FMO DATABASE

FMODB ID: YZ3Q2

Calculation Name: 3VFI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VFI

Chain ID: A

ChEMBL ID:

UniProt ID: C4NT42

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	104
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-857218.29029
FMO2-HF: Nuclear repulsion	813017.376239
FMO2-HF: Total energy	-44200.914051
FMO2-MP2: Total energy	-44323.176444

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(A:2:LEU)

Summations of interaction energy for fragment #1(A:2:LEU)

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.
-10.981	-1.929	9.444	-5.065	-13.43	-0.023

Interaction energy analysis for fragmet #1(A:2:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : -0.004

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	A	4	SER	0	0.008	0.002	3.501	-1.867	-0.140	0.009	-0.834	-0.902	0.002
4	A	5	LEU	0	-0.045	-0.022	6.068	0.317	0.317	0.000	0.000	0.000	0.000
5	A	6	SER	0	0.057	0.034	8.968	-0.031	-0.031	0.000	0.000	0.000	0.000
6	A	7	ASP	-1	-0.748	-0.881	12.544	-0.200	-0.200	0.000	0.000	0.000	0.000
7	A	8	SER	0	-0.139	-0.068	15.478	0.033	0.033	0.000	0.000	0.000	0.000
8	A	9	ASP	-1	-0.802	-0.898	11.838	-0.140	-0.140	0.000	0.000	0.000	0.000
9	A	10	PHE	0	-0.008	-0.002	12.559	0.029	0.029	0.000	0.000	0.000	0.000
10	A	11	GLN	0	0.005	-0.018	14.330	0.028	0.028	0.000	0.000	0.000	0.000
11	A	12	LEU	0	0.026	0.020	15.026	0.007	0.007	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-0.899	-0.960	10.788	0.141	0.141	0.000	0.000	0.000	0.000
13	A	14	VAL	0	-0.047	-0.021	11.234	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	15	ARG	1	0.844	0.928	13.729	0.132	0.132	0.000	0.000	0.000	0.000
15	A	16	GLN	0	-0.007	-0.015	17.204	0.021	0.021	0.000	0.000	0.000	0.000
16	A	17	HIS	0	-0.052	-0.001	12.461	-0.017	-0.017	0.000	0.000	0.000	0.000
17	A	18	PRO	0	-0.006	-0.003	15.606	-0.021	-0.021	0.000	0.000	0.000	0.000
18	A	19	ASP	-1	-0.853	-0.917	11.906	0.155	0.155	0.000	0.000	0.000	0.000
19	A	20	PRO	0	0.009	0.005	11.873	-0.033	-0.033	0.000	0.000	0.000	0.000
20	A	21	ILE	0	-0.022	-0.009	7.267	0.020	0.020	0.000	0.000	0.000	0.000
21	A	22	ILE	0	-0.005	0.008	5.813	0.012	0.012	0.000	0.000	0.000	0.000
22	A	23	ILE	0	0.004	-0.001	5.824	-0.151	-0.151	0.000	0.000	0.000	0.000
23	A	24	MET	0	-0.032	-0.004	5.295	0.053	0.053	0.000	0.000	0.000	0.000
24	A	25	PHE	0	0.033	0.000	7.259	-0.118	-0.118	0.000	0.000	0.000	0.000
25	A	26	THR	0	-0.022	-0.045	7.678	-0.022	-0.022	0.000	0.000	0.000	0.000
26	A	27	GLY	0	0.111	0.048	10.232	0.045	0.045	0.000	0.000	0.000	0.000
27	A	28	SER	0	0.062	0.033	12.862	-0.036	-0.036	0.000	0.000	0.000	0.000
28	A	29	TRP	0	-0.041	-0.015	14.469	0.000	0.000	0.000	0.000	0.000	0.000
29	A	30	CYS	0	-0.080	0.022	13.642	0.008	0.008	0.000	0.000	0.000	0.000
30	A	31	GLN	0	0.085	0.032	13.744	-0.074	-0.074	0.000	0.000	0.000	0.000
31	A	32	PRO	0	0.023	-0.017	14.005	-0.025	-0.025	0.000	0.000	0.000	0.000
32	A	33	CYS	0	0.036	0.011	10.020	-0.013	-0.013	0.000	0.000	0.000	0.000
33	A	34	LYS	1	0.855	0.950	9.243	0.292	0.292	0.000	0.000	0.000	0.000
34	A	35	LYS	1	0.928	0.959	10.352	0.287	0.287	0.000	0.000	0.000	0.000
35	A	36	MET	0	0.029	0.043	8.549	0.040	0.040	0.000	0.000	0.000	0.000
36	A	37	LYS	1	0.957	0.998	5.359	1.371	1.371	0.000	0.000	0.000	0.000
37	A	38	PRO	0	0.040	0.034	5.435	-0.174	-0.174	0.000	0.000	0.000	0.000
38	A	39	THR	0	0.001	0.007	7.144	0.033	0.033	0.000	0.000	0.000	0.000
39	A	40	PHE	0	0.004	-0.005	2.460	-0.920	-0.177	1.479	-0.452	-1.770	-0.002
40	A	41	GLU	-1	-0.841	-0.912	2.208	-4.887	-3.875	2.412	-0.808	-2.616	-0.005
41	A	42	GLU	-1	-0.962	-0.978	3.647	-0.094	-0.014	0.005	0.063	-0.148	0.000
42	A	43	MET	0	-0.093	-0.027	6.300	0.207	0.207	0.000	0.000	0.000	0.000
43	A	44	ALA	0	0.040	0.010	2.525	-0.570	-0.095	1.013	-0.429	-1.059	-0.001
44	A	45	SER	0	-0.056	-0.041	4.405	0.279	0.366	-0.001	-0.015	-0.071	0.000
45	A	46	GLN	0	-0.008	-0.004	6.255	0.062	0.062	0.000	0.000	0.000	0.000
46	A	47	MET	0	-0.016	0.002	7.774	0.013	0.013	0.000	0.000	0.000	0.000
47	A	48	GLU	-1	-0.894	-0.937	6.826	0.980	0.980	0.000	0.000	0.000	0.000
48	A	49	GLY	0	-0.036	-0.015	8.122	-0.010	-0.010	0.000	0.000	0.000	0.000
49	A	50	ASP	-1	-0.963	-0.958	10.310	0.044	0.044	0.000	0.000	0.000	0.000
50	A	51	ILE	0	-0.059	-0.049	8.430	-0.037	-0.037	0.000	0.000	0.000	0.000
51	A	52	ARG	1	0.837	0.926	6.051	-0.009	-0.009	0.000	0.000	0.000	0.000
52	A	53	PHE	0	0.016	0.001	2.389	-1.124	-0.340	1.137	-0.402	-1.518	0.001
53	A	54	ALA	0	-0.022	-0.009	2.795	-2.796	-0.459	0.543	-1.195	-1.685	-0.012
54	A	55	TYR	0	-0.075	-0.074	2.330	-1.473	0.325	2.848	-0.992	-3.654	-0.006
55	A	56	MET	0	-0.029	-0.004	5.317	0.066	0.075	-0.001	-0.001	-0.007	0.000
56	A	57	ASP	-1	-0.859	-0.928	8.870	-0.552	-0.552	0.000	0.000	0.000	0.000
57	A	58	ALA	0	0.011	-0.026	10.992	0.062	0.062	0.000	0.000	0.000	0.000
58	A	59	GLU	-1	-1.016	-1.005	14.444	-0.246	-0.246	0.000	0.000	0.000	0.000
59	A	60	ASP	-1	-0.907	-0.933	12.351	-0.370	-0.370	0.000	0.000	0.000	0.000
60	A	61	ALA	0	-0.030	-0.028	12.587	0.022	0.022	0.000	0.000	0.000	0.000
61	A	62	GLU	-1	-0.906	-0.950	14.700	-0.178	-0.178	0.000	0.000	0.000	0.000
62	A	63	LYS	1	0.876	0.923	18.322	0.140	0.140	0.000	0.000	0.000	0.000
63	A	64	THR	0	0.030	-0.006	13.872	0.016	0.016	0.000	0.000	0.000	0.000
64	A	65	MET	0	-0.005	0.003	14.913	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	66	ALA	0	-0.051	-0.006	17.167	0.015	0.015	0.000	0.000	0.000	0.000
66	A	67	GLU	-1	-0.943	-0.972	19.163	-0.133	-0.133	0.000	0.000	0.000	0.000
67	A	68	LEU	0	-0.035	-0.016	15.114	0.009	0.009	0.000	0.000	0.000	0.000
68	A	69	ASN	0	-0.087	-0.057	19.005	-0.008	-0.008	0.000	0.000	0.000	0.000
69	A	70	ILE	0	0.035	0.040	14.144	0.000	0.000	0.000	0.000	0.000	0.000
70	A	71	ARG	1	0.803	0.905	17.848	0.189	0.189	0.000	0.000	0.000	0.000
71	A	72	THR	0	0.003	0.005	16.174	-0.009	-0.009	0.000	0.000	0.000	0.000
72	A	73	LEU	0	0.020	0.074	12.629	-0.029	-0.029	0.000	0.000	0.000	0.000
73	A	74	PRO	0	0.033	-0.066	10.037	0.028	0.028	0.000	0.000	0.000	0.000
74	A	75	SER	0	0.019	-0.022	11.387	0.060	0.060	0.000	0.000	0.000	0.000
75	A	76	LEU	0	-0.039	-0.011	8.012	-0.080	-0.080	0.000	0.000	0.000	0.000
76	A	77	ALA	0	0.028	0.026	10.090	0.056	0.056	0.000	0.000	0.000	0.000
77	A	78	LEU	0	-0.002	0.019	10.450	-0.043	-0.043	0.000	0.000	0.000	0.000
78	A	79	PHE	0	0.005	-0.012	11.513	0.026	0.026	0.000	0.000	0.000	0.000
79	A	80	VAL	0	0.027	0.001	13.359	0.005	0.005	0.000	0.000	0.000	0.000
80	A	81	ASP	-1	-0.891	-0.936	16.112	-0.021	-0.021	0.000	0.000	0.000	0.000
81	A	82	GLY	0	0.046	0.038	16.323	0.001	0.001	0.000	0.000	0.000	0.000
82	A	83	MET	0	-0.090	-0.054	17.319	-0.012	-0.012	0.000	0.000	0.000	0.000
83	A	84	ILE	0	-0.051	-0.024	15.039	-0.008	-0.008	0.000	0.000	0.000	0.000
84	A	85	ARG	1	0.900	0.953	15.705	0.100	0.100	0.000	0.000	0.000	0.000
85	A	86	GLU	-1	-0.867	-0.935	15.813	-0.147	-0.147	0.000	0.000	0.000	0.000
86	A	87	VAL	0	-0.021	-0.028	14.757	-0.030	-0.030	0.000	0.000	0.000	0.000
87	A	88	PHE	0	-0.021	0.002	13.782	0.020	0.020	0.000	0.000	0.000	0.000
88	A	89	SER	0	0.012	-0.003	14.374	-0.031	-0.031	0.000	0.000	0.000	0.000
89	A	90	GLY	0	-0.001	-0.004	14.728	0.024	0.024	0.000	0.000	0.000	0.000
90	A	91	THR	0	-0.065	-0.051	12.783	-0.022	-0.022	0.000	0.000	0.000	0.000
91	A	92	MET	0	0.021	0.013	12.118	0.040	0.040	0.000	0.000	0.000	0.000
92	A	93	ASN	0	0.017	0.021	12.231	-0.047	-0.047	0.000	0.000	0.000	0.000
93	A	94	LYS	1	0.998	0.969	10.745	0.242	0.242	0.000	0.000	0.000	0.000
94	A	95	SER	0	-0.042	-0.025	12.519	0.006	0.006	0.000	0.000	0.000	0.000
95	A	96	ASP	-1	-0.874	-0.936	15.557	-0.174	-0.174	0.000	0.000	0.000	0.000
96	A	97	LEU	0	0.004	0.006	7.517	0.006	0.006	0.000	0.000	0.000	0.000
97	A	98	ARG	1	0.898	0.936	12.257	0.148	0.148	0.000	0.000	0.000	0.000
98	A	99	TYR	0	-0.023	-0.006	13.261	0.023	0.023	0.000	0.000	0.000	0.000
99	A	100	TRP	0	0.025	0.001	11.219	0.006	0.006	0.000	0.000	0.000	0.000
100	A	101	ILE	0	0.031	0.011	8.937	0.008	0.008	0.000	0.000	0.000	0.000
101	A	102	ASN	0	0.001	-0.009	13.401	0.023	0.023	0.000	0.000	0.000	0.000
102	A	103	ASN	0	-0.062	-0.020	16.173	0.024	0.024	0.000	0.000	0.000	0.000
103	A	104	ASN	0	-0.021	0.003	15.919	0.025	0.025	0.000	0.000	0.000	0.000
104	A	105	ILE	0	-0.051	-0.026	13.245	0.013	0.013	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:LEU)