FMO DATABASE

FMODB ID: VQKG1

Calculation Name: 1ID1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ID1

Chain ID: A

ChEMBL ID:

UniProt ID: P31069

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	153
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1374652.391544
FMO2-HF: Nuclear repulsion	1315422.844052
FMO2-HF: Total energy	-59229.547492
FMO2-MP2: Total energy	-59400.714333

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:3:HIS)

Summations of interaction energy for fragment #1(A:3: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.
-12.547	-20.289	26.456	-7.136	-11.579	0.047

Interaction energy analysis for fragmet #1(A:3:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : -0.012

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	5	LYS	1	0.923	0.954	2.734	4.823	7.531	0.186	-1.012	-1.883	0.001
4	A	6	ASP	-1	-0.912	-0.977	4.875	-2.053	-1.947	-0.001	-0.010	-0.095	0.000
5	A	7	HIS	0	0.014	0.013	7.048	-0.762	-0.762	0.000	0.000	0.000	0.000
6	A	8	PHE	0	-0.003	0.002	9.460	0.451	0.451	0.000	0.000	0.000	0.000
7	A	9	ILE	0	0.038	0.031	8.968	-0.096	-0.096	0.000	0.000	0.000	0.000
8	A	10	VAL	0	-0.013	-0.010	12.292	0.022	0.022	0.000	0.000	0.000	0.000
9	A	11	CYS	0	-0.008	0.002	15.319	0.070	0.070	0.000	0.000	0.000	0.000
10	A	12	GLY	0	0.032	0.007	17.183	-0.023	-0.023	0.000	0.000	0.000	0.000
11	A	13	HIS	0	0.020	0.017	19.086	-0.029	-0.029	0.000	0.000	0.000	0.000
12	A	14	SER	0	0.036	0.026	21.403	-0.026	-0.026	0.000	0.000	0.000	0.000
13	A	15	ILE	0	0.046	0.005	23.688	-0.025	-0.025	0.000	0.000	0.000	0.000
14	A	16	LEU	0	0.018	0.014	24.447	-0.027	-0.027	0.000	0.000	0.000	0.000
15	A	17	ALA	0	0.026	0.025	20.148	-0.031	-0.031	0.000	0.000	0.000	0.000
16	A	18	ILE	0	0.032	0.017	20.371	-0.050	-0.050	0.000	0.000	0.000	0.000
17	A	19	ASN	0	-0.006	-0.016	21.021	-0.050	-0.050	0.000	0.000	0.000	0.000
18	A	20	THR	0	-0.027	-0.024	19.877	-0.028	-0.028	0.000	0.000	0.000	0.000
19	A	21	ILE	0	0.011	0.008	15.779	-0.051	-0.051	0.000	0.000	0.000	0.000
20	A	22	LEU	0	0.029	0.025	17.887	-0.085	-0.085	0.000	0.000	0.000	0.000
21	A	23	GLN	0	-0.055	-0.028	20.188	-0.054	-0.054	0.000	0.000	0.000	0.000
22	A	24	LEU	0	-0.006	-0.005	16.347	-0.032	-0.032	0.000	0.000	0.000	0.000
23	A	25	ASN	0	0.013	0.007	14.260	0.018	0.018	0.000	0.000	0.000	0.000
24	A	26	GLN	0	-0.020	-0.014	17.291	-0.043	-0.043	0.000	0.000	0.000	0.000
25	A	27	ARG	1	0.819	0.923	18.904	0.439	0.439	0.000	0.000	0.000	0.000
26	A	28	GLY	0	0.012	0.007	16.541	0.000	0.000	0.000	0.000	0.000	0.000
27	A	29	GLN	0	-0.019	-0.001	13.637	-0.289	-0.289	0.000	0.000	0.000	0.000
28	A	30	ASN	0	-0.003	-0.003	9.160	0.018	0.018	0.000	0.000	0.000	0.000
29	A	31	VAL	0	-0.016	-0.019	11.300	0.152	0.152	0.000	0.000	0.000	0.000
30	A	32	THR	0	-0.017	-0.001	7.641	-0.215	-0.215	0.000	0.000	0.000	0.000
31	A	33	VAL	0	-0.012	0.000	10.244	0.137	0.137	0.000	0.000	0.000	0.000
32	A	34	ILE	0	0.003	0.015	11.615	0.104	0.104	0.000	0.000	0.000	0.000
33	A	35	SER	0	-0.014	-0.021	14.250	-0.059	-0.059	0.000	0.000	0.000	0.000
34	A	36	ASN	0	0.014	0.012	17.390	0.003	0.003	0.000	0.000	0.000	0.000
35	A	37	LEU	0	-0.008	-0.008	19.889	-0.011	-0.011	0.000	0.000	0.000	0.000
36	A	38	PRO	0	0.007	0.004	20.519	0.024	0.024	0.000	0.000	0.000	0.000
37	A	39	GLU	-1	-0.852	-0.933	20.209	-0.069	-0.069	0.000	0.000	0.000	0.000
38	A	40	ASP	-1	-0.848	-0.932	20.934	-0.113	-0.113	0.000	0.000	0.000	0.000
39	A	41	ASP	-1	-0.832	-0.937	22.913	-0.049	-0.049	0.000	0.000	0.000	0.000
40	A	42	ILE	0	-0.042	-0.015	16.184	-0.023	-0.023	0.000	0.000	0.000	0.000
41	A	43	LYS	1	0.814	0.916	18.379	0.048	0.048	0.000	0.000	0.000	0.000
42	A	44	GLN	0	-0.021	-0.013	20.063	-0.048	-0.048	0.000	0.000	0.000	0.000
43	A	45	LEU	0	-0.036	-0.012	17.433	-0.026	-0.026	0.000	0.000	0.000	0.000
44	A	46	GLU	-1	-0.887	-0.967	14.565	-0.320	-0.320	0.000	0.000	0.000	0.000
45	A	47	GLN	0	-0.025	-0.012	17.280	-0.049	-0.049	0.000	0.000	0.000	0.000
46	A	48	ARG	1	0.859	0.951	20.160	0.244	0.244	0.000	0.000	0.000	0.000
47	A	49	LEU	0	-0.080	-0.050	15.743	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	50	GLY	0	0.005	0.007	17.897	-0.028	-0.028	0.000	0.000	0.000	0.000
49	A	51	ASP	-1	-0.873	-0.922	16.063	-0.954	-0.954	0.000	0.000	0.000	0.000
50	A	52	ASN	0	-0.120	-0.069	11.409	-0.333	-0.333	0.000	0.000	0.000	0.000
51	A	53	ALA	0	-0.007	0.013	11.807	-0.097	-0.097	0.000	0.000	0.000	0.000
52	A	54	ASP	-1	-0.759	-0.864	7.163	-0.174	-0.174	0.000	0.000	0.000	0.000
53	A	55	VAL	0	0.015	0.000	9.866	0.181	0.181	0.000	0.000	0.000	0.000
54	A	56	ILE	0	-0.045	-0.029	7.503	0.176	0.176	0.000	0.000	0.000	0.000
55	A	57	PRO	0	-0.013	0.001	11.428	0.016	0.016	0.000	0.000	0.000	0.000
56	A	58	GLY	0	-0.005	-0.020	14.459	0.096	0.096	0.000	0.000	0.000	0.000
57	A	59	ASP	-1	-0.841	-0.912	16.057	0.334	0.334	0.000	0.000	0.000	0.000
58	A	60	SER	0	0.006	-0.024	15.687	0.062	0.062	0.000	0.000	0.000	0.000
59	A	61	ASN	0	-0.011	-0.020	16.723	0.049	0.049	0.000	0.000	0.000	0.000
60	A	62	ASP	-1	-0.849	-0.898	16.612	0.809	0.809	0.000	0.000	0.000	0.000
61	A	63	SER	0	0.099	0.015	15.043	0.069	0.069	0.000	0.000	0.000	0.000
62	A	64	SER	0	-0.094	-0.048	12.829	0.223	0.223	0.000	0.000	0.000	0.000
63	A	65	VAL	0	-0.003	-0.006	11.034	0.327	0.327	0.000	0.000	0.000	0.000
64	A	66	LEU	0	0.036	0.038	10.108	0.255	0.255	0.000	0.000	0.000	0.000
65	A	67	LYS	1	0.975	0.995	8.474	-2.769	-2.769	0.000	0.000	0.000	0.000
66	A	68	LYS	1	0.875	0.948	6.669	-0.889	-0.889	0.000	0.000	0.000	0.000
67	A	69	ALA	0	0.001	-0.017	5.359	1.296	1.296	0.000	0.000	0.000	0.000
68	A	70	GLY	0	-0.028	-0.012	5.484	-0.269	-0.269	0.000	0.000	0.000	0.000
69	A	71	ILE	0	0.023	-0.009	6.158	-0.343	-0.343	0.000	0.000	0.000	0.000
70	A	72	ASP	-1	-0.872	-0.931	7.792	2.656	2.656	0.000	0.000	0.000	0.000
71	A	73	ARG	1	0.819	0.910	1.989	-16.862	-27.418	26.271	-6.114	-9.601	0.046
72	A	74	CYS	0	-0.059	0.003	7.038	-0.980	-0.980	0.000	0.000	0.000	0.000
73	A	75	ARG	1	0.872	0.944	9.576	0.909	0.909	0.000	0.000	0.000	0.000
74	A	76	ALA	0	-0.037	-0.031	12.416	0.085	0.085	0.000	0.000	0.000	0.000
75	A	77	ILE	0	0.021	0.020	13.754	-0.064	-0.064	0.000	0.000	0.000	0.000
76	A	78	LEU	0	-0.055	-0.041	15.253	-0.029	-0.029	0.000	0.000	0.000	0.000
77	A	79	ALA	0	0.022	0.028	17.958	0.008	0.008	0.000	0.000	0.000	0.000
78	A	80	LEU	0	-0.022	-0.022	20.148	-0.029	-0.029	0.000	0.000	0.000	0.000
79	A	81	SER	0	0.005	-0.007	22.081	-0.030	-0.030	0.000	0.000	0.000	0.000
80	A	82	ASP	-1	-0.871	-0.941	23.598	0.005	0.005	0.000	0.000	0.000	0.000
81	A	83	ASN	0	0.013	0.026	25.821	0.009	0.009	0.000	0.000	0.000	0.000
82	A	84	ASP	-1	-0.723	-0.871	25.924	0.101	0.101	0.000	0.000	0.000	0.000
83	A	85	ALA	0	-0.050	-0.016	27.121	0.014	0.014	0.000	0.000	0.000	0.000
84	A	86	ASP	-1	-0.824	-0.926	22.588	0.250	0.250	0.000	0.000	0.000	0.000
85	A	87	ASN	0	-0.005	-0.003	22.258	0.057	0.057	0.000	0.000	0.000	0.000
86	A	88	ALA	0	-0.007	-0.013	22.630	0.024	0.024	0.000	0.000	0.000	0.000
87	A	89	PHE	0	0.015	0.013	21.586	0.020	0.020	0.000	0.000	0.000	0.000
88	A	90	VAL	0	0.030	0.025	17.182	0.053	0.053	0.000	0.000	0.000	0.000
89	A	91	VAL	0	-0.039	-0.032	18.728	0.057	0.057	0.000	0.000	0.000	0.000
90	A	92	LEU	0	-0.032	-0.015	20.555	0.035	0.035	0.000	0.000	0.000	0.000
91	A	93	SER	0	0.026	0.003	17.669	0.039	0.039	0.000	0.000	0.000	0.000
92	A	94	ALA	0	0.001	-0.001	16.147	0.085	0.085	0.000	0.000	0.000	0.000
93	A	95	LYS	1	0.844	0.925	17.124	-0.291	-0.291	0.000	0.000	0.000	0.000
94	A	96	ASP	-1	-0.955	-0.970	19.792	0.673	0.673	0.000	0.000	0.000	0.000
95	A	97	MET	0	-0.102	-0.027	12.137	0.083	0.083	0.000	0.000	0.000	0.000
96	A	98	SER	0	-0.064	-0.066	13.976	0.141	0.141	0.000	0.000	0.000	0.000
97	A	99	SER	0	-0.034	-0.015	15.838	-0.076	-0.076	0.000	0.000	0.000	0.000
98	A	100	ASP	-1	-0.888	-0.916	15.139	0.810	0.810	0.000	0.000	0.000	0.000
99	A	101	VAL	0	-0.004	0.014	14.103	-0.085	-0.085	0.000	0.000	0.000	0.000
100	A	102	LYS	1	0.957	0.978	15.644	-0.029	-0.029	0.000	0.000	0.000	0.000
101	A	103	THR	0	-0.027	-0.018	17.174	-0.013	-0.013	0.000	0.000	0.000	0.000
102	A	104	VAL	0	-0.008	-0.007	19.573	-0.039	-0.039	0.000	0.000	0.000	0.000
103	A	105	LEU	0	-0.003	-0.003	20.996	0.019	0.019	0.000	0.000	0.000	0.000
104	A	106	ALA	0	0.013	0.018	23.673	-0.021	-0.021	0.000	0.000	0.000	0.000
105	A	107	VAL	0	-0.065	-0.030	26.036	0.019	0.019	0.000	0.000	0.000	0.000
106	A	108	SER	0	0.002	-0.018	28.335	-0.020	-0.020	0.000	0.000	0.000	0.000
107	A	109	ASP	-1	-0.848	-0.926	30.477	0.043	0.043	0.000	0.000	0.000	0.000
108	A	110	SER	0	-0.036	-0.024	33.771	0.008	0.008	0.000	0.000	0.000	0.000
109	A	111	LYS	1	0.908	0.951	35.284	-0.045	-0.045	0.000	0.000	0.000	0.000
110	A	112	ASN	0	-0.033	-0.033	32.304	0.011	0.011	0.000	0.000	0.000	0.000
111	A	113	LEU	0	0.020	0.033	31.960	0.014	0.014	0.000	0.000	0.000	0.000
112	A	114	ASN	0	0.055	-0.010	32.808	0.007	0.007	0.000	0.000	0.000	0.000
113	A	115	LYS	1	0.901	0.962	32.766	-0.104	-0.104	0.000	0.000	0.000	0.000
114	A	116	ILE	0	0.058	0.029	28.051	0.014	0.014	0.000	0.000	0.000	0.000
115	A	117	LYS	1	0.949	0.981	28.940	-0.072	-0.072	0.000	0.000	0.000	0.000
116	A	118	MET	0	-0.037	-0.022	30.542	0.010	0.010	0.000	0.000	0.000	0.000
117	A	119	VAL	0	-0.027	0.004	25.684	0.012	0.012	0.000	0.000	0.000	0.000
118	A	120	HIS	0	-0.106	-0.052	25.741	0.016	0.016	0.000	0.000	0.000	0.000
119	A	121	PRO	0	-0.012	0.009	23.725	0.021	0.021	0.000	0.000	0.000	0.000
120	A	122	ASP	-1	-0.785	-0.892	20.610	0.230	0.230	0.000	0.000	0.000	0.000
121	A	123	ILE	0	-0.050	-0.027	22.224	-0.034	-0.034	0.000	0.000	0.000	0.000
122	A	124	ILE	0	-0.017	-0.003	24.782	0.019	0.019	0.000	0.000	0.000	0.000
123	A	125	LEU	0	0.021	0.008	26.349	-0.017	-0.017	0.000	0.000	0.000	0.000
124	A	126	SER	0	0.019	0.010	28.344	0.004	0.004	0.000	0.000	0.000	0.000
125	A	127	PRO	0	0.018	-0.004	29.268	-0.008	-0.008	0.000	0.000	0.000	0.000
126	A	128	GLN	0	0.062	0.020	31.895	-0.006	-0.006	0.000	0.000	0.000	0.000
127	A	129	LEU	0	-0.027	-0.012	34.980	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	130	PHE	0	0.046	0.029	31.321	-0.004	-0.004	0.000	0.000	0.000	0.000
129	A	131	GLY	0	0.041	0.015	34.626	-0.006	-0.006	0.000	0.000	0.000	0.000
130	A	132	SER	0	-0.064	-0.025	36.233	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	133	GLU	-1	-0.860	-0.943	37.895	-0.011	-0.011	0.000	0.000	0.000	0.000
132	A	134	ILE	0	0.013	0.003	34.118	-0.003	-0.003	0.000	0.000	0.000	0.000
133	A	135	LEU	0	-0.017	-0.013	38.615	-0.003	-0.003	0.000	0.000	0.000	0.000
134	A	136	ALA	0	-0.017	-0.005	41.251	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	137	ARG	1	0.889	0.946	39.133	0.026	0.026	0.000	0.000	0.000	0.000
136	A	138	VAL	0	0.011	0.008	39.886	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	139	LEU	0	-0.067	-0.036	42.968	-0.002	-0.002	0.000	0.000	0.000	0.000
138	A	140	ASN	0	-0.135	-0.072	45.921	0.002	0.002	0.000	0.000	0.000	0.000
139	A	141	GLY	0	-0.022	-0.008	46.562	0.002	0.002	0.000	0.000	0.000	0.000
140	A	142	GLU	-1	-0.873	-0.915	43.862	-0.031	-0.031	0.000	0.000	0.000	0.000
141	A	143	GLU	-1	-0.965	-0.979	41.520	-0.079	-0.079	0.000	0.000	0.000	0.000
142	A	144	ILE	0	-0.022	-0.024	36.139	0.006	0.006	0.000	0.000	0.000	0.000
143	A	145	ASN	0	0.037	0.022	36.429	-0.010	-0.010	0.000	0.000	0.000	0.000
144	A	146	ASN	0	0.019	-0.027	28.769	0.010	0.010	0.000	0.000	0.000	0.000
145	A	147	ASP	-1	-0.852	-0.928	31.781	-0.055	-0.055	0.000	0.000	0.000	0.000
146	A	148	MET	0	-0.073	-0.019	33.328	0.011	0.011	0.000	0.000	0.000	0.000
147	A	149	LEU	0	0.004	0.005	30.489	0.006	0.006	0.000	0.000	0.000	0.000
148	A	150	VAL	0	0.009	-0.005	27.483	0.007	0.007	0.000	0.000	0.000	0.000
149	A	151	SER	0	-0.013	-0.002	29.705	0.019	0.019	0.000	0.000	0.000	0.000
150	A	152	MET	0	-0.063	-0.012	32.318	0.008	0.008	0.000	0.000	0.000	0.000
151	A	153	LEU	0	-0.065	-0.022	26.858	0.002	0.002	0.000	0.000	0.000	0.000
152	A	154	LEU	0	-0.046	-0.024	25.137	0.016	0.016	0.000	0.000	0.000	0.000
153	A	155	ASN	0	-0.034	-0.005	27.530	-0.012	-0.012	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:HIS)