FMO DATABASE

FMODB ID: 94V82

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

Total energy (hartree)

FMO2-HF: Electronic energy	-618772.822752
FMO2-HF: Nuclear repulsion	582856.827515
FMO2-HF: Total energy	-35915.995238
FMO2-MP2: Total energy	-36022.150643

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.
-26.222	-23.203	27.747	-9.077	-21.685	-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 : -0.035 / q_NPA : -0.023

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	0.035	0.015	2.425	-1.977	1.424	1.629	-2.259	-2.771	-0.012
4	B	4	ILE	0	-0.019	-0.010	4.902	-0.433	-0.380	-0.001	-0.006	-0.045	0.000
5	B	5	VAL	0	0.016	0.005	7.682	0.453	0.453	0.000	0.000	0.000	0.000
6	B	6	ALA	0	-0.017	-0.006	10.898	-0.154	-0.154	0.000	0.000	0.000	0.000
7	B	7	ILE	0	-0.028	-0.004	13.803	0.088	0.088	0.000	0.000	0.000	0.000
8	B	8	VAL	0	0.026	0.008	16.936	-0.046	-0.046	0.000	0.000	0.000	0.000
9	B	9	ARG	1	0.894	0.929	19.665	0.034	0.034	0.000	0.000	0.000	0.000
10	B	10	PRO	0	0.050	0.023	22.615	0.017	0.017	0.000	0.000	0.000	0.000
11	B	11	GLU	-1	-0.873	-0.939	24.062	0.077	0.077	0.000	0.000	0.000	0.000
12	B	12	LYS	1	0.904	0.961	22.097	-0.030	-0.030	0.000	0.000	0.000	0.000
13	B	13	LEU	0	0.006	0.013	18.057	0.011	0.011	0.000	0.000	0.000	0.000
14	B	14	ASN	0	0.013	-0.004	19.978	0.050	0.050	0.000	0.000	0.000	0.000
15	B	15	GLU	-1	-0.909	-0.956	21.134	0.083	0.083	0.000	0.000	0.000	0.000
16	B	16	VAL	0	0.028	0.007	15.845	0.001	0.001	0.000	0.000	0.000	0.000
17	B	17	LEU	0	-0.005	-0.012	15.724	0.042	0.042	0.000	0.000	0.000	0.000
18	B	18	LYS	1	0.931	0.982	16.452	-0.098	-0.098	0.000	0.000	0.000	0.000
19	B	19	ALA	0	0.007	-0.003	16.924	0.010	0.010	0.000	0.000	0.000	0.000
20	B	20	LEU	0	-0.011	-0.009	11.202	-0.008	-0.008	0.000	0.000	0.000	0.000
21	B	21	PHE	0	-0.036	-0.026	12.399	0.076	0.076	0.000	0.000	0.000	0.000
22	B	22	GLN	0	-0.051	-0.030	14.304	-0.025	-0.025	0.000	0.000	0.000	0.000
23	B	23	ALA	0	-0.046	-0.003	12.033	-0.037	-0.037	0.000	0.000	0.000	0.000
24	B	24	GLU	-1	-0.929	-0.945	10.364	0.313	0.313	0.000	0.000	0.000	0.000
25	B	25	VAL	0	-0.004	-0.004	7.002	0.035	0.035	0.000	0.000	0.000	0.000
26	B	26	ARG	1	0.871	0.930	2.917	-2.268	-1.814	2.890	-0.606	-2.738	-0.002
27	B	27	GLY	0	0.007	0.003	5.301	0.503	0.503	0.000	0.000	0.000	0.000
28	B	28	LEU	0	-0.019	-0.012	7.520	0.363	0.363	0.000	0.000	0.000	0.000
29	B	29	THR	0	-0.010	0.005	9.790	-0.211	-0.211	0.000	0.000	0.000	0.000
30	B	30	LEU	0	0.016	-0.001	12.448	-0.060	-0.060	0.000	0.000	0.000	0.000
31	B	31	SER	0	-0.028	-0.009	15.439	-0.023	-0.023	0.000	0.000	0.000	0.000
32	B	32	ARG	1	0.998	1.001	18.734	-0.260	-0.260	0.000	0.000	0.000	0.000
33	B	33	VAL	0	-0.008	-0.004	19.108	0.007	0.007	0.000	0.000	0.000	0.000
34	B	34	GLN	0	0.057	0.022	22.247	-0.014	-0.014	0.000	0.000	0.000	0.000
35	B	35	GLY	0	-0.044	-0.016	24.101	-0.011	-0.011	0.000	0.000	0.000	0.000
36	B	36	HIS	0	0.066	0.013	24.883	0.004	0.004	0.000	0.000	0.000	0.000
37	B	37	GLY	0	-0.032	-0.003	26.353	-0.019	-0.019	0.000	0.000	0.000	0.000
38	B	53	MET	0	-0.047	-0.036	33.147	-0.001	-0.001	0.000	0.000	0.000	0.000
39	B	54	GLU	-1	-0.920	-0.952	33.552	0.028	0.028	0.000	0.000	0.000	0.000
40	B	55	LEU	0	-0.060	-0.020	28.176	-0.006	-0.006	0.000	0.000	0.000	0.000
41	B	56	HIS	0	0.014	0.000	27.653	0.009	0.009	0.000	0.000	0.000	0.000
42	B	57	GLU	-1	-0.905	-0.944	25.927	0.116	0.116	0.000	0.000	0.000	0.000
43	B	58	LYS	1	0.866	0.929	21.187	-0.026	-0.026	0.000	0.000	0.000	0.000
44	B	59	VAL	0	0.010	0.006	17.779	0.026	0.026	0.000	0.000	0.000	0.000
45	B	60	ARG	1	0.858	0.915	12.400	-0.401	-0.401	0.000	0.000	0.000	0.000
46	B	61	LEU	0	-0.018	-0.020	12.742	0.076	0.076	0.000	0.000	0.000	0.000
47	B	62	GLU	-1	-0.859	-0.910	8.767	0.544	0.544	0.000	0.000	0.000	0.000
48	B	63	ILE	0	-0.001	-0.018	6.725	0.249	0.249	0.000	0.000	0.000	0.000
49	B	64	GLY	0	0.026	0.036	3.175	-1.286	-1.487	1.772	-0.628	-0.942	0.004
50	B	65	VAL	0	-0.007	-0.017	2.472	0.154	-0.208	1.709	1.113	-2.460	-0.004
51	B	66	SER	0	0.014	0.010	2.053	-6.502	-4.642	6.433	-3.789	-4.505	-0.014
52	B	67	GLU	-1	-0.772	-0.899	1.985	-12.154	-17.462	12.029	-2.001	-4.720	-0.047
53	B	68	PRO	0	-0.012	0.002	4.858	0.341	0.423	-0.001	-0.007	-0.073	0.000
54	B	69	PHE	0	0.036	0.006	6.893	0.186	0.186	0.000	0.000	0.000	0.000
55	B	70	VAL	0	0.027	0.034	5.355	0.272	0.272	0.000	0.000	0.000	0.000
56	B	71	LYS	1	0.899	0.958	7.874	0.745	0.745	0.000	0.000	0.000	0.000
57	B	72	PRO	0	0.008	-0.014	10.604	0.116	0.116	0.000	0.000	0.000	0.000
58	B	73	THR	0	0.037	0.024	8.878	0.187	0.187	0.000	0.000	0.000	0.000
59	B	74	VAL	0	-0.003	-0.011	10.179	0.100	0.100	0.000	0.000	0.000	0.000
60	B	75	GLU	-1	-0.874	-0.945	12.474	-0.305	-0.305	0.000	0.000	0.000	0.000
61	B	76	ALA	0	-0.001	0.010	14.240	0.043	0.043	0.000	0.000	0.000	0.000
62	B	77	ILE	0	-0.007	-0.004	11.220	0.038	0.038	0.000	0.000	0.000	0.000
63	B	78	LEU	0	-0.021	-0.014	15.656	0.016	0.016	0.000	0.000	0.000	0.000
64	B	79	LYS	1	0.913	0.951	18.075	0.081	0.081	0.000	0.000	0.000	0.000
65	B	80	ALA	0	-0.025	0.001	18.748	0.010	0.010	0.000	0.000	0.000	0.000
66	B	81	ALA	0	0.020	-0.008	18.879	0.014	0.014	0.000	0.000	0.000	0.000
67	B	82	ARG	1	0.888	0.966	20.840	0.137	0.137	0.000	0.000	0.000	0.000
68	B	83	THR	0	-0.051	-0.080	23.202	0.013	0.013	0.000	0.000	0.000	0.000
69	B	84	GLY	0	-0.059	-0.029	26.308	-0.002	-0.002	0.000	0.000	0.000	0.000
70	B	85	GLU	-1	-0.934	-0.945	28.002	-0.038	-0.038	0.000	0.000	0.000	0.000
71	B	86	VAL	0	0.023	-0.005	27.253	-0.006	-0.006	0.000	0.000	0.000	0.000
72	B	87	GLY	0	0.005	-0.001	26.026	0.014	0.014	0.000	0.000	0.000	0.000
73	B	88	ASP	-1	-0.700	-0.799	22.631	-0.040	-0.040	0.000	0.000	0.000	0.000
74	B	89	GLY	0	-0.021	0.003	20.291	0.019	0.019	0.000	0.000	0.000	0.000
75	B	90	LYS	1	0.911	0.953	17.463	0.206	0.206	0.000	0.000	0.000	0.000
76	B	91	ILE	0	0.034	0.011	11.946	0.063	0.063	0.000	0.000	0.000	0.000
77	B	92	PHE	0	-0.043	-0.013	12.095	-0.068	-0.068	0.000	0.000	0.000	0.000
78	B	93	VAL	0	0.024	0.011	7.492	0.080	0.080	0.000	0.000	0.000	0.000
79	B	94	LEU	0	-0.016	-0.009	7.762	0.021	0.021	0.000	0.000	0.000	0.000
80	B	95	PRO	0	-0.018	-0.012	5.774	-1.094	-1.094	0.000	0.000	0.000	0.000
81	B	96	VAL	0	-0.002	-0.007	3.075	0.384	1.346	0.052	-0.218	-0.796	-0.001
82	B	97	GLU	-1	-0.945	-0.962	3.932	-2.586	-2.407	0.000	-0.075	-0.104	0.000
83	B	98	LYS	1	0.987	0.995	5.867	-0.093	-0.093	0.000	0.000	0.000	0.000
84	B	99	VAL	0	-0.012	0.001	2.788	-1.731	-0.589	1.200	-0.401	-1.940	0.001
85	B	100	TYR	0	0.051	0.030	5.447	-0.382	-0.382	0.000	0.000	0.000	0.000
86	B	101	ARG	1	0.785	0.899	4.429	-1.505	-1.387	-0.001	-0.004	-0.112	0.000
87	B	102	ILE	0	0.049	0.007	7.947	-0.258	-0.258	0.000	0.000	0.000	0.000
88	B	103	ARG	1	0.910	0.958	9.913	-1.007	-1.007	0.000	0.000	0.000	0.000
89	B	104	THR	0	0.005	-0.017	10.709	-0.050	-0.050	0.000	0.000	0.000	0.000
90	B	105	GLY	0	0.031	0.035	11.845	-0.102	-0.102	0.000	0.000	0.000	0.000
91	B	106	GLU	-1	-0.936	-0.964	9.167	0.872	0.872	0.000	0.000	0.000	0.000
92	B	107	GLU	-1	-0.905	-0.954	7.900	1.195	1.195	0.000	0.000	0.000	0.000
93	B	108	ASP	-1	-0.938	-0.977	3.488	0.573	1.212	0.036	-0.196	-0.479	-0.001

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