FMO DATABASE

FMODB ID: 53VRZ

Calculation Name: 3VC8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VC8

Chain ID: A

ChEMBL ID:

UniProt ID: P0C6X9

Base Structure: X-ray

Registration Date: 2023-06-19

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	81
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-554702.215356
FMO2-HF: Nuclear repulsion	520976.238209
FMO2-HF: Total energy	-33725.977147
FMO2-MP2: Total energy	-33820.745021

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:1:THR)

Summations of interaction energy for fragment #1(A:1: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.
-51.949	-54.663	35.257	-17.893	-14.649	-0.079

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.054

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	3	GLU	-1	-0.763	-0.886	2.755	-1.927	1.914	0.542	-1.761	-2.622	0.003
4	A	4	GLU	-1	-0.877	-0.897	1.634	-49.110	-57.164	34.671	-15.719	-10.898	-0.083
5	A	5	MET	0	0.011	0.007	3.116	-0.521	0.484	0.030	-0.333	-0.703	0.001
6	A	6	ALA	0	0.015	0.024	5.114	0.282	0.385	-0.001	-0.006	-0.095	0.000
7	A	7	LEU	0	-0.019	-0.005	6.720	0.068	0.068	0.000	0.000	0.000	0.000
8	A	8	THR	0	-0.057	-0.028	7.237	-0.041	-0.041	0.000	0.000	0.000	0.000
9	A	9	THR	0	-0.013	-0.020	9.778	0.125	0.125	0.000	0.000	0.000	0.000
10	A	10	PHE	0	-0.020	-0.005	9.148	-0.024	-0.024	0.000	0.000	0.000	0.000
11	A	11	MET	0	0.017	0.025	12.728	0.026	0.026	0.000	0.000	0.000	0.000
12	A	12	ILE	0	0.018	0.029	12.428	0.015	0.015	0.000	0.000	0.000	0.000
13	A	13	THR	0	0.019	0.009	14.214	0.011	0.011	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.895	0.923	15.157	-0.053	-0.053	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.837	-0.890	13.355	0.309	0.309	0.000	0.000	0.000	0.000
16	A	16	SER	0	0.036	-0.009	10.578	0.078	0.078	0.000	0.000	0.000	0.000
17	A	17	TYR	0	0.005	-0.017	10.415	0.066	0.066	0.000	0.000	0.000	0.000
18	A	18	CYS	0	-0.005	-0.005	11.237	0.037	0.037	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.819	0.902	8.039	-0.364	-0.364	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.020	0.011	5.879	0.229	0.229	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.877	0.940	7.258	-0.236	-0.236	0.000	0.000	0.000	0.000
22	A	22	ASN	0	-0.008	0.002	9.148	-0.057	-0.057	0.000	0.000	0.000	0.000
23	A	23	SER	0	-0.085	-0.037	3.348	-0.336	-0.124	0.016	-0.063	-0.165	0.000
24	A	24	VAL	0	-0.023	-0.011	4.579	-0.155	0.024	-0.001	-0.011	-0.166	0.000
25	A	25	SER	0	0.028	0.023	7.158	-0.068	-0.068	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.791	-0.896	10.515	0.243	0.243	0.000	0.000	0.000	0.000
27	A	27	VAL	0	0.033	0.014	13.329	-0.016	-0.016	0.000	0.000	0.000	0.000
28	A	28	ALA	0	0.000	0.005	9.097	-0.018	-0.018	0.000	0.000	0.000	0.000
29	A	29	PHE	0	0.030	0.013	10.400	0.003	0.003	0.000	0.000	0.000	0.000
30	A	30	ASN	0	0.002	-0.024	11.437	-0.027	-0.027	0.000	0.000	0.000	0.000
31	A	31	ARG	1	0.851	0.930	11.895	-0.334	-0.334	0.000	0.000	0.000	0.000
32	A	32	TYR	0	-0.026	-0.043	6.758	-0.126	-0.126	0.000	0.000	0.000	0.000
33	A	33	LEU	0	0.026	0.022	12.958	-0.030	-0.030	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.081	-0.049	15.755	-0.023	-0.023	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.030	-0.013	14.254	-0.018	-0.018	0.000	0.000	0.000	0.000
36	A	36	TYR	0	-0.001	-0.002	16.653	-0.012	-0.012	0.000	0.000	0.000	0.000
37	A	37	ASN	0	0.005	-0.016	18.099	-0.014	-0.014	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.856	0.949	16.899	-0.173	-0.173	0.000	0.000	0.000	0.000
39	A	39	TYR	0	-0.011	-0.052	15.414	-0.019	-0.019	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.898	0.962	19.505	-0.051	-0.051	0.000	0.000	0.000	0.000
41	A	41	TYR	0	0.006	-0.003	21.367	-0.012	-0.012	0.000	0.000	0.000	0.000
42	A	42	PHE	0	0.010	0.015	20.980	0.001	0.001	0.000	0.000	0.000	0.000
43	A	43	SER	0	-0.023	-0.007	23.290	-0.010	-0.010	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.017	0.004	25.305	0.000	0.000	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.934	0.966	23.499	0.021	0.021	0.000	0.000	0.000	0.000
46	A	46	MET	0	0.001	0.010	17.039	0.005	0.005	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.815	-0.894	16.863	0.062	0.062	0.000	0.000	0.000	0.000
48	A	48	THR	0	0.033	-0.012	13.540	0.028	0.028	0.000	0.000	0.000	0.000
49	A	49	ALA	0	-0.025	-0.002	12.459	0.049	0.049	0.000	0.000	0.000	0.000
50	A	50	ALA	0	0.033	0.010	12.856	0.075	0.075	0.000	0.000	0.000	0.000
51	A	51	TYR	0	-0.045	-0.037	12.493	0.024	0.024	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.970	0.984	8.693	-0.083	-0.083	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.736	-0.826	9.891	0.359	0.359	0.000	0.000	0.000	0.000
54	A	54	ALA	0	0.014	0.005	11.728	-0.010	-0.010	0.000	0.000	0.000	0.000
55	A	55	ALA	0	-0.007	-0.004	9.787	-0.039	-0.039	0.000	0.000	0.000	0.000
56	A	56	CYS	0	-0.043	-0.006	6.758	-0.034	-0.034	0.000	0.000	0.000	0.000
57	A	57	SER	0	-0.012	-0.026	9.580	-0.058	-0.058	0.000	0.000	0.000	0.000
58	A	58	GLN	0	-0.023	-0.010	13.208	-0.020	-0.020	0.000	0.000	0.000	0.000
59	A	59	LEU	0	-0.005	0.016	7.824	-0.025	-0.025	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.026	0.014	11.595	-0.010	-0.010	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.931	0.956	12.767	-0.096	-0.096	0.000	0.000	0.000	0.000
62	A	62	ALA	0	-0.016	0.020	14.355	-0.008	-0.008	0.000	0.000	0.000	0.000
63	A	63	MET	0	-0.009	-0.001	10.162	-0.016	-0.016	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.829	-0.890	14.830	0.136	0.136	0.000	0.000	0.000	0.000
65	A	65	THR	0	-0.075	-0.051	17.548	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	66	PHE	0	-0.049	-0.021	16.659	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	67	ASN	0	0.004	0.021	17.190	0.010	0.010	0.000	0.000	0.000	0.000
68	A	68	HIS	1	0.820	0.880	19.246	-0.126	-0.126	0.000	0.000	0.000	0.000
69	A	69	ASN	0	-0.032	-0.021	22.425	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	70	ASN	0	0.010	0.007	23.335	-0.010	-0.010	0.000	0.000	0.000	0.000
71	A	71	GLY	0	0.085	0.054	23.003	0.008	0.008	0.000	0.000	0.000	0.000
72	A	72	ASN	0	-0.083	-0.041	22.933	0.003	0.003	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.832	-0.913	18.761	0.070	0.070	0.000	0.000	0.000	0.000
74	A	74	VAL	0	-0.014	-0.013	17.311	-0.006	-0.006	0.000	0.000	0.000	0.000
75	A	75	LEU	0	0.028	0.005	16.064	-0.005	-0.005	0.000	0.000	0.000	0.000
76	A	76	TYR	0	-0.053	-0.038	10.690	0.051	0.051	0.000	0.000	0.000	0.000
77	A	77	GLN	0	0.013	-0.011	14.206	-0.024	-0.024	0.000	0.000	0.000	0.000
78	A	78	PRO	0	0.007	0.024	12.121	0.041	0.041	0.000	0.000	0.000	0.000
79	A	79	PRO	0	-0.002	0.001	13.271	0.001	0.001	0.000	0.000	0.000	0.000
80	A	80	THR	0	0.016	0.004	16.484	-0.019	-0.019	0.000	0.000	0.000	0.000
81	A	81	ALA	0	-0.015	0.018	16.686	-0.006	-0.006	0.000	0.000	0.000	0.000

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