FMO DATABASE

FMODB ID: 6Y8LZ

Calculation Name: 2V9A-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2V9A

Chain ID: A

ChEMBL ID:

UniProt ID: P52687

Base Structure: X-ray

Registration Date: 2023-09-23

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	OptAll
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	105
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-742321.322141
FMO2-HF: Nuclear repulsion	702323.342122
FMO2-HF: Total energy	-39997.980019
FMO2-MP2: Total energy	-40114.633336

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:4:THR)

Summations of interaction energy for fragment #1(A:4:THR)

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.
-7.158	-3.409	0.595	-1.472	-2.872	0.006

Interaction energy analysis for fragmet #1(A:4:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : -0.011

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	6	GLU	-1	-0.810	-0.876	3.324	3.669	5.305	0.006	-0.672	-0.970	0.001
4	A	7	ARG	1	0.787	0.867	2.778	-7.529	-5.713	0.589	-0.758	-1.647	0.005
5	A	8	LEU	0	0.033	0.040	4.139	-0.791	-0.494	0.000	-0.042	-0.255	0.000
6	A	9	HIS	0	-0.051	-0.047	6.687	-0.180	-0.180	0.000	0.000	0.000	0.000
7	A	10	TYR	0	0.050	0.017	7.282	-0.136	-0.136	0.000	0.000	0.000	0.000
8	A	11	GLN	0	0.008	0.016	9.505	-0.138	-0.138	0.000	0.000	0.000	0.000
9	A	12	VAL	0	0.025	0.015	11.537	-0.003	-0.003	0.000	0.000	0.000	0.000
10	A	13	GLY	0	-0.009	-0.012	13.519	0.018	0.018	0.000	0.000	0.000	0.000
11	A	14	GLN	0	-0.003	-0.006	14.881	-0.011	-0.011	0.000	0.000	0.000	0.000
12	A	15	ARG	1	0.836	0.883	16.264	0.153	0.153	0.000	0.000	0.000	0.000
13	A	16	ALA	0	0.015	0.013	18.002	0.005	0.005	0.000	0.000	0.000	0.000
14	A	17	LEU	0	-0.044	-0.023	19.294	0.009	0.009	0.000	0.000	0.000	0.000
15	A	18	ILE	0	0.038	0.021	19.525	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	19	GLN	0	0.053	0.047	21.500	0.017	0.017	0.000	0.000	0.000	0.000
17	A	20	ALA	0	0.005	-0.001	23.752	0.002	0.002	0.000	0.000	0.000	0.000
18	A	21	MET	0	-0.038	-0.025	24.069	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	22	GLN	0	-0.007	-0.004	26.094	0.003	0.003	0.000	0.000	0.000	0.000
20	A	23	ILE	0	0.012	-0.002	26.966	0.001	0.001	0.000	0.000	0.000	0.000
21	A	24	SER	0	-0.050	-0.037	29.574	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	25	ALA	0	0.031	0.018	31.440	0.004	0.004	0.000	0.000	0.000	0.000
23	A	26	MET	0	-0.019	0.002	30.502	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	27	PRO	0	0.057	0.024	34.954	0.006	0.006	0.000	0.000	0.000	0.000
25	A	28	GLU	-1	-0.790	-0.875	37.839	-0.006	-0.006	0.000	0.000	0.000	0.000
26	A	29	LEU	0	-0.008	-0.006	33.392	0.004	0.004	0.000	0.000	0.000	0.000
27	A	30	VAL	0	0.001	0.003	36.949	0.006	0.006	0.000	0.000	0.000	0.000
28	A	31	GLU	-1	-0.797	-0.889	38.989	0.014	0.014	0.000	0.000	0.000	0.000
29	A	32	ALA	0	-0.018	-0.004	39.529	0.003	0.003	0.000	0.000	0.000	0.000
30	A	33	VAL	0	-0.044	-0.030	36.773	0.004	0.004	0.000	0.000	0.000	0.000
31	A	34	GLN	0	-0.047	-0.024	40.194	0.001	0.001	0.000	0.000	0.000	0.000
32	A	35	LYS	1	0.810	0.895	43.265	-0.012	-0.012	0.000	0.000	0.000	0.000
33	A	36	ARG	1	0.841	0.910	42.105	-0.055	-0.055	0.000	0.000	0.000	0.000
34	A	37	ASP	-1	-0.803	-0.893	43.248	0.019	0.019	0.000	0.000	0.000	0.000
35	A	38	LEU	0	0.012	-0.022	40.402	0.000	0.000	0.000	0.000	0.000	0.000
36	A	39	ALA	0	-0.018	0.013	40.360	0.000	0.000	0.000	0.000	0.000	0.000
37	A	40	ARG	1	0.856	0.900	40.471	0.001	0.001	0.000	0.000	0.000	0.000
38	A	41	ILE	0	0.007	-0.011	35.946	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	42	LYS	1	0.915	0.966	36.378	-0.029	-0.029	0.000	0.000	0.000	0.000
40	A	43	ALA	0	-0.016	-0.014	36.343	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	44	LEU	0	-0.043	-0.007	35.541	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	45	ILE	0	-0.020	-0.018	30.752	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	46	ASP	-1	-0.818	-0.916	31.406	0.027	0.027	0.000	0.000	0.000	0.000
44	A	47	PRO	0	0.013	0.009	31.753	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	48	MET	0	0.007	0.007	28.209	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	49	ARG	1	0.792	0.892	27.058	-0.047	-0.047	0.000	0.000	0.000	0.000
47	A	50	SER	0	-0.004	0.004	26.801	0.004	0.004	0.000	0.000	0.000	0.000
48	A	51	PHE	0	-0.040	-0.019	26.812	-0.013	-0.013	0.000	0.000	0.000	0.000
49	A	52	SER	0	-0.067	-0.032	22.817	-0.014	-0.014	0.000	0.000	0.000	0.000
50	A	53	ASP	-1	-0.750	-0.843	18.002	-0.138	-0.138	0.000	0.000	0.000	0.000
51	A	54	ALA	0	-0.047	-0.017	19.709	0.021	0.021	0.000	0.000	0.000	0.000
52	A	55	THR	0	0.013	-0.018	19.246	-0.012	-0.012	0.000	0.000	0.000	0.000
53	A	56	TYR	0	-0.052	-0.020	21.944	0.015	0.015	0.000	0.000	0.000	0.000
54	A	57	ILE	0	0.053	0.026	24.352	0.003	0.003	0.000	0.000	0.000	0.000
55	A	58	THR	0	-0.061	-0.020	27.075	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	59	VAL	0	0.080	0.042	29.451	0.001	0.001	0.000	0.000	0.000	0.000
57	A	60	GLY	0	-0.045	-0.004	32.316	0.005	0.005	0.000	0.000	0.000	0.000
58	A	61	ASP	-1	-0.751	-0.850	34.263	0.064	0.064	0.000	0.000	0.000	0.000
59	A	62	ALA	0	0.027	0.028	36.102	0.008	0.008	0.000	0.000	0.000	0.000
60	A	63	SER	0	-0.040	-0.040	37.152	0.005	0.005	0.000	0.000	0.000	0.000
61	A	64	GLY	0	0.007	0.011	34.645	0.007	0.007	0.000	0.000	0.000	0.000
62	A	65	GLN	0	-0.026	-0.012	35.284	0.003	0.003	0.000	0.000	0.000	0.000
63	A	66	ARG	1	0.860	0.914	33.084	-0.113	-0.113	0.000	0.000	0.000	0.000
64	A	67	LEU	0	0.013	0.004	35.121	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	90	ASN	0	-0.013	-0.027	30.731	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	91	ALA	0	0.053	0.020	31.671	0.002	0.002	0.000	0.000	0.000	0.000
67	A	92	LYS	1	0.959	1.005	25.573	-0.175	-0.175	0.000	0.000	0.000	0.000
68	A	93	SER	0	0.041	0.003	25.232	0.009	0.009	0.000	0.000	0.000	0.000
69	A	94	TYR	0	-0.071	-0.041	22.272	0.016	0.016	0.000	0.000	0.000	0.000
70	A	95	VAL	0	0.059	0.030	16.428	-0.013	-0.013	0.000	0.000	0.000	0.000
71	A	96	SER	0	-0.081	-0.021	19.703	0.016	0.016	0.000	0.000	0.000	0.000
72	A	97	VAL	0	0.048	0.012	14.432	-0.011	-0.011	0.000	0.000	0.000	0.000
73	A	98	ARG	1	0.942	0.978	17.698	-0.363	-0.363	0.000	0.000	0.000	0.000
74	A	99	LYS	1	0.944	0.952	10.856	-1.404	-1.404	0.000	0.000	0.000	0.000
75	A	100	GLY	0	0.023	0.018	16.538	-0.025	-0.025	0.000	0.000	0.000	0.000
76	A	101	SER	0	-0.024	-0.008	18.435	-0.056	-0.056	0.000	0.000	0.000	0.000
77	A	102	LEU	0	0.027	0.018	16.994	0.026	0.026	0.000	0.000	0.000	0.000
78	A	103	GLY	0	0.070	0.063	13.602	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	104	SER	0	-0.042	-0.034	12.741	0.092	0.092	0.000	0.000	0.000	0.000
80	A	105	SER	0	-0.021	-0.003	15.153	-0.075	-0.075	0.000	0.000	0.000	0.000
81	A	106	LEU	0	0.002	0.012	12.052	0.038	0.038	0.000	0.000	0.000	0.000
82	A	107	ARG	1	0.904	0.937	16.632	-0.341	-0.341	0.000	0.000	0.000	0.000
83	A	108	GLY	0	0.049	0.037	20.093	0.021	0.021	0.000	0.000	0.000	0.000
84	A	109	LYS	1	0.850	0.912	21.248	-0.239	-0.239	0.000	0.000	0.000	0.000
85	A	110	SER	0	0.045	0.015	24.785	0.002	0.002	0.000	0.000	0.000	0.000
86	A	111	PRO	0	0.014	0.020	27.617	0.000	0.000	0.000	0.000	0.000	0.000
87	A	112	ILE	0	0.011	0.038	31.308	-0.009	-0.009	0.000	0.000	0.000	0.000
88	A	113	GLN	0	-0.008	-0.023	32.595	0.013	0.013	0.000	0.000	0.000	0.000
89	A	114	ASP	-1	-0.762	-0.857	36.905	0.023	0.023	0.000	0.000	0.000	0.000
90	A	115	ALA	0	0.018	0.010	39.959	0.000	0.000	0.000	0.000	0.000	0.000
91	A	116	THR	0	-0.078	-0.069	42.252	0.001	0.001	0.000	0.000	0.000	0.000
92	A	117	GLY	0	-0.008	0.000	38.321	0.002	0.002	0.000	0.000	0.000	0.000
93	A	118	LYS	1	0.919	0.960	37.756	-0.036	-0.036	0.000	0.000	0.000	0.000
94	A	119	VAL	0	-0.007	-0.006	34.688	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	120	ILE	0	-0.001	-0.006	37.134	0.001	0.001	0.000	0.000	0.000	0.000
96	A	121	GLY	0	0.010	-0.004	35.631	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	122	ILE	0	-0.105	-0.032	28.399	0.005	0.005	0.000	0.000	0.000	0.000
98	A	123	VAL	0	0.052	0.040	27.333	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	124	SER	0	-0.074	-0.049	24.321	0.022	0.022	0.000	0.000	0.000	0.000
100	A	125	VAL	0	0.038	0.034	21.899	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	126	GLY	0	-0.008	-0.028	20.759	0.025	0.025	0.000	0.000	0.000	0.000
102	A	127	TYR	0	0.014	-0.011	16.669	-0.034	-0.034	0.000	0.000	0.000	0.000
103	A	128	THR	0	0.023	0.017	15.742	0.047	0.047	0.000	0.000	0.000	0.000
104	A	129	ILE	0	-0.036	-0.009	9.646	-0.070	-0.070	0.000	0.000	0.000	0.000
105	A	130	GLU	-1	-0.900	-0.950	9.894	0.508	0.508	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:4:THR)