FMO DATABASE

FMODB ID: Z623N

Calculation Name: 1Y12-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Y12

Chain ID: A

ChEMBL ID:

UniProt ID: Q9I747

Base Structure: X-ray

Registration Date: 2023-06-21

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	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	161
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1411437.969148
FMO2-HF: Nuclear repulsion	1349926.939036
FMO2-HF: Total energy	-61511.030112
FMO2-MP2: Total energy	-61687.672105

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:2:ALA)

Summations of interaction energy for fragment #1(A:2:ALA)

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.
-3.792	-1.867	0.167	-0.859	-1.233	0.003

Interaction energy analysis for fragmet #1(A:2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / q_NPA : -0.024

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	4	ASP	-1	-0.726	-0.844	3.882	-3.662	-2.505	-0.010	-0.553	-0.594	0.002
4	A	5	MET	0	-0.079	-0.037	5.451	0.754	0.754	0.000	0.000	0.000	0.000
5	A	6	PHE	0	0.032	0.023	8.665	-0.019	-0.019	0.000	0.000	0.000	0.000
6	A	7	ILE	0	0.008	0.000	12.196	0.077	0.077	0.000	0.000	0.000	0.000
7	A	8	LYS	1	0.868	0.932	15.621	0.141	0.141	0.000	0.000	0.000	0.000
8	A	9	ILE	0	0.021	-0.008	19.107	0.023	0.023	0.000	0.000	0.000	0.000
9	A	10	GLY	0	0.019	0.011	22.062	0.001	0.001	0.000	0.000	0.000	0.000
10	A	11	ASP	-1	-0.896	-0.932	24.365	-0.123	-0.123	0.000	0.000	0.000	0.000
11	A	12	VAL	0	-0.045	-0.005	22.756	-0.002	-0.002	0.000	0.000	0.000	0.000
12	A	13	LYS	1	0.864	0.928	21.779	0.175	0.175	0.000	0.000	0.000	0.000
13	A	14	GLY	0	0.047	0.007	18.530	0.012	0.012	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.933	-0.977	17.550	-0.251	-0.251	0.000	0.000	0.000	0.000
15	A	16	SER	0	-0.059	-0.023	12.766	-0.023	-0.023	0.000	0.000	0.000	0.000
16	A	17	LYS	1	0.921	0.939	14.042	0.466	0.466	0.000	0.000	0.000	0.000
17	A	18	ASP	-1	-0.728	-0.829	12.205	-0.618	-0.618	0.000	0.000	0.000	0.000
18	A	19	LYS	1	0.893	0.959	13.809	0.390	0.390	0.000	0.000	0.000	0.000
19	A	20	THR	0	-0.002	-0.006	15.500	0.030	0.030	0.000	0.000	0.000	0.000
20	A	21	HIS	1	0.762	0.847	13.998	0.380	0.380	0.000	0.000	0.000	0.000
21	A	22	ALA	0	0.029	0.021	16.170	-0.020	-0.020	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.877	-0.923	18.004	-0.163	-0.163	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.850	-0.904	15.759	-0.260	-0.260	0.000	0.000	0.000	0.000
24	A	25	ILE	0	-0.020	-0.023	14.624	-0.011	-0.011	0.000	0.000	0.000	0.000
25	A	26	ASP	-1	-0.827	-0.902	10.491	-0.664	-0.664	0.000	0.000	0.000	0.000
26	A	27	VAL	0	-0.070	-0.034	10.021	0.080	0.080	0.000	0.000	0.000	0.000
27	A	28	LEU	0	0.001	0.000	7.968	-0.174	-0.174	0.000	0.000	0.000	0.000
28	A	29	ALA	0	0.008	0.000	7.624	-0.032	-0.032	0.000	0.000	0.000	0.000
29	A	30	TRP	0	-0.008	-0.018	9.485	0.040	0.040	0.000	0.000	0.000	0.000
30	A	31	SER	0	0.002	0.009	12.592	0.049	0.049	0.000	0.000	0.000	0.000
31	A	32	TRP	0	-0.022	-0.019	15.347	-0.019	-0.019	0.000	0.000	0.000	0.000
32	A	33	GLY	0	0.046	0.025	17.977	0.026	0.026	0.000	0.000	0.000	0.000
33	A	34	MET	0	-0.023	-0.008	20.607	-0.016	-0.016	0.000	0.000	0.000	0.000
34	A	35	SER	0	0.000	0.018	24.239	0.011	0.011	0.000	0.000	0.000	0.000
35	A	36	GLN	0	0.036	-0.003	27.185	-0.008	-0.008	0.000	0.000	0.000	0.000
36	A	37	SER	0	0.024	0.017	30.573	0.002	0.002	0.000	0.000	0.000	0.000
37	A	38	GLY	0	-0.011	0.008	34.017	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	39	SER	0	-0.032	-0.024	34.644	0.005	0.005	0.000	0.000	0.000	0.000
39	A	40	MET	0	0.017	-0.004	35.455	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	41	HIS	0	0.011	-0.001	35.827	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	42	MET	0	-0.015	0.015	40.530	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	43	GLY	0	0.026	0.028	42.323	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	44	GLY	0	0.020	-0.006	43.988	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	45	GLY	0	-0.033	-0.016	44.792	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	46	GLY	0	-0.010	0.000	41.352	0.001	0.001	0.000	0.000	0.000	0.000
46	A	47	GLY	0	0.036	0.023	40.438	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	48	ALA	0	-0.026	-0.023	38.726	0.003	0.003	0.000	0.000	0.000	0.000
48	A	49	GLY	0	0.004	-0.002	36.458	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	50	LYS	1	0.930	0.972	34.296	-0.021	-0.021	0.000	0.000	0.000	0.000
50	A	51	VAL	0	0.020	0.013	28.049	0.003	0.003	0.000	0.000	0.000	0.000
51	A	52	ASN	0	-0.059	-0.032	28.740	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	53	VAL	0	0.017	-0.001	24.055	0.008	0.008	0.000	0.000	0.000	0.000
53	A	54	GLN	0	-0.005	0.003	21.764	0.003	0.003	0.000	0.000	0.000	0.000
54	A	55	ASP	-1	-0.721	-0.832	23.341	-0.031	-0.031	0.000	0.000	0.000	0.000
55	A	56	LEU	0	-0.079	-0.025	16.542	0.008	0.008	0.000	0.000	0.000	0.000
56	A	57	SER	0	-0.004	-0.004	17.999	-0.012	-0.012	0.000	0.000	0.000	0.000
57	A	58	PHE	0	-0.017	-0.026	13.848	0.006	0.006	0.000	0.000	0.000	0.000
58	A	59	THR	0	0.027	0.012	12.161	0.025	0.025	0.000	0.000	0.000	0.000
59	A	60	LYS	1	0.758	0.861	12.446	0.172	0.172	0.000	0.000	0.000	0.000
60	A	61	TYR	0	0.090	0.026	10.882	-0.011	-0.011	0.000	0.000	0.000	0.000
61	A	62	ILE	0	-0.048	0.000	15.353	0.012	0.012	0.000	0.000	0.000	0.000
62	A	63	ASP	-1	-0.767	-0.852	17.880	-0.281	-0.281	0.000	0.000	0.000	0.000
63	A	64	LYS	1	0.847	0.908	20.046	0.243	0.243	0.000	0.000	0.000	0.000
64	A	65	SER	0	-0.034	-0.046	19.699	0.020	0.020	0.000	0.000	0.000	0.000
65	A	66	THR	0	-0.011	-0.034	20.993	0.011	0.011	0.000	0.000	0.000	0.000
66	A	67	PRO	0	0.026	0.002	22.937	0.014	0.014	0.000	0.000	0.000	0.000
67	A	68	ASN	0	-0.031	-0.008	25.264	0.020	0.020	0.000	0.000	0.000	0.000
68	A	69	LEU	0	0.000	0.000	20.309	0.011	0.011	0.000	0.000	0.000	0.000
69	A	70	MET	0	0.039	0.017	24.345	0.012	0.012	0.000	0.000	0.000	0.000
70	A	71	MET	0	0.006	0.024	27.313	0.012	0.012	0.000	0.000	0.000	0.000
71	A	72	ALA	0	-0.024	-0.003	27.367	0.008	0.008	0.000	0.000	0.000	0.000
72	A	73	CYS	0	-0.022	0.000	27.184	0.008	0.008	0.000	0.000	0.000	0.000
73	A	74	SER	0	-0.022	-0.029	29.254	0.008	0.008	0.000	0.000	0.000	0.000
74	A	75	SER	0	-0.092	-0.051	32.341	0.006	0.006	0.000	0.000	0.000	0.000
75	A	76	GLY	0	0.017	0.019	32.920	0.003	0.003	0.000	0.000	0.000	0.000
76	A	77	LYS	1	0.849	0.929	32.111	0.059	0.059	0.000	0.000	0.000	0.000
77	A	78	HIS	0	-0.028	-0.018	29.315	-0.006	-0.006	0.000	0.000	0.000	0.000
78	A	79	TYR	0	0.028	0.012	26.087	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	80	PRO	0	0.015	-0.004	28.325	0.004	0.004	0.000	0.000	0.000	0.000
80	A	81	GLN	0	-0.041	-0.040	23.961	0.006	0.006	0.000	0.000	0.000	0.000
81	A	82	ALA	0	0.031	0.028	21.080	-0.009	-0.009	0.000	0.000	0.000	0.000
82	A	83	LYS	1	0.897	0.946	18.210	0.114	0.114	0.000	0.000	0.000	0.000
83	A	84	LEU	0	0.055	0.052	12.375	-0.029	-0.029	0.000	0.000	0.000	0.000
84	A	85	THR	0	-0.020	-0.021	13.166	0.081	0.081	0.000	0.000	0.000	0.000
85	A	86	ILE	0	0.002	0.011	8.003	-0.117	-0.117	0.000	0.000	0.000	0.000
86	A	87	ARG	1	0.741	0.838	8.649	0.923	0.923	0.000	0.000	0.000	0.000
87	A	88	LYS	1	0.847	0.922	6.978	-1.056	-1.056	0.000	0.000	0.000	0.000
88	A	89	ALA	0	0.059	0.028	2.847	-1.033	-0.407	0.178	-0.295	-0.509	0.001
89	A	90	GLY	0	-0.002	0.007	4.768	0.470	0.612	-0.001	-0.011	-0.130	0.000
90	A	91	GLY	0	0.017	0.022	7.478	0.158	0.158	0.000	0.000	0.000	0.000
91	A	92	GLU	-1	-0.898	-0.980	10.384	-0.308	-0.308	0.000	0.000	0.000	0.000
92	A	93	ASN	0	-0.059	-0.025	13.458	0.090	0.090	0.000	0.000	0.000	0.000
93	A	94	GLN	0	-0.052	-0.007	8.045	0.137	0.137	0.000	0.000	0.000	0.000
94	A	95	VAL	0	-0.015	-0.025	11.822	-0.046	-0.046	0.000	0.000	0.000	0.000
95	A	96	GLU	-1	-0.784	-0.889	11.636	-0.265	-0.265	0.000	0.000	0.000	0.000
96	A	97	TYR	0	-0.041	-0.020	7.985	0.135	0.135	0.000	0.000	0.000	0.000
97	A	98	LEU	0	-0.002	0.005	11.667	0.061	0.061	0.000	0.000	0.000	0.000
98	A	99	ILE	0	-0.007	0.003	13.263	-0.072	-0.072	0.000	0.000	0.000	0.000
99	A	100	ILE	0	0.000	0.006	15.512	0.036	0.036	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.027	-0.012	17.996	-0.035	-0.035	0.000	0.000	0.000	0.000
101	A	102	LEU	0	0.005	0.008	20.351	0.018	0.018	0.000	0.000	0.000	0.000
102	A	103	LYS	1	0.959	0.952	23.617	0.021	0.021	0.000	0.000	0.000	0.000
103	A	104	GLU	-1	-0.826	-0.887	27.333	-0.028	-0.028	0.000	0.000	0.000	0.000
104	A	105	VAL	0	-0.001	0.003	23.394	0.004	0.004	0.000	0.000	0.000	0.000
105	A	106	LEU	0	0.047	0.029	26.831	-0.008	-0.008	0.000	0.000	0.000	0.000
106	A	107	VAL	0	-0.003	-0.004	23.661	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	108	SER	0	-0.012	-0.023	25.367	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	109	SER	0	-0.024	-0.030	24.001	0.004	0.004	0.000	0.000	0.000	0.000
109	A	110	VAL	0	0.040	0.008	22.216	-0.010	-0.010	0.000	0.000	0.000	0.000
110	A	111	SER	0	-0.054	-0.024	21.975	0.016	0.016	0.000	0.000	0.000	0.000
111	A	112	THR	0	0.006	-0.026	20.952	-0.013	-0.013	0.000	0.000	0.000	0.000
112	A	113	GLY	0	0.010	0.006	21.455	0.016	0.016	0.000	0.000	0.000	0.000
113	A	114	GLY	0	-0.004	-0.008	20.765	-0.019	-0.019	0.000	0.000	0.000	0.000
114	A	115	SER	0	-0.108	-0.075	19.205	0.016	0.016	0.000	0.000	0.000	0.000
115	A	116	GLY	0	-0.014	-0.014	21.627	0.014	0.014	0.000	0.000	0.000	0.000
116	A	117	GLY	0	-0.034	-0.028	21.049	0.010	0.010	0.000	0.000	0.000	0.000
117	A	118	GLU	-1	-0.821	-0.863	16.961	-0.175	-0.175	0.000	0.000	0.000	0.000
118	A	119	ASP	-1	-0.884	-0.938	15.351	-0.330	-0.330	0.000	0.000	0.000	0.000
119	A	120	ARG	1	0.874	0.939	13.091	0.438	0.438	0.000	0.000	0.000	0.000
120	A	121	LEU	0	0.057	0.029	16.076	-0.013	-0.013	0.000	0.000	0.000	0.000
121	A	122	THR	0	-0.038	-0.016	13.661	-0.023	-0.023	0.000	0.000	0.000	0.000
122	A	123	GLU	-1	-0.756	-0.833	16.558	-0.149	-0.149	0.000	0.000	0.000	0.000
123	A	124	ASN	0	-0.007	0.009	16.314	-0.037	-0.037	0.000	0.000	0.000	0.000
124	A	125	VAL	0	0.014	0.005	18.175	0.012	0.012	0.000	0.000	0.000	0.000
125	A	126	THR	0	-0.021	-0.001	19.096	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	127	LEU	0	-0.035	-0.014	19.766	-0.004	-0.004	0.000	0.000	0.000	0.000
127	A	128	ASN	0	-0.003	-0.006	23.122	0.010	0.010	0.000	0.000	0.000	0.000
128	A	129	PHE	0	0.015	-0.013	22.434	-0.007	-0.007	0.000	0.000	0.000	0.000
129	A	130	ALA	0	0.013	0.023	27.456	0.007	0.007	0.000	0.000	0.000	0.000
130	A	131	GLN	0	-0.033	-0.019	27.994	0.006	0.006	0.000	0.000	0.000	0.000
131	A	132	VAL	0	0.002	0.014	22.055	-0.010	-0.010	0.000	0.000	0.000	0.000
132	A	133	GLN	0	-0.041	-0.041	22.885	0.005	0.005	0.000	0.000	0.000	0.000
133	A	134	VAL	0	-0.017	-0.006	17.893	-0.014	-0.014	0.000	0.000	0.000	0.000
134	A	135	ASP	-1	-0.779	-0.858	18.787	0.039	0.039	0.000	0.000	0.000	0.000
135	A	136	TYR	0	0.042	0.009	13.034	-0.002	-0.002	0.000	0.000	0.000	0.000
136	A	137	GLN	0	-0.041	-0.016	15.837	-0.052	-0.052	0.000	0.000	0.000	0.000
137	A	138	PRO	0	0.017	0.014	15.718	0.058	0.058	0.000	0.000	0.000	0.000
138	A	139	GLN	0	-0.012	-0.023	11.916	0.032	0.032	0.000	0.000	0.000	0.000
139	A	140	LYS	1	0.858	0.913	16.705	-0.154	-0.154	0.000	0.000	0.000	0.000
140	A	141	ALA	0	0.004	-0.008	15.932	0.042	0.042	0.000	0.000	0.000	0.000
141	A	142	ASP	-1	-0.858	-0.923	15.473	0.264	0.264	0.000	0.000	0.000	0.000
142	A	143	GLY	0	0.014	0.022	13.619	-0.005	-0.005	0.000	0.000	0.000	0.000
143	A	144	ALA	0	0.007	0.017	14.252	-0.034	-0.034	0.000	0.000	0.000	0.000
144	A	145	LYS	1	0.893	0.928	17.403	-0.028	-0.028	0.000	0.000	0.000	0.000
145	A	146	ASP	-1	-0.890	-0.923	18.661	0.180	0.180	0.000	0.000	0.000	0.000
146	A	147	GLY	0	0.057	0.030	21.010	0.005	0.005	0.000	0.000	0.000	0.000
147	A	148	GLY	0	-0.001	0.005	22.618	-0.006	-0.006	0.000	0.000	0.000	0.000
148	A	149	PRO	0	-0.036	-0.020	20.273	0.017	0.017	0.000	0.000	0.000	0.000
149	A	150	VAL	0	0.038	0.016	20.232	-0.013	-0.013	0.000	0.000	0.000	0.000
150	A	151	LYS	1	0.777	0.865	20.935	-0.041	-0.041	0.000	0.000	0.000	0.000
151	A	152	TYR	0	0.040	0.021	22.500	0.004	0.004	0.000	0.000	0.000	0.000
152	A	153	GLY	0	0.033	0.019	23.704	-0.008	-0.008	0.000	0.000	0.000	0.000
153	A	154	TRP	0	-0.019	0.002	26.078	0.006	0.006	0.000	0.000	0.000	0.000
154	A	155	ASN	0	0.001	-0.010	28.088	-0.007	-0.007	0.000	0.000	0.000	0.000
155	A	156	ILE	0	0.026	0.004	26.363	0.005	0.005	0.000	0.000	0.000	0.000
156	A	157	ARG	1	0.832	0.895	30.933	0.022	0.022	0.000	0.000	0.000	0.000
157	A	158	GLN	0	-0.022	-0.014	34.018	-0.003	-0.003	0.000	0.000	0.000	0.000
158	A	159	ASN	0	-0.045	-0.014	33.412	0.003	0.003	0.000	0.000	0.000	0.000
159	A	160	VAL	0	0.018	0.017	33.336	0.003	0.003	0.000	0.000	0.000	0.000
160	A	161	GLN	0	0.031	0.014	30.498	0.002	0.002	0.000	0.000	0.000	0.000
161	A	162	ALA	0	-0.050	-0.020	28.194	-0.005	-0.005	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:2:ALA)