FMO DATABASE

FMODB ID: K3KY3

Calculation Name: 1GVP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1GVP

Chain ID: A

ChEMBL ID:

UniProt ID: P69543

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	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	87
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-541566.376666
FMO2-HF: Nuclear repulsion	507683.275001
FMO2-HF: Total energy	-33883.101665
FMO2-MP2: Total energy	-33981.786526

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:1:MET)

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

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.
-3.087	0.463	0.915	-1.966	-2.499	-0.011

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.036 / q_NPA : 0.022

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	3	LYS	1	0.905	0.962	3.792	0.224	1.908	0.000	-0.788	-0.896	0.004
4	A	4	VAL	0	0.009	0.002	5.610	0.784	0.784	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.846	-0.913	8.537	-0.682	-0.682	0.000	0.000	0.000	0.000
6	A	6	ILE	0	-0.019	0.015	11.770	0.086	0.086	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.880	0.914	15.112	0.536	0.536	0.000	0.000	0.000	0.000
8	A	8	PRO	0	0.059	0.007	18.022	0.025	0.025	0.000	0.000	0.000	0.000
9	A	9	SER	0	-0.015	-0.006	21.222	0.010	0.010	0.000	0.000	0.000	0.000
10	A	10	GLN	0	0.003	0.002	17.273	-0.024	-0.024	0.000	0.000	0.000	0.000
11	A	11	ALA	0	-0.007	0.007	19.756	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	12	GLN	0	0.047	0.037	21.127	0.011	0.011	0.000	0.000	0.000	0.000
13	A	13	PHE	0	-0.061	-0.020	22.200	-0.012	-0.012	0.000	0.000	0.000	0.000
14	A	14	THR	0	-0.026	-0.011	23.537	0.007	0.007	0.000	0.000	0.000	0.000
15	A	15	THR	0	0.042	-0.008	25.320	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.867	0.934	24.368	0.011	0.011	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.001	-0.018	29.232	0.001	0.001	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.017	0.016	31.900	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.009	0.000	34.252	0.001	0.001	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.009	0.003	33.638	0.002	0.002	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.978	0.972	33.201	-0.048	-0.048	0.000	0.000	0.000	0.000
22	A	22	GLN	0	0.039	0.028	35.713	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	23	GLY	0	0.029	0.019	38.111	0.000	0.000	0.000	0.000	0.000	0.000
24	A	24	LYS	1	0.943	0.978	29.993	-0.041	-0.041	0.000	0.000	0.000	0.000
25	A	25	PRO	0	0.044	0.024	34.839	0.001	0.001	0.000	0.000	0.000	0.000
26	A	26	TYR	0	-0.072	-0.042	29.132	0.005	0.005	0.000	0.000	0.000	0.000
27	A	27	SER	0	0.031	-0.004	29.582	-0.007	-0.007	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.016	-0.010	23.816	0.006	0.006	0.000	0.000	0.000	0.000
29	A	29	ASN	0	0.074	0.060	23.252	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.782	-0.867	21.141	-0.024	-0.024	0.000	0.000	0.000	0.000
31	A	31	GLN	0	0.000	-0.005	18.013	0.013	0.013	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.021	-0.012	18.509	0.006	0.006	0.000	0.000	0.000	0.000
33	A	33	CYS	0	-0.030	-0.008	13.377	-0.020	-0.020	0.000	0.000	0.000	0.000
34	A	34	TYR	0	0.017	-0.002	13.698	0.080	0.080	0.000	0.000	0.000	0.000
35	A	35	VAL	0	0.006	-0.002	8.417	-0.151	-0.151	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.843	-0.920	8.181	-0.945	-0.945	0.000	0.000	0.000	0.000
37	A	37	LEU	0	0.008	-0.006	7.622	-0.218	-0.218	0.000	0.000	0.000	0.000
38	A	38	GLY	0	-0.020	0.016	9.414	0.141	0.141	0.000	0.000	0.000	0.000
39	A	39	ASN	0	-0.065	-0.039	10.756	0.146	0.146	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.888	-0.949	14.266	-0.320	-0.320	0.000	0.000	0.000	0.000
41	A	41	TYR	0	-0.027	-0.010	16.211	-0.016	-0.016	0.000	0.000	0.000	0.000
42	A	42	PRO	0	-0.042	-0.021	12.384	0.009	0.009	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.054	0.042	12.355	0.094	0.094	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.029	-0.015	14.355	-0.059	-0.059	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.000	0.003	13.051	0.052	0.052	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.828	0.897	16.189	0.052	0.052	0.000	0.000	0.000	0.000
47	A	47	ILE	0	0.009	0.008	13.425	0.030	0.030	0.000	0.000	0.000	0.000
48	A	48	THR	0	-0.028	-0.021	17.065	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.012	-0.004	18.177	0.015	0.015	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.772	-0.864	17.928	0.106	0.106	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.966	-0.992	20.643	0.017	0.017	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.014	0.009	23.603	0.004	0.004	0.000	0.000	0.000	0.000
53	A	53	GLN	0	-0.027	0.011	16.021	0.015	0.015	0.000	0.000	0.000	0.000
54	A	54	PRO	0	0.008	-0.001	20.025	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	55	ALA	0	0.002	-0.008	19.388	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	56	TYR	0	0.010	0.013	13.661	0.001	0.001	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.069	0.037	16.583	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	58	PRO	0	0.001	-0.006	15.856	-0.049	-0.049	0.000	0.000	0.000	0.000
59	A	59	GLY	0	0.011	0.020	14.180	0.035	0.035	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.015	-0.007	8.826	-0.050	-0.050	0.000	0.000	0.000	0.000
61	A	61	TYR	0	-0.049	-0.054	8.006	0.197	0.197	0.000	0.000	0.000	0.000
62	A	62	THR	0	-0.014	-0.022	2.518	-4.283	-2.603	0.916	-1.163	-1.433	-0.015
63	A	63	VAL	0	-0.004	0.000	4.257	0.699	0.885	-0.001	-0.015	-0.170	0.000
64	A	64	HIS	0	0.054	0.057	5.425	0.529	0.529	0.000	0.000	0.000	0.000
65	A	65	LEU	0	0.063	0.018	5.601	0.124	0.124	0.000	0.000	0.000	0.000
66	A	66	SER	0	0.013	-0.014	8.869	-0.018	-0.018	0.000	0.000	0.000	0.000
67	A	67	SER	0	-0.022	-0.002	9.320	-0.149	-0.149	0.000	0.000	0.000	0.000
68	A	68	PHE	0	-0.041	-0.020	6.388	0.046	0.046	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.847	0.916	11.647	-0.348	-0.348	0.000	0.000	0.000	0.000
70	A	70	VAL	0	0.018	0.015	13.995	0.049	0.049	0.000	0.000	0.000	0.000
71	A	71	GLY	0	0.020	0.004	15.753	-0.028	-0.028	0.000	0.000	0.000	0.000
72	A	72	GLN	0	-0.047	-0.034	18.325	-0.007	-0.007	0.000	0.000	0.000	0.000
73	A	73	PHE	0	0.008	0.000	20.361	-0.019	-0.019	0.000	0.000	0.000	0.000
74	A	74	GLY	0	0.012	0.016	18.762	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	75	SER	0	0.008	0.009	15.476	0.014	0.014	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.001	0.002	8.542	-0.023	-0.023	0.000	0.000	0.000	0.000
77	A	77	MET	0	-0.014	-0.004	12.943	-0.023	-0.023	0.000	0.000	0.000	0.000
78	A	78	ILE	0	0.050	0.026	9.953	0.068	0.068	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.858	-0.907	12.848	0.136	0.136	0.000	0.000	0.000	0.000
80	A	80	ARG	1	0.831	0.899	14.540	-0.122	-0.122	0.000	0.000	0.000	0.000
81	A	81	LEU	0	0.012	0.007	9.034	0.078	0.078	0.000	0.000	0.000	0.000
82	A	82	ARG	1	0.787	0.854	11.362	-0.276	-0.276	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.023	-0.006	8.547	0.018	0.018	0.000	0.000	0.000	0.000
84	A	84	VAL	0	0.011	-0.002	6.933	0.148	0.148	0.000	0.000	0.000	0.000
85	A	85	PRO	0	0.022	0.013	7.955	-0.275	-0.275	0.000	0.000	0.000	0.000
86	A	86	ALA	0	0.003	-0.004	6.490	0.096	0.096	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.925	0.977	7.103	0.446	0.446	0.000	0.000	0.000	0.000

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