FMO DATABASE

FMODB ID: G5L11

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1042422.148515
FMO2-HF: Nuclear repulsion	993112.073875
FMO2-HF: Total energy	-49310.07464
FMO2-MP2: Total energy	-49454.839649

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.
-36.257	-40.861	22.818	-10.214	-8.001	-0.093

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 : -0.025 / q_NPA : -0.038

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	0.854	0.904	3.868	1.667	2.639	-0.009	-0.411	-0.552	0.002
4	A	3	PHE	0	-0.035	-0.027	6.454	-0.267	-0.267	0.000	0.000	0.000	0.000
5	A	4	GLU	-1	-0.763	-0.876	9.458	-0.048	-0.048	0.000	0.000	0.000	0.000
6	A	5	ASN	0	-0.052	-0.036	12.383	0.021	0.021	0.000	0.000	0.000	0.000
7	A	6	THR	0	0.038	0.027	13.893	0.010	0.010	0.000	0.000	0.000	0.000
8	A	7	GLY	0	0.032	0.019	16.531	-0.007	-0.007	0.000	0.000	0.000	0.000
9	A	8	LEU	0	0.000	0.007	15.051	-0.006	-0.006	0.000	0.000	0.000	0.000
10	A	9	GLU	-1	-0.836	-0.897	13.637	0.282	0.282	0.000	0.000	0.000	0.000
11	A	10	ASN	0	-0.017	-0.017	17.290	0.001	0.001	0.000	0.000	0.000	0.000
12	A	11	GLN	0	-0.019	-0.004	20.037	-0.036	-0.036	0.000	0.000	0.000	0.000
13	A	12	THR	0	-0.009	0.000	21.478	0.025	0.025	0.000	0.000	0.000	0.000
14	A	13	VAL	0	0.019	0.006	21.901	-0.014	-0.014	0.000	0.000	0.000	0.000
15	A	14	GLU	-1	-0.723	-0.818	24.475	0.177	0.177	0.000	0.000	0.000	0.000
16	A	15	LEU	0	0.003	-0.005	22.135	0.006	0.006	0.000	0.000	0.000	0.000
17	A	16	SER	0	-0.044	-0.031	24.663	0.013	0.013	0.000	0.000	0.000	0.000
18	A	17	ARG	1	0.938	0.948	26.815	-0.149	-0.149	0.000	0.000	0.000	0.000
19	A	18	LEU	0	-0.012	0.002	19.014	0.004	0.004	0.000	0.000	0.000	0.000
20	A	19	ASP	-1	-0.744	-0.829	22.240	0.347	0.347	0.000	0.000	0.000	0.000
21	A	20	ASP	-1	-0.886	-0.937	23.603	0.191	0.191	0.000	0.000	0.000	0.000
22	A	21	ILE	0	-0.079	-0.047	21.388	-0.009	-0.009	0.000	0.000	0.000	0.000
23	A	22	MET	0	-0.047	-0.024	17.423	0.033	0.033	0.000	0.000	0.000	0.000
24	A	23	GLU	-1	-0.920	-0.954	20.606	0.227	0.227	0.000	0.000	0.000	0.000
25	A	24	ARG	1	0.839	0.919	22.928	-0.189	-0.189	0.000	0.000	0.000	0.000
26	A	25	LEU	0	-0.036	-0.004	20.190	-0.019	-0.019	0.000	0.000	0.000	0.000
27	A	26	GLY	0	-0.013	-0.001	19.583	0.019	0.019	0.000	0.000	0.000	0.000
28	A	27	PHE	0	-0.054	-0.045	13.586	0.041	0.041	0.000	0.000	0.000	0.000
29	A	28	VAL	0	0.004	0.005	17.169	-0.053	-0.053	0.000	0.000	0.000	0.000
30	A	29	ARG	1	0.834	0.890	16.950	-0.270	-0.270	0.000	0.000	0.000	0.000
31	A	30	ALA	0	-0.036	-0.020	13.829	-0.012	-0.012	0.000	0.000	0.000	0.000
32	A	31	ALA	0	0.003	-0.019	13.383	0.001	0.001	0.000	0.000	0.000	0.000
33	A	32	GLN	0	0.014	0.006	15.506	-0.023	-0.023	0.000	0.000	0.000	0.000
34	A	33	TRP	0	0.024	0.016	13.674	-0.048	-0.048	0.000	0.000	0.000	0.000
35	A	34	ASP	-1	-0.880	-0.945	15.800	0.557	0.557	0.000	0.000	0.000	0.000
36	A	35	TYR	0	-0.025	-0.029	18.662	-0.024	-0.024	0.000	0.000	0.000	0.000
37	A	36	GLU	-1	-0.916	-0.929	18.698	0.361	0.361	0.000	0.000	0.000	0.000
38	A	37	ARG	1	0.828	0.894	11.994	-0.726	-0.726	0.000	0.000	0.000	0.000
39	A	38	VAL	0	0.014	0.028	17.421	-0.012	-0.012	0.000	0.000	0.000	0.000
40	A	39	THR	0	0.009	-0.008	12.113	0.102	0.102	0.000	0.000	0.000	0.000
41	A	40	TYR	0	-0.027	-0.035	13.900	-0.064	-0.064	0.000	0.000	0.000	0.000
42	A	41	ASP	-1	-0.783	-0.868	11.554	1.230	1.230	0.000	0.000	0.000	0.000
43	A	42	ARG	1	0.905	0.963	13.157	-0.443	-0.443	0.000	0.000	0.000	0.000
44	A	43	LYS	1	0.857	0.906	12.672	-0.549	-0.549	0.000	0.000	0.000	0.000
45	A	44	TYR	0	0.033	0.010	12.375	-0.111	-0.111	0.000	0.000	0.000	0.000
46	A	45	VAL	0	-0.016	-0.001	13.136	-0.020	-0.020	0.000	0.000	0.000	0.000
47	A	46	VAL	0	-0.033	-0.014	12.667	-0.017	-0.017	0.000	0.000	0.000	0.000
48	A	47	LYS	1	0.951	0.982	15.781	0.248	0.248	0.000	0.000	0.000	0.000
49	A	48	GLU	-1	-0.880	-0.953	13.039	-0.295	-0.295	0.000	0.000	0.000	0.000
50	A	49	GLY	0	0.049	0.033	12.683	-0.082	-0.082	0.000	0.000	0.000	0.000
51	A	50	THR	0	-0.117	-0.065	11.440	0.077	0.077	0.000	0.000	0.000	0.000
52	A	51	TYR	0	0.098	0.054	7.051	-0.057	-0.057	0.000	0.000	0.000	0.000
53	A	52	TYR	0	-0.072	-0.045	6.601	0.111	0.111	0.000	0.000	0.000	0.000
54	A	53	LEU	0	-0.004	0.027	8.137	0.600	0.600	0.000	0.000	0.000	0.000
55	A	54	ARG	1	0.861	0.901	8.307	-1.700	-1.700	0.000	0.000	0.000	0.000
56	A	55	VAL	0	0.031	0.021	9.978	0.062	0.062	0.000	0.000	0.000	0.000
57	A	56	GLN	0	0.009	-0.011	11.621	0.039	0.039	0.000	0.000	0.000	0.000
58	A	57	GLY	0	0.018	0.009	13.394	-0.045	-0.045	0.000	0.000	0.000	0.000
59	A	58	TYR	0	0.000	0.009	16.278	0.023	0.023	0.000	0.000	0.000	0.000
60	A	59	ALA	0	0.039	0.020	18.627	-0.025	-0.025	0.000	0.000	0.000	0.000
61	A	60	ILE	0	-0.064	-0.028	22.413	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	61	GLU	-1	-0.852	-0.915	24.158	0.147	0.147	0.000	0.000	0.000	0.000
63	A	62	GLY	0	-0.014	-0.003	26.413	0.012	0.012	0.000	0.000	0.000	0.000
64	A	63	ASN	0	-0.049	-0.051	25.407	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	64	VAL	0	0.046	0.022	20.829	-0.011	-0.011	0.000	0.000	0.000	0.000
66	A	65	ASP	-1	-0.883	-0.924	23.745	0.259	0.259	0.000	0.000	0.000	0.000
67	A	66	SER	0	-0.063	-0.018	26.856	-0.022	-0.022	0.000	0.000	0.000	0.000
68	A	67	ARG	1	0.847	0.897	27.773	-0.155	-0.155	0.000	0.000	0.000	0.000
69	A	68	TYR	0	-0.097	-0.063	29.535	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	69	ALA	0	0.068	0.034	25.219	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	70	LEU	0	-0.028	0.018	25.388	0.006	0.006	0.000	0.000	0.000	0.000
72	A	71	ILE	0	0.008	-0.004	19.441	0.017	0.017	0.000	0.000	0.000	0.000
73	A	72	LYS	1	0.858	0.924	17.239	-0.322	-0.322	0.000	0.000	0.000	0.000
74	A	73	LEU	0	0.011	0.002	16.147	0.048	0.048	0.000	0.000	0.000	0.000
75	A	74	LEU	0	-0.023	-0.018	12.040	-0.059	-0.059	0.000	0.000	0.000	0.000
76	A	75	THR	0	-0.055	-0.049	9.596	0.018	0.018	0.000	0.000	0.000	0.000
77	A	76	PRO	0	-0.027	0.005	9.361	0.172	0.172	0.000	0.000	0.000	0.000
78	A	77	ILE	0	0.021	0.003	4.301	-0.494	-0.377	-0.001	-0.011	-0.105	0.000
79	A	78	MET	0	-0.062	-0.025	5.430	-1.010	-1.010	0.000	0.000	0.000	0.000
80	A	79	GLY	0	0.025	0.029	3.743	3.486	4.103	0.063	-0.293	-0.388	0.001
81	A	80	LYS	1	0.896	0.940	4.464	0.983	1.106	-0.001	-0.008	-0.114	0.000
82	A	81	HIS	0	0.018	0.007	5.953	-0.187	-0.187	0.000	0.000	0.000	0.000
83	A	82	TYR	0	-0.061	-0.041	7.905	0.166	0.166	0.000	0.000	0.000	0.000
84	A	83	TYR	0	-0.059	-0.036	11.786	0.075	0.075	0.000	0.000	0.000	0.000
85	A	84	PRO	0	0.010	-0.020	15.496	0.008	0.008	0.000	0.000	0.000	0.000
86	A	85	HIS	0	-0.013	-0.015	16.378	-0.024	-0.024	0.000	0.000	0.000	0.000
87	A	86	GLY	0	0.056	0.023	12.260	-0.054	-0.054	0.000	0.000	0.000	0.000
88	A	87	VAL	0	-0.060	-0.028	13.037	0.063	0.063	0.000	0.000	0.000	0.000
89	A	88	GLU	-1	-0.858	-0.889	7.042	-2.431	-2.431	0.000	0.000	0.000	0.000
90	A	89	TYR	0	-0.014	-0.004	11.575	0.134	0.134	0.000	0.000	0.000	0.000
91	A	90	GLY	0	-0.016	-0.013	8.265	-0.244	-0.244	0.000	0.000	0.000	0.000
92	A	91	ASP	-1	-0.972	-0.981	8.291	-0.655	-0.655	0.000	0.000	0.000	0.000
93	A	92	ASP	-1	-0.828	-0.918	6.862	-2.216	-2.216	0.000	0.000	0.000	0.000
94	A	93	GLU	-1	-0.843	-0.909	1.665	-36.049	-43.348	22.348	-9.059	-5.990	-0.099
95	A	94	HIS	0	-0.050	-0.025	5.991	0.355	0.355	0.000	0.000	0.000	0.000
96	A	95	PHE	0	0.023	-0.008	2.483	-0.155	0.711	0.418	-0.432	-0.852	0.003
97	A	96	PRO	0	-0.011	0.008	8.329	0.122	0.122	0.000	0.000	0.000	0.000
98	A	97	SER	0	0.088	0.030	11.813	0.135	0.135	0.000	0.000	0.000	0.000
99	A	98	SER	0	0.026	0.021	13.364	0.072	0.072	0.000	0.000	0.000	0.000
100	A	99	LEU	0	0.016	0.011	10.812	0.057	0.057	0.000	0.000	0.000	0.000
101	A	100	VAL	0	0.039	0.019	9.201	0.142	0.142	0.000	0.000	0.000	0.000
102	A	101	SER	0	0.014	-0.005	11.687	0.070	0.070	0.000	0.000	0.000	0.000
103	A	102	GLN	0	-0.063	-0.040	15.185	0.057	0.057	0.000	0.000	0.000	0.000
104	A	103	CYS	0	-0.035	0.001	11.565	0.096	0.096	0.000	0.000	0.000	0.000
105	A	104	GLN	0	0.030	0.009	13.308	0.013	0.013	0.000	0.000	0.000	0.000
106	A	105	ASN	0	-0.008	-0.003	15.204	-0.004	-0.004	0.000	0.000	0.000	0.000
107	A	106	VAL	0	-0.017	-0.003	15.734	0.000	0.000	0.000	0.000	0.000	0.000
108	A	107	LEU	0	-0.002	-0.002	11.918	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	108	ALA	0	0.013	0.017	16.611	-0.016	-0.016	0.000	0.000	0.000	0.000
110	A	109	GLN	0	-0.023	-0.015	19.863	0.000	0.000	0.000	0.000	0.000	0.000
111	A	110	VAL	0	0.033	0.009	17.303	-0.008	-0.008	0.000	0.000	0.000	0.000
112	A	111	LYS	1	0.818	0.901	19.429	-0.182	-0.182	0.000	0.000	0.000	0.000
113	A	112	SER	0	-0.027	-0.018	21.072	-0.017	-0.017	0.000	0.000	0.000	0.000
114	A	113	GLU	-1	-0.810	-0.897	23.587	0.142	0.142	0.000	0.000	0.000	0.000
115	A	114	LEU	0	0.015	0.007	20.075	-0.005	-0.005	0.000	0.000	0.000	0.000
116	A	115	GLU	-1	-0.823	-0.920	24.374	0.118	0.118	0.000	0.000	0.000	0.000
117	A	116	LYS	1	0.807	0.904	26.579	-0.137	-0.137	0.000	0.000	0.000	0.000
118	A	117	ILE	0	0.014	0.013	26.024	-0.006	-0.006	0.000	0.000	0.000	0.000
119	A	118	LYS	1	0.804	0.923	26.490	-0.117	-0.117	0.000	0.000	0.000	0.000
120	A	119	GLU	-1	-0.915	-0.965	28.884	0.101	0.101	0.000	0.000	0.000	0.000
121	A	120	GLU	-1	-1.038	-0.997	31.539	0.106	0.106	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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