FMO DATABASE

FMODB ID: 14KMZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1181475.615746
FMO2-HF: Nuclear repulsion	1128474.744549
FMO2-HF: Total energy	-53000.871196
FMO2-MP2: Total energy	-53156.987692

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.
-7.853	-2.551	0.761	-1.643	-4.419	-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 : -0.028 / q_NPA : -0.025

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	0.853	0.910	2.953	-0.578	1.141	0.032	-0.681	-1.069	0.002
4	A	8	PRO	0	0.032	0.047	5.755	-0.345	-0.345	0.000	0.000	0.000	0.000
5	A	9	THR	0	0.041	0.014	8.696	-0.153	-0.153	0.000	0.000	0.000	0.000
6	A	10	HIS	0	-0.018	-0.014	12.267	0.106	0.106	0.000	0.000	0.000	0.000
7	A	11	LEU	0	0.017	0.024	14.625	-0.016	-0.016	0.000	0.000	0.000	0.000
8	A	12	PRO	0	-0.069	-0.021	13.814	0.076	0.076	0.000	0.000	0.000	0.000
9	A	13	ILE	0	-0.010	0.005	9.757	-0.001	-0.001	0.000	0.000	0.000	0.000
10	A	14	SER	0	-0.045	-0.031	11.336	0.263	0.263	0.000	0.000	0.000	0.000
11	A	15	LYS	1	0.933	0.947	8.084	-2.002	-2.002	0.000	0.000	0.000	0.000
12	A	16	PRO	0	0.001	-0.003	8.719	0.054	0.054	0.000	0.000	0.000	0.000
13	A	17	PHE	0	0.098	0.059	9.889	-0.103	-0.103	0.000	0.000	0.000	0.000
14	A	18	HIS	0	0.006	-0.006	4.813	0.458	0.458	0.000	0.000	0.000	0.000
15	A	19	ALA	0	-0.028	-0.010	5.311	-0.456	-0.456	0.000	0.000	0.000	0.000
16	A	20	LEU	0	0.033	0.032	7.001	-0.216	-0.216	0.000	0.000	0.000	0.000
17	A	21	LEU	0	0.003	0.001	6.024	-0.153	-0.153	0.000	0.000	0.000	0.000
18	A	22	ALA	0	-0.030	-0.039	2.692	-0.959	-0.458	0.298	-0.165	-0.635	0.000
19	A	23	ASN	0	-0.036	-0.015	3.899	-0.238	-0.137	0.001	0.006	-0.107	0.000
20	A	24	ILE	0	0.090	0.037	7.267	-0.050	-0.050	0.000	0.000	0.000	0.000
21	A	25	LEU	0	-0.030	0.002	3.532	-0.344	-0.101	0.007	-0.042	-0.208	0.000
22	A	26	SER	0	-0.058	-0.036	5.489	0.257	0.257	0.000	0.000	0.000	0.000
23	A	27	GLU	-1	-0.945	-0.976	7.008	-0.177	-0.177	0.000	0.000	0.000	0.000
24	A	28	HIS	0	-0.003	0.013	9.731	0.096	0.096	0.000	0.000	0.000	0.000
25	A	29	GLN	0	-0.107	-0.051	6.341	-0.222	-0.222	0.000	0.000	0.000	0.000
26	A	30	ALA	0	-0.051	-0.012	10.054	0.085	0.085	0.000	0.000	0.000	0.000
27	A	40	GLU	-1	-0.996	-1.021	12.001	-0.552	-0.552	0.000	0.000	0.000	0.000
28	A	41	VAL	0	-0.069	-0.025	9.133	0.023	0.023	0.000	0.000	0.000	0.000
29	A	42	VAL	0	0.066	0.033	12.333	-0.006	-0.006	0.000	0.000	0.000	0.000
30	A	43	MET	0	-0.043	-0.011	8.048	0.039	0.039	0.000	0.000	0.000	0.000
31	A	44	ASN	0	-0.052	-0.029	14.195	0.024	0.024	0.000	0.000	0.000	0.000
32	A	45	PHE	0	0.025	0.010	12.414	-0.007	-0.007	0.000	0.000	0.000	0.000
33	A	46	ARG	1	0.940	0.947	18.459	0.206	0.206	0.000	0.000	0.000	0.000
34	A	47	ASP	-1	-0.684	-0.791	22.206	-0.051	-0.051	0.000	0.000	0.000	0.000
35	A	48	SER	0	-0.140	-0.108	24.922	0.003	0.003	0.000	0.000	0.000	0.000
36	A	49	SER	0	-0.064	-0.073	27.509	0.005	0.005	0.000	0.000	0.000	0.000
37	A	50	TYR	0	-0.040	-0.003	27.701	0.005	0.005	0.000	0.000	0.000	0.000
38	A	51	SER	0	-0.029	-0.029	29.704	-0.006	-0.006	0.000	0.000	0.000	0.000
39	A	52	ALA	0	-0.015	-0.031	32.985	0.004	0.004	0.000	0.000	0.000	0.000
40	A	53	GLU	-1	-1.027	-1.020	34.889	-0.016	-0.016	0.000	0.000	0.000	0.000
41	A	54	ASP	-1	-0.878	-0.903	34.676	-0.027	-0.027	0.000	0.000	0.000	0.000
42	A	55	GLY	0	-0.081	-0.026	32.244	0.005	0.005	0.000	0.000	0.000	0.000
43	A	56	GLY	0	0.088	0.034	29.326	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	57	PHE	0	-0.111	-0.065	23.815	0.009	0.009	0.000	0.000	0.000	0.000
45	A	58	HIS	1	0.815	0.900	24.135	0.021	0.021	0.000	0.000	0.000	0.000
46	A	59	PRO	0	0.009	0.011	22.362	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	60	VAL	0	-0.021	-0.011	16.829	0.011	0.011	0.000	0.000	0.000	0.000
48	A	61	GLU	-1	-0.876	-0.885	17.320	-0.281	-0.281	0.000	0.000	0.000	0.000
49	A	62	ILE	0	-0.026	-0.015	11.503	0.034	0.034	0.000	0.000	0.000	0.000
50	A	63	ALA	0	0.021	0.038	13.086	-0.066	-0.066	0.000	0.000	0.000	0.000
51	A	64	LEU	0	-0.004	-0.002	6.920	-0.057	-0.057	0.000	0.000	0.000	0.000
52	A	65	SER	0	0.039	0.041	9.647	0.004	0.004	0.000	0.000	0.000	0.000
53	A	66	GLN	0	-0.013	-0.027	7.438	-0.106	-0.106	0.000	0.000	0.000	0.000
54	A	67	SER	0	-0.028	-0.011	7.401	0.326	0.326	0.000	0.000	0.000	0.000
55	A	68	SER	0	0.000	-0.008	9.059	-0.020	-0.020	0.000	0.000	0.000	0.000
56	A	69	ASP	-1	-0.939	-0.961	7.754	-0.732	-0.732	0.000	0.000	0.000	0.000
57	A	70	GLY	0	-0.005	-0.001	6.196	0.117	0.117	0.000	0.000	0.000	0.000
58	A	71	GLN	0	-0.096	-0.040	2.937	-1.485	-0.201	0.210	-0.398	-1.096	-0.002
59	A	72	TRP	0	0.052	0.015	2.870	-0.409	1.078	0.214	-0.353	-1.348	-0.001
60	A	73	CYS	0	-0.021	-0.011	5.132	0.147	0.114	-0.001	-0.010	0.044	0.000
61	A	74	ILE	0	-0.022	-0.015	8.205	-0.014	-0.014	0.000	0.000	0.000	0.000
62	A	75	GLU	-1	-0.871	-0.949	10.029	-0.412	-0.412	0.000	0.000	0.000	0.000
63	A	76	TYR	0	-0.049	-0.082	13.392	0.073	0.073	0.000	0.000	0.000	0.000
64	A	77	ILE	0	-0.039	-0.012	13.294	-0.046	-0.046	0.000	0.000	0.000	0.000
65	A	78	THR	0	-0.032	-0.042	16.521	0.027	0.027	0.000	0.000	0.000	0.000
66	A	79	ASP	-1	-0.811	-0.880	19.948	-0.049	-0.049	0.000	0.000	0.000	0.000
67	A	80	PHE	0	0.045	-0.001	21.256	0.007	0.007	0.000	0.000	0.000	0.000
68	A	81	ALA	0	0.012	-0.014	25.360	0.006	0.006	0.000	0.000	0.000	0.000
69	A	82	TYR	0	0.002	0.015	28.653	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	83	VAL	0	0.002	0.020	32.180	0.008	0.008	0.000	0.000	0.000	0.000
71	A	84	GLY	0	-0.024	-0.017	34.665	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	85	ASN	0	-0.012	-0.014	37.950	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	86	HIS	0	-0.019	-0.025	40.711	0.001	0.001	0.000	0.000	0.000	0.000
74	A	87	PHE	0	-0.033	-0.010	40.358	0.000	0.000	0.000	0.000	0.000	0.000
75	A	88	PRO	0	-0.012	0.021	35.798	0.000	0.000	0.000	0.000	0.000	0.000
76	A	89	GLU	-1	-0.914	-0.972	33.173	-0.072	-0.072	0.000	0.000	0.000	0.000
77	A	90	LEU	0	-0.045	-0.028	27.135	0.004	0.004	0.000	0.000	0.000	0.000
78	A	91	GLU	-1	-0.899	-0.943	29.472	-0.055	-0.055	0.000	0.000	0.000	0.000
79	A	92	ARG	1	0.921	0.953	23.874	0.123	0.123	0.000	0.000	0.000	0.000
80	A	93	CYS	0	-0.054	-0.019	25.455	0.012	0.012	0.000	0.000	0.000	0.000
81	A	94	LEU	0	-0.048	-0.033	22.728	0.016	0.016	0.000	0.000	0.000	0.000
82	A	95	ASP	-1	-0.863	-0.906	20.977	-0.132	-0.132	0.000	0.000	0.000	0.000
83	A	96	PHE	0	-0.015	-0.019	17.559	0.040	0.040	0.000	0.000	0.000	0.000
84	A	97	ASP	-1	-0.805	-0.907	17.616	-0.194	-0.194	0.000	0.000	0.000	0.000
85	A	98	PHE	0	-0.027	-0.049	14.067	0.065	0.065	0.000	0.000	0.000	0.000
86	A	99	GLN	0	-0.042	-0.010	15.650	0.052	0.052	0.000	0.000	0.000	0.000
87	A	100	ARG	1	0.908	0.957	17.256	0.116	0.116	0.000	0.000	0.000	0.000
88	A	101	GLY	0	-0.030	0.000	19.334	0.021	0.021	0.000	0.000	0.000	0.000
89	A	102	ASP	-1	-0.929	-0.961	20.263	-0.009	-0.009	0.000	0.000	0.000	0.000
90	A	103	PHE	0	-0.026	-0.026	21.439	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	104	PHE	0	-0.004	-0.010	23.246	0.001	0.001	0.000	0.000	0.000	0.000
92	A	105	THR	0	-0.019	0.013	25.307	0.000	0.000	0.000	0.000	0.000	0.000
93	A	106	ALA	0	0.045	0.022	28.051	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	107	TYR	0	-0.038	-0.027	31.361	0.000	0.000	0.000	0.000	0.000	0.000
95	A	108	HIS	0	-0.012	-0.023	28.996	-0.006	-0.006	0.000	0.000	0.000	0.000
96	A	109	GLY	0	0.011	0.020	30.943	0.001	0.001	0.000	0.000	0.000	0.000
97	A	110	TRP	0	-0.004	-0.007	24.518	0.002	0.002	0.000	0.000	0.000	0.000
98	A	111	ASN	0	-0.064	-0.030	26.840	0.006	0.006	0.000	0.000	0.000	0.000
99	A	112	PRO	0	0.085	0.049	24.176	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	113	ILE	0	-0.002	-0.009	18.302	0.019	0.019	0.000	0.000	0.000	0.000
101	A	114	VAL	0	-0.024	-0.022	19.316	0.020	0.020	0.000	0.000	0.000	0.000
102	A	115	GLY	0	-0.004	0.007	20.555	0.028	0.028	0.000	0.000	0.000	0.000
103	A	116	ASN	0	-0.052	-0.017	22.842	0.003	0.003	0.000	0.000	0.000	0.000
104	A	117	ARG	1	0.975	0.970	23.373	-0.091	-0.091	0.000	0.000	0.000	0.000
105	A	118	ASP	-1	-0.879	-0.944	25.476	0.083	0.083	0.000	0.000	0.000	0.000
106	A	119	ALA	0	0.029	0.027	21.942	0.001	0.001	0.000	0.000	0.000	0.000
107	A	120	ARG	1	0.953	0.975	19.056	-0.282	-0.282	0.000	0.000	0.000	0.000
108	A	121	GLU	-1	-0.954	-0.984	21.116	0.174	0.174	0.000	0.000	0.000	0.000
109	A	122	LEU	0	0.016	0.016	23.307	0.003	0.003	0.000	0.000	0.000	0.000
110	A	123	TYR	0	-0.004	-0.023	13.529	-0.030	-0.030	0.000	0.000	0.000	0.000
111	A	124	GLN	0	-0.057	-0.033	18.677	0.052	0.052	0.000	0.000	0.000	0.000
112	A	125	LEU	0	-0.027	-0.006	19.737	0.006	0.006	0.000	0.000	0.000	0.000
113	A	126	TRP	0	0.019	0.021	15.544	0.005	0.005	0.000	0.000	0.000	0.000
114	A	127	GLU	-1	-0.745	-0.864	13.427	0.419	0.419	0.000	0.000	0.000	0.000
115	A	128	SER	0	-0.006	-0.006	17.350	0.010	0.010	0.000	0.000	0.000	0.000
116	A	129	ASN	0	-0.039	-0.013	19.462	0.004	0.004	0.000	0.000	0.000	0.000
117	A	130	PHE	0	0.031	0.013	13.575	-0.002	-0.002	0.000	0.000	0.000	0.000
118	A	131	LEU	0	0.003	-0.015	12.830	-0.006	-0.006	0.000	0.000	0.000	0.000
119	A	132	ALA	0	-0.013	0.003	16.757	-0.006	-0.006	0.000	0.000	0.000	0.000
120	A	133	TYR	0	-0.013	-0.009	19.847	-0.009	-0.009	0.000	0.000	0.000	0.000
121	A	134	VAL	0	0.031	0.015	14.330	-0.013	-0.013	0.000	0.000	0.000	0.000
122	A	135	ALA	0	-0.053	-0.018	17.179	-0.010	-0.010	0.000	0.000	0.000	0.000
123	A	136	THR	0	-0.123	-0.059	18.169	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	137	GLU	-1	-0.956	-0.977	19.808	-0.035	-0.035	0.000	0.000	0.000	0.000
125	A	138	ALA	0	-0.036	-0.018	21.129	-0.005	-0.005	0.000	0.000	0.000	0.000
126	A	139	PHE	0	-0.069	-0.046	18.627	-0.005	-0.005	0.000	0.000	0.000	0.000
127	A	140	ASP	-1	-0.787	-0.842	20.819	-0.092	-0.092	0.000	0.000	0.000	0.000
128	A	141	ASP	-1	-0.961	-0.974	21.633	-0.182	-0.182	0.000	0.000	0.000	0.000
129	A	142	ILE	0	0.009	0.001	14.729	-0.004	-0.004	0.000	0.000	0.000	0.000
130	A	143	SER	0	-0.024	-0.002	17.175	-0.007	-0.007	0.000	0.000	0.000	0.000
131	A	144	LEU	0	-0.002	-0.008	10.004	-0.032	-0.032	0.000	0.000	0.000	0.000
132	A	145	THR	0	-0.025	-0.011	14.627	0.019	0.019	0.000	0.000	0.000	0.000

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