FMO DATABASE

FMODB ID: 4JV1N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-401270.263938
FMO2-HF: Nuclear repulsion	374172.444623
FMO2-HF: Total energy	-27097.819314
FMO2-MP2: Total energy	-27176.715659

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.
-8.55	-7.606	12.76	-5.241	-8.467	-0.018

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 : -0.015 / q_NPA : -0.031

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	-0.005	-0.007	3.553	-2.526	-0.669	0.004	-0.736	-1.125	0.001
4	A	6	LEU	0	-0.021	0.023	3.683	-0.175	0.267	0.003	-0.111	-0.335	0.000
5	A	7	GLY	0	0.026	0.009	5.561	0.270	0.270	0.000	0.000	0.000	0.000
6	A	8	SER	0	-0.061	-0.040	8.107	0.122	0.122	0.000	0.000	0.000	0.000
7	A	9	ILE	0	-0.049	-0.031	10.388	-0.099	-0.099	0.000	0.000	0.000	0.000
8	A	10	VAL	0	0.032	0.023	9.844	0.060	0.060	0.000	0.000	0.000	0.000
9	A	11	SER	0	-0.025	-0.020	13.103	-0.083	-0.083	0.000	0.000	0.000	0.000
10	A	12	ILE	0	0.059	0.025	10.744	0.075	0.075	0.000	0.000	0.000	0.000
11	A	13	ASN	0	-0.016	-0.014	14.707	-0.097	-0.097	0.000	0.000	0.000	0.000
12	A	14	CYS	0	0.026	0.012	15.898	0.044	0.044	0.000	0.000	0.000	0.000
13	A	15	GLY	0	0.028	0.025	18.338	-0.018	-0.018	0.000	0.000	0.000	0.000
14	A	16	ASP	-1	-0.917	-0.967	21.691	0.165	0.165	0.000	0.000	0.000	0.000
15	A	17	SER	0	-0.038	-0.022	24.452	-0.017	-0.017	0.000	0.000	0.000	0.000
16	A	18	LEU	0	-0.004	0.007	19.824	-0.016	-0.016	0.000	0.000	0.000	0.000
17	A	19	GLY	0	-0.001	0.005	22.332	-0.013	-0.013	0.000	0.000	0.000	0.000
18	A	20	VAL	0	0.020	0.012	18.759	0.022	0.022	0.000	0.000	0.000	0.000
19	A	21	TYR	0	-0.025	-0.004	16.375	-0.058	-0.058	0.000	0.000	0.000	0.000
20	A	22	GLN	0	0.001	-0.002	16.183	0.070	0.070	0.000	0.000	0.000	0.000
21	A	23	GLY	0	0.027	0.008	15.001	-0.047	-0.047	0.000	0.000	0.000	0.000
22	A	24	ARG	1	0.906	0.963	11.748	0.054	0.054	0.000	0.000	0.000	0.000
23	A	25	VAL	0	0.032	0.025	6.130	-0.048	-0.048	0.000	0.000	0.000	0.000
24	A	26	SER	0	-0.025	-0.018	8.967	-0.082	-0.082	0.000	0.000	0.000	0.000
25	A	27	ALA	0	0.032	0.014	6.509	-0.155	-0.155	0.000	0.000	0.000	0.000
26	A	28	VAL	0	-0.004	-0.004	2.147	-0.610	-0.025	3.205	-1.570	-2.220	0.000
27	A	29	ASP	-1	-0.838	-0.903	3.109	-3.488	-2.298	0.114	-0.684	-0.621	-0.007
28	A	30	GLN	0	0.001	-0.034	2.133	-2.452	-5.726	9.436	-2.106	-4.056	-0.012
29	A	31	VAL	0	-0.036	-0.003	4.710	0.260	0.297	-0.001	-0.032	-0.005	0.000
30	A	32	SER	0	-0.009	-0.007	8.334	0.209	0.209	0.000	0.000	0.000	0.000
31	A	33	GLN	0	-0.056	-0.009	7.442	0.145	0.145	0.000	0.000	0.000	0.000
32	A	34	THR	0	-0.019	-0.011	7.237	0.106	0.106	0.000	0.000	0.000	0.000
33	A	35	ILE	0	0.003	0.008	6.396	0.031	0.031	0.000	0.000	0.000	0.000
34	A	36	SER	0	0.037	0.033	7.795	0.016	0.016	0.000	0.000	0.000	0.000
35	A	37	LEU	0	-0.015	0.001	9.769	-0.025	-0.025	0.000	0.000	0.000	0.000
36	A	38	THR	0	0.012	0.009	12.503	-0.021	-0.021	0.000	0.000	0.000	0.000
37	A	39	ARG	1	0.870	0.914	15.038	0.097	0.097	0.000	0.000	0.000	0.000
38	A	40	PRO	0	0.029	0.031	16.273	0.016	0.016	0.000	0.000	0.000	0.000
39	A	41	PHE	0	0.016	-0.006	18.044	-0.019	-0.019	0.000	0.000	0.000	0.000
40	A	42	HIS	1	0.884	0.931	19.906	-0.108	-0.108	0.000	0.000	0.000	0.000
41	A	43	ASN	0	0.014	0.009	22.444	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	44	GLY	0	0.022	0.017	24.628	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	45	VAL	0	-0.010	-0.001	25.498	-0.010	-0.010	0.000	0.000	0.000	0.000
44	A	46	LYS	1	0.923	0.973	22.169	0.012	0.012	0.000	0.000	0.000	0.000
45	A	47	CYS	0	-0.031	-0.018	19.989	0.002	0.002	0.000	0.000	0.000	0.000
46	A	48	LEU	0	0.013	-0.005	23.029	-0.011	-0.011	0.000	0.000	0.000	0.000
47	A	49	VAL	0	0.001	0.009	19.386	-0.012	-0.012	0.000	0.000	0.000	0.000
48	A	50	PRO	0	-0.025	-0.013	19.421	0.014	0.014	0.000	0.000	0.000	0.000
49	A	51	GLU	-1	-0.871	-0.950	12.188	-0.299	-0.299	0.000	0.000	0.000	0.000
50	A	52	VAL	0	-0.033	-0.003	15.016	0.003	0.003	0.000	0.000	0.000	0.000
51	A	53	THR	0	0.017	-0.008	10.572	0.009	0.009	0.000	0.000	0.000	0.000
52	A	54	PHE	0	-0.023	-0.011	11.647	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	55	ARG	1	0.910	0.930	10.934	-0.147	-0.147	0.000	0.000	0.000	0.000
54	A	56	ALA	0	0.028	-0.003	8.797	0.011	0.011	0.000	0.000	0.000	0.000
55	A	57	GLY	0	-0.019	-0.010	10.862	0.006	0.006	0.000	0.000	0.000	0.000
56	A	58	ASP	-1	-0.851	-0.910	14.225	0.203	0.203	0.000	0.000	0.000	0.000
57	A	59	ILE	0	-0.075	-0.029	10.798	-0.035	-0.035	0.000	0.000	0.000	0.000
58	A	60	THR	0	-0.024	-0.015	14.937	0.042	0.042	0.000	0.000	0.000	0.000
59	A	61	GLU	-1	-0.900	-0.962	16.135	0.423	0.423	0.000	0.000	0.000	0.000
60	A	62	LEU	0	-0.018	0.003	9.012	-0.036	-0.036	0.000	0.000	0.000	0.000
61	A	63	LYS	1	0.912	0.958	13.535	-0.307	-0.307	0.000	0.000	0.000	0.000
62	A	64	ILE	0	0.022	-0.003	11.217	-0.009	-0.009	0.000	0.000	0.000	0.000
63	A	65	LEU	0	-0.090	-0.044	13.758	-0.046	-0.046	0.000	0.000	0.000	0.000
64	A	66	GLU	-1	-0.913	-0.943	14.453	0.163	0.163	0.000	0.000	0.000	0.000
65	A	67	ILE	0	0.002	-0.008	12.120	0.047	0.047	0.000	0.000	0.000	0.000
66	A	68	PRO	0	0.008	0.012	8.285	-0.067	-0.067	0.000	0.000	0.000	0.000
67	A	69	GLY	0	0.024	0.016	11.250	0.034	0.034	0.000	0.000	0.000	0.000
68	A	70	PRO	0	0.016	-0.001	11.910	-0.012	-0.012	0.000	0.000	0.000	0.000
69	A	71	GLY	0	-0.008	0.008	13.550	-0.008	-0.008	0.000	0.000	0.000	0.000
70	A	72	ASH	0	-0.021	-0.028	10.914	-0.010	-0.010	0.000	0.000	0.000	0.000
71	A	73	ASN	0	-0.004	-0.015	7.718	0.001	0.001	0.000	0.000	0.000	0.000
72	A	74	GLN	0	0.004	0.021	4.764	-0.102	0.005	-0.001	-0.002	-0.105	0.000

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