FMO DATABASE

FMODB ID: KGR23

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1591782.997439
FMO2-HF: Nuclear repulsion	1528049.058787
FMO2-HF: Total energy	-63733.938652
FMO2-MP2: Total energy	-63917.636394

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.
-40.287	-32.544	24.959	-9.448	-23.253	-0.096

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 : -0.038 / 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	0.049	0.008	2.411	-2.722	-0.580	1.660	-1.606	-2.197	-0.012
4	A	4	SER	0	-0.003	-0.001	4.494	0.774	1.014	-0.001	-0.014	-0.224	0.000
5	A	5	LEU	0	0.061	0.025	2.508	-1.383	0.055	0.602	-0.389	-1.651	0.000
6	A	6	ARG	1	0.999	0.996	2.390	-1.233	0.799	5.550	-2.700	-4.881	0.010
7	A	7	LYS	1	0.947	0.965	3.631	0.424	-3.067	0.038	4.022	-0.569	0.002
8	A	8	ALA	0	0.015	0.018	7.012	-0.367	-0.367	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.026	0.002	4.756	-0.895	-0.644	0.002	-0.042	-0.211	0.000
10	A	10	ALA	0	-0.001	-0.007	6.632	-0.770	-0.770	0.000	0.000	0.000	0.000
11	A	11	ALA	0	-0.027	-0.009	8.187	-0.397	-0.397	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.005	-0.004	9.953	-0.211	-0.211	0.000	0.000	0.000	0.000
13	A	13	ILE	0	0.004	0.013	7.477	-0.185	-0.185	0.000	0.000	0.000	0.000
14	A	14	GLY	0	-0.008	0.003	11.351	-0.117	-0.117	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.019	-0.008	14.230	-0.058	-0.058	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.009	0.009	14.314	-0.043	-0.043	0.000	0.000	0.000	0.000
17	A	17	ALA	0	-0.012	-0.026	12.810	0.095	0.095	0.000	0.000	0.000	0.000
18	A	18	ILE	0	-0.013	-0.007	13.394	0.060	0.060	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.033	0.021	14.065	0.044	0.044	0.000	0.000	0.000	0.000
20	A	20	ILE	0	0.012	0.010	8.098	0.138	0.138	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.011	0.006	10.072	0.185	0.185	0.000	0.000	0.000	0.000
22	A	22	SER	0	-0.017	-0.014	12.234	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	23	VAL	0	-0.033	-0.001	7.710	-0.014	-0.014	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.038	-0.005	6.348	0.138	0.138	0.000	0.000	0.000	0.000
25	A	25	ILE	0	0.030	0.011	9.146	-0.099	-0.099	0.000	0.000	0.000	0.000
26	A	26	THR	0	-0.053	-0.038	12.330	-0.062	-0.062	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.075	0.040	9.399	-0.063	-0.063	0.000	0.000	0.000	0.000
28	A	28	PRO	0	-0.052	-0.035	7.702	-0.040	-0.040	0.000	0.000	0.000	0.000
29	A	29	SER	0	0.021	0.019	10.495	-0.072	-0.072	0.000	0.000	0.000	0.000
30	A	30	GLY	0	-0.030	-0.003	13.452	-0.088	-0.088	0.000	0.000	0.000	0.000
31	A	31	ASN	0	-0.089	-0.067	14.805	-0.108	-0.108	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.902	-0.944	12.489	0.368	0.368	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.033	0.018	9.897	0.125	0.125	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.084	-0.036	7.111	-0.109	-0.109	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.861	-0.907	10.657	0.053	0.053	0.000	0.000	0.000	0.000
36	A	36	GLY	0	0.021	0.017	14.371	0.031	0.031	0.000	0.000	0.000	0.000
37	A	37	VAL	0	-0.016	-0.022	16.960	0.007	0.007	0.000	0.000	0.000	0.000
38	A	38	SER	0	-0.020	0.001	19.446	-0.007	-0.007	0.000	0.000	0.000	0.000
39	A	39	TYR	0	0.031	0.003	20.596	0.004	0.004	0.000	0.000	0.000	0.000
40	A	40	ILE	0	0.024	0.025	25.856	-0.005	-0.005	0.000	0.000	0.000	0.000
41	A	41	PRO	0	-0.027	-0.006	27.557	0.003	0.003	0.000	0.000	0.000	0.000
42	A	42	TYR	0	0.006	-0.001	22.096	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.947	0.979	28.092	-0.037	-0.037	0.000	0.000	0.000	0.000
44	A	44	ASP	-1	-0.795	-0.909	24.705	0.040	0.040	0.000	0.000	0.000	0.000
45	A	45	ILE	0	-0.018	-0.007	24.620	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	46	VAL	0	-0.035	-0.011	26.642	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	47	GLY	0	-0.044	-0.023	29.060	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	48	VAL	0	0.003	-0.004	27.843	0.000	0.000	0.000	0.000	0.000	0.000
49	A	49	TRP	0	-0.035	-0.019	28.298	0.006	0.006	0.000	0.000	0.000	0.000
50	A	50	THR	0	-0.008	0.006	23.244	0.001	0.001	0.000	0.000	0.000	0.000
51	A	51	VAL	0	0.020	0.007	25.132	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	52	CYS	0	-0.032	-0.002	21.818	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	53	HIS	0	0.030	0.019	17.568	0.001	0.001	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.051	0.025	19.102	0.001	0.001	0.000	0.000	0.000	0.000
55	A	55	HIS	1	0.754	0.851	21.004	-0.133	-0.133	0.000	0.000	0.000	0.000
56	A	56	THR	0	0.052	0.011	23.704	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	57	GLY	0	0.014	0.000	26.693	0.001	0.001	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.916	0.948	30.007	-0.037	-0.037	0.000	0.000	0.000	0.000
59	A	59	ASP	-1	-0.846	-0.895	30.048	0.093	0.093	0.000	0.000	0.000	0.000
60	A	60	ILE	0	-0.031	0.002	27.844	0.008	0.008	0.000	0.000	0.000	0.000
61	A	61	MET	0	0.023	0.004	31.796	-0.008	-0.008	0.000	0.000	0.000	0.000
62	A	62	LEU	0	0.029	-0.009	33.074	0.006	0.006	0.000	0.000	0.000	0.000
63	A	63	GLY	0	0.008	0.018	34.036	0.002	0.002	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.793	0.901	30.787	-0.119	-0.119	0.000	0.000	0.000	0.000
65	A	65	THR	0	0.032	0.013	29.712	0.003	0.003	0.000	0.000	0.000	0.000
66	A	66	TYR	0	-0.025	-0.029	27.036	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	67	THR	0	0.023	-0.009	27.155	0.012	0.012	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.953	0.945	20.753	-0.267	-0.267	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.005	0.010	23.008	0.016	0.016	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.754	-0.851	25.082	0.140	0.140	0.000	0.000	0.000	0.000
71	A	72	LYS	1	0.959	0.981	16.472	-0.463	-0.463	0.000	0.000	0.000	0.000
72	A	73	ALA	0	0.020	0.006	21.508	0.004	0.004	0.000	0.000	0.000	0.000
73	A	74	LEU	0	-0.019	-0.009	24.230	-0.010	-0.010	0.000	0.000	0.000	0.000
74	A	75	LEU	0	0.042	0.034	16.378	-0.008	-0.008	0.000	0.000	0.000	0.000
75	A	76	ASN	0	-0.024	-0.004	20.497	0.014	0.014	0.000	0.000	0.000	0.000
76	A	77	LYS	1	0.982	0.983	21.492	-0.131	-0.131	0.000	0.000	0.000	0.000
77	A	78	ASP	-1	-0.794	-0.864	21.833	0.112	0.112	0.000	0.000	0.000	0.000
78	A	79	LEU	0	0.007	-0.003	16.164	-0.022	-0.022	0.000	0.000	0.000	0.000
79	A	80	ALA	0	0.002	0.008	20.085	-0.021	-0.021	0.000	0.000	0.000	0.000
80	A	81	THR	0	-0.051	-0.041	22.537	-0.027	-0.027	0.000	0.000	0.000	0.000
81	A	82	VAL	0	0.036	0.026	18.480	-0.021	-0.021	0.000	0.000	0.000	0.000
82	A	83	ALA	0	0.001	-0.001	19.737	-0.027	-0.027	0.000	0.000	0.000	0.000
83	A	84	ARG	1	0.887	0.937	20.947	-0.091	-0.091	0.000	0.000	0.000	0.000
84	A	85	GLN	0	-0.040	-0.006	23.529	-0.019	-0.019	0.000	0.000	0.000	0.000
85	A	86	ILE	0	0.053	0.015	17.685	-0.015	-0.015	0.000	0.000	0.000	0.000
86	A	87	ASN	0	0.043	0.024	19.493	-0.037	-0.037	0.000	0.000	0.000	0.000
87	A	88	PRO	0	0.021	0.028	22.064	-0.014	-0.014	0.000	0.000	0.000	0.000
88	A	89	TYR	0	-0.034	-0.028	23.639	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	90	ILE	0	-0.042	-0.006	17.880	-0.021	-0.021	0.000	0.000	0.000	0.000
90	A	91	LYS	1	0.872	0.920	21.940	0.089	0.089	0.000	0.000	0.000	0.000
91	A	92	VAL	0	0.016	0.026	19.357	0.006	0.006	0.000	0.000	0.000	0.000
92	A	93	ASP	-1	-0.881	-0.931	19.071	-0.088	-0.088	0.000	0.000	0.000	0.000
93	A	94	ILE	0	-0.068	-0.045	14.406	-0.047	-0.047	0.000	0.000	0.000	0.000
94	A	95	PRO	0	0.016	0.002	10.967	0.045	0.045	0.000	0.000	0.000	0.000
95	A	96	GLU	-1	-0.728	-0.865	12.635	0.086	0.086	0.000	0.000	0.000	0.000
96	A	97	THR	0	0.007	-0.001	6.873	0.046	0.046	0.000	0.000	0.000	0.000
97	A	98	MET	0	0.002	0.002	8.926	-0.009	-0.009	0.000	0.000	0.000	0.000
98	A	99	ARG	1	0.923	0.955	10.406	0.035	0.035	0.000	0.000	0.000	0.000
99	A	100	GLY	0	0.019	0.001	11.022	0.019	0.019	0.000	0.000	0.000	0.000
100	A	101	ALA	0	-0.020	-0.014	8.199	0.079	0.079	0.000	0.000	0.000	0.000
101	A	102	LEU	0	-0.010	-0.010	10.097	-0.021	-0.021	0.000	0.000	0.000	0.000
102	A	103	TYR	0	0.000	0.004	13.679	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	104	SER	0	0.025	-0.008	11.390	0.046	0.046	0.000	0.000	0.000	0.000
104	A	105	PHE	0	0.011	0.009	13.257	-0.025	-0.025	0.000	0.000	0.000	0.000
105	A	106	VAL	0	-0.036	-0.021	14.640	0.000	0.000	0.000	0.000	0.000	0.000
106	A	107	TYR	0	-0.084	-0.050	16.155	0.006	0.006	0.000	0.000	0.000	0.000
107	A	108	ASN	0	-0.022	0.010	15.268	-0.046	-0.046	0.000	0.000	0.000	0.000
108	A	109	VAL	0	-0.010	-0.004	17.344	-0.005	-0.005	0.000	0.000	0.000	0.000
109	A	110	GLY	0	0.060	0.045	19.825	-0.006	-0.006	0.000	0.000	0.000	0.000
110	A	111	ALA	0	0.036	-0.009	22.285	-0.021	-0.021	0.000	0.000	0.000	0.000
111	A	112	GLY	0	-0.027	-0.012	23.580	-0.013	-0.013	0.000	0.000	0.000	0.000
112	A	113	ASN	0	0.012	-0.011	22.437	-0.015	-0.015	0.000	0.000	0.000	0.000
113	A	114	PHE	0	0.039	0.021	17.451	-0.017	-0.017	0.000	0.000	0.000	0.000
114	A	115	ARG	1	0.861	0.931	21.828	0.018	0.018	0.000	0.000	0.000	0.000
115	A	116	THR	0	0.012	0.019	24.843	-0.008	-0.008	0.000	0.000	0.000	0.000
116	A	117	SER	0	-0.031	-0.003	20.941	-0.021	-0.021	0.000	0.000	0.000	0.000
117	A	118	THR	0	-0.008	-0.030	21.984	0.009	0.009	0.000	0.000	0.000	0.000
118	A	119	LEU	0	-0.010	-0.002	15.072	-0.010	-0.010	0.000	0.000	0.000	0.000
119	A	120	LEU	0	0.014	0.010	19.270	-0.018	-0.018	0.000	0.000	0.000	0.000
120	A	121	ARG	1	0.900	0.954	20.980	0.171	0.171	0.000	0.000	0.000	0.000
121	A	122	LYS	1	0.877	0.922	19.510	0.346	0.346	0.000	0.000	0.000	0.000
122	A	123	ILE	0	0.018	0.017	16.523	-0.008	-0.008	0.000	0.000	0.000	0.000
123	A	124	ASN	0	-0.001	-0.002	19.479	0.003	0.003	0.000	0.000	0.000	0.000
124	A	125	GLN	0	-0.028	0.002	22.711	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	126	GLY	0	0.046	0.021	20.753	0.002	0.002	0.000	0.000	0.000	0.000
126	A	127	ASP	-1	-0.818	-0.889	18.908	-0.455	-0.455	0.000	0.000	0.000	0.000
127	A	128	ILE	0	0.011	-0.016	13.511	-0.040	-0.040	0.000	0.000	0.000	0.000
128	A	129	LYS	1	0.881	0.937	10.804	1.104	1.104	0.000	0.000	0.000	0.000
129	A	130	GLY	0	0.049	0.036	14.238	-0.077	-0.077	0.000	0.000	0.000	0.000
130	A	131	ALA	0	-0.041	-0.031	15.477	0.003	0.003	0.000	0.000	0.000	0.000
131	A	132	CYS	0	-0.067	-0.022	4.698	0.357	0.406	-0.002	-0.002	-0.045	0.000
132	A	133	ASP	-1	-0.744	-0.849	12.140	-1.085	-1.085	0.000	0.000	0.000	0.000
133	A	134	GLN	0	-0.018	-0.002	13.769	0.098	0.098	0.000	0.000	0.000	0.000
134	A	135	LEU	0	0.012	0.018	10.586	0.084	0.084	0.000	0.000	0.000	0.000
135	A	136	ARG	1	0.785	0.847	9.453	1.237	1.237	0.000	0.000	0.000	0.000
136	A	137	ARG	1	0.864	0.935	14.192	0.348	0.348	0.000	0.000	0.000	0.000
137	A	138	TRP	0	-0.044	-0.007	16.045	0.072	0.072	0.000	0.000	0.000	0.000
138	A	139	THR	0	0.012	-0.009	14.336	0.021	0.021	0.000	0.000	0.000	0.000
139	A	140	TYR	0	0.025	0.002	17.063	0.041	0.041	0.000	0.000	0.000	0.000
140	A	141	ALA	0	0.041	0.019	20.750	0.004	0.004	0.000	0.000	0.000	0.000
141	A	142	GLY	0	0.025	0.018	23.072	0.005	0.005	0.000	0.000	0.000	0.000
142	A	143	GLY	0	0.014	0.012	25.921	0.004	0.004	0.000	0.000	0.000	0.000
143	A	144	LYS	1	0.895	0.970	21.124	0.043	0.043	0.000	0.000	0.000	0.000
144	A	145	GLN	0	0.062	0.034	17.086	-0.037	-0.037	0.000	0.000	0.000	0.000
145	A	146	TRP	0	0.048	0.002	17.517	0.030	0.030	0.000	0.000	0.000	0.000
146	A	147	LYS	1	0.935	0.940	12.636	0.111	0.111	0.000	0.000	0.000	0.000
147	A	148	GLY	0	0.056	0.026	12.490	-0.024	-0.024	0.000	0.000	0.000	0.000
148	A	149	LEU	0	0.039	0.028	12.050	-0.004	-0.004	0.000	0.000	0.000	0.000
149	A	150	MET	0	-0.029	0.006	12.183	-0.045	-0.045	0.000	0.000	0.000	0.000
150	A	151	THR	0	0.016	0.003	7.907	-0.154	-0.154	0.000	0.000	0.000	0.000
151	A	152	ARG	1	0.787	0.884	7.482	-0.301	-0.301	0.000	0.000	0.000	0.000
152	A	153	ARG	1	0.794	0.871	8.516	0.137	0.137	0.000	0.000	0.000	0.000
153	A	154	GLU	-1	-0.765	-0.844	6.445	-1.645	-1.645	0.000	0.000	0.000	0.000
154	A	155	ILE	0	0.010	0.014	2.581	-1.877	-1.008	0.666	-0.312	-1.224	-0.001
155	A	156	GLU	-1	-0.745	-0.858	4.978	-0.292	-0.234	-0.001	-0.002	-0.055	0.000
156	A	157	ARG	1	0.834	0.887	7.615	1.707	1.707	0.000	0.000	0.000	0.000
157	A	158	GLU	-1	-0.849	-0.929	2.062	-31.474	-28.199	12.327	-7.423	-8.178	-0.093
158	A	159	ILE	0	-0.046	-0.023	2.296	-0.239	-0.519	2.868	-0.519	-2.069	-0.001
159	A	161	LEU	0	-0.005	-0.013	6.712	0.361	0.361	0.000	0.000	0.000	0.000
160	A	162	TRP	0	-0.008	0.003	2.535	-1.467	-0.307	1.250	-0.461	-1.949	-0.001
161	A	163	GLY	0	-0.037	-0.019	5.672	0.210	0.210	0.000	0.000	0.000	0.000
162	A	164	GLN	0	0.036	0.011	9.337	-0.058	-0.058	0.000	0.000	0.000	0.000
163	A	165	GLN	0	0.031	0.036	7.124	0.098	0.098	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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