FMO DATABASE

FMODB ID: 7GQYK

Calculation Name: 3FB9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FB9

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H2

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:

Apendix: None

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	89
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-626287.152145
FMO2-HF: Nuclear repulsion	590253.558654
FMO2-HF: Total energy	-36033.593491
FMO2-MP2: Total energy	-36138.579903

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:0:GLY)

Summations of interaction energy for fragment #1(A:0: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.
-0.37	0.241	0	-0.268	-0.344	0.001

Interaction energy analysis for fragmet #1(A:0:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / q_NPA : -0.012

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].	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	2	SER	0	0.047	0.014	3.852	-0.654	-0.043	-0.268	-0.344	0.001
4	A	3	ASP	-1	-0.882	-0.965	6.397	-0.609	-0.609	0.000	0.000	0.000
5	A	4	ALA	0	0.004	0.008	9.041	0.219	0.219	0.000	0.000	0.000
6	A	5	PHE	0	-0.039	-0.032	7.677	0.242	0.242	0.000	0.000	0.000
7	A	6	THR	0	-0.028	0.002	8.627	0.140	0.140	0.000	0.000	0.000
8	A	7	ASP	-1	-0.834	-0.923	10.327	-0.160	-0.160	0.000	0.000	0.000
9	A	8	VAL	0	-0.045	-0.025	13.496	0.040	0.040	0.000	0.000	0.000
10	A	9	ALA	0	0.002	0.014	12.779	0.057	0.057	0.000	0.000	0.000
11	A	10	LYS	1	0.971	0.987	11.838	0.215	0.215	0.000	0.000	0.000
12	A	11	MET	0	0.004	0.009	15.321	0.053	0.053	0.000	0.000	0.000
13	A	12	LYS	1	0.875	0.950	18.247	0.262	0.262	0.000	0.000	0.000
14	A	13	LYS	1	0.914	0.966	17.865	0.205	0.205	0.000	0.000	0.000
15	A	14	ILE	0	0.048	0.036	17.837	0.024	0.024	0.000	0.000	0.000
16	A	15	LYS	1	0.849	0.921	21.033	0.132	0.132	0.000	0.000	0.000
17	A	16	GLU	-1	-0.945	-0.977	22.257	-0.187	-0.187	0.000	0.000	0.000
18	A	17	GLU	-1	-0.903	-0.963	20.704	-0.133	-0.133	0.000	0.000	0.000
19	A	18	ILE	0	0.017	0.006	24.683	0.012	0.012	0.000	0.000	0.000
20	A	19	LYS	1	0.934	0.971	26.962	0.103	0.103	0.000	0.000	0.000
21	A	20	ALA	0	-0.070	-0.040	27.690	0.006	0.006	0.000	0.000	0.000
22	A	21	HIS	0	0.019	0.018	28.378	-0.001	-0.001	0.000	0.000	0.000
23	A	22	GLU	-1	-0.916	-0.954	30.422	-0.045	-0.045	0.000	0.000	0.000
24	A	23	GLY	0	-0.051	-0.030	33.158	0.001	0.001	0.000	0.000	0.000
25	A	24	GLN	0	-0.045	-0.024	32.453	0.001	0.001	0.000	0.000	0.000
26	A	25	VAL	0	0.020	0.006	32.449	0.001	0.001	0.000	0.000	0.000
27	A	26	VAL	0	-0.003	0.008	28.256	-0.004	-0.004	0.000	0.000	0.000
28	A	27	GLU	-1	-0.839	-0.904	27.641	0.027	0.027	0.000	0.000	0.000
29	A	28	MET	0	-0.043	-0.027	25.998	-0.005	-0.005	0.000	0.000	0.000
30	A	29	THR	0	-0.030	-0.017	24.406	0.008	0.008	0.000	0.000	0.000
31	A	30	LEU	0	-0.036	-0.020	24.625	-0.005	-0.005	0.000	0.000	0.000
32	A	31	GLU	-1	-0.925	-0.934	17.541	0.138	0.138	0.000	0.000	0.000
33	A	32	ASN	0	0.020	-0.012	22.030	0.001	0.001	0.000	0.000	0.000
34	A	33	GLY	0	-0.002	0.016	21.469	0.019	0.019	0.000	0.000	0.000
35	A	34	ARG	1	0.940	0.954	20.784	-0.194	-0.194	0.000	0.000	0.000
36	A	35	LYS	1	0.854	0.938	22.246	-0.092	-0.092	0.000	0.000	0.000
37	A	36	ARG	1	1.013	1.013	18.792	-0.114	-0.114	0.000	0.000	0.000
38	A	37	GLN	0	0.028	-0.006	25.957	-0.001	-0.001	0.000	0.000	0.000
39	A	38	LYS	1	0.922	0.954	29.023	-0.043	-0.043	0.000	0.000	0.000
40	A	39	ASN	0	0.000	-0.011	26.970	0.004	0.004	0.000	0.000	0.000
41	A	40	ARG	1	0.813	0.927	29.544	-0.010	-0.010	0.000	0.000	0.000
42	A	41	LEU	0	0.015	0.002	30.934	-0.003	-0.003	0.000	0.000	0.000
43	A	42	GLY	0	0.022	0.000	32.678	0.002	0.002	0.000	0.000	0.000
44	A	43	LYS	1	0.932	0.982	33.461	0.024	0.024	0.000	0.000	0.000
45	A	44	LEU	0	-0.010	-0.003	29.399	0.002	0.002	0.000	0.000	0.000
46	A	45	ILE	0	-0.068	-0.043	33.255	-0.003	-0.003	0.000	0.000	0.000
47	A	46	GLU	-1	-0.869	-0.924	34.694	-0.036	-0.036	0.000	0.000	0.000
48	A	47	VAL	0	0.006	0.003	29.883	-0.001	-0.001	0.000	0.000	0.000
49	A	48	TYR	0	0.019	0.015	31.574	0.000	0.000	0.000	0.000	0.000
50	A	49	PRO	0	-0.018	-0.013	30.040	-0.005	-0.005	0.000	0.000	0.000
51	A	50	SER	0	-0.062	-0.038	28.298	-0.008	-0.008	0.000	0.000	0.000
52	A	51	LEU	0	-0.019	-0.012	28.147	0.001	0.001	0.000	0.000	0.000
53	A	52	PHE	0	0.020	0.022	25.504	-0.004	-0.004	0.000	0.000	0.000
54	A	53	ILE	0	0.020	0.007	30.717	0.005	0.005	0.000	0.000	0.000
55	A	54	VAL	0	0.007	0.008	30.323	-0.003	-0.003	0.000	0.000	0.000
56	A	55	GLU	-1	-0.962	-0.975	33.655	-0.009	-0.009	0.000	0.000	0.000
57	A	56	PHE	0	0.022	-0.014	30.893	0.000	0.000	0.000	0.000	0.000
58	A	57	GLY	0	0.053	0.016	36.769	0.000	0.000	0.000	0.000	0.000
59	A	58	ASP	-1	-0.815	-0.917	39.496	-0.003	-0.003	0.000	0.000	0.000
60	A	59	VAL	0	-0.012	0.018	35.745	-0.002	-0.002	0.000	0.000	0.000
61	A	60	GLU	-1	-0.948	-0.982	38.941	-0.001	-0.001	0.000	0.000	0.000
62	A	61	GLY	0	-0.019	-0.014	38.643	0.000	0.000	0.000	0.000	0.000
63	A	62	ASP	-1	-0.865	-0.942	35.511	0.018	0.018	0.000	0.000	0.000
64	A	63	LYS	1	0.819	0.932	38.233	0.002	0.002	0.000	0.000	0.000
65	A	64	GLN	0	-0.080	-0.044	38.270	0.004	0.004	0.000	0.000	0.000
66	A	65	VAL	0	-0.037	-0.017	42.072	-0.002	-0.002	0.000	0.000	0.000
67	A	66	ASN	0	-0.043	-0.019	41.199	-0.002	-0.002	0.000	0.000	0.000
68	A	67	VAL	0	0.058	0.037	41.063	0.001	0.001	0.000	0.000	0.000
69	A	68	TYR	0	-0.072	-0.019	35.235	0.001	0.001	0.000	0.000	0.000
70	A	69	VAL	0	0.047	0.023	37.073	-0.001	-0.001	0.000	0.000	0.000
71	A	70	GLU	-1	-0.879	-0.942	31.363	0.009	0.009	0.000	0.000	0.000
72	A	71	SER	0	-0.054	-0.024	32.297	-0.003	-0.003	0.000	0.000	0.000
73	A	72	PHE	0	0.057	0.031	26.774	0.005	0.005	0.000	0.000	0.000
74	A	73	THR	0	0.001	0.000	25.329	-0.010	-0.010	0.000	0.000	0.000
75	A	74	TYR	0	0.046	-0.019	22.729	-0.003	-0.003	0.000	0.000	0.000
76	A	75	SER	0	0.004	-0.002	20.821	-0.014	-0.014	0.000	0.000	0.000
77	A	76	ASP	-1	-0.845	-0.906	20.544	-0.013	-0.013	0.000	0.000	0.000
78	A	77	ILE	0	0.000	0.003	19.801	0.011	0.011	0.000	0.000	0.000
79	A	78	LEU	0	-0.017	-0.025	15.123	-0.001	-0.001	0.000	0.000	0.000
80	A	79	THR	0	-0.113	-0.075	15.975	-0.001	-0.001	0.000	0.000	0.000
81	A	80	GLU	-1	-0.957	-0.974	14.317	0.067	0.067	0.000	0.000	0.000
82	A	81	LYS	1	1.006	1.028	18.360	0.004	0.004	0.000	0.000	0.000
83	A	82	ASN	0	-0.053	-0.048	21.693	0.005	0.005	0.000	0.000	0.000
84	A	83	LEU	0	-0.008	-0.002	19.026	-0.009	-0.009	0.000	0.000	0.000
85	A	84	ILE	0	-0.007	-0.014	21.844	0.003	0.003	0.000	0.000	0.000
86	A	85	HIS	0	-0.004	0.005	22.395	-0.010	-0.010	0.000	0.000	0.000
87	A	86	TYR	0	0.039	0.008	22.515	0.007	0.007	0.000	0.000	0.000
88	A	87	LEU	0	-0.051	-0.010	26.984	-0.001	-0.001	0.000	0.000	0.000
89	A	88	ASP	-1	-0.936	-0.971	29.804	-0.046	-0.046	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:GLY)