FMO DATABASE

FMODB ID: LNN39

Calculation Name: 5X5J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5X5J

Chain ID: A

ChEMBL ID:

UniProt ID: Q6TA00

Base Structure: X-ray

Registration Date: 2023-09-21

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	120
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1049456.211792
FMO2-HF: Nuclear repulsion	1001627.166292
FMO2-HF: Total energy	-47829.0455
FMO2-MP2: Total energy	-47967.856354

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(A:10:CYS)

Summations of interaction energy for fragment #1(A:10:CYS)

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.
-6.116	-2.845	8.101	-3.303	-8.07	-0.008

Interaction energy analysis for fragmet #1(A:10:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.054 / q_NPA : -0.033

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	A	12	ASP	-1	-0.877	-0.930	3.867	-1.604	-0.499	-0.001	-0.427	-0.678	0.001
4	A	13	LYS	1	0.806	0.898	2.834	1.146	1.899	0.237	-0.250	-0.740	-0.001
5	A	14	VAL	0	0.006	0.006	5.437	0.137	0.137	0.000	0.000	0.000	0.000
6	A	15	ILE	0	-0.014	-0.013	4.823	0.089	0.089	0.000	0.000	0.000	0.000
7	A	16	LEU	0	-0.004	-0.004	8.816	0.134	0.134	0.000	0.000	0.000	0.000
8	A	17	VAL	0	0.008	0.000	11.647	0.025	0.025	0.000	0.000	0.000	0.000
9	A	18	VAL	0	-0.013	-0.013	13.958	0.022	0.022	0.000	0.000	0.000	0.000
10	A	19	GLH	0	-0.055	-0.076	17.431	0.012	0.012	0.000	0.000	0.000	0.000
11	A	20	ASP	-1	-0.817	-0.887	19.532	-0.053	-0.053	0.000	0.000	0.000	0.000
12	A	21	ASP	-1	-0.896	-0.942	21.950	-0.024	-0.024	0.000	0.000	0.000	0.000
13	A	22	TYR	0	0.027	-0.006	21.004	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	23	ASP	-1	-0.848	-0.914	20.475	-0.015	-0.015	0.000	0.000	0.000	0.000
15	A	24	ILE	0	-0.014	-0.018	18.180	0.009	0.009	0.000	0.000	0.000	0.000
16	A	25	GLY	0	0.006	-0.003	16.796	0.005	0.005	0.000	0.000	0.000	0.000
17	A	26	ASP	-1	-0.806	-0.887	15.726	-0.043	-0.043	0.000	0.000	0.000	0.000
18	A	27	ILE	0	-0.060	-0.019	15.722	0.022	0.022	0.000	0.000	0.000	0.000
19	A	28	ILE	0	-0.011	-0.011	11.706	0.038	0.038	0.000	0.000	0.000	0.000
20	A	29	GLU	-1	-0.796	-0.876	11.362	-0.071	-0.071	0.000	0.000	0.000	0.000
21	A	30	ASN	0	-0.015	-0.022	11.327	0.036	0.036	0.000	0.000	0.000	0.000
22	A	31	TYR	0	0.006	-0.002	10.017	0.030	0.030	0.000	0.000	0.000	0.000
23	A	32	LEU	0	0.005	-0.007	6.486	0.183	0.183	0.000	0.000	0.000	0.000
24	A	33	LYS	1	0.882	0.928	6.626	0.223	0.223	0.000	0.000	0.000	0.000
25	A	34	ARG	1	0.795	0.910	9.128	-0.203	-0.203	0.000	0.000	0.000	0.000
26	A	35	GLU	-1	-0.895	-0.937	3.739	0.373	0.808	0.079	-0.102	-0.411	-0.001
27	A	36	GLY	0	-0.007	0.006	4.291	0.326	0.750	0.051	-0.191	-0.283	-0.001
28	A	37	MET	0	-0.061	-0.018	3.026	-3.080	-1.967	1.965	-0.699	-2.379	-0.004
29	A	38	SER	0	-0.011	-0.011	5.506	0.697	0.697	0.000	0.000	0.000	0.000
30	A	39	VAL	0	-0.051	-0.031	8.223	-0.108	-0.108	0.000	0.000	0.000	0.000
31	A	40	ILE	0	-0.006	0.006	10.827	0.064	0.064	0.000	0.000	0.000	0.000
32	A	41	ARG	1	0.812	0.883	13.981	0.083	0.083	0.000	0.000	0.000	0.000
33	A	42	ALA	0	-0.016	-0.010	16.687	0.007	0.007	0.000	0.000	0.000	0.000
34	A	43	MET	0	0.026	0.016	19.380	0.001	0.001	0.000	0.000	0.000	0.000
35	A	44	ASN	0	0.005	-0.007	22.274	0.005	0.005	0.000	0.000	0.000	0.000
36	A	45	GLY	0	0.079	0.027	22.462	-0.011	-0.011	0.000	0.000	0.000	0.000
37	A	46	LYS	1	0.823	0.892	23.269	0.065	0.065	0.000	0.000	0.000	0.000
38	A	47	GLN	0	0.028	0.016	21.574	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	48	ALA	0	0.028	0.021	18.952	-0.014	-0.014	0.000	0.000	0.000	0.000
40	A	49	ILE	0	-0.015	-0.013	19.199	-0.018	-0.018	0.000	0.000	0.000	0.000
41	A	50	GLU	-1	-0.874	-0.917	21.431	-0.131	-0.131	0.000	0.000	0.000	0.000
42	A	51	LEU	0	0.011	0.003	17.334	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	52	HIS	0	0.035	0.016	15.436	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	53	ALA	0	-0.080	-0.041	17.761	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	54	SER	0	-0.028	-0.025	20.286	-0.004	-0.004	0.000	0.000	0.000	0.000
46	A	55	GLN	0	-0.034	-0.012	15.198	-0.006	-0.006	0.000	0.000	0.000	0.000
47	A	56	PRO	0	-0.016	-0.001	12.891	0.001	0.001	0.000	0.000	0.000	0.000
48	A	57	ILE	0	-0.049	-0.023	11.297	-0.092	-0.092	0.000	0.000	0.000	0.000
49	A	58	ASP	-1	-0.807	-0.885	7.215	-1.121	-1.121	0.000	0.000	0.000	0.000
50	A	59	LEU	0	-0.052	-0.031	7.139	0.057	0.057	0.000	0.000	0.000	0.000
51	A	60	ILE	0	-0.012	-0.003	9.485	0.015	0.015	0.000	0.000	0.000	0.000
52	A	61	LEU	0	-0.004	0.003	9.772	0.022	0.022	0.000	0.000	0.000	0.000
53	A	62	LEU	0	0.011	-0.003	13.198	0.008	0.008	0.000	0.000	0.000	0.000
54	A	63	ASP	-1	-0.739	-0.807	16.985	-0.051	-0.051	0.000	0.000	0.000	0.000
55	A	64	ILE	0	-0.015	-0.009	19.934	-0.006	-0.006	0.000	0.000	0.000	0.000
56	A	65	LYS	1	0.797	0.892	23.112	0.049	0.049	0.000	0.000	0.000	0.000
57	A	66	LEU	0	0.003	-0.012	21.240	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	67	PRO	0	-0.004	-0.001	25.314	0.003	0.003	0.000	0.000	0.000	0.000
59	A	68	GLU	-1	-0.816	-0.893	27.611	-0.070	-0.070	0.000	0.000	0.000	0.000
60	A	69	LEU	0	-0.039	-0.017	26.680	0.000	0.000	0.000	0.000	0.000	0.000
61	A	70	ASN	0	0.067	0.035	26.762	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	71	GLY	0	0.082	0.035	23.279	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	72	TRP	0	0.046	0.009	22.234	-0.016	-0.016	0.000	0.000	0.000	0.000
64	A	73	GLU	-1	-0.832	-0.908	24.391	-0.089	-0.089	0.000	0.000	0.000	0.000
65	A	74	VAL	0	-0.054	-0.010	21.151	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	75	LEU	0	0.003	0.011	18.272	-0.010	-0.010	0.000	0.000	0.000	0.000
67	A	76	ASN	0	-0.052	-0.033	21.328	-0.013	-0.013	0.000	0.000	0.000	0.000
68	A	77	LYS	1	0.902	0.934	24.364	0.091	0.091	0.000	0.000	0.000	0.000
69	A	78	ILE	0	0.013	0.019	17.730	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	79	ARG	1	0.803	0.876	15.687	0.218	0.218	0.000	0.000	0.000	0.000
71	A	80	GLN	0	-0.046	-0.011	21.635	0.004	0.004	0.000	0.000	0.000	0.000
72	A	81	LYS	1	0.797	0.895	19.490	0.197	0.197	0.000	0.000	0.000	0.000
73	A	82	ALA	0	-0.010	-0.016	17.771	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	83	GLN	0	0.016	0.000	17.645	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	84	THR	0	0.027	0.034	12.262	0.009	0.009	0.000	0.000	0.000	0.000
76	A	85	PRO	0	0.034	0.031	10.518	0.048	0.048	0.000	0.000	0.000	0.000
77	A	86	VAL	0	-0.024	-0.019	12.255	-0.031	-0.031	0.000	0.000	0.000	0.000
78	A	87	ILE	0	-0.004	0.005	9.708	0.024	0.024	0.000	0.000	0.000	0.000
79	A	88	MET	0	-0.033	-0.007	13.718	0.002	0.002	0.000	0.000	0.000	0.000
80	A	89	LEU	0	0.024	0.013	14.657	0.016	0.016	0.000	0.000	0.000	0.000
81	A	90	THR	0	-0.013	-0.064	18.272	0.001	0.001	0.000	0.000	0.000	0.000
82	A	91	ALA	0	0.042	0.009	21.749	0.006	0.006	0.000	0.000	0.000	0.000
83	A	92	LEU	0	-0.059	-0.038	24.056	0.004	0.004	0.000	0.000	0.000	0.000
84	A	93	ASP	-1	-0.858	-0.898	25.905	-0.028	-0.028	0.000	0.000	0.000	0.000
85	A	94	GLN	0	-0.067	-0.044	29.296	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	95	ASP	-1	-0.900	-0.962	28.565	-0.052	-0.052	0.000	0.000	0.000	0.000
87	A	96	ILE	0	-0.029	-0.034	25.519	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	97	ASP	-1	-0.861	-0.920	26.533	-0.059	-0.059	0.000	0.000	0.000	0.000
89	A	98	LYS	1	0.970	0.987	26.142	0.056	0.056	0.000	0.000	0.000	0.000
90	A	99	VAL	0	-0.016	-0.021	24.559	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	100	MET	0	0.014	0.045	21.689	-0.010	-0.010	0.000	0.000	0.000	0.000
92	A	101	ALA	0	0.015	-0.003	21.789	-0.009	-0.009	0.000	0.000	0.000	0.000
93	A	102	LEU	0	-0.082	-0.032	23.106	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	103	ARG	1	0.857	0.947	17.465	0.143	0.143	0.000	0.000	0.000	0.000
95	A	104	ILE	0	-0.042	0.007	17.173	-0.019	-0.019	0.000	0.000	0.000	0.000
96	A	105	GLY	0	0.026	0.012	19.258	0.013	0.013	0.000	0.000	0.000	0.000
97	A	106	ALA	0	-0.028	-0.029	14.810	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	107	ASP	-1	-0.767	-0.869	13.807	-0.272	-0.272	0.000	0.000	0.000	0.000
99	A	108	ASP	-1	-0.795	-0.888	13.160	-0.096	-0.096	0.000	0.000	0.000	0.000
100	A	109	PHE	0	-0.076	-0.054	15.113	-0.005	-0.005	0.000	0.000	0.000	0.000
101	A	110	VAL	0	0.018	0.012	14.025	0.011	0.011	0.000	0.000	0.000	0.000
102	A	111	VAL	0	0.021	0.019	17.198	-0.007	-0.007	0.000	0.000	0.000	0.000
103	A	112	LYS	1	0.815	0.913	19.875	0.061	0.061	0.000	0.000	0.000	0.000
104	A	113	PRO	0	0.010	-0.004	21.748	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	114	PHE	0	0.069	0.023	15.722	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	115	ASN	0	0.039	0.028	15.595	0.024	0.024	0.000	0.000	0.000	0.000
107	A	116	PRO	0	0.034	0.006	13.589	0.007	0.007	0.000	0.000	0.000	0.000
108	A	117	ASN	0	-0.005	-0.020	10.930	0.086	0.086	0.000	0.000	0.000	0.000
109	A	118	GLU	-1	-0.865	-0.908	10.782	0.053	0.053	0.000	0.000	0.000	0.000
110	A	119	VAL	0	0.005	0.003	10.160	-0.009	-0.009	0.000	0.000	0.000	0.000
111	A	120	ILE	0	-0.004	0.013	5.600	-0.121	-0.060	-0.001	-0.004	-0.056	0.000
112	A	121	ALA	0	0.028	0.017	6.667	0.268	0.268	0.000	0.000	0.000	0.000
113	A	122	ARG	1	0.792	0.867	8.417	-0.057	-0.057	0.000	0.000	0.000	0.000
114	A	123	VAL	0	0.017	0.006	4.459	-0.270	-0.191	-0.001	-0.009	-0.070	0.000
115	A	124	GLN	0	-0.029	-0.035	2.732	-2.827	-4.143	5.372	-1.414	-2.643	-0.001
116	A	125	ALA	0	-0.072	-0.034	4.658	-0.793	-0.718	-0.001	-0.015	-0.059	0.000
117	A	126	VAL	0	-0.024	-0.021	7.873	-0.072	-0.072	0.000	0.000	0.000	0.000
118	A	127	LEU	0	-0.006	-0.004	2.718	-0.775	-0.233	0.401	-0.192	-0.751	-0.001
119	A	128	ARG	1	0.892	0.965	5.723	0.649	0.649	0.000	0.000	0.000	0.000
120	A	129	ARG	1	0.829	0.934	7.040	0.435	0.435	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:10:CYS)