FMO DATABASE

FMODB ID: G5Y21

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	OptAll
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	-1379066.606753
FMO2-HF: Nuclear repulsion	1319835.813354
FMO2-HF: Total energy	-59230.7934
FMO2-MP2: Total energy	-59401.806858

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.
-12.293	-9.589	10.243	-4.592	-8.356	0.028

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 : -0.021 / q_NPA : -0.018

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	0.866	0.908	2.472	3.971	7.063	0.784	-1.459	-2.417	-0.002
4	A	6	ASP	-1	-0.842	-0.895	4.471	-2.154	-1.995	0.000	-0.029	-0.130	0.000
5	A	7	HIS	0	-0.003	0.004	6.556	-0.898	-0.898	0.000	0.000	0.000	0.000
6	A	8	PHE	0	-0.009	-0.010	9.604	0.357	0.357	0.000	0.000	0.000	0.000
7	A	9	ILE	0	0.016	0.010	9.270	-0.060	-0.060	0.000	0.000	0.000	0.000
8	A	10	VAL	0	-0.010	-0.003	12.670	0.035	0.035	0.000	0.000	0.000	0.000
9	A	11	CYS	0	-0.017	0.004	15.736	0.064	0.064	0.000	0.000	0.000	0.000
10	A	12	GLY	0	0.043	0.009	17.356	-0.025	-0.025	0.000	0.000	0.000	0.000
11	A	13	HIS	0	0.040	0.032	19.286	-0.010	-0.010	0.000	0.000	0.000	0.000
12	A	14	SER	0	0.047	0.037	21.862	-0.030	-0.030	0.000	0.000	0.000	0.000
13	A	15	ILE	0	0.004	-0.012	24.253	-0.022	-0.022	0.000	0.000	0.000	0.000
14	A	16	LEU	0	-0.002	0.005	24.678	-0.026	-0.026	0.000	0.000	0.000	0.000
15	A	17	ALA	0	0.032	0.031	20.396	-0.031	-0.031	0.000	0.000	0.000	0.000
16	A	18	ILE	0	0.029	0.013	20.834	-0.045	-0.045	0.000	0.000	0.000	0.000
17	A	19	ASN	0	0.015	-0.008	21.489	-0.049	-0.049	0.000	0.000	0.000	0.000
18	A	20	THR	0	-0.038	-0.025	19.961	-0.035	-0.035	0.000	0.000	0.000	0.000
19	A	21	ILE	0	0.019	0.008	16.009	-0.052	-0.052	0.000	0.000	0.000	0.000
20	A	22	LEU	0	0.027	0.029	18.204	-0.084	-0.084	0.000	0.000	0.000	0.000
21	A	23	GLN	0	0.017	0.014	20.395	-0.072	-0.072	0.000	0.000	0.000	0.000
22	A	24	LEU	0	0.000	0.005	16.472	-0.030	-0.030	0.000	0.000	0.000	0.000
23	A	25	ASN	0	0.007	-0.002	14.302	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	26	GLN	0	-0.026	-0.019	17.524	-0.039	-0.039	0.000	0.000	0.000	0.000
25	A	27	ARG	1	0.801	0.897	19.070	0.395	0.395	0.000	0.000	0.000	0.000
26	A	28	GLY	0	0.021	0.018	16.659	-0.033	-0.033	0.000	0.000	0.000	0.000
27	A	29	GLN	0	-0.046	-0.014	13.871	-0.190	-0.190	0.000	0.000	0.000	0.000
28	A	30	ASN	0	0.025	0.014	9.283	0.030	0.030	0.000	0.000	0.000	0.000
29	A	31	VAL	0	-0.030	-0.026	11.365	0.109	0.109	0.000	0.000	0.000	0.000
30	A	32	THR	0	-0.013	-0.006	8.305	-0.083	-0.083	0.000	0.000	0.000	0.000
31	A	33	VAL	0	-0.021	-0.010	10.767	0.014	0.014	0.000	0.000	0.000	0.000
32	A	34	ILE	0	-0.028	-0.014	11.938	0.138	0.138	0.000	0.000	0.000	0.000
33	A	35	SER	0	0.002	-0.016	14.713	-0.070	-0.070	0.000	0.000	0.000	0.000
34	A	36	ASN	0	0.008	-0.010	17.944	0.005	0.005	0.000	0.000	0.000	0.000
35	A	37	LEU	0	-0.017	0.005	20.414	-0.017	-0.017	0.000	0.000	0.000	0.000
36	A	38	PRO	0	0.008	0.002	21.197	0.027	0.027	0.000	0.000	0.000	0.000
37	A	39	GLU	-1	-0.825	-0.914	20.576	0.051	0.051	0.000	0.000	0.000	0.000
38	A	40	ASP	-1	-0.835	-0.912	21.336	-0.018	-0.018	0.000	0.000	0.000	0.000
39	A	41	ASP	-1	-0.852	-0.937	23.374	0.043	0.043	0.000	0.000	0.000	0.000
40	A	42	ILE	0	-0.040	-0.014	17.034	-0.016	-0.016	0.000	0.000	0.000	0.000
41	A	43	LYS	1	0.823	0.909	19.185	-0.051	-0.051	0.000	0.000	0.000	0.000
42	A	44	GLN	0	-0.071	-0.038	20.386	-0.047	-0.047	0.000	0.000	0.000	0.000
43	A	45	LEU	0	-0.038	-0.020	18.107	-0.030	-0.030	0.000	0.000	0.000	0.000
44	A	46	GLU	-1	-0.898	-0.970	15.422	-0.043	-0.043	0.000	0.000	0.000	0.000
45	A	47	GLN	0	-0.046	-0.026	17.902	-0.068	-0.068	0.000	0.000	0.000	0.000
46	A	48	ARG	1	0.845	0.946	20.883	0.134	0.134	0.000	0.000	0.000	0.000
47	A	49	LEU	0	-0.070	-0.038	16.535	-0.012	-0.012	0.000	0.000	0.000	0.000
48	A	50	GLY	0	0.018	0.004	18.375	-0.044	-0.044	0.000	0.000	0.000	0.000
49	A	51	ASP	-1	-0.900	-0.942	16.000	-0.689	-0.689	0.000	0.000	0.000	0.000
50	A	52	ASN	0	-0.076	-0.055	11.347	-0.231	-0.231	0.000	0.000	0.000	0.000
51	A	53	ALA	0	0.002	0.016	12.171	-0.058	-0.058	0.000	0.000	0.000	0.000
52	A	54	ASP	-1	-0.750	-0.812	7.847	0.581	0.581	0.000	0.000	0.000	0.000
53	A	55	VAL	0	-0.003	-0.007	10.447	0.128	0.128	0.000	0.000	0.000	0.000
54	A	56	ILE	0	-0.055	-0.025	8.176	0.158	0.158	0.000	0.000	0.000	0.000
55	A	57	PRO	0	0.027	0.014	12.195	-0.031	-0.031	0.000	0.000	0.000	0.000
56	A	58	GLY	0	-0.027	-0.029	15.081	0.090	0.090	0.000	0.000	0.000	0.000
57	A	59	ASP	-1	-0.817	-0.907	16.439	0.357	0.357	0.000	0.000	0.000	0.000
58	A	60	SER	0	0.019	-0.004	16.003	0.054	0.054	0.000	0.000	0.000	0.000
59	A	61	ASN	0	-0.052	-0.039	17.064	0.031	0.031	0.000	0.000	0.000	0.000
60	A	62	ASP	-1	-0.784	-0.857	15.706	0.949	0.949	0.000	0.000	0.000	0.000
61	A	63	SER	0	0.075	0.012	15.187	0.058	0.058	0.000	0.000	0.000	0.000
62	A	64	SER	0	-0.122	-0.087	12.814	0.248	0.248	0.000	0.000	0.000	0.000
63	A	65	VAL	0	-0.003	-0.014	11.040	0.317	0.317	0.000	0.000	0.000	0.000
64	A	66	LEU	0	0.060	0.041	10.395	0.175	0.175	0.000	0.000	0.000	0.000
65	A	67	LYS	1	0.883	0.953	7.657	-3.673	-3.673	0.000	0.000	0.000	0.000
66	A	68	LYS	1	0.881	0.941	6.731	-0.583	-0.583	0.000	0.000	0.000	0.000
67	A	69	ALA	0	0.037	0.015	5.703	0.741	0.741	0.000	0.000	0.000	0.000
68	A	70	GLY	0	-0.007	0.002	6.046	-0.294	-0.294	0.000	0.000	0.000	0.000
69	A	71	ILE	0	0.060	-0.001	6.865	-0.424	-0.424	0.000	0.000	0.000	0.000
70	A	72	ASP	-1	-0.740	-0.867	6.690	4.824	4.824	0.000	0.000	0.000	0.000
71	A	73	ARG	1	0.763	0.883	2.079	-17.927	-18.474	9.459	-3.104	-5.809	0.030
72	A	74	CYS	0	-0.081	-0.009	6.112	-1.274	-1.274	0.000	0.000	0.000	0.000
73	A	75	ARG	1	0.818	0.894	8.991	1.136	1.136	0.000	0.000	0.000	0.000
74	A	76	ALA	0	-0.013	-0.026	12.000	0.083	0.083	0.000	0.000	0.000	0.000
75	A	77	ILE	0	0.009	0.013	13.757	-0.059	-0.059	0.000	0.000	0.000	0.000
76	A	78	LEU	0	-0.038	-0.028	15.489	-0.030	-0.030	0.000	0.000	0.000	0.000
77	A	79	ALA	0	0.025	0.029	18.362	0.009	0.009	0.000	0.000	0.000	0.000
78	A	80	LEU	0	-0.005	-0.012	20.209	-0.038	-0.038	0.000	0.000	0.000	0.000
79	A	81	SER	0	0.033	0.010	22.123	-0.025	-0.025	0.000	0.000	0.000	0.000
80	A	82	ASP	-1	-0.889	-0.951	23.625	0.056	0.056	0.000	0.000	0.000	0.000
81	A	83	ASN	0	-0.022	-0.030	26.279	-0.017	-0.017	0.000	0.000	0.000	0.000
82	A	84	ASP	-1	-0.732	-0.839	26.260	0.134	0.134	0.000	0.000	0.000	0.000
83	A	85	ALA	0	-0.043	-0.008	27.466	0.013	0.013	0.000	0.000	0.000	0.000
84	A	86	ASP	-1	-0.757	-0.851	22.810	0.291	0.291	0.000	0.000	0.000	0.000
85	A	87	ASN	0	-0.045	-0.020	22.710	0.048	0.048	0.000	0.000	0.000	0.000
86	A	88	ALA	0	0.020	-0.008	22.938	0.019	0.019	0.000	0.000	0.000	0.000
87	A	89	PHE	0	-0.003	0.002	21.519	0.017	0.017	0.000	0.000	0.000	0.000
88	A	90	VAL	0	0.026	0.008	17.529	0.053	0.053	0.000	0.000	0.000	0.000
89	A	91	VAL	0	-0.022	-0.010	18.922	0.060	0.060	0.000	0.000	0.000	0.000
90	A	92	LEU	0	-0.027	-0.008	20.609	0.034	0.034	0.000	0.000	0.000	0.000
91	A	93	SER	0	0.015	0.006	17.747	0.026	0.026	0.000	0.000	0.000	0.000
92	A	94	ALA	0	-0.014	-0.006	16.066	0.104	0.104	0.000	0.000	0.000	0.000
93	A	95	LYS	1	0.775	0.860	16.659	-0.306	-0.306	0.000	0.000	0.000	0.000
94	A	96	ASP	-1	-0.954	-0.969	19.333	0.686	0.686	0.000	0.000	0.000	0.000
95	A	97	MET	0	-0.076	-0.025	12.415	0.056	0.056	0.000	0.000	0.000	0.000
96	A	98	SER	0	-0.066	-0.055	13.097	0.260	0.260	0.000	0.000	0.000	0.000
97	A	99	SER	0	-0.033	0.014	15.206	-0.088	-0.088	0.000	0.000	0.000	0.000
98	A	100	ASP	-1	-0.880	-0.941	13.639	0.813	0.813	0.000	0.000	0.000	0.000
99	A	101	VAL	0	-0.026	-0.001	12.526	-0.121	-0.121	0.000	0.000	0.000	0.000
100	A	102	LYS	1	0.943	0.987	14.542	0.032	0.032	0.000	0.000	0.000	0.000
101	A	103	THR	0	-0.033	-0.051	16.035	0.007	0.007	0.000	0.000	0.000	0.000
102	A	104	VAL	0	-0.015	-0.017	18.764	-0.047	-0.047	0.000	0.000	0.000	0.000
103	A	105	LEU	0	-0.003	0.008	21.155	0.025	0.025	0.000	0.000	0.000	0.000
104	A	106	ALA	0	0.001	0.002	23.997	-0.026	-0.026	0.000	0.000	0.000	0.000
105	A	107	VAL	0	-0.085	-0.046	26.309	0.020	0.020	0.000	0.000	0.000	0.000
106	A	108	SER	0	0.014	-0.030	28.632	-0.019	-0.019	0.000	0.000	0.000	0.000
107	A	109	ASP	-1	-0.848	-0.930	30.646	0.067	0.067	0.000	0.000	0.000	0.000
108	A	110	SER	0	-0.009	0.004	33.818	0.007	0.007	0.000	0.000	0.000	0.000
109	A	111	LYS	1	0.890	0.931	35.869	-0.059	-0.059	0.000	0.000	0.000	0.000
110	A	112	ASN	0	0.012	-0.009	32.118	0.012	0.012	0.000	0.000	0.000	0.000
111	A	113	LEU	0	0.007	0.027	31.968	0.013	0.013	0.000	0.000	0.000	0.000
112	A	114	ASN	0	0.026	-0.020	32.851	0.005	0.005	0.000	0.000	0.000	0.000
113	A	115	LYS	1	0.856	0.934	33.025	-0.116	-0.116	0.000	0.000	0.000	0.000
114	A	116	ILE	0	0.040	0.012	28.353	0.014	0.014	0.000	0.000	0.000	0.000
115	A	117	LYS	1	0.938	0.983	28.727	-0.084	-0.084	0.000	0.000	0.000	0.000
116	A	118	MET	0	-0.031	-0.008	29.803	0.010	0.010	0.000	0.000	0.000	0.000
117	A	119	VAL	0	-0.023	0.000	25.889	0.011	0.011	0.000	0.000	0.000	0.000
118	A	120	HIS	0	-0.080	-0.035	25.185	0.011	0.011	0.000	0.000	0.000	0.000
119	A	121	PRO	0	0.053	0.044	22.912	0.020	0.020	0.000	0.000	0.000	0.000
120	A	122	ASP	-1	-0.772	-0.847	20.072	0.244	0.244	0.000	0.000	0.000	0.000
121	A	123	ILE	0	-0.049	-0.024	21.190	-0.038	-0.038	0.000	0.000	0.000	0.000
122	A	124	ILE	0	-0.020	-0.008	24.225	0.023	0.023	0.000	0.000	0.000	0.000
123	A	125	LEU	0	0.024	0.017	26.451	-0.021	-0.021	0.000	0.000	0.000	0.000
124	A	126	SER	0	0.024	0.007	28.458	0.012	0.012	0.000	0.000	0.000	0.000
125	A	127	PRO	0	0.023	0.008	29.715	-0.008	-0.008	0.000	0.000	0.000	0.000
126	A	128	GLN	0	0.040	0.018	32.389	-0.005	-0.005	0.000	0.000	0.000	0.000
127	A	129	LEU	0	0.000	0.009	35.370	-0.004	-0.004	0.000	0.000	0.000	0.000
128	A	130	PHE	0	0.063	0.033	30.647	-0.005	-0.005	0.000	0.000	0.000	0.000
129	A	131	GLY	0	0.042	0.021	34.653	-0.007	-0.007	0.000	0.000	0.000	0.000
130	A	132	SER	0	-0.075	-0.049	36.513	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	133	GLU	-1	-0.801	-0.887	37.669	-0.010	-0.010	0.000	0.000	0.000	0.000
132	A	134	ILE	0	0.018	0.009	33.750	-0.004	-0.004	0.000	0.000	0.000	0.000
133	A	135	LEU	0	-0.032	-0.019	38.376	-0.004	-0.004	0.000	0.000	0.000	0.000
134	A	136	ALA	0	-0.021	-0.008	41.392	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	137	ARG	1	0.789	0.857	39.337	0.020	0.020	0.000	0.000	0.000	0.000
136	A	138	VAL	0	0.011	0.007	40.088	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	139	LEU	0	-0.074	-0.039	43.083	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	140	ASN	0	-0.109	-0.054	45.961	0.002	0.002	0.000	0.000	0.000	0.000
139	A	141	GLY	0	-0.017	-0.003	46.469	0.001	0.001	0.000	0.000	0.000	0.000
140	A	142	GLU	-1	-0.863	-0.905	43.053	-0.028	-0.028	0.000	0.000	0.000	0.000
141	A	143	GLU	-1	-0.947	-0.972	40.868	-0.079	-0.079	0.000	0.000	0.000	0.000
142	A	144	ILE	0	-0.032	-0.026	35.590	0.006	0.006	0.000	0.000	0.000	0.000
143	A	145	ASN	0	-0.018	-0.030	35.487	-0.005	-0.005	0.000	0.000	0.000	0.000
144	A	146	ASN	0	-0.018	-0.021	28.577	0.004	0.004	0.000	0.000	0.000	0.000
145	A	147	ASP	-1	-0.800	-0.892	31.434	-0.069	-0.069	0.000	0.000	0.000	0.000
146	A	148	MET	0	-0.024	0.004	32.626	0.010	0.010	0.000	0.000	0.000	0.000
147	A	149	LEU	0	0.018	0.007	30.556	0.007	0.007	0.000	0.000	0.000	0.000
148	A	150	VAL	0	-0.009	-0.012	27.030	0.005	0.005	0.000	0.000	0.000	0.000
149	A	151	SER	0	-0.011	-0.015	29.159	0.017	0.017	0.000	0.000	0.000	0.000
150	A	152	MET	0	-0.078	-0.013	31.733	0.009	0.009	0.000	0.000	0.000	0.000
151	A	153	LEU	0	-0.048	-0.013	26.862	0.003	0.003	0.000	0.000	0.000	0.000
152	A	154	LEU	0	-0.027	-0.011	24.468	0.016	0.016	0.000	0.000	0.000	0.000
153	A	155	ASN	0	-0.050	-0.027	26.390	-0.009	-0.009	0.000	0.000	0.000	0.000

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