FMO DATABASE

FMODB ID: QY79Y

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1407048.791111
FMO2-HF: Nuclear repulsion	1348136.106131
FMO2-HF: Total energy	-58912.684981
FMO2-MP2: Total energy	-59086.056359

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.
-25.853	-20.635	10.106	-5.522	-9.8	0.044

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 : 0.073 / q_NPA : 0.034

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	-0.842	-0.895	2.440	-3.748	-0.371	3.188	-2.711	-3.854	0.024
4	A	5	ASN	0	0.009	0.010	2.000	-12.110	-11.498	6.862	-2.479	-4.994	0.020
5	A	6	THR	0	-0.008	0.002	3.746	-2.992	-2.459	0.023	-0.206	-0.350	0.001
6	A	7	ILE	0	0.001	0.000	5.802	-0.715	-0.715	0.000	0.000	0.000	0.000
7	A	8	LYS	1	0.856	0.913	6.547	-2.011	-2.011	0.000	0.000	0.000	0.000
8	A	9	SER	0	-0.009	-0.001	7.920	-0.591	-0.591	0.000	0.000	0.000	0.000
9	A	10	ALA	0	0.031	0.008	9.774	-0.282	-0.282	0.000	0.000	0.000	0.000
10	A	11	TYR	0	-0.036	-0.029	11.143	-0.134	-0.134	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.847	-0.906	11.752	0.909	0.909	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-0.818	-0.906	13.944	0.360	0.360	0.000	0.000	0.000	0.000
13	A	14	SER	0	-0.073	-0.050	15.494	-0.097	-0.097	0.000	0.000	0.000	0.000
14	A	15	LEU	0	-0.043	-0.005	16.729	-0.064	-0.064	0.000	0.000	0.000	0.000
15	A	16	ASN	0	-0.070	-0.030	18.812	-0.074	-0.074	0.000	0.000	0.000	0.000
16	A	17	ASN	0	-0.106	-0.064	20.710	-0.046	-0.046	0.000	0.000	0.000	0.000
17	A	18	ALA	0	0.035	0.031	18.822	-0.033	-0.033	0.000	0.000	0.000	0.000
18	A	19	ARG	1	0.750	0.858	12.120	-0.419	-0.419	0.000	0.000	0.000	0.000
19	A	20	PHE	0	-0.023	-0.019	18.260	-0.021	-0.021	0.000	0.000	0.000	0.000
20	A	21	GLY	0	0.015	0.009	17.781	-0.032	-0.032	0.000	0.000	0.000	0.000
21	A	22	ASP	-1	-0.932	-0.954	13.189	0.299	0.299	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.869	0.930	10.159	-0.485	-0.485	0.000	0.000	0.000	0.000
23	A	24	ILE	0	0.036	0.017	10.719	-0.032	-0.032	0.000	0.000	0.000	0.000
24	A	25	GLU	-1	-0.796	-0.919	6.235	0.035	0.035	0.000	0.000	0.000	0.000
25	A	26	GLU	-1	-0.812	-0.876	5.762	-0.071	-0.071	0.000	0.000	0.000	0.000
26	A	27	ILE	0	0.005	0.006	7.424	-0.107	-0.107	0.000	0.000	0.000	0.000
27	A	28	ASP	-1	-0.872	-0.931	6.615	-0.287	-0.287	0.000	0.000	0.000	0.000
28	A	29	ALA	0	-0.050	-0.031	3.344	-0.574	-0.192	0.036	-0.106	-0.312	-0.001
29	A	30	ILE	0	0.014	0.008	4.492	0.130	0.281	-0.001	-0.010	-0.139	0.000
30	A	31	GLN	0	-0.007	-0.002	7.197	0.060	0.060	0.000	0.000	0.000	0.000
31	A	32	SER	0	0.008	0.007	4.507	0.133	0.217	-0.001	-0.006	-0.077	0.000
32	A	33	THR	0	-0.066	-0.021	4.610	-0.082	-0.003	-0.001	-0.004	-0.074	0.000
33	A	34	ILE	0	-0.010	-0.007	6.380	0.062	0.062	0.000	0.000	0.000	0.000
34	A	35	LYS	1	0.893	0.935	9.649	0.195	0.195	0.000	0.000	0.000	0.000
35	A	36	SER	0	-0.080	-0.046	7.306	-0.043	-0.043	0.000	0.000	0.000	0.000
36	A	37	ALA	0	-0.004	0.007	9.945	-0.063	-0.063	0.000	0.000	0.000	0.000
37	A	38	LYS	1	0.892	0.949	11.471	0.425	0.425	0.000	0.000	0.000	0.000
38	A	39	ASN	0	-0.024	0.007	13.865	0.075	0.075	0.000	0.000	0.000	0.000
39	A	40	VAL	0	0.008	0.007	14.791	0.004	0.004	0.000	0.000	0.000	0.000
40	A	41	THR	0	0.047	0.027	16.688	0.002	0.002	0.000	0.000	0.000	0.000
41	A	42	VAL	0	-0.014	-0.009	18.830	0.017	0.017	0.000	0.000	0.000	0.000
42	A	43	ALA	0	0.027	0.012	21.394	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	44	THR	0	-0.103	-0.065	23.073	0.013	0.013	0.000	0.000	0.000	0.000
44	A	45	SER	0	0.119	0.055	26.601	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	46	ASN	0	-0.096	-0.053	29.620	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	47	GLU	-1	-0.756	-0.898	29.709	-0.040	-0.040	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.784	0.881	30.349	0.006	0.006	0.000	0.000	0.000	0.000
48	A	49	LYS	1	0.932	0.954	27.654	-0.008	-0.008	0.000	0.000	0.000	0.000
49	A	50	PHE	0	0.045	0.028	23.341	0.002	0.002	0.000	0.000	0.000	0.000
50	A	51	LYS	1	0.890	0.924	25.637	0.044	0.044	0.000	0.000	0.000	0.000
51	A	52	VAL	0	-0.026	-0.006	25.937	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	53	VAL	0	-0.011	-0.013	20.938	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	54	SER	0	0.076	0.034	21.971	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	55	ASP	-1	-0.863	-0.884	22.572	-0.067	-0.067	0.000	0.000	0.000	0.000
55	A	56	ILE	0	-0.063	-0.031	20.108	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	57	ILE	0	0.031	0.001	16.521	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	58	SER	0	0.002	-0.012	18.089	-0.022	-0.022	0.000	0.000	0.000	0.000
58	A	59	ARG	1	0.824	0.914	20.386	0.062	0.062	0.000	0.000	0.000	0.000
59	A	60	ILE	0	-0.072	-0.033	14.834	0.002	0.002	0.000	0.000	0.000	0.000
60	A	61	THR	0	-0.028	-0.011	13.593	-0.019	-0.019	0.000	0.000	0.000	0.000
61	A	62	ASP	-1	-0.899	-0.955	15.469	-0.247	-0.247	0.000	0.000	0.000	0.000
62	A	63	ALA	0	-0.016	-0.004	15.761	-0.031	-0.031	0.000	0.000	0.000	0.000
63	A	64	ASN	0	-0.030	-0.009	17.453	0.040	0.040	0.000	0.000	0.000	0.000
64	A	65	ILE	0	-0.016	-0.010	18.807	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	66	SER	0	0.021	0.006	20.733	0.008	0.008	0.000	0.000	0.000	0.000
66	A	67	MET	0	-0.058	-0.012	22.236	0.010	0.010	0.000	0.000	0.000	0.000
67	A	68	LEU	0	0.006	0.002	22.254	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	69	GLU	-1	-0.923	-0.957	24.459	-0.055	-0.055	0.000	0.000	0.000	0.000
69	A	70	ILE	0	-0.031	-0.012	25.199	0.006	0.006	0.000	0.000	0.000	0.000
70	A	71	PRO	0	0.008	0.005	27.602	0.004	0.004	0.000	0.000	0.000	0.000
71	A	72	THR	0	0.072	0.023	25.547	0.006	0.006	0.000	0.000	0.000	0.000
72	A	73	ASN	0	-0.009	-0.006	28.523	0.006	0.006	0.000	0.000	0.000	0.000
73	A	74	SER	0	0.058	0.033	29.931	0.005	0.005	0.000	0.000	0.000	0.000
74	A	75	ALA	0	0.058	0.029	27.017	0.006	0.006	0.000	0.000	0.000	0.000
75	A	76	ASP	-1	-0.876	-0.922	28.927	0.057	0.057	0.000	0.000	0.000	0.000
76	A	77	LEU	0	-0.016	0.003	31.710	0.000	0.000	0.000	0.000	0.000	0.000
77	A	78	THR	0	-0.021	-0.006	28.015	0.009	0.009	0.000	0.000	0.000	0.000
78	A	79	ARG	1	0.971	0.961	28.579	-0.122	-0.122	0.000	0.000	0.000	0.000
79	A	80	MET	0	0.009	0.007	23.525	0.000	0.000	0.000	0.000	0.000	0.000
80	A	81	PRO	0	-0.024	0.009	25.307	0.004	0.004	0.000	0.000	0.000	0.000
81	A	82	ALA	0	0.017	0.014	23.375	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	83	LEU	0	0.068	0.028	18.706	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	84	ASN	0	0.013	-0.022	21.111	0.013	0.013	0.000	0.000	0.000	0.000
84	A	85	LYS	1	0.773	0.878	23.439	-0.052	-0.052	0.000	0.000	0.000	0.000
85	A	86	GLY	0	0.024	0.007	19.524	-0.014	-0.014	0.000	0.000	0.000	0.000
86	A	87	LEU	0	0.013	0.001	17.524	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	88	ILE	0	0.027	0.030	19.854	-0.009	-0.009	0.000	0.000	0.000	0.000
88	A	89	ALA	0	-0.007	0.015	19.232	-0.014	-0.014	0.000	0.000	0.000	0.000
89	A	90	VAL	0	-0.055	-0.025	14.913	-0.016	-0.016	0.000	0.000	0.000	0.000
90	A	91	ASP	-1	-0.921	-0.954	17.163	0.118	0.118	0.000	0.000	0.000	0.000
91	A	92	SER	0	-0.118	-0.076	19.504	-0.017	-0.017	0.000	0.000	0.000	0.000
92	A	93	SER	0	-0.061	-0.034	18.751	-0.022	-0.022	0.000	0.000	0.000	0.000
93	A	94	ASP	-1	-0.887	-0.943	15.521	-0.154	-0.154	0.000	0.000	0.000	0.000
94	A	95	ALA	0	-0.072	-0.023	14.881	-0.050	-0.050	0.000	0.000	0.000	0.000
95	A	96	ASP	-1	-0.829	-0.926	10.344	-0.460	-0.460	0.000	0.000	0.000	0.000
96	A	97	LEU	0	-0.075	-0.046	10.527	0.034	0.034	0.000	0.000	0.000	0.000
97	A	98	ILE	0	0.009	0.017	12.967	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	99	ILE	0	-0.020	0.001	16.117	0.024	0.024	0.000	0.000	0.000	0.000
99	A	100	THR	0	-0.008	-0.012	18.513	-0.011	-0.011	0.000	0.000	0.000	0.000
100	A	101	ARG	1	0.823	0.871	21.298	-0.026	-0.026	0.000	0.000	0.000	0.000
101	A	102	GLY	0	-0.028	-0.015	24.258	-0.005	-0.005	0.000	0.000	0.000	0.000
102	A	103	ARG	1	0.817	0.907	27.112	-0.063	-0.063	0.000	0.000	0.000	0.000
103	A	104	LEU	0	0.050	0.030	25.471	0.007	0.007	0.000	0.000	0.000	0.000
104	A	105	GLY	0	0.054	0.021	27.148	0.013	0.013	0.000	0.000	0.000	0.000
105	A	106	ILE	0	0.017	0.021	29.870	-0.006	-0.006	0.000	0.000	0.000	0.000
106	A	107	PRO	0	0.027	0.011	33.543	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	108	GLY	0	0.022	0.017	35.407	0.000	0.000	0.000	0.000	0.000	0.000
108	A	109	SER	0	-0.063	-0.046	31.333	0.000	0.000	0.000	0.000	0.000	0.000
109	A	110	GLY	0	0.030	0.016	31.078	0.002	0.002	0.000	0.000	0.000	0.000
110	A	111	SER	0	-0.072	-0.034	27.844	0.002	0.002	0.000	0.000	0.000	0.000
111	A	112	LEU	0	0.032	0.019	21.591	0.001	0.001	0.000	0.000	0.000	0.000
112	A	113	LEU	0	-0.020	-0.003	19.461	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	114	LEU	0	-0.006	-0.011	17.528	0.012	0.012	0.000	0.000	0.000	0.000
114	A	115	ILE	0	0.024	0.014	13.128	-0.023	-0.023	0.000	0.000	0.000	0.000
115	A	116	MET	0	-0.029	-0.009	13.326	0.032	0.032	0.000	0.000	0.000	0.000
116	A	117	ASP	-1	-0.699	-0.857	7.874	0.582	0.582	0.000	0.000	0.000	0.000
117	A	118	LYS	1	1.029	1.020	6.466	0.352	0.352	0.000	0.000	0.000	0.000
118	A	119	LYS	1	0.813	0.901	7.500	-1.110	-1.110	0.000	0.000	0.000	0.000
119	A	120	GLY	0	0.050	0.034	11.893	0.030	0.030	0.000	0.000	0.000	0.000
120	A	121	ARG	1	0.728	0.847	5.988	-2.024	-2.024	0.000	0.000	0.000	0.000
121	A	122	ILE	0	-0.006	-0.010	12.247	-0.098	-0.098	0.000	0.000	0.000	0.000
122	A	123	LEU	0	-0.017	0.000	8.363	0.051	0.051	0.000	0.000	0.000	0.000
123	A	124	THR	0	-0.012	-0.026	11.775	-0.015	-0.015	0.000	0.000	0.000	0.000
124	A	125	GLY	0	0.021	0.002	14.993	0.009	0.009	0.000	0.000	0.000	0.000
125	A	126	SER	0	-0.069	-0.047	18.651	-0.004	-0.004	0.000	0.000	0.000	0.000
126	A	127	VAL	0	0.023	0.006	22.191	0.004	0.004	0.000	0.000	0.000	0.000
127	A	128	SER	0	-0.040	-0.042	25.740	-0.007	-0.007	0.000	0.000	0.000	0.000
128	A	129	PRO	0	0.031	0.009	29.101	0.004	0.004	0.000	0.000	0.000	0.000
129	A	130	SER	0	0.037	0.014	32.640	-0.004	-0.004	0.000	0.000	0.000	0.000
130	A	131	SER	0	0.052	0.034	34.784	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	132	ILE	0	0.003	-0.005	36.995	-0.003	-0.003	0.000	0.000	0.000	0.000
132	A	133	ILE	0	-0.009	-0.002	36.797	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	134	HIS	0	0.039	0.026	34.240	0.000	0.000	0.000	0.000	0.000	0.000
134	A	135	LYS	1	0.817	0.908	36.745	-0.023	-0.023	0.000	0.000	0.000	0.000
135	A	136	ASN	0	0.017	-0.016	32.922	-0.002	-0.002	0.000	0.000	0.000	0.000
136	A	137	PRO	0	0.023	0.017	35.212	0.001	0.001	0.000	0.000	0.000	0.000
137	A	138	ILE	0	0.005	-0.003	31.052	0.000	0.000	0.000	0.000	0.000	0.000
138	A	139	ASP	-1	-0.747	-0.870	30.781	-0.008	-0.008	0.000	0.000	0.000	0.000
139	A	140	LYS	1	1.022	1.012	29.825	0.005	0.005	0.000	0.000	0.000	0.000
140	A	141	THR	0	-0.041	-0.010	29.290	0.000	0.000	0.000	0.000	0.000	0.000
141	A	142	VAL	0	-0.007	0.001	25.382	0.003	0.003	0.000	0.000	0.000	0.000
142	A	143	GLU	-1	-0.906	-0.949	25.199	-0.017	-0.017	0.000	0.000	0.000	0.000
143	A	144	LEU	0	0.020	0.014	24.866	-0.002	-0.002	0.000	0.000	0.000	0.000
144	A	145	GLU	-1	-0.716	-0.798	23.734	0.034	0.034	0.000	0.000	0.000	0.000
145	A	146	LEU	0	0.032	0.038	18.706	0.007	0.007	0.000	0.000	0.000	0.000
146	A	147	ILE	0	0.036	0.012	19.967	-0.005	-0.005	0.000	0.000	0.000	0.000
147	A	148	THR	0	-0.019	-0.019	20.798	-0.001	-0.001	0.000	0.000	0.000	0.000
148	A	149	ALA	0	-0.043	-0.018	17.846	0.005	0.005	0.000	0.000	0.000	0.000
149	A	150	LEU	0	0.020	0.019	15.123	0.001	0.001	0.000	0.000	0.000	0.000
150	A	151	GLU	-1	-0.791	-0.893	16.277	-0.020	-0.020	0.000	0.000	0.000	0.000
151	A	152	ARG	1	0.844	0.936	15.929	-0.106	-0.106	0.000	0.000	0.000	0.000
152	A	153	ILE	0	-0.037	-0.010	11.970	0.016	0.016	0.000	0.000	0.000	0.000
153	A	154	GLY	0	0.020	0.006	13.059	-0.042	-0.042	0.000	0.000	0.000	0.000
154	A	155	ILE	0	-0.057	-0.019	11.769	-0.015	-0.015	0.000	0.000	0.000	0.000
155	A	156	VAL	0	-0.002	-0.004	15.967	0.014	0.014	0.000	0.000	0.000	0.000
156	A	157	VAL	0	0.021	0.016	19.244	-0.008	-0.008	0.000	0.000	0.000	0.000
157	A	158	LYS	1	0.885	0.939	21.597	0.026	0.026	0.000	0.000	0.000	0.000

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