FMO DATABASE

FMODB ID: LZ7J9

Calculation Name: 3GPV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GPV

Chain ID: A

ChEMBL ID:

UniProt ID: Q6HKH9

Base Structure: X-ray

Registration Date: 2023-06-22

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	114
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-924384.643411
FMO2-HF: Nuclear repulsion	876055.562476
FMO2-HF: Total energy	-48329.080935
FMO2-MP2: Total energy	-48467.55692

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:20:MET)

Summations of interaction energy for fragment #1(A:20: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.
-5.304	0.374	4.317	-2.761	-7.236	-0.012

Interaction energy analysis for fragmet #1(A:20:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.039 / q_NPA : 0.021

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

Sort

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	22	TYR	0	0.000	0.012	2.553	-4.450	0.337	4.291	-2.596	-6.483	-0.013
4	A	23	THR	0	0.065	0.029	3.987	0.403	0.516	0.002	-0.011	-0.104	0.000
5	A	24	ILE	0	0.069	0.023	7.298	-0.075	-0.075	0.000	0.000	0.000	0.000
6	A	25	GLY	0	-0.016	-0.013	10.093	0.036	0.036	0.000	0.000	0.000	0.000
7	A	26	GLN	0	0.019	0.010	3.029	-0.584	-0.238	0.023	-0.092	-0.278	0.001
8	A	27	VAL	0	0.073	0.036	7.611	0.028	0.028	0.000	0.000	0.000	0.000
9	A	28	ALA	0	-0.033	-0.019	9.551	0.094	0.094	0.000	0.000	0.000	0.000
10	A	29	LYS	1	0.941	0.978	10.446	0.356	0.356	0.000	0.000	0.000	0.000
11	A	30	MET	0	-0.044	-0.025	5.570	0.115	0.115	0.000	0.000	0.000	0.000
12	A	31	GLN	0	0.001	0.005	11.391	0.126	0.126	0.000	0.000	0.000	0.000
13	A	32	HIS	0	-0.054	-0.002	14.719	0.098	0.098	0.000	0.000	0.000	0.000
14	A	33	LEU	0	-0.003	0.006	15.914	0.045	0.045	0.000	0.000	0.000	0.000
15	A	34	THR	0	0.019	-0.017	16.332	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	35	ILE	0	0.038	-0.002	13.741	-0.036	-0.036	0.000	0.000	0.000	0.000
17	A	36	SER	0	-0.006	-0.011	16.213	-0.020	-0.020	0.000	0.000	0.000	0.000
18	A	37	GLN	0	0.065	0.058	18.942	-0.007	-0.007	0.000	0.000	0.000	0.000
19	A	38	ILE	0	0.050	0.037	13.033	0.003	0.003	0.000	0.000	0.000	0.000
20	A	39	ARG	1	0.989	0.983	14.953	0.298	0.298	0.000	0.000	0.000	0.000
21	A	40	TYR	0	-0.028	0.000	17.885	0.020	0.020	0.000	0.000	0.000	0.000
22	A	41	TYR	0	0.056	0.020	17.778	0.046	0.046	0.000	0.000	0.000	0.000
23	A	42	ASP	-1	-0.803	-0.880	16.065	-0.556	-0.556	0.000	0.000	0.000	0.000
24	A	43	LYS	1	0.942	0.974	18.428	0.254	0.254	0.000	0.000	0.000	0.000
25	A	44	GLN	0	-0.050	-0.027	21.881	0.005	0.005	0.000	0.000	0.000	0.000
26	A	45	GLY	0	0.003	-0.003	21.601	0.021	0.021	0.000	0.000	0.000	0.000
27	A	46	LEU	0	-0.035	-0.016	19.354	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	47	PHE	0	-0.013	-0.015	14.917	-0.050	-0.050	0.000	0.000	0.000	0.000
29	A	48	PRO	0	0.005	0.011	16.459	-0.033	-0.033	0.000	0.000	0.000	0.000
30	A	49	PHE	0	0.070	0.026	12.583	0.015	0.015	0.000	0.000	0.000	0.000
31	A	50	LEU	0	-0.077	-0.016	11.402	-0.150	-0.150	0.000	0.000	0.000	0.000
32	A	51	GLN	0	0.073	0.048	7.915	-0.191	-0.191	0.000	0.000	0.000	0.000
33	A	52	ARG	1	0.877	0.919	11.684	0.288	0.288	0.000	0.000	0.000	0.000
34	A	53	ASN	0	0.027	0.021	7.375	0.025	0.025	0.000	0.000	0.000	0.000
35	A	54	GLU	-1	-0.827	-0.931	9.780	0.247	0.247	0.000	0.000	0.000	0.000
36	A	55	LYS	1	0.891	0.950	9.181	-0.701	-0.701	0.000	0.000	0.000	0.000
37	A	56	GLY	0	0.012	0.013	13.054	-0.037	-0.037	0.000	0.000	0.000	0.000
38	A	57	ASP	-1	-0.926	-0.965	9.538	-0.497	-0.497	0.000	0.000	0.000	0.000
39	A	58	ARG	1	0.800	0.885	11.197	0.407	0.407	0.000	0.000	0.000	0.000
40	A	59	ILE	0	-0.059	-0.026	6.816	-0.031	-0.031	0.000	0.000	0.000	0.000
41	A	60	PHE	0	0.043	-0.007	6.921	0.197	0.197	0.000	0.000	0.000	0.000
42	A	61	ASN	0	0.048	0.034	4.926	-0.998	-0.998	0.000	0.000	0.000	0.000
43	A	62	GLU	-1	-0.808	-0.940	3.753	-3.022	-2.590	0.001	-0.062	-0.371	0.000
44	A	63	GLU	-1	-0.874	-0.920	6.113	-0.604	-0.604	0.000	0.000	0.000	0.000
45	A	64	ALA	0	-0.002	0.003	8.773	0.279	0.279	0.000	0.000	0.000	0.000
46	A	65	LEU	0	-0.030	-0.016	5.789	0.329	0.329	0.000	0.000	0.000	0.000
47	A	66	LYS	1	0.935	0.973	8.180	1.980	1.980	0.000	0.000	0.000	0.000
48	A	67	TYR	0	-0.033	-0.024	12.389	0.213	0.213	0.000	0.000	0.000	0.000
49	A	68	LEU	0	-0.058	-0.031	11.848	0.143	0.143	0.000	0.000	0.000	0.000
50	A	69	GLU	-1	-0.939	-0.966	13.642	-0.692	-0.692	0.000	0.000	0.000	0.000
51	A	70	MET	0	0.037	0.023	15.332	0.123	0.123	0.000	0.000	0.000	0.000
52	A	71	ILE	0	-0.025	-0.007	16.326	0.083	0.083	0.000	0.000	0.000	0.000
53	A	72	LEU	0	-0.024	-0.018	15.870	0.077	0.077	0.000	0.000	0.000	0.000
54	A	73	CYS	0	0.029	0.028	19.410	0.069	0.069	0.000	0.000	0.000	0.000
55	A	74	LEU	0	0.020	0.005	21.365	0.054	0.054	0.000	0.000	0.000	0.000
56	A	75	LYS	1	0.897	0.949	22.199	0.393	0.393	0.000	0.000	0.000	0.000
57	A	76	ASN	0	-0.077	-0.048	21.454	0.045	0.045	0.000	0.000	0.000	0.000
58	A	77	THR	0	-0.041	-0.024	24.994	0.025	0.025	0.000	0.000	0.000	0.000
59	A	78	GLY	0	0.015	0.008	27.444	0.016	0.016	0.000	0.000	0.000	0.000
60	A	79	MET	0	-0.021	0.024	26.226	0.012	0.012	0.000	0.000	0.000	0.000
61	A	80	PRO	0	-0.006	-0.013	27.401	-0.012	-0.012	0.000	0.000	0.000	0.000
62	A	81	ILE	0	0.072	0.023	24.776	-0.011	-0.011	0.000	0.000	0.000	0.000
63	A	82	GLN	0	0.028	0.006	25.920	-0.035	-0.035	0.000	0.000	0.000	0.000
64	A	83	LYS	1	0.913	0.959	27.722	0.240	0.240	0.000	0.000	0.000	0.000
65	A	84	ILE	0	0.012	0.008	21.768	-0.012	-0.012	0.000	0.000	0.000	0.000
66	A	85	LYS	1	0.871	0.929	22.926	0.301	0.301	0.000	0.000	0.000	0.000
67	A	86	GLN	0	0.038	0.042	23.871	-0.011	-0.011	0.000	0.000	0.000	0.000
68	A	87	PHE	0	0.000	-0.010	19.902	0.003	0.003	0.000	0.000	0.000	0.000
69	A	88	ILE	0	-0.029	-0.019	18.471	-0.022	-0.022	0.000	0.000	0.000	0.000
70	A	89	ASP	-1	-0.892	-0.951	20.379	-0.413	-0.413	0.000	0.000	0.000	0.000
71	A	90	TRP	0	-0.015	-0.029	22.511	0.002	0.002	0.000	0.000	0.000	0.000
72	A	91	SER	0	-0.069	-0.047	18.539	0.009	0.009	0.000	0.000	0.000	0.000
73	A	92	MET	0	-0.023	0.005	17.221	-0.045	-0.045	0.000	0.000	0.000	0.000
74	A	93	GLU	-1	-0.916	-0.952	19.247	-0.295	-0.295	0.000	0.000	0.000	0.000
75	A	94	GLY	0	0.056	0.040	20.911	0.023	0.023	0.000	0.000	0.000	0.000
76	A	95	ASP	-1	-0.977	-0.995	21.924	-0.290	-0.290	0.000	0.000	0.000	0.000
77	A	96	SER	0	0.053	0.025	23.898	0.026	0.026	0.000	0.000	0.000	0.000
78	A	97	THR	0	-0.009	0.000	24.113	0.013	0.013	0.000	0.000	0.000	0.000
79	A	98	ILE	0	-0.005	0.000	22.941	-0.007	-0.007	0.000	0.000	0.000	0.000
80	A	99	LEU	0	0.021	0.001	25.830	0.000	0.000	0.000	0.000	0.000	0.000
81	A	100	HIS	0	0.013	0.011	27.931	0.008	0.008	0.000	0.000	0.000	0.000
82	A	101	ARG	1	0.892	0.942	20.397	0.425	0.425	0.000	0.000	0.000	0.000
83	A	102	LEU	0	0.006	0.019	26.169	0.000	0.000	0.000	0.000	0.000	0.000
84	A	103	LYS	1	0.967	0.983	27.606	0.204	0.204	0.000	0.000	0.000	0.000
85	A	104	LEU	0	-0.025	-0.013	26.347	0.011	0.011	0.000	0.000	0.000	0.000
86	A	105	MET	0	0.005	0.002	24.097	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	106	LYS	1	0.993	1.001	27.277	0.217	0.217	0.000	0.000	0.000	0.000
88	A	107	GLN	0	-0.012	0.006	30.620	0.011	0.011	0.000	0.000	0.000	0.000
89	A	108	GLN	0	0.019	0.004	26.764	0.022	0.022	0.000	0.000	0.000	0.000
90	A	109	GLU	-1	-0.908	-0.942	28.982	-0.230	-0.230	0.000	0.000	0.000	0.000
91	A	110	ALA	0	0.004	-0.003	30.202	0.011	0.011	0.000	0.000	0.000	0.000
92	A	111	ASN	0	-0.049	-0.040	31.429	0.021	0.021	0.000	0.000	0.000	0.000
93	A	112	VAL	0	-0.017	-0.013	27.878	0.006	0.006	0.000	0.000	0.000	0.000
94	A	113	LEU	0	0.006	0.007	31.302	0.008	0.008	0.000	0.000	0.000	0.000
95	A	114	GLN	0	-0.037	-0.023	33.954	0.011	0.011	0.000	0.000	0.000	0.000
96	A	115	LEU	0	0.028	0.018	30.921	0.008	0.008	0.000	0.000	0.000	0.000
97	A	116	ILE	0	-0.005	0.018	30.679	0.007	0.007	0.000	0.000	0.000	0.000
98	A	117	GLN	0	0.041	0.031	34.556	0.015	0.015	0.000	0.000	0.000	0.000
99	A	118	ASP	-1	-0.868	-0.938	37.786	-0.134	-0.134	0.000	0.000	0.000	0.000
100	A	119	THR	0	-0.113	-0.079	34.212	0.006	0.006	0.000	0.000	0.000	0.000
101	A	120	GLU	-1	-0.904	-0.950	36.952	-0.137	-0.137	0.000	0.000	0.000	0.000
102	A	121	LYS	1	0.927	0.969	39.026	0.111	0.111	0.000	0.000	0.000	0.000
103	A	122	ASN	0	-0.005	-0.018	39.190	0.015	0.015	0.000	0.000	0.000	0.000
104	A	123	LEU	0	0.038	0.034	37.451	0.006	0.006	0.000	0.000	0.000	0.000
105	A	124	LYS	1	0.991	0.995	40.523	0.098	0.098	0.000	0.000	0.000	0.000
106	A	125	LYS	1	0.891	0.946	43.844	0.116	0.116	0.000	0.000	0.000	0.000
107	A	126	ILE	0	-0.011	-0.007	40.684	0.006	0.006	0.000	0.000	0.000	0.000
108	A	127	GLN	0	0.044	0.008	40.917	0.005	0.005	0.000	0.000	0.000	0.000
109	A	128	GLN	0	-0.013	-0.006	44.618	0.002	0.002	0.000	0.000	0.000	0.000
110	A	129	LYS	1	0.892	0.961	46.477	0.084	0.084	0.000	0.000	0.000	0.000
111	A	130	ILE	0	0.017	0.004	42.527	0.003	0.003	0.000	0.000	0.000	0.000
112	A	131	ALA	0	-0.008	0.006	47.127	0.003	0.003	0.000	0.000	0.000	0.000
113	A	132	LYS	1	0.895	0.948	49.946	0.067	0.067	0.000	0.000	0.000	0.000
114	A	133	TYR	0	-0.016	0.002	47.013	0.005	0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:20:MET)