FMO DATABASE

FMODB ID: MNMVZ

Calculation Name: 3F1I-S-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3F1I

Chain ID: S

ChEMBL ID:
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UniProt ID: O14964

Base Structure: X-ray

Registration Date: 2023-09-20

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	77
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-394778.055903
FMO2-HF: Nuclear repulsion	361880.980149
FMO2-HF: Total energy	-32897.075754
FMO2-MP2: Total energy	-32987.720763

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(S:301:PHE)

Summations of interaction energy for fragment #1(S:301:PHE)

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.
-15.091	-6.444	3.724	-3.176	-9.197	-0.001

Interaction energy analysis for fragmet #1(S:301:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.026 / q_NPA : -0.031

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

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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	S	303	ASP	-1	-0.909	-0.988	3.725	-1.836	-0.175	0.001	-0.526	-1.136	0.001
4	S	304	GLU	-1	-0.879	-0.961	5.600	-0.465	-0.465	0.000	0.000	0.000	0.000
5	S	305	ASP	-1	-0.853	-0.904	8.820	-0.484	-0.484	0.000	0.000	0.000	0.000
6	S	306	LYS	1	0.836	0.914	4.380	-0.333	-0.164	-0.001	-0.009	-0.160	0.000
7	S	307	MET	0	-0.016	-0.015	6.931	0.130	0.130	0.000	0.000	0.000	0.000
8	S	308	ASP	-1	-0.902	-0.934	10.104	-0.486	-0.486	0.000	0.000	0.000	0.000
9	S	309	GLN	0	-0.062	-0.036	12.510	0.039	0.039	0.000	0.000	0.000	0.000
10	S	310	LEU	0	0.020	0.014	9.610	0.066	0.066	0.000	0.000	0.000	0.000
11	S	311	LEU	0	-0.002	0.005	12.851	0.075	0.075	0.000	0.000	0.000	0.000
12	S	312	GLN	0	-0.020	-0.021	15.101	0.063	0.063	0.000	0.000	0.000	0.000
13	S	313	MET	0	-0.019	0.015	14.951	0.026	0.026	0.000	0.000	0.000	0.000
14	S	314	LEU	0	0.019	0.026	13.910	0.037	0.037	0.000	0.000	0.000	0.000
15	S	315	GLN	0	-0.047	-0.029	17.974	0.045	0.045	0.000	0.000	0.000	0.000
16	S	316	SER	0	-0.119	-0.068	20.591	0.033	0.033	0.000	0.000	0.000	0.000
17	S	317	THR	0	-0.019	-0.016	20.257	0.021	0.021	0.000	0.000	0.000	0.000
18	S	318	ASP	-1	-0.872	-0.941	22.764	-0.166	-0.166	0.000	0.000	0.000	0.000
19	S	319	PRO	0	-0.033	-0.032	25.306	0.001	0.001	0.000	0.000	0.000	0.000
20	S	320	SER	0	-0.102	-0.051	26.267	0.007	0.007	0.000	0.000	0.000	0.000
21	S	321	ASP	-1	-0.874	-0.925	25.493	-0.181	-0.181	0.000	0.000	0.000	0.000
22	S	322	ASP	-1	-0.990	-0.986	28.029	-0.126	-0.126	0.000	0.000	0.000	0.000
23	S	323	GLN	0	-0.121	-0.059	24.467	0.010	0.010	0.000	0.000	0.000	0.000
24	S	324	PRO	0	-0.056	-0.025	21.242	-0.010	-0.010	0.000	0.000	0.000	0.000
25	S	325	ASP	-1	-0.847	-0.916	16.828	-0.335	-0.335	0.000	0.000	0.000	0.000
26	S	326	LEU	0	-0.010	-0.018	17.097	0.020	0.020	0.000	0.000	0.000	0.000
27	S	327	PRO	0	-0.007	-0.021	15.059	-0.036	-0.036	0.000	0.000	0.000	0.000
28	S	328	GLU	-1	-0.950	-0.976	12.941	-0.313	-0.313	0.000	0.000	0.000	0.000
29	S	329	LEU	0	0.028	0.021	11.832	-0.062	-0.062	0.000	0.000	0.000	0.000
30	S	330	LEU	0	0.060	0.022	11.605	-0.096	-0.096	0.000	0.000	0.000	0.000
31	S	331	HIS	0	-0.048	-0.021	7.004	-0.185	-0.185	0.000	0.000	0.000	0.000
32	S	332	LEU	0	0.013	-0.009	7.152	-0.178	-0.178	0.000	0.000	0.000	0.000
33	S	333	GLU	-1	-0.893	-0.938	7.411	-1.044	-1.044	0.000	0.000	0.000	0.000
34	S	334	ALA	0	-0.026	-0.015	6.807	-0.263	-0.263	0.000	0.000	0.000	0.000
35	S	335	MET	0	-0.091	-0.044	2.581	-2.046	-0.888	1.947	-0.716	-2.389	0.008
36	S	336	CYS	0	0.013	-0.004	2.958	-4.438	-2.950	0.173	-0.679	-0.982	-0.007
37	S	337	HIS	0	0.006	0.012	5.350	-0.404	-0.335	-0.001	-0.004	-0.065	0.000
38	S	338	GLN	0	-0.033	-0.028	2.725	-0.308	0.648	0.443	-0.312	-1.087	0.000
39	S	339	MET	0	-0.057	0.003	2.598	-2.073	-0.110	0.790	-0.617	-2.136	-0.003
40	S	340	GLY	0	0.017	0.024	3.778	1.064	1.218	0.008	-0.028	-0.134	0.000
41	S	341	PRO	0	0.046	0.011	6.350	0.326	0.326	0.000	0.000	0.000	0.000
42	S	342	LEU	0	-0.011	0.005	2.825	-0.764	0.265	0.364	-0.285	-1.108	0.000
43	S	343	ILE	0	-0.028	-0.017	6.426	0.438	0.438	0.000	0.000	0.000	0.000
44	S	344	ASP	-1	-0.880	-0.945	8.453	-0.330	-0.330	0.000	0.000	0.000	0.000
45	S	345	GLU	-1	-0.955	-0.960	9.366	0.678	0.678	0.000	0.000	0.000	0.000
46	S	346	LYS	1	0.906	0.951	7.296	-1.264	-1.264	0.000	0.000	0.000	0.000
47	S	347	LEU	0	-0.020	-0.014	11.474	0.030	0.030	0.000	0.000	0.000	0.000
48	S	348	GLU	-1	-0.850	-0.912	14.304	0.124	0.124	0.000	0.000	0.000	0.000
49	S	349	ASP	-1	-0.933	-0.960	13.040	0.394	0.394	0.000	0.000	0.000	0.000
50	S	350	ILE	0	-0.089	-0.055	13.866	0.004	0.004	0.000	0.000	0.000	0.000
51	S	351	ASP	-1	-0.875	-0.944	17.231	-0.044	-0.044	0.000	0.000	0.000	0.000
52	S	352	ARG	1	0.859	0.929	16.852	-0.201	-0.201	0.000	0.000	0.000	0.000
53	S	353	LYS	1	0.954	0.975	16.004	-0.326	-0.326	0.000	0.000	0.000	0.000
54	S	354	HIS	0	-0.013	0.009	21.397	-0.010	-0.010	0.000	0.000	0.000	0.000
55	S	355	SER	0	-0.014	-0.019	23.188	-0.009	-0.009	0.000	0.000	0.000	0.000
56	S	356	GLU	-1	-0.922	-0.962	23.804	0.128	0.128	0.000	0.000	0.000	0.000
57	S	357	LEU	0	-0.044	-0.034	24.065	-0.004	-0.004	0.000	0.000	0.000	0.000
58	S	358	SER	0	-0.047	-0.013	27.064	-0.007	-0.007	0.000	0.000	0.000	0.000
59	S	359	GLU	-1	-0.891	-0.953	28.893	0.025	0.025	0.000	0.000	0.000	0.000
60	S	360	LEU	0	-0.031	-0.011	30.232	-0.002	-0.002	0.000	0.000	0.000	0.000
61	S	361	ASN	0	-0.003	-0.010	31.172	-0.001	-0.001	0.000	0.000	0.000	0.000
62	S	362	VAL	0	0.042	0.020	32.947	-0.004	-0.004	0.000	0.000	0.000	0.000
63	S	363	LYS	1	0.945	0.976	34.945	-0.040	-0.040	0.000	0.000	0.000	0.000
64	S	364	VAL	0	-0.025	-0.010	34.729	-0.001	-0.001	0.000	0.000	0.000	0.000
65	S	365	MET	0	-0.004	-0.013	36.505	-0.003	-0.003	0.000	0.000	0.000	0.000
66	S	366	GLU	-1	-0.929	-0.960	39.017	0.014	0.014	0.000	0.000	0.000	0.000
67	S	367	ALA	0	-0.020	0.002	40.533	-0.001	-0.001	0.000	0.000	0.000	0.000
68	S	368	LEU	0	-0.023	-0.016	39.554	-0.001	-0.001	0.000	0.000	0.000	0.000
69	S	369	SER	0	0.005	0.000	43.179	-0.003	-0.003	0.000	0.000	0.000	0.000
70	S	370	LEU	0	-0.053	-0.018	45.026	-0.002	-0.002	0.000	0.000	0.000	0.000
71	S	371	TYR	0	0.019	0.007	46.271	-0.001	-0.001	0.000	0.000	0.000	0.000
72	S	372	THR	0	-0.003	-0.017	46.849	-0.001	-0.001	0.000	0.000	0.000	0.000
73	S	373	LYS	1	0.910	0.947	47.341	-0.012	-0.012	0.000	0.000	0.000	0.000
74	S	374	LEU	0	0.003	0.009	50.046	-0.001	-0.001	0.000	0.000	0.000	0.000
75	S	375	MET	0	-0.072	-0.025	51.183	0.000	0.000	0.000	0.000	0.000	0.000
76	S	376	ASN	0	-0.088	-0.036	53.767	-0.001	-0.001	0.000	0.000	0.000	0.000
77	S	377	GLU	-1	-0.986	-0.975	55.560	0.012	0.012	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(S:301:PHE)