FMO DATABASE

FMODB ID: ZN65N

Calculation Name: 5IIP-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5IIP

Chain ID: D

ChEMBL ID:

UniProt ID: A0A160

Base Structure: X-ray

Registration Date: 2023-09-26

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	OptH
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	117
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-946178.811843
FMO2-HF: Nuclear repulsion	899449.778064
FMO2-HF: Total energy	-46729.033779
FMO2-MP2: Total energy	-46866.09395

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(D:253:GLY)

Summations of interaction energy for fragment #1(D:253:GLY)

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.
-4.293	-1.363	0.192	-1.305	-1.818	-0.002

Interaction energy analysis for fragmet #1(D:253:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : -0.001

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	D	255	MET	0	-0.059	0.007	2.898	-2.356	0.423	0.195	-1.280	-1.695	-0.002
4	D	256	ILE	0	0.012	0.013	4.685	-0.744	-0.754	-0.001	-0.008	0.019	0.000
5	D	257	LYS	1	1.002	0.978	7.754	0.392	0.392	0.000	0.000	0.000	0.000
6	D	258	PRO	0	-0.013	0.012	9.650	0.051	0.051	0.000	0.000	0.000	0.000
7	D	259	ILE	0	-0.018	-0.005	12.414	-0.030	-0.030	0.000	0.000	0.000	0.000
8	D	260	THR	0	-0.012	-0.014	15.438	0.019	0.019	0.000	0.000	0.000	0.000
9	D	261	ILE	0	-0.009	-0.004	17.984	-0.006	-0.006	0.000	0.000	0.000	0.000
10	D	262	GLN	0	0.024	0.020	20.821	0.008	0.008	0.000	0.000	0.000	0.000
11	D	263	ALA	0	0.033	-0.001	23.166	0.006	0.006	0.000	0.000	0.000	0.000
12	D	264	GLU	-1	-0.930	-0.968	25.098	-0.021	-0.021	0.000	0.000	0.000	0.000
13	D	265	ALA	0	-0.049	0.002	26.342	0.000	0.000	0.000	0.000	0.000	0.000
14	D	266	THR	0	-0.017	-0.028	28.237	0.006	0.006	0.000	0.000	0.000	0.000
15	D	267	LEU	0	0.051	0.017	28.096	-0.002	-0.002	0.000	0.000	0.000	0.000
16	D	268	ASN	0	-0.013	-0.016	29.139	0.001	0.001	0.000	0.000	0.000	0.000
17	D	269	ASP	-1	-0.828	-0.903	27.589	-0.023	-0.023	0.000	0.000	0.000	0.000
18	D	270	ALA	0	0.013	-0.003	25.060	-0.005	-0.005	0.000	0.000	0.000	0.000
19	D	271	VAL	0	0.028	0.018	25.253	0.000	0.000	0.000	0.000	0.000	0.000
20	D	272	HIS	0	-0.014	-0.004	27.224	-0.002	-0.002	0.000	0.000	0.000	0.000
21	D	273	ILE	0	-0.014	-0.013	21.569	-0.007	-0.007	0.000	0.000	0.000	0.000
22	D	274	MET	0	-0.005	0.044	21.924	-0.008	-0.008	0.000	0.000	0.000	0.000
23	D	275	ARG	1	0.945	1.014	23.341	0.031	0.031	0.000	0.000	0.000	0.000
24	D	276	GLN	0	-0.093	-0.063	23.736	-0.006	-0.006	0.000	0.000	0.000	0.000
25	D	277	LYS	1	0.946	0.975	18.710	0.076	0.076	0.000	0.000	0.000	0.000
26	D	278	ARG	1	0.922	0.952	20.389	0.011	0.011	0.000	0.000	0.000	0.000
27	D	279	VAL	0	-0.046	-0.019	17.178	0.003	0.003	0.000	0.000	0.000	0.000
28	D	280	ASP	-1	-0.905	-0.964	19.533	0.061	0.061	0.000	0.000	0.000	0.000
29	D	281	THR	0	0.364	0.477	17.969	-0.004	-0.004	0.000	0.000	0.000	0.000
30	D	282	ILE	0	-0.030	-0.013	17.928	-0.010	-0.010	0.000	0.000	0.000	0.000
31	D	283	PHE	0	0.003	-0.009	14.197	0.020	0.020	0.000	0.000	0.000	0.000
32	D	284	VAL	0	0.007	0.008	17.581	-0.019	-0.019	0.000	0.000	0.000	0.000
33	D	285	VAL	0	0.006	0.004	16.070	0.008	0.008	0.000	0.000	0.000	0.000
34	D	286	ASP	-1	-0.787	-0.891	19.272	-0.029	-0.029	0.000	0.000	0.000	0.000
35	D	287	SER	0	-0.018	-0.010	20.792	-0.012	-0.012	0.000	0.000	0.000	0.000
36	D	288	ASN	0	-0.046	-0.025	20.398	-0.015	-0.015	0.000	0.000	0.000	0.000
37	D	289	ASN	0	-0.033	-0.030	15.533	-0.016	-0.016	0.000	0.000	0.000	0.000
38	D	290	HIS	0	-0.030	-0.014	15.948	-0.006	-0.006	0.000	0.000	0.000	0.000
39	D	291	LEU	0	-0.037	-0.021	14.136	0.002	0.002	0.000	0.000	0.000	0.000
40	D	292	LEU	0	-0.046	-0.024	17.097	0.008	0.008	0.000	0.000	0.000	0.000
41	D	293	GLY	0	0.011	-0.014	19.457	0.006	0.006	0.000	0.000	0.000	0.000
42	D	294	PHE	0	-0.069	-0.029	16.684	0.001	0.001	0.000	0.000	0.000	0.000
43	D	295	LEU	0	0.182	-0.029	19.983	-0.005	-0.005	0.000	0.000	0.000	0.000
44	D	296	ASP	-1	-1.346	-1.377	21.134	0.074	0.074	0.000	0.000	0.000	0.000
45	D	297	ILE	0	0.010	-0.002	23.066	-0.007	-0.007	0.000	0.000	0.000	0.000
46	D	298	GLU	-1	-0.948	-0.976	26.213	0.036	0.036	0.000	0.000	0.000	0.000
47	D	299	ASP	-1	-0.852	-0.943	24.657	0.059	0.059	0.000	0.000	0.000	0.000
48	D	300	ILE	0	-0.005	-0.012	25.062	-0.006	-0.006	0.000	0.000	0.000	0.000
49	D	301	ASN	0	-0.036	-0.010	28.811	-0.008	-0.008	0.000	0.000	0.000	0.000
50	D	302	GLN	0	-0.051	-0.032	29.096	-0.005	-0.005	0.000	0.000	0.000	0.000
51	D	303	GLY	0	0.023	0.023	31.471	-0.002	-0.002	0.000	0.000	0.000	0.000
52	D	304	ILE	0	-0.015	-0.006	32.295	-0.003	-0.003	0.000	0.000	0.000	0.000
53	D	305	ARG	1	0.901	0.964	34.911	-0.022	-0.022	0.000	0.000	0.000	0.000
54	D	306	GLY	0	0.003	0.007	36.350	0.002	0.002	0.000	0.000	0.000	0.000
55	D	307	HIS	0	-0.067	-0.042	36.911	0.000	0.000	0.000	0.000	0.000	0.000
56	D	308	LYS	1	0.971	0.997	33.323	-0.024	-0.024	0.000	0.000	0.000	0.000
57	D	309	SER	0	0.031	0.016	32.155	-0.002	-0.002	0.000	0.000	0.000	0.000
58	D	310	LEU	0	0.027	0.040	24.890	0.004	0.004	0.000	0.000	0.000	0.000
59	D	311	ARG	1	0.979	0.965	26.395	-0.002	-0.002	0.000	0.000	0.000	0.000
60	D	312	ASP	-1	-0.924	-0.963	28.146	0.025	0.025	0.000	0.000	0.000	0.000
61	D	313	THR	0	-0.070	-0.060	27.933	0.003	0.003	0.000	0.000	0.000	0.000
62	D	314	MET	0	-0.079	-0.003	23.468	0.004	0.004	0.000	0.000	0.000	0.000
63	D	315	GLN	0	-0.003	0.006	22.704	0.005	0.005	0.000	0.000	0.000	0.000
64	D	316	GLN	0	0.007	-0.018	21.881	0.004	0.004	0.000	0.000	0.000	0.000
65	D	317	HIS	0	-0.033	0.004	21.581	0.011	0.011	0.000	0.000	0.000	0.000
66	D	318	ILE	0	0.030	0.010	16.087	0.012	0.012	0.000	0.000	0.000	0.000
67	D	319	TYR	0	-0.059	-0.019	13.020	-0.006	-0.006	0.000	0.000	0.000	0.000
68	D	320	THR	0	-0.002	-0.008	12.254	0.019	0.019	0.000	0.000	0.000	0.000
69	D	321	VAL	0	0.005	-0.015	7.641	0.032	0.032	0.000	0.000	0.000	0.000
70	D	322	GLN	0	0.085	0.047	8.940	-0.041	-0.041	0.000	0.000	0.000	0.000
71	D	323	ILE	0	0.001	-0.007	4.105	0.146	0.241	-0.001	-0.015	-0.079	0.000
72	D	324	ASP	-1	-0.969	-0.966	4.887	-0.284	-0.218	-0.001	-0.002	-0.063	0.000
73	D	325	SER	0	0.006	0.017	6.738	0.074	0.074	0.000	0.000	0.000	0.000
74	D	326	LYS	1	0.970	0.976	5.663	-0.176	-0.176	0.000	0.000	0.000	0.000
75	D	327	LEU	0	0.058	0.028	6.010	-0.069	-0.069	0.000	0.000	0.000	0.000
76	D	328	GLN	0	0.016	-0.022	7.580	-0.194	-0.194	0.000	0.000	0.000	0.000
77	D	329	ASP	-1	-0.994	-0.988	10.547	0.300	0.300	0.000	0.000	0.000	0.000
78	D	330	SER	0	0.011	0.013	9.421	-0.042	-0.042	0.000	0.000	0.000	0.000
79	D	331	VAL	0	0.043	0.019	11.215	-0.085	-0.085	0.000	0.000	0.000	0.000
80	D	332	ARG	1	0.979	0.979	12.553	-0.395	-0.395	0.000	0.000	0.000	0.000
81	D	333	THR	0	-0.038	-0.017	15.145	-0.071	-0.071	0.000	0.000	0.000	0.000
82	D	334	ILE	0	0.025	0.011	10.642	-0.068	-0.068	0.000	0.000	0.000	0.000
83	D	335	LEU	0	-0.011	0.003	14.888	-0.056	-0.056	0.000	0.000	0.000	0.000
84	D	336	LYS	1	0.935	0.965	17.013	-0.284	-0.284	0.000	0.000	0.000	0.000
85	D	337	ARG	1	0.929	0.987	18.453	-0.263	-0.263	0.000	0.000	0.000	0.000
86	D	338	ASN	0	0.034	0.001	19.502	0.018	0.018	0.000	0.000	0.000	0.000
87	D	339	VAL	0	-0.041	-0.004	15.520	-0.018	-0.018	0.000	0.000	0.000	0.000
88	D	340	ARG	1	1.037	0.997	16.099	-0.091	-0.091	0.000	0.000	0.000	0.000
89	D	341	ASN	0	-0.015	0.002	13.298	0.013	0.013	0.000	0.000	0.000	0.000
90	D	342	VAL	0	0.018	0.013	10.349	-0.044	-0.044	0.000	0.000	0.000	0.000
91	D	343	PRO	0	0.003	-0.002	9.595	0.115	0.115	0.000	0.000	0.000	0.000
92	D	344	VAL	0	-0.011	-0.009	4.895	0.100	0.100	0.000	0.000	0.000	0.000
93	D	345	VAL	0	-0.012	-0.016	8.058	-0.151	-0.151	0.000	0.000	0.000	0.000
94	D	346	ASP	-1	-0.745	-0.851	9.466	-0.091	-0.091	0.000	0.000	0.000	0.000
95	D	347	ASP	-1	-0.938	-1.027	11.082	0.073	0.073	0.000	0.000	0.000	0.000
96	D	348	GLN	0	0.206	0.191	14.004	0.021	0.021	0.000	0.000	0.000	0.000
97	D	349	GLN	0	-0.087	0.046	14.565	-0.023	-0.023	0.000	0.000	0.000	0.000
98	D	350	ARG	0	-0.263	-0.269	13.501	0.023	0.023	0.000	0.000	0.000	0.000
99	D	351	LEU	0	-0.031	-0.008	10.770	-0.006	-0.006	0.000	0.000	0.000	0.000
100	D	352	VAL	0	0.030	0.011	6.849	-0.050	-0.050	0.000	0.000	0.000	0.000
101	D	353	GLY	0	-0.057	-0.046	6.258	-0.187	-0.187	0.000	0.000	0.000	0.000
102	D	354	LEU	0	-0.015	0.004	7.340	0.175	0.175	0.000	0.000	0.000	0.000
103	D	355	ILE	0	0.024	0.013	5.634	0.019	0.019	0.000	0.000	0.000	0.000
104	D	356	THR	0	0.020	0.013	8.275	-0.079	-0.079	0.000	0.000	0.000	0.000
105	D	357	ARG	1	0.927	0.948	11.560	-0.187	-0.187	0.000	0.000	0.000	0.000
106	D	358	ALA	0	-0.050	-0.029	14.051	0.008	0.008	0.000	0.000	0.000	0.000
107	D	359	ASN	0	0.105	0.042	9.946	-0.062	-0.062	0.000	0.000	0.000	0.000
108	D	360	VAL	0	-0.020	0.001	9.614	0.018	0.018	0.000	0.000	0.000	0.000
109	D	361	VAL	0	-0.036	-0.028	11.677	-0.026	-0.026	0.000	0.000	0.000	0.000
110	D	362	ASP	-1	-0.865	-0.928	13.726	0.108	0.108	0.000	0.000	0.000	0.000
111	D	363	ILE	0	0.053	0.051	8.119	0.004	0.004	0.000	0.000	0.000	0.000
112	D	364	VAL	0	-0.020	0.052	12.260	-0.024	-0.024	0.000	0.000	0.000	0.000
113	D	365	TYR	0	-0.066	-0.039	14.066	-0.034	-0.034	0.000	0.000	0.000	0.000
114	D	366	ASP	-1	-0.857	-0.932	14.772	0.044	0.044	0.000	0.000	0.000	0.000
115	D	367	THR	0	-0.189	-0.156	12.981	-0.009	-0.009	0.000	0.000	0.000	0.000
116	D	368	ILE	0	-0.100	-0.040	15.094	-0.019	-0.019	0.000	0.000	0.000	0.000
117	D	369	TRP	0	-0.029	-0.007	18.428	-0.010	-0.010	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:253:GLY)