FMO DATABASE

FMODB ID: 82YRY

Calculation Name: 3VH5-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VH5

Chain ID: D

ChEMBL ID:

UniProt ID: E1BSW7

Base Structure: X-ray

Registration Date: 2023-06-20

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	75
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-425277.864599
FMO2-HF: Nuclear repulsion	395753.142276
FMO2-HF: Total energy	-29524.722323
FMO2-MP2: Total energy	-29612.554267

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(D:6:GLY)

Summations of interaction energy for fragment #1(D:6:GLY)

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.
1.427	2.94	-0.017	-0.861	-0.635	0.001

Interaction energy analysis for fragmet #1(D:6:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.006

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	D	8	PHE	0	-0.005	0.019	3.863	1.183	2.564	-0.016	-0.807	-0.558	0.001
4	D	9	ARG	1	0.983	0.987	7.352	-1.171	-1.171	0.000	0.000	0.000	0.000
5	D	10	LYS	1	0.932	0.944	8.804	-0.018	-0.018	0.000	0.000	0.000	0.000
6	D	11	GLU	-1	-0.791	-0.877	12.175	0.245	0.245	0.000	0.000	0.000	0.000
7	D	12	THR	0	-0.033	-0.021	11.060	0.033	0.033	0.000	0.000	0.000	0.000
8	D	13	VAL	0	0.029	0.023	11.260	-0.027	-0.027	0.000	0.000	0.000	0.000
9	D	14	GLU	-1	-0.817	-0.899	13.988	0.066	0.066	0.000	0.000	0.000	0.000
10	D	15	ARG	1	0.850	0.901	16.745	-0.220	-0.220	0.000	0.000	0.000	0.000
11	D	16	LEU	0	0.022	0.024	14.518	-0.014	-0.014	0.000	0.000	0.000	0.000
12	D	17	LEU	0	0.010	0.005	17.183	-0.024	-0.024	0.000	0.000	0.000	0.000
13	D	18	ARG	1	0.835	0.890	19.822	-0.096	-0.096	0.000	0.000	0.000	0.000
14	D	19	LEU	0	-0.045	-0.006	20.663	-0.006	-0.006	0.000	0.000	0.000	0.000
15	D	20	HIS	0	-0.020	-0.016	20.254	-0.008	-0.008	0.000	0.000	0.000	0.000
16	D	21	PHE	0	-0.039	-0.015	21.924	-0.013	-0.013	0.000	0.000	0.000	0.000
17	D	22	ARG	1	0.980	0.992	26.229	-0.006	-0.006	0.000	0.000	0.000	0.000
18	D	23	ASP	-1	-0.799	-0.879	29.296	0.016	0.016	0.000	0.000	0.000	0.000
19	D	24	GLY	0	0.078	0.049	29.211	0.001	0.001	0.000	0.000	0.000	0.000
20	D	25	ARG	1	0.845	0.904	29.439	-0.007	-0.007	0.000	0.000	0.000	0.000
21	D	26	THR	0	-0.026	-0.007	25.350	-0.004	-0.004	0.000	0.000	0.000	0.000
22	D	27	ARG	1	0.832	0.898	23.649	-0.036	-0.036	0.000	0.000	0.000	0.000
23	D	28	VAL	0	0.035	0.020	18.394	-0.010	-0.010	0.000	0.000	0.000	0.000
24	D	29	ASN	0	0.015	-0.003	20.417	0.001	0.001	0.000	0.000	0.000	0.000
25	D	30	GLY	0	0.034	0.008	17.484	-0.003	-0.003	0.000	0.000	0.000	0.000
26	D	31	ASP	-1	-0.796	-0.876	15.928	-0.088	-0.088	0.000	0.000	0.000	0.000
27	D	32	ALA	0	0.043	0.011	16.135	-0.036	-0.036	0.000	0.000	0.000	0.000
28	D	33	LEU	0	-0.009	-0.006	14.239	-0.014	-0.014	0.000	0.000	0.000	0.000
29	D	34	LEU	0	-0.031	-0.014	10.871	0.003	0.003	0.000	0.000	0.000	0.000
30	D	35	LEU	0	0.020	0.011	11.898	-0.094	-0.094	0.000	0.000	0.000	0.000
31	D	36	MET	0	0.027	0.013	13.737	-0.046	-0.046	0.000	0.000	0.000	0.000
32	D	37	ALA	0	-0.019	-0.003	8.773	0.011	0.011	0.000	0.000	0.000	0.000
33	D	38	GLU	-1	-0.794	-0.888	7.810	-1.638	-1.638	0.000	0.000	0.000	0.000
34	D	39	LEU	0	-0.004	0.015	10.143	-0.049	-0.049	0.000	0.000	0.000	0.000
35	D	40	LEU	0	0.021	0.003	10.783	0.007	0.007	0.000	0.000	0.000	0.000
36	D	41	LYS	1	0.780	0.869	4.300	2.252	2.384	-0.001	-0.054	-0.077	0.000
37	D	42	VAL	0	-0.020	-0.016	8.130	-0.085	-0.085	0.000	0.000	0.000	0.000
38	D	43	PHE	0	0.013	0.017	10.903	0.039	0.039	0.000	0.000	0.000	0.000
39	D	44	VAL	0	0.020	0.001	7.876	0.037	0.037	0.000	0.000	0.000	0.000
40	D	45	ARG	1	0.910	0.955	6.411	1.205	1.205	0.000	0.000	0.000	0.000
41	D	46	GLU	-1	-0.710	-0.812	9.728	-0.237	-0.237	0.000	0.000	0.000	0.000
42	D	47	ALA	0	0.001	0.004	13.071	0.045	0.045	0.000	0.000	0.000	0.000
43	D	48	ALA	0	-0.002	0.000	10.885	0.031	0.031	0.000	0.000	0.000	0.000
44	D	49	ALA	0	-0.023	-0.009	12.839	0.024	0.024	0.000	0.000	0.000	0.000
45	D	50	ARG	1	0.730	0.837	14.350	0.204	0.204	0.000	0.000	0.000	0.000
46	D	51	ALA	0	0.051	0.033	16.191	0.019	0.019	0.000	0.000	0.000	0.000
47	D	52	ALA	0	0.014	0.002	15.389	0.016	0.016	0.000	0.000	0.000	0.000
48	D	53	ARG	1	0.817	0.869	16.448	0.256	0.256	0.000	0.000	0.000	0.000
49	D	54	GLN	0	-0.060	-0.031	19.959	0.008	0.008	0.000	0.000	0.000	0.000
50	D	55	ALA	0	0.044	0.021	20.256	0.008	0.008	0.000	0.000	0.000	0.000
51	D	56	GLN	0	-0.003	-0.009	18.664	-0.003	-0.003	0.000	0.000	0.000	0.000
52	D	57	ALA	0	-0.056	-0.022	22.867	0.005	0.005	0.000	0.000	0.000	0.000
53	D	58	GLU	-1	-0.868	-0.920	25.295	-0.049	-0.049	0.000	0.000	0.000	0.000
54	D	59	ASP	-1	-0.967	-0.971	26.303	-0.059	-0.059	0.000	0.000	0.000	0.000
55	D	60	LEU	0	-0.061	-0.021	23.662	0.007	0.007	0.000	0.000	0.000	0.000
56	D	61	GLU	-1	-0.956	-0.984	20.838	-0.078	-0.078	0.000	0.000	0.000	0.000
57	D	62	LYS	1	0.728	0.839	19.273	-0.009	-0.009	0.000	0.000	0.000	0.000
58	D	63	VAL	0	0.005	0.001	16.626	-0.005	-0.005	0.000	0.000	0.000	0.000
59	D	64	ASP	-1	-0.806	-0.878	18.921	0.014	0.014	0.000	0.000	0.000	0.000
60	D	65	ILE	0	0.000	-0.008	20.036	-0.009	-0.009	0.000	0.000	0.000	0.000
61	D	66	GLU	-1	-0.825	-0.919	21.030	-0.009	-0.009	0.000	0.000	0.000	0.000
62	D	67	HIS	0	-0.007	-0.008	20.248	-0.009	-0.009	0.000	0.000	0.000	0.000
63	D	68	VAL	0	-0.026	-0.014	17.109	-0.015	-0.015	0.000	0.000	0.000	0.000
64	D	69	GLU	-1	-0.925	-0.968	19.667	-0.005	-0.005	0.000	0.000	0.000	0.000
65	D	70	LYS	1	0.841	0.926	22.988	0.067	0.067	0.000	0.000	0.000	0.000
66	D	71	VAL	0	-0.055	-0.037	19.039	-0.009	-0.009	0.000	0.000	0.000	0.000
67	D	72	LEU	0	-0.006	0.010	18.971	-0.011	-0.011	0.000	0.000	0.000	0.000
68	D	73	PRO	0	0.013	-0.005	21.255	-0.006	-0.006	0.000	0.000	0.000	0.000
69	D	74	GLN	0	-0.021	-0.020	23.345	0.006	0.006	0.000	0.000	0.000	0.000
70	D	75	LEU	0	-0.049	-0.022	16.214	-0.011	-0.011	0.000	0.000	0.000	0.000
71	D	76	LEU	0	-0.050	-0.044	19.973	-0.009	-0.009	0.000	0.000	0.000	0.000
72	D	77	LEU	0	-0.037	0.004	21.998	0.003	0.003	0.000	0.000	0.000	0.000
73	D	78	ASP	-1	-0.774	-0.853	21.450	-0.131	-0.131	0.000	0.000	0.000	0.000
74	D	79	PHE	0	-0.054	-0.025	15.403	-0.028	-0.028	0.000	0.000	0.000	0.000
75	D	80	VAL	0	-0.013	0.000	19.052	0.020	0.020	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:6:GLY)