FMO DATABASE

FMODB ID: GN3J1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-424839.93703
FMO2-HF: Nuclear repulsion	395315.36715
FMO2-HF: Total energy	-29524.56988
FMO2-MP2: Total energy	-29612.436094

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.
1.197	2.974	-0.026	-1.012	-0.74	0.003

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 : 0.018 / q_NPA : 0.001

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	0.002	0.019	3.792	0.439	2.137	-0.025	-0.986	-0.688	0.003
4	D	9	ARG	1	0.990	0.992	7.027	-0.917	-0.917	0.000	0.000	0.000	0.000
5	D	10	LYS	1	1.001	0.991	8.631	0.123	0.123	0.000	0.000	0.000	0.000
6	D	11	GLU	-1	-0.816	-0.887	12.073	0.167	0.167	0.000	0.000	0.000	0.000
7	D	12	THR	0	-0.031	-0.018	10.968	0.024	0.024	0.000	0.000	0.000	0.000
8	D	13	VAL	0	0.043	0.024	11.156	-0.002	-0.002	0.000	0.000	0.000	0.000
9	D	14	GLU	-1	-0.861	-0.927	13.823	0.034	0.034	0.000	0.000	0.000	0.000
10	D	15	ARG	1	0.865	0.913	16.566	-0.145	-0.145	0.000	0.000	0.000	0.000
11	D	16	LEU	0	0.013	0.016	14.672	-0.006	-0.006	0.000	0.000	0.000	0.000
12	D	17	LEU	0	0.012	0.003	17.252	-0.014	-0.014	0.000	0.000	0.000	0.000
13	D	18	ARG	1	0.838	0.900	19.688	-0.054	-0.054	0.000	0.000	0.000	0.000
14	D	19	LEU	0	-0.044	-0.006	20.949	-0.004	-0.004	0.000	0.000	0.000	0.000
15	D	20	HIS	0	-0.016	-0.020	20.379	-0.001	-0.001	0.000	0.000	0.000	0.000
16	D	21	PHE	0	-0.052	-0.009	22.016	-0.010	-0.010	0.000	0.000	0.000	0.000
17	D	22	ARG	1	1.012	1.001	26.295	-0.010	-0.010	0.000	0.000	0.000	0.000
18	D	23	ASP	-1	-0.806	-0.883	29.242	0.007	0.007	0.000	0.000	0.000	0.000
19	D	24	GLY	0	0.075	0.049	29.155	0.000	0.000	0.000	0.000	0.000	0.000
20	D	25	ARG	1	0.854	0.911	29.235	0.002	0.002	0.000	0.000	0.000	0.000
21	D	26	THR	0	-0.031	-0.008	25.633	-0.006	-0.006	0.000	0.000	0.000	0.000
22	D	27	ARG	1	0.835	0.896	24.273	-0.011	-0.011	0.000	0.000	0.000	0.000
23	D	28	VAL	0	0.039	0.021	19.026	-0.006	-0.006	0.000	0.000	0.000	0.000
24	D	29	ASN	0	0.003	-0.003	20.811	0.000	0.000	0.000	0.000	0.000	0.000
25	D	30	GLY	0	0.034	0.000	17.693	-0.005	-0.005	0.000	0.000	0.000	0.000
26	D	31	ASP	-1	-0.808	-0.903	16.405	-0.157	-0.157	0.000	0.000	0.000	0.000
27	D	32	ALA	0	0.041	0.018	16.705	-0.033	-0.033	0.000	0.000	0.000	0.000
28	D	33	LEU	0	-0.011	0.000	14.787	-0.014	-0.014	0.000	0.000	0.000	0.000
29	D	34	LEU	0	-0.029	-0.017	11.431	-0.007	-0.007	0.000	0.000	0.000	0.000
30	D	35	LEU	0	0.013	0.008	12.186	-0.086	-0.086	0.000	0.000	0.000	0.000
31	D	36	MET	0	0.021	0.009	13.799	-0.039	-0.039	0.000	0.000	0.000	0.000
32	D	37	ALA	0	-0.017	0.000	9.212	0.023	0.023	0.000	0.000	0.000	0.000
33	D	38	GLU	-1	-0.818	-0.899	8.125	-1.520	-1.520	0.000	0.000	0.000	0.000
34	D	39	LEU	0	0.009	0.015	10.704	-0.021	-0.021	0.000	0.000	0.000	0.000
35	D	40	LEU	0	0.017	-0.003	11.096	0.030	0.030	0.000	0.000	0.000	0.000
36	D	41	LYS	1	0.794	0.877	4.800	2.185	2.264	-0.001	-0.026	-0.052	0.000
37	D	42	VAL	0	-0.018	-0.010	8.489	0.023	0.023	0.000	0.000	0.000	0.000
38	D	43	PHE	0	0.015	0.023	11.047	0.056	0.056	0.000	0.000	0.000	0.000
39	D	44	VAL	0	0.016	-0.002	8.234	0.042	0.042	0.000	0.000	0.000	0.000
40	D	45	ARG	1	0.909	0.951	5.968	1.002	1.002	0.000	0.000	0.000	0.000
41	D	46	GLU	-1	-0.779	-0.870	9.739	-0.177	-0.177	0.000	0.000	0.000	0.000
42	D	47	ALA	0	0.011	-0.001	13.320	0.025	0.025	0.000	0.000	0.000	0.000
43	D	48	ALA	0	-0.014	-0.005	10.865	0.016	0.016	0.000	0.000	0.000	0.000
44	D	49	ALA	0	-0.017	-0.009	12.824	0.000	0.000	0.000	0.000	0.000	0.000
45	D	50	ARG	1	0.738	0.839	14.208	0.108	0.108	0.000	0.000	0.000	0.000
46	D	51	ALA	0	0.042	0.025	16.331	0.006	0.006	0.000	0.000	0.000	0.000
47	D	52	ALA	0	0.015	0.002	15.132	0.005	0.005	0.000	0.000	0.000	0.000
48	D	53	ARG	1	0.897	0.943	16.216	0.149	0.149	0.000	0.000	0.000	0.000
49	D	54	GLN	0	-0.054	-0.027	19.814	-0.002	-0.002	0.000	0.000	0.000	0.000
50	D	55	ALA	0	0.041	0.016	20.134	0.003	0.003	0.000	0.000	0.000	0.000
51	D	56	GLN	0	-0.010	-0.008	18.687	-0.011	-0.011	0.000	0.000	0.000	0.000
52	D	57	ALA	0	-0.062	-0.017	22.622	0.000	0.000	0.000	0.000	0.000	0.000
53	D	58	GLU	-1	-0.877	-0.925	25.192	0.010	0.010	0.000	0.000	0.000	0.000
54	D	59	ASP	-1	-0.975	-0.979	25.973	-0.013	-0.013	0.000	0.000	0.000	0.000
55	D	60	LEU	0	-0.042	-0.009	23.646	0.008	0.008	0.000	0.000	0.000	0.000
56	D	61	GLU	-1	-0.955	-0.987	20.650	-0.003	-0.003	0.000	0.000	0.000	0.000
57	D	62	LYS	1	0.722	0.838	19.163	-0.092	-0.092	0.000	0.000	0.000	0.000
58	D	63	VAL	0	-0.003	0.001	16.357	-0.007	-0.007	0.000	0.000	0.000	0.000
59	D	64	ASP	-1	-0.796	-0.876	18.689	0.120	0.120	0.000	0.000	0.000	0.000
60	D	65	ILE	0	-0.016	-0.013	20.298	-0.002	-0.002	0.000	0.000	0.000	0.000
61	D	66	GLU	-1	-0.824	-0.920	21.295	0.064	0.064	0.000	0.000	0.000	0.000
62	D	67	HIS	0	0.012	0.005	20.348	-0.002	-0.002	0.000	0.000	0.000	0.000
63	D	68	VAL	0	-0.033	-0.027	17.264	-0.013	-0.013	0.000	0.000	0.000	0.000
64	D	69	GLU	-1	-0.936	-0.971	19.826	0.062	0.062	0.000	0.000	0.000	0.000
65	D	70	LYS	1	0.856	0.935	23.109	0.002	0.002	0.000	0.000	0.000	0.000
66	D	71	VAL	0	-0.065	-0.045	18.824	-0.011	-0.011	0.000	0.000	0.000	0.000
67	D	72	LEU	0	-0.009	0.009	19.373	-0.012	-0.012	0.000	0.000	0.000	0.000
68	D	73	PRO	0	0.009	0.006	21.541	-0.009	-0.009	0.000	0.000	0.000	0.000
69	D	74	GLN	0	-0.021	-0.023	23.478	0.001	0.001	0.000	0.000	0.000	0.000
70	D	75	LEU	0	-0.016	0.004	16.436	-0.011	-0.011	0.000	0.000	0.000	0.000
71	D	76	LEU	0	-0.045	-0.046	19.893	-0.012	-0.012	0.000	0.000	0.000	0.000
72	D	77	LEU	0	-0.051	-0.014	21.924	-0.004	-0.004	0.000	0.000	0.000	0.000
73	D	78	ASP	-1	-0.778	-0.852	21.503	-0.081	-0.081	0.000	0.000	0.000	0.000
74	D	79	PHE	0	-0.099	-0.037	15.266	-0.020	-0.020	0.000	0.000	0.000	0.000
75	D	80	VAL	0	0.011	0.003	19.192	0.011	0.011	0.000	0.000	0.000	0.000

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