FMO DATABASE

FMODB ID: 17VRZ

Calculation Name: 3SDL-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3SDL

Chain ID: B

ChEMBL ID:

UniProt ID: P05161

Base Structure: X-ray

Registration Date: 2023-06-26

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	97
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-682417.7161
FMO2-HF: Nuclear repulsion	642655.054064
FMO2-HF: Total energy	-39762.662036
FMO2-MP2: Total energy	-39876.829265

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:THR)

Summations of interaction energy for fragment #1(B:7: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.
-2.957	-0.672	2.929	-2.088	-3.124	0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / 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	GLN	0	0.005	0.001	2.333	-1.936	0.311	2.930	-2.085	-3.091	0.001
4	B	10	ILE	0	0.002	-0.002	4.853	0.184	0.222	-0.001	-0.003	-0.033	0.000
5	B	11	GLU	-1	-0.954	-0.961	8.462	-0.553	-0.553	0.000	0.000	0.000	0.000
6	B	12	VAL	0	-0.021	-0.009	10.984	0.091	0.091	0.000	0.000	0.000	0.000
7	B	13	GLY	0	0.078	0.036	13.419	0.034	0.034	0.000	0.000	0.000	0.000
8	B	14	PRO	0	0.022	-0.011	16.983	0.031	0.031	0.000	0.000	0.000	0.000
9	B	15	GLY	0	-0.011	-0.007	19.520	0.030	0.030	0.000	0.000	0.000	0.000
10	B	16	ALA	0	0.047	0.030	14.990	0.031	0.031	0.000	0.000	0.000	0.000
11	B	17	THR	0	0.009	0.008	17.129	0.046	0.046	0.000	0.000	0.000	0.000
12	B	18	ASN	0	0.052	0.015	18.449	0.049	0.049	0.000	0.000	0.000	0.000
13	B	19	ALA	0	0.010	0.014	17.899	0.023	0.023	0.000	0.000	0.000	0.000
14	B	20	THR	0	0.009	-0.004	14.466	0.030	0.030	0.000	0.000	0.000	0.000
15	B	21	ILE	0	-0.048	-0.013	17.031	0.047	0.047	0.000	0.000	0.000	0.000
16	B	22	ASN	0	0.070	0.031	20.087	0.028	0.028	0.000	0.000	0.000	0.000
17	B	23	PHE	0	0.089	0.048	14.425	0.011	0.011	0.000	0.000	0.000	0.000
18	B	24	GLU	-1	-0.848	-0.924	14.727	0.381	0.381	0.000	0.000	0.000	0.000
19	B	25	ALA	0	-0.023	-0.018	18.565	0.020	0.020	0.000	0.000	0.000	0.000
20	B	26	GLY	0	0.026	0.011	21.517	-0.003	-0.003	0.000	0.000	0.000	0.000
21	B	27	ILE	0	0.003	0.010	16.823	0.011	0.011	0.000	0.000	0.000	0.000
22	B	28	LEU	0	-0.027	-0.022	20.197	0.017	0.017	0.000	0.000	0.000	0.000
23	B	29	GLU	-1	-0.783	-0.878	22.679	0.152	0.152	0.000	0.000	0.000	0.000
24	B	30	CYS	0	-0.039	-0.024	22.059	-0.011	-0.011	0.000	0.000	0.000	0.000
25	B	31	TYR	0	-0.032	-0.015	17.498	0.014	0.014	0.000	0.000	0.000	0.000
26	B	32	GLU	-1	-0.884	-0.965	23.824	0.179	0.179	0.000	0.000	0.000	0.000
27	B	33	ARG	1	0.880	0.931	27.390	-0.150	-0.150	0.000	0.000	0.000	0.000
28	B	34	PHE	0	0.032	0.020	24.825	-0.008	-0.008	0.000	0.000	0.000	0.000
29	B	35	SER	0	-0.006	-0.014	27.359	-0.002	-0.002	0.000	0.000	0.000	0.000
30	B	36	TRP	0	-0.037	-0.013	28.835	-0.009	-0.009	0.000	0.000	0.000	0.000
31	B	37	GLN	0	-0.073	-0.037	30.176	-0.019	-0.019	0.000	0.000	0.000	0.000
32	B	38	ARG	1	0.876	0.937	32.065	-0.158	-0.158	0.000	0.000	0.000	0.000
33	B	39	ALA	0	0.054	0.038	28.055	0.002	0.002	0.000	0.000	0.000	0.000
34	B	40	LEU	0	-0.077	-0.003	23.171	0.027	0.027	0.000	0.000	0.000	0.000
35	B	41	ASP	-1	-0.808	-0.889	24.112	0.394	0.394	0.000	0.000	0.000	0.000
36	B	42	TYR	0	0.072	0.008	26.346	0.006	0.006	0.000	0.000	0.000	0.000
37	B	43	PRO	0	0.026	0.004	22.552	0.002	0.002	0.000	0.000	0.000	0.000
38	B	44	GLY	0	0.018	0.003	22.002	0.026	0.026	0.000	0.000	0.000	0.000
39	B	45	GLN	0	-0.045	-0.047	23.086	-0.013	-0.013	0.000	0.000	0.000	0.000
40	B	46	ASP	-1	-0.864	-0.900	22.785	0.356	0.356	0.000	0.000	0.000	0.000
41	B	47	ARG	1	0.943	0.957	17.602	-0.574	-0.574	0.000	0.000	0.000	0.000
42	B	48	LEU	0	-0.004	0.026	20.876	-0.002	-0.002	0.000	0.000	0.000	0.000
43	B	49	HIS	0	0.063	0.015	23.188	-0.018	-0.018	0.000	0.000	0.000	0.000
44	B	50	ARG	1	0.822	0.891	20.388	-0.392	-0.392	0.000	0.000	0.000	0.000
45	B	51	LEU	0	-0.027	-0.002	18.003	-0.012	-0.012	0.000	0.000	0.000	0.000
46	B	52	LYS	1	1.014	1.012	20.783	-0.192	-0.192	0.000	0.000	0.000	0.000
47	B	53	ARG	1	0.941	0.976	24.066	-0.260	-0.260	0.000	0.000	0.000	0.000
48	B	54	LYS	1	0.982	0.987	16.065	-0.462	-0.462	0.000	0.000	0.000	0.000
49	B	55	LEU	0	-0.018	0.023	20.255	-0.023	-0.023	0.000	0.000	0.000	0.000
50	B	56	GLU	-1	-0.882	-0.941	22.191	0.095	0.095	0.000	0.000	0.000	0.000
51	B	57	SER	0	-0.075	-0.052	23.333	-0.015	-0.015	0.000	0.000	0.000	0.000
52	B	58	ARG	1	0.869	0.895	16.868	-0.227	-0.227	0.000	0.000	0.000	0.000
53	B	59	ILE	0	0.027	0.031	22.922	-0.022	-0.022	0.000	0.000	0.000	0.000
54	B	60	LYS	1	0.960	0.980	25.599	-0.101	-0.101	0.000	0.000	0.000	0.000
55	B	61	THR	0	-0.064	-0.033	24.080	-0.013	-0.013	0.000	0.000	0.000	0.000
56	B	62	HIS	0	-0.002	-0.009	23.116	-0.013	-0.013	0.000	0.000	0.000	0.000
57	B	63	ASN	0	0.020	-0.010	25.586	-0.016	-0.016	0.000	0.000	0.000	0.000
58	B	64	LYS	1	0.893	0.956	28.778	-0.036	-0.036	0.000	0.000	0.000	0.000
59	B	65	SER	0	-0.012	0.001	27.164	-0.001	-0.001	0.000	0.000	0.000	0.000
60	B	66	GLU	-1	-0.936	-0.951	26.955	-0.051	-0.051	0.000	0.000	0.000	0.000
61	B	67	PRO	0	0.000	-0.012	30.369	0.006	0.006	0.000	0.000	0.000	0.000
62	B	68	GLU	-1	-0.828	-0.930	33.189	0.018	0.018	0.000	0.000	0.000	0.000
63	B	69	ASN	0	-0.032	-0.010	35.194	0.008	0.008	0.000	0.000	0.000	0.000
64	B	70	LYS	1	0.957	0.978	28.719	0.048	0.048	0.000	0.000	0.000	0.000
65	B	71	ARG	1	0.845	0.945	29.967	-0.019	-0.019	0.000	0.000	0.000	0.000
66	B	72	MET	0	0.029	0.021	28.142	0.005	0.005	0.000	0.000	0.000	0.000
67	B	73	SER	0	-0.024	-0.012	29.264	0.009	0.009	0.000	0.000	0.000	0.000
68	B	74	LEU	0	0.031	-0.008	25.559	0.002	0.002	0.000	0.000	0.000	0.000
69	B	75	GLU	-1	-0.896	-0.955	27.911	0.120	0.120	0.000	0.000	0.000	0.000
70	B	76	GLU	-1	-0.807	-0.893	30.191	0.047	0.047	0.000	0.000	0.000	0.000
71	B	77	ARG	1	0.807	0.880	24.778	-0.055	-0.055	0.000	0.000	0.000	0.000
72	B	78	LYS	1	0.879	0.966	25.493	-0.151	-0.151	0.000	0.000	0.000	0.000
73	B	79	ALA	0	-0.005	0.007	26.104	0.003	0.003	0.000	0.000	0.000	0.000
74	B	80	ILE	0	-0.028	-0.021	24.378	-0.005	-0.005	0.000	0.000	0.000	0.000
75	B	81	GLY	0	0.065	0.027	22.349	-0.006	-0.006	0.000	0.000	0.000	0.000
76	B	82	VAL	0	-0.021	-0.031	22.446	0.009	0.009	0.000	0.000	0.000	0.000
77	B	83	LYS	1	0.917	0.985	24.801	-0.038	-0.038	0.000	0.000	0.000	0.000
78	B	84	MET	0	-0.015	-0.007	20.370	-0.002	-0.002	0.000	0.000	0.000	0.000
79	B	85	MET	0	-0.021	-0.013	19.338	0.008	0.008	0.000	0.000	0.000	0.000
80	B	86	LYS	1	0.917	0.978	21.506	-0.076	-0.076	0.000	0.000	0.000	0.000
81	B	87	VAL	0	0.053	0.034	21.647	0.002	0.002	0.000	0.000	0.000	0.000
82	B	88	LEU	0	-0.025	-0.011	16.660	-0.007	-0.007	0.000	0.000	0.000	0.000
83	B	89	LEU	0	-0.072	-0.036	20.018	0.007	0.007	0.000	0.000	0.000	0.000
84	B	90	PHE	0	-0.008	0.000	21.420	0.012	0.012	0.000	0.000	0.000	0.000
85	B	91	MET	0	-0.102	-0.038	18.012	-0.010	-0.010	0.000	0.000	0.000	0.000
86	B	92	ASP	-1	-0.832	-0.928	21.851	-0.020	-0.020	0.000	0.000	0.000	0.000
87	B	93	PRO	0	-0.065	-0.043	24.455	0.011	0.011	0.000	0.000	0.000	0.000
88	B	94	SER	0	-0.025	-0.029	26.372	0.001	0.001	0.000	0.000	0.000	0.000
89	B	95	ALA	0	0.024	0.041	29.693	0.007	0.007	0.000	0.000	0.000	0.000
90	B	96	GLY	0	0.048	0.044	27.406	0.008	0.008	0.000	0.000	0.000	0.000
91	B	97	ILE	0	-0.104	-0.071	27.126	0.016	0.016	0.000	0.000	0.000	0.000
92	B	98	GLU	-1	-0.972	-0.994	28.937	0.007	0.007	0.000	0.000	0.000	0.000
93	B	99	GLY	0	0.009	-0.004	32.511	0.005	0.005	0.000	0.000	0.000	0.000
94	B	100	PHE	0	-0.118	-0.063	34.050	-0.001	-0.001	0.000	0.000	0.000	0.000
95	B	101	GLU	-1	-0.839	-0.931	29.894	0.043	0.043	0.000	0.000	0.000	0.000
96	B	102	PRO	0	-0.039	0.000	31.266	0.002	0.002	0.000	0.000	0.000	0.000
97	B	103	TYR	0	-0.005	0.004	28.419	0.004	0.004	0.000	0.000	0.000	0.000

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