FMO DATABASE

FMODB ID: R5QZ8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-541803.77989
FMO2-HF: Nuclear repulsion	507921.693639
FMO2-HF: Total energy	-33882.086252
FMO2-MP2: Total energy	-33980.763473

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.
-3.871	-0.73	0.223	-1.407	-1.956	-0.008

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 : 0.014 / q_NPA : 0.003

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	1.009	1.008	3.564	-0.789	0.381	0.006	-0.472	-0.704	0.002
4	A	4	VAL	0	0.007	0.002	5.798	-0.021	-0.021	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.886	-0.950	8.705	0.256	0.256	0.000	0.000	0.000	0.000
6	A	6	ILE	0	-0.015	0.023	11.774	-0.013	-0.013	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.925	0.940	14.993	-0.132	-0.132	0.000	0.000	0.000	0.000
8	A	8	PRO	0	0.033	-0.012	17.863	-0.004	-0.004	0.000	0.000	0.000	0.000
9	A	9	SER	0	-0.012	-0.001	21.149	-0.002	-0.002	0.000	0.000	0.000	0.000
10	A	10	GLN	0	0.014	0.009	17.138	0.002	0.002	0.000	0.000	0.000	0.000
11	A	11	ALA	0	0.015	0.017	19.972	0.003	0.003	0.000	0.000	0.000	0.000
12	A	12	GLN	0	0.019	0.033	21.094	0.000	0.000	0.000	0.000	0.000	0.000
13	A	13	PHE	0	-0.022	-0.011	22.241	0.005	0.005	0.000	0.000	0.000	0.000
14	A	14	THR	0	-0.012	-0.001	23.746	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	15	THR	0	0.004	-0.017	25.730	0.004	0.004	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.917	0.972	26.064	-0.086	-0.086	0.000	0.000	0.000	0.000
17	A	17	SER	0	0.005	-0.012	29.108	0.002	0.002	0.000	0.000	0.000	0.000
18	A	18	GLY	0	-0.009	-0.008	31.767	0.000	0.000	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.013	0.027	33.890	0.000	0.000	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.006	0.005	32.940	0.000	0.000	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.983	0.966	32.995	-0.048	-0.048	0.000	0.000	0.000	0.000
22	A	22	GLN	0	-0.007	0.010	34.690	0.000	0.000	0.000	0.000	0.000	0.000
23	A	23	GLY	0	0.039	0.024	37.629	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	24	LYS	1	0.963	0.975	30.374	-0.057	-0.057	0.000	0.000	0.000	0.000
25	A	25	PRO	0	0.026	0.008	34.213	0.003	0.003	0.000	0.000	0.000	0.000
26	A	26	TYR	0	-0.045	-0.012	28.983	0.001	0.001	0.000	0.000	0.000	0.000
27	A	27	SER	0	0.036	0.005	29.262	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.028	-0.015	23.954	0.005	0.005	0.000	0.000	0.000	0.000
29	A	29	ASN	0	0.083	0.056	23.081	-0.008	-0.008	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.835	-0.913	21.072	0.108	0.108	0.000	0.000	0.000	0.000
31	A	31	GLN	0	0.011	0.001	18.027	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.025	-0.012	18.382	0.009	0.009	0.000	0.000	0.000	0.000
33	A	33	CYS	0	-0.038	0.001	13.439	0.001	0.001	0.000	0.000	0.000	0.000
34	A	34	TYR	0	0.016	0.003	13.834	0.001	0.001	0.000	0.000	0.000	0.000
35	A	35	VAL	0	0.008	-0.002	8.157	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.877	-0.948	8.276	0.097	0.097	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.035	-0.027	7.352	-0.156	-0.156	0.000	0.000	0.000	0.000
38	A	38	GLY	0	-0.009	0.017	9.018	-0.025	-0.025	0.000	0.000	0.000	0.000
39	A	39	ASN	0	-0.069	-0.033	10.469	0.023	0.023	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.907	-0.956	13.974	0.020	0.020	0.000	0.000	0.000	0.000
41	A	41	TYR	0	-0.016	-0.002	16.062	0.013	0.013	0.000	0.000	0.000	0.000
42	A	42	PRO	0	-0.040	-0.032	12.719	-0.010	-0.010	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.035	0.036	12.098	0.007	0.007	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.045	-0.030	14.129	0.005	0.005	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.005	0.008	12.275	0.006	0.006	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.845	0.898	15.475	-0.105	-0.105	0.000	0.000	0.000	0.000
47	A	47	ILE	0	0.026	0.021	13.971	0.021	0.021	0.000	0.000	0.000	0.000
48	A	48	THR	0	-0.030	-0.016	16.730	-0.018	-0.018	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.012	-0.018	17.803	0.018	0.018	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.846	-0.916	17.691	0.162	0.162	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.966	-0.993	20.367	0.061	0.061	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.003	0.003	23.312	0.001	0.001	0.000	0.000	0.000	0.000
53	A	53	GLN	0	-0.022	0.009	16.567	0.008	0.008	0.000	0.000	0.000	0.000
54	A	54	PRO	0	-0.028	-0.026	20.597	0.001	0.001	0.000	0.000	0.000	0.000
55	A	55	ALA	0	0.022	0.012	19.770	0.006	0.006	0.000	0.000	0.000	0.000
56	A	56	TYR	0	0.010	0.013	13.923	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.054	0.031	17.019	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	58	PRO	0	-0.017	-0.020	15.964	0.006	0.006	0.000	0.000	0.000	0.000
59	A	59	GLY	0	0.016	0.015	14.090	0.000	0.000	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.017	-0.002	8.915	0.007	0.007	0.000	0.000	0.000	0.000
61	A	61	TYR	0	-0.045	-0.049	8.160	0.010	0.010	0.000	0.000	0.000	0.000
62	A	62	THR	0	0.001	0.002	2.827	-2.863	-1.201	0.219	-0.917	-0.963	-0.010
63	A	63	VAL	0	-0.001	-0.005	4.574	0.201	0.395	-0.001	-0.012	-0.181	0.000
64	A	64	HIS	0	0.058	0.075	5.641	0.298	0.298	0.000	0.000	0.000	0.000
65	A	65	LEU	0	0.082	0.023	6.769	0.178	0.178	0.000	0.000	0.000	0.000
66	A	66	SER	0	-0.034	-0.049	9.104	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	67	SER	0	0.008	0.000	9.203	-0.112	-0.112	0.000	0.000	0.000	0.000
68	A	68	PHE	0	-0.050	-0.012	5.254	-0.191	-0.076	-0.001	-0.006	-0.108	0.000
69	A	69	LYS	1	0.888	0.953	10.931	-0.307	-0.307	0.000	0.000	0.000	0.000
70	A	70	VAL	0	0.007	0.007	13.270	0.022	0.022	0.000	0.000	0.000	0.000
71	A	71	GLY	0	0.008	-0.006	15.032	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	72	GLN	0	-0.017	-0.017	17.423	-0.014	-0.014	0.000	0.000	0.000	0.000
73	A	73	PHE	0	-0.014	-0.015	19.453	-0.011	-0.011	0.000	0.000	0.000	0.000
74	A	74	GLY	0	0.024	0.026	18.089	-0.011	-0.011	0.000	0.000	0.000	0.000
75	A	75	SER	0	0.008	0.014	14.107	-0.010	-0.010	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.028	-0.017	7.679	0.006	0.006	0.000	0.000	0.000	0.000
77	A	77	MET	0	0.032	0.013	11.911	0.001	0.001	0.000	0.000	0.000	0.000
78	A	78	ILE	0	-0.003	0.002	8.692	0.060	0.060	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.897	-0.954	11.958	0.127	0.127	0.000	0.000	0.000	0.000
80	A	80	ARG	1	0.960	0.971	13.956	-0.194	-0.194	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.022	-0.008	8.857	0.058	0.058	0.000	0.000	0.000	0.000
82	A	82	ARG	1	0.801	0.896	11.110	-0.315	-0.315	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.023	-0.006	8.987	0.052	0.052	0.000	0.000	0.000	0.000
84	A	84	VAL	0	0.020	0.012	7.550	0.012	0.012	0.000	0.000	0.000	0.000
85	A	85	PRO	0	-0.005	-0.027	8.483	-0.047	-0.047	0.000	0.000	0.000	0.000
86	A	86	ALA	0	0.027	0.005	6.833	-0.048	-0.048	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.928	0.996	7.436	-0.136	-0.136	0.000	0.000	0.000	0.000

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