FMO DATABASE

FMODB ID: 4JNLN

Calculation Name: 3HDE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HDE

Chain ID: A

ChEMBL ID:

UniProt ID: P27359

Base Structure: X-ray

Registration Date: 2023-09-20

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	163
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1595603.212793
FMO2-HF: Nuclear repulsion	1531869.132603
FMO2-HF: Total energy	-63734.08019
FMO2-MP2: Total energy	-63917.780285

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:1:MET)

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

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.
-45.282	-39.955	29.876	-11.712	-23.489	-0.097

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / q_NPA : 0.002

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	3	PRO	0	0.018	-0.001	3.087	-0.888	1.364	0.149	-1.165	-1.236	-0.003
4	A	4	SER	0	0.006	0.010	4.681	0.630	0.844	-0.001	-0.012	-0.200	0.000
5	A	5	LEU	0	0.068	0.028	2.446	-1.182	-0.063	0.491	-0.326	-1.284	0.001
6	A	6	ARG	1	0.987	0.988	2.247	-4.321	-4.261	8.014	-2.610	-5.464	0.015
7	A	7	LYS	1	0.958	0.969	3.695	-1.125	-3.110	0.034	2.419	-0.468	0.000
8	A	8	ALA	0	0.017	0.018	7.426	-0.389	-0.389	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.021	-0.001	4.898	-0.844	-0.637	0.001	-0.029	-0.179	0.000
10	A	10	ALA	0	-0.007	-0.010	6.640	-0.760	-0.760	0.000	0.000	0.000	0.000
11	A	11	ALA	0	-0.016	-0.001	8.243	-0.454	-0.454	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.003	-0.003	10.075	-0.239	-0.239	0.000	0.000	0.000	0.000
13	A	13	ILE	0	-0.013	-0.005	7.807	-0.218	-0.218	0.000	0.000	0.000	0.000
14	A	14	GLY	0	-0.005	0.006	11.513	-0.142	-0.142	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.009	-0.002	14.423	-0.068	-0.068	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.015	0.009	14.304	-0.048	-0.048	0.000	0.000	0.000	0.000
17	A	17	ALA	0	-0.011	-0.022	12.694	0.087	0.087	0.000	0.000	0.000	0.000
18	A	18	ILE	0	-0.017	-0.010	13.473	0.024	0.024	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.027	0.024	14.209	0.028	0.028	0.000	0.000	0.000	0.000
20	A	20	ILE	0	0.015	0.008	8.233	0.112	0.112	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.011	0.009	10.554	0.122	0.122	0.000	0.000	0.000	0.000
22	A	22	SER	0	0.002	0.005	12.449	0.009	0.009	0.000	0.000	0.000	0.000
23	A	23	VAL	0	-0.017	0.010	8.277	-0.010	-0.010	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.046	-0.011	6.599	0.166	0.166	0.000	0.000	0.000	0.000
25	A	25	ILE	0	0.018	0.004	9.208	-0.062	-0.062	0.000	0.000	0.000	0.000
26	A	26	THR	0	-0.066	-0.051	12.442	-0.030	-0.030	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.084	0.045	9.092	-0.033	-0.033	0.000	0.000	0.000	0.000
28	A	28	PRO	0	-0.068	-0.052	7.961	-0.034	-0.034	0.000	0.000	0.000	0.000
29	A	29	SER	0	0.022	0.024	10.660	-0.081	-0.081	0.000	0.000	0.000	0.000
30	A	30	GLY	0	-0.022	0.005	13.398	-0.092	-0.092	0.000	0.000	0.000	0.000
31	A	31	ASN	0	-0.098	-0.075	14.536	-0.131	-0.131	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.900	-0.939	12.338	0.430	0.430	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.025	0.010	9.781	0.153	0.153	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.054	-0.025	7.168	-0.119	-0.119	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.799	-0.875	10.791	-0.107	-0.107	0.000	0.000	0.000	0.000
36	A	36	GLY	0	0.009	0.017	14.622	0.042	0.042	0.000	0.000	0.000	0.000
37	A	37	VAL	0	-0.017	-0.017	17.559	0.002	0.002	0.000	0.000	0.000	0.000
38	A	38	SER	0	-0.022	-0.013	19.593	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	39	TYR	0	0.031	-0.001	20.512	0.005	0.005	0.000	0.000	0.000	0.000
40	A	40	ILE	0	0.037	0.028	25.948	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	41	PRO	0	-0.022	0.001	27.526	0.002	0.002	0.000	0.000	0.000	0.000
42	A	42	TYR	0	0.000	0.009	22.233	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.943	0.976	28.827	-0.012	-0.012	0.000	0.000	0.000	0.000
44	A	44	ASP	-1	-0.782	-0.901	25.196	-0.014	-0.014	0.000	0.000	0.000	0.000
45	A	45	ILE	0	-0.032	-0.012	24.787	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	46	VAL	0	-0.044	-0.022	26.998	-0.005	-0.005	0.000	0.000	0.000	0.000
47	A	47	GLY	0	-0.024	-0.002	29.369	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.019	-0.018	27.920	0.005	0.005	0.000	0.000	0.000	0.000
49	A	49	TRP	0	-0.004	-0.005	28.656	0.006	0.006	0.000	0.000	0.000	0.000
50	A	50	THR	0	-0.004	-0.005	23.647	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	51	VAL	0	0.011	0.003	25.327	0.004	0.004	0.000	0.000	0.000	0.000
52	A	52	CYS	0	-0.019	0.002	21.833	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	53	HIS	0	0.031	0.016	17.513	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.052	0.027	19.010	-0.008	-0.008	0.000	0.000	0.000	0.000
55	A	55	HIS	1	0.766	0.858	20.861	-0.099	-0.099	0.000	0.000	0.000	0.000
56	A	56	THR	0	0.044	0.007	23.577	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	57	GLY	0	0.011	-0.001	26.710	0.000	0.000	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.929	0.951	30.045	-0.011	-0.011	0.000	0.000	0.000	0.000
59	A	59	ASP	-1	-0.822	-0.882	29.721	0.070	0.070	0.000	0.000	0.000	0.000
60	A	60	ILE	0	-0.048	-0.009	27.804	0.009	0.009	0.000	0.000	0.000	0.000
61	A	61	MET	0	0.041	0.012	31.751	-0.008	-0.008	0.000	0.000	0.000	0.000
62	A	62	LEU	0	0.012	-0.008	33.255	0.006	0.006	0.000	0.000	0.000	0.000
63	A	63	GLY	0	0.022	0.023	33.935	0.002	0.002	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.769	0.882	30.789	-0.112	-0.112	0.000	0.000	0.000	0.000
65	A	65	THR	0	0.028	0.010	29.630	0.002	0.002	0.000	0.000	0.000	0.000
66	A	66	TYR	0	-0.033	-0.019	27.050	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	67	THR	0	0.020	-0.023	26.981	0.015	0.015	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.939	0.943	20.826	-0.283	-0.283	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.018	0.022	22.572	0.016	0.016	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.749	-0.838	24.566	0.136	0.136	0.000	0.000	0.000	0.000
71	A	72	LYS	1	0.938	0.967	15.938	-0.491	-0.491	0.000	0.000	0.000	0.000
72	A	73	ALA	0	0.016	0.007	21.227	0.002	0.002	0.000	0.000	0.000	0.000
73	A	74	LEU	0	-0.033	-0.022	24.212	-0.013	-0.013	0.000	0.000	0.000	0.000
74	A	75	LEU	0	0.030	0.028	16.325	-0.009	-0.009	0.000	0.000	0.000	0.000
75	A	76	ASN	0	-0.004	0.002	20.616	0.003	0.003	0.000	0.000	0.000	0.000
76	A	77	LYS	1	0.962	0.980	21.764	-0.119	-0.119	0.000	0.000	0.000	0.000
77	A	78	ASP	-1	-0.782	-0.849	21.747	0.059	0.059	0.000	0.000	0.000	0.000
78	A	79	LEU	0	0.008	0.001	16.072	-0.030	-0.030	0.000	0.000	0.000	0.000
79	A	80	ALA	0	0.021	0.012	19.905	-0.027	-0.027	0.000	0.000	0.000	0.000
80	A	81	THR	0	-0.076	-0.057	22.229	-0.023	-0.023	0.000	0.000	0.000	0.000
81	A	82	VAL	0	0.017	0.007	18.178	-0.020	-0.020	0.000	0.000	0.000	0.000
82	A	83	ALA	0	0.009	0.004	19.542	-0.029	-0.029	0.000	0.000	0.000	0.000
83	A	84	ARG	1	0.895	0.947	20.682	-0.049	-0.049	0.000	0.000	0.000	0.000
84	A	85	GLN	0	-0.026	-0.003	23.263	-0.024	-0.024	0.000	0.000	0.000	0.000
85	A	86	ILE	0	0.035	0.014	17.484	-0.014	-0.014	0.000	0.000	0.000	0.000
86	A	87	ASN	0	0.025	0.009	19.181	-0.039	-0.039	0.000	0.000	0.000	0.000
87	A	88	PRO	0	0.025	0.025	21.934	-0.010	-0.010	0.000	0.000	0.000	0.000
88	A	89	TYR	0	-0.023	-0.020	23.702	0.001	0.001	0.000	0.000	0.000	0.000
89	A	90	ILE	0	-0.014	0.005	17.787	-0.021	-0.021	0.000	0.000	0.000	0.000
90	A	91	LYS	1	0.849	0.914	21.883	0.146	0.146	0.000	0.000	0.000	0.000
91	A	92	VAL	0	0.020	0.023	19.325	0.008	0.008	0.000	0.000	0.000	0.000
92	A	93	ASP	-1	-0.879	-0.932	18.745	-0.127	-0.127	0.000	0.000	0.000	0.000
93	A	94	ILE	0	-0.045	-0.034	14.053	-0.058	-0.058	0.000	0.000	0.000	0.000
94	A	95	PRO	0	0.016	0.005	10.556	0.059	0.059	0.000	0.000	0.000	0.000
95	A	96	GLU	-1	-0.746	-0.863	12.145	0.009	0.009	0.000	0.000	0.000	0.000
96	A	97	THR	0	0.004	0.003	6.746	0.051	0.051	0.000	0.000	0.000	0.000
97	A	98	MET	0	0.027	0.025	8.771	-0.078	-0.078	0.000	0.000	0.000	0.000
98	A	99	ARG	1	0.892	0.931	10.138	0.087	0.087	0.000	0.000	0.000	0.000
99	A	100	GLY	0	0.034	0.014	11.316	0.010	0.010	0.000	0.000	0.000	0.000
100	A	101	ALA	0	-0.015	-0.014	7.997	0.063	0.063	0.000	0.000	0.000	0.000
101	A	102	LEU	0	-0.028	-0.017	9.913	-0.020	-0.020	0.000	0.000	0.000	0.000
102	A	103	TYR	0	0.001	0.001	13.397	0.016	0.016	0.000	0.000	0.000	0.000
103	A	104	SER	0	0.001	-0.022	11.064	0.079	0.079	0.000	0.000	0.000	0.000
104	A	105	PHE	0	0.012	0.010	12.631	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	106	VAL	0	-0.030	-0.024	14.004	0.032	0.032	0.000	0.000	0.000	0.000
106	A	107	TYR	0	-0.081	-0.058	16.349	0.022	0.022	0.000	0.000	0.000	0.000
107	A	108	ASN	0	-0.015	0.004	15.796	-0.044	-0.044	0.000	0.000	0.000	0.000
108	A	109	VAL	0	-0.020	0.004	17.353	-0.011	-0.011	0.000	0.000	0.000	0.000
109	A	110	GLY	0	0.048	0.041	19.916	0.008	0.008	0.000	0.000	0.000	0.000
110	A	111	ALA	0	0.025	-0.013	22.000	-0.026	-0.026	0.000	0.000	0.000	0.000
111	A	112	GLY	0	-0.014	-0.002	23.028	-0.011	-0.011	0.000	0.000	0.000	0.000
112	A	113	ASN	0	0.032	0.012	21.822	-0.011	-0.011	0.000	0.000	0.000	0.000
113	A	114	PHE	0	0.045	0.018	16.941	-0.017	-0.017	0.000	0.000	0.000	0.000
114	A	115	ARG	1	0.848	0.926	21.196	0.084	0.084	0.000	0.000	0.000	0.000
115	A	116	THR	0	0.021	0.017	24.502	-0.004	-0.004	0.000	0.000	0.000	0.000
116	A	117	SER	0	-0.032	-0.006	20.500	-0.023	-0.023	0.000	0.000	0.000	0.000
117	A	118	THR	0	-0.005	-0.020	21.261	0.015	0.015	0.000	0.000	0.000	0.000
118	A	119	LEU	0	0.018	0.011	14.561	-0.005	-0.005	0.000	0.000	0.000	0.000
119	A	120	LEU	0	0.024	0.019	18.757	-0.016	-0.016	0.000	0.000	0.000	0.000
120	A	121	ARG	1	0.861	0.925	20.553	0.250	0.250	0.000	0.000	0.000	0.000
121	A	122	LYS	1	0.814	0.895	19.198	0.448	0.448	0.000	0.000	0.000	0.000
122	A	123	ILE	0	0.021	0.010	16.135	-0.006	-0.006	0.000	0.000	0.000	0.000
123	A	124	ASN	0	-0.019	-0.020	19.102	0.009	0.009	0.000	0.000	0.000	0.000
124	A	125	GLN	0	0.002	0.018	22.167	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	126	GLY	0	0.056	0.031	20.436	0.006	0.006	0.000	0.000	0.000	0.000
126	A	127	ASP	-1	-0.796	-0.867	18.320	-0.599	-0.599	0.000	0.000	0.000	0.000
127	A	128	ILE	0	0.023	-0.012	13.070	-0.047	-0.047	0.000	0.000	0.000	0.000
128	A	129	LYS	1	0.841	0.912	10.738	1.195	1.195	0.000	0.000	0.000	0.000
129	A	130	GLY	0	0.067	0.031	13.844	-0.116	-0.116	0.000	0.000	0.000	0.000
130	A	131	ALA	0	-0.033	-0.029	15.498	0.005	0.005	0.000	0.000	0.000	0.000
131	A	132	CYS	0	-0.078	-0.026	4.579	0.662	0.721	-0.002	-0.005	-0.052	0.000
132	A	133	ASP	-1	-0.763	-0.868	11.759	-1.404	-1.404	0.000	0.000	0.000	0.000
133	A	134	GLN	0	-0.036	-0.012	13.633	0.132	0.132	0.000	0.000	0.000	0.000
134	A	135	LEU	0	0.013	0.015	10.120	0.101	0.101	0.000	0.000	0.000	0.000
135	A	136	ARG	1	0.771	0.830	9.673	1.488	1.488	0.000	0.000	0.000	0.000
136	A	137	ARG	1	0.871	0.941	14.178	0.485	0.485	0.000	0.000	0.000	0.000
137	A	138	TRP	0	-0.039	-0.001	16.099	0.094	0.094	0.000	0.000	0.000	0.000
138	A	139	THR	0	0.024	-0.002	14.197	0.015	0.015	0.000	0.000	0.000	0.000
139	A	140	TYR	0	0.023	-0.001	16.859	0.057	0.057	0.000	0.000	0.000	0.000
140	A	141	ALA	0	0.035	0.016	20.520	0.002	0.002	0.000	0.000	0.000	0.000
141	A	142	GLY	0	0.025	0.017	22.870	0.006	0.006	0.000	0.000	0.000	0.000
142	A	143	GLY	0	0.030	0.022	26.100	0.008	0.008	0.000	0.000	0.000	0.000
143	A	144	LYS	1	0.884	0.969	21.125	0.106	0.106	0.000	0.000	0.000	0.000
144	A	145	GLN	0	0.060	0.033	16.905	-0.056	-0.056	0.000	0.000	0.000	0.000
145	A	146	TRP	0	0.034	-0.011	17.493	0.047	0.047	0.000	0.000	0.000	0.000
146	A	147	LYS	1	0.940	0.946	12.620	0.203	0.203	0.000	0.000	0.000	0.000
147	A	148	GLY	0	0.053	0.028	12.068	-0.039	-0.039	0.000	0.000	0.000	0.000
148	A	149	LEU	0	0.036	0.027	11.696	-0.036	-0.036	0.000	0.000	0.000	0.000
149	A	150	MET	0	-0.017	0.008	12.164	-0.068	-0.068	0.000	0.000	0.000	0.000
150	A	151	THR	0	0.013	0.006	7.488	-0.226	-0.226	0.000	0.000	0.000	0.000
151	A	152	ARG	1	0.763	0.868	7.261	-0.222	-0.222	0.000	0.000	0.000	0.000
152	A	153	ARG	1	0.780	0.869	8.615	0.249	0.249	0.000	0.000	0.000	0.000
153	A	154	GLU	-1	-0.763	-0.844	6.206	-2.046	-2.046	0.000	0.000	0.000	0.000
154	A	155	ILE	0	0.007	0.012	2.580	-1.924	-1.013	1.208	-0.645	-1.474	-0.002
155	A	156	GLU	-1	-0.734	-0.850	4.690	-0.977	-0.915	-0.001	-0.005	-0.056	0.000
156	A	157	ARG	1	0.842	0.904	7.285	2.139	2.139	0.000	0.000	0.000	0.000
157	A	158	GLU	-1	-0.838	-0.923	1.903	-34.808	-33.331	15.738	-8.376	-8.838	-0.102
158	A	159	ILE	0	-0.051	-0.035	2.273	0.245	0.163	2.428	-0.366	-1.980	-0.001
159	A	161	LEU	0	0.015	-0.002	6.662	0.406	0.406	0.000	0.000	0.000	0.000
160	A	162	TRP	0	0.016	0.012	2.352	-0.900	0.133	1.817	-0.592	-2.258	-0.005
161	A	163	GLY	0	-0.039	-0.023	5.643	0.341	0.341	0.000	0.000	0.000	0.000
162	A	164	GLN	0	0.024	0.008	9.102	0.021	0.021	0.000	0.000	0.000	0.000
163	A	165	GLN	0	0.038	0.049	6.945	-0.018	-0.018	0.000	0.000	0.000	0.000

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