FMO DATABASE

FMODB ID: R9LL8

Calculation Name: 5D5X-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D5X

Chain ID: B

ChEMBL ID:

UniProt ID: G0SB31

Base Structure: X-ray

Registration Date: 2023-06-22

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	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	103
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-893085.740963
FMO2-HF: Nuclear repulsion	849911.499662
FMO2-HF: Total energy	-43174.241301
FMO2-MP2: Total energy	-43303.214819

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:41:SER)

Summations of interaction energy for fragment #1(B:41: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.
-25.869	-26.131	16.465	-9.137	-7.065	0.028

Interaction energy analysis for fragmet #1(B:41:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.056 / q_NPA : 0.045

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	43	PHE	0	-0.004	-0.002	3.046	-3.749	-0.354	0.014	-1.805	-1.604	0.000
4	B	44	VAL	0	0.088	0.047	3.450	-0.497	-0.007	0.012	-0.106	-0.396	0.000
5	B	45	ARG	1	0.923	0.964	4.107	4.749	5.218	-0.001	-0.189	-0.279	0.001
6	B	46	LYS	1	0.866	0.926	6.794	0.490	0.490	0.000	0.000	0.000	0.000
7	B	47	LEU	0	-0.023	-0.002	7.868	0.132	0.132	0.000	0.000	0.000	0.000
8	B	48	TYR	0	-0.008	-0.024	9.385	0.025	0.025	0.000	0.000	0.000	0.000
9	B	49	LYS	1	0.849	0.923	10.994	0.473	0.473	0.000	0.000	0.000	0.000
10	B	50	MET	0	-0.071	-0.030	12.418	0.091	0.091	0.000	0.000	0.000	0.000
11	B	51	LEU	0	-0.004	0.002	13.901	0.051	0.051	0.000	0.000	0.000	0.000
12	B	52	GLU	-1	-0.815	-0.887	14.532	-0.548	-0.548	0.000	0.000	0.000	0.000
13	B	53	ASP	-1	-0.861	-0.909	17.831	-0.107	-0.107	0.000	0.000	0.000	0.000
14	B	54	PRO	0	0.032	-0.003	19.958	0.031	0.031	0.000	0.000	0.000	0.000
15	B	55	SER	0	-0.063	-0.042	22.499	0.025	0.025	0.000	0.000	0.000	0.000
16	B	56	TYR	0	0.020	-0.020	17.250	0.025	0.025	0.000	0.000	0.000	0.000
17	B	57	HIS	0	0.023	0.030	22.610	0.031	0.031	0.000	0.000	0.000	0.000
18	B	58	SER	0	0.001	-0.015	24.282	0.005	0.005	0.000	0.000	0.000	0.000
19	B	59	VAL	0	-0.026	-0.007	21.523	0.016	0.016	0.000	0.000	0.000	0.000
20	B	60	VAL	0	-0.054	-0.048	17.160	0.035	0.035	0.000	0.000	0.000	0.000
21	B	61	ARG	1	0.892	0.963	19.603	-0.066	-0.066	0.000	0.000	0.000	0.000
22	B	62	TRP	0	0.025	0.003	13.328	0.035	0.035	0.000	0.000	0.000	0.000
23	B	63	SER	0	0.001	0.002	19.413	0.000	0.000	0.000	0.000	0.000	0.000
24	B	64	ASP	-1	-0.855	-0.908	21.855	0.002	0.002	0.000	0.000	0.000	0.000
25	B	65	ASP	-1	-0.898	-0.939	23.075	-0.002	-0.002	0.000	0.000	0.000	0.000
26	B	66	GLY	0	-0.049	-0.015	20.100	-0.018	-0.018	0.000	0.000	0.000	0.000
27	B	67	ASP	-1	-0.815	-0.906	17.874	0.022	0.022	0.000	0.000	0.000	0.000
28	B	68	SER	0	-0.057	-0.067	16.357	0.029	0.029	0.000	0.000	0.000	0.000
29	B	69	PHE	0	-0.013	-0.006	12.828	-0.022	-0.022	0.000	0.000	0.000	0.000
30	B	70	VAL	0	0.049	0.016	17.374	0.056	0.056	0.000	0.000	0.000	0.000
31	B	71	VAL	0	-0.052	-0.011	17.690	-0.019	-0.019	0.000	0.000	0.000	0.000
32	B	72	LEU	0	-0.003	0.003	20.403	0.010	0.010	0.000	0.000	0.000	0.000
33	B	73	GLU	-1	-0.697	-0.821	24.222	0.083	0.083	0.000	0.000	0.000	0.000
34	B	74	ASN	0	0.037	-0.011	21.770	-0.017	-0.017	0.000	0.000	0.000	0.000
35	B	75	GLU	-1	-0.779	-0.848	22.309	0.203	0.203	0.000	0.000	0.000	0.000
36	B	76	LYS	1	0.853	0.916	23.971	-0.062	-0.062	0.000	0.000	0.000	0.000
37	B	77	PHE	0	0.051	0.022	15.081	0.003	0.003	0.000	0.000	0.000	0.000
38	B	78	THR	0	-0.042	-0.051	19.198	0.030	0.030	0.000	0.000	0.000	0.000
39	B	79	LYS	1	0.834	0.884	20.149	-0.162	-0.162	0.000	0.000	0.000	0.000
40	B	80	THR	0	-0.046	-0.019	21.429	-0.024	-0.024	0.000	0.000	0.000	0.000
41	B	81	ILE	0	0.011	0.020	16.501	-0.006	-0.006	0.000	0.000	0.000	0.000
42	B	82	LEU	0	-0.039	-0.010	14.038	0.010	0.010	0.000	0.000	0.000	0.000
43	B	83	PRO	0	-0.008	-0.008	15.078	0.031	0.031	0.000	0.000	0.000	0.000
44	B	84	LYS	1	0.877	0.953	16.457	0.068	0.068	0.000	0.000	0.000	0.000
45	B	85	HIS	0	0.016	0.030	12.149	-0.048	-0.048	0.000	0.000	0.000	0.000
46	B	86	PHE	0	-0.055	-0.043	7.999	0.083	0.083	0.000	0.000	0.000	0.000
47	B	87	LYS	1	0.921	0.976	12.047	-0.027	-0.027	0.000	0.000	0.000	0.000
48	B	88	HIS	0	-0.010	0.001	12.350	-0.065	-0.065	0.000	0.000	0.000	0.000
49	B	89	SER	0	0.055	0.020	16.473	-0.024	-0.024	0.000	0.000	0.000	0.000
50	B	90	ASN	0	0.011	0.002	17.366	-0.059	-0.059	0.000	0.000	0.000	0.000
51	B	91	PHE	0	0.086	0.032	16.610	0.095	0.095	0.000	0.000	0.000	0.000
52	B	92	ALA	0	0.038	0.026	16.787	0.058	0.058	0.000	0.000	0.000	0.000
53	B	93	SER	0	-0.004	-0.013	14.003	0.061	0.061	0.000	0.000	0.000	0.000
54	B	94	PHE	0	-0.002	0.008	11.449	0.234	0.234	0.000	0.000	0.000	0.000
55	B	95	VAL	0	0.062	0.034	12.162	0.144	0.144	0.000	0.000	0.000	0.000
56	B	96	ARG	1	0.888	0.951	13.382	-1.014	-1.014	0.000	0.000	0.000	0.000
57	B	97	GLN	0	0.014	0.002	6.473	0.063	0.063	0.000	0.000	0.000	0.000
58	B	98	LEU	0	0.035	0.022	8.835	0.414	0.414	0.000	0.000	0.000	0.000
59	B	99	ASN	0	0.053	0.023	10.458	0.088	0.088	0.000	0.000	0.000	0.000
60	B	100	LYS	1	0.805	0.909	8.588	-2.224	-2.224	0.000	0.000	0.000	0.000
61	B	101	TYR	0	-0.044	-0.043	1.743	-8.471	-14.562	16.307	-6.359	-3.857	0.022
62	B	102	ASP	-1	-0.750	-0.854	7.779	0.556	0.556	0.000	0.000	0.000	0.000
63	B	103	PHE	0	-0.030	0.005	7.682	-0.174	-0.174	0.000	0.000	0.000	0.000
64	B	104	HIS	0	-0.023	-0.019	12.488	0.052	0.052	0.000	0.000	0.000	0.000
65	B	105	LYS	1	0.845	0.941	16.251	-0.331	-0.331	0.000	0.000	0.000	0.000
66	B	106	VAL	0	0.037	0.020	19.041	0.002	0.002	0.000	0.000	0.000	0.000
67	B	107	ARG	1	0.798	0.892	21.599	-0.207	-0.207	0.000	0.000	0.000	0.000
68	B	108	HIS	0	0.059	0.031	25.022	0.000	0.000	0.000	0.000	0.000	0.000
69	B	109	ASN	0	-0.001	0.007	27.380	0.018	0.018	0.000	0.000	0.000	0.000
70	B	110	ASP	-1	-1.001	-1.004	31.110	0.101	0.101	0.000	0.000	0.000	0.000
71	B	111	GLU	-1	-0.803	-0.893	32.880	0.069	0.069	0.000	0.000	0.000	0.000
72	B	112	ASN	0	-0.088	-0.053	34.578	-0.006	-0.006	0.000	0.000	0.000	0.000
73	B	113	GLY	0	0.069	0.042	33.203	-0.001	-0.001	0.000	0.000	0.000	0.000
74	B	114	GLU	-1	-0.893	-0.947	28.068	0.084	0.084	0.000	0.000	0.000	0.000
75	B	115	SER	0	-0.129	-0.058	30.036	0.008	0.008	0.000	0.000	0.000	0.000
76	B	116	PRO	0	-0.025	-0.002	27.922	0.001	0.001	0.000	0.000	0.000	0.000
77	B	117	TYR	0	-0.054	-0.086	24.077	0.000	0.000	0.000	0.000	0.000	0.000
78	B	118	GLY	0	0.032	0.019	27.873	-0.004	-0.004	0.000	0.000	0.000	0.000
79	B	119	ARG	1	0.905	0.934	28.424	-0.114	-0.114	0.000	0.000	0.000	0.000
80	B	120	ASP	-1	-0.879	-0.933	27.552	0.151	0.151	0.000	0.000	0.000	0.000
81	B	121	ALA	0	-0.002	0.014	24.424	0.019	0.019	0.000	0.000	0.000	0.000
82	B	122	TRP	0	-0.069	-0.070	19.635	0.051	0.051	0.000	0.000	0.000	0.000
83	B	123	GLU	-1	-0.723	-0.824	19.548	0.154	0.154	0.000	0.000	0.000	0.000
84	B	124	PHE	0	-0.057	-0.041	14.692	0.062	0.062	0.000	0.000	0.000	0.000
85	B	125	LYS	1	0.851	0.928	15.642	-0.158	-0.158	0.000	0.000	0.000	0.000
86	B	126	HIS	0	0.047	0.012	9.775	-0.061	-0.061	0.000	0.000	0.000	0.000
87	B	127	PRO	0	0.044	0.029	13.597	-0.071	-0.071	0.000	0.000	0.000	0.000
88	B	128	GLU	-1	-0.858	-0.907	11.120	-0.138	-0.138	0.000	0.000	0.000	0.000
89	B	129	PHE	0	-0.056	-0.028	9.335	-0.130	-0.130	0.000	0.000	0.000	0.000
90	B	130	ARG	1	0.935	0.957	12.115	0.165	0.165	0.000	0.000	0.000	0.000
91	B	131	ALA	0	0.031	0.022	14.712	-0.086	-0.086	0.000	0.000	0.000	0.000
92	B	132	ASP	-1	-0.848	-0.928	16.864	-0.253	-0.253	0.000	0.000	0.000	0.000
93	B	133	ARG	1	0.769	0.867	13.685	0.351	0.351	0.000	0.000	0.000	0.000
94	B	134	LYS	1	0.878	0.928	12.311	0.635	0.635	0.000	0.000	0.000	0.000
95	B	135	ASP	-1	-0.853	-0.914	11.426	-0.730	-0.730	0.000	0.000	0.000	0.000
96	B	136	ASN	0	-0.031	-0.015	11.342	-0.067	-0.067	0.000	0.000	0.000	0.000
97	B	137	LEU	0	-0.018	-0.011	6.817	0.022	0.022	0.000	0.000	0.000	0.000
98	B	138	ASP	-1	-0.915	-0.953	5.316	-3.456	-3.456	0.000	0.000	0.000	0.000
99	B	139	ASN	0	-0.011	-0.023	6.397	0.526	0.526	0.000	0.000	0.000	0.000
100	B	140	ILE	0	-0.046	0.004	5.990	0.440	0.440	0.000	0.000	0.000	0.000
101	B	141	ARG	1	0.878	0.935	4.342	-0.277	-0.139	-0.001	-0.023	-0.114	0.000
102	B	142	ARG	1	0.865	0.924	3.037	-12.342	-11.005	0.134	-0.655	-0.815	0.005
103	B	143	LYS	1	0.849	0.915	7.183	-1.500	-1.500	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:41:SER)