FMO DATABASE

FMODB ID: 17RJZ

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	OptAll
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	-859873.256477
FMO2-HF: Nuclear repulsion	815671.061518
FMO2-HF: Total energy	-44202.194959
FMO2-MP2: Total energy	-44324.40021

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.
-10.676	-2.23	11.407	-5.235	-14.613	-0.032

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 : -0.003 / q_NPA : -0.008

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	-0.001	0.006	3.780	-1.583	-0.216	-0.001	-0.624	-0.742	0.002
4	A	5	LEU	0	-0.054	-0.022	6.194	0.311	0.311	0.000	0.000	0.000	0.000
5	A	6	SER	0	0.071	0.017	8.928	0.002	0.002	0.000	0.000	0.000	0.000
6	A	7	ASP	-1	-0.746	-0.873	12.618	-0.238	-0.238	0.000	0.000	0.000	0.000
7	A	8	SER	0	-0.108	-0.052	15.536	0.033	0.033	0.000	0.000	0.000	0.000
8	A	9	ASP	-1	-0.775	-0.858	11.309	-0.203	-0.203	0.000	0.000	0.000	0.000
9	A	10	PHE	0	0.011	0.006	12.502	0.021	0.021	0.000	0.000	0.000	0.000
10	A	11	GLN	0	0.042	0.000	13.846	0.012	0.012	0.000	0.000	0.000	0.000
11	A	12	LEU	0	0.011	0.019	15.169	0.014	0.014	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-0.794	-0.907	10.436	-0.070	-0.070	0.000	0.000	0.000	0.000
13	A	14	VAL	0	-0.022	-0.008	10.799	-0.038	-0.038	0.000	0.000	0.000	0.000
14	A	15	ARG	1	0.789	0.900	13.439	0.202	0.202	0.000	0.000	0.000	0.000
15	A	16	GLN	0	-0.040	-0.011	16.631	0.031	0.031	0.000	0.000	0.000	0.000
16	A	17	HIS	0	-0.049	-0.012	11.907	-0.009	-0.009	0.000	0.000	0.000	0.000
17	A	18	PRO	0	-0.018	-0.001	15.051	-0.024	-0.024	0.000	0.000	0.000	0.000
18	A	19	ASP	-1	-0.870	-0.929	11.337	-0.021	-0.021	0.000	0.000	0.000	0.000
19	A	20	PRO	0	0.009	0.004	11.568	-0.046	-0.046	0.000	0.000	0.000	0.000
20	A	21	ILE	0	-0.027	-0.009	7.123	-0.028	-0.028	0.000	0.000	0.000	0.000
21	A	22	ILE	0	-0.015	0.009	5.670	0.068	0.068	0.000	0.000	0.000	0.000
22	A	23	ILE	0	0.006	0.001	5.882	-0.272	-0.272	0.000	0.000	0.000	0.000
23	A	24	MET	0	-0.048	-0.008	5.497	0.155	0.155	0.000	0.000	0.000	0.000
24	A	25	PHE	0	0.044	0.011	7.244	-0.105	-0.105	0.000	0.000	0.000	0.000
25	A	26	THR	0	-0.046	-0.068	7.654	0.015	0.015	0.000	0.000	0.000	0.000
26	A	27	GLY	0	0.092	0.035	10.609	0.040	0.040	0.000	0.000	0.000	0.000
27	A	28	SER	0	0.009	0.007	13.198	-0.015	-0.015	0.000	0.000	0.000	0.000
28	A	29	TRP	0	-0.001	-0.002	14.442	0.013	0.013	0.000	0.000	0.000	0.000
29	A	30	CYS	0	-0.033	0.058	13.511	0.019	0.019	0.000	0.000	0.000	0.000
30	A	31	GLN	0	0.074	0.019	13.655	-0.047	-0.047	0.000	0.000	0.000	0.000
31	A	32	PRO	0	-0.019	-0.018	14.522	-0.005	-0.005	0.000	0.000	0.000	0.000
32	A	33	CYS	0	0.039	0.011	9.982	-0.022	-0.022	0.000	0.000	0.000	0.000
33	A	34	LYS	1	0.824	0.910	9.387	0.217	0.217	0.000	0.000	0.000	0.000
34	A	35	LYS	1	0.893	0.950	10.621	0.241	0.241	0.000	0.000	0.000	0.000
35	A	36	MET	0	0.034	0.044	8.526	0.033	0.033	0.000	0.000	0.000	0.000
36	A	37	LYS	1	0.917	0.972	5.379	1.027	1.027	0.000	0.000	0.000	0.000
37	A	38	PRO	0	0.053	0.043	4.925	-0.172	-0.077	-0.001	0.000	-0.093	0.000
38	A	39	THR	0	-0.002	0.001	6.642	0.001	0.001	0.000	0.000	0.000	0.000
39	A	40	PHE	0	-0.005	-0.011	2.396	-0.848	-0.337	2.050	-0.534	-2.026	-0.004
40	A	41	GLU	-1	-0.818	-0.887	2.300	-3.226	-2.354	2.989	-1.034	-2.827	-0.002
41	A	42	GLU	-1	-0.881	-0.963	3.241	0.169	-0.171	0.015	0.528	-0.203	0.000
42	A	43	MET	0	-0.109	-0.040	5.861	0.149	0.149	0.000	0.000	0.000	0.000
43	A	44	ALA	0	0.060	0.033	2.501	-0.559	-0.201	1.284	-0.498	-1.143	-0.001
44	A	45	SER	0	-0.058	-0.039	4.349	0.205	0.299	-0.001	-0.020	-0.072	0.000
45	A	46	GLN	0	-0.035	-0.018	6.380	0.080	0.080	0.000	0.000	0.000	0.000
46	A	47	MET	0	-0.004	0.003	7.568	-0.009	-0.009	0.000	0.000	0.000	0.000
47	A	48	GLU	-1	-0.947	-0.954	6.218	0.651	0.651	0.000	0.000	0.000	0.000
48	A	49	GLY	0	-0.003	-0.001	7.812	0.059	0.059	0.000	0.000	0.000	0.000
49	A	50	ASP	-1	-0.964	-0.968	10.688	-0.087	-0.087	0.000	0.000	0.000	0.000
50	A	51	ILE	0	-0.051	-0.043	7.816	-0.014	-0.014	0.000	0.000	0.000	0.000
51	A	52	ARG	1	0.829	0.916	5.844	0.196	0.196	0.000	0.000	0.000	0.000
52	A	53	PHE	0	0.014	-0.006	2.288	-1.021	-0.381	1.958	-0.602	-1.996	0.001
53	A	54	ALA	0	-0.007	0.001	2.599	-4.005	-1.274	1.245	-1.686	-2.290	-0.021
54	A	55	TYR	0	-0.070	-0.089	2.557	-1.452	0.643	1.870	-0.765	-3.200	-0.007
55	A	56	MET	0	-0.005	0.001	5.358	0.068	0.091	-0.001	0.000	-0.021	0.000
56	A	57	ASP	-1	-0.826	-0.932	9.059	-0.443	-0.443	0.000	0.000	0.000	0.000
57	A	58	ALA	0	0.041	-0.004	10.951	0.048	0.048	0.000	0.000	0.000	0.000
58	A	59	GLU	-1	-0.968	-0.964	14.486	-0.197	-0.197	0.000	0.000	0.000	0.000
59	A	60	ASP	-1	-0.897	-0.937	12.528	-0.260	-0.260	0.000	0.000	0.000	0.000
60	A	61	ALA	0	-0.036	-0.018	12.609	0.004	0.004	0.000	0.000	0.000	0.000
61	A	62	GLU	-1	-0.858	-0.917	14.740	-0.148	-0.148	0.000	0.000	0.000	0.000
62	A	63	LYS	1	0.804	0.884	18.462	0.161	0.161	0.000	0.000	0.000	0.000
63	A	64	THR	0	0.017	-0.018	13.652	0.010	0.010	0.000	0.000	0.000	0.000
64	A	65	MET	0	-0.010	-0.005	15.047	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	66	ALA	0	-0.070	-0.012	17.316	0.016	0.016	0.000	0.000	0.000	0.000
66	A	67	GLU	-1	-0.861	-0.930	19.123	-0.175	-0.175	0.000	0.000	0.000	0.000
67	A	68	LEU	0	-0.026	-0.007	14.853	0.006	0.006	0.000	0.000	0.000	0.000
68	A	69	ASN	0	-0.042	-0.030	18.905	0.000	0.000	0.000	0.000	0.000	0.000
69	A	70	ILE	0	0.031	0.038	13.997	0.005	0.005	0.000	0.000	0.000	0.000
70	A	71	ARG	1	0.792	0.887	17.885	0.198	0.198	0.000	0.000	0.000	0.000
71	A	72	THR	0	0.003	0.004	16.585	0.007	0.007	0.000	0.000	0.000	0.000
72	A	73	LEU	0	0.028	0.051	13.199	-0.030	-0.030	0.000	0.000	0.000	0.000
73	A	74	PRO	0	-0.014	-0.059	10.468	0.029	0.029	0.000	0.000	0.000	0.000
74	A	75	SER	0	-0.011	-0.015	11.663	0.068	0.068	0.000	0.000	0.000	0.000
75	A	76	LEU	0	-0.039	-0.008	8.045	-0.080	-0.080	0.000	0.000	0.000	0.000
76	A	77	ALA	0	0.025	0.011	10.111	0.066	0.066	0.000	0.000	0.000	0.000
77	A	78	LEU	0	0.003	0.019	10.428	-0.079	-0.079	0.000	0.000	0.000	0.000
78	A	79	PHE	0	0.017	-0.013	11.608	0.049	0.049	0.000	0.000	0.000	0.000
79	A	80	VAL	0	0.044	0.014	13.083	-0.017	-0.017	0.000	0.000	0.000	0.000
80	A	81	ASP	-1	-0.802	-0.888	15.745	-0.113	-0.113	0.000	0.000	0.000	0.000
81	A	82	GLY	0	0.025	0.039	16.630	0.013	0.013	0.000	0.000	0.000	0.000
82	A	83	MET	0	-0.071	-0.048	17.684	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	84	ILE	0	-0.029	-0.010	14.918	-0.017	-0.017	0.000	0.000	0.000	0.000
84	A	85	ARG	1	0.813	0.893	16.007	0.174	0.174	0.000	0.000	0.000	0.000
85	A	86	GLU	-1	-0.844	-0.916	15.923	-0.175	-0.175	0.000	0.000	0.000	0.000
86	A	87	VAL	0	-0.043	-0.037	14.784	-0.041	-0.041	0.000	0.000	0.000	0.000
87	A	88	PHE	0	-0.006	-0.001	13.756	0.025	0.025	0.000	0.000	0.000	0.000
88	A	89	SER	0	-0.002	-0.009	14.527	-0.030	-0.030	0.000	0.000	0.000	0.000
89	A	90	GLY	0	0.010	0.004	15.090	0.027	0.027	0.000	0.000	0.000	0.000
90	A	91	THR	0	-0.055	-0.045	12.652	-0.028	-0.028	0.000	0.000	0.000	0.000
91	A	92	MET	0	-0.011	0.001	12.504	0.035	0.035	0.000	0.000	0.000	0.000
92	A	93	ASN	0	-0.026	-0.006	12.607	-0.022	-0.022	0.000	0.000	0.000	0.000
93	A	94	LYS	1	0.908	0.951	9.466	0.279	0.279	0.000	0.000	0.000	0.000
94	A	95	SER	0	-0.040	-0.026	12.456	0.002	0.002	0.000	0.000	0.000	0.000
95	A	96	ASP	-1	-0.811	-0.916	15.495	-0.194	-0.194	0.000	0.000	0.000	0.000
96	A	97	LEU	0	0.022	0.020	7.596	0.000	0.000	0.000	0.000	0.000	0.000
97	A	98	ARG	1	0.923	0.953	11.914	0.185	0.185	0.000	0.000	0.000	0.000
98	A	99	TYR	0	-0.062	-0.031	13.107	0.011	0.011	0.000	0.000	0.000	0.000
99	A	100	TRP	0	0.027	0.002	11.179	0.002	0.002	0.000	0.000	0.000	0.000
100	A	101	ILE	0	0.034	0.014	8.934	0.003	0.003	0.000	0.000	0.000	0.000
101	A	102	ASN	0	-0.018	-0.004	13.365	0.000	0.000	0.000	0.000	0.000	0.000
102	A	103	ASN	0	-0.057	-0.019	16.129	0.026	0.026	0.000	0.000	0.000	0.000
103	A	104	ASN	0	0.003	0.012	15.951	0.033	0.033	0.000	0.000	0.000	0.000
104	A	105	ILE	0	-0.058	-0.038	14.193	-0.012	-0.012	0.000	0.000	0.000	0.000

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