FMO DATABASE

FMODB ID: MV1NZ

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	OptHSide
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	-618849.488331
FMO2-HF: Nuclear repulsion	582932.887225
FMO2-HF: Total energy	-35916.601106
FMO2-MP2: Total energy	-36022.714437

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.
-28.494	-20.896	22.527	-9.688	-20.441	-0.072

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 : -0.029 / q_NPA : -0.005

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	0.032	0.014	2.525	-2.524	1.232	1.109	-2.256	-2.609	-0.009
4	B	4	ILE	0	-0.017	-0.008	4.945	-0.321	-0.269	-0.001	-0.005	-0.045	0.000
5	B	5	VAL	0	0.019	0.005	7.778	0.398	0.398	0.000	0.000	0.000	0.000
6	B	6	ALA	0	-0.014	-0.003	10.960	-0.129	-0.129	0.000	0.000	0.000	0.000
7	B	7	ILE	0	-0.022	-0.004	13.887	0.075	0.075	0.000	0.000	0.000	0.000
8	B	8	VAL	0	0.021	0.004	17.048	-0.037	-0.037	0.000	0.000	0.000	0.000
9	B	9	ARG	1	0.844	0.901	19.750	0.015	0.015	0.000	0.000	0.000	0.000
10	B	10	PRO	0	0.040	0.017	22.694	0.018	0.018	0.000	0.000	0.000	0.000
11	B	11	GLU	-1	-0.833	-0.914	24.126	0.069	0.069	0.000	0.000	0.000	0.000
12	B	12	LYS	1	0.810	0.905	22.071	-0.045	-0.045	0.000	0.000	0.000	0.000
13	B	13	LEU	0	0.005	0.011	18.287	0.014	0.014	0.000	0.000	0.000	0.000
14	B	14	ASN	0	0.012	-0.004	20.054	0.046	0.046	0.000	0.000	0.000	0.000
15	B	15	GLU	-1	-0.846	-0.914	21.327	0.092	0.092	0.000	0.000	0.000	0.000
16	B	16	VAL	0	0.022	0.003	15.981	0.006	0.006	0.000	0.000	0.000	0.000
17	B	17	LEU	0	-0.003	-0.008	15.762	0.043	0.043	0.000	0.000	0.000	0.000
18	B	18	LYS	1	0.934	0.986	16.897	-0.112	-0.112	0.000	0.000	0.000	0.000
19	B	19	ALA	0	-0.007	-0.010	17.021	0.013	0.013	0.000	0.000	0.000	0.000
20	B	20	LEU	0	-0.004	-0.007	11.157	0.003	0.003	0.000	0.000	0.000	0.000
21	B	21	PHE	0	-0.023	-0.019	12.843	0.077	0.077	0.000	0.000	0.000	0.000
22	B	22	GLN	0	-0.048	-0.031	14.695	-0.016	-0.016	0.000	0.000	0.000	0.000
23	B	23	ALA	0	-0.053	-0.009	12.346	-0.030	-0.030	0.000	0.000	0.000	0.000
24	B	24	GLU	-1	-0.926	-0.942	10.685	0.423	0.423	0.000	0.000	0.000	0.000
25	B	25	VAL	0	-0.014	-0.009	7.428	0.068	0.068	0.000	0.000	0.000	0.000
26	B	26	ARG	1	0.854	0.923	2.621	-2.437	-1.756	2.168	-0.521	-2.329	-0.002
27	B	27	GLY	0	0.010	0.005	5.569	0.427	0.427	0.000	0.000	0.000	0.000
28	B	28	LEU	0	-0.027	-0.014	7.610	0.321	0.321	0.000	0.000	0.000	0.000
29	B	29	THR	0	-0.013	0.001	9.877	-0.155	-0.155	0.000	0.000	0.000	0.000
30	B	30	LEU	0	0.028	0.008	12.528	-0.055	-0.055	0.000	0.000	0.000	0.000
31	B	31	SER	0	-0.025	-0.011	15.545	-0.020	-0.020	0.000	0.000	0.000	0.000
32	B	32	ARG	1	0.995	1.002	18.772	-0.208	-0.208	0.000	0.000	0.000	0.000
33	B	33	VAL	0	-0.011	-0.007	19.163	0.002	0.002	0.000	0.000	0.000	0.000
34	B	34	GLN	0	0.055	0.019	22.259	-0.011	-0.011	0.000	0.000	0.000	0.000
35	B	35	GLY	0	-0.033	-0.008	24.127	-0.012	-0.012	0.000	0.000	0.000	0.000
36	B	36	HIS	0	0.034	0.000	24.926	0.007	0.007	0.000	0.000	0.000	0.000
37	B	37	GLY	0	-0.012	0.005	26.411	-0.017	-0.017	0.000	0.000	0.000	0.000
38	B	53	MET	0	-0.028	-0.016	33.248	-0.002	-0.002	0.000	0.000	0.000	0.000
39	B	54	GLU	-1	-0.929	-0.965	33.586	0.018	0.018	0.000	0.000	0.000	0.000
40	B	55	LEU	0	-0.066	-0.029	27.936	-0.007	-0.007	0.000	0.000	0.000	0.000
41	B	56	HIS	0	0.007	0.004	27.818	0.008	0.008	0.000	0.000	0.000	0.000
42	B	57	GLU	-1	-0.904	-0.948	25.943	0.106	0.106	0.000	0.000	0.000	0.000
43	B	58	LYS	1	0.864	0.924	21.326	-0.022	-0.022	0.000	0.000	0.000	0.000
44	B	59	VAL	0	0.007	0.007	18.011	0.022	0.022	0.000	0.000	0.000	0.000
45	B	60	ARG	1	0.819	0.880	12.074	-0.313	-0.313	0.000	0.000	0.000	0.000
46	B	61	LEU	0	-0.017	-0.020	12.830	0.067	0.067	0.000	0.000	0.000	0.000
47	B	62	GLU	-1	-0.813	-0.872	8.891	0.341	0.341	0.000	0.000	0.000	0.000
48	B	63	ILE	0	0.000	-0.017	6.931	0.237	0.237	0.000	0.000	0.000	0.000
49	B	64	GLY	0	0.034	0.042	3.305	-1.444	-1.225	1.010	-0.496	-0.734	0.002
50	B	65	VAL	0	-0.010	-0.019	2.597	-0.144	0.406	1.015	0.452	-2.017	-0.003
51	B	66	SER	0	0.015	0.008	2.055	-6.745	-4.582	5.572	-3.593	-4.142	-0.016
52	B	67	GLU	-1	-0.741	-0.869	2.063	-11.740	-13.715	7.813	-1.914	-3.924	-0.041
53	B	68	PRO	0	-0.017	-0.001	4.849	0.126	0.202	-0.001	-0.007	-0.068	0.000
54	B	69	PHE	0	0.032	0.005	6.894	0.072	0.072	0.000	0.000	0.000	0.000
55	B	70	VAL	0	0.022	0.030	5.265	0.186	0.186	0.000	0.000	0.000	0.000
56	B	71	LYS	1	0.867	0.924	7.887	0.519	0.519	0.000	0.000	0.000	0.000
57	B	72	PRO	0	0.024	0.009	10.570	0.074	0.074	0.000	0.000	0.000	0.000
58	B	73	THR	0	0.022	0.010	8.962	0.151	0.151	0.000	0.000	0.000	0.000
59	B	74	VAL	0	-0.004	-0.015	10.270	0.067	0.067	0.000	0.000	0.000	0.000
60	B	75	GLU	-1	-0.828	-0.907	12.631	-0.210	-0.210	0.000	0.000	0.000	0.000
61	B	76	ALA	0	-0.012	0.003	14.229	0.028	0.028	0.000	0.000	0.000	0.000
62	B	77	ILE	0	-0.003	-0.002	11.280	0.023	0.023	0.000	0.000	0.000	0.000
63	B	78	LEU	0	-0.008	-0.008	15.790	0.007	0.007	0.000	0.000	0.000	0.000
64	B	79	LYS	1	0.910	0.950	18.219	0.024	0.024	0.000	0.000	0.000	0.000
65	B	80	ALA	0	-0.013	0.004	18.854	0.006	0.006	0.000	0.000	0.000	0.000
66	B	81	ALA	0	0.018	-0.007	18.949	0.010	0.010	0.000	0.000	0.000	0.000
67	B	82	ARG	1	0.890	0.967	20.960	0.097	0.097	0.000	0.000	0.000	0.000
68	B	83	THR	0	-0.033	-0.063	23.333	0.012	0.012	0.000	0.000	0.000	0.000
69	B	84	GLY	0	-0.082	-0.038	26.426	-0.002	-0.002	0.000	0.000	0.000	0.000
70	B	85	GLU	-1	-0.892	-0.919	28.109	-0.022	-0.022	0.000	0.000	0.000	0.000
71	B	86	VAL	0	-0.004	-0.020	27.370	-0.005	-0.005	0.000	0.000	0.000	0.000
72	B	87	GLY	0	0.033	0.015	26.123	0.011	0.011	0.000	0.000	0.000	0.000
73	B	88	ASP	-1	-0.697	-0.806	22.749	-0.028	-0.028	0.000	0.000	0.000	0.000
74	B	89	GLY	0	-0.018	0.004	20.387	0.017	0.017	0.000	0.000	0.000	0.000
75	B	90	LYS	1	0.905	0.949	17.636	0.180	0.180	0.000	0.000	0.000	0.000
76	B	91	ILE	0	0.031	0.007	12.092	0.054	0.054	0.000	0.000	0.000	0.000
77	B	92	PHE	0	-0.046	-0.013	12.234	-0.058	-0.058	0.000	0.000	0.000	0.000
78	B	93	VAL	0	0.019	0.008	7.576	0.056	0.056	0.000	0.000	0.000	0.000
79	B	94	LEU	0	-0.012	-0.004	7.833	0.027	0.027	0.000	0.000	0.000	0.000
80	B	95	PRO	0	0.014	0.001	6.026	-1.026	-1.026	0.000	0.000	0.000	0.000
81	B	96	VAL	0	-0.023	-0.021	3.141	0.202	1.117	0.038	-0.206	-0.748	-0.001
82	B	97	GLU	-1	-0.929	-0.949	3.896	-3.199	-3.019	0.000	-0.093	-0.088	0.000
83	B	98	LYS	1	0.841	0.899	5.639	-0.015	-0.015	0.000	0.000	0.000	0.000
84	B	99	VAL	0	0.001	-0.003	2.426	-1.334	-1.272	3.743	-0.805	-3.000	0.000
85	B	100	TYR	0	-0.013	-0.025	5.388	-0.432	-0.381	-0.001	-0.004	-0.047	0.000
86	B	101	ARG	1	0.753	0.871	4.544	-0.883	-0.773	-0.001	-0.002	-0.107	0.000
87	B	102	ILE	0	0.036	0.001	7.681	-0.216	-0.216	0.000	0.000	0.000	0.000
88	B	103	ARG	1	0.917	0.964	10.427	-0.811	-0.811	0.000	0.000	0.000	0.000
89	B	104	THR	0	0.008	-0.017	10.318	-0.043	-0.043	0.000	0.000	0.000	0.000
90	B	105	GLY	0	0.029	0.034	11.548	-0.081	-0.081	0.000	0.000	0.000	0.000
91	B	106	GLU	-1	-0.879	-0.918	9.174	0.709	0.709	0.000	0.000	0.000	0.000
92	B	107	GLU	-1	-0.743	-0.830	7.726	0.568	0.568	0.000	0.000	0.000	0.000
93	B	108	ASP	-1	-0.912	-0.962	3.472	0.275	1.033	0.063	-0.238	-0.583	-0.002

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