FMO DATABASE

FMODB ID: 7GR7K

Calculation Name: 5D6H-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D6H

Chain ID: B

ChEMBL ID:

UniProt ID: Q6XBY4

Base Structure: X-ray

Registration Date: 2023-06-20

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	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	107
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-668521.653816
FMO2-HF: Nuclear repulsion	629043.072854
FMO2-HF: Total energy	-39478.580962
FMO2-MP2: Total energy	-39594.134376

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:7:HIS)

Summations of interaction energy for fragment #1(B:7:HIS)

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.
-12.933	-8.89	2.11	-2.423	-3.729	-0.009

Interaction energy analysis for fragmet #1(B:7:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : -0.002

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	B	9	HIS	0	-0.045	-0.021	2.535	-9.794	-6.042	2.111	-2.401	-3.462	-0.009
4	B	10	SER	0	-0.041	-0.022	3.950	2.081	2.372	-0.001	-0.022	-0.267	0.000
5	B	11	THR	0	-0.014	-0.017	5.893	-0.201	-0.201	0.000	0.000	0.000	0.000
6	B	12	GLY	0	-0.009	0.008	8.753	0.178	0.178	0.000	0.000	0.000	0.000
7	B	13	CYS	0	-0.065	-0.025	10.592	0.094	0.094	0.000	0.000	0.000	0.000
8	B	14	THR	0	-0.014	-0.001	14.180	0.061	0.061	0.000	0.000	0.000	0.000
9	B	15	VAL	0	-0.002	-0.019	16.752	0.066	0.066	0.000	0.000	0.000	0.000
10	B	16	GLY	0	-0.016	0.039	20.142	0.022	0.022	0.000	0.000	0.000	0.000
11	B	17	GLY	0	0.018	0.003	23.000	0.033	0.033	0.000	0.000	0.000	0.000
12	B	18	SER	0	-0.013	-0.020	22.738	0.045	0.045	0.000	0.000	0.000	0.000
13	B	28	GLY	0	0.033	0.023	32.713	0.003	0.003	0.000	0.000	0.000	0.000
14	B	29	THR	0	-0.070	-0.053	32.918	-0.011	-0.011	0.000	0.000	0.000	0.000
15	B	30	LEU	0	0.043	0.021	35.236	0.004	0.004	0.000	0.000	0.000	0.000
16	B	31	ASN	0	-0.007	0.006	38.346	-0.001	-0.001	0.000	0.000	0.000	0.000
17	B	32	PHE	0	0.032	0.038	41.831	0.005	0.005	0.000	0.000	0.000	0.000
18	B	43	LEU	0	0.028	0.015	52.898	-0.001	-0.001	0.000	0.000	0.000	0.000
19	B	44	THR	0	0.013	-0.006	56.242	-0.002	-0.002	0.000	0.000	0.000	0.000
20	B	45	ALA	0	-0.029	-0.014	55.787	0.002	0.002	0.000	0.000	0.000	0.000
21	B	46	GLU	-1	-0.977	-0.974	54.798	-0.137	-0.137	0.000	0.000	0.000	0.000
22	B	47	VAL	0	-0.056	-0.036	55.181	-0.005	-0.005	0.000	0.000	0.000	0.000
23	B	48	ALA	0	0.052	0.038	53.522	0.004	0.004	0.000	0.000	0.000	0.000
24	B	49	SER	0	-0.043	-0.015	48.240	-0.006	-0.006	0.000	0.000	0.000	0.000
25	B	50	ALA	0	-0.018	0.005	47.235	0.000	0.000	0.000	0.000	0.000	0.000
26	B	51	ALA	0	-0.017	-0.031	42.697	-0.005	-0.005	0.000	0.000	0.000	0.000
27	B	52	THR	0	0.004	-0.011	39.624	0.005	0.005	0.000	0.000	0.000	0.000
28	B	53	GLY	0	-0.010	-0.005	36.510	-0.003	-0.003	0.000	0.000	0.000	0.000
29	B	54	GLY	0	0.034	0.027	33.462	0.008	0.008	0.000	0.000	0.000	0.000
30	B	55	ASN	0	-0.066	-0.039	29.047	0.010	0.010	0.000	0.000	0.000	0.000
31	B	56	ILE	0	0.040	0.034	25.367	-0.017	-0.017	0.000	0.000	0.000	0.000
32	B	57	SER	0	-0.010	-0.008	22.426	0.009	0.009	0.000	0.000	0.000	0.000
33	B	58	VAL	0	0.027	0.007	18.623	-0.032	-0.032	0.000	0.000	0.000	0.000
34	B	59	THR	0	-0.022	-0.014	15.776	0.089	0.089	0.000	0.000	0.000	0.000
35	B	61	ASP	-1	-0.753	-0.876	8.499	-3.563	-3.563	0.000	0.000	0.000	0.000
36	B	62	GLY	0	0.049	0.032	9.356	-0.442	-0.442	0.000	0.000	0.000	0.000
37	B	63	THR	0	-0.086	-0.048	8.865	0.160	0.160	0.000	0.000	0.000	0.000
38	B	64	ASP	-1	-0.954	-0.979	11.602	-0.809	-0.809	0.000	0.000	0.000	0.000
39	B	65	PRO	0	-0.033	-0.005	14.209	-0.154	-0.154	0.000	0.000	0.000	0.000
40	B	66	VAL	0	-0.006	0.001	13.938	-0.074	-0.074	0.000	0.000	0.000	0.000
41	B	67	ASP	-1	-0.816	-0.896	16.970	-0.592	-0.592	0.000	0.000	0.000	0.000
42	B	68	PHE	0	-0.048	-0.034	19.484	-0.074	-0.074	0.000	0.000	0.000	0.000
43	B	69	THR	0	-0.026	-0.006	21.708	0.078	0.078	0.000	0.000	0.000	0.000
44	B	70	VAL	0	-0.016	-0.008	25.088	-0.032	-0.032	0.000	0.000	0.000	0.000
45	B	71	ALA	0	-0.002	0.003	27.500	0.034	0.034	0.000	0.000	0.000	0.000
46	B	72	ILE	0	-0.017	-0.010	30.662	-0.018	-0.018	0.000	0.000	0.000	0.000
47	B	73	ASP	-1	-0.838	-0.910	33.238	-0.322	-0.322	0.000	0.000	0.000	0.000
48	B	93	TYR	0	-0.098	-0.051	44.101	-0.004	-0.004	0.000	0.000	0.000	0.000
49	B	94	ASN	0	0.058	0.025	41.130	-0.007	-0.007	0.000	0.000	0.000	0.000
50	B	95	VAL	0	0.009	0.011	35.739	0.001	0.001	0.000	0.000	0.000	0.000
51	B	96	TYR	0	0.014	0.006	36.726	0.000	0.000	0.000	0.000	0.000	0.000
52	B	97	ARG	1	0.859	0.921	27.766	0.429	0.429	0.000	0.000	0.000	0.000
53	B	98	ASP	-1	-0.844	-0.903	33.459	-0.266	-0.266	0.000	0.000	0.000	0.000
54	B	99	ALA	0	0.043	0.025	36.075	0.007	0.007	0.000	0.000	0.000	0.000
55	B	100	ALA	0	-0.038	-0.027	37.747	0.006	0.006	0.000	0.000	0.000	0.000
56	B	101	ARG	1	0.879	0.944	39.544	0.224	0.224	0.000	0.000	0.000	0.000
57	B	102	THR	0	-0.025	-0.027	39.931	0.009	0.009	0.000	0.000	0.000	0.000
58	B	103	ASN	0	-0.024	-0.017	34.317	0.000	0.000	0.000	0.000	0.000	0.000
59	B	104	LEU	0	-0.009	-0.005	36.892	-0.012	-0.012	0.000	0.000	0.000	0.000
60	B	105	TYR	0	-0.023	-0.014	30.603	-0.019	-0.019	0.000	0.000	0.000	0.000
61	B	106	VAL	0	-0.024	-0.011	35.863	0.010	0.010	0.000	0.000	0.000	0.000
62	B	107	VAL	0	0.051	0.025	36.130	-0.017	-0.017	0.000	0.000	0.000	0.000
63	B	108	ASN	0	-0.034	-0.028	34.281	-0.005	-0.005	0.000	0.000	0.000	0.000
64	B	109	GLN	0	-0.032	-0.011	34.223	-0.004	-0.004	0.000	0.000	0.000	0.000
65	B	110	PRO	0	-0.028	-0.013	28.931	-0.006	-0.006	0.000	0.000	0.000	0.000
66	B	111	GLN	0	0.031	0.041	29.390	0.025	0.025	0.000	0.000	0.000	0.000
67	B	112	GLN	0	0.014	0.000	24.368	-0.026	-0.026	0.000	0.000	0.000	0.000
68	B	113	PHE	0	-0.013	-0.009	23.812	0.046	0.046	0.000	0.000	0.000	0.000
69	B	114	THR	0	0.028	0.000	20.880	-0.042	-0.042	0.000	0.000	0.000	0.000
70	B	115	THR	0	-0.019	-0.004	17.612	-0.020	-0.020	0.000	0.000	0.000	0.000
71	B	116	VAL	0	0.048	0.017	17.702	0.013	0.013	0.000	0.000	0.000	0.000
72	B	117	SER	0	0.063	0.028	14.177	0.044	0.044	0.000	0.000	0.000	0.000
73	B	118	GLY	0	-0.003	-0.006	16.101	0.013	0.013	0.000	0.000	0.000	0.000
74	B	119	GLN	0	-0.120	-0.059	18.720	0.104	0.104	0.000	0.000	0.000	0.000
75	B	120	ALA	0	0.050	0.067	18.955	-0.037	-0.037	0.000	0.000	0.000	0.000
76	B	121	THR	0	0.014	-0.027	19.914	0.045	0.045	0.000	0.000	0.000	0.000
77	B	122	ALA	0	-0.045	-0.008	22.584	-0.031	-0.031	0.000	0.000	0.000	0.000
78	B	123	VAL	0	0.038	0.009	24.484	0.002	0.002	0.000	0.000	0.000	0.000
79	B	124	PRO	0	-0.047	-0.010	27.167	0.015	0.015	0.000	0.000	0.000	0.000
80	B	125	ILE	0	0.028	0.009	30.371	0.005	0.005	0.000	0.000	0.000	0.000
81	B	126	PHE	0	-0.027	-0.021	33.438	0.012	0.012	0.000	0.000	0.000	0.000
82	B	127	GLY	0	0.052	0.029	37.110	0.002	0.002	0.000	0.000	0.000	0.000
83	B	128	ALA	0	-0.040	-0.040	39.929	0.009	0.009	0.000	0.000	0.000	0.000
84	B	129	ILE	0	0.030	0.067	43.611	-0.002	-0.002	0.000	0.000	0.000	0.000
85	B	130	ALA	0	0.009	-0.050	47.038	0.004	0.004	0.000	0.000	0.000	0.000
86	B	131	PRO	0	0.021	0.066	50.455	0.007	0.007	0.000	0.000	0.000	0.000
87	B	132	ASN	0	0.035	-0.035	51.567	-0.005	-0.005	0.000	0.000	0.000	0.000
88	B	133	THR	0	0.023	-0.008	49.901	0.001	0.001	0.000	0.000	0.000	0.000
89	B	134	GLY	0	-0.066	-0.064	46.551	-0.001	-0.001	0.000	0.000	0.000	0.000
90	B	135	THR	0	0.027	0.035	43.454	-0.006	-0.006	0.000	0.000	0.000	0.000
91	B	136	PRO	0	0.009	0.013	44.787	0.001	0.001	0.000	0.000	0.000	0.000
92	B	137	LYS	1	0.951	0.964	45.868	0.201	0.201	0.000	0.000	0.000	0.000
93	B	138	ALA	0	0.009	0.009	47.691	-0.007	-0.007	0.000	0.000	0.000	0.000
94	B	139	GLN	0	-0.004	0.009	50.390	0.003	0.003	0.000	0.000	0.000	0.000
95	B	140	GLY	0	-0.013	-0.003	49.741	-0.006	-0.006	0.000	0.000	0.000	0.000
96	B	141	ASP	-1	-0.830	-0.914	47.254	-0.194	-0.194	0.000	0.000	0.000	0.000
97	B	142	TYR	0	-0.044	-0.041	47.072	-0.009	-0.009	0.000	0.000	0.000	0.000
98	B	143	LYS	1	0.839	0.912	42.339	0.213	0.213	0.000	0.000	0.000	0.000
99	B	144	ASP	-1	-0.883	-0.954	40.782	-0.254	-0.254	0.000	0.000	0.000	0.000
100	B	145	THR	0	-0.091	-0.040	36.300	-0.009	-0.009	0.000	0.000	0.000	0.000
101	B	146	LEU	0	0.012	0.018	35.362	0.003	0.003	0.000	0.000	0.000	0.000
102	B	147	LEU	0	-0.004	0.002	30.650	-0.020	-0.020	0.000	0.000	0.000	0.000
103	B	148	VAL	0	-0.019	-0.019	27.910	0.006	0.006	0.000	0.000	0.000	0.000
104	B	149	THR	0	-0.026	-0.006	26.408	-0.028	-0.028	0.000	0.000	0.000	0.000
105	B	150	VAL	0	0.008	0.002	21.632	0.017	0.017	0.000	0.000	0.000	0.000
106	B	151	ASN	0	-0.061	-0.042	22.791	-0.045	-0.045	0.000	0.000	0.000	0.000
107	B	152	PHE	0	0.075	0.035	17.641	-0.024	-0.024	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:7:HIS)