FMO DATABASE

FMODB ID: VQ8M1

Calculation Name: 2R5X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2R5X

Chain ID: A

ChEMBL ID:

UniProt ID: Q5L106

Base Structure: X-ray

Registration Date: 2023-09-20

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

DOI:

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	121
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1039308.582743
FMO2-HF: Nuclear repulsion	989999.910454
FMO2-HF: Total energy	-49308.672289
FMO2-MP2: Total energy	-49453.32847

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:0:SER)

Summations of interaction energy for fragment #1(A:0:SER)

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.
-14.906	-8.202	0.716	-3.372	-4.048	-0.018

Interaction energy analysis for fragmet #1(A:0:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.046 / q_NPA : 0.009

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	2	LYS	1	0.968	0.976	3.791	-1.417	-0.365	-0.011	-0.434	-0.607	0.003
4	A	3	PHE	0	-0.049	-0.031	6.147	-0.121	-0.121	0.000	0.000	0.000	0.000
5	A	4	GLU	-1	-0.854	-0.936	9.686	0.500	0.500	0.000	0.000	0.000	0.000
6	A	5	ASN	0	-0.058	-0.038	12.206	-0.023	-0.023	0.000	0.000	0.000	0.000
7	A	6	THR	0	0.057	0.032	13.541	-0.025	-0.025	0.000	0.000	0.000	0.000
8	A	7	GLY	0	0.022	0.004	16.342	-0.023	-0.023	0.000	0.000	0.000	0.000
9	A	8	LEU	0	0.005	0.004	14.495	-0.019	-0.019	0.000	0.000	0.000	0.000
10	A	9	GLU	-1	-0.867	-0.919	13.298	0.398	0.398	0.000	0.000	0.000	0.000
11	A	10	ASN	0	-0.034	-0.024	17.037	-0.008	-0.008	0.000	0.000	0.000	0.000
12	A	11	GLN	0	-0.023	0.005	20.058	-0.031	-0.031	0.000	0.000	0.000	0.000
13	A	12	THR	0	-0.004	0.002	21.210	0.020	0.020	0.000	0.000	0.000	0.000
14	A	13	VAL	0	0.010	0.007	21.659	-0.012	-0.012	0.000	0.000	0.000	0.000
15	A	14	GLU	-1	-0.877	-0.937	24.089	0.140	0.140	0.000	0.000	0.000	0.000
16	A	15	LEU	0	0.013	-0.001	21.652	0.009	0.009	0.000	0.000	0.000	0.000
17	A	16	SER	0	-0.004	0.000	24.005	0.006	0.006	0.000	0.000	0.000	0.000
18	A	17	ARG	1	0.989	0.998	26.300	-0.131	-0.131	0.000	0.000	0.000	0.000
19	A	18	LEU	0	-0.013	-0.001	18.436	0.005	0.005	0.000	0.000	0.000	0.000
20	A	19	ASP	-1	-0.787	-0.920	21.634	0.223	0.223	0.000	0.000	0.000	0.000
21	A	20	ASP	-1	-0.903	-0.937	22.764	0.148	0.148	0.000	0.000	0.000	0.000
22	A	21	ILE	0	-0.067	-0.034	20.771	0.000	0.000	0.000	0.000	0.000	0.000
23	A	22	MET	0	-0.059	-0.037	17.116	0.020	0.020	0.000	0.000	0.000	0.000
24	A	23	GLU	-1	-0.926	-0.952	19.678	0.164	0.164	0.000	0.000	0.000	0.000
25	A	24	ARG	1	0.897	0.950	21.966	-0.163	-0.163	0.000	0.000	0.000	0.000
26	A	25	LEU	0	-0.073	-0.025	19.254	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	26	GLY	0	-0.021	-0.010	18.631	0.025	0.025	0.000	0.000	0.000	0.000
28	A	27	PHE	0	-0.065	-0.034	12.668	0.023	0.023	0.000	0.000	0.000	0.000
29	A	28	VAL	0	0.014	0.009	16.291	-0.031	-0.031	0.000	0.000	0.000	0.000
30	A	29	ARG	1	0.889	0.944	16.080	-0.192	-0.192	0.000	0.000	0.000	0.000
31	A	30	ALA	0	-0.031	-0.019	13.246	-0.016	-0.016	0.000	0.000	0.000	0.000
32	A	31	ALA	0	-0.021	-0.033	12.887	0.006	0.006	0.000	0.000	0.000	0.000
33	A	32	GLN	0	-0.004	-0.011	14.996	0.001	0.001	0.000	0.000	0.000	0.000
34	A	33	TRP	0	0.026	0.024	13.610	-0.023	-0.023	0.000	0.000	0.000	0.000
35	A	34	ASP	-1	-0.910	-0.956	15.678	0.337	0.337	0.000	0.000	0.000	0.000
36	A	35	TYR	0	0.043	0.022	18.409	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	36	GLU	-1	-0.968	-0.973	18.593	0.246	0.246	0.000	0.000	0.000	0.000
38	A	37	ARG	1	0.840	0.903	10.837	-0.610	-0.610	0.000	0.000	0.000	0.000
39	A	38	VAL	0	0.016	0.027	17.201	-0.019	-0.019	0.000	0.000	0.000	0.000
40	A	39	THR	0	0.017	-0.008	11.586	0.075	0.075	0.000	0.000	0.000	0.000
41	A	40	TYR	0	-0.033	-0.011	13.342	-0.044	-0.044	0.000	0.000	0.000	0.000
42	A	41	ASP	-1	-0.786	-0.863	10.625	0.590	0.590	0.000	0.000	0.000	0.000
43	A	42	ARG	1	0.922	0.975	12.009	-0.354	-0.354	0.000	0.000	0.000	0.000
44	A	43	LYS	1	0.930	0.961	12.014	-0.218	-0.218	0.000	0.000	0.000	0.000
45	A	44	TYR	0	0.022	0.008	11.847	-0.066	-0.066	0.000	0.000	0.000	0.000
46	A	45	VAL	0	-0.034	-0.013	13.218	0.026	0.026	0.000	0.000	0.000	0.000
47	A	46	VAL	0	-0.016	-0.009	13.600	-0.006	-0.006	0.000	0.000	0.000	0.000
48	A	47	LYS	1	0.980	0.983	16.491	0.034	0.034	0.000	0.000	0.000	0.000
49	A	48	GLU	-1	-0.906	-0.959	13.132	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	49	GLY	0	0.050	0.038	13.164	-0.045	-0.045	0.000	0.000	0.000	0.000
51	A	50	THR	0	-0.079	-0.032	11.178	0.022	0.022	0.000	0.000	0.000	0.000
52	A	51	TYR	0	0.067	0.043	7.650	-0.054	-0.054	0.000	0.000	0.000	0.000
53	A	52	TYR	0	-0.044	-0.024	6.470	-0.105	-0.105	0.000	0.000	0.000	0.000
54	A	53	LEU	0	-0.008	0.010	7.252	0.273	0.273	0.000	0.000	0.000	0.000
55	A	54	ARG	1	0.844	0.880	7.254	-0.756	-0.756	0.000	0.000	0.000	0.000
56	A	55	VAL	0	0.020	0.007	9.144	0.072	0.072	0.000	0.000	0.000	0.000
57	A	56	GLN	0	0.011	-0.007	10.997	0.056	0.056	0.000	0.000	0.000	0.000
58	A	57	GLY	0	0.028	0.014	13.038	0.008	0.008	0.000	0.000	0.000	0.000
59	A	58	TYR	0	0.018	0.022	16.253	0.009	0.009	0.000	0.000	0.000	0.000
60	A	59	ALA	0	0.028	0.009	18.521	-0.010	-0.010	0.000	0.000	0.000	0.000
61	A	60	ILE	0	-0.067	-0.024	22.297	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	61	GLU	-1	-0.894	-0.949	23.823	0.129	0.129	0.000	0.000	0.000	0.000
63	A	62	GLY	0	-0.018	0.006	26.477	0.006	0.006	0.000	0.000	0.000	0.000
64	A	63	ASN	0	0.010	-0.018	25.455	0.001	0.001	0.000	0.000	0.000	0.000
65	A	64	VAL	0	0.036	0.014	20.533	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	65	ASP	-1	-0.948	-0.961	23.611	0.156	0.156	0.000	0.000	0.000	0.000
67	A	66	SER	0	-0.077	-0.024	26.469	-0.015	-0.015	0.000	0.000	0.000	0.000
68	A	67	ARG	1	0.962	0.978	27.197	-0.108	-0.108	0.000	0.000	0.000	0.000
69	A	68	TYR	0	-0.038	-0.016	28.323	0.007	0.007	0.000	0.000	0.000	0.000
70	A	69	ALA	0	0.050	0.021	25.048	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	70	LEU	0	-0.010	0.006	25.224	0.004	0.004	0.000	0.000	0.000	0.000
72	A	71	ILE	0	0.001	-0.005	19.183	0.012	0.012	0.000	0.000	0.000	0.000
73	A	72	LYS	1	0.912	0.965	16.352	-0.363	-0.363	0.000	0.000	0.000	0.000
74	A	73	LEU	0	-0.006	-0.012	15.741	0.032	0.032	0.000	0.000	0.000	0.000
75	A	74	LEU	0	-0.031	-0.027	11.761	-0.014	-0.014	0.000	0.000	0.000	0.000
76	A	75	THR	0	-0.033	-0.031	8.802	0.005	0.005	0.000	0.000	0.000	0.000
77	A	76	PRO	0	-0.028	0.003	9.025	0.129	0.129	0.000	0.000	0.000	0.000
78	A	77	ILE	0	0.003	0.000	3.624	-0.221	0.000	0.002	-0.037	-0.186	0.000
79	A	78	MET	0	-0.032	-0.025	4.354	-0.751	-0.632	-0.001	-0.018	-0.100	0.000
80	A	79	GLY	0	0.006	0.022	3.145	2.559	3.434	0.224	-0.496	-0.603	-0.002
81	A	80	LYS	1	0.900	0.932	4.166	0.151	0.221	-0.001	-0.003	-0.066	0.000
82	A	81	HIS	0	-0.006	0.000	6.311	-0.451	-0.451	0.000	0.000	0.000	0.000
83	A	82	TYR	0	-0.039	-0.001	8.384	0.285	0.285	0.000	0.000	0.000	0.000
84	A	83	TYR	0	-0.092	-0.053	11.940	-0.018	-0.018	0.000	0.000	0.000	0.000
85	A	84	PRO	0	-0.001	-0.011	15.549	0.025	0.025	0.000	0.000	0.000	0.000
86	A	85	HIS	0	-0.070	-0.075	15.697	0.010	0.010	0.000	0.000	0.000	0.000
87	A	86	GLY	0	0.126	0.063	12.758	0.006	0.006	0.000	0.000	0.000	0.000
88	A	87	VAL	0	-0.053	-0.048	13.748	-0.032	-0.032	0.000	0.000	0.000	0.000
89	A	88	GLU	-1	-0.827	-0.866	7.813	-1.416	-1.416	0.000	0.000	0.000	0.000
90	A	89	TYR	0	-0.017	-0.005	12.394	0.036	0.036	0.000	0.000	0.000	0.000
91	A	90	GLY	0	-0.021	-0.019	9.780	-0.153	-0.153	0.000	0.000	0.000	0.000
92	A	91	ASP	-1	-0.968	-0.988	9.020	-1.041	-1.041	0.000	0.000	0.000	0.000
93	A	92	ASP	-1	-0.909	-0.949	6.897	-2.290	-2.290	0.000	0.000	0.000	0.000
94	A	93	GLU	-1	-0.941	-0.967	2.813	-9.534	-5.922	0.339	-2.058	-1.893	-0.022
95	A	94	HIS	0	-0.010	0.001	6.707	0.267	0.267	0.000	0.000	0.000	0.000
96	A	95	PHE	0	0.023	-0.012	3.204	-1.109	-0.354	0.164	-0.326	-0.593	0.003
97	A	96	PRO	0	-0.012	0.006	9.117	-0.127	-0.127	0.000	0.000	0.000	0.000
98	A	97	SER	0	0.072	0.018	12.152	0.096	0.096	0.000	0.000	0.000	0.000
99	A	98	SER	0	0.010	0.002	14.165	0.045	0.045	0.000	0.000	0.000	0.000
100	A	99	LEU	0	0.051	0.016	10.645	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	100	VAL	0	0.035	0.016	9.503	0.075	0.075	0.000	0.000	0.000	0.000
102	A	101	SER	0	-0.005	-0.001	11.832	-0.012	-0.012	0.000	0.000	0.000	0.000
103	A	102	GLN	0	-0.032	-0.017	14.861	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	103	CYS	0	-0.019	-0.002	10.825	0.025	0.025	0.000	0.000	0.000	0.000
105	A	104	GLN	0	0.027	0.006	12.839	-0.030	-0.030	0.000	0.000	0.000	0.000
106	A	105	ASN	0	-0.016	-0.005	14.559	-0.024	-0.024	0.000	0.000	0.000	0.000
107	A	106	VAL	0	-0.013	0.002	14.969	-0.018	-0.018	0.000	0.000	0.000	0.000
108	A	107	LEU	0	0.002	-0.002	11.091	-0.019	-0.019	0.000	0.000	0.000	0.000
109	A	108	ALA	0	0.014	0.019	15.753	-0.021	-0.021	0.000	0.000	0.000	0.000
110	A	109	GLN	0	-0.021	-0.017	19.085	-0.011	-0.011	0.000	0.000	0.000	0.000
111	A	110	VAL	0	0.024	0.014	16.208	-0.013	-0.013	0.000	0.000	0.000	0.000
112	A	111	LYS	1	0.825	0.902	19.120	-0.229	-0.229	0.000	0.000	0.000	0.000
113	A	112	SER	0	-0.028	-0.017	20.607	-0.018	-0.018	0.000	0.000	0.000	0.000
114	A	113	GLU	-1	-0.831	-0.924	22.865	0.141	0.141	0.000	0.000	0.000	0.000
115	A	114	LEU	0	-0.020	-0.015	19.666	-0.008	-0.008	0.000	0.000	0.000	0.000
116	A	115	GLU	-1	-0.919	-0.977	24.044	0.151	0.151	0.000	0.000	0.000	0.000
117	A	116	LYS	1	0.830	0.927	26.387	-0.147	-0.147	0.000	0.000	0.000	0.000
118	A	117	ILE	0	0.009	0.014	25.886	-0.007	-0.007	0.000	0.000	0.000	0.000
119	A	118	LYS	1	0.894	0.964	25.785	-0.156	-0.156	0.000	0.000	0.000	0.000
120	A	119	GLU	-1	-0.952	-0.975	28.920	0.108	0.108	0.000	0.000	0.000	0.000
121	A	120	GLU	-1	-1.035	-1.003	31.310	0.098	0.098	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:0:SER)