000	0.000
69	C	283	ASP	0	0.158	-0.095	26.302	0.018	0.018	0.000	0.000	0.000	0.000
70	C	283	ASP	-1	-0.927	-0.785	26.288	-0.199	-0.199	0.000	0.000	0.000	0.000
71	C	284	SER	0	0.022	-0.081	24.239	-0.030	-0.030	0.000	0.000	0.000	0.000
72	C	284	SER	0	-0.031	0.044	25.366	0.005	0.005	0.000	0.000	0.000	0.000
73	C	285	ALA	0	0.094	-0.109	23.535	-0.019	-0.019	0.000	0.000	0.000	0.000
74	C	285	ALA	0	-0.048	0.139	26.352	0.004	0.004	0.000	0.000	0.000	0.000
75	C	286	GLN	0	0.092	-0.119	23.203	-0.008	-0.008	0.000	0.000	0.000	0.000
76	C	286	GLN	0	-0.059	0.136	23.692	-0.003	-0.003	0.000	0.000	0.000	0.000
77	C	287	VAL	0	0.083	-0.099	20.305	-0.024	-0.024	0.000	0.000	0.000	0.000
78	C	287	VAL	0	-0.106	0.102	19.228	-0.005	-0.005	0.000	0.000	0.000	0.000
79	C	288	ALA	0	0.090	-0.108	18.735	-0.062	-0.062	0.000	0.000	0.000	0.000
80	C	288	ALA	0	-0.073	0.099	20.676	0.007	0.007	0.000	0.000	0.000	0.000
81	C	289	ARG	0	0.089	-0.080	18.625	-0.019	-0.019	0.000	0.000	0.000	0.000
82	C	289	ARG	1	0.867	1.062	21.188	0.227	0.227	0.000	0.000	0.000	0.000
83	C	290	LEU	0	0.058	-0.108	18.153	0.007	0.007	0.000	0.000	0.000	0.000
84	C	290	LEU	0	-0.097	0.092	17.883	-0.006	-0.006	0.000	0.000	0.000	0.000
85	C	291	TRP	0	0.098	-0.086	14.504	-0.066	-0.066	0.000	0.000	0.000	0.000
86	C	291	TRP	0	-0.063	0.083	10.073	-0.021	-0.021	0.000	0.000	0.000	0.000
87	C	292	GLY	0	0.002	-0.116	13.923	-0.043	-0.043	0.000	0.000	0.000	0.000
88	C	293	ILE	0	0.099	0.030	15.043	0.020	0.020	0.000	0.000	0.000	0.000
89	C	293	ILE	0	-0.082	0.092	15.976	0.002	0.002	0.000	0.000	0.000	0.000
90	C	294	ARG	0	0.044	-0.099	12.720	0.034	0.034	0.000	0.000	0.000	0.000
91	C	294	ARG	1	0.749	0.994	10.507	0.949	0.949	0.000	0.000	0.000	0.000
92	C	295	LYS	0	0.040	-0.092	10.146	-0.197	-0.197	0.000	0.000	0.000	0.000
93	C	295	LYS	1	0.711	0.987	7.203	1.111	1.111	0.000	0.000	0.000	0.000
94	C	296	ASN	0	0.134	-0.045	11.119	0.090	0.090	0.000	0.000	0.000	0.000
95	C	296	ASN	0	-0.072	0.088	12.521	-0.011	-0.011	0.000	0.000	0.000	0.000
96	C	297	ARG	0	0.042	-0.106	13.779	0.084	0.084	0.000	0.000	0.000	0.000
97	C	297	ARG	1	0.817	1.032	11.775	-0.026	-0.026	0.000	0.000	0.000	0.000
98	C	298	PRO	0	0.120	-0.068	15.467	-0.028	-0.028	0.000	0.000	0.000	0.000
99	C	299	ALA	0	0.160	0.040	19.059	-0.010	-0.010	0.000	0.000	0.000	0.000
100	C	299	ALA	0	-0.076	0.109	19.972	0.006	0.006	0.000	0.000	0.000	0.000
101	C	300	MET	0	0.019	-0.138	18.026	0.024	0.024	0.000	0.000	0.000	0.000
102	C	300	MET	0	-0.105	0.108	15.057	-0.002	-0.002	0.000	0.000	0.000	0.000
103	C	301	ASN	0	0.027	-0.084	19.139	0.004	0.004	0.000	0.000	0.000	0.000
104	C	301	ASN	0	-0.077	0.054	22.623	-0.004	-0.004	0.000	0.000	0.000	0.000
105	C	302	TYR	0	0.184	-0.080	20.652	-0.022	-0.022	0.000	0.000	0.000	0.000
106	C	302	TYR	0	-0.008	0.146	22.710	0.004	0.004	0.000	0.000	0.000	0.000
107	C	303	ASP	0	0.052	-0.107	22.132	-0.026	-0.026	0.000	0.000	0.000	0.000
108	C	303	ASP	-1	-0.867	-0.773	23.867	-0.127	-0.127	0.000	0.000	0.000	0.000
109	C	304	LYS	0	0.082	-0.110	19.538	-0.002	-0.002	0.000	0.000	0.000	0.000
110	C	304	LYS	1	0.839	1.077	18.512	0.108	0.108	0.000	0.000	0.000	0.000
111	C	305	LEU	0	0.127	-0.078	17.202	-0.012	-0.012	0.000	0.000	0.000	0.000
112	C	305	LEU	0	-0.080	0.113	16.977	-0.001	-0.001	0.000	0.000	0.000	0.000
113	C	306	SER	0	0.041	-0.104	18.112	-0.042	-0.042	0.000	0.000	0.000	0.000
114	C	306	SER	0	-0.059	0.070	22.350	0.013	0.013	0.000	0.000	0.000	0.000
115	C	307	ARG	0	0.047	-0.124	20.353	-0.009	-0.009	0.000	0.000	0.000	0.000
116	C	307	ARG	1	0.796	1.030	19.609	0.143	0.143	0.000	0.000	0.000	0.000
117	C	308	SER	0	0.038	-0.084	15.625	0.036	0.036	0.000	0.000	0.000	0.000
118	C	308	SER	0	-0.050	0.061	14.679	-0.014	-0.014	0.000	0.000	0.000	0.000
119	C	309	ILE	0	0.057	-0.086	16.689	-0.030	-0.030	0.000	0.000	0.000	0.000
120	C	309	ILE	0	-0.066	0.091	17.673	-0.002	-0.002	0.000	0.000	0.000	0.000
121	C	310	ARG	0	0.092	-0.064	18.310	-0.012	-0.012	0.000	0.000	0.000	0.000
122	C	310	ARG	1	0.822	1.040	21.376	0.179	0.179	0.000	0.000	0.000	0.000
123	C	311	GLN	0	0.027	-0.124	16.969	0.030	0.030	0.000	0.000	0.000	0.000
124	C	311	GLN	0	-0.038	0.116	16.230	0.007	0.007	0.000	0.000	0.000	0.000
125	C	312	TYR	0	0.033	-0.107	16.730	0.016	0.016	0.000	0.000	0.000	0.000
126	C	312	TYR	0	-0.057	0.098	11.162	-0.043	-0.043	0.000	0.000	0.000	0.000
127	C	313	TYR	0	0.082	-0.052	17.395	-0.015	-0.015	0.000	0.000	0.000	0.000
128	C	313	TYR	0	-0.034	0.082	21.220	0.001	0.001	0.000	0.000	0.000	0.000
129	C	314	LYS	0	0.128	-0.046	20.920	-0.006	-0.006	0.000	0.000	0.000	0.000
130	C	314	LYS	1	0.877	1.069	20.127	0.102	0.102	0.000	0.000	0.000	0.000
131	C	315	LYS	0	0.026	-0.127	16.722	0.036	0.036	0.000	0.000	0.000	0.000
132	C	315	LYS	1	0.877	1.063	14.126	0.231	0.231	0.000	0.000	0.000	0.000
133	C	316	GLY	0	0.067	-0.045	18.156	-0.015	-0.015	0.000	0.000	0.000	0.000
134	C	317	ILE	0	0.099	0.014	16.174	0.008	0.008	0.000	0.000	0.000	0.000
135	C	317	ILE	0	-0.120	0.078	13.494	-0.011	-0.011	0.000	0.000	0.000	0.000
136	C	318	ILE	0	0.092	-0.094	17.666	-0.020	-0.020	0.000	0.000	0.000	0.000
137	C	318	ILE	0	-0.105	0.065	16.259	-0.010	-0.010	0.000	0.000	0.000	0.000
138	C	319	ARG	0	0.046	-0.083	19.670	0.010	0.010	0.000	0.000	0.000	0.000
139	C	319	ARG	1	0.758	0.959	23.517	0.196	0.196	0.000	0.000	0.000	0.000
140	C	320	LYS	0	0.014	-0.139	23.303	-0.021	-0.021	0.000	0.000	0.000	0.000
141	C	320	LYS	1	0.794	1.051	25.536	0.203	0.203	0.000	0.000	0.000	0.000
142	C	321	PRO	0	0.009	-0.101	26.521	-0.001	-0.001	0.000	0.000	0.000	0.000
143	C	322	ASP	0	0.081	0.021	28.909	0.003	0.003	0.000	0.000	0.000	0.000
144	C	322	ASP	-1	-0.832	-0.776	31.388	-0.160	-0.160	0.000	0.000	0.000	0.000
145	C	323	ILE	0	0.076	-0.096	32.057	0.009	0.009	0.000	0.000	0.000	0.000
146	C	323	ILE	0	-0.071	0.130	34.423	0.000	0.000	0.000	0.000	0.000	0.000
147	C	324	SER	0	0.121	-0.078	30.758	-0.010	-0.010	0.000	0.000	0.000	0.000
148	C	324	SER	0	-0.046	0.076	30.871	-0.003	-0.003	0.000	0.000	0.000	0.000
149	C	325	GLN	0	0.047	-0.093	30.362	0.011	0.011	0.000	0.000	0.000	0.000
150	C	325	GLN	0	-0.087	0.086	31.049	-0.002	-0.002	0.000	0.000	0.000	0.000
151	C	326	ARG	0	0.097	-0.105	29.515	-0.014	-0.014	0.000	0.000	0.000	0.000
152	C	326	ARG	1	0.918	1.092	31.118	0.125	0.125	0.000	0.000	0.000	0.000
153	C	327	LEU	0	-0.044	-0.118	26.481	0.001	0.001	0.000	0.000	0.000	0.000
154	C	327	LEU	0	-0.021	0.116	26.377	0.001	0.001	0.000	0.000	0.000	0.000
155	C	328	VAL	0	0.139	-0.123	25.945	-0.025	-0.025	0.000	0.000	0.000	0.000
156	C	328	VAL	0	-0.058	0.138	27.867	0.001	0.001	0.000	0.000	0.000	0.000
157	C	329	TYR	0	-0.021	-0.098	23.130	0.020	0.020	0.000	0.000	0.000	0.000
158	C	329	TYR	0	-0.109	0.041	22.404	0.000	0.000	0.000	0.000	0.000	0.000
159	C	330	GLN	0	0.199	-0.077	23.416	-0.004	-0.004	0.000	0.000	0.000	0.000
160	C	330	GLN	0	-0.081	0.123	24.266	0.019	0.019	0.000	0.000	0.000	0.000
161	C	331	PHE	0	0.010	-0.090	20.014	0.003	0.003	0.000	0.000	0.000	0.000
162	C	331	PHE	0	-0.091	0.053	16.419	-0.020	-0.020	0.000	0.000	0.000	0.000
163	C	332	VAL	0	0.116	-0.080	20.256	0.020	0.020	0.000	0.000	0.000	0.000
164	C	332	VAL	0	-0.101	0.101	20.406	0.002	0.002	0.000	0.000	0.000	0.000
165	C	333	HIS	0	0.114	-0.032	19.106	0.034	0.034	0.000	0.000	0.000	0.000
166	C	333	HIS	0	-0.078	0.086	18.253	-0.015	-0.015	0.000	0.000	0.000	0.000
167	C	334	PRO	0	-0.002	-0.113	19.221	-0.053	-0.053	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:247:GLN)