FMO DATABASE

FMODB ID: 72V6K

Calculation Name: 1VFJ-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VFJ

Chain ID: B

ChEMBL ID:

UniProt ID: P83820

Base Structure: X-ray

Registration Date: 2023-09-19

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	93
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-620013.46945
FMO2-HF: Nuclear repulsion	584096.585594
FMO2-HF: Total energy	-35916.883856
FMO2-MP2: Total energy	-36022.961646

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(B:1:MET)

Summations of interaction energy for fragment #1(B:1:MET)

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.
-31.615	-26.089	25.226	-10.134	-20.619	-0.076

Interaction energy analysis for fragmet #1(B:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.034 / 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	B	3	LEU	0	0.024	0.018	2.578	-1.962	1.497	1.055	-2.059	-2.456	-0.008
4	B	4	ILE	0	-0.010	0.001	4.679	-0.441	-0.376	-0.001	-0.008	-0.055	0.000
5	B	5	VAL	0	0.006	0.002	7.492	0.450	0.450	0.000	0.000	0.000	0.000
6	B	6	ALA	0	-0.005	-0.006	10.672	-0.167	-0.167	0.000	0.000	0.000	0.000
7	B	7	ILE	0	-0.023	-0.002	13.862	0.074	0.074	0.000	0.000	0.000	0.000
8	B	8	VAL	0	0.014	0.002	17.060	-0.048	-0.048	0.000	0.000	0.000	0.000
9	B	9	ARG	1	0.828	0.875	19.775	-0.025	-0.025	0.000	0.000	0.000	0.000
10	B	10	PRO	0	0.003	0.009	22.531	0.020	0.020	0.000	0.000	0.000	0.000
11	B	11	GLU	-1	-0.819	-0.907	23.993	0.112	0.112	0.000	0.000	0.000	0.000
12	B	12	LYS	1	0.801	0.906	22.141	-0.079	-0.079	0.000	0.000	0.000	0.000
13	B	13	LEU	0	0.002	0.010	18.420	0.015	0.015	0.000	0.000	0.000	0.000
14	B	14	ASN	0	0.008	-0.009	20.124	0.049	0.049	0.000	0.000	0.000	0.000
15	B	15	GLU	-1	-0.850	-0.914	21.461	0.113	0.113	0.000	0.000	0.000	0.000
16	B	16	VAL	0	0.009	-0.005	16.000	0.008	0.008	0.000	0.000	0.000	0.000
17	B	17	LEU	0	0.007	0.004	15.666	0.045	0.045	0.000	0.000	0.000	0.000
18	B	18	LYS	1	0.942	0.989	16.760	-0.129	-0.129	0.000	0.000	0.000	0.000
19	B	19	ALA	0	-0.026	-0.018	16.752	0.006	0.006	0.000	0.000	0.000	0.000
20	B	20	LEU	0	0.005	-0.006	10.972	0.005	0.005	0.000	0.000	0.000	0.000
21	B	21	PHE	0	-0.009	-0.015	12.698	0.073	0.073	0.000	0.000	0.000	0.000
22	B	22	GLN	0	-0.042	-0.033	14.552	-0.013	-0.013	0.000	0.000	0.000	0.000
23	B	23	ALA	0	-0.031	-0.002	12.204	-0.053	-0.053	0.000	0.000	0.000	0.000
24	B	24	GLU	-1	-0.965	-0.970	10.977	0.371	0.371	0.000	0.000	0.000	0.000
25	B	25	VAL	0	-0.035	-0.009	7.685	0.092	0.092	0.000	0.000	0.000	0.000
26	B	26	ARG	1	0.865	0.915	2.503	-2.427	-1.673	2.066	-0.489	-2.331	-0.002
27	B	27	GLY	0	0.019	0.015	5.718	-0.110	-0.110	0.000	0.000	0.000	0.000
28	B	28	LEU	0	-0.043	-0.020	7.125	0.535	0.535	0.000	0.000	0.000	0.000
29	B	29	THR	0	-0.018	0.003	9.558	-0.224	-0.224	0.000	0.000	0.000	0.000
30	B	30	LEU	0	0.018	-0.004	12.292	-0.043	-0.043	0.000	0.000	0.000	0.000
31	B	31	SER	0	-0.011	0.004	15.480	-0.022	-0.022	0.000	0.000	0.000	0.000
32	B	32	ARG	1	0.888	0.940	18.531	-0.234	-0.234	0.000	0.000	0.000	0.000
33	B	33	VAL	0	-0.011	-0.011	19.224	0.005	0.005	0.000	0.000	0.000	0.000
34	B	34	GLN	0	0.058	0.022	22.320	-0.018	-0.018	0.000	0.000	0.000	0.000
35	B	35	GLY	0	-0.021	-0.001	24.059	-0.002	-0.002	0.000	0.000	0.000	0.000
36	B	36	HIS	0	0.037	-0.002	25.008	-0.001	-0.001	0.000	0.000	0.000	0.000
37	B	37	GLY	0	-0.019	0.004	26.349	-0.012	-0.012	0.000	0.000	0.000	0.000
38	B	53	MET	0	-0.025	-0.012	33.157	-0.002	-0.002	0.000	0.000	0.000	0.000
39	B	54	GLU	-1	-0.891	-0.952	33.230	0.052	0.052	0.000	0.000	0.000	0.000
40	B	55	LEU	0	-0.108	-0.052	28.150	-0.003	-0.003	0.000	0.000	0.000	0.000
41	B	56	HIS	0	0.027	0.021	27.892	0.006	0.006	0.000	0.000	0.000	0.000
42	B	57	GLU	-1	-0.853	-0.917	25.782	0.169	0.169	0.000	0.000	0.000	0.000
43	B	58	LYS	1	0.871	0.925	21.298	-0.085	-0.085	0.000	0.000	0.000	0.000
44	B	59	VAL	0	-0.002	-0.002	17.814	0.021	0.021	0.000	0.000	0.000	0.000
45	B	60	ARG	1	0.839	0.898	11.879	-0.553	-0.553	0.000	0.000	0.000	0.000
46	B	61	LEU	0	0.002	-0.010	12.994	0.061	0.061	0.000	0.000	0.000	0.000
47	B	62	GLU	-1	-0.826	-0.884	8.699	0.670	0.670	0.000	0.000	0.000	0.000
48	B	63	ILE	0	0.006	-0.009	7.023	0.169	0.169	0.000	0.000	0.000	0.000
49	B	64	GLY	0	0.032	0.032	3.228	-0.777	-0.902	1.867	-0.781	-0.960	0.005
50	B	65	VAL	0	-0.016	-0.015	2.753	-0.510	-1.163	1.099	1.603	-2.049	-0.004
51	B	66	SER	0	0.055	0.029	2.036	-7.100	-5.126	6.471	-4.395	-4.050	-0.019
52	B	67	GLU	-1	-0.749	-0.873	2.019	-14.912	-16.269	7.374	-2.306	-3.712	-0.044
53	B	68	PRO	0	-0.019	-0.007	5.097	0.260	0.325	-0.001	-0.005	-0.059	0.000
54	B	69	PHE	0	0.041	0.015	6.976	0.102	0.102	0.000	0.000	0.000	0.000
55	B	70	VAL	0	-0.003	0.018	4.909	0.236	0.236	0.000	0.000	0.000	0.000
56	B	71	LYS	1	0.872	0.920	7.539	0.556	0.556	0.000	0.000	0.000	0.000
57	B	72	PRO	0	0.025	0.011	10.497	0.086	0.086	0.000	0.000	0.000	0.000
58	B	73	THR	0	0.020	0.001	8.910	0.164	0.164	0.000	0.000	0.000	0.000
59	B	74	VAL	0	0.000	-0.003	10.484	0.081	0.081	0.000	0.000	0.000	0.000
60	B	75	GLU	-1	-0.820	-0.900	12.818	-0.216	-0.216	0.000	0.000	0.000	0.000
61	B	76	ALA	0	-0.017	-0.002	14.096	0.029	0.029	0.000	0.000	0.000	0.000
62	B	77	ILE	0	0.012	0.002	11.255	0.025	0.025	0.000	0.000	0.000	0.000
63	B	78	LEU	0	-0.017	-0.011	15.774	0.006	0.006	0.000	0.000	0.000	0.000
64	B	79	LYS	1	0.904	0.949	18.309	0.002	0.002	0.000	0.000	0.000	0.000
65	B	80	ALA	0	-0.001	0.017	18.752	0.003	0.003	0.000	0.000	0.000	0.000
66	B	81	ALA	0	0.026	-0.004	18.792	0.005	0.005	0.000	0.000	0.000	0.000
67	B	82	ARG	1	0.884	0.958	20.825	0.059	0.059	0.000	0.000	0.000	0.000
68	B	83	THR	0	-0.066	-0.073	23.469	0.010	0.010	0.000	0.000	0.000	0.000
69	B	84	GLY	0	-0.065	-0.040	26.755	-0.006	-0.006	0.000	0.000	0.000	0.000
70	B	85	GLU	-1	-0.862	-0.896	28.306	0.008	0.008	0.000	0.000	0.000	0.000
71	B	86	VAL	0	-0.008	-0.020	27.428	-0.003	-0.003	0.000	0.000	0.000	0.000
72	B	87	GLY	0	0.036	0.013	26.435	0.006	0.006	0.000	0.000	0.000	0.000
73	B	88	ASP	-1	-0.721	-0.805	22.919	0.019	0.019	0.000	0.000	0.000	0.000
74	B	89	GLY	0	0.053	0.007	20.236	0.029	0.029	0.000	0.000	0.000	0.000
75	B	90	LYS	1	0.883	0.950	17.703	0.071	0.071	0.000	0.000	0.000	0.000
76	B	91	ILE	0	0.013	0.005	12.205	0.062	0.062	0.000	0.000	0.000	0.000
77	B	92	PHE	0	-0.034	-0.006	11.963	-0.062	-0.062	0.000	0.000	0.000	0.000
78	B	93	VAL	0	0.020	-0.002	7.344	0.105	0.105	0.000	0.000	0.000	0.000
79	B	94	LEU	0	0.002	0.011	7.665	-0.116	-0.116	0.000	0.000	0.000	0.000
80	B	95	PRO	0	0.024	-0.003	6.265	-0.882	-0.882	0.000	0.000	0.000	0.000
81	B	96	VAL	0	-0.028	-0.024	3.132	-0.163	0.822	0.076	-0.224	-0.837	0.000
82	B	97	GLU	-1	-0.925	-0.948	4.545	-2.656	-2.623	-0.001	-0.014	-0.018	0.000
83	B	98	LYS	1	0.841	0.905	6.286	0.055	0.055	0.000	0.000	0.000	0.000
84	B	99	VAL	0	-0.006	-0.015	2.395	-0.827	-1.550	5.128	-1.131	-3.275	-0.001
85	B	100	TYR	0	-0.026	-0.025	5.271	-0.391	-0.391	0.000	0.000	0.000	0.000
86	B	101	ARG	1	0.814	0.894	4.768	-0.603	-0.500	-0.001	-0.002	-0.100	0.000
87	B	102	ILE	0	0.051	0.014	7.452	-0.182	-0.182	0.000	0.000	0.000	0.000
88	B	103	ARG	1	0.924	0.962	10.539	-0.681	-0.681	0.000	0.000	0.000	0.000
89	B	104	THR	0	-0.036	-0.034	10.425	-0.041	-0.041	0.000	0.000	0.000	0.000
90	B	105	GLY	0	0.028	0.030	11.665	-0.063	-0.063	0.000	0.000	0.000	0.000
91	B	106	GLU	-1	-0.871	-0.911	9.251	0.486	0.486	0.000	0.000	0.000	0.000
92	B	107	GLU	-1	-0.751	-0.829	7.135	0.310	0.310	0.000	0.000	0.000	0.000
93	B	108	ASP	-1	-0.934	-0.971	3.358	-0.667	0.279	0.094	-0.323	-0.717	-0.003

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Interactive mode: IFIE and PIEDA for fragment #1(B:1:MET)