FMO DATABASE

FMODB ID: G5N81

Calculation Name: 1DCF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1DCF

Chain ID: A

ChEMBL ID:

UniProt ID: P49333

Base Structure: X-ray

Registration Date: 2023-09-21

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	134
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1208995.064567
FMO2-HF: Nuclear repulsion	1154535.964547
FMO2-HF: Total energy	-54459.10002
FMO2-MP2: Total energy	-54612.464427

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:HIS)

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

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.
-17.253	-7.49	4.414	-5.648	-8.528	0.003

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.042 / q_NPA : 0.026

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	SER	0	-0.039	-0.020	3.767	-2.019	1.192	0.106	-1.458	-1.860	0.006
4	A	4	ASN	0	-0.028	-0.001	5.602	-1.044	-0.900	-0.001	-0.007	-0.136	0.000
5	A	5	PHE	0	0.063	0.018	4.717	-0.255	-0.196	-0.001	-0.006	-0.051	0.000
6	A	6	THR	0	-0.004	-0.022	10.493	-0.067	-0.067	0.000	0.000	0.000	0.000
7	A	7	GLY	0	-0.018	0.002	13.933	0.017	0.017	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.021	-0.001	10.930	0.006	0.006	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.874	0.946	14.745	0.027	0.027	0.000	0.000	0.000	0.000
10	A	10	VAL	0	0.000	0.008	13.266	0.019	0.019	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.041	-0.027	16.739	-0.013	-0.013	0.000	0.000	0.000	0.000
12	A	12	VAL	0	-0.006	-0.004	16.710	-0.006	-0.006	0.000	0.000	0.000	0.000
13	A	13	MET	0	-0.016	-0.006	19.295	0.011	0.011	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.777	-0.886	21.007	-0.225	-0.225	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.836	-0.912	23.123	-0.143	-0.143	0.000	0.000	0.000	0.000
16	A	16	ASN	0	0.015	0.015	24.291	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.021	-0.002	24.216	-0.011	-0.011	0.000	0.000	0.000	0.000
18	A	18	VAL	0	0.039	0.021	22.940	-0.012	-0.012	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.026	-0.032	20.533	-0.040	-0.040	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.891	0.951	19.570	0.122	0.122	0.000	0.000	0.000	0.000
21	A	21	MET	0	-0.051	-0.027	19.984	-0.014	-0.014	0.000	0.000	0.000	0.000
22	A	22	VAL	0	-0.005	-0.011	16.740	-0.018	-0.018	0.000	0.000	0.000	0.000
23	A	23	THR	0	-0.004	-0.009	14.729	-0.061	-0.061	0.000	0.000	0.000	0.000
24	A	24	LYS	1	0.890	0.937	15.184	0.158	0.158	0.000	0.000	0.000	0.000
25	A	25	GLY	0	0.019	0.009	16.546	0.003	0.003	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.006	-0.003	11.907	-0.024	-0.024	0.000	0.000	0.000	0.000
27	A	27	LEU	0	0.015	0.003	11.045	-0.035	-0.035	0.000	0.000	0.000	0.000
28	A	28	VAL	0	-0.002	-0.004	13.052	0.048	0.048	0.000	0.000	0.000	0.000
29	A	29	HIS	0	-0.026	0.001	11.148	0.075	0.075	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.046	-0.023	7.575	-0.033	-0.033	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.032	0.020	11.066	0.110	0.110	0.000	0.000	0.000	0.000
32	A	32	CYS	0	-0.051	-0.011	12.104	0.054	0.054	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.892	-0.946	14.756	-0.104	-0.104	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.025	-0.013	16.091	0.012	0.012	0.000	0.000	0.000	0.000
35	A	35	THR	0	-0.021	0.006	18.803	0.007	0.007	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.025	-0.021	20.610	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	37	VAL	0	-0.029	-0.008	22.834	0.011	0.011	0.000	0.000	0.000	0.000
38	A	38	SER	0	-0.031	-0.024	24.501	-0.012	-0.012	0.000	0.000	0.000	0.000
39	A	39	SER	0	0.054	0.016	27.034	0.006	0.006	0.000	0.000	0.000	0.000
40	A	40	ASN	0	0.066	0.013	27.197	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.840	-0.912	28.755	-0.039	-0.039	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.844	-0.921	28.618	-0.090	-0.090	0.000	0.000	0.000	0.000
43	A	43	CYS	0	0.012	0.007	24.181	0.000	0.000	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.007	0.006	26.452	0.006	0.006	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.864	0.937	28.686	0.058	0.058	0.000	0.000	0.000	0.000
46	A	46	VAL	0	-0.026	-0.008	25.152	0.003	0.003	0.000	0.000	0.000	0.000
47	A	47	VAL	0	-0.013	0.011	22.425	0.002	0.002	0.000	0.000	0.000	0.000
48	A	48	SER	0	0.012	0.002	24.080	0.009	0.009	0.000	0.000	0.000	0.000
49	A	49	HIS	0	0.061	0.019	23.088	0.003	0.003	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.882	-0.912	22.108	-0.027	-0.027	0.000	0.000	0.000	0.000
51	A	51	HIS	0	-0.034	-0.034	19.400	0.007	0.007	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.912	0.945	15.588	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	53	VAL	0	0.024	0.015	12.277	0.028	0.028	0.000	0.000	0.000	0.000
54	A	54	VAL	0	0.000	0.001	15.673	-0.029	-0.029	0.000	0.000	0.000	0.000
55	A	55	PHE	0	0.019	0.016	10.845	0.006	0.006	0.000	0.000	0.000	0.000
56	A	56	MET	0	-0.014	-0.011	16.351	0.007	0.007	0.000	0.000	0.000	0.000
57	A	57	ASP	-1	-0.742	-0.847	18.749	-0.216	-0.216	0.000	0.000	0.000	0.000
58	A	58	VAL	0	-0.054	-0.040	19.654	0.026	0.026	0.000	0.000	0.000	0.000
59	A	59	CYS	0	-0.063	-0.036	21.402	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	60	MET	0	-0.018	0.024	23.699	0.001	0.001	0.000	0.000	0.000	0.000
61	A	61	PRO	0	0.009	0.010	26.632	0.001	0.001	0.000	0.000	0.000	0.000
62	A	62	GLY	0	-0.006	-0.004	28.870	0.006	0.006	0.000	0.000	0.000	0.000
63	A	63	VAL	0	0.041	-0.002	26.580	-0.006	-0.006	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.904	-0.944	27.946	-0.058	-0.058	0.000	0.000	0.000	0.000
65	A	65	ASN	0	-0.032	-0.037	24.262	0.013	0.013	0.000	0.000	0.000	0.000
66	A	66	TYR	0	0.062	0.017	21.095	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	67	GLN	0	0.042	0.016	24.961	0.012	0.012	0.000	0.000	0.000	0.000
68	A	68	ILE	0	-0.046	-0.016	23.976	0.008	0.008	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.117	0.047	22.321	0.003	0.003	0.000	0.000	0.000	0.000
70	A	70	LEU	0	0.019	0.036	23.972	0.010	0.010	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.908	0.945	27.039	0.036	0.036	0.000	0.000	0.000	0.000
72	A	72	ILE	0	0.008	-0.004	22.713	0.001	0.001	0.000	0.000	0.000	0.000
73	A	73	HIS	0	-0.009	0.013	21.964	0.019	0.019	0.000	0.000	0.000	0.000
74	A	74	GLU	-1	-0.835	-0.892	26.145	0.019	0.019	0.000	0.000	0.000	0.000
75	A	75	LYS	1	0.804	0.880	27.698	0.027	0.027	0.000	0.000	0.000	0.000
76	A	76	PHE	0	-0.034	-0.016	24.547	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	77	THR	0	-0.036	-0.006	27.662	0.007	0.007	0.000	0.000	0.000	0.000
78	A	78	LYS	1	0.769	0.869	29.831	-0.013	-0.013	0.000	0.000	0.000	0.000
79	A	79	GLN	0	-0.022	-0.026	30.445	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	80	ARG	1	0.928	0.969	29.437	-0.009	-0.009	0.000	0.000	0.000	0.000
81	A	81	HIS	0	0.011	0.018	25.390	0.009	0.009	0.000	0.000	0.000	0.000
82	A	82	GLN	0	0.065	0.021	21.388	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	83	ARG	1	0.786	0.887	18.580	-0.097	-0.097	0.000	0.000	0.000	0.000
84	A	84	PRO	0	-0.035	-0.004	18.787	0.013	0.013	0.000	0.000	0.000	0.000
85	A	85	LEU	0	0.031	0.011	13.041	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	86	LEU	0	-0.052	-0.022	16.594	-0.039	-0.039	0.000	0.000	0.000	0.000
87	A	87	VAL	0	0.023	0.008	11.780	0.020	0.020	0.000	0.000	0.000	0.000
88	A	88	ALA	0	0.007	0.008	14.906	-0.023	-0.023	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.005	0.007	14.434	-0.047	-0.047	0.000	0.000	0.000	0.000
90	A	90	SER	0	0.040	-0.007	16.583	0.028	0.028	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.050	0.025	17.452	-0.046	-0.046	0.000	0.000	0.000	0.000
92	A	92	ASN	0	-0.012	0.008	18.964	0.008	0.008	0.000	0.000	0.000	0.000
93	A	93	THR	0	0.109	0.052	14.417	0.010	0.010	0.000	0.000	0.000	0.000
94	A	94	ASP	-1	-0.838	-0.914	17.854	-0.029	-0.029	0.000	0.000	0.000	0.000
95	A	95	LYS	1	0.895	0.937	20.937	-0.034	-0.034	0.000	0.000	0.000	0.000
96	A	96	SER	0	-0.006	0.011	22.902	0.010	0.010	0.000	0.000	0.000	0.000
97	A	97	THR	0	0.008	-0.017	18.582	0.011	0.011	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.918	0.954	17.075	-0.014	-0.014	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.833	-0.925	20.117	0.064	0.064	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.846	0.929	23.015	0.066	0.066	0.000	0.000	0.000	0.000
101	A	101	CYS	0	-0.024	-0.021	18.652	-0.008	-0.008	0.000	0.000	0.000	0.000
102	A	102	MET	0	0.021	0.022	19.222	0.008	0.008	0.000	0.000	0.000	0.000
103	A	103	SER	0	-0.022	-0.003	21.985	0.005	0.005	0.000	0.000	0.000	0.000
104	A	104	PHE	0	-0.075	-0.057	23.814	-0.005	-0.005	0.000	0.000	0.000	0.000
105	A	105	GLY	0	0.021	0.018	22.097	-0.009	-0.009	0.000	0.000	0.000	0.000
106	A	106	LEU	0	-0.064	-0.034	17.671	0.002	0.002	0.000	0.000	0.000	0.000
107	A	107	ASP	-1	-0.760	-0.853	15.081	0.130	0.130	0.000	0.000	0.000	0.000
108	A	108	GLY	0	0.023	0.013	12.490	0.065	0.065	0.000	0.000	0.000	0.000
109	A	109	VAL	0	-0.065	-0.045	12.528	-0.028	-0.028	0.000	0.000	0.000	0.000
110	A	110	LEU	0	-0.015	0.003	8.895	-0.026	-0.026	0.000	0.000	0.000	0.000
111	A	111	LEU	0	-0.035	-0.002	12.448	0.070	0.070	0.000	0.000	0.000	0.000
112	A	112	LYS	1	0.816	0.901	13.701	0.175	0.175	0.000	0.000	0.000	0.000
113	A	113	PRO	0	0.002	-0.025	16.325	0.044	0.044	0.000	0.000	0.000	0.000
114	A	114	VAL	0	-0.005	0.006	11.937	-0.040	-0.040	0.000	0.000	0.000	0.000
115	A	115	SER	0	-0.033	-0.042	9.174	0.082	0.082	0.000	0.000	0.000	0.000
116	A	116	LEU	0	0.025	0.001	7.717	-0.127	-0.127	0.000	0.000	0.000	0.000
117	A	117	ASP	-1	-0.889	-0.917	4.923	-3.267	-3.267	0.000	0.000	0.000	0.000
118	A	118	ASN	0	0.053	0.017	4.844	-1.073	-1.004	-0.001	-0.001	-0.066	0.000
119	A	119	ILE	0	0.009	0.003	6.732	0.332	0.332	0.000	0.000	0.000	0.000
120	A	120	ARG	1	0.878	0.930	2.470	1.535	2.616	0.715	-0.574	-1.222	0.003
121	A	121	ASP	-1	-0.907	-0.939	2.476	-0.850	0.744	0.633	-0.888	-1.339	-0.007
122	A	122	VAL	0	0.043	0.023	3.138	2.535	2.345	0.032	0.414	-0.257	-0.001
123	A	123	LEU	0	-0.037	-0.015	6.271	0.364	0.364	0.000	0.000	0.000	0.000
124	A	124	SER	0	-0.004	-0.015	2.276	-7.944	-6.741	2.811	-1.602	-2.411	0.015
125	A	125	ASP	-1	-0.825	-0.893	5.477	0.659	0.659	0.000	0.000	0.000	0.000
126	A	126	LEU	0	-0.094	-0.053	7.233	-0.353	-0.353	0.000	0.000	0.000	0.000
127	A	127	LEU	0	-0.074	-0.044	8.731	-0.172	-0.172	0.000	0.000	0.000	0.000
128	A	128	GLU	-1	-0.918	-0.954	3.250	-5.199	-2.607	0.120	-1.526	-1.186	-0.013
129	A	129	PRO	0	-0.059	-0.031	7.641	0.092	0.092	0.000	0.000	0.000	0.000
130	A	130	ARG	1	0.872	0.931	8.851	-0.791	-0.791	0.000	0.000	0.000	0.000
131	A	131	VAL	0	-0.028	-0.019	11.296	-0.080	-0.080	0.000	0.000	0.000	0.000
132	A	132	LEU	0	-0.044	-0.015	14.334	0.059	0.059	0.000	0.000	0.000	0.000
133	A	133	TYR	0	-0.010	-0.003	13.313	-0.041	-0.041	0.000	0.000	0.000	0.000
134	A	134	GLU	-1	-0.942	-0.968	18.276	0.344	0.344	0.000	0.000	0.000	0.000

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