FMO DATABASE

FMODB ID: 5JV1Z

Calculation Name: 2VC8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VC8

Chain ID: A

ChEMBL ID:

UniProt ID: Q96F86

Base Structure: X-ray

Registration Date: 2023-09-23

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	72
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-401517.976616
FMO2-HF: Nuclear repulsion	374419.787505
FMO2-HF: Total energy	-27098.18911
FMO2-MP2: Total energy	-27177.081581

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:3:THR)

Summations of interaction energy for fragment #1(A:3:THR)

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.
-3.443	1.444	5.915	-3.907	-6.894	-0.014

Interaction energy analysis for fragmet #1(A:3:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : -0.014

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	5	TRP	0	0.012	0.002	3.573	-1.756	0.208	0.006	-0.783	-1.187	0.001
4	A	6	LEU	0	-0.016	0.019	3.581	0.544	1.019	0.006	-0.123	-0.358	0.000
5	A	7	GLY	0	0.040	0.018	5.500	0.066	0.066	0.000	0.000	0.000	0.000
6	A	8	SER	0	-0.054	-0.028	8.129	0.401	0.401	0.000	0.000	0.000	0.000
7	A	9	ILE	0	-0.056	-0.035	10.415	0.024	0.024	0.000	0.000	0.000	0.000
8	A	10	VAL	0	0.031	0.021	9.859	0.043	0.043	0.000	0.000	0.000	0.000
9	A	11	SER	0	-0.023	-0.040	13.121	-0.021	-0.021	0.000	0.000	0.000	0.000
10	A	12	ILE	0	0.045	0.019	10.421	0.053	0.053	0.000	0.000	0.000	0.000
11	A	13	ASN	0	-0.030	-0.017	14.713	-0.057	-0.057	0.000	0.000	0.000	0.000
12	A	14	CYS	0	0.034	0.017	16.013	0.042	0.042	0.000	0.000	0.000	0.000
13	A	15	GLY	0	0.027	0.023	18.335	0.003	0.003	0.000	0.000	0.000	0.000
14	A	16	ASP	-1	-0.923	-0.971	21.687	0.132	0.132	0.000	0.000	0.000	0.000
15	A	17	SER	0	-0.031	-0.014	24.240	-0.010	-0.010	0.000	0.000	0.000	0.000
16	A	18	LEU	0	0.008	0.011	19.911	-0.015	-0.015	0.000	0.000	0.000	0.000
17	A	19	GLY	0	0.013	0.018	22.334	-0.022	-0.022	0.000	0.000	0.000	0.000
18	A	20	VAL	0	0.018	0.012	18.772	0.020	0.020	0.000	0.000	0.000	0.000
19	A	21	TYR	0	-0.046	-0.026	16.373	-0.043	-0.043	0.000	0.000	0.000	0.000
20	A	22	GLN	0	0.015	0.024	16.191	0.040	0.040	0.000	0.000	0.000	0.000
21	A	23	GLY	0	0.028	0.010	15.021	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	24	ARG	1	0.877	0.942	11.812	0.611	0.611	0.000	0.000	0.000	0.000
23	A	25	VAL	0	0.030	0.022	6.130	0.075	0.075	0.000	0.000	0.000	0.000
24	A	26	SER	0	-0.022	-0.014	8.934	-0.257	-0.257	0.000	0.000	0.000	0.000
25	A	27	ALA	0	0.050	0.015	6.641	-0.137	-0.137	0.000	0.000	0.000	0.000
26	A	28	VAL	0	-0.014	-0.010	2.276	-0.936	-0.053	2.195	-1.165	-1.912	0.000
27	A	29	ASP	-1	-0.808	-0.871	3.211	-1.154	-0.209	0.086	-0.515	-0.516	-0.005
28	A	30	GLN	0	0.005	-0.025	2.221	-0.861	-0.358	3.624	-1.307	-2.820	-0.010
29	A	31	VAL	0	-0.044	-0.010	4.929	0.082	0.091	-0.001	-0.012	0.005	0.000
30	A	32	SER	0	-0.025	-0.034	8.427	0.009	0.009	0.000	0.000	0.000	0.000
31	A	33	GLN	0	-0.064	-0.014	7.402	-0.023	-0.023	0.000	0.000	0.000	0.000
32	A	34	THR	0	-0.018	-0.011	7.197	-0.048	-0.048	0.000	0.000	0.000	0.000
33	A	35	ILE	0	0.001	0.009	6.299	0.088	0.088	0.000	0.000	0.000	0.000
34	A	36	SER	0	0.011	-0.001	7.794	0.052	0.052	0.000	0.000	0.000	0.000
35	A	37	LEU	0	-0.033	-0.010	9.782	-0.138	-0.138	0.000	0.000	0.000	0.000
36	A	38	THR	0	0.003	0.004	12.517	0.031	0.031	0.000	0.000	0.000	0.000
37	A	39	ARG	1	0.876	0.914	15.055	0.271	0.271	0.000	0.000	0.000	0.000
38	A	40	PRO	0	0.058	0.043	16.206	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	41	PHE	0	0.013	-0.002	18.059	0.006	0.006	0.000	0.000	0.000	0.000
40	A	42	HIS	1	0.891	0.939	19.919	-0.038	-0.038	0.000	0.000	0.000	0.000
41	A	43	ASN	0	0.004	0.001	22.455	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	44	GLY	0	0.033	0.023	24.636	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	45	VAL	0	-0.009	0.000	25.520	-0.010	-0.010	0.000	0.000	0.000	0.000
44	A	46	LYS	1	0.894	0.951	22.257	0.095	0.095	0.000	0.000	0.000	0.000
45	A	47	CYS	0	-0.038	-0.017	20.900	0.016	0.016	0.000	0.000	0.000	0.000
46	A	48	LEU	0	0.012	-0.005	23.041	-0.016	-0.016	0.000	0.000	0.000	0.000
47	A	49	VAL	0	0.000	0.009	19.577	-0.009	-0.009	0.000	0.000	0.000	0.000
48	A	50	PRO	0	-0.019	-0.010	19.510	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	51	GLU	-1	-0.855	-0.917	12.124	-0.277	-0.277	0.000	0.000	0.000	0.000
50	A	52	VAL	0	-0.029	-0.002	15.042	0.027	0.027	0.000	0.000	0.000	0.000
51	A	53	THR	0	0.016	-0.001	10.467	-0.019	-0.019	0.000	0.000	0.000	0.000
52	A	54	PHE	0	-0.019	-0.012	11.640	0.004	0.004	0.000	0.000	0.000	0.000
53	A	55	ARG	1	0.872	0.884	10.926	-0.266	-0.266	0.000	0.000	0.000	0.000
54	A	56	ALA	0	0.023	-0.006	8.756	-0.040	-0.040	0.000	0.000	0.000	0.000
55	A	57	GLY	0	-0.006	-0.003	10.848	-0.033	-0.033	0.000	0.000	0.000	0.000
56	A	58	ASP	-1	-0.815	-0.864	14.216	0.283	0.283	0.000	0.000	0.000	0.000
57	A	59	ILE	0	-0.079	-0.029	10.743	-0.064	-0.064	0.000	0.000	0.000	0.000
58	A	60	THR	0	-0.010	-0.007	14.930	0.039	0.039	0.000	0.000	0.000	0.000
59	A	61	GLU	-1	-0.875	-0.956	16.179	0.203	0.203	0.000	0.000	0.000	0.000
60	A	62	LEU	0	-0.010	0.005	8.925	-0.030	-0.030	0.000	0.000	0.000	0.000
61	A	63	LYS	1	0.859	0.943	13.540	-0.136	-0.136	0.000	0.000	0.000	0.000
62	A	64	ILE	0	0.037	0.000	11.307	-0.020	-0.020	0.000	0.000	0.000	0.000
63	A	65	LEU	0	-0.094	-0.044	13.775	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	66	GLU	-1	-0.905	-0.946	14.472	-0.313	-0.313	0.000	0.000	0.000	0.000
65	A	67	ILE	0	0.010	0.003	12.138	-0.032	-0.032	0.000	0.000	0.000	0.000
66	A	68	PRO	0	0.004	0.007	8.320	0.111	0.111	0.000	0.000	0.000	0.000
67	A	69	GLY	0	0.019	0.017	11.152	0.103	0.103	0.000	0.000	0.000	0.000
68	A	70	PRO	0	0.014	-0.004	11.702	-0.197	-0.197	0.000	0.000	0.000	0.000
69	A	71	GLY	0	-0.010	0.007	12.934	0.004	0.004	0.000	0.000	0.000	0.000
70	A	72	ASH	0	-0.020	-0.029	10.522	-0.250	-0.250	0.000	0.000	0.000	0.000
71	A	73	ASN	0	-0.002	-0.013	7.587	0.343	0.343	0.000	0.000	0.000	0.000
72	A	74	GLN	0	0.008	0.023	4.786	-0.015	0.093	-0.001	-0.002	-0.106	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:THR)