FMO DATABASE

FMODB ID: JQVJ9

Calculation Name: 3HD4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HD4

Chain ID: A

ChEMBL ID:

UniProt ID: P03416

Base Structure: X-ray

Registration Date: 2023-09-23

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	OptH
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	131
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1128542.200325
FMO2-HF: Nuclear repulsion	1077889.450944
FMO2-HF: Total energy	-50652.749381
FMO2-MP2: Total energy	-50804.942225

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:64:PRO)

Summations of interaction energy for fragment #1(A:64:PRO)

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.
-1.791	0.738	-0.007	-1.065	-1.456	0

Interaction energy analysis for fragmet #1(A:64:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.015

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].
3	A	66	TYR	0	0.009	0.014	3.803	-0.782	1.747	-0.007	-1.065	-1.456
4	A	67	SER	0	0.011	0.008	5.553	0.275	0.275	0.000	0.000	0.000
5	A	68	TRP	0	0.047	0.011	8.697	0.138	0.138	0.000	0.000	0.000
6	A	69	PHE	0	-0.002	0.011	11.618	0.097	0.097	0.000	0.000	0.000
7	A	70	SER	0	-0.010	-0.003	11.540	-0.044	-0.044	0.000	0.000	0.000
8	A	71	GLY	0	0.020	0.015	12.436	-0.039	-0.039	0.000	0.000	0.000
9	A	72	ILE	0	-0.006	0.007	13.066	0.046	0.046	0.000	0.000	0.000
10	A	73	THR	0	-0.044	-0.055	15.254	-0.017	-0.017	0.000	0.000	0.000
11	A	74	GLN	0	-0.001	0.014	16.702	-0.004	-0.004	0.000	0.000	0.000
12	A	75	PHE	0	-0.034	-0.031	19.025	0.019	0.019	0.000	0.000	0.000
13	A	76	GLN	0	-0.020	-0.002	21.839	0.004	0.004	0.000	0.000	0.000
14	A	77	LYS	1	0.946	0.952	22.444	-0.015	-0.015	0.000	0.000	0.000
15	A	78	GLY	0	0.014	0.001	23.667	0.003	0.003	0.000	0.000	0.000
16	A	79	LYS	1	0.906	0.987	24.002	0.045	0.045	0.000	0.000	0.000
17	A	80	GLU	-1	-0.887	-0.948	22.717	-0.108	-0.108	0.000	0.000	0.000
18	A	81	PHE	0	-0.054	-0.026	17.620	0.003	0.003	0.000	0.000	0.000
19	A	82	GLN	0	-0.005	-0.010	20.948	-0.015	-0.015	0.000	0.000	0.000
20	A	83	PHE	0	0.006	0.006	19.757	0.007	0.007	0.000	0.000	0.000
21	A	84	ALA	0	0.046	0.027	24.654	-0.002	-0.002	0.000	0.000	0.000
22	A	85	GLU	-1	-0.888	-0.950	26.792	-0.136	-0.136	0.000	0.000	0.000
23	A	86	GLY	0	0.004	0.012	26.663	0.010	0.010	0.000	0.000	0.000
24	A	87	GLN	0	-0.060	-0.043	25.872	0.001	0.001	0.000	0.000	0.000
25	A	88	GLY	0	0.071	0.015	22.128	-0.009	-0.009	0.000	0.000	0.000
26	A	89	VAL	0	-0.052	0.006	19.109	-0.023	-0.023	0.000	0.000	0.000
27	A	90	PRO	0	-0.022	0.000	16.343	0.030	0.030	0.000	0.000	0.000
28	A	91	ILE	0	-0.038	-0.016	19.634	-0.009	-0.009	0.000	0.000	0.000
29	A	92	ALA	0	0.018	-0.003	19.422	0.005	0.005	0.000	0.000	0.000
30	A	93	ASN	0	-0.014	-0.019	21.534	0.002	0.002	0.000	0.000	0.000
31	A	94	GLY	0	0.017	0.010	22.430	-0.008	-0.008	0.000	0.000	0.000
32	A	95	ILE	0	-0.016	0.009	19.429	-0.007	-0.007	0.000	0.000	0.000
33	A	96	PRO	0	0.023	0.023	22.985	0.011	0.011	0.000	0.000	0.000
34	A	97	ALA	0	0.054	0.006	24.582	-0.015	-0.015	0.000	0.000	0.000
35	A	98	SER	0	0.019	0.011	25.671	-0.005	-0.005	0.000	0.000	0.000
36	A	99	GLU	-1	-0.826	-0.917	21.207	-0.263	-0.263	0.000	0.000	0.000
37	A	100	GLN	0	-0.081	-0.047	20.782	-0.019	-0.019	0.000	0.000	0.000
38	A	101	LYS	1	0.932	0.971	20.117	0.262	0.262	0.000	0.000	0.000
39	A	102	GLY	0	0.020	0.003	16.737	-0.037	-0.037	0.000	0.000	0.000
40	A	103	TYR	0	-0.016	-0.004	10.356	0.007	0.007	0.000	0.000	0.000
41	A	104	TRP	0	-0.044	-0.023	14.129	-0.068	-0.068	0.000	0.000	0.000
42	A	105	TYR	0	0.028	0.009	6.679	0.018	0.018	0.000	0.000	0.000
43	A	106	ARG	1	0.920	0.964	10.978	0.196	0.196	0.000	0.000	0.000
44	A	107	HIS	0	0.033	0.023	5.110	-0.097	-0.097	0.000	0.000	0.000
45	A	108	ASN	0	0.021	-0.027	9.359	0.084	0.084	0.000	0.000	0.000
46	A	109	ARG	1	0.942	0.957	10.834	0.020	0.020	0.000	0.000	0.000
47	A	110	ARG	1	0.903	0.976	10.365	-0.047	-0.047	0.000	0.000	0.000
48	A	111	SER	0	-0.010	-0.027	12.367	-0.034	-0.034	0.000	0.000	0.000
49	A	112	PHE	0	-0.011	0.009	12.948	0.047	0.047	0.000	0.000	0.000
50	A	113	LYS	1	0.903	0.963	15.213	-0.224	-0.224	0.000	0.000	0.000
51	A	114	THR	0	-0.026	-0.044	17.039	0.018	0.018	0.000	0.000	0.000
52	A	115	PRO	0	0.019	-0.008	20.264	0.003	0.003	0.000	0.000	0.000
53	A	116	ASP	-1	-0.784	-0.842	22.149	0.133	0.133	0.000	0.000	0.000
54	A	117	GLY	0	0.010	-0.016	21.654	0.003	0.003	0.000	0.000	0.000
55	A	118	GLN	0	-0.028	-0.005	22.424	-0.009	-0.009	0.000	0.000	0.000
56	A	119	GLN	0	-0.058	-0.019	16.365	0.027	0.027	0.000	0.000	0.000
57	A	120	LYS	1	0.979	0.993	18.472	-0.152	-0.152	0.000	0.000	0.000
58	A	121	GLN	0	0.014	-0.005	17.318	0.010	0.010	0.000	0.000	0.000
59	A	122	LEU	0	-0.054	-0.023	13.741	-0.003	-0.003	0.000	0.000	0.000
60	A	123	LEU	0	0.003	0.012	16.113	-0.012	-0.012	0.000	0.000	0.000
61	A	124	PRO	0	0.023	0.013	13.685	0.022	0.022	0.000	0.000	0.000
62	A	125	ARG	1	0.847	0.937	11.150	-0.025	-0.025	0.000	0.000	0.000
63	A	126	TRP	0	0.027	0.015	11.399	-0.035	-0.035	0.000	0.000	0.000
64	A	127	TYR	0	0.033	-0.005	8.407	0.107	0.107	0.000	0.000	0.000
65	A	128	PHE	0	0.063	0.041	11.273	-0.045	-0.045	0.000	0.000	0.000
66	A	129	TYR	0	-0.034	-0.021	5.760	0.064	0.064	0.000	0.000	0.000
67	A	130	TYR	0	0.094	0.046	12.406	0.079	0.079	0.000	0.000	0.000
68	A	131	LEU	0	0.041	0.018	14.018	-0.083	-0.083	0.000	0.000	0.000
69	A	132	GLY	0	0.034	0.031	14.906	0.026	0.026	0.000	0.000	0.000
70	A	133	THR	0	-0.077	-0.043	11.170	-0.060	-0.060	0.000	0.000	0.000
71	A	134	GLY	0	0.032	0.001	7.467	0.080	0.080	0.000	0.000	0.000
72	A	135	PRO	0	-0.062	-0.033	5.949	0.034	0.034	0.000	0.000	0.000
73	A	136	HIS	0	-0.003	-0.016	7.012	0.144	0.144	0.000	0.000	0.000
74	A	137	ALA	0	-0.028	0.007	9.942	0.126	0.126	0.000	0.000	0.000
75	A	138	GLY	0	-0.026	-0.020	11.771	0.080	0.080	0.000	0.000	0.000
76	A	139	ALA	0	-0.044	-0.006	14.135	0.054	0.054	0.000	0.000	0.000
77	A	140	SER	0	0.001	-0.001	16.037	-0.008	-0.008	0.000	0.000	0.000
78	A	141	TYR	0	0.007	-0.014	19.314	-0.007	-0.007	0.000	0.000	0.000
79	A	142	GLY	0	-0.006	-0.010	20.096	0.022	0.022	0.000	0.000	0.000
80	A	143	ASP	-1	-0.838	-0.900	18.328	-0.257	-0.257	0.000	0.000	0.000
81	A	144	SER	0	-0.060	-0.025	19.136	-0.017	-0.017	0.000	0.000	0.000
82	A	145	ILE	0	0.029	0.009	13.962	0.000	0.000	0.000	0.000	0.000
83	A	146	GLU	-1	-0.927	-0.962	16.928	-0.145	-0.145	0.000	0.000	0.000
84	A	147	GLY	0	-0.095	-0.052	14.128	-0.028	-0.028	0.000	0.000	0.000
85	A	148	VAL	0	0.034	0.020	13.105	-0.065	-0.065	0.000	0.000	0.000
86	A	149	PHE	0	-0.017	0.003	15.550	0.039	0.039	0.000	0.000	0.000
87	A	150	TRP	0	-0.012	-0.007	15.908	-0.036	-0.036	0.000	0.000	0.000
88	A	151	VAL	0	-0.038	-0.014	18.818	0.025	0.025	0.000	0.000	0.000
89	A	152	ALA	0	0.051	0.001	20.790	-0.025	-0.025	0.000	0.000	0.000
90	A	153	ASN	0	0.006	0.022	23.370	0.022	0.022	0.000	0.000	0.000
91	A	154	SER	0	0.034	-0.001	26.310	-0.005	-0.005	0.000	0.000	0.000
92	A	155	GLN	0	-0.054	-0.026	29.075	0.005	0.005	0.000	0.000	0.000
93	A	156	ALA	0	-0.026	0.000	24.256	-0.001	-0.001	0.000	0.000	0.000
94	A	157	ASP	-1	-0.826	-0.903	26.000	-0.166	-0.166	0.000	0.000	0.000
95	A	158	THR	0	-0.056	-0.055	22.963	-0.014	-0.014	0.000	0.000	0.000
96	A	159	ASN	0	-0.008	-0.003	22.792	-0.019	-0.019	0.000	0.000	0.000
97	A	160	THR	0	-0.018	0.005	22.981	-0.009	-0.009	0.000	0.000	0.000
98	A	161	ARG	1	0.913	0.950	14.482	0.438	0.438	0.000	0.000	0.000
99	A	162	SER	0	-0.045	-0.009	16.813	0.017	0.017	0.000	0.000	0.000
100	A	163	ASP	-1	-0.884	-0.949	18.563	-0.251	-0.251	0.000	0.000	0.000
101	A	164	ILE	0	-0.140	-0.065	15.683	0.014	0.014	0.000	0.000	0.000
102	A	165	VAL	0	-0.008	-0.004	13.315	-0.059	-0.059	0.000	0.000	0.000
103	A	166	GLU	-1	-0.826	-0.919	8.447	-1.562	-1.562	0.000	0.000	0.000
104	A	167	ARG	1	0.798	0.892	8.029	0.384	0.384	0.000	0.000	0.000
105	A	168	ASP	-1	-0.770	-0.863	8.762	-0.287	-0.287	0.000	0.000	0.000
106	A	169	PRO	0	-0.073	-0.049	6.913	0.084	0.084	0.000	0.000	0.000
107	A	170	SER	0	-0.099	-0.057	9.902	0.080	0.080	0.000	0.000	0.000
108	A	171	SER	0	0.005	0.000	12.415	-0.004	-0.004	0.000	0.000	0.000
109	A	172	HIS	0	-0.020	-0.008	13.246	-0.022	-0.022	0.000	0.000	0.000
110	A	173	GLU	-1	-0.904	-0.941	12.134	0.099	0.099	0.000	0.000	0.000
111	A	174	ALA	0	-0.069	-0.030	10.621	-0.055	-0.055	0.000	0.000	0.000
112	A	175	ILE	0	0.009	0.002	12.615	0.061	0.061	0.000	0.000	0.000
113	A	176	PRO	0	-0.032	-0.035	15.463	-0.023	-0.023	0.000	0.000	0.000
114	A	177	THR	0	0.025	0.008	15.435	-0.023	-0.023	0.000	0.000	0.000
115	A	178	ARG	1	0.879	0.942	18.058	0.087	0.087	0.000	0.000	0.000
116	A	179	PHE	0	0.033	0.015	19.327	-0.015	-0.015	0.000	0.000	0.000
117	A	180	ALA	0	0.055	0.034	23.801	0.011	0.011	0.000	0.000	0.000
118	A	181	PRO	0	0.014	0.010	27.181	0.001	0.001	0.000	0.000	0.000
119	A	182	GLY	0	0.030	0.018	29.974	-0.001	-0.001	0.000	0.000	0.000
120	A	183	THR	0	-0.057	-0.043	24.549	-0.005	-0.005	0.000	0.000	0.000
121	A	184	VAL	0	-0.026	-0.007	27.527	0.006	0.006	0.000	0.000	0.000
122	A	185	LEU	0	-0.010	-0.002	22.420	-0.009	-0.009	0.000	0.000	0.000
123	A	186	PRO	0	-0.012	0.020	21.585	0.012	0.012	0.000	0.000	0.000
124	A	187	GLN	0	0.034	-0.006	24.362	0.006	0.006	0.000	0.000	0.000
125	A	188	GLY	0	0.013	-0.002	24.595	-0.003	-0.003	0.000	0.000	0.000
126	A	189	PHE	0	0.006	0.000	18.181	0.003	0.003	0.000	0.000	0.000
127	A	190	TYR	0	-0.002	-0.003	18.905	0.001	0.001	0.000	0.000	0.000
128	A	191	VAL	0	0.019	0.014	18.049	-0.006	-0.006	0.000	0.000	0.000
129	A	192	GLU	-1	-0.833	-0.894	14.466	0.057	0.057	0.000	0.000	0.000
130	A	193	GLY	0	0.022	0.019	17.293	-0.017	-0.017	0.000	0.000	0.000
131	A	194	SER	0	-0.029	-0.010	18.892	-0.010	-0.010	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:64:PRO)