FMO DATABASE

FMODB ID: Q1KRY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-541717.827369
FMO2-HF: Nuclear repulsion	507835.034148
FMO2-HF: Total energy	-33882.793221
FMO2-MP2: Total energy	-33981.455381

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.
-2.923	0.864	0.198	-1.883	-2.103	-0.003

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 : 0.051 / q_NPA : 0.033

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	0.904	0.952	3.708	-0.206	1.695	-0.002	-0.991	-0.908	0.006
4	A	4	VAL	0	0.012	-0.001	5.605	0.721	0.721	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.827	-0.906	8.793	-0.595	-0.595	0.000	0.000	0.000	0.000
6	A	6	ILE	0	-0.022	0.017	11.849	0.078	0.078	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.891	0.915	15.076	0.506	0.506	0.000	0.000	0.000	0.000
8	A	8	PRO	0	0.036	-0.009	17.873	0.027	0.027	0.000	0.000	0.000	0.000
9	A	9	SER	0	-0.016	-0.007	21.210	0.011	0.011	0.000	0.000	0.000	0.000
10	A	10	GLN	0	0.002	0.007	17.343	-0.018	-0.018	0.000	0.000	0.000	0.000
11	A	11	ALA	0	0.009	0.018	20.046	0.003	0.003	0.000	0.000	0.000	0.000
12	A	12	GLN	0	0.043	0.040	21.167	0.014	0.014	0.000	0.000	0.000	0.000
13	A	13	PHE	0	-0.037	-0.009	22.386	-0.010	-0.010	0.000	0.000	0.000	0.000
14	A	14	THR	0	-0.013	-0.006	23.802	0.002	0.002	0.000	0.000	0.000	0.000
15	A	15	THR	0	-0.016	-0.039	25.840	0.001	0.001	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.880	0.946	24.797	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	17	SER	0	0.016	-0.009	29.251	0.003	0.003	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.011	0.002	31.904	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.015	0.026	34.033	0.002	0.002	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.003	0.003	33.313	0.001	0.001	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.976	0.965	33.078	-0.049	-0.049	0.000	0.000	0.000	0.000
22	A	22	GLN	0	0.007	0.018	35.297	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	23	GLY	0	0.035	0.023	37.904	0.000	0.000	0.000	0.000	0.000	0.000
24	A	24	LYS	1	0.965	0.979	30.391	-0.059	-0.059	0.000	0.000	0.000	0.000
25	A	25	PRO	0	0.029	0.011	34.483	0.002	0.002	0.000	0.000	0.000	0.000
26	A	26	TYR	0	-0.074	-0.034	29.175	0.006	0.006	0.000	0.000	0.000	0.000
27	A	27	SER	0	0.037	0.001	29.380	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.024	-0.010	23.880	0.008	0.008	0.000	0.000	0.000	0.000
29	A	29	ASN	0	0.082	0.057	23.336	-0.009	-0.009	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.810	-0.880	21.207	-0.014	-0.014	0.000	0.000	0.000	0.000
31	A	31	GLN	0	0.005	-0.002	18.353	0.011	0.011	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.032	-0.016	18.494	0.006	0.006	0.000	0.000	0.000	0.000
33	A	33	CYS	0	-0.040	-0.008	13.539	-0.024	-0.024	0.000	0.000	0.000	0.000
34	A	34	TYR	0	0.027	0.003	13.771	0.064	0.064	0.000	0.000	0.000	0.000
35	A	35	VAL	0	0.024	0.005	8.348	-0.148	-0.148	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.830	-0.908	8.069	-1.090	-1.090	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.013	-0.018	7.550	-0.330	-0.330	0.000	0.000	0.000	0.000
38	A	38	GLY	0	-0.003	0.019	9.179	0.104	0.104	0.000	0.000	0.000	0.000
39	A	39	ASN	0	-0.066	-0.026	10.583	0.124	0.124	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.908	-0.959	14.106	-0.347	-0.347	0.000	0.000	0.000	0.000
41	A	41	TYR	0	-0.008	0.002	15.900	-0.027	-0.027	0.000	0.000	0.000	0.000
42	A	42	PRO	0	-0.050	-0.034	12.383	-0.006	-0.006	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.041	0.030	12.357	0.105	0.105	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.039	-0.023	14.313	-0.051	-0.051	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.004	0.005	12.449	0.050	0.050	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.851	0.910	15.665	0.045	0.045	0.000	0.000	0.000	0.000
47	A	47	ILE	0	0.024	0.017	13.920	0.033	0.033	0.000	0.000	0.000	0.000
48	A	48	THR	0	-0.046	-0.028	16.879	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.017	-0.008	18.108	0.021	0.021	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.784	-0.878	17.844	0.160	0.160	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.960	-0.988	20.470	0.041	0.041	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.009	0.006	23.399	0.006	0.006	0.000	0.000	0.000	0.000
53	A	53	GLN	0	-0.008	0.025	16.371	0.012	0.012	0.000	0.000	0.000	0.000
54	A	54	PRO	0	-0.020	-0.021	20.582	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	55	ALA	0	0.013	0.002	19.801	0.000	0.000	0.000	0.000	0.000	0.000
56	A	56	TYR	0	0.010	0.010	13.913	0.006	0.006	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.073	0.041	17.068	-0.008	-0.008	0.000	0.000	0.000	0.000
58	A	58	PRO	0	-0.012	-0.016	16.031	-0.040	-0.040	0.000	0.000	0.000	0.000
59	A	59	GLY	0	0.008	0.013	14.173	0.036	0.036	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.022	-0.004	8.700	-0.055	-0.055	0.000	0.000	0.000	0.000
61	A	61	TYR	0	-0.047	-0.052	8.223	0.212	0.212	0.000	0.000	0.000	0.000
62	A	62	THR	0	0.001	-0.005	2.861	-2.827	-1.219	0.202	-0.878	-0.933	-0.009
63	A	63	VAL	0	-0.004	-0.009	4.684	0.500	0.682	-0.001	-0.011	-0.171	0.000
64	A	64	HIS	0	0.059	0.058	5.691	0.613	0.613	0.000	0.000	0.000	0.000
65	A	65	LEU	0	0.059	0.010	5.981	0.114	0.114	0.000	0.000	0.000	0.000
66	A	66	SER	0	-0.008	-0.019	8.929	-0.034	-0.034	0.000	0.000	0.000	0.000
67	A	67	SER	0	0.001	0.003	9.345	-0.178	-0.178	0.000	0.000	0.000	0.000
68	A	68	PHE	0	-0.029	-0.002	5.665	-0.149	-0.053	-0.001	-0.003	-0.091	0.000
69	A	69	LYS	1	0.881	0.935	11.132	-0.365	-0.365	0.000	0.000	0.000	0.000
70	A	70	VAL	0	0.008	0.008	13.676	0.039	0.039	0.000	0.000	0.000	0.000
71	A	71	GLY	0	0.003	-0.010	15.403	-0.029	-0.029	0.000	0.000	0.000	0.000
72	A	72	GLN	0	-0.017	-0.014	17.952	-0.009	-0.009	0.000	0.000	0.000	0.000
73	A	73	PHE	0	-0.015	-0.017	20.161	-0.016	-0.016	0.000	0.000	0.000	0.000
74	A	74	GLY	0	0.027	0.026	18.585	-0.006	-0.006	0.000	0.000	0.000	0.000
75	A	75	SER	0	0.002	0.013	14.969	0.011	0.011	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.021	-0.014	8.248	-0.012	-0.012	0.000	0.000	0.000	0.000
77	A	77	MET	0	0.014	0.013	12.519	-0.015	-0.015	0.000	0.000	0.000	0.000
78	A	78	ILE	0	0.017	0.004	9.119	0.082	0.082	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.874	-0.928	12.270	0.152	0.152	0.000	0.000	0.000	0.000
80	A	80	ARG	1	0.849	0.909	14.222	-0.177	-0.177	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.012	-0.003	8.907	0.091	0.091	0.000	0.000	0.000	0.000
82	A	82	ARG	1	0.802	0.879	11.215	-0.362	-0.362	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.020	-0.002	8.896	0.059	0.059	0.000	0.000	0.000	0.000
84	A	84	VAL	0	0.018	0.005	7.437	0.114	0.114	0.000	0.000	0.000	0.000
85	A	85	PRO	0	-0.007	-0.018	8.507	-0.221	-0.221	0.000	0.000	0.000	0.000
86	A	86	ALA	0	0.025	0.002	6.885	0.096	0.096	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.928	0.995	7.467	0.291	0.291	0.000	0.000	0.000	0.000

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