FMO DATABASE

FMODB ID: GN971

Calculation Name: 4AGH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4AGH

Chain ID: A

ChEMBL ID:

UniProt ID: G4NEJ8

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	80
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-465462.519808
FMO2-HF: Nuclear repulsion	434090.649792
FMO2-HF: Total energy	-31371.870016
FMO2-MP2: Total energy	-31463.772933

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:38:GLY)

Summations of interaction energy for fragment #1(A:38: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.
0.254	2.185	-0.011	-0.97	-0.952	0.003

Interaction energy analysis for fragmet #1(A:38:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.047 / q_NPA : 0.023

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	40	GLN	0	-0.031	-0.030	3.862	0.589	2.279	-0.011	-0.890	-0.790	0.003
4	A	41	VAL	0	0.018	0.005	6.737	0.127	0.127	0.000	0.000	0.000	0.000
5	A	42	ASP	-1	-0.839	-0.906	10.569	-0.825	-0.825	0.000	0.000	0.000	0.000
6	A	43	ALA	0	-0.003	-0.006	13.296	0.076	0.076	0.000	0.000	0.000	0.000
7	A	44	GLU	-1	-0.973	-0.991	16.750	-0.511	-0.511	0.000	0.000	0.000	0.000
8	A	45	GLY	0	-0.018	0.007	15.612	0.058	0.058	0.000	0.000	0.000	0.000
9	A	46	ASN	0	-0.101	-0.068	14.130	0.077	0.077	0.000	0.000	0.000	0.000
10	A	47	PRO	0	0.001	0.012	9.749	-0.128	-0.128	0.000	0.000	0.000	0.000
11	A	48	PHE	0	-0.025	-0.032	8.085	0.128	0.128	0.000	0.000	0.000	0.000
12	A	49	TRP	0	0.027	0.015	3.588	-0.871	-0.630	0.000	-0.080	-0.162	0.000
13	A	50	GLU	-1	-0.795	-0.881	5.218	-0.883	-0.883	0.000	0.000	0.000	0.000
14	A	51	ILE	0	-0.035	-0.025	6.360	-0.126	-0.126	0.000	0.000	0.000	0.000
15	A	52	SER	0	-0.011	-0.014	9.146	0.247	0.247	0.000	0.000	0.000	0.000
16	A	53	ASP	-1	-0.844	-0.914	10.631	-0.568	-0.568	0.000	0.000	0.000	0.000
17	A	54	LYS	1	0.855	0.929	12.045	0.376	0.376	0.000	0.000	0.000	0.000
18	A	55	ARG	1	0.800	0.893	12.138	0.532	0.532	0.000	0.000	0.000	0.000
19	A	56	ARG	1	0.895	0.938	9.715	1.116	1.116	0.000	0.000	0.000	0.000
20	A	57	VAL	0	0.006	-0.005	9.447	0.290	0.290	0.000	0.000	0.000	0.000
21	A	58	GLY	0	0.053	0.022	9.673	-0.417	-0.417	0.000	0.000	0.000	0.000
22	A	59	ILE	0	-0.060	-0.013	11.922	0.192	0.192	0.000	0.000	0.000	0.000
23	A	60	SER	0	0.069	0.052	14.355	-0.011	-0.011	0.000	0.000	0.000	0.000
24	A	61	GLN	0	-0.023	-0.029	17.411	0.072	0.072	0.000	0.000	0.000	0.000
25	A	62	PHE	0	0.062	0.016	20.635	0.024	0.024	0.000	0.000	0.000	0.000
26	A	63	LYS	1	0.833	0.909	24.245	0.239	0.239	0.000	0.000	0.000	0.000
27	A	64	LYS	1	0.963	0.986	24.304	0.208	0.208	0.000	0.000	0.000	0.000
28	A	65	MET	0	0.014	0.030	24.031	0.012	0.012	0.000	0.000	0.000	0.000
29	A	66	ASP	-1	-0.833	-0.909	18.326	-0.421	-0.421	0.000	0.000	0.000	0.000
30	A	67	PHE	0	-0.053	-0.036	19.127	0.041	0.041	0.000	0.000	0.000	0.000
31	A	68	ILE	0	-0.006	0.003	13.840	-0.068	-0.068	0.000	0.000	0.000	0.000
32	A	69	ASN	0	-0.071	-0.039	15.276	0.131	0.131	0.000	0.000	0.000	0.000
33	A	70	ILE	0	0.026	0.011	14.029	-0.126	-0.126	0.000	0.000	0.000	0.000
34	A	71	ARG	1	0.813	0.903	14.596	0.593	0.593	0.000	0.000	0.000	0.000
35	A	72	GLU	-1	-0.764	-0.848	14.786	-0.472	-0.472	0.000	0.000	0.000	0.000
36	A	73	TYR	0	-0.006	-0.009	14.783	0.008	0.008	0.000	0.000	0.000	0.000
37	A	74	TYR	0	-0.023	-0.014	16.994	0.027	0.027	0.000	0.000	0.000	0.000
38	A	75	GLU	-1	-0.833	-0.927	18.832	-0.351	-0.351	0.000	0.000	0.000	0.000
39	A	76	ALA	0	-0.040	-0.024	20.378	0.035	0.035	0.000	0.000	0.000	0.000
40	A	77	GLY	0	0.011	0.007	23.203	-0.007	-0.007	0.000	0.000	0.000	0.000
41	A	78	GLY	0	0.029	0.025	20.327	0.011	0.011	0.000	0.000	0.000	0.000
42	A	79	GLU	-1	-0.802	-0.874	18.868	-0.374	-0.374	0.000	0.000	0.000	0.000
43	A	80	MET	0	0.008	0.003	13.896	0.041	0.041	0.000	0.000	0.000	0.000
44	A	81	LYS	1	0.796	0.882	17.358	0.294	0.294	0.000	0.000	0.000	0.000
45	A	82	PRO	0	0.032	0.027	18.051	-0.004	-0.004	0.000	0.000	0.000	0.000
46	A	83	GLY	0	0.034	0.009	18.973	0.061	0.061	0.000	0.000	0.000	0.000
47	A	84	LYS	1	0.936	0.955	21.114	0.244	0.244	0.000	0.000	0.000	0.000
48	A	85	LYS	1	0.864	0.918	20.606	0.320	0.320	0.000	0.000	0.000	0.000
49	A	86	GLY	0	0.084	0.035	19.303	-0.052	-0.052	0.000	0.000	0.000	0.000
50	A	87	ILE	0	-0.041	-0.010	19.099	0.048	0.048	0.000	0.000	0.000	0.000
51	A	88	GLY	0	0.069	0.022	18.718	-0.066	-0.066	0.000	0.000	0.000	0.000
52	A	89	LEU	0	-0.037	-0.002	17.740	0.049	0.049	0.000	0.000	0.000	0.000
53	A	90	THR	0	0.024	-0.015	20.015	-0.033	-0.033	0.000	0.000	0.000	0.000
54	A	91	VAL	0	0.093	0.034	19.368	-0.017	-0.017	0.000	0.000	0.000	0.000
55	A	92	ASP	-1	-0.844	-0.896	20.905	-0.225	-0.225	0.000	0.000	0.000	0.000
56	A	93	GLN	0	0.006	0.004	22.387	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	94	TYR	0	0.032	0.022	13.310	-0.008	-0.008	0.000	0.000	0.000	0.000
58	A	95	THR	0	0.028	0.000	18.930	0.022	0.022	0.000	0.000	0.000	0.000
59	A	96	ALA	0	-0.049	-0.011	20.383	0.031	0.031	0.000	0.000	0.000	0.000
60	A	97	PHE	0	0.037	0.013	15.163	0.021	0.021	0.000	0.000	0.000	0.000
61	A	98	LEU	0	0.001	-0.008	14.928	0.022	0.022	0.000	0.000	0.000	0.000
62	A	99	LYS	1	0.860	0.917	18.780	0.208	0.208	0.000	0.000	0.000	0.000
63	A	100	ALA	0	0.006	0.015	21.891	0.022	0.022	0.000	0.000	0.000	0.000
64	A	101	ILE	0	-0.005	0.009	15.310	0.014	0.014	0.000	0.000	0.000	0.000
65	A	102	PRO	0	0.022	0.012	19.569	0.017	0.017	0.000	0.000	0.000	0.000
66	A	103	ALA	0	0.001	0.007	21.733	0.016	0.016	0.000	0.000	0.000	0.000
67	A	104	ILE	0	-0.016	-0.010	19.739	0.006	0.006	0.000	0.000	0.000	0.000
68	A	105	ASN	0	0.031	0.003	16.753	-0.020	-0.020	0.000	0.000	0.000	0.000
69	A	106	ALA	0	-0.022	-0.002	20.541	0.018	0.018	0.000	0.000	0.000	0.000
70	A	107	GLU	-1	-0.791	-0.882	24.208	-0.061	-0.061	0.000	0.000	0.000	0.000
71	A	108	LEU	0	-0.045	-0.026	18.824	0.002	0.002	0.000	0.000	0.000	0.000
72	A	109	ARG	1	0.854	0.919	19.008	0.001	0.001	0.000	0.000	0.000	0.000
73	A	110	SER	0	-0.063	-0.013	23.897	0.012	0.012	0.000	0.000	0.000	0.000
74	A	111	ARG	1	0.768	0.862	25.191	0.089	0.089	0.000	0.000	0.000	0.000
75	A	112	GLY	0	0.001	0.005	25.762	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	113	HIS	0	-0.074	-0.032	20.142	0.008	0.008	0.000	0.000	0.000	0.000
77	A	114	ASP	-1	-0.887	-0.948	19.043	0.112	0.112	0.000	0.000	0.000	0.000
78	A	115	ILE	0	-0.052	-0.028	16.162	-0.024	-0.024	0.000	0.000	0.000	0.000
79	A	116	THR	0	0.058	0.038	13.903	0.003	0.003	0.000	0.000	0.000	0.000
80	A	117	ASP	-1	-0.923	-0.954	16.294	0.047	0.047	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:38:GLY)