FMO DATABASE

FMODB ID: 6G56Z

Calculation Name: 3DSP-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3DSP

Chain ID: A

ChEMBL ID:

UniProt ID: Q58AD3

Base Structure: X-ray

Registration Date: 2025-07-08

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	OptHSide
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	124
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-380806.657376
FMO2-HF: Nuclear repulsion	353182.803071
FMO2-HF: Total energy	-27623.854305
FMO2-MP2: Total energy	-27698.871166

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:1:VAL)

Summations of interaction energy for fragment #1(A:1: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.
-5.351	-4.385	4.467	-1.782	-3.653	-0.024

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.128 / q_NPA : 0.039

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	2	ASP	-1	-0.876	-0.771	4.726	-1.133	-0.848	-0.001	-0.094	-0.191	0.000
5	A	3	MET	0	0.066	-0.120	3.832	-1.171	-0.233	-0.007	-0.417	-0.514	0.001
6	A	3	MET	0	-0.092	0.100	4.296	-0.697	-0.474	0.000	-0.094	-0.129	0.000
7	A	4	SER	0	0.026	-0.078	5.618	0.316	0.404	-0.002	-0.002	-0.084	0.000
8	A	4	SER	0	-0.059	0.037	8.131	0.171	0.171	0.000	0.000	0.000	0.000
9	A	5	ASN	0	0.062	-0.050	7.801	0.192	0.192	0.000	0.000	0.000	0.000
10	A	5	ASN	0	-0.130	0.040	8.639	0.133	0.133	0.000	0.000	0.000	0.000
11	A	6	VAL	0	0.127	-0.114	6.404	0.474	0.474	0.000	0.000	0.000	0.000
12	A	6	VAL	0	-0.123	0.100	4.241	-0.263	-0.211	0.001	-0.022	-0.031	0.000
13	A	7	VAL	0	0.061	-0.108	7.574	0.127	0.127	0.000	0.000	0.000	0.000
14	A	7	VAL	0	-0.090	0.109	11.115	0.047	0.047	0.000	0.000	0.000	0.000
15	A	8	LYS	0	0.052	-0.124	9.451	0.142	0.142	0.000	0.000	0.000	0.000
16	A	8	LYS	1	0.847	1.074	11.530	0.858	0.858	0.000	0.000	0.000	0.000
17	A	9	THR	0	0.033	-0.092	8.377	-0.245	-0.245	0.000	0.000	0.000	0.000
18	A	9	THR	0	-0.004	0.097	7.352	-0.436	-0.436	0.000	0.000	0.000	0.000
19	A	10	TYR	0	0.025	-0.088	9.102	0.215	0.215	0.000	0.000	0.000	0.000
20	A	10	TYR	0	-0.053	0.102	11.276	0.068	0.068	0.000	0.000	0.000	0.000
21	A	11	ASP	0	0.190	-0.044	10.445	-0.156	-0.156	0.000	0.000	0.000	0.000
22	A	11	ASP	-1	-0.915	-0.787	10.268	-1.321	-1.321	0.000	0.000	0.000	0.000
23	A	12	LEU	0	0.144	-0.101	11.952	0.117	0.117	0.000	0.000	0.000	0.000
24	A	12	LEU	0	-0.075	0.116	11.954	0.015	0.015	0.000	0.000	0.000	0.000
25	A	13	GLN	0	0.070	-0.133	13.949	-0.020	-0.020	0.000	0.000	0.000	0.000
26	A	13	GLN	0	-0.035	0.108	18.077	-0.008	-0.008	0.000	0.000	0.000	0.000
27	A	14	ASP	0	-0.035	-0.096	15.550	0.037	0.037	0.000	0.000	0.000	0.000
28	A	14	ASP	-1	-0.914	-0.786	13.727	-0.329	-0.329	0.000	0.000	0.000	0.000
29	A	15	GLY	0	-0.032	-0.135	12.669	0.108	0.108	0.000	0.000	0.000	0.000
30	A	16	SER	0	-0.002	0.022	9.296	-0.078	-0.078	0.000	0.000	0.000	0.000
31	A	16	SER	0	-0.044	0.020	9.937	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	17	LYS	0	0.017	-0.121	7.424	0.203	0.203	0.000	0.000	0.000	0.000
33	A	17	LYS	1	0.820	1.028	6.258	1.308	1.308	0.000	0.000	0.000	0.000
34	A	18	VAL	0	0.107	-0.096	7.444	-0.185	-0.185	0.000	0.000	0.000	0.000
35	A	18	VAL	0	-0.064	0.121	9.620	0.050	0.050	0.000	0.000	0.000	0.000
36	A	19	HIS	0	0.050	-0.091	5.038	0.215	0.254	-0.001	-0.018	-0.020	0.000
37	A	19	HIS	1	0.708	0.945	3.666	5.470	5.202	0.200	0.381	-0.313	-0.001
38	A	20	VAL	0	0.147	-0.085	6.537	0.238	0.238	0.000	0.000	0.000	0.000
39	A	20	VAL	0	-0.075	0.122	10.417	0.031	0.031	0.000	0.000	0.000	0.000
40	A	21	PHE	0	0.087	-0.084	8.721	-0.300	-0.300	0.000	0.000	0.000	0.000
41	A	21	PHE	0	-0.086	0.090	4.226	-0.191	-0.082	-0.001	-0.041	-0.067	0.000
42	A	22	LYS	0	0.183	-0.053	9.211	0.181	0.181	0.000	0.000	0.000	0.000
43	A	22	LYS	1	0.857	1.069	12.266	0.537	0.537	0.000	0.000	0.000	0.000
44	A	23	ASP	0	-0.042	-0.148	12.070	0.092	0.092	0.000	0.000	0.000	0.000
45	A	23	ASP	-1	-0.857	-0.796	11.624	-0.542	-0.542	0.000	0.000	0.000	0.000
46	A	24	GLY	0	-0.008	-0.113	12.909	0.103	0.103	0.000	0.000	0.000	0.000
47	A	25	LYS	0	0.099	0.021	10.671	0.046	0.046	0.000	0.000	0.000	0.000
48	A	25	LYS	1	0.821	1.024	10.008	0.261	0.261	0.000	0.000	0.000	0.000
49	A	26	MET	0	0.037	-0.136	9.119	-0.268	-0.268	0.000	0.000	0.000	0.000
50	A	26	MET	0	-0.083	0.148	10.498	0.008	0.008	0.000	0.000	0.000	0.000
51	A	27	GLY	0	-0.005	-0.120	5.907	0.303	0.303	0.000	0.000	0.000	0.000
52	A	28	MET	0	0.128	0.024	6.884	-0.608	-0.608	0.000	0.000	0.000	0.000
53	A	28	MET	0	-0.123	0.095	9.078	0.094	0.094	0.000	0.000	0.000	0.000
54	A	29	GLU	0	0.021	-0.122	4.570	0.558	0.639	-0.002	-0.015	-0.065	0.000
55	A	29	GLU	-1	-0.842	-0.755	2.071	-8.605	-9.332	4.284	-1.454	-2.102	-0.024
56	A	30	ASN	0	0.175	-0.028	6.041	-0.319	-0.319	0.000	0.000	0.000	0.000
57	A	30	ASN	0	-0.086	0.047	8.822	0.120	0.120	0.000	0.000	0.000	0.000
58	A	31	LYS	0	0.101	-0.083	7.658	-0.090	-0.090	0.000	0.000	0.000	0.000
59	A	31	LYS	1	0.816	1.044	11.744	0.045	0.045	0.000	0.000	0.000	0.000
60	A	32	PHE	0	0.001	-0.114	9.144	-0.124	-0.124	0.000	0.000	0.000	0.000
61	A	32	PHE	0	-0.072	0.089	9.880	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	33	GLY	0	0.107	-0.058	4.788	0.345	0.375	-0.002	-0.001	-0.027	0.000
63	A	34	LYS	0	0.030	-0.021	4.619	1.924	2.040	-0.002	-0.005	-0.110	0.000
64	A	34	LYS	1	0.773	1.030	6.341	-2.795	-2.795	0.000	0.000	0.000	0.000
65	A	35	SER	0	0.142	-0.069	6.179	-0.740	-0.740	0.000	0.000	0.000	0.000
66	A	35	SER	0	-0.034	0.090	6.048	0.204	0.204	0.000	0.000	0.000	0.000
67	A	36	MET	0	0.007	-0.095	6.843	0.042	0.042	0.000	0.000	0.000	0.000
68	A	36	MET	0	-0.099	0.085	8.791	-0.041	-0.041	0.000	0.000	0.000	0.000
69	A	37	ASN	0	0.131	-0.080	9.920	-0.135	-0.135	0.000	0.000	0.000	0.000
70	A	37	ASN	0	-0.112	0.080	12.988	0.047	0.047	0.000	0.000	0.000	0.000
71	A	38	MET	0	0.129	-0.103	12.385	0.020	0.020	0.000	0.000	0.000	0.000
72	A	38	MET	0	-0.102	0.129	10.148	-0.009	-0.009	0.000	0.000	0.000	0.000
73	A	39	PRO	0	-0.050	-0.124	13.048	0.043	0.043	0.000	0.000	0.000	0.000
74	A	40	GLU	0	0.102	-0.020	16.648	-0.064	-0.064	0.000	0.000	0.000	0.000
75	A	40	GLU	-1	-0.894	-0.766	18.741	-0.143	-0.143	0.000	0.000	0.000	0.000
76	A	41	GLY	0	-0.068	-0.151	18.911	0.030	0.030	0.000	0.000	0.000	0.000
77	A	42	LYS	0	0.105	0.021	19.688	0.028	0.028	0.000	0.000	0.000	0.000
78	A	42	LYS	1	0.865	1.062	16.900	0.205	0.205	0.000	0.000	0.000	0.000
79	A	43	VAL	0	0.098	-0.086	19.112	-0.039	-0.039	0.000	0.000	0.000	0.000
80	A	43	VAL	0	-0.055	0.109	21.609	0.003	0.003	0.000	0.000	0.000	0.000
81	A	44	MET	0	-0.020	-0.140	16.627	0.052	0.052	0.000	0.000	0.000	0.000
82	A	44	MET	0	-0.115	0.097	14.176	-0.011	-0.011	0.000	0.000	0.000	0.000
83	A	45	GLU	0	0.181	-0.106	18.047	-0.042	-0.042	0.000	0.000	0.000	0.000
84	A	45	GLU	-1	-0.904	-0.755	19.933	-0.243	-0.243	0.000	0.000	0.000	0.000
85	A	46	THR	0	-0.052	-0.117	16.124	-0.013	-0.013	0.000	0.000	0.000	0.000
86	A	46	THR	0	-0.062	0.013	15.613	0.012	0.012	0.000	0.000	0.000	0.000
87	A	47	ARG	0	0.165	-0.029	15.883	0.064	0.064	0.000	0.000	0.000	0.000
88	A	47	ARG	1	0.712	0.973	12.334	0.682	0.682	0.000	0.000	0.000	0.000
89	A	48	ASP	0	-0.045	-0.150	17.431	0.055	0.055	0.000	0.000	0.000	0.000
90	A	48	ASP	-1	-0.884	-0.794	17.496	-0.600	-0.600	0.000	0.000	0.000	0.000
91	A	49	GLY	0	0.027	-0.091	19.162	0.024	0.024	0.000	0.000	0.000	0.000
92	A	50	THR	0	0.076	0.085	20.045	0.044	0.044	0.000	0.000	0.000	0.000
93	A	50	THR	0	-0.027	0.055	18.767	-0.006	-0.006	0.000	0.000	0.000	0.000
94	A	51	LYS	0	0.007	-0.109	19.560	-0.013	-0.013	0.000	0.000	0.000	0.000
95	A	51	LYS	1	0.823	0.997	21.131	0.248	0.248	0.000	0.000	0.000	0.000
96	A	52	ILE	0	0.060	-0.084	16.849	0.021	0.021	0.000	0.000	0.000	0.000
97	A	52	ILE	0	-0.066	0.079	13.744	-0.021	-0.021	0.000	0.000	0.000	0.000
98	A	53	ILE	0	0.082	-0.073	18.304	0.016	0.016	0.000	0.000	0.000	0.000
99	A	53	ILE	0	-0.078	0.101	20.371	0.008	0.008	0.000	0.000	0.000	0.000
100	A	54	MET	0	0.130	-0.104	16.189	-0.026	-0.026	0.000	0.000	0.000	0.000
101	A	54	MET	0	-0.096	0.118	14.651	0.004	0.004	0.000	0.000	0.000	0.000
102	A	55	LYS	0	0.089	-0.138	17.515	0.046	0.046	0.000	0.000	0.000	0.000
103	A	55	LYS	1	0.781	1.030	21.535	0.145	0.145	0.000	0.000	0.000	0.000
104	A	56	GLY	0	0.039	-0.070	20.269	-0.013	-0.013	0.000	0.000	0.000	0.000
105	A	57	ASN	0	0.066	0.047	16.141	-0.007	-0.007	0.000	0.000	0.000	0.000
106	A	57	ASN	0	-0.131	0.043	14.616	-0.009	-0.009	0.000	0.000	0.000	0.000
107	A	58	GLU	0	0.123	-0.146	16.655	-0.056	-0.056	0.000	0.000	0.000	0.000
108	A	58	GLU	-1	-0.957	-0.807	18.894	-0.294	-0.294	0.000	0.000	0.000	0.000
109	A	59	ILE	0	0.008	-0.116	15.739	0.041	0.041	0.000	0.000	0.000	0.000
110	A	59	ILE	0	-0.068	0.069	13.294	-0.019	-0.019	0.000	0.000	0.000	0.000
111	A	60	PHE	0	0.062	-0.082	16.988	-0.013	-0.013	0.000	0.000	0.000	0.000
112	A	60	PHE	0	-0.106	0.106	20.059	0.007	0.007	0.000	0.000	0.000	0.000
113	A	61	ARG	0	0.158	-0.100	19.100	-0.025	-0.025	0.000	0.000	0.000	0.000
114	A	61	ARG	1	0.736	0.982	17.989	0.423	0.423	0.000	0.000	0.000	0.000
115	A	62	LEU	0	0.032	-0.123	20.587	0.021	0.021	0.000	0.000	0.000	0.000
116	A	62	LEU	0	-0.092	0.096	22.933	0.002	0.002	0.000	0.000	0.000	0.000
117	A	63	ASP	0	0.125	-0.095	23.792	-0.027	-0.027	0.000	0.000	0.000	0.000
118	A	63	ASP	-1	-0.962	-0.816	26.921	-0.235	-0.235	0.000	0.000	0.000	0.000
119	A	64	GLU	0	0.081	-0.082	25.977	0.020	0.020	0.000	0.000	0.000	0.000
120	A	64	GLU	-1	-0.884	-0.821	23.280	-0.352	-0.352	0.000	0.000	0.000	0.000
121	A	65	ALA	0	0.055	-0.081	27.248	0.009	0.009	0.000	0.000	0.000	0.000
122	A	65	ALA	0	-0.090	0.100	30.147	0.002	0.002	0.000	0.000	0.000	0.000
123	A	66	LEU	0	-0.157	-0.161	28.981	0.017	0.017	0.000	0.000	0.000	0.000
124	A	66	LEU	0	-0.006	-0.007	30.275	0.002	0.002	0.000	0.000	0.000	0.000

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