FMO DATABASE

FMODB ID: GNRV1

Calculation Name: 2C5J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2C5J

Chain ID: A

ChEMBL ID:

UniProt ID: Q03322

Base Structure: X-ray

Registration Date: 2023-03-13

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	OptHSide
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	87
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-483011.456715
FMO2-HF: Nuclear repulsion	447268.818979
FMO2-HF: Total energy	-35742.637737
FMO2-MP2: Total energy	-35847.80476

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:6:ASP)

Summations of interaction energy for fragment #1(A:6:ASP)

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.
-11.321	-7.958	20.874	-11.505	-12.734	0.137

Interaction energy analysis for fragmet #1(A:6:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.815 / q_NPA : -0.925

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	8	PHE	0	0.045	0.034	2.481	-21.659	-15.821	1.900	-3.464	-4.275	0.040
4	A	9	GLN	0	-0.034	-0.034	1.783	-53.194	-56.381	18.928	-7.704	-8.038	0.093
5	A	10	GLN	0	-0.083	-0.050	3.721	-12.140	-11.428	0.046	-0.337	-0.421	0.004
6	A	11	VAL	0	0.049	0.028	5.926	-5.784	-5.784	0.000	0.000	0.000	0.000
7	A	12	VAL	0	0.014	0.024	6.719	-5.769	-5.769	0.000	0.000	0.000	0.000
8	A	13	LYS	1	0.748	0.860	7.814	-30.550	-30.550	0.000	0.000	0.000	0.000
9	A	14	ASP	-1	-0.775	-0.880	9.763	24.323	24.323	0.000	0.000	0.000	0.000
10	A	15	THR	0	0.053	0.026	11.398	-2.763	-2.763	0.000	0.000	0.000	0.000
11	A	16	LYS	1	0.953	0.979	12.349	-24.561	-24.561	0.000	0.000	0.000	0.000
12	A	17	GLU	-1	-0.886	-0.926	12.939	19.593	19.593	0.000	0.000	0.000	0.000
13	A	18	GLN	0	-0.013	-0.008	15.621	-0.547	-0.547	0.000	0.000	0.000	0.000
14	A	19	LEU	0	0.049	0.024	16.031	-1.212	-1.212	0.000	0.000	0.000	0.000
15	A	20	ASN	0	-0.047	-0.029	17.391	-1.311	-1.311	0.000	0.000	0.000	0.000
16	A	21	ARG	1	0.846	0.915	15.562	-18.633	-18.633	0.000	0.000	0.000	0.000
17	A	22	ILE	0	0.078	0.053	20.968	-0.694	-0.694	0.000	0.000	0.000	0.000
18	A	23	ASN	0	0.012	0.007	22.943	-0.860	-0.860	0.000	0.000	0.000	0.000
19	A	24	ASN	0	-0.028	-0.029	23.303	-0.798	-0.798	0.000	0.000	0.000	0.000
20	A	25	TYR	0	-0.090	-0.067	26.068	-0.448	-0.448	0.000	0.000	0.000	0.000
21	A	26	ILE	0	0.110	0.055	26.638	-0.396	-0.396	0.000	0.000	0.000	0.000
22	A	27	THR	0	-0.062	-0.018	28.250	-0.420	-0.420	0.000	0.000	0.000	0.000
23	A	28	ARG	1	0.917	0.954	26.558	-11.476	-11.476	0.000	0.000	0.000	0.000
24	A	29	HIS	1	0.836	0.924	31.320	-9.978	-9.978	0.000	0.000	0.000	0.000
25	A	30	ASN	0	-0.016	0.007	32.202	-0.323	-0.323	0.000	0.000	0.000	0.000
26	A	31	THR	0	-0.116	-0.062	34.710	-0.183	-0.183	0.000	0.000	0.000	0.000
27	A	32	ALA	0	-0.041	-0.008	36.419	-0.264	-0.264	0.000	0.000	0.000	0.000
28	A	33	GLY	0	0.003	0.010	38.350	-0.037	-0.037	0.000	0.000	0.000	0.000
29	A	34	ASP	-1	-0.985	-1.004	41.052	7.420	7.420	0.000	0.000	0.000	0.000
30	A	35	ASP	-1	-0.895	-0.951	36.403	8.909	8.909	0.000	0.000	0.000	0.000
31	A	36	ASP	-1	-0.851	-0.941	32.530	10.154	10.154	0.000	0.000	0.000	0.000
32	A	37	GLN	0	-0.103	-0.035	31.363	-0.040	-0.040	0.000	0.000	0.000	0.000
33	A	38	GLU	-1	-0.936	-0.968	31.918	9.324	9.324	0.000	0.000	0.000	0.000
34	A	39	GLU	-1	-0.965	-0.987	30.983	9.783	9.783	0.000	0.000	0.000	0.000
35	A	40	GLU	-1	-0.776	-0.899	28.741	10.403	10.403	0.000	0.000	0.000	0.000
36	A	41	ILE	0	-0.036	-0.012	26.144	0.646	0.646	0.000	0.000	0.000	0.000
37	A	42	GLN	0	0.022	0.022	25.933	0.579	0.579	0.000	0.000	0.000	0.000
38	A	43	ASP	-1	-0.837	-0.907	26.223	11.705	11.705	0.000	0.000	0.000	0.000
39	A	44	ILE	0	0.011	0.005	21.480	0.641	0.641	0.000	0.000	0.000	0.000
40	A	45	LEU	0	-0.070	-0.042	21.500	0.892	0.892	0.000	0.000	0.000	0.000
41	A	46	LYS	1	0.849	0.916	21.631	-10.918	-10.918	0.000	0.000	0.000	0.000
42	A	47	ASP	-1	-0.871	-0.922	19.836	15.208	15.208	0.000	0.000	0.000	0.000
43	A	48	VAL	0	-0.078	-0.046	16.445	1.287	1.287	0.000	0.000	0.000	0.000
44	A	49	GLU	-1	-0.948	-0.981	16.865	15.112	15.112	0.000	0.000	0.000	0.000
45	A	50	GLU	-1	-0.962	-0.979	17.957	16.641	16.641	0.000	0.000	0.000	0.000
46	A	51	THR	0	0.003	-0.010	12.619	1.352	1.352	0.000	0.000	0.000	0.000
47	A	52	ILE	0	-0.044	-0.022	13.236	2.232	2.232	0.000	0.000	0.000	0.000
48	A	53	VAL	0	0.003	0.007	13.993	0.889	0.889	0.000	0.000	0.000	0.000
49	A	54	ASP	-1	-0.849	-0.906	12.726	21.366	21.366	0.000	0.000	0.000	0.000
50	A	55	LEU	0	-0.063	-0.030	7.948	2.458	2.458	0.000	0.000	0.000	0.000
51	A	56	ASP	-1	-0.876	-0.930	10.790	23.352	23.352	0.000	0.000	0.000	0.000
52	A	57	ARG	1	0.815	0.878	13.415	-18.632	-18.632	0.000	0.000	0.000	0.000
53	A	58	SER	0	-0.044	-0.025	8.511	1.426	1.426	0.000	0.000	0.000	0.000
54	A	59	ILE	0	0.023	0.013	9.024	1.267	1.267	0.000	0.000	0.000	0.000
55	A	60	ILE	0	-0.049	-0.026	10.659	-1.055	-1.055	0.000	0.000	0.000	0.000
56	A	61	VAL	0	-0.030	-0.020	11.431	-1.211	-1.211	0.000	0.000	0.000	0.000
57	A	62	MET	0	-0.005	0.014	7.666	1.652	1.652	0.000	0.000	0.000	0.000
58	A	63	LYS	1	0.968	0.980	10.776	-21.445	-21.445	0.000	0.000	0.000	0.000
59	A	64	ARG	1	0.792	0.892	13.931	-20.862	-20.862	0.000	0.000	0.000	0.000
60	A	65	ASP	-1	-0.763	-0.877	12.249	21.948	21.948	0.000	0.000	0.000	0.000
61	A	66	GLU	-1	-0.928	-0.959	10.608	27.679	27.679	0.000	0.000	0.000	0.000
62	A	67	ASN	0	-0.052	-0.036	14.347	-0.981	-0.981	0.000	0.000	0.000	0.000
63	A	68	GLU	-1	-0.929	-0.962	17.335	15.742	15.742	0.000	0.000	0.000	0.000
64	A	69	ASP	-1	-0.811	-0.880	15.268	18.968	18.968	0.000	0.000	0.000	0.000
65	A	70	VAL	0	-0.045	-0.021	17.305	-0.939	-0.939	0.000	0.000	0.000	0.000
66	A	71	SER	0	0.013	0.008	19.539	-0.857	-0.857	0.000	0.000	0.000	0.000
67	A	72	GLY	0	0.003	0.010	21.069	-0.777	-0.777	0.000	0.000	0.000	0.000
68	A	73	ARG	1	0.814	0.878	15.824	-19.175	-19.175	0.000	0.000	0.000	0.000
69	A	74	GLU	-1	-0.915	-0.962	22.492	12.537	12.537	0.000	0.000	0.000	0.000
70	A	75	ALA	0	-0.037	-0.025	25.286	-0.708	-0.708	0.000	0.000	0.000	0.000
71	A	76	GLN	0	-0.003	-0.003	23.112	-0.229	-0.229	0.000	0.000	0.000	0.000
72	A	77	VAL	0	-0.001	-0.002	25.939	-0.559	-0.559	0.000	0.000	0.000	0.000
73	A	78	LYS	1	0.954	0.973	28.489	-10.222	-10.222	0.000	0.000	0.000	0.000
74	A	79	ASN	0	0.028	0.022	30.241	-0.713	-0.713	0.000	0.000	0.000	0.000
75	A	80	ILE	0	0.016	0.010	28.852	-0.377	-0.377	0.000	0.000	0.000	0.000
76	A	81	LYS	1	0.919	0.968	31.601	-10.438	-10.438	0.000	0.000	0.000	0.000
77	A	82	GLN	0	0.028	0.015	34.766	-0.156	-0.156	0.000	0.000	0.000	0.000
78	A	83	GLN	0	-0.029	-0.023	34.679	-0.506	-0.506	0.000	0.000	0.000	0.000
79	A	84	LEU	0	-0.017	-0.012	36.770	-0.256	-0.256	0.000	0.000	0.000	0.000
80	A	85	ASP	-1	-0.849	-0.917	38.515	7.962	7.962	0.000	0.000	0.000	0.000
81	A	86	ALA	0	-0.005	-0.007	40.406	-0.238	-0.238	0.000	0.000	0.000	0.000
82	A	87	LEU	0	-0.038	-0.023	40.314	-0.227	-0.227	0.000	0.000	0.000	0.000
83	A	88	LYS	1	0.846	0.920	40.056	-8.120	-8.120	0.000	0.000	0.000	0.000
84	A	89	LEU	0	0.051	0.034	44.677	-0.146	-0.146	0.000	0.000	0.000	0.000
85	A	90	ARG	1	0.889	0.942	44.806	-7.152	-7.152	0.000	0.000	0.000	0.000
86	A	91	PHE	0	-0.070	-0.039	46.470	-0.126	-0.126	0.000	0.000	0.000	0.000
87	A	92	ASP	-1	-0.991	-0.969	48.376	6.294	6.294	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:ASP)