FMO DATABASE

FMODB ID: VQ5G1

Calculation Name: 3DGP-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DGP

Chain ID: B

ChEMBL ID:

UniProt ID: Q02939

Base Structure: X-ray

Registration Date: 2023-09-21

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	63
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-343136.3532
FMO2-HF: Nuclear repulsion	318237.27117
FMO2-HF: Total energy	-24899.082029
FMO2-MP2: Total energy	-24971.814115

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(B:2:ALA)

Summations of interaction energy for fragment #1(B:2:ALA)

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.
1.25	2.721	-0.015	-0.804	-0.652	0.002

Interaction energy analysis for fragmet #1(B:2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.034 / 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	B	4	ALA	0	0.036	0.025	3.882	0.704	2.175	-0.015	-0.804	-0.652	0.002
4	B	5	ARG	1	0.867	0.915	6.571	-0.584	-0.584	0.000	0.000	0.000	0.000
5	B	6	LYS	1	0.958	0.977	10.392	0.122	0.122	0.000	0.000	0.000	0.000
6	B	7	GLY	0	0.027	0.002	13.655	0.026	0.026	0.000	0.000	0.000	0.000
7	B	8	ALA	0	-0.014	0.003	16.140	-0.015	-0.015	0.000	0.000	0.000	0.000
8	B	9	LEU	0	0.017	0.015	15.567	0.020	0.020	0.000	0.000	0.000	0.000
9	B	10	VAL	0	-0.022	-0.010	17.770	-0.031	-0.031	0.000	0.000	0.000	0.000
10	B	11	GLN	0	0.043	0.024	20.576	0.037	0.037	0.000	0.000	0.000	0.000
11	B	12	CYS	0	-0.089	-0.029	22.747	-0.014	-0.014	0.000	0.000	0.000	0.000
12	B	13	ASP	-1	-0.737	-0.839	25.754	0.110	0.110	0.000	0.000	0.000	0.000
13	B	14	PRO	0	0.082	0.017	27.456	0.002	0.002	0.000	0.000	0.000	0.000
14	B	15	SER	0	-0.076	-0.042	28.469	0.000	0.000	0.000	0.000	0.000	0.000
15	B	16	ILE	0	0.034	0.001	27.931	-0.001	-0.001	0.000	0.000	0.000	0.000
16	B	17	LYS	1	0.832	0.921	22.392	-0.220	-0.220	0.000	0.000	0.000	0.000
17	B	18	ALA	0	0.012	0.003	26.770	0.004	0.004	0.000	0.000	0.000	0.000
18	B	19	LEU	0	-0.007	-0.004	29.284	-0.003	-0.003	0.000	0.000	0.000	0.000
19	B	20	ILE	0	0.001	-0.008	24.720	-0.004	-0.004	0.000	0.000	0.000	0.000
20	B	21	LEU	0	0.017	0.013	23.519	-0.002	-0.002	0.000	0.000	0.000	0.000
21	B	22	GLN	0	-0.036	-0.019	27.319	-0.009	-0.009	0.000	0.000	0.000	0.000
22	B	23	ILE	0	-0.019	-0.003	29.412	-0.007	-0.007	0.000	0.000	0.000	0.000
23	B	24	ASP	-1	-0.821	-0.920	25.117	0.127	0.127	0.000	0.000	0.000	0.000
24	B	25	ALA	0	-0.001	-0.002	27.842	-0.006	-0.006	0.000	0.000	0.000	0.000
25	B	26	LYS	1	0.873	0.945	29.849	-0.076	-0.076	0.000	0.000	0.000	0.000
26	B	27	MET	0	-0.026	-0.007	30.088	-0.007	-0.007	0.000	0.000	0.000	0.000
27	B	28	SER	0	-0.039	-0.008	26.862	-0.005	-0.005	0.000	0.000	0.000	0.000
28	B	29	ASP	-1	-0.809	-0.890	23.152	0.078	0.078	0.000	0.000	0.000	0.000
29	B	30	ILE	0	-0.021	0.006	24.539	-0.010	-0.010	0.000	0.000	0.000	0.000
30	B	31	VAL	0	-0.007	-0.016	20.679	0.005	0.005	0.000	0.000	0.000	0.000
31	B	32	LEU	0	-0.093	-0.044	16.571	-0.003	-0.003	0.000	0.000	0.000	0.000
32	B	33	GLU	-1	-0.850	-0.922	12.609	0.703	0.703	0.000	0.000	0.000	0.000
33	B	34	GLU	-1	-0.852	-0.925	17.121	0.195	0.195	0.000	0.000	0.000	0.000
34	B	35	LEU	0	-0.080	-0.036	13.696	0.049	0.049	0.000	0.000	0.000	0.000
35	B	36	ASP	-1	-0.713	-0.834	16.851	0.284	0.284	0.000	0.000	0.000	0.000
36	B	37	ASP	-1	-0.895	-0.949	19.839	0.188	0.188	0.000	0.000	0.000	0.000
37	B	38	THR	0	-0.099	-0.055	22.060	-0.023	-0.023	0.000	0.000	0.000	0.000
38	B	39	HIS	1	0.774	0.847	18.305	-0.237	-0.237	0.000	0.000	0.000	0.000
39	B	40	LEU	0	0.048	0.033	19.106	0.019	0.019	0.000	0.000	0.000	0.000
40	B	41	LEU	0	-0.012	0.001	13.524	-0.011	-0.011	0.000	0.000	0.000	0.000
41	B	42	VAL	0	0.026	0.011	17.499	-0.006	-0.006	0.000	0.000	0.000	0.000
42	B	43	ASN	0	0.036	0.023	19.321	-0.012	-0.012	0.000	0.000	0.000	0.000
43	B	44	PRO	0	0.004	-0.019	19.041	-0.008	-0.008	0.000	0.000	0.000	0.000
44	B	45	SER	0	-0.065	-0.042	21.753	-0.007	-0.007	0.000	0.000	0.000	0.000
45	B	46	LYS	1	0.832	0.899	24.522	-0.076	-0.076	0.000	0.000	0.000	0.000
46	B	47	VAL	0	0.005	0.017	22.763	0.003	0.003	0.000	0.000	0.000	0.000
47	B	48	GLU	-1	-0.772	-0.887	25.751	0.049	0.049	0.000	0.000	0.000	0.000
48	B	49	PHE	0	0.013	0.013	29.191	-0.002	-0.002	0.000	0.000	0.000	0.000
49	B	50	VAL	0	0.041	0.017	26.244	-0.001	-0.001	0.000	0.000	0.000	0.000
50	B	51	LYS	1	0.813	0.894	27.022	-0.055	-0.055	0.000	0.000	0.000	0.000
51	B	52	HIS	0	-0.004	-0.011	30.766	-0.001	-0.001	0.000	0.000	0.000	0.000
52	B	53	GLU	-1	-0.889	-0.944	32.388	0.055	0.055	0.000	0.000	0.000	0.000
53	B	54	LEU	0	-0.014	-0.003	28.928	-0.001	-0.001	0.000	0.000	0.000	0.000
54	B	55	ASN	0	0.010	0.003	33.458	-0.002	-0.002	0.000	0.000	0.000	0.000
55	B	56	ARG	1	0.919	0.987	36.210	-0.040	-0.040	0.000	0.000	0.000	0.000
56	B	57	LEU	0	0.016	-0.001	34.284	-0.002	-0.002	0.000	0.000	0.000	0.000
57	B	58	LEU	0	0.025	0.022	35.203	-0.002	-0.002	0.000	0.000	0.000	0.000
58	B	59	SER	0	-0.037	-0.030	38.653	-0.004	-0.004	0.000	0.000	0.000	0.000
59	B	60	LYS	1	0.812	0.883	41.242	-0.041	-0.041	0.000	0.000	0.000	0.000
60	B	61	ASN	0	0.053	0.041	41.643	-0.001	-0.001	0.000	0.000	0.000	0.000
61	B	62	ILE	0	-0.016	-0.013	43.441	-0.001	-0.001	0.000	0.000	0.000	0.000
62	B	63	TYR	0	-0.034	-0.009	45.290	-0.002	-0.002	0.000	0.000	0.000	0.000
63	B	64	ASN	0	-0.042	-0.007	42.708	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:2:ALA)