FMO DATABASE

FMODB ID: 5JRLZ

Calculation Name: 2H3R-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2H3R

Chain ID: B

ChEMBL ID:

UniProt ID: P88989

Base Structure: X-ray

Registration Date: 2023-09-22

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	88
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-453684.710397
FMO2-HF: Nuclear repulsion	419027.435627
FMO2-HF: Total energy	-34657.27477
FMO2-MP2: Total energy	-34757.752174

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(B:8:LYS)

Summations of interaction energy for fragment #1(B:8:LYS)

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.
29.19	33.862	1.919	-2.474	-4.117	0.001

Interaction energy analysis for fragmet #1(B:8:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.077 / q_NPA : 1.025

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

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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	B	10	TYR	0	0.025	0.011	3.127	-0.182	1.651	0.056	-0.590	-1.299	0.005
4	B	11	GLU	-1	-0.907	-0.958	2.187	-44.787	-43.533	1.806	-1.390	-1.670	-0.003
5	B	12	GLU	-1	-0.856	-0.920	3.162	-54.685	-53.100	0.057	-0.494	-1.148	-0.001
6	B	13	MET	0	0.012	0.013	5.814	5.017	5.017	0.000	0.000	0.000	0.000
7	B	14	VAL	0	-0.001	0.004	6.976	2.769	2.769	0.000	0.000	0.000	0.000
8	B	15	LYS	1	0.849	0.913	5.535	48.642	48.642	0.000	0.000	0.000	0.000
9	B	16	GLU	-1	-0.927	-0.961	9.611	-22.368	-22.368	0.000	0.000	0.000	0.000
10	B	17	VAL	0	-0.031	-0.019	11.562	2.320	2.320	0.000	0.000	0.000	0.000
11	B	18	GLU	-1	-0.929	-0.963	12.898	-15.681	-15.681	0.000	0.000	0.000	0.000
12	B	19	ARG	1	0.953	0.972	9.598	27.594	27.594	0.000	0.000	0.000	0.000
13	B	20	LEU	0	0.055	0.022	15.154	1.418	1.418	0.000	0.000	0.000	0.000
14	B	21	LYS	1	0.889	0.953	16.985	17.032	17.032	0.000	0.000	0.000	0.000
15	B	22	LEU	0	-0.030	-0.010	17.386	1.121	1.121	0.000	0.000	0.000	0.000
16	B	23	GLU	-1	-0.925	-0.957	19.316	-14.823	-14.823	0.000	0.000	0.000	0.000
17	B	24	ASN	0	0.005	-0.015	20.951	0.717	0.717	0.000	0.000	0.000	0.000
18	B	25	LYS	1	0.927	0.975	22.995	12.593	12.593	0.000	0.000	0.000	0.000
19	B	26	THR	0	0.053	0.026	24.106	0.737	0.737	0.000	0.000	0.000	0.000
20	B	27	LEU	0	0.015	0.002	23.566	0.616	0.616	0.000	0.000	0.000	0.000
21	B	28	LYS	1	0.903	0.949	25.845	11.980	11.980	0.000	0.000	0.000	0.000
22	B	29	GLN	0	-0.042	-0.026	28.774	0.225	0.225	0.000	0.000	0.000	0.000
23	B	30	LYS	1	0.998	0.981	27.455	11.647	11.647	0.000	0.000	0.000	0.000
24	B	31	VAL	0	0.018	0.020	30.309	0.276	0.276	0.000	0.000	0.000	0.000
25	B	32	LYS	1	0.908	0.969	32.054	9.799	9.799	0.000	0.000	0.000	0.000
26	B	33	SER	0	-0.076	-0.017	34.836	0.303	0.303	0.000	0.000	0.000	0.000
27	B	34	SER	0	-0.004	0.004	35.821	0.004	0.004	0.000	0.000	0.000	0.000
28	B	42	SER	0	0.061	0.030	37.061	0.137	0.137	0.000	0.000	0.000	0.000
29	B	43	ILE	0	-0.043	-0.028	30.733	-0.139	-0.139	0.000	0.000	0.000	0.000
30	B	44	LEU	0	0.045	0.030	29.816	0.065	0.065	0.000	0.000	0.000	0.000
31	B	45	THR	0	0.009	-0.006	29.344	-0.400	-0.400	0.000	0.000	0.000	0.000
32	B	46	ALA	0	-0.024	-0.027	25.074	0.047	0.047	0.000	0.000	0.000	0.000
33	B	47	ALA	0	0.093	0.036	26.839	0.012	0.012	0.000	0.000	0.000	0.000
34	B	48	LYS	1	0.967	1.006	28.775	8.546	8.546	0.000	0.000	0.000	0.000
35	B	49	ARG	1	0.978	0.968	24.393	11.406	11.406	0.000	0.000	0.000	0.000
36	B	50	GLU	-1	-0.903	-0.944	25.855	-10.571	-10.571	0.000	0.000	0.000	0.000
37	B	51	SER	0	0.002	0.006	28.753	0.239	0.239	0.000	0.000	0.000	0.000
38	B	52	ILE	0	0.044	0.015	32.314	0.218	0.218	0.000	0.000	0.000	0.000
39	B	53	ILE	0	0.016	0.041	28.142	0.199	0.199	0.000	0.000	0.000	0.000
40	B	54	VAL	0	0.030	0.030	29.154	0.170	0.170	0.000	0.000	0.000	0.000
41	B	55	SER	0	-0.042	-0.013	31.527	0.237	0.237	0.000	0.000	0.000	0.000
42	B	56	SER	0	0.007	-0.057	34.120	0.192	0.192	0.000	0.000	0.000	0.000
43	B	57	SER	0	-0.022	-0.018	31.095	0.069	0.069	0.000	0.000	0.000	0.000
44	B	58	ARG	1	0.936	0.978	32.489	8.446	8.446	0.000	0.000	0.000	0.000
45	B	59	ALA	0	0.001	0.025	35.399	0.167	0.167	0.000	0.000	0.000	0.000
46	B	60	LEU	0	0.065	0.014	34.853	0.130	0.130	0.000	0.000	0.000	0.000
47	B	61	GLY	0	0.004	0.008	35.697	0.066	0.066	0.000	0.000	0.000	0.000
48	B	62	ALA	0	0.014	-0.002	36.292	0.129	0.129	0.000	0.000	0.000	0.000
49	B	63	VAL	0	-0.022	0.002	39.647	0.204	0.204	0.000	0.000	0.000	0.000
50	B	64	ALA	0	0.009	-0.009	37.079	0.131	0.131	0.000	0.000	0.000	0.000
51	B	65	MET	0	-0.007	-0.023	37.747	0.027	0.027	0.000	0.000	0.000	0.000
52	B	66	ARG	1	0.969	0.997	40.041	6.688	6.688	0.000	0.000	0.000	0.000
53	B	67	LYS	1	0.849	0.906	41.215	7.227	7.227	0.000	0.000	0.000	0.000
54	B	68	ILE	0	0.008	0.013	37.331	0.071	0.071	0.000	0.000	0.000	0.000
55	B	69	GLU	-1	-0.813	-0.879	41.827	-6.202	-6.202	0.000	0.000	0.000	0.000
56	B	70	ALA	0	-0.017	-0.011	44.434	0.135	0.135	0.000	0.000	0.000	0.000
57	B	71	LYS	1	0.863	0.906	41.954	7.092	7.092	0.000	0.000	0.000	0.000
58	B	72	VAL	0	0.025	0.013	42.117	0.050	0.050	0.000	0.000	0.000	0.000
59	B	73	ARG	1	0.875	0.913	45.001	6.073	6.073	0.000	0.000	0.000	0.000
60	B	74	SER	0	-0.051	-0.014	48.492	0.109	0.109	0.000	0.000	0.000	0.000
61	B	75	ARG	1	0.865	0.915	41.907	6.921	6.921	0.000	0.000	0.000	0.000
62	B	76	ALA	0	0.007	0.017	48.202	-0.017	-0.017	0.000	0.000	0.000	0.000
63	B	77	ALA	0	0.001	0.009	49.607	0.091	0.091	0.000	0.000	0.000	0.000
64	B	78	LYS	1	0.900	0.936	52.824	5.648	5.648	0.000	0.000	0.000	0.000
65	B	79	ALA	0	0.009	0.029	50.411	0.032	0.032	0.000	0.000	0.000	0.000
66	B	80	VAL	0	0.026	0.015	52.493	0.037	0.037	0.000	0.000	0.000	0.000
67	B	81	THR	0	0.007	0.012	53.171	0.019	0.019	0.000	0.000	0.000	0.000
68	B	82	GLU	-1	-0.876	-0.956	49.950	-5.769	-5.769	0.000	0.000	0.000	0.000
69	B	83	GLN	0	-0.007	-0.005	48.517	-0.157	-0.157	0.000	0.000	0.000	0.000
70	B	84	GLU	-1	-0.888	-0.948	47.993	-5.729	-5.729	0.000	0.000	0.000	0.000
71	B	85	LEU	0	0.026	0.001	46.695	-0.105	-0.105	0.000	0.000	0.000	0.000
72	B	86	THR	0	-0.012	0.000	43.424	-0.173	-0.173	0.000	0.000	0.000	0.000
73	B	87	SER	0	-0.031	-0.024	43.389	-0.188	-0.188	0.000	0.000	0.000	0.000
74	B	88	LEU	0	-0.056	-0.015	43.243	-0.165	-0.165	0.000	0.000	0.000	0.000
75	B	89	LEU	0	-0.045	-0.043	41.620	-0.133	-0.133	0.000	0.000	0.000	0.000
76	B	90	GLN	0	-0.053	0.005	37.727	-0.307	-0.307	0.000	0.000	0.000	0.000
77	B	91	SER	0	0.042	0.010	37.193	-0.164	-0.164	0.000	0.000	0.000	0.000
78	B	92	LEU	0	0.001	0.023	38.098	-0.057	-0.057	0.000	0.000	0.000	0.000
79	B	93	THR	0	0.001	0.000	35.915	-0.223	-0.223	0.000	0.000	0.000	0.000
80	B	94	LEU	0	-0.057	-0.039	37.505	0.257	0.257	0.000	0.000	0.000	0.000
81	B	95	ARG	1	0.996	1.011	37.229	7.554	7.554	0.000	0.000	0.000	0.000
82	B	96	VAL	0	-0.019	-0.017	36.618	0.272	0.272	0.000	0.000	0.000	0.000
83	B	97	ASP	-1	-0.852	-0.906	37.205	-7.828	-7.828	0.000	0.000	0.000	0.000
84	B	98	VAL	0	-0.055	-0.008	36.167	0.210	0.210	0.000	0.000	0.000	0.000
85	B	99	SER	0	0.065	0.024	37.981	-0.257	-0.257	0.000	0.000	0.000	0.000
86	B	100	MET	0	-0.028	-0.030	37.302	0.046	0.046	0.000	0.000	0.000	0.000
87	B	101	GLU	-1	-0.960	-0.972	40.069	-7.015	-7.015	0.000	0.000	0.000	0.000
88	B	102	GLU	-1	-0.931	-0.949	42.156	-6.864	-6.864	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:8:LYS)