FMO DATABASE

FMODB ID: 6NYMZ

Calculation Name: 2FGG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FGG

Chain ID: A

ChEMBL ID:

UniProt ID: P9WL61

Base Structure: X-ray

Registration Date: 2023-06-22

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	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	84
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-456347.907915
FMO2-HF: Nuclear repulsion	424389.144078
FMO2-HF: Total energy	-31958.763836
FMO2-MP2: Total energy	-32051.989969

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:4:SER)

Summations of interaction energy for fragment #1(A:4:SER)

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.
-8.166	-18.112	9.296	4.322	-3.673	0.033

Interaction energy analysis for fragmet #1(A:4:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.031 / q_NPA : 0.002

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	6	HIS	0	-0.047	-0.040	2.044	-5.808	-15.754	9.296	4.322	-3.673	0.033
4	A	7	VAL	0	-0.026	-0.008	5.126	-1.082	-1.082	0.000	0.000	0.000	0.000
5	A	8	GLY	0	0.026	0.026	7.317	-0.792	-0.792	0.000	0.000	0.000	0.000
6	A	9	LYS	1	0.921	0.947	10.756	-0.379	-0.379	0.000	0.000	0.000	0.000
7	A	10	THR	0	0.024	0.012	13.989	-0.051	-0.051	0.000	0.000	0.000	0.000
8	A	11	CYS	0	-0.042	-0.024	17.626	-0.018	-0.018	0.000	0.000	0.000	0.000
9	A	12	GLN	0	0.005	0.003	21.112	0.018	0.018	0.000	0.000	0.000	0.000
10	A	13	ILE	0	0.022	0.013	24.746	-0.008	-0.008	0.000	0.000	0.000	0.000
11	A	14	ASP	-1	-0.837	-0.899	27.584	0.195	0.195	0.000	0.000	0.000	0.000
12	A	15	VAL	0	-0.029	-0.020	30.727	-0.013	-0.013	0.000	0.000	0.000	0.000
13	A	16	LEU	0	-0.041	-0.009	33.341	0.005	0.005	0.000	0.000	0.000	0.000
14	A	17	ILE	0	0.009	-0.011	36.905	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	18	GLU	-1	-0.763	-0.864	40.143	0.078	0.078	0.000	0.000	0.000	0.000
16	A	19	GLU	-1	-0.823	-0.905	43.712	0.065	0.065	0.000	0.000	0.000	0.000
17	A	20	HIS	0	-0.135	-0.063	45.408	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	21	ASP	-1	-0.852	-0.927	49.800	0.049	0.049	0.000	0.000	0.000	0.000
19	A	22	GLU	-1	-0.855	-0.915	51.607	0.032	0.032	0.000	0.000	0.000	0.000
20	A	23	ARG	1	0.769	0.870	47.532	-0.034	-0.034	0.000	0.000	0.000	0.000
21	A	24	THR	0	0.034	0.025	44.050	0.002	0.002	0.000	0.000	0.000	0.000
22	A	25	ARG	1	0.782	0.876	41.521	-0.064	-0.064	0.000	0.000	0.000	0.000
23	A	26	ALA	0	0.005	0.009	37.373	0.005	0.005	0.000	0.000	0.000	0.000
24	A	27	LYS	1	0.805	0.882	36.344	-0.085	-0.085	0.000	0.000	0.000	0.000
25	A	28	ALA	0	0.049	0.019	31.279	0.007	0.007	0.000	0.000	0.000	0.000
26	A	29	ARG	1	0.829	0.909	30.053	-0.165	-0.165	0.000	0.000	0.000	0.000
27	A	30	LEU	0	0.041	0.012	23.452	0.014	0.014	0.000	0.000	0.000	0.000
28	A	31	SER	0	-0.034	-0.021	25.317	-0.011	-0.011	0.000	0.000	0.000	0.000
29	A	32	TRP	0	0.044	0.014	18.008	0.045	0.045	0.000	0.000	0.000	0.000
30	A	33	ALA	0	0.017	0.014	21.989	-0.016	-0.016	0.000	0.000	0.000	0.000
31	A	34	GLY	0	0.023	0.013	23.006	-0.021	-0.021	0.000	0.000	0.000	0.000
32	A	35	ARG	1	0.876	0.943	25.461	-0.081	-0.081	0.000	0.000	0.000	0.000
33	A	36	GLN	0	0.008	0.002	27.481	0.016	0.016	0.000	0.000	0.000	0.000
34	A	37	MET	0	-0.002	0.020	26.843	-0.009	-0.009	0.000	0.000	0.000	0.000
35	A	38	VAL	0	0.008	-0.017	30.064	0.014	0.014	0.000	0.000	0.000	0.000
36	A	39	GLY	0	0.014	0.058	32.349	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	40	VAL	0	-0.042	-0.050	33.797	0.008	0.008	0.000	0.000	0.000	0.000
38	A	41	GLY	0	-0.004	-0.002	37.465	-0.006	-0.006	0.000	0.000	0.000	0.000
39	A	42	LEU	0	-0.022	-0.018	39.414	0.002	0.002	0.000	0.000	0.000	0.000
40	A	43	ALA	0	-0.020	-0.006	43.010	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	44	ARG	1	0.950	0.963	45.538	-0.021	-0.021	0.000	0.000	0.000	0.000
42	A	45	LEU	0	-0.040	-0.008	46.052	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	46	ASP	-1	-0.812	-0.872	49.785	0.029	0.029	0.000	0.000	0.000	0.000
44	A	47	PRO	0	-0.082	-0.059	52.660	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	48	ALA	0	0.006	-0.008	54.946	0.002	0.002	0.000	0.000	0.000	0.000
46	A	49	ASP	-1	-0.951	-0.966	55.990	0.028	0.028	0.000	0.000	0.000	0.000
47	A	50	GLU	-1	-0.936	-0.948	52.010	0.042	0.042	0.000	0.000	0.000	0.000
48	A	51	PRO	0	-0.080	-0.056	49.548	0.001	0.001	0.000	0.000	0.000	0.000
49	A	52	VAL	0	0.084	0.018	47.038	0.001	0.001	0.000	0.000	0.000	0.000
50	A	53	ALA	0	0.010	0.022	46.062	0.000	0.000	0.000	0.000	0.000	0.000
51	A	54	GLN	0	-0.034	-0.021	40.973	0.001	0.001	0.000	0.000	0.000	0.000
52	A	55	ILE	0	0.034	0.023	42.501	0.001	0.001	0.000	0.000	0.000	0.000
53	A	56	GLY	0	-0.021	-0.027	43.937	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	57	ASP	-1	-0.805	-0.902	40.877	0.066	0.066	0.000	0.000	0.000	0.000
55	A	58	GLU	-1	-0.879	-0.939	38.332	0.059	0.059	0.000	0.000	0.000	0.000
56	A	59	LEU	0	-0.030	-0.010	38.081	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	60	ALA	0	-0.022	-0.008	39.567	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	61	ILE	0	0.049	0.004	34.217	0.001	0.001	0.000	0.000	0.000	0.000
59	A	62	ALA	0	0.002	0.009	34.724	0.002	0.002	0.000	0.000	0.000	0.000
60	A	63	ARG	1	0.855	0.942	34.980	-0.034	-0.034	0.000	0.000	0.000	0.000
61	A	64	ALA	0	0.022	0.026	35.134	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	65	LEU	0	0.007	-0.012	29.478	0.003	0.003	0.000	0.000	0.000	0.000
63	A	66	SER	0	-0.024	-0.022	30.901	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	67	ASP	-1	-0.836	-0.891	32.707	0.039	0.039	0.000	0.000	0.000	0.000
65	A	68	LEU	0	0.027	0.006	27.710	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	69	ALA	0	-0.009	0.000	27.903	0.001	0.001	0.000	0.000	0.000	0.000
67	A	70	ASN	0	-0.018	-0.023	28.603	-0.017	-0.017	0.000	0.000	0.000	0.000
68	A	71	GLN	0	-0.071	-0.056	30.263	0.000	0.000	0.000	0.000	0.000	0.000
69	A	72	LEU	0	-0.004	-0.005	23.692	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	73	PHE	0	-0.015	0.006	25.619	-0.011	-0.011	0.000	0.000	0.000	0.000
71	A	74	ALA	0	0.007	0.006	27.655	-0.013	-0.013	0.000	0.000	0.000	0.000
72	A	75	LEU	0	-0.048	-0.022	24.511	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	76	THR	0	-0.028	-0.031	22.572	-0.008	-0.008	0.000	0.000	0.000	0.000
74	A	77	SER	0	-0.005	-0.008	24.692	-0.019	-0.019	0.000	0.000	0.000	0.000
75	A	78	SER	0	-0.075	-0.041	27.439	-0.009	-0.009	0.000	0.000	0.000	0.000
76	A	79	ASP	-1	-0.863	-0.944	22.944	-0.004	-0.004	0.000	0.000	0.000	0.000
77	A	80	ILE	0	-0.033	-0.009	22.489	-0.017	-0.017	0.000	0.000	0.000	0.000
78	A	81	GLU	-1	-0.904	-0.944	24.329	-0.120	-0.120	0.000	0.000	0.000	0.000
79	A	82	ALA	0	-0.076	-0.033	25.759	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	83	SER	0	-0.124	-0.057	21.735	-0.012	-0.012	0.000	0.000	0.000	0.000
81	A	84	THR	0	-0.037	-0.043	23.544	-0.029	-0.029	0.000	0.000	0.000	0.000
82	A	85	HIS	0	0.007	0.023	26.115	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	86	GLN	0	0.065	0.030	25.025	0.009	0.009	0.000	0.000	0.000	0.000
84	A	87	PRO	0	-0.086	-0.030	28.388	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:SER)