FMO DATABASE

FMODB ID: JQ289

Calculation Name: 3HDC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HDC

Chain ID: A

ChEMBL ID:

UniProt ID: Q39VV7

Base Structure: X-ray

Registration Date: 2023-09-22

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	150
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1417401.490149
FMO2-HF: Nuclear repulsion	1358930.631586
FMO2-HF: Total energy	-58470.858563
FMO2-MP2: Total energy	-58642.809522

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:20:SER)

Summations of interaction energy for fragment #1(A:20:SER)

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.
0.766	2.106	-0.024	-0.578	-0.739	0.002

Interaction energy analysis for fragmet #1(A:20:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.022

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	22	ALA	0	0.013	0.010	3.800	1.060	2.400	-0.024	-0.578	-0.739	0.002
4	A	23	PRO	0	0.021	0.016	6.553	-0.013	-0.013	0.000	0.000	0.000	0.000
5	A	24	GLY	0	0.034	0.012	9.137	-0.146	-0.146	0.000	0.000	0.000	0.000
6	A	25	LYS	1	0.899	0.942	12.706	0.066	0.066	0.000	0.000	0.000	0.000
7	A	26	ALA	0	0.018	0.012	15.399	0.004	0.004	0.000	0.000	0.000	0.000
8	A	27	GLU	-1	-0.939	-0.967	17.347	0.028	0.028	0.000	0.000	0.000	0.000
9	A	28	SER	0	-0.063	-0.034	20.397	0.018	0.018	0.000	0.000	0.000	0.000
10	A	29	ASP	-1	-0.877	-0.939	21.915	0.071	0.071	0.000	0.000	0.000	0.000
11	A	30	ALA	0	-0.045	-0.008	23.660	0.000	0.000	0.000	0.000	0.000	0.000
12	A	31	PRO	0	-0.008	-0.005	25.652	-0.006	-0.006	0.000	0.000	0.000	0.000
13	A	32	LEU	0	-0.014	-0.014	27.671	0.004	0.004	0.000	0.000	0.000	0.000
14	A	33	VAL	0	0.022	0.009	28.882	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	34	ARG	1	0.934	0.965	28.778	-0.032	-0.032	0.000	0.000	0.000	0.000
16	A	35	THR	0	0.012	0.001	31.700	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	36	GLY	0	-0.019	-0.012	33.773	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	37	ALA	0	-0.015	-0.001	34.992	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	38	LEU	0	-0.019	-0.014	36.827	0.001	0.001	0.000	0.000	0.000	0.000
20	A	39	ALA	0	0.005	0.005	36.889	0.002	0.002	0.000	0.000	0.000	0.000
21	A	40	PRO	0	0.019	0.019	33.785	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	41	ASN	0	0.025	0.025	36.797	0.000	0.000	0.000	0.000	0.000	0.000
23	A	42	PHE	0	0.017	0.003	38.338	0.003	0.003	0.000	0.000	0.000	0.000
24	A	43	LYS	1	0.969	0.976	40.380	-0.028	-0.028	0.000	0.000	0.000	0.000
25	A	44	LEU	0	-0.026	0.001	38.869	0.001	0.001	0.000	0.000	0.000	0.000
26	A	45	PRO	0	0.046	0.039	42.434	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	46	THR	0	-0.024	-0.028	44.897	0.001	0.001	0.000	0.000	0.000	0.000
28	A	47	LEU	0	-0.019	-0.026	46.870	0.000	0.000	0.000	0.000	0.000	0.000
29	A	48	SER	0	-0.018	-0.004	49.060	0.000	0.000	0.000	0.000	0.000	0.000
30	A	49	GLY	0	0.004	0.014	49.197	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	50	GLU	-1	-0.907	-0.934	50.273	0.021	0.021	0.000	0.000	0.000	0.000
32	A	51	ASN	0	-0.026	-0.027	46.550	0.002	0.002	0.000	0.000	0.000	0.000
33	A	52	LYS	1	0.921	0.963	46.654	-0.026	-0.026	0.000	0.000	0.000	0.000
34	A	53	SER	0	-0.033	-0.028	44.513	0.002	0.002	0.000	0.000	0.000	0.000
35	A	54	LEU	0	0.038	0.017	40.115	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	55	ALA	0	-0.017	-0.017	43.875	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	56	GLN	0	0.030	0.021	45.958	0.000	0.000	0.000	0.000	0.000	0.000
38	A	57	TYR	0	0.003	-0.002	46.532	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	58	ARG	1	0.966	0.996	42.655	-0.024	-0.024	0.000	0.000	0.000	0.000
40	A	59	GLY	0	-0.013	-0.005	48.531	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	60	LYS	1	0.876	0.943	49.278	-0.018	-0.018	0.000	0.000	0.000	0.000
42	A	61	ILE	0	0.022	0.028	44.729	0.001	0.001	0.000	0.000	0.000	0.000
43	A	62	VAL	0	-0.022	-0.015	42.714	0.000	0.000	0.000	0.000	0.000	0.000
44	A	63	LEU	0	0.003	0.011	41.083	0.001	0.001	0.000	0.000	0.000	0.000
45	A	64	VAL	0	-0.001	-0.008	37.422	0.000	0.000	0.000	0.000	0.000	0.000
46	A	65	ASN	0	-0.007	-0.006	37.445	0.002	0.002	0.000	0.000	0.000	0.000
47	A	66	PHE	0	-0.005	0.004	33.774	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	67	TRP	0	-0.008	-0.023	35.259	0.002	0.002	0.000	0.000	0.000	0.000
49	A	68	ALA	0	0.051	0.005	34.695	0.001	0.001	0.000	0.000	0.000	0.000
50	A	69	SER	0	-0.039	-0.038	36.590	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	70	TRP	0	0.028	0.015	30.429	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	71	CYS	0	-0.027	0.004	33.024	0.001	0.001	0.000	0.000	0.000	0.000
53	A	72	PRO	0	0.021	-0.001	34.152	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	73	TYR	0	0.097	0.037	31.441	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	74	CYS	0	-0.050	0.005	35.060	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	75	ARG	1	0.846	0.930	37.728	-0.046	-0.046	0.000	0.000	0.000	0.000
57	A	76	ASP	-1	-0.883	-0.949	39.057	0.037	0.037	0.000	0.000	0.000	0.000
58	A	77	GLU	-1	-0.834	-0.926	38.322	0.039	0.039	0.000	0.000	0.000	0.000
59	A	78	MET	0	-0.045	-0.014	41.270	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	79	PRO	0	0.014	-0.004	43.907	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	80	SER	0	0.047	0.032	43.145	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	81	MET	0	0.016	0.011	40.337	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	82	ASP	-1	-0.769	-0.878	45.327	0.022	0.022	0.000	0.000	0.000	0.000
64	A	83	ARG	1	0.855	0.923	47.418	-0.024	-0.024	0.000	0.000	0.000	0.000
65	A	84	LEU	0	-0.014	0.006	45.146	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	85	VAL	0	-0.015	-0.006	47.454	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	86	LYS	1	0.738	0.845	50.006	-0.022	-0.022	0.000	0.000	0.000	0.000
68	A	87	SER	0	-0.078	-0.023	51.580	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	88	PHE	0	-0.035	-0.015	49.109	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	89	PRO	0	0.031	0.022	53.667	0.000	0.000	0.000	0.000	0.000	0.000
71	A	90	LYS	1	1.009	0.991	54.857	-0.016	-0.016	0.000	0.000	0.000	0.000
72	A	91	GLY	0	-0.022	-0.014	53.061	0.000	0.000	0.000	0.000	0.000	0.000
73	A	92	ASP	-1	-0.900	-0.955	52.341	0.016	0.016	0.000	0.000	0.000	0.000
74	A	93	LEU	0	-0.045	-0.012	45.550	0.000	0.000	0.000	0.000	0.000	0.000
75	A	94	VAL	0	-0.041	-0.017	46.602	0.000	0.000	0.000	0.000	0.000	0.000
76	A	95	VAL	0	0.071	0.035	42.980	0.001	0.001	0.000	0.000	0.000	0.000
77	A	96	LEU	0	-0.060	-0.029	42.097	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	97	ALA	0	0.055	0.032	41.074	0.002	0.002	0.000	0.000	0.000	0.000
79	A	98	VAL	0	0.006	-0.002	37.353	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	99	ASN	0	-0.056	-0.043	37.743	0.004	0.004	0.000	0.000	0.000	0.000
81	A	100	VAL	0	0.032	-0.003	32.994	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	101	GLU	-1	-0.801	-0.867	34.573	0.052	0.052	0.000	0.000	0.000	0.000
83	A	102	LYS	1	0.975	0.993	35.061	-0.054	-0.054	0.000	0.000	0.000	0.000
84	A	103	ARG	1	0.942	0.961	37.058	-0.038	-0.038	0.000	0.000	0.000	0.000
85	A	104	PHE	0	0.026	0.020	40.491	0.001	0.001	0.000	0.000	0.000	0.000
86	A	105	PRO	0	0.016	0.015	41.072	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	106	GLU	-1	-0.908	-0.986	43.558	0.026	0.026	0.000	0.000	0.000	0.000
88	A	107	LYS	1	1.016	1.001	46.842	-0.031	-0.031	0.000	0.000	0.000	0.000
89	A	108	TYR	0	0.019	0.006	43.039	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	109	ARG	1	0.913	0.970	46.225	-0.031	-0.031	0.000	0.000	0.000	0.000
91	A	110	ARG	1	0.902	0.957	49.850	-0.025	-0.025	0.000	0.000	0.000	0.000
92	A	111	ALA	0	0.003	0.015	48.997	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	112	PRO	0	0.008	0.024	51.008	0.000	0.000	0.000	0.000	0.000	0.000
94	A	113	VAL	0	0.000	-0.006	47.741	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	114	SER	0	-0.016	-0.008	50.593	0.000	0.000	0.000	0.000	0.000	0.000
96	A	115	PHE	0	-0.011	-0.012	45.338	0.001	0.001	0.000	0.000	0.000	0.000
97	A	116	ASN	0	-0.037	0.001	46.587	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	117	PHE	0	0.032	0.008	43.697	0.001	0.001	0.000	0.000	0.000	0.000
99	A	118	LEU	0	-0.007	-0.005	41.974	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	119	SER	0	-0.020	0.002	40.327	0.002	0.002	0.000	0.000	0.000	0.000
101	A	120	ASP	-1	-0.757	-0.903	34.825	0.052	0.052	0.000	0.000	0.000	0.000
102	A	121	ALA	0	0.012	0.010	36.187	0.003	0.003	0.000	0.000	0.000	0.000
103	A	122	THR	0	-0.016	-0.015	35.191	0.003	0.003	0.000	0.000	0.000	0.000
104	A	123	GLY	0	0.055	0.040	32.156	0.003	0.003	0.000	0.000	0.000	0.000
105	A	124	GLN	0	-0.017	-0.012	30.843	0.001	0.001	0.000	0.000	0.000	0.000
106	A	125	VAL	0	-0.034	-0.023	32.735	0.001	0.001	0.000	0.000	0.000	0.000
107	A	126	GLN	0	0.019	-0.007	30.177	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	127	GLN	0	-0.021	-0.005	25.600	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	128	ARG	1	0.850	0.908	28.672	-0.043	-0.043	0.000	0.000	0.000	0.000
110	A	129	TYR	0	-0.043	-0.039	30.770	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	130	GLY	0	0.014	0.015	27.086	0.000	0.000	0.000	0.000	0.000	0.000
112	A	131	ALA	0	-0.014	0.014	27.195	0.004	0.004	0.000	0.000	0.000	0.000
113	A	132	ASN	0	-0.035	-0.026	23.336	-0.005	-0.005	0.000	0.000	0.000	0.000
114	A	133	ARG	1	0.944	0.974	23.893	-0.097	-0.097	0.000	0.000	0.000	0.000
115	A	134	LEU	0	-0.011	0.018	27.934	-0.005	-0.005	0.000	0.000	0.000	0.000
116	A	135	PRO	0	0.034	-0.002	31.618	0.002	0.002	0.000	0.000	0.000	0.000
117	A	136	ASP	-1	-0.819	-0.915	30.244	0.068	0.068	0.000	0.000	0.000	0.000
118	A	137	THR	0	-0.008	0.008	33.093	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	138	PHE	0	-0.015	-0.010	30.929	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	139	ILE	0	0.016	0.015	36.490	-0.002	-0.002	0.000	0.000	0.000	0.000
121	A	140	VAL	0	-0.030	-0.015	39.226	0.000	0.000	0.000	0.000	0.000	0.000
122	A	141	ASP	-1	-0.752	-0.882	41.194	0.020	0.020	0.000	0.000	0.000	0.000
123	A	142	ARG	1	1.002	1.005	44.053	-0.016	-0.016	0.000	0.000	0.000	0.000
124	A	143	LYS	1	0.934	0.954	45.589	-0.015	-0.015	0.000	0.000	0.000	0.000
125	A	144	GLY	0	-0.006	0.004	43.196	0.000	0.000	0.000	0.000	0.000	0.000
126	A	145	ILE	0	-0.018	0.005	38.831	0.002	0.002	0.000	0.000	0.000	0.000
127	A	146	ILE	0	-0.008	0.010	34.589	0.000	0.000	0.000	0.000	0.000	0.000
128	A	147	ARG	1	0.909	0.947	37.055	-0.020	-0.020	0.000	0.000	0.000	0.000
129	A	148	GLN	0	-0.010	-0.008	34.371	-0.003	-0.003	0.000	0.000	0.000	0.000
130	A	149	ARG	1	0.925	0.969	27.176	-0.063	-0.063	0.000	0.000	0.000	0.000
131	A	150	VAL	0	-0.015	-0.011	33.034	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	151	THR	0	-0.034	-0.014	28.062	0.002	0.002	0.000	0.000	0.000	0.000
133	A	152	GLY	0	0.003	0.001	31.355	0.000	0.000	0.000	0.000	0.000	0.000
134	A	153	GLY	0	-0.021	-0.004	32.764	-0.002	-0.002	0.000	0.000	0.000	0.000
135	A	154	ILE	0	-0.038	-0.017	36.141	-0.001	-0.001	0.000	0.000	0.000	0.000
136	A	155	GLU	-1	-0.899	-0.947	38.432	0.026	0.026	0.000	0.000	0.000	0.000
137	A	156	TRP	0	-0.044	-0.061	38.041	-0.002	-0.002	0.000	0.000	0.000	0.000
138	A	157	ASP	-1	-0.803	-0.903	43.402	0.022	0.022	0.000	0.000	0.000	0.000
139	A	158	ALA	0	0.033	0.022	43.784	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	159	PRO	0	0.047	0.010	45.818	0.000	0.000	0.000	0.000	0.000	0.000
141	A	160	LYS	1	0.965	0.979	39.364	-0.021	-0.021	0.000	0.000	0.000	0.000
142	A	161	VAL	0	0.017	0.022	41.365	0.000	0.000	0.000	0.000	0.000	0.000
143	A	162	VAL	0	0.055	0.027	43.860	0.000	0.000	0.000	0.000	0.000	0.000
144	A	163	SER	0	-0.051	-0.028	46.749	-0.001	-0.001	0.000	0.000	0.000	0.000
145	A	164	TYR	0	0.036	0.014	39.546	0.000	0.000	0.000	0.000	0.000	0.000
146	A	165	LEU	0	0.023	0.012	43.000	0.000	0.000	0.000	0.000	0.000	0.000
147	A	166	LYS	1	0.961	0.978	45.955	-0.016	-0.016	0.000	0.000	0.000	0.000
148	A	167	SER	0	-0.113	-0.052	45.513	-0.001	-0.001	0.000	0.000	0.000	0.000
149	A	168	LEU	0	-0.056	-0.034	42.961	0.000	0.000	0.000	0.000	0.000	0.000
150	A	169	GLU	-1	-0.975	-0.977	47.285	0.015	0.015	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:20:SER)