FMO DATABASE

FMODB ID: K9713

Calculation Name: 5D5P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D5P

Chain ID: A

ChEMBL ID:

UniProt ID: Q6LX55

Base Structure: X-ray

Registration Date: 2023-06-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	157
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1408896.441646
FMO2-HF: Nuclear repulsion	1349983.383923
FMO2-HF: Total energy	-58913.057723
FMO2-MP2: Total energy	-59086.41628

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:2:ASN)

Summations of interaction energy for fragment #1(A:2:ASN)

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.
-29.965	-27.844	14.453	-6.736	-9.834	0.058

Interaction energy analysis for fragmet #1(A:2:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.094 / q_NPA : 0.053

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	A	4	GLU	-1	-0.839	-0.883	2.311	-4.711	-1.432	3.064	-2.728	-3.615	0.023
4	A	5	ASN	0	-0.023	-0.019	1.916	-16.198	-18.592	11.309	-3.691	-5.223	0.035
5	A	6	THR	0	-0.014	-0.004	3.528	-3.040	-2.519	0.010	-0.188	-0.343	0.000
6	A	7	ILE	0	0.024	0.015	6.062	-0.676	-0.676	0.000	0.000	0.000	0.000
7	A	8	LYS	1	0.809	0.898	6.775	-2.269	-2.269	0.000	0.000	0.000	0.000
8	A	9	SER	0	0.012	0.008	8.198	-0.610	-0.610	0.000	0.000	0.000	0.000
9	A	10	ALA	0	0.030	0.015	9.997	-0.283	-0.283	0.000	0.000	0.000	0.000
10	A	11	TYR	0	-0.015	-0.005	11.469	-0.150	-0.150	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.796	-0.880	11.684	1.149	1.149	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-0.815	-0.915	14.055	0.460	0.460	0.000	0.000	0.000	0.000
13	A	14	SER	0	-0.076	-0.053	15.632	-0.116	-0.116	0.000	0.000	0.000	0.000
14	A	15	LEU	0	-0.053	-0.022	16.673	-0.070	-0.070	0.000	0.000	0.000	0.000
15	A	16	ASN	0	-0.089	-0.048	18.607	-0.086	-0.086	0.000	0.000	0.000	0.000
16	A	17	ASN	0	-0.097	-0.047	20.447	-0.058	-0.058	0.000	0.000	0.000	0.000
17	A	18	ALA	0	0.038	0.026	18.905	-0.036	-0.036	0.000	0.000	0.000	0.000
18	A	19	ARG	1	0.751	0.861	11.942	-0.502	-0.502	0.000	0.000	0.000	0.000
19	A	20	PHE	0	-0.037	-0.032	18.164	-0.026	-0.026	0.000	0.000	0.000	0.000
20	A	21	GLY	0	0.000	0.000	17.827	-0.039	-0.039	0.000	0.000	0.000	0.000
21	A	22	ASP	-1	-0.917	-0.936	13.376	0.360	0.360	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.856	0.916	9.504	-0.707	-0.707	0.000	0.000	0.000	0.000
23	A	24	ILE	0	0.019	0.014	10.493	-0.033	-0.033	0.000	0.000	0.000	0.000
24	A	25	GLU	-1	-0.778	-0.912	5.877	0.207	0.207	0.000	0.000	0.000	0.000
25	A	26	GLU	-1	-0.799	-0.865	5.707	0.123	0.123	0.000	0.000	0.000	0.000
26	A	27	ILE	0	0.005	0.011	7.543	-0.099	-0.099	0.000	0.000	0.000	0.000
27	A	28	ASP	-1	-0.868	-0.931	6.709	-0.206	-0.206	0.000	0.000	0.000	0.000
28	A	29	ALA	0	-0.035	-0.021	3.145	-0.483	-0.104	0.073	-0.108	-0.343	0.000
29	A	30	ILE	0	0.008	0.007	4.256	-0.211	-0.062	-0.001	-0.007	-0.141	0.000
30	A	31	GLN	0	0.013	0.006	7.164	-0.055	-0.055	0.000	0.000	0.000	0.000
31	A	32	SER	0	0.010	0.007	4.353	0.104	0.201	-0.001	-0.009	-0.086	0.000
32	A	33	THR	0	-0.076	-0.032	4.582	-0.370	-0.280	-0.001	-0.005	-0.083	0.000
33	A	34	ILE	0	-0.021	-0.017	6.438	0.064	0.064	0.000	0.000	0.000	0.000
34	A	35	LYS	1	0.884	0.929	9.651	0.245	0.245	0.000	0.000	0.000	0.000
35	A	36	SER	0	-0.055	-0.036	7.362	-0.083	-0.083	0.000	0.000	0.000	0.000
36	A	37	ALA	0	0.000	0.013	9.932	-0.057	-0.057	0.000	0.000	0.000	0.000
37	A	38	LYS	1	0.789	0.875	11.079	0.709	0.709	0.000	0.000	0.000	0.000
38	A	39	ASN	0	-0.044	-0.008	13.739	0.148	0.148	0.000	0.000	0.000	0.000
39	A	40	VAL	0	-0.001	-0.004	14.362	-0.028	-0.028	0.000	0.000	0.000	0.000
40	A	41	THR	0	0.032	0.026	16.476	0.025	0.025	0.000	0.000	0.000	0.000
41	A	42	VAL	0	-0.015	-0.018	18.565	0.017	0.017	0.000	0.000	0.000	0.000
42	A	43	ALA	0	0.050	0.029	21.106	0.006	0.006	0.000	0.000	0.000	0.000
43	A	44	THR	0	-0.125	-0.081	22.825	0.023	0.023	0.000	0.000	0.000	0.000
44	A	45	SER	0	0.126	0.056	26.294	-0.008	-0.008	0.000	0.000	0.000	0.000
45	A	46	ASN	0	-0.080	-0.053	29.185	0.005	0.005	0.000	0.000	0.000	0.000
46	A	47	GLU	-1	-0.765	-0.910	29.778	-0.104	-0.104	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.788	0.886	29.937	0.045	0.045	0.000	0.000	0.000	0.000
48	A	49	LYS	1	0.942	0.963	27.863	0.045	0.045	0.000	0.000	0.000	0.000
49	A	50	PHE	0	0.037	0.032	22.912	0.001	0.001	0.000	0.000	0.000	0.000
50	A	51	LYS	1	0.894	0.926	25.382	0.097	0.097	0.000	0.000	0.000	0.000
51	A	52	VAL	0	-0.030	-0.008	26.002	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	53	VAL	0	0.005	-0.003	20.844	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	54	SER	0	0.063	0.028	22.036	-0.018	-0.018	0.000	0.000	0.000	0.000
54	A	55	ASP	-1	-0.858	-0.889	22.804	-0.130	-0.130	0.000	0.000	0.000	0.000
55	A	56	ILE	0	-0.064	-0.029	20.017	0.001	0.001	0.000	0.000	0.000	0.000
56	A	57	ILE	0	0.032	0.000	16.654	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	58	SER	0	0.014	-0.007	18.289	-0.030	-0.030	0.000	0.000	0.000	0.000
58	A	59	ARG	1	0.822	0.915	20.620	0.121	0.121	0.000	0.000	0.000	0.000
59	A	60	ILE	0	-0.082	-0.039	14.928	0.013	0.013	0.000	0.000	0.000	0.000
60	A	61	THR	0	-0.026	-0.013	13.494	-0.033	-0.033	0.000	0.000	0.000	0.000
61	A	62	ASP	-1	-0.849	-0.911	15.301	-0.430	-0.430	0.000	0.000	0.000	0.000
62	A	63	ALA	0	-0.003	-0.001	15.525	-0.059	-0.059	0.000	0.000	0.000	0.000
63	A	64	ASN	0	-0.018	0.000	17.381	0.075	0.075	0.000	0.000	0.000	0.000
64	A	65	ILE	0	0.011	0.003	18.281	-0.019	-0.019	0.000	0.000	0.000	0.000
65	A	66	SER	0	-0.033	-0.025	20.482	0.016	0.016	0.000	0.000	0.000	0.000
66	A	67	MET	0	-0.053	0.000	22.071	0.005	0.005	0.000	0.000	0.000	0.000
67	A	68	LEU	0	0.036	0.024	22.348	-0.012	-0.012	0.000	0.000	0.000	0.000
68	A	69	GLU	-1	-0.910	-0.956	24.648	-0.136	-0.136	0.000	0.000	0.000	0.000
69	A	70	ILE	0	-0.023	-0.002	24.885	0.013	0.013	0.000	0.000	0.000	0.000
70	A	71	PRO	0	-0.016	-0.016	27.530	0.003	0.003	0.000	0.000	0.000	0.000
71	A	72	THR	0	0.055	0.030	25.104	0.009	0.009	0.000	0.000	0.000	0.000
72	A	73	ASN	0	-0.020	-0.019	28.003	0.005	0.005	0.000	0.000	0.000	0.000
73	A	74	SER	0	0.041	0.024	29.443	0.007	0.007	0.000	0.000	0.000	0.000
74	A	75	ALA	0	0.074	0.042	26.643	0.008	0.008	0.000	0.000	0.000	0.000
75	A	76	ASP	-1	-0.845	-0.904	28.556	0.003	0.003	0.000	0.000	0.000	0.000
76	A	77	LEU	0	-0.014	0.007	31.240	0.004	0.004	0.000	0.000	0.000	0.000
77	A	78	THR	0	-0.034	-0.019	27.998	0.009	0.009	0.000	0.000	0.000	0.000
78	A	79	ARG	1	0.975	0.958	28.594	-0.086	-0.086	0.000	0.000	0.000	0.000
79	A	80	MET	0	0.009	0.014	23.241	0.006	0.006	0.000	0.000	0.000	0.000
80	A	81	PRO	0	-0.031	0.008	24.864	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	82	ALA	0	0.026	0.018	23.362	-0.006	-0.006	0.000	0.000	0.000	0.000
82	A	83	LEU	0	0.068	0.041	18.152	-0.014	-0.014	0.000	0.000	0.000	0.000
83	A	84	ASN	0	0.007	-0.013	20.654	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	85	LYS	1	0.769	0.871	22.948	0.008	0.008	0.000	0.000	0.000	0.000
85	A	86	GLY	0	0.030	0.011	19.088	-0.019	-0.019	0.000	0.000	0.000	0.000
86	A	87	LEU	0	-0.005	-0.005	17.298	-0.018	-0.018	0.000	0.000	0.000	0.000
87	A	88	ILE	0	0.023	0.016	19.548	-0.015	-0.015	0.000	0.000	0.000	0.000
88	A	89	ALA	0	0.013	0.021	18.913	-0.013	-0.013	0.000	0.000	0.000	0.000
89	A	90	VAL	0	-0.029	-0.005	14.753	-0.027	-0.027	0.000	0.000	0.000	0.000
90	A	91	ASP	-1	-0.938	-0.974	17.120	-0.025	-0.025	0.000	0.000	0.000	0.000
91	A	92	SER	0	-0.108	-0.076	19.742	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	93	SER	0	-0.015	-0.012	18.700	-0.017	-0.017	0.000	0.000	0.000	0.000
93	A	94	ASP	-1	-0.892	-0.934	15.533	-0.353	-0.353	0.000	0.000	0.000	0.000
94	A	95	ALA	0	-0.058	-0.023	14.606	-0.084	-0.084	0.000	0.000	0.000	0.000
95	A	96	ASP	-1	-0.810	-0.914	9.948	-0.913	-0.913	0.000	0.000	0.000	0.000
96	A	97	LEU	0	-0.064	-0.032	10.168	0.007	0.007	0.000	0.000	0.000	0.000
97	A	98	ILE	0	0.027	0.021	12.479	0.030	0.030	0.000	0.000	0.000	0.000
98	A	99	ILE	0	-0.028	-0.008	15.442	0.024	0.024	0.000	0.000	0.000	0.000
99	A	100	THR	0	-0.003	-0.014	18.093	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	101	ARG	1	0.828	0.876	20.952	0.032	0.032	0.000	0.000	0.000	0.000
101	A	102	GLY	0	-0.022	-0.010	24.205	-0.004	-0.004	0.000	0.000	0.000	0.000
102	A	103	ARG	1	0.799	0.894	26.981	-0.022	-0.022	0.000	0.000	0.000	0.000
103	A	104	LEU	0	0.013	0.008	25.978	0.003	0.003	0.000	0.000	0.000	0.000
104	A	105	GLY	0	0.069	0.016	26.960	0.010	0.010	0.000	0.000	0.000	0.000
105	A	106	ILE	0	0.027	0.036	29.560	-0.007	-0.007	0.000	0.000	0.000	0.000
106	A	107	PRO	0	0.036	0.011	33.375	-0.003	-0.003	0.000	0.000	0.000	0.000
107	A	108	GLY	0	0.012	0.008	35.829	0.003	0.003	0.000	0.000	0.000	0.000
108	A	109	SER	0	-0.054	-0.048	31.655	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	110	GLY	0	0.043	0.032	31.635	0.003	0.003	0.000	0.000	0.000	0.000
110	A	111	SER	0	-0.054	-0.024	28.162	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	112	LEU	0	0.000	0.002	21.882	0.006	0.006	0.000	0.000	0.000	0.000
112	A	113	LEU	0	-0.019	-0.002	19.999	-0.008	-0.008	0.000	0.000	0.000	0.000
113	A	114	LEU	0	-0.002	-0.013	17.481	0.017	0.017	0.000	0.000	0.000	0.000
114	A	115	ILE	0	0.031	0.018	13.082	-0.024	-0.024	0.000	0.000	0.000	0.000
115	A	116	MET	0	-0.024	-0.012	12.715	0.049	0.049	0.000	0.000	0.000	0.000
116	A	117	ASP	-1	-0.689	-0.830	7.583	-0.163	-0.163	0.000	0.000	0.000	0.000
117	A	118	LYS	1	0.960	0.984	5.531	1.276	1.276	0.000	0.000	0.000	0.000
118	A	119	LYS	1	0.810	0.904	7.118	-0.415	-0.415	0.000	0.000	0.000	0.000
119	A	120	GLY	0	0.035	0.023	11.676	0.103	0.103	0.000	0.000	0.000	0.000
120	A	121	ARG	1	0.733	0.833	6.433	-1.054	-1.054	0.000	0.000	0.000	0.000
121	A	122	ILE	0	-0.003	-0.010	11.906	-0.103	-0.103	0.000	0.000	0.000	0.000
122	A	123	LEU	0	-0.015	0.002	8.280	0.072	0.072	0.000	0.000	0.000	0.000
123	A	124	THR	0	-0.018	-0.030	11.691	0.023	0.023	0.000	0.000	0.000	0.000
124	A	125	GLY	0	0.015	-0.001	14.869	-0.007	-0.007	0.000	0.000	0.000	0.000
125	A	126	SER	0	-0.067	-0.047	18.617	0.005	0.005	0.000	0.000	0.000	0.000
126	A	127	VAL	0	0.029	0.009	22.214	0.001	0.001	0.000	0.000	0.000	0.000
127	A	128	SER	0	-0.028	-0.037	25.858	-0.004	-0.004	0.000	0.000	0.000	0.000
128	A	129	PRO	0	0.038	0.010	29.400	0.003	0.003	0.000	0.000	0.000	0.000
129	A	130	SER	0	0.027	0.024	32.989	-0.006	-0.006	0.000	0.000	0.000	0.000
130	A	131	SER	0	0.044	0.026	35.100	0.001	0.001	0.000	0.000	0.000	0.000
131	A	132	ILE	0	0.018	0.013	37.316	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	133	ILE	0	-0.018	-0.001	37.112	0.000	0.000	0.000	0.000	0.000	0.000
133	A	134	HIS	0	0.049	0.027	34.134	0.002	0.002	0.000	0.000	0.000	0.000
134	A	135	LYS	1	0.812	0.885	37.782	-0.002	-0.002	0.000	0.000	0.000	0.000
135	A	136	ASN	0	0.014	-0.004	32.748	0.001	0.001	0.000	0.000	0.000	0.000
136	A	137	PRO	0	0.032	0.012	35.119	0.000	0.000	0.000	0.000	0.000	0.000
137	A	138	ILE	0	0.008	0.001	31.296	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	139	ASP	-1	-0.774	-0.877	30.824	-0.051	-0.051	0.000	0.000	0.000	0.000
139	A	140	LYS	1	0.928	0.930	29.764	0.040	0.040	0.000	0.000	0.000	0.000
140	A	141	THR	0	-0.052	-0.006	29.190	0.002	0.002	0.000	0.000	0.000	0.000
141	A	142	VAL	0	0.019	0.016	25.291	0.002	0.002	0.000	0.000	0.000	0.000
142	A	143	GLU	-1	-0.841	-0.888	25.144	-0.057	-0.057	0.000	0.000	0.000	0.000
143	A	144	LEU	0	0.025	0.018	25.050	-0.003	-0.003	0.000	0.000	0.000	0.000
144	A	145	GLU	-1	-0.737	-0.816	24.017	-0.017	-0.017	0.000	0.000	0.000	0.000
145	A	146	LEU	0	0.036	0.040	18.756	0.005	0.005	0.000	0.000	0.000	0.000
146	A	147	ILE	0	0.030	0.015	20.007	-0.008	-0.008	0.000	0.000	0.000	0.000
147	A	148	THR	0	-0.027	-0.026	20.524	0.002	0.002	0.000	0.000	0.000	0.000
148	A	149	ALA	0	-0.038	-0.016	17.989	0.009	0.009	0.000	0.000	0.000	0.000
149	A	150	LEU	0	0.029	0.031	15.165	-0.002	-0.002	0.000	0.000	0.000	0.000
150	A	151	GLU	-1	-0.776	-0.889	16.159	-0.050	-0.050	0.000	0.000	0.000	0.000
151	A	152	ARG	1	0.859	0.939	15.359	-0.058	-0.058	0.000	0.000	0.000	0.000
152	A	153	ILE	0	-0.035	-0.009	11.937	0.021	0.021	0.000	0.000	0.000	0.000
153	A	154	GLY	0	0.027	0.008	12.979	-0.031	-0.031	0.000	0.000	0.000	0.000
154	A	155	ILE	0	-0.066	-0.025	11.700	-0.013	-0.013	0.000	0.000	0.000	0.000
155	A	156	VAL	0	0.015	0.007	15.843	0.008	0.008	0.000	0.000	0.000	0.000
156	A	157	VAL	0	0.001	0.004	19.237	-0.013	-0.013	0.000	0.000	0.000	0.000
157	A	158	LYS	1	0.846	0.918	21.684	0.057	0.057	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ASN)