FMO DATABASE

FMODB ID: VR7Z1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-464650.702767
FMO2-HF: Nuclear repulsion	433279.407964
FMO2-HF: Total energy	-31371.294803
FMO2-MP2: Total energy	-31463.171075

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.
-1.432	0.13	-0.004	-0.574	-0.983	0.001

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 : 0.016 / q_NPA : -0.007

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	-0.021	-0.020	3.808	0.574	1.653	-0.009	-0.415	-0.656	0.001
4	A	41	VAL	0	0.016	0.010	6.514	0.401	0.401	0.000	0.000	0.000	0.000
5	A	42	ASP	-1	-0.872	-0.939	10.288	-0.679	-0.679	0.000	0.000	0.000	0.000
6	A	43	ALA	0	0.002	-0.011	12.729	0.063	0.063	0.000	0.000	0.000	0.000
7	A	44	GLU	-1	-0.995	-0.997	16.029	-0.368	-0.368	0.000	0.000	0.000	0.000
8	A	45	GLY	0	-0.050	-0.013	15.026	0.056	0.056	0.000	0.000	0.000	0.000
9	A	46	ASN	0	-0.060	-0.030	13.720	0.096	0.096	0.000	0.000	0.000	0.000
10	A	47	PRO	0	-0.001	0.015	9.192	-0.160	-0.160	0.000	0.000	0.000	0.000
11	A	48	PHE	0	-0.020	-0.038	7.952	0.244	0.244	0.000	0.000	0.000	0.000
12	A	49	TRP	0	0.023	0.012	3.693	-2.088	-1.748	0.006	-0.153	-0.192	0.000
13	A	50	GLU	-1	-0.876	-0.934	4.541	-1.266	-1.123	-0.001	-0.006	-0.135	0.000
14	A	51	ILE	0	-0.042	-0.032	5.939	0.348	0.348	0.000	0.000	0.000	0.000
15	A	52	SER	0	-0.041	-0.037	8.682	0.140	0.140	0.000	0.000	0.000	0.000
16	A	53	ASP	-1	-0.816	-0.898	9.924	-0.621	-0.621	0.000	0.000	0.000	0.000
17	A	54	LYS	1	0.937	0.969	11.984	0.232	0.232	0.000	0.000	0.000	0.000
18	A	55	ARG	1	0.802	0.903	12.101	0.213	0.213	0.000	0.000	0.000	0.000
19	A	56	ARG	1	1.000	1.017	9.393	0.830	0.830	0.000	0.000	0.000	0.000
20	A	57	VAL	0	0.011	-0.006	9.006	0.194	0.194	0.000	0.000	0.000	0.000
21	A	58	GLY	0	0.057	0.031	9.203	-0.227	-0.227	0.000	0.000	0.000	0.000
22	A	59	ILE	0	-0.035	-0.007	11.487	0.145	0.145	0.000	0.000	0.000	0.000
23	A	60	SER	0	0.048	0.038	14.046	-0.055	-0.055	0.000	0.000	0.000	0.000
24	A	61	GLN	0	-0.029	-0.026	17.158	0.039	0.039	0.000	0.000	0.000	0.000
25	A	62	PHE	0	0.031	0.003	20.187	-0.007	-0.007	0.000	0.000	0.000	0.000
26	A	63	LYS	1	0.885	0.936	23.774	0.106	0.106	0.000	0.000	0.000	0.000
27	A	64	LYS	1	0.948	0.971	23.942	0.074	0.074	0.000	0.000	0.000	0.000
28	A	65	MET	0	0.023	0.033	23.462	0.015	0.015	0.000	0.000	0.000	0.000
29	A	66	ASP	-1	-0.829	-0.905	17.928	-0.100	-0.100	0.000	0.000	0.000	0.000
30	A	67	PHE	0	-0.064	-0.044	18.533	0.028	0.028	0.000	0.000	0.000	0.000
31	A	68	ILE	0	0.020	0.018	13.761	-0.037	-0.037	0.000	0.000	0.000	0.000
32	A	69	ASN	0	-0.069	-0.043	14.821	0.062	0.062	0.000	0.000	0.000	0.000
33	A	70	ILE	0	0.043	0.034	13.683	-0.058	-0.058	0.000	0.000	0.000	0.000
34	A	71	ARG	1	0.866	0.922	14.013	0.258	0.258	0.000	0.000	0.000	0.000
35	A	72	GLU	-1	-0.872	-0.921	14.291	-0.268	-0.268	0.000	0.000	0.000	0.000
36	A	73	TYR	0	-0.019	-0.019	14.419	0.021	0.021	0.000	0.000	0.000	0.000
37	A	74	TYR	0	-0.054	-0.033	16.557	0.022	0.022	0.000	0.000	0.000	0.000
38	A	75	GLU	-1	-0.844	-0.928	18.254	-0.407	-0.407	0.000	0.000	0.000	0.000
39	A	76	ALA	0	-0.071	-0.047	19.856	0.038	0.038	0.000	0.000	0.000	0.000
40	A	77	GLY	0	-0.004	0.001	22.859	-0.009	-0.009	0.000	0.000	0.000	0.000
41	A	78	GLY	0	0.005	0.014	20.662	0.001	0.001	0.000	0.000	0.000	0.000
42	A	79	GLU	-1	-0.925	-0.947	18.916	-0.373	-0.373	0.000	0.000	0.000	0.000
43	A	80	MET	0	-0.022	-0.017	13.128	0.044	0.044	0.000	0.000	0.000	0.000
44	A	81	LYS	1	0.963	0.978	17.108	0.245	0.245	0.000	0.000	0.000	0.000
45	A	82	PRO	0	0.028	0.033	17.700	0.004	0.004	0.000	0.000	0.000	0.000
46	A	83	GLY	0	0.043	0.011	18.633	0.037	0.037	0.000	0.000	0.000	0.000
47	A	84	LYS	1	0.939	0.947	20.864	0.148	0.148	0.000	0.000	0.000	0.000
48	A	85	LYS	1	0.944	0.985	20.208	0.159	0.159	0.000	0.000	0.000	0.000
49	A	86	GLY	0	0.081	0.025	18.813	-0.032	-0.032	0.000	0.000	0.000	0.000
50	A	87	ILE	0	-0.066	-0.023	18.550	0.016	0.016	0.000	0.000	0.000	0.000
51	A	88	GLY	0	0.047	0.030	18.345	-0.020	-0.020	0.000	0.000	0.000	0.000
52	A	89	LEU	0	-0.028	-0.008	17.736	0.017	0.017	0.000	0.000	0.000	0.000
53	A	90	THR	0	0.064	0.029	19.849	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	91	VAL	0	0.103	0.038	18.970	0.015	0.015	0.000	0.000	0.000	0.000
55	A	92	ASP	-1	-0.887	-0.940	20.823	0.073	0.073	0.000	0.000	0.000	0.000
56	A	93	GLN	0	-0.035	-0.020	22.449	0.006	0.006	0.000	0.000	0.000	0.000
57	A	94	TYR	0	0.031	0.020	13.701	0.014	0.014	0.000	0.000	0.000	0.000
58	A	95	THR	0	0.019	-0.005	19.451	0.032	0.032	0.000	0.000	0.000	0.000
59	A	96	ALA	0	-0.040	-0.017	20.868	0.018	0.018	0.000	0.000	0.000	0.000
60	A	97	PHE	0	0.018	0.005	15.773	0.003	0.003	0.000	0.000	0.000	0.000
61	A	98	LEU	0	0.004	-0.008	15.704	0.017	0.017	0.000	0.000	0.000	0.000
62	A	99	LYS	1	0.897	0.946	19.600	-0.119	-0.119	0.000	0.000	0.000	0.000
63	A	100	ALA	0	0.008	0.011	22.730	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	101	ILE	0	0.007	0.016	16.385	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	102	PRO	0	0.023	0.020	20.647	0.000	0.000	0.000	0.000	0.000	0.000
66	A	103	ALA	0	0.008	0.004	22.736	-0.007	-0.007	0.000	0.000	0.000	0.000
67	A	104	ILE	0	-0.008	-0.003	20.551	-0.013	-0.013	0.000	0.000	0.000	0.000
68	A	105	ASN	0	0.035	-0.003	18.094	-0.022	-0.022	0.000	0.000	0.000	0.000
69	A	106	ALA	0	-0.026	-0.006	21.707	-0.005	-0.005	0.000	0.000	0.000	0.000
70	A	107	GLU	-1	-0.812	-0.878	25.330	0.079	0.079	0.000	0.000	0.000	0.000
71	A	108	LEU	0	-0.036	-0.031	19.725	-0.013	-0.013	0.000	0.000	0.000	0.000
72	A	109	ARG	1	0.909	0.953	20.371	-0.275	-0.275	0.000	0.000	0.000	0.000
73	A	110	SER	0	-0.048	-0.006	24.775	-0.011	-0.011	0.000	0.000	0.000	0.000
74	A	111	ARG	1	0.753	0.852	25.710	-0.084	-0.084	0.000	0.000	0.000	0.000
75	A	112	GLY	0	0.004	0.009	26.241	-0.010	-0.010	0.000	0.000	0.000	0.000
76	A	113	HIS	0	-0.070	-0.027	20.598	0.007	0.007	0.000	0.000	0.000	0.000
77	A	114	ASP	-1	-0.892	-0.945	19.483	0.285	0.285	0.000	0.000	0.000	0.000
78	A	115	ILE	0	-0.038	-0.020	17.226	0.022	0.022	0.000	0.000	0.000	0.000
79	A	116	THR	0	0.030	0.009	15.281	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	117	ASP	-1	-0.986	-0.984	17.116	0.484	0.484	0.000	0.000	0.000	0.000

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