FMO DATABASE

FMODB ID: G6711

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

Total energy (hartree)

FMO2-HF: Electronic energy	-682613.582701
FMO2-HF: Nuclear repulsion	642850.243363
FMO2-HF: Total energy	-39763.339338
FMO2-MP2: Total energy	-39877.489576

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.
-1.465	1.581	0.422	-1.406	-2.062	-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 : -0.022 / q_NPA : -0.024

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	-0.041	-0.029	2.707	-1.697	1.311	0.423	-1.404	-2.027	-0.001
4	B	10	ILE	0	0.003	-0.006	5.018	0.362	0.400	-0.001	-0.002	-0.035	0.000
5	B	11	GLU	-1	-0.947	-0.958	8.491	-0.375	-0.375	0.000	0.000	0.000	0.000
6	B	12	VAL	0	-0.020	-0.011	10.863	0.087	0.087	0.000	0.000	0.000	0.000
7	B	13	GLY	0	0.087	0.045	13.419	0.046	0.046	0.000	0.000	0.000	0.000
8	B	14	PRO	0	0.016	-0.016	16.968	0.008	0.008	0.000	0.000	0.000	0.000
9	B	15	GLY	0	-0.012	-0.003	19.539	0.010	0.010	0.000	0.000	0.000	0.000
10	B	16	ALA	0	0.053	0.031	14.817	0.024	0.024	0.000	0.000	0.000	0.000
11	B	17	THR	0	0.008	0.015	16.972	0.020	0.020	0.000	0.000	0.000	0.000
12	B	18	ASN	0	0.061	0.022	18.284	0.026	0.026	0.000	0.000	0.000	0.000
13	B	19	ALA	0	0.006	0.014	17.843	0.016	0.016	0.000	0.000	0.000	0.000
14	B	20	THR	0	0.003	-0.018	14.413	0.023	0.023	0.000	0.000	0.000	0.000
15	B	21	ILE	0	-0.052	-0.018	17.088	0.026	0.026	0.000	0.000	0.000	0.000
16	B	22	ASN	0	0.062	0.029	20.115	0.013	0.013	0.000	0.000	0.000	0.000
17	B	23	PHE	0	0.096	0.050	14.379	0.009	0.009	0.000	0.000	0.000	0.000
18	B	24	GLU	-1	-0.809	-0.908	15.882	0.114	0.114	0.000	0.000	0.000	0.000
19	B	25	ALA	0	-0.021	-0.012	18.548	0.009	0.009	0.000	0.000	0.000	0.000
20	B	26	GLY	0	0.029	0.014	21.495	0.000	0.000	0.000	0.000	0.000	0.000
21	B	27	ILE	0	-0.002	0.008	16.629	0.009	0.009	0.000	0.000	0.000	0.000
22	B	28	LEU	0	-0.018	-0.017	20.040	0.009	0.009	0.000	0.000	0.000	0.000
23	B	29	GLU	-1	-0.773	-0.857	22.521	0.086	0.086	0.000	0.000	0.000	0.000
24	B	30	CYS	0	-0.036	-0.021	21.812	-0.001	-0.001	0.000	0.000	0.000	0.000
25	B	31	TYR	0	-0.018	-0.011	17.354	0.003	0.003	0.000	0.000	0.000	0.000
26	B	32	GLU	-1	-0.774	-0.886	23.537	0.076	0.076	0.000	0.000	0.000	0.000
27	B	33	ARG	1	0.879	0.925	27.129	-0.098	-0.098	0.000	0.000	0.000	0.000
28	B	34	PHE	0	0.032	0.016	24.609	-0.003	-0.003	0.000	0.000	0.000	0.000
29	B	35	SER	0	0.025	-0.002	27.002	-0.001	-0.001	0.000	0.000	0.000	0.000
30	B	36	TRP	0	-0.063	-0.024	28.478	-0.006	-0.006	0.000	0.000	0.000	0.000
31	B	37	GLN	0	-0.068	-0.033	29.754	-0.009	-0.009	0.000	0.000	0.000	0.000
32	B	38	ARG	1	0.873	0.935	31.680	-0.082	-0.082	0.000	0.000	0.000	0.000
33	B	39	ALA	0	0.050	0.036	27.639	0.001	0.001	0.000	0.000	0.000	0.000
34	B	40	LEU	0	-0.065	-0.001	22.796	0.014	0.014	0.000	0.000	0.000	0.000
35	B	41	ASP	-1	-0.790	-0.881	23.548	0.185	0.185	0.000	0.000	0.000	0.000
36	B	42	TYR	0	0.074	0.010	25.918	0.001	0.001	0.000	0.000	0.000	0.000
37	B	43	PRO	0	0.026	0.004	22.157	-0.003	-0.003	0.000	0.000	0.000	0.000
38	B	44	GLY	0	0.012	-0.007	21.604	0.007	0.007	0.000	0.000	0.000	0.000
39	B	45	GLN	0	-0.033	-0.036	22.681	-0.010	-0.010	0.000	0.000	0.000	0.000
40	B	46	ASP	-1	-0.829	-0.886	22.920	0.099	0.099	0.000	0.000	0.000	0.000
41	B	47	ARG	1	0.905	0.958	17.327	-0.257	-0.257	0.000	0.000	0.000	0.000
42	B	48	LEU	0	-0.004	0.021	20.568	-0.004	-0.004	0.000	0.000	0.000	0.000
43	B	49	HIS	0	0.061	0.015	22.862	-0.013	-0.013	0.000	0.000	0.000	0.000
44	B	50	ARG	1	0.787	0.870	20.271	-0.113	-0.113	0.000	0.000	0.000	0.000
45	B	51	LEU	0	-0.028	-0.001	17.808	-0.016	-0.016	0.000	0.000	0.000	0.000
46	B	52	LYS	1	0.905	0.940	20.545	-0.080	-0.080	0.000	0.000	0.000	0.000
47	B	53	ARG	1	0.955	0.985	23.897	-0.074	-0.074	0.000	0.000	0.000	0.000
48	B	54	LYS	1	0.938	0.979	15.774	-0.127	-0.127	0.000	0.000	0.000	0.000
49	B	55	LEU	0	-0.012	0.010	20.541	-0.017	-0.017	0.000	0.000	0.000	0.000
50	B	56	GLU	-1	-0.808	-0.891	22.060	0.007	0.007	0.000	0.000	0.000	0.000
51	B	57	SER	0	-0.075	-0.042	23.136	-0.011	-0.011	0.000	0.000	0.000	0.000
52	B	58	ARG	1	0.850	0.891	16.265	-0.037	-0.037	0.000	0.000	0.000	0.000
53	B	59	ILE	0	0.016	0.018	22.898	-0.011	-0.011	0.000	0.000	0.000	0.000
54	B	60	LYS	1	0.902	0.940	25.563	-0.010	-0.010	0.000	0.000	0.000	0.000
55	B	61	THR	0	-0.070	-0.048	24.177	-0.006	-0.006	0.000	0.000	0.000	0.000
56	B	62	HIS	0	-0.006	-0.003	23.615	-0.003	-0.003	0.000	0.000	0.000	0.000
57	B	63	ASN	0	0.006	-0.017	25.647	-0.004	-0.004	0.000	0.000	0.000	0.000
58	B	64	LYS	1	0.916	0.974	28.504	0.047	0.047	0.000	0.000	0.000	0.000
59	B	65	SER	0	-0.012	0.002	27.098	-0.003	-0.003	0.000	0.000	0.000	0.000
60	B	66	GLU	-1	-0.837	-0.900	27.091	-0.049	-0.049	0.000	0.000	0.000	0.000
61	B	67	PRO	0	0.015	0.000	30.251	0.004	0.004	0.000	0.000	0.000	0.000
62	B	68	GLU	-1	-0.822	-0.920	33.012	-0.014	-0.014	0.000	0.000	0.000	0.000
63	B	69	ASN	0	-0.021	-0.007	35.061	0.005	0.005	0.000	0.000	0.000	0.000
64	B	70	LYS	1	0.828	0.905	28.110	0.042	0.042	0.000	0.000	0.000	0.000
65	B	71	ARG	1	0.843	0.938	29.854	0.015	0.015	0.000	0.000	0.000	0.000
66	B	72	MET	0	0.000	0.017	28.191	0.006	0.006	0.000	0.000	0.000	0.000
67	B	73	SER	0	-0.043	-0.050	29.218	-0.001	-0.001	0.000	0.000	0.000	0.000
68	B	74	LEU	0	0.025	-0.007	25.574	0.004	0.004	0.000	0.000	0.000	0.000
69	B	75	GLU	-1	-0.820	-0.917	27.933	0.060	0.060	0.000	0.000	0.000	0.000
70	B	76	GLU	-1	-0.788	-0.859	30.195	0.021	0.021	0.000	0.000	0.000	0.000
71	B	77	ARG	1	0.821	0.884	24.754	0.002	0.002	0.000	0.000	0.000	0.000
72	B	78	LYS	1	0.777	0.893	25.473	-0.065	-0.065	0.000	0.000	0.000	0.000
73	B	79	ALA	0	-0.021	-0.003	26.083	0.008	0.008	0.000	0.000	0.000	0.000
74	B	80	ILE	0	-0.023	-0.018	24.455	0.004	0.004	0.000	0.000	0.000	0.000
75	B	81	GLY	0	0.064	0.028	22.378	0.003	0.003	0.000	0.000	0.000	0.000
76	B	82	VAL	0	-0.023	-0.032	22.412	0.014	0.014	0.000	0.000	0.000	0.000
77	B	83	LYS	1	0.930	0.988	24.720	-0.040	-0.040	0.000	0.000	0.000	0.000
78	B	84	MET	0	-0.008	-0.001	20.419	0.004	0.004	0.000	0.000	0.000	0.000
79	B	85	MET	0	-0.016	-0.010	18.635	0.020	0.020	0.000	0.000	0.000	0.000
80	B	86	LYS	1	0.906	0.971	21.409	-0.071	-0.071	0.000	0.000	0.000	0.000
81	B	87	VAL	0	0.037	0.029	21.810	0.007	0.007	0.000	0.000	0.000	0.000
82	B	88	LEU	0	-0.016	-0.007	16.735	0.008	0.008	0.000	0.000	0.000	0.000
83	B	89	LEU	0	-0.073	-0.038	19.893	0.019	0.019	0.000	0.000	0.000	0.000
84	B	90	PHE	0	-0.013	-0.002	21.220	0.013	0.013	0.000	0.000	0.000	0.000
85	B	91	MET	0	-0.091	-0.037	17.939	0.002	0.002	0.000	0.000	0.000	0.000
86	B	92	ASP	-1	-0.759	-0.872	21.762	0.093	0.093	0.000	0.000	0.000	0.000
87	B	93	PRO	0	-0.081	-0.046	24.385	-0.003	-0.003	0.000	0.000	0.000	0.000
88	B	94	SER	0	-0.043	-0.054	26.402	-0.011	-0.011	0.000	0.000	0.000	0.000
89	B	95	ALA	0	-0.014	0.018	29.691	0.004	0.004	0.000	0.000	0.000	0.000
90	B	96	GLY	0	0.052	0.046	27.342	0.002	0.002	0.000	0.000	0.000	0.000
91	B	97	ILE	0	-0.102	-0.071	26.966	0.003	0.003	0.000	0.000	0.000	0.000
92	B	98	GLU	-1	-0.953	-0.987	28.920	0.054	0.054	0.000	0.000	0.000	0.000
93	B	99	GLY	0	0.000	-0.009	32.522	-0.002	-0.002	0.000	0.000	0.000	0.000
94	B	100	PHE	0	-0.119	-0.065	33.902	0.001	0.001	0.000	0.000	0.000	0.000
95	B	101	GLU	-1	-0.807	-0.912	29.991	0.100	0.100	0.000	0.000	0.000	0.000
96	B	102	PRO	0	-0.042	-0.007	31.073	0.004	0.004	0.000	0.000	0.000	0.000
97	B	103	TYR	0	-0.035	-0.004	28.193	0.003	0.003	0.000	0.000	0.000	0.000

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