FMO DATABASE

FMODB ID: 2N87R

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

Total energy (hartree)

FMO2-HF: Electronic energy	-741797.329296
FMO2-HF: Nuclear repulsion	701799.714757
FMO2-HF: Total energy	-39997.614539
FMO2-MP2: Total energy	-40114.30181

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.
-11.556	-7.115	2.344	-2.531	-4.256	0.013

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 : -0.010 / 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	6	GLU	-1	-0.781	-0.858	3.014	3.302	5.671	0.059	-1.040	-1.388	0.002
4	A	7	ARG	1	0.763	0.851	2.554	-10.754	-8.960	2.285	-1.439	-2.641	0.011
5	A	8	LEU	0	0.040	0.058	4.318	-1.166	-0.888	0.000	-0.052	-0.227	0.000
6	A	9	HIS	0	-0.013	-0.040	6.557	-0.261	-0.261	0.000	0.000	0.000	0.000
7	A	10	TYR	0	0.012	0.009	7.176	-0.053	-0.053	0.000	0.000	0.000	0.000
8	A	11	GLN	0	0.051	0.041	9.705	-0.202	-0.202	0.000	0.000	0.000	0.000
9	A	12	VAL	0	0.026	0.009	11.612	-0.009	-0.009	0.000	0.000	0.000	0.000
10	A	13	GLY	0	-0.039	-0.034	13.059	-0.023	-0.023	0.000	0.000	0.000	0.000
11	A	14	GLN	0	-0.003	-0.007	14.403	-0.013	-0.013	0.000	0.000	0.000	0.000
12	A	15	ARG	1	0.851	0.902	16.083	0.045	0.045	0.000	0.000	0.000	0.000
13	A	16	ALA	0	0.003	0.003	17.659	-0.006	-0.006	0.000	0.000	0.000	0.000
14	A	17	LEU	0	-0.028	-0.013	18.859	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	18	ILE	0	0.042	0.022	19.801	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	19	GLN	0	0.066	0.054	21.730	0.021	0.021	0.000	0.000	0.000	0.000
17	A	20	ALA	0	-0.015	-0.001	23.377	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	21	MET	0	-0.036	-0.029	23.732	-0.006	-0.006	0.000	0.000	0.000	0.000
19	A	22	GLN	0	-0.015	-0.003	26.047	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	23	ILE	0	0.033	0.004	26.603	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	24	SER	0	-0.060	-0.032	29.366	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	25	ALA	0	0.017	0.006	31.252	0.001	0.001	0.000	0.000	0.000	0.000
23	A	26	MET	0	-0.039	-0.006	30.650	-0.007	-0.007	0.000	0.000	0.000	0.000
24	A	27	PRO	0	0.094	0.038	34.881	0.006	0.006	0.000	0.000	0.000	0.000
25	A	28	GLU	-1	-0.793	-0.870	37.995	0.016	0.016	0.000	0.000	0.000	0.000
26	A	29	LEU	0	-0.005	-0.004	33.199	0.004	0.004	0.000	0.000	0.000	0.000
27	A	30	VAL	0	0.002	-0.002	36.397	0.006	0.006	0.000	0.000	0.000	0.000
28	A	31	GLU	-1	-0.821	-0.901	38.580	0.032	0.032	0.000	0.000	0.000	0.000
29	A	32	ALA	0	-0.014	-0.009	39.483	0.002	0.002	0.000	0.000	0.000	0.000
30	A	33	VAL	0	-0.049	-0.034	36.416	0.004	0.004	0.000	0.000	0.000	0.000
31	A	34	GLN	0	-0.046	-0.009	39.848	0.001	0.001	0.000	0.000	0.000	0.000
32	A	35	LYS	1	0.818	0.899	42.898	-0.031	-0.031	0.000	0.000	0.000	0.000
33	A	36	ARG	1	0.856	0.929	41.881	-0.077	-0.077	0.000	0.000	0.000	0.000
34	A	37	ASP	-1	-0.791	-0.894	43.009	0.039	0.039	0.000	0.000	0.000	0.000
35	A	38	LEU	0	-0.003	-0.031	40.053	0.000	0.000	0.000	0.000	0.000	0.000
36	A	39	ALA	0	-0.011	0.012	40.282	0.002	0.002	0.000	0.000	0.000	0.000
37	A	40	ARG	1	0.872	0.909	40.666	-0.021	-0.021	0.000	0.000	0.000	0.000
38	A	41	ILE	0	-0.009	-0.020	35.832	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	42	LYS	1	0.923	0.971	36.342	-0.054	-0.054	0.000	0.000	0.000	0.000
40	A	43	ALA	0	-0.019	-0.008	36.747	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	44	LEU	0	-0.049	-0.014	35.785	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	45	ILE	0	-0.018	-0.022	30.641	0.003	0.003	0.000	0.000	0.000	0.000
43	A	46	ASP	-1	-0.821	-0.906	31.359	0.063	0.063	0.000	0.000	0.000	0.000
44	A	47	PRO	0	0.008	0.009	31.694	0.000	0.000	0.000	0.000	0.000	0.000
45	A	48	MET	0	0.010	0.002	28.437	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	49	ARG	1	0.795	0.898	27.186	-0.086	-0.086	0.000	0.000	0.000	0.000
47	A	50	SER	0	0.028	0.017	26.248	0.003	0.003	0.000	0.000	0.000	0.000
48	A	51	PHE	0	-0.070	-0.021	26.628	-0.011	-0.011	0.000	0.000	0.000	0.000
49	A	52	SER	0	-0.034	-0.009	22.945	-0.009	-0.009	0.000	0.000	0.000	0.000
50	A	53	ASP	-1	-0.761	-0.863	18.251	-0.031	-0.031	0.000	0.000	0.000	0.000
51	A	54	ALA	0	-0.033	-0.014	19.665	0.034	0.034	0.000	0.000	0.000	0.000
52	A	55	THR	0	-0.003	0.009	19.784	0.014	0.014	0.000	0.000	0.000	0.000
53	A	56	TYR	0	-0.009	-0.004	22.013	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	57	ILE	0	0.054	0.034	24.429	0.009	0.009	0.000	0.000	0.000	0.000
55	A	58	THR	0	-0.039	-0.018	27.080	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	59	VAL	0	0.123	0.070	29.581	0.003	0.003	0.000	0.000	0.000	0.000
57	A	60	GLY	0	-0.042	0.045	32.465	0.003	0.003	0.000	0.000	0.000	0.000
58	A	61	ASP	-1	-0.774	-0.882	33.920	0.087	0.087	0.000	0.000	0.000	0.000
59	A	62	ALA	0	0.030	0.020	35.729	0.009	0.009	0.000	0.000	0.000	0.000
60	A	63	SER	0	-0.037	-0.029	37.001	0.004	0.004	0.000	0.000	0.000	0.000
61	A	64	GLY	0	0.014	0.013	34.583	0.009	0.009	0.000	0.000	0.000	0.000
62	A	65	GLN	0	-0.037	-0.017	35.201	0.004	0.004	0.000	0.000	0.000	0.000
63	A	66	ARG	1	0.859	0.912	32.677	-0.145	-0.145	0.000	0.000	0.000	0.000
64	A	67	LEU	0	-0.028	-0.058	34.896	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	90	ASN	0	-0.042	-0.032	30.508	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	91	ALA	0	0.086	0.037	31.860	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	92	LYS	1	0.951	0.990	25.379	-0.215	-0.215	0.000	0.000	0.000	0.000
68	A	93	SER	0	0.045	0.013	24.908	0.010	0.010	0.000	0.000	0.000	0.000
69	A	94	TYR	0	-0.077	-0.037	21.683	0.015	0.015	0.000	0.000	0.000	0.000
70	A	95	VAL	0	0.062	0.029	16.226	-0.013	-0.013	0.000	0.000	0.000	0.000
71	A	96	SER	0	-0.107	-0.037	19.203	0.025	0.025	0.000	0.000	0.000	0.000
72	A	97	VAL	0	0.064	0.015	14.103	0.011	0.011	0.000	0.000	0.000	0.000
73	A	98	ARG	1	0.938	0.981	17.302	-0.398	-0.398	0.000	0.000	0.000	0.000
74	A	99	LYS	1	0.934	0.946	11.016	-1.561	-1.561	0.000	0.000	0.000	0.000
75	A	100	GLY	0	0.017	0.010	16.665	-0.046	-0.046	0.000	0.000	0.000	0.000
76	A	101	SER	0	-0.036	-0.011	18.422	-0.041	-0.041	0.000	0.000	0.000	0.000
77	A	102	LEU	0	0.046	0.036	16.971	0.003	0.003	0.000	0.000	0.000	0.000
78	A	103	GLY	0	0.082	0.065	13.503	-0.008	-0.008	0.000	0.000	0.000	0.000
79	A	104	SER	0	-0.057	-0.038	12.682	0.052	0.052	0.000	0.000	0.000	0.000
80	A	105	SER	0	-0.020	-0.003	15.012	-0.060	-0.060	0.000	0.000	0.000	0.000
81	A	106	LEU	0	-0.007	-0.005	12.064	0.015	0.015	0.000	0.000	0.000	0.000
82	A	107	ARG	1	0.902	0.941	16.779	-0.425	-0.425	0.000	0.000	0.000	0.000
83	A	108	GLY	0	0.054	0.035	20.204	0.017	0.017	0.000	0.000	0.000	0.000
84	A	109	LYS	1	0.874	0.936	21.199	-0.294	-0.294	0.000	0.000	0.000	0.000
85	A	110	SER	0	0.045	0.018	24.659	0.003	0.003	0.000	0.000	0.000	0.000
86	A	111	PRO	0	0.004	0.011	27.406	0.000	0.000	0.000	0.000	0.000	0.000
87	A	112	ILE	0	0.019	0.036	31.120	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	113	GLN	0	-0.014	-0.011	32.215	0.010	0.010	0.000	0.000	0.000	0.000
89	A	114	ASP	-1	-0.780	-0.881	36.520	0.041	0.041	0.000	0.000	0.000	0.000
90	A	115	ALA	0	-0.004	0.001	39.449	0.000	0.000	0.000	0.000	0.000	0.000
91	A	116	THR	0	-0.037	-0.044	41.834	0.000	0.000	0.000	0.000	0.000	0.000
92	A	117	GLY	0	-0.012	-0.001	37.754	0.002	0.002	0.000	0.000	0.000	0.000
93	A	118	LYS	1	0.921	0.959	37.351	-0.056	-0.056	0.000	0.000	0.000	0.000
94	A	119	VAL	0	0.001	-0.008	34.374	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	120	ILE	0	0.009	0.005	36.868	0.002	0.002	0.000	0.000	0.000	0.000
96	A	121	GLY	0	0.010	-0.004	35.442	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	122	ILE	0	-0.109	-0.043	28.333	0.007	0.007	0.000	0.000	0.000	0.000
98	A	123	VAL	0	0.045	0.038	27.239	0.002	0.002	0.000	0.000	0.000	0.000
99	A	124	SER	0	-0.047	-0.043	25.052	0.021	0.021	0.000	0.000	0.000	0.000
100	A	125	VAL	0	0.000	0.013	21.980	0.003	0.003	0.000	0.000	0.000	0.000
101	A	126	GLY	0	-0.031	-0.037	21.175	0.031	0.031	0.000	0.000	0.000	0.000
102	A	127	TYR	0	0.008	-0.034	16.649	-0.034	-0.034	0.000	0.000	0.000	0.000
103	A	128	THR	0	-0.002	-0.024	15.994	0.065	0.065	0.000	0.000	0.000	0.000
104	A	129	ILE	0	-0.037	-0.010	9.430	-0.060	-0.060	0.000	0.000	0.000	0.000
105	A	130	GLU	-1	-0.904	-0.947	9.980	0.621	0.621	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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