FMO DATABASE

FMODB ID: RY748

Calculation Name: 4DFC-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4DFC

Chain ID: A

ChEMBL ID:

UniProt ID: P30958

Base Structure: X-ray

Registration Date: 2025-07-10

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	OptH
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	162
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-607997.41149
FMO2-HF: Nuclear repulsion	573432.68269
FMO2-HF: Total energy	-34564.7288
FMO2-MP2: Total energy	-34664.679402

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(A:129:VAL)

Summations of interaction energy for fragment #1(A:129:VAL)

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.
1.764	2.844	7.535	-4.86	-3.757	-0.022

Interaction energy analysis for fragmet #1(A:129:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.144 / q_NPA : 0.022

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	A	130	MET	0	-0.061	0.136	3.681	-0.313	0.129	0.013	-0.169	-0.287	0.000
5	A	131	LYS	0	0.149	-0.041	3.852	-1.187	0.350	-0.015	-0.862	-0.659	0.000
6	A	131	LYS	1	0.759	0.987	3.767	6.191	6.335	-0.001	-0.045	-0.098	0.000
7	A	132	LYS	0	0.153	-0.077	6.968	0.296	0.296	0.000	0.000	0.000	0.000
8	A	132	LYS	1	0.832	1.080	11.366	0.403	0.403	0.000	0.000	0.000	0.000
9	A	133	GLY	0	-0.045	-0.108	10.659	-0.173	-0.173	0.000	0.000	0.000	0.000
10	A	134	GLN	0	0.113	0.021	8.749	0.027	0.027	0.000	0.000	0.000	0.000
11	A	134	GLN	0	-0.116	0.094	4.809	-0.683	-0.683	0.000	0.000	0.000	0.000
12	A	135	ARG	0	0.113	-0.103	10.281	0.155	0.155	0.000	0.000	0.000	0.000
13	A	135	ARG	1	0.784	1.044	12.920	0.221	0.221	0.000	0.000	0.000	0.000
14	A	136	LEU	0	-0.015	-0.123	9.662	-0.167	-0.167	0.000	0.000	0.000	0.000
15	A	136	LEU	0	-0.091	0.099	7.630	0.041	0.041	0.000	0.000	0.000	0.000
16	A	137	SER	0	0.168	-0.037	11.110	-0.009	-0.009	0.000	0.000	0.000	0.000
17	A	137	SER	0	-0.050	0.052	12.697	0.010	0.010	0.000	0.000	0.000	0.000
18	A	138	ARG	0	0.087	-0.100	12.263	0.166	0.166	0.000	0.000	0.000	0.000
19	A	138	ARG	1	0.829	1.062	13.755	-0.444	-0.444	0.000	0.000	0.000	0.000
20	A	139	ASP	0	0.071	-0.121	14.048	0.139	0.139	0.000	0.000	0.000	0.000
21	A	139	ASP	-1	-0.954	-0.837	17.108	0.450	0.450	0.000	0.000	0.000	0.000
22	A	140	ALA	0	0.036	-0.094	12.562	0.026	0.026	0.000	0.000	0.000	0.000
23	A	140	ALA	0	-0.077	0.079	11.835	-0.020	-0.020	0.000	0.000	0.000	0.000
24	A	141	LEU	0	0.144	-0.094	10.146	0.112	0.112	0.000	0.000	0.000	0.000
25	A	141	LEU	0	-0.090	0.117	7.925	0.004	0.004	0.000	0.000	0.000	0.000
26	A	142	ARG	0	0.096	-0.059	10.968	0.210	0.210	0.000	0.000	0.000	0.000
27	A	142	ARG	1	0.847	1.065	14.385	-0.593	-0.593	0.000	0.000	0.000	0.000
28	A	143	THR	0	0.062	-0.068	14.218	0.049	0.049	0.000	0.000	0.000	0.000
29	A	143	THR	0	-0.029	0.067	15.242	-0.008	-0.008	0.000	0.000	0.000	0.000
30	A	144	GLN	0	0.119	-0.074	10.817	-0.127	-0.127	0.000	0.000	0.000	0.000
31	A	144	GLN	0	-0.127	0.073	7.078	0.059	0.059	0.000	0.000	0.000	0.000
32	A	145	LEU	0	0.026	-0.134	11.543	0.095	0.095	0.000	0.000	0.000	0.000
33	A	145	LEU	0	-0.036	0.100	9.280	0.044	0.044	0.000	0.000	0.000	0.000
34	A	146	ASP	0	0.147	-0.061	12.238	0.006	0.006	0.000	0.000	0.000	0.000
35	A	146	ASP	-1	-0.960	-0.810	16.626	0.751	0.751	0.000	0.000	0.000	0.000
36	A	147	SER	0	0.025	-0.094	15.023	-0.064	-0.064	0.000	0.000	0.000	0.000
37	A	147	SER	0	-0.099	0.057	14.478	-0.052	-0.052	0.000	0.000	0.000	0.000
38	A	148	ALA	0	0.023	-0.118	11.700	-0.188	-0.188	0.000	0.000	0.000	0.000
39	A	148	ALA	0	-0.099	0.095	11.164	0.094	0.094	0.000	0.000	0.000	0.000
40	A	149	GLY	0	-0.080	-0.133	13.153	0.012	0.012	0.000	0.000	0.000	0.000
41	A	150	TYR	0	0.049	-0.015	14.086	-0.094	-0.094	0.000	0.000	0.000	0.000
42	A	150	TYR	0	-0.086	0.094	9.644	0.134	0.134	0.000	0.000	0.000	0.000
43	A	151	ARG	0	0.061	-0.113	15.309	-0.044	-0.044	0.000	0.000	0.000	0.000
44	A	151	ARG	1	0.893	1.091	18.859	-0.602	-0.602	0.000	0.000	0.000	0.000
45	A	152	HIS	0	0.154	-0.042	17.544	0.061	0.061	0.000	0.000	0.000	0.000
46	A	152	HIS	0	-0.142	0.053	18.654	-0.009	-0.009	0.000	0.000	0.000	0.000
47	A	153	VAL	0	-0.043	-0.160	19.220	-0.050	-0.050	0.000	0.000	0.000	0.000
48	A	153	VAL	0	-0.044	0.136	18.961	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	154	ASP	0	0.068	-0.111	20.728	0.028	0.028	0.000	0.000	0.000	0.000
50	A	154	ASP	-1	-0.940	-0.829	24.489	0.315	0.315	0.000	0.000	0.000	0.000
51	A	155	GLN	0	0.087	-0.137	21.462	0.003	0.003	0.000	0.000	0.000	0.000
52	A	155	GLN	0	-0.143	0.078	22.427	-0.018	-0.018	0.000	0.000	0.000	0.000
53	A	156	VAL	0	0.015	-0.084	17.320	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	156	VAL	0	-0.095	0.097	15.531	0.006	0.006	0.000	0.000	0.000	0.000
55	A	157	MET	0	0.120	-0.089	18.780	-0.027	-0.027	0.000	0.000	0.000	0.000
56	A	157	MET	0	-0.122	0.093	21.808	-0.008	-0.008	0.000	0.000	0.000	0.000
57	A	158	GLU	0	0.124	-0.092	18.688	-0.018	-0.018	0.000	0.000	0.000	0.000
58	A	158	GLU	-1	-1.052	-0.878	19.589	0.432	0.432	0.000	0.000	0.000	0.000
59	A	159	HIS	0	0.060	-0.137	15.131	0.063	0.063	0.000	0.000	0.000	0.000
60	A	159	HIS	0	-0.119	0.093	15.237	-0.032	-0.032	0.000	0.000	0.000	0.000
61	A	160	GLY	0	0.010	-0.085	13.841	-0.051	-0.051	0.000	0.000	0.000	0.000
62	A	161	GLU	0	0.014	-0.047	14.838	-0.009	-0.009	0.000	0.000	0.000	0.000
63	A	161	GLU	-1	-0.887	-0.793	16.892	0.517	0.517	0.000	0.000	0.000	0.000
64	A	162	TYR	0	0.090	-0.075	14.135	0.110	0.110	0.000	0.000	0.000	0.000
65	A	162	TYR	0	-0.150	0.005	13.378	0.002	0.002	0.000	0.000	0.000	0.000
66	A	163	ALA	0	0.166	-0.103	15.164	-0.057	-0.057	0.000	0.000	0.000	0.000
67	A	163	ALA	0	-0.072	0.137	17.886	-0.012	-0.012	0.000	0.000	0.000	0.000
68	A	164	THR	0	-0.060	-0.094	16.585	0.045	0.045	0.000	0.000	0.000	0.000
69	A	164	THR	0	-0.080	0.044	16.585	-0.017	-0.017	0.000	0.000	0.000	0.000
70	A	165	ARG	0	0.111	-0.127	18.773	-0.032	-0.032	0.000	0.000	0.000	0.000
71	A	165	ARG	1	0.756	1.039	19.296	-0.363	-0.363	0.000	0.000	0.000	0.000
72	A	166	GLY	0	0.044	-0.081	20.352	-0.016	-0.016	0.000	0.000	0.000	0.000
73	A	167	ALA	0	0.104	-0.062	18.980	0.056	0.056	0.000	0.000	0.000	0.000
74	A	167	ALA	0	0.000	0.175	18.888	-0.009	-0.009	0.000	0.000	0.000	0.000
75	A	168	LEU	0	0.035	-0.109	16.391	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	168	LEU	0	-0.083	0.106	17.241	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	169	LEU	0	0.129	-0.072	13.680	-0.030	-0.030	0.000	0.000	0.000	0.000
78	A	169	LEU	0	-0.138	0.077	11.183	0.013	0.013	0.000	0.000	0.000	0.000
79	A	170	ASP	0	0.094	-0.089	12.995	0.063	0.063	0.000	0.000	0.000	0.000
80	A	170	ASP	-1	-0.839	-0.764	15.648	0.417	0.417	0.000	0.000	0.000	0.000
81	A	171	LEU	0	0.152	-0.073	10.562	-0.043	-0.043	0.000	0.000	0.000	0.000
82	A	171	LEU	0	-0.132	0.092	7.828	0.076	0.076	0.000	0.000	0.000	0.000
83	A	172	PHE	0	0.125	-0.107	11.461	0.022	0.022	0.000	0.000	0.000	0.000
84	A	172	PHE	0	-0.097	0.120	12.566	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	173	PRO	0	-0.035	-0.116	7.677	0.038	0.038	0.000	0.000	0.000	0.000
86	A	174	MET	0	0.123	0.008	9.775	-0.278	-0.278	0.000	0.000	0.000	0.000
87	A	174	MET	0	-0.093	0.099	11.843	-0.072	-0.072	0.000	0.000	0.000	0.000
88	A	175	GLY	0	-0.031	-0.116	10.857	0.155	0.155	0.000	0.000	0.000	0.000
89	A	176	SER	0	0.042	0.039	10.411	-0.159	-0.159	0.000	0.000	0.000	0.000
90	A	176	SER	0	-0.072	0.041	9.447	0.027	0.027	0.000	0.000	0.000	0.000
91	A	177	GLU	0	0.016	-0.109	11.491	0.027	0.027	0.000	0.000	0.000	0.000
92	A	177	GLU	-1	-0.911	-0.860	12.713	0.316	0.316	0.000	0.000	0.000	0.000
93	A	178	LEU	0	0.018	-0.124	13.050	-0.010	-0.010	0.000	0.000	0.000	0.000
94	A	178	LEU	0	-0.084	0.126	12.152	-0.019	-0.019	0.000	0.000	0.000	0.000
95	A	179	PRO	0	-0.006	-0.090	11.744	0.154	0.154	0.000	0.000	0.000	0.000
96	A	180	TYR	0	0.119	0.004	10.015	-0.157	-0.157	0.000	0.000	0.000	0.000
97	A	180	TYR	0	-0.083	0.085	9.026	-0.021	-0.021	0.000	0.000	0.000	0.000
98	A	181	ARG	0	0.119	-0.083	11.488	0.145	0.145	0.000	0.000	0.000	0.000
99	A	181	ARG	1	0.671	0.979	14.892	-0.332	-0.332	0.000	0.000	0.000	0.000
100	A	182	LEU	0	0.013	-0.146	11.240	-0.135	-0.135	0.000	0.000	0.000	0.000
101	A	182	LEU	0	-0.070	0.105	7.981	0.047	0.047	0.000	0.000	0.000	0.000
102	A	183	ASP	0	0.139	-0.099	12.318	0.078	0.078	0.000	0.000	0.000	0.000
103	A	183	ASP	-1	-1.016	-0.856	15.905	0.079	0.079	0.000	0.000	0.000	0.000
104	A	184	PHE	0	0.036	-0.087	14.918	-0.081	-0.081	0.000	0.000	0.000	0.000
105	A	184	PHE	0	-0.137	0.061	10.865	0.051	0.051	0.000	0.000	0.000	0.000
106	A	185	PHE	0	0.223	-0.062	15.932	0.029	0.029	0.000	0.000	0.000	0.000
107	A	185	PHE	0	-0.125	0.090	18.228	-0.005	-0.005	0.000	0.000	0.000	0.000
108	A	186	ASP	0	0.015	-0.100	17.866	-0.027	-0.027	0.000	0.000	0.000	0.000
109	A	186	ASP	-1	-1.034	-0.901	19.116	0.020	0.020	0.000	0.000	0.000	0.000
110	A	187	ASP	0	0.050	-0.111	15.625	0.065	0.065	0.000	0.000	0.000	0.000
111	A	187	ASP	-1	-0.915	-0.833	15.160	-0.093	-0.093	0.000	0.000	0.000	0.000
112	A	188	GLU	0	0.130	-0.109	13.566	0.013	0.013	0.000	0.000	0.000	0.000
113	A	188	GLU	-1	-1.001	-0.843	13.694	-0.375	-0.375	0.000	0.000	0.000	0.000
114	A	189	ILE	0	0.026	-0.146	11.047	0.115	0.115	0.000	0.000	0.000	0.000
115	A	189	ILE	0	-0.116	0.106	8.449	0.031	0.031	0.000	0.000	0.000	0.000
116	A	190	ASP	0	0.129	-0.096	12.532	-0.158	-0.158	0.000	0.000	0.000	0.000
117	A	190	ASP	-1	-1.019	-0.830	16.559	-0.136	-0.136	0.000	0.000	0.000	0.000
118	A	191	SER	0	-0.031	-0.127	13.686	-0.096	-0.096	0.000	0.000	0.000	0.000
119	A	191	SER	0	-0.015	0.081	15.066	0.033	0.033	0.000	0.000	0.000	0.000
120	A	192	LEU	0	0.045	-0.145	9.987	0.120	0.120	0.000	0.000	0.000	0.000
121	A	192	LEU	0	-0.062	0.144	7.544	0.037	0.037	0.000	0.000	0.000	0.000
122	A	193	ARG	0	0.066	-0.072	11.361	-0.090	-0.090	0.000	0.000	0.000	0.000
123	A	193	ARG	1	0.851	1.072	15.288	0.013	0.013	0.000	0.000	0.000	0.000
124	A	194	VAL	0	0.184	-0.096	13.322	0.123	0.123	0.000	0.000	0.000	0.000
125	A	194	VAL	0	-0.032	0.154	12.602	0.000	0.000	0.000	0.000	0.000	0.000
126	A	195	PHE	0	0.006	-0.089	14.350	-0.069	-0.069	0.000	0.000	0.000	0.000
127	A	195	PHE	0	-0.123	0.075	14.188	-0.004	-0.004	0.000	0.000	0.000	0.000
128	A	196	ASP	0	0.155	-0.071	17.005	0.053	0.053	0.000	0.000	0.000	0.000
129	A	196	ASP	-1	-0.904	-0.828	20.938	0.203	0.203	0.000	0.000	0.000	0.000
130	A	197	VAL	0	0.034	-0.160	19.781	-0.010	-0.010	0.000	0.000	0.000	0.000
131	A	197	VAL	0	-0.032	0.158	18.341	0.006	0.006	0.000	0.000	0.000	0.000
132	A	198	ASP	0	0.144	-0.069	20.483	0.008	0.008	0.000	0.000	0.000	0.000
133	A	198	ASP	-1	-1.019	-0.848	24.685	0.231	0.231	0.000	0.000	0.000	0.000
134	A	199	SER	0	0.004	-0.104	23.926	-0.007	-0.007	0.000	0.000	0.000	0.000
135	A	199	SER	0	-0.131	0.012	23.578	-0.008	-0.008	0.000	0.000	0.000	0.000
136	A	200	GLN	0	0.060	-0.104	21.139	-0.016	-0.016	0.000	0.000	0.000	0.000
137	A	200	GLN	0	-0.113	0.102	20.402	0.000	0.000	0.000	0.000	0.000	0.000
138	A	201	ARG	0	0.039	-0.114	21.701	0.006	0.006	0.000	0.000	0.000	0.000
139	A	201	ARG	1	0.840	1.057	23.346	-0.117	-0.117	0.000	0.000	0.000	0.000
140	A	202	THR	0	0.081	-0.061	18.577	0.023	0.023	0.000	0.000	0.000	0.000
141	A	202	THR	0	-0.126	-0.012	18.497	-0.008	-0.008	0.000	0.000	0.000	0.000
142	A	203	LEU	0	0.055	-0.083	18.143	-0.026	-0.026	0.000	0.000	0.000	0.000
143	A	203	LEU	0	-0.121	0.090	17.778	-0.004	-0.004	0.000	0.000	0.000	0.000
144	A	204	GLU	0	0.077	-0.115	17.950	0.002	0.002	0.000	0.000	0.000	0.000
145	A	204	GLU	-1	-0.951	-0.832	15.872	0.020	0.020	0.000	0.000	0.000	0.000
146	A	205	GLU	0	0.051	-0.123	14.750	0.062	0.062	0.000	0.000	0.000	0.000
147	A	205	GLU	-1	-0.979	-0.865	14.076	-0.262	-0.262	0.000	0.000	0.000	0.000
148	A	206	VAL	0	0.001	-0.136	11.047	-0.014	-0.014	0.000	0.000	0.000	0.000
149	A	206	VAL	0	-0.065	0.115	9.596	-0.002	-0.002	0.000	0.000	0.000	0.000
150	A	207	GLU	0	0.146	-0.084	10.707	0.061	0.061	0.000	0.000	0.000	0.000
151	A	207	GLU	-1	-1.003	-0.850	10.498	-0.603	-0.603	0.000	0.000	0.000	0.000
152	A	208	ALA	0	0.095	-0.117	6.459	-0.053	-0.053	0.000	0.000	0.000	0.000
153	A	208	ALA	0	-0.124	0.076	5.375	-0.218	-0.213	-0.001	-0.001	-0.003	0.000
154	A	209	ILE	0	0.016	-0.119	4.702	-0.135	-0.045	-0.002	-0.027	-0.062	0.000
155	A	209	ILE	0	-0.048	0.140	4.054	0.035	0.130	0.000	-0.031	-0.065	0.000
156	A	210	ASN	0	0.153	-0.055	1.895	0.315	-0.657	7.324	-4.904	-1.449	-0.022
157	A	210	ASN	0	-0.118	0.049	3.678	-2.504	-2.383	0.011	0.077	-0.209	-0.001
158	A	211	LEU	0	0.113	-0.125	2.893	0.263	-1.015	0.095	1.572	-0.389	-0.002
159	A	211	LEU	0	-0.092	0.142	3.362	-0.268	0.506	0.112	-0.441	-0.444	0.003
160	A	212	LEU	0	0.059	-0.145	4.358	-0.884	-0.762	-0.001	-0.029	-0.092	0.000
161	A	212	LEU	0	-0.057	0.154	7.848	-0.121	-0.121	0.000	0.000	0.000	0.000
162	A	213	PRO	0	0.004	-0.094	6.545	0.009	0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:129:VAL)