FMO DATABASE

FMODB ID: 6N39Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1409160.777724
FMO2-HF: Nuclear repulsion	1347650.027287
FMO2-HF: Total energy	-61510.750436
FMO2-MP2: Total energy	-61687.396287

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.
-4.917	-2.708	0.391	-1.103	-1.496	0.004

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 : -0.021 / 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	4	ASP	-1	-0.795	-0.870	3.788	-4.275	-2.952	-0.005	-0.652	-0.665	0.002
4	A	5	MET	0	-0.070	-0.036	5.513	0.721	0.721	0.000	0.000	0.000	0.000
5	A	6	PHE	0	0.025	0.024	8.715	-0.001	-0.001	0.000	0.000	0.000	0.000
6	A	7	ILE	0	0.011	0.000	12.340	0.075	0.075	0.000	0.000	0.000	0.000
7	A	8	LYS	1	0.899	0.962	15.636	0.185	0.185	0.000	0.000	0.000	0.000
8	A	9	ILE	0	0.019	0.004	19.172	0.027	0.027	0.000	0.000	0.000	0.000
9	A	10	GLY	0	0.028	0.011	21.929	0.002	0.002	0.000	0.000	0.000	0.000
10	A	11	ASP	-1	-0.918	-0.955	24.488	-0.151	-0.151	0.000	0.000	0.000	0.000
11	A	12	VAL	0	-0.057	-0.020	23.057	0.000	0.000	0.000	0.000	0.000	0.000
12	A	13	LYS	1	0.854	0.927	22.213	0.201	0.201	0.000	0.000	0.000	0.000
13	A	14	GLY	0	0.043	0.016	18.732	0.009	0.009	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.905	-0.966	17.966	-0.284	-0.284	0.000	0.000	0.000	0.000
15	A	16	SER	0	-0.052	-0.018	13.009	-0.019	-0.019	0.000	0.000	0.000	0.000
16	A	17	LYS	1	0.943	0.950	14.186	0.518	0.518	0.000	0.000	0.000	0.000
17	A	18	ASP	-1	-0.778	-0.854	11.854	-0.693	-0.693	0.000	0.000	0.000	0.000
18	A	19	LYS	1	0.930	0.968	13.859	0.381	0.381	0.000	0.000	0.000	0.000
19	A	20	THR	0	0.010	-0.011	15.288	0.026	0.026	0.000	0.000	0.000	0.000
20	A	21	HIS	1	0.750	0.849	14.095	0.447	0.447	0.000	0.000	0.000	0.000
21	A	22	ALA	0	0.019	0.016	16.235	-0.021	-0.021	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.880	-0.939	18.063	-0.191	-0.191	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.848	-0.895	16.130	-0.321	-0.321	0.000	0.000	0.000	0.000
24	A	25	ILE	0	-0.031	-0.032	14.979	-0.014	-0.014	0.000	0.000	0.000	0.000
25	A	26	ASP	-1	-0.831	-0.898	10.994	-0.764	-0.764	0.000	0.000	0.000	0.000
26	A	27	VAL	0	-0.058	-0.032	9.964	0.091	0.091	0.000	0.000	0.000	0.000
27	A	28	LEU	0	0.000	-0.012	8.062	-0.202	-0.202	0.000	0.000	0.000	0.000
28	A	29	ALA	0	0.002	0.000	7.681	-0.046	-0.046	0.000	0.000	0.000	0.000
29	A	30	TRP	0	0.002	-0.008	9.640	0.071	0.071	0.000	0.000	0.000	0.000
30	A	31	SER	0	0.011	0.013	12.392	0.034	0.034	0.000	0.000	0.000	0.000
31	A	32	TRP	0	-0.044	-0.038	15.132	-0.012	-0.012	0.000	0.000	0.000	0.000
32	A	33	GLY	0	0.042	0.027	18.179	0.020	0.020	0.000	0.000	0.000	0.000
33	A	34	MET	0	-0.013	-0.004	21.010	-0.008	-0.008	0.000	0.000	0.000	0.000
34	A	35	SER	0	-0.003	0.013	24.554	0.011	0.011	0.000	0.000	0.000	0.000
35	A	36	GLN	0	0.040	0.013	27.377	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	37	SER	0	0.030	0.014	30.568	0.002	0.002	0.000	0.000	0.000	0.000
37	A	38	GLY	0	-0.036	-0.005	33.920	0.000	0.000	0.000	0.000	0.000	0.000
38	A	39	SER	0	-0.009	-0.012	34.785	0.004	0.004	0.000	0.000	0.000	0.000
39	A	40	MET	0	0.014	-0.009	35.152	0.000	0.000	0.000	0.000	0.000	0.000
40	A	41	HIS	0	-0.020	-0.010	35.909	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	42	MET	0	-0.029	0.010	40.421	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	43	GLY	0	0.024	0.017	42.223	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	44	GLY	0	0.008	-0.001	43.938	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	45	GLY	0	0.006	0.019	43.663	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	46	GLY	0	-0.032	-0.032	40.948	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	47	GLY	0	0.105	0.052	40.572	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	48	ALA	0	-0.056	-0.032	38.542	0.002	0.002	0.000	0.000	0.000	0.000
48	A	49	GLY	0	0.009	0.006	36.466	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	50	LYS	1	0.939	0.965	34.504	0.004	0.004	0.000	0.000	0.000	0.000
50	A	51	VAL	0	0.018	0.009	28.040	0.003	0.003	0.000	0.000	0.000	0.000
51	A	52	ASN	0	-0.072	-0.031	28.578	-0.007	-0.007	0.000	0.000	0.000	0.000
52	A	53	VAL	0	0.018	-0.007	24.269	0.005	0.005	0.000	0.000	0.000	0.000
53	A	54	GLN	0	-0.008	0.002	21.720	0.005	0.005	0.000	0.000	0.000	0.000
54	A	55	ASP	-1	-0.715	-0.824	22.958	-0.082	-0.082	0.000	0.000	0.000	0.000
55	A	56	LEU	0	-0.079	-0.024	16.009	0.005	0.005	0.000	0.000	0.000	0.000
56	A	57	SER	0	-0.002	-0.004	17.122	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	58	PHE	0	-0.002	-0.016	13.644	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	59	THR	0	0.017	0.008	12.078	0.032	0.032	0.000	0.000	0.000	0.000
59	A	60	LYS	1	0.776	0.882	12.492	0.219	0.219	0.000	0.000	0.000	0.000
60	A	61	TYR	0	0.077	0.019	11.318	-0.014	-0.014	0.000	0.000	0.000	0.000
61	A	62	ILE	0	-0.041	0.001	15.751	0.014	0.014	0.000	0.000	0.000	0.000
62	A	63	ASP	-1	-0.771	-0.857	18.344	-0.339	-0.339	0.000	0.000	0.000	0.000
63	A	64	LYS	1	0.860	0.923	20.494	0.274	0.274	0.000	0.000	0.000	0.000
64	A	65	SER	0	-0.057	-0.060	20.150	0.023	0.023	0.000	0.000	0.000	0.000
65	A	66	THR	0	-0.025	-0.042	21.378	0.011	0.011	0.000	0.000	0.000	0.000
66	A	67	PRO	0	0.029	0.006	23.337	0.014	0.014	0.000	0.000	0.000	0.000
67	A	68	ASN	0	-0.035	-0.013	25.614	0.023	0.023	0.000	0.000	0.000	0.000
68	A	69	LEU	0	0.022	0.013	20.604	0.012	0.012	0.000	0.000	0.000	0.000
69	A	70	MET	0	0.029	0.016	24.537	0.014	0.014	0.000	0.000	0.000	0.000
70	A	71	MET	0	0.013	0.023	27.570	0.014	0.014	0.000	0.000	0.000	0.000
71	A	72	ALA	0	-0.025	-0.003	27.246	0.009	0.009	0.000	0.000	0.000	0.000
72	A	73	CYS	0	-0.051	-0.022	27.044	0.009	0.009	0.000	0.000	0.000	0.000
73	A	74	SER	0	-0.028	-0.016	29.017	0.009	0.009	0.000	0.000	0.000	0.000
74	A	75	SER	0	-0.122	-0.082	32.464	0.008	0.008	0.000	0.000	0.000	0.000
75	A	76	GLY	0	0.036	0.027	32.018	0.006	0.006	0.000	0.000	0.000	0.000
76	A	77	LYS	1	0.886	0.948	32.353	0.082	0.082	0.000	0.000	0.000	0.000
77	A	78	HIS	0	-0.041	-0.016	29.571	-0.008	-0.008	0.000	0.000	0.000	0.000
78	A	79	TYR	0	0.016	0.003	26.121	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	80	PRO	0	0.038	0.013	28.438	0.004	0.004	0.000	0.000	0.000	0.000
80	A	81	GLN	0	-0.033	-0.033	23.505	0.001	0.001	0.000	0.000	0.000	0.000
81	A	82	ALA	0	0.028	0.028	20.596	-0.010	-0.010	0.000	0.000	0.000	0.000
82	A	83	LYS	1	0.913	0.960	17.864	0.165	0.165	0.000	0.000	0.000	0.000
83	A	84	LEU	0	0.032	0.030	12.137	-0.029	-0.029	0.000	0.000	0.000	0.000
84	A	85	THR	0	-0.012	-0.011	12.765	0.089	0.089	0.000	0.000	0.000	0.000
85	A	86	ILE	0	-0.010	-0.001	8.085	-0.137	-0.137	0.000	0.000	0.000	0.000
86	A	87	ARG	1	0.769	0.856	8.628	1.117	1.117	0.000	0.000	0.000	0.000
87	A	88	LYS	1	0.848	0.917	6.660	-1.225	-1.225	0.000	0.000	0.000	0.000
88	A	89	ALA	0	0.080	0.038	2.868	-1.256	-0.522	0.397	-0.437	-0.694	0.002
89	A	90	GLY	0	0.012	0.006	4.570	0.542	0.694	-0.001	-0.014	-0.137	0.000
90	A	91	GLY	0	0.030	0.024	7.096	0.053	0.053	0.000	0.000	0.000	0.000
91	A	92	GLU	-1	-0.906	-0.974	9.638	-0.307	-0.307	0.000	0.000	0.000	0.000
92	A	93	ASN	0	-0.047	-0.024	12.809	0.060	0.060	0.000	0.000	0.000	0.000
93	A	94	GLN	0	-0.071	-0.017	8.113	0.045	0.045	0.000	0.000	0.000	0.000
94	A	95	VAL	0	-0.010	-0.011	11.548	-0.077	-0.077	0.000	0.000	0.000	0.000
95	A	96	GLU	-1	-0.813	-0.902	11.250	-0.315	-0.315	0.000	0.000	0.000	0.000
96	A	97	TYR	0	-0.021	-0.016	7.644	0.087	0.087	0.000	0.000	0.000	0.000
97	A	98	LEU	0	0.018	0.017	11.762	0.055	0.055	0.000	0.000	0.000	0.000
98	A	99	ILE	0	0.008	0.015	13.387	-0.081	-0.081	0.000	0.000	0.000	0.000
99	A	100	ILE	0	0.009	0.008	15.639	0.044	0.044	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.058	-0.028	18.108	-0.032	-0.032	0.000	0.000	0.000	0.000
101	A	102	LEU	0	0.006	0.013	19.860	0.021	0.021	0.000	0.000	0.000	0.000
102	A	103	LYS	1	0.940	0.949	23.337	0.053	0.053	0.000	0.000	0.000	0.000
103	A	104	GLU	-1	-0.831	-0.903	26.949	-0.055	-0.055	0.000	0.000	0.000	0.000
104	A	105	VAL	0	-0.018	-0.017	23.284	0.003	0.003	0.000	0.000	0.000	0.000
105	A	106	LEU	0	0.058	0.037	26.693	-0.004	-0.004	0.000	0.000	0.000	0.000
106	A	107	VAL	0	0.001	-0.005	23.704	-0.006	-0.006	0.000	0.000	0.000	0.000
107	A	108	SER	0	0.001	-0.022	25.021	0.002	0.002	0.000	0.000	0.000	0.000
108	A	109	SER	0	-0.025	-0.027	23.553	0.007	0.007	0.000	0.000	0.000	0.000
109	A	110	VAL	0	0.034	0.001	22.324	-0.014	-0.014	0.000	0.000	0.000	0.000
110	A	111	SER	0	-0.041	-0.006	21.708	0.018	0.018	0.000	0.000	0.000	0.000
111	A	112	THR	0	0.013	-0.020	21.064	-0.019	-0.019	0.000	0.000	0.000	0.000
112	A	113	GLY	0	0.000	0.001	22.155	0.018	0.018	0.000	0.000	0.000	0.000
113	A	114	GLY	0	0.009	0.001	21.555	-0.020	-0.020	0.000	0.000	0.000	0.000
114	A	115	SER	0	-0.114	-0.072	19.483	0.021	0.021	0.000	0.000	0.000	0.000
115	A	116	GLY	0	0.007	0.006	22.305	0.016	0.016	0.000	0.000	0.000	0.000
116	A	117	GLY	0	-0.031	-0.027	21.640	-0.003	-0.003	0.000	0.000	0.000	0.000
117	A	118	GLU	-1	-0.834	-0.881	17.885	-0.239	-0.239	0.000	0.000	0.000	0.000
118	A	119	ASP	-1	-0.907	-0.959	16.075	-0.368	-0.368	0.000	0.000	0.000	0.000
119	A	120	ARG	1	0.881	0.943	13.111	0.517	0.517	0.000	0.000	0.000	0.000
120	A	121	LEU	0	0.054	0.037	16.711	-0.008	-0.008	0.000	0.000	0.000	0.000
121	A	122	THR	0	-0.038	-0.019	13.678	-0.030	-0.030	0.000	0.000	0.000	0.000
122	A	123	GLU	-1	-0.765	-0.846	16.744	-0.196	-0.196	0.000	0.000	0.000	0.000
123	A	124	ASN	0	-0.005	0.006	16.218	-0.055	-0.055	0.000	0.000	0.000	0.000
124	A	125	VAL	0	0.019	0.009	17.918	0.023	0.023	0.000	0.000	0.000	0.000
125	A	126	THR	0	-0.022	-0.005	18.889	-0.007	-0.007	0.000	0.000	0.000	0.000
126	A	127	LEU	0	-0.039	-0.015	19.578	0.002	0.002	0.000	0.000	0.000	0.000
127	A	128	ASN	0	-0.008	-0.012	22.769	0.011	0.011	0.000	0.000	0.000	0.000
128	A	129	PHE	0	0.010	-0.006	22.043	-0.006	-0.006	0.000	0.000	0.000	0.000
129	A	130	ALA	0	0.011	0.023	26.853	0.008	0.008	0.000	0.000	0.000	0.000
130	A	131	GLN	0	-0.032	-0.026	27.661	0.010	0.010	0.000	0.000	0.000	0.000
131	A	132	VAL	0	0.007	0.015	21.898	-0.012	-0.012	0.000	0.000	0.000	0.000
132	A	133	GLN	0	-0.039	-0.032	22.540	0.012	0.012	0.000	0.000	0.000	0.000
133	A	134	VAL	0	-0.004	-0.007	17.627	-0.019	-0.019	0.000	0.000	0.000	0.000
134	A	135	ASP	-1	-0.789	-0.861	18.685	0.009	0.009	0.000	0.000	0.000	0.000
135	A	136	TYR	0	0.047	0.012	12.857	-0.007	-0.007	0.000	0.000	0.000	0.000
136	A	137	GLN	0	-0.035	-0.025	15.459	-0.036	-0.036	0.000	0.000	0.000	0.000
137	A	138	PRO	0	0.016	0.015	15.110	0.053	0.053	0.000	0.000	0.000	0.000
138	A	139	GLN	0	-0.018	-0.015	11.788	0.024	0.024	0.000	0.000	0.000	0.000
139	A	140	LYS	1	0.869	0.907	16.222	-0.192	-0.192	0.000	0.000	0.000	0.000
140	A	141	ALA	0	-0.014	-0.014	16.034	0.052	0.052	0.000	0.000	0.000	0.000
141	A	142	ASP	-1	-0.861	-0.927	15.368	0.375	0.375	0.000	0.000	0.000	0.000
142	A	143	GLY	0	0.003	0.017	13.679	0.025	0.025	0.000	0.000	0.000	0.000
143	A	144	ALA	0	0.024	0.027	14.334	-0.057	-0.057	0.000	0.000	0.000	0.000
144	A	145	LYS	1	0.904	0.947	17.479	-0.025	-0.025	0.000	0.000	0.000	0.000
145	A	146	ASP	-1	-0.884	-0.928	18.800	0.206	0.206	0.000	0.000	0.000	0.000
146	A	147	GLY	0	0.034	0.024	20.639	-0.005	-0.005	0.000	0.000	0.000	0.000
147	A	148	GLY	0	-0.006	-0.003	21.957	-0.003	-0.003	0.000	0.000	0.000	0.000
148	A	149	PRO	0	-0.009	-0.011	19.907	0.016	0.016	0.000	0.000	0.000	0.000
149	A	150	VAL	0	0.016	0.003	20.052	-0.009	-0.009	0.000	0.000	0.000	0.000
150	A	151	LYS	1	0.777	0.869	20.600	-0.009	-0.009	0.000	0.000	0.000	0.000
151	A	152	TYR	0	0.037	0.021	22.251	0.004	0.004	0.000	0.000	0.000	0.000
152	A	153	GLY	0	0.055	0.030	23.679	-0.012	-0.012	0.000	0.000	0.000	0.000
153	A	154	TRP	0	-0.027	-0.005	26.374	0.010	0.010	0.000	0.000	0.000	0.000
154	A	155	ASN	0	0.012	0.002	28.228	-0.010	-0.010	0.000	0.000	0.000	0.000
155	A	156	ILE	0	0.031	0.006	26.257	0.006	0.006	0.000	0.000	0.000	0.000
156	A	157	ARG	1	0.833	0.904	30.865	0.051	0.051	0.000	0.000	0.000	0.000
157	A	158	GLN	0	-0.030	-0.031	33.746	-0.002	-0.002	0.000	0.000	0.000	0.000
158	A	159	ASN	0	-0.037	-0.003	33.578	0.003	0.003	0.000	0.000	0.000	0.000
159	A	160	VAL	0	0.011	0.014	33.639	0.005	0.005	0.000	0.000	0.000	0.000
160	A	161	GLN	0	0.023	0.012	30.613	-0.002	-0.002	0.000	0.000	0.000	0.000
161	A	162	ALA	0	-0.053	-0.022	28.626	-0.002	-0.002	0.000	0.000	0.000	0.000

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