FMO DATABASE

FMODB ID: GNGJ1

Calculation Name: 2V1L-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2V1L

Chain ID: A

ChEMBL ID:

UniProt ID: Q9KR41

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	132
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1182128.187955
FMO2-HF: Nuclear repulsion	1129126.454797
FMO2-HF: Total energy	-53001.733158
FMO2-MP2: Total energy	-53157.856995

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:5:LEU)

Summations of interaction energy for fragment #1(A:5:LEU)

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.
-7.272	-2.139	1.666	-1.728	-5.068	-0.001

Interaction energy analysis for fragmet #1(A:5:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : -0.023

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	7	LYS	1	0.885	0.933	3.100	0.586	2.309	0.028	-0.670	-1.081	0.002
4	A	8	PRO	0	0.003	0.028	5.680	-0.332	-0.332	0.000	0.000	0.000	0.000
5	A	9	THR	0	0.031	0.006	8.620	-0.123	-0.123	0.000	0.000	0.000	0.000
6	A	10	HIS	0	-0.007	-0.011	12.185	0.114	0.114	0.000	0.000	0.000	0.000
7	A	11	LEU	0	0.017	0.027	14.558	-0.004	-0.004	0.000	0.000	0.000	0.000
8	A	12	PRO	0	-0.072	-0.025	13.729	0.061	0.061	0.000	0.000	0.000	0.000
9	A	13	ILE	0	-0.010	0.004	9.755	0.008	0.008	0.000	0.000	0.000	0.000
10	A	14	SER	0	-0.059	-0.051	11.218	0.238	0.238	0.000	0.000	0.000	0.000
11	A	15	LYS	1	0.963	0.961	7.764	-2.179	-2.179	0.000	0.000	0.000	0.000
12	A	16	PRO	0	-0.009	-0.011	8.619	0.073	0.073	0.000	0.000	0.000	0.000
13	A	17	PHE	0	0.089	0.061	9.969	-0.087	-0.087	0.000	0.000	0.000	0.000
14	A	18	HIS	0	0.000	-0.008	4.732	0.380	0.455	-0.001	-0.003	-0.070	0.000
15	A	19	ALA	0	-0.030	-0.014	5.020	-0.454	-0.374	-0.001	-0.002	-0.077	0.000
16	A	20	LEU	0	0.039	0.036	6.694	-0.184	-0.184	0.000	0.000	0.000	0.000
17	A	21	LEU	0	0.017	0.008	5.961	-0.137	-0.137	0.000	0.000	0.000	0.000
18	A	22	ALA	0	-0.030	-0.037	2.539	-0.907	-0.458	0.580	-0.219	-0.810	-0.001
19	A	23	ASN	0	-0.096	-0.046	3.835	-0.208	-0.115	0.003	0.026	-0.122	0.000
20	A	24	ILE	0	0.097	0.040	7.243	-0.059	-0.059	0.000	0.000	0.000	0.000
21	A	25	LEU	0	-0.032	0.001	3.407	-0.415	-0.124	0.011	-0.054	-0.247	0.000
22	A	26	SER	0	-0.056	-0.032	5.560	0.231	0.231	0.000	0.000	0.000	0.000
23	A	27	GLU	-1	-0.889	-0.948	7.058	-0.100	-0.100	0.000	0.000	0.000	0.000
24	A	28	HIS	0	-0.001	0.012	9.687	0.069	0.069	0.000	0.000	0.000	0.000
25	A	29	GLN	0	-0.110	-0.056	6.482	-0.214	-0.214	0.000	0.000	0.000	0.000
26	A	30	ALA	0	-0.042	-0.006	10.213	0.067	0.067	0.000	0.000	0.000	0.000
27	A	40	GLU	-1	-1.002	-1.027	11.689	-0.545	-0.545	0.000	0.000	0.000	0.000
28	A	41	VAL	0	-0.049	-0.025	8.987	0.027	0.027	0.000	0.000	0.000	0.000
29	A	42	VAL	0	0.059	0.033	12.299	-0.014	-0.014	0.000	0.000	0.000	0.000
30	A	43	MET	0	-0.039	-0.007	7.826	0.040	0.040	0.000	0.000	0.000	0.000
31	A	44	ASN	0	-0.068	-0.046	13.927	0.023	0.023	0.000	0.000	0.000	0.000
32	A	45	PHE	0	0.018	0.005	12.282	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	46	ARG	1	0.807	0.845	18.407	0.183	0.183	0.000	0.000	0.000	0.000
34	A	47	ASP	-1	-0.699	-0.806	22.156	-0.033	-0.033	0.000	0.000	0.000	0.000
35	A	48	SER	0	-0.138	-0.110	24.842	0.001	0.001	0.000	0.000	0.000	0.000
36	A	49	SER	0	-0.078	-0.069	27.440	0.003	0.003	0.000	0.000	0.000	0.000
37	A	50	TYR	0	-0.036	0.001	27.592	0.003	0.003	0.000	0.000	0.000	0.000
38	A	51	SER	0	-0.032	-0.055	29.608	-0.007	-0.007	0.000	0.000	0.000	0.000
39	A	52	ALA	0	-0.028	-0.032	32.894	0.003	0.003	0.000	0.000	0.000	0.000
40	A	53	GLU	-1	-0.998	-1.008	34.784	-0.015	-0.015	0.000	0.000	0.000	0.000
41	A	54	ASP	-1	-0.883	-0.893	34.530	-0.021	-0.021	0.000	0.000	0.000	0.000
42	A	55	GLY	0	-0.065	-0.018	32.091	0.005	0.005	0.000	0.000	0.000	0.000
43	A	56	GLY	0	0.085	0.033	29.175	-0.005	-0.005	0.000	0.000	0.000	0.000
44	A	57	PHE	0	-0.108	-0.069	23.655	0.007	0.007	0.000	0.000	0.000	0.000
45	A	58	HIS	1	0.810	0.888	23.877	0.017	0.017	0.000	0.000	0.000	0.000
46	A	59	PRO	0	0.023	0.015	22.274	0.000	0.000	0.000	0.000	0.000	0.000
47	A	60	VAL	0	-0.037	-0.016	16.821	0.008	0.008	0.000	0.000	0.000	0.000
48	A	61	GLU	-1	-0.858	-0.900	17.054	-0.269	-0.269	0.000	0.000	0.000	0.000
49	A	62	ILE	0	-0.028	-0.015	11.283	0.027	0.027	0.000	0.000	0.000	0.000
50	A	63	ALA	0	0.018	0.034	12.907	-0.057	-0.057	0.000	0.000	0.000	0.000
51	A	64	LEU	0	0.007	0.001	6.728	-0.074	-0.074	0.000	0.000	0.000	0.000
52	A	65	SER	0	0.008	0.001	9.578	0.023	0.023	0.000	0.000	0.000	0.000
53	A	66	GLN	0	-0.050	-0.027	7.207	-0.122	-0.122	0.000	0.000	0.000	0.000
54	A	67	SER	0	0.008	-0.007	7.252	0.337	0.337	0.000	0.000	0.000	0.000
55	A	68	SER	0	-0.014	-0.014	8.964	0.027	0.027	0.000	0.000	0.000	0.000
56	A	69	ASP	-1	-0.929	-0.947	7.444	-1.014	-1.014	0.000	0.000	0.000	0.000
57	A	70	GLY	0	0.004	0.005	6.373	0.108	0.108	0.000	0.000	0.000	0.000
58	A	71	GLN	0	-0.138	-0.069	2.803	-1.643	-0.550	0.271	-0.356	-1.007	-0.001
59	A	72	TRP	0	0.063	0.019	2.469	-0.325	1.030	0.776	-0.441	-1.690	-0.001
60	A	73	CYS	0	-0.014	-0.011	5.126	-0.064	-0.090	-0.001	-0.009	0.036	0.000
61	A	74	ILE	0	-0.023	-0.013	8.054	0.025	0.025	0.000	0.000	0.000	0.000
62	A	75	GLU	-1	-0.821	-0.897	9.764	-0.472	-0.472	0.000	0.000	0.000	0.000
63	A	76	TYR	0	-0.051	-0.054	13.176	0.072	0.072	0.000	0.000	0.000	0.000
64	A	77	ILE	0	-0.034	-0.008	13.104	-0.041	-0.041	0.000	0.000	0.000	0.000
65	A	78	THR	0	-0.023	-0.029	16.196	0.024	0.024	0.000	0.000	0.000	0.000
66	A	79	ASP	-1	-0.777	-0.849	19.649	-0.040	-0.040	0.000	0.000	0.000	0.000
67	A	80	PHE	0	0.051	0.001	20.917	0.004	0.004	0.000	0.000	0.000	0.000
68	A	81	ALA	0	0.001	-0.015	25.147	0.007	0.007	0.000	0.000	0.000	0.000
69	A	82	TYR	0	0.012	0.018	28.534	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	83	VAL	0	-0.008	0.015	31.793	0.008	0.008	0.000	0.000	0.000	0.000
71	A	84	GLY	0	-0.024	-0.017	34.423	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	85	ASN	0	-0.012	-0.010	37.752	0.000	0.000	0.000	0.000	0.000	0.000
73	A	86	HIS	0	-0.034	-0.028	40.502	0.001	0.001	0.000	0.000	0.000	0.000
74	A	87	PHE	0	-0.025	-0.014	39.927	0.000	0.000	0.000	0.000	0.000	0.000
75	A	88	PRO	0	-0.022	0.019	35.678	0.000	0.000	0.000	0.000	0.000	0.000
76	A	89	GLU	-1	-0.916	-0.967	33.021	-0.070	-0.070	0.000	0.000	0.000	0.000
77	A	90	LEU	0	-0.040	-0.024	27.006	0.004	0.004	0.000	0.000	0.000	0.000
78	A	91	GLU	-1	-0.897	-0.945	29.152	-0.058	-0.058	0.000	0.000	0.000	0.000
79	A	92	ARG	1	0.852	0.902	22.810	0.138	0.138	0.000	0.000	0.000	0.000
80	A	93	CYS	0	-0.047	-0.019	25.117	0.012	0.012	0.000	0.000	0.000	0.000
81	A	94	LEU	0	-0.061	-0.034	22.637	0.015	0.015	0.000	0.000	0.000	0.000
82	A	95	ASP	-1	-0.798	-0.863	20.831	-0.144	-0.144	0.000	0.000	0.000	0.000
83	A	96	PHE	0	-0.022	-0.023	17.249	0.036	0.036	0.000	0.000	0.000	0.000
84	A	97	ASP	-1	-0.811	-0.909	17.303	-0.216	-0.216	0.000	0.000	0.000	0.000
85	A	98	PHE	0	-0.003	-0.042	13.761	0.060	0.060	0.000	0.000	0.000	0.000
86	A	99	GLN	0	-0.052	-0.014	15.172	0.055	0.055	0.000	0.000	0.000	0.000
87	A	100	ARG	1	0.836	0.921	17.068	0.123	0.123	0.000	0.000	0.000	0.000
88	A	101	GLY	0	-0.033	-0.005	19.241	0.022	0.022	0.000	0.000	0.000	0.000
89	A	102	ASP	-1	-0.875	-0.932	20.185	-0.035	-0.035	0.000	0.000	0.000	0.000
90	A	103	PHE	0	-0.024	-0.024	21.134	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	104	PHE	0	0.020	0.003	22.916	0.003	0.003	0.000	0.000	0.000	0.000
92	A	105	THR	0	-0.029	-0.014	24.958	0.008	0.008	0.000	0.000	0.000	0.000
93	A	106	ALA	0	0.044	0.031	27.696	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	107	TYR	0	-0.038	-0.024	31.014	0.000	0.000	0.000	0.000	0.000	0.000
95	A	108	HIS	0	-0.028	-0.030	28.812	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	109	GLY	0	0.009	0.017	30.615	0.000	0.000	0.000	0.000	0.000	0.000
97	A	110	TRP	0	-0.013	-0.013	23.876	0.003	0.003	0.000	0.000	0.000	0.000
98	A	111	ASN	0	-0.061	-0.026	26.528	0.008	0.008	0.000	0.000	0.000	0.000
99	A	112	PRO	0	0.089	0.050	24.096	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	113	ILE	0	0.000	-0.001	18.176	0.019	0.019	0.000	0.000	0.000	0.000
101	A	114	VAL	0	-0.033	-0.024	19.534	0.021	0.021	0.000	0.000	0.000	0.000
102	A	115	GLY	0	0.005	0.012	20.476	0.025	0.025	0.000	0.000	0.000	0.000
103	A	116	ASN	0	-0.060	-0.028	22.759	0.008	0.008	0.000	0.000	0.000	0.000
104	A	117	ARG	1	0.879	0.917	23.289	-0.069	-0.069	0.000	0.000	0.000	0.000
105	A	118	ASP	-1	-0.796	-0.889	25.391	0.068	0.068	0.000	0.000	0.000	0.000
106	A	119	ALA	0	0.037	0.035	21.882	0.002	0.002	0.000	0.000	0.000	0.000
107	A	120	ARG	1	0.905	0.948	18.863	-0.249	-0.249	0.000	0.000	0.000	0.000
108	A	121	GLU	-1	-0.918	-0.966	21.037	0.169	0.169	0.000	0.000	0.000	0.000
109	A	122	LEU	0	0.012	0.015	23.238	0.006	0.006	0.000	0.000	0.000	0.000
110	A	123	TYR	0	-0.005	-0.036	13.510	-0.028	-0.028	0.000	0.000	0.000	0.000
111	A	124	GLN	0	-0.030	-0.009	18.603	0.046	0.046	0.000	0.000	0.000	0.000
112	A	125	LEU	0	-0.016	0.000	19.661	0.009	0.009	0.000	0.000	0.000	0.000
113	A	126	TRP	0	0.006	0.003	15.527	0.007	0.007	0.000	0.000	0.000	0.000
114	A	127	GLU	-1	-0.729	-0.827	13.298	0.396	0.396	0.000	0.000	0.000	0.000
115	A	128	SER	0	0.009	0.001	17.053	0.016	0.016	0.000	0.000	0.000	0.000
116	A	129	ASN	0	-0.096	-0.049	19.272	-0.010	-0.010	0.000	0.000	0.000	0.000
117	A	130	PHE	0	0.055	0.025	13.531	0.001	0.001	0.000	0.000	0.000	0.000
118	A	131	LEU	0	-0.001	-0.015	12.536	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	132	ALA	0	-0.023	-0.001	16.484	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	133	TYR	0	-0.018	-0.010	19.806	-0.010	-0.010	0.000	0.000	0.000	0.000
121	A	134	VAL	0	0.040	0.020	14.110	-0.011	-0.011	0.000	0.000	0.000	0.000
122	A	135	ALA	0	-0.054	-0.017	16.935	-0.006	-0.006	0.000	0.000	0.000	0.000
123	A	136	THR	0	-0.122	-0.072	17.949	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	137	GLU	-1	-0.962	-0.977	19.513	-0.005	-0.005	0.000	0.000	0.000	0.000
125	A	138	ALA	0	-0.034	-0.014	20.985	-0.007	-0.007	0.000	0.000	0.000	0.000
126	A	139	PHE	0	-0.062	-0.044	18.348	-0.007	-0.007	0.000	0.000	0.000	0.000
127	A	140	ASP	-1	-0.784	-0.838	20.750	-0.070	-0.070	0.000	0.000	0.000	0.000
128	A	141	ASP	-1	-0.835	-0.881	21.382	-0.157	-0.157	0.000	0.000	0.000	0.000
129	A	142	ILE	0	0.005	0.003	14.681	-0.006	-0.006	0.000	0.000	0.000	0.000
130	A	143	SER	0	0.010	0.018	16.962	0.002	0.002	0.000	0.000	0.000	0.000
131	A	144	LEU	0	-0.028	-0.016	9.971	-0.033	-0.033	0.000	0.000	0.000	0.000
132	A	145	THR	0	-0.017	-0.006	14.472	0.018	0.018	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:LEU)