FMO DATABASE

FMODB ID: K3523

Calculation Name: 1YQ5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YQ5

Chain ID: A

ChEMBL ID:

UniProt ID: P22536

Base Structure: X-ray

Registration Date: 2023-06-20

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	144
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1135604.071063
FMO2-HF: Nuclear repulsion	1084402.172642
FMO2-HF: Total energy	-51201.898421
FMO2-MP2: Total energy	-51349.990133

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:197:GLY)

Summations of interaction energy for fragment #1(A:197:GLY)

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.
0.383	2.04	-0.013	-1.027	-0.617	0.004

Interaction energy analysis for fragmet #1(A:197:GLY)

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 : 0.024

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	199	VAL	0	-0.024	-0.007	3.858	-0.225	1.432	-0.013	-1.027	-0.617	0.004
4	A	200	THR	0	-0.002	-0.022	6.568	-0.027	-0.027	0.000	0.000	0.000	0.000
5	A	201	ASP	-1	-0.765	-0.856	8.663	-0.677	-0.677	0.000	0.000	0.000	0.000
6	A	202	ALA	0	-0.010	-0.011	11.669	-0.019	-0.019	0.000	0.000	0.000	0.000
7	A	203	LEU	0	-0.018	0.009	13.475	0.027	0.027	0.000	0.000	0.000	0.000
8	A	204	SER	0	-0.035	-0.025	16.963	0.031	0.031	0.000	0.000	0.000	0.000
9	A	205	LEU	0	-0.003	-0.008	18.825	0.007	0.007	0.000	0.000	0.000	0.000
10	A	206	MET	0	0.034	0.032	22.639	0.017	0.017	0.000	0.000	0.000	0.000
11	A	207	TYR	0	-0.043	-0.025	25.546	0.007	0.007	0.000	0.000	0.000	0.000
12	A	208	SER	0	0.071	0.003	28.708	0.012	0.012	0.000	0.000	0.000	0.000
13	A	209	THR	0	-0.027	-0.003	32.206	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	210	SER	0	-0.001	0.005	34.011	0.007	0.007	0.000	0.000	0.000	0.000
15	A	211	THR	0	-0.084	-0.044	29.170	0.001	0.001	0.000	0.000	0.000	0.000
16	A	212	GLY	0	0.058	0.015	30.641	-0.011	-0.011	0.000	0.000	0.000	0.000
17	A	213	GLY	0	0.018	0.031	32.694	0.002	0.002	0.000	0.000	0.000	0.000
18	A	214	PRO	0	-0.016	-0.002	33.885	0.006	0.006	0.000	0.000	0.000	0.000
19	A	215	ALA	0	0.042	0.007	37.527	0.000	0.000	0.000	0.000	0.000	0.000
20	A	216	SER	0	-0.012	-0.024	39.787	0.003	0.003	0.000	0.000	0.000	0.000
21	A	217	ILE	0	-0.046	0.005	34.161	0.000	0.000	0.000	0.000	0.000	0.000
22	A	218	ALA	0	0.023	0.000	38.666	0.004	0.004	0.000	0.000	0.000	0.000
23	A	219	ALA	0	0.030	0.015	39.941	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	220	ASN	0	-0.056	-0.037	40.302	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	221	ALA	0	0.027	0.024	39.718	0.002	0.002	0.000	0.000	0.000	0.000
26	A	222	LEU	0	0.020	0.019	33.684	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	223	THR	0	0.030	0.021	35.868	0.002	0.002	0.000	0.000	0.000	0.000
28	A	224	ASP	-1	-0.823	-0.879	31.246	-0.139	-0.139	0.000	0.000	0.000	0.000
29	A	225	PHE	0	-0.006	-0.014	29.129	0.005	0.005	0.000	0.000	0.000	0.000
30	A	226	ASP	-1	-0.793	-0.846	30.092	-0.188	-0.188	0.000	0.000	0.000	0.000
31	A	227	LEU	0	-0.007	-0.009	25.235	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	228	SER	0	-0.072	-0.059	27.479	-0.019	-0.019	0.000	0.000	0.000	0.000
33	A	229	GLY	0	0.033	0.001	28.824	-0.010	-0.010	0.000	0.000	0.000	0.000
34	A	230	ALA	0	-0.016	0.008	26.177	0.004	0.004	0.000	0.000	0.000	0.000
35	A	231	LEU	0	0.009	0.010	25.129	-0.015	-0.015	0.000	0.000	0.000	0.000
36	A	232	THR	0	0.002	-0.010	20.357	0.005	0.005	0.000	0.000	0.000	0.000
37	A	233	VAL	0	-0.002	0.015	19.431	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	234	ASN	0	0.011	-0.004	13.053	-0.019	-0.019	0.000	0.000	0.000	0.000
39	A	235	SER	0	0.018	-0.003	16.184	0.065	0.065	0.000	0.000	0.000	0.000
40	A	236	VAL	0	-0.018	0.003	9.847	-0.032	-0.032	0.000	0.000	0.000	0.000
41	A	237	GLY	0	0.042	0.038	12.916	0.025	0.025	0.000	0.000	0.000	0.000
42	A	238	THR	0	-0.032	-0.031	13.529	0.075	0.075	0.000	0.000	0.000	0.000
43	A	239	GLY	0	-0.053	-0.032	15.302	0.073	0.073	0.000	0.000	0.000	0.000
44	A	240	LEU	0	0.002	0.012	14.520	0.046	0.046	0.000	0.000	0.000	0.000
45	A	241	THR	0	0.000	0.002	17.927	-0.008	-0.008	0.000	0.000	0.000	0.000
46	A	242	LYS	1	0.849	0.933	21.262	0.314	0.314	0.000	0.000	0.000	0.000
47	A	243	SER	0	-0.009	-0.033	24.228	0.008	0.008	0.000	0.000	0.000	0.000
48	A	244	ALA	0	0.051	0.018	27.630	0.001	0.001	0.000	0.000	0.000	0.000
49	A	245	ALA	0	-0.043	-0.013	29.255	0.013	0.013	0.000	0.000	0.000	0.000
50	A	246	GLY	0	0.020	0.007	26.499	0.008	0.008	0.000	0.000	0.000	0.000
51	A	247	ILE	0	-0.043	-0.021	19.788	-0.013	-0.013	0.000	0.000	0.000	0.000
52	A	248	GLN	0	0.007	0.017	22.514	0.020	0.020	0.000	0.000	0.000	0.000
53	A	249	LEU	0	0.009	-0.003	18.308	-0.040	-0.040	0.000	0.000	0.000	0.000
54	A	250	ALA	0	-0.027	-0.004	18.781	0.033	0.033	0.000	0.000	0.000	0.000
55	A	251	ALA	0	0.057	0.003	19.700	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	252	GLY	0	0.036	0.021	19.410	-0.022	-0.022	0.000	0.000	0.000	0.000
57	A	253	LYS	1	0.821	0.910	13.534	0.686	0.686	0.000	0.000	0.000	0.000
58	A	254	SER	0	0.075	0.044	16.413	-0.029	-0.029	0.000	0.000	0.000	0.000
59	A	255	GLY	0	0.011	0.009	14.269	-0.037	-0.037	0.000	0.000	0.000	0.000
60	A	256	LEU	0	-0.008	-0.001	12.885	0.011	0.011	0.000	0.000	0.000	0.000
61	A	257	TYR	0	-0.003	-0.019	12.875	-0.146	-0.146	0.000	0.000	0.000	0.000
62	A	258	GLN	0	0.020	0.026	13.335	0.102	0.102	0.000	0.000	0.000	0.000
63	A	259	ILE	0	-0.015	-0.025	15.031	-0.066	-0.066	0.000	0.000	0.000	0.000
64	A	260	THR	0	-0.009	-0.018	18.231	0.029	0.029	0.000	0.000	0.000	0.000
65	A	261	MET	0	-0.052	-0.002	20.178	-0.025	-0.025	0.000	0.000	0.000	0.000
66	A	262	THR	0	-0.035	-0.008	22.791	0.021	0.021	0.000	0.000	0.000	0.000
67	A	263	VAL	0	0.031	0.011	25.609	-0.007	-0.007	0.000	0.000	0.000	0.000
68	A	264	LYS	1	0.871	0.947	29.072	0.116	0.116	0.000	0.000	0.000	0.000
69	A	265	ASN	0	0.076	0.023	31.503	-0.009	-0.009	0.000	0.000	0.000	0.000
70	A	266	ASN	0	0.039	0.005	33.994	0.006	0.006	0.000	0.000	0.000	0.000
71	A	267	THR	0	0.011	0.027	36.788	0.003	0.003	0.000	0.000	0.000	0.000
72	A	268	VAL	0	0.003	0.019	38.598	0.004	0.004	0.000	0.000	0.000	0.000
73	A	269	THR	0	-0.015	-0.001	38.216	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	270	THR	0	0.043	0.022	40.149	0.004	0.004	0.000	0.000	0.000	0.000
75	A	271	GLY	0	0.031	0.030	40.724	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	272	ASN	0	-0.065	-0.061	36.858	0.001	0.001	0.000	0.000	0.000	0.000
77	A	273	TYR	0	0.020	-0.008	33.223	-0.005	-0.005	0.000	0.000	0.000	0.000
78	A	274	LEU	0	-0.014	-0.004	33.950	0.003	0.003	0.000	0.000	0.000	0.000
79	A	275	LEU	0	-0.014	-0.019	27.862	-0.009	-0.009	0.000	0.000	0.000	0.000
80	A	276	ARG	1	0.845	0.900	29.369	0.123	0.123	0.000	0.000	0.000	0.000
81	A	277	VAL	0	-0.012	-0.003	23.016	-0.012	-0.012	0.000	0.000	0.000	0.000
82	A	278	LYS	1	0.851	0.907	26.287	0.142	0.142	0.000	0.000	0.000	0.000
83	A	279	TYR	0	0.013	-0.014	22.515	-0.030	-0.030	0.000	0.000	0.000	0.000
84	A	280	GLY	0	0.028	0.023	25.532	0.013	0.013	0.000	0.000	0.000	0.000
85	A	281	SER	0	-0.040	-0.020	28.060	0.001	0.001	0.000	0.000	0.000	0.000
86	A	282	SER	0	-0.014	0.003	26.644	0.012	0.012	0.000	0.000	0.000	0.000
87	A	283	ASP	-1	-0.923	-0.975	27.993	-0.110	-0.110	0.000	0.000	0.000	0.000
88	A	284	PHE	0	0.027	0.015	24.588	0.008	0.008	0.000	0.000	0.000	0.000
89	A	285	VAL	0	0.018	0.001	27.967	-0.011	-0.011	0.000	0.000	0.000	0.000
90	A	286	VAL	0	-0.021	-0.008	28.111	0.006	0.006	0.000	0.000	0.000	0.000
91	A	287	ALA	0	0.016	0.010	30.946	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	288	CYS	0	-0.048	-0.011	30.609	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	289	PRO	0	0.050	0.030	33.346	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	290	ALA	0	-0.001	0.018	35.742	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	291	SER	0	0.014	-0.010	36.630	0.006	0.006	0.000	0.000	0.000	0.000
96	A	292	SER	0	0.002	-0.026	37.733	-0.004	-0.004	0.000	0.000	0.000	0.000
97	A	293	LEU	0	-0.027	-0.002	35.055	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	294	THR	0	-0.030	-0.001	32.416	-0.004	-0.004	0.000	0.000	0.000	0.000
99	A	295	ALA	0	0.030	0.036	34.096	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	296	GLY	0	-0.006	-0.037	31.819	-0.008	-0.008	0.000	0.000	0.000	0.000
101	A	297	GLY	0	0.034	0.018	30.091	0.010	0.010	0.000	0.000	0.000	0.000
102	A	298	THR	0	-0.063	-0.053	23.780	-0.017	-0.017	0.000	0.000	0.000	0.000
103	A	299	ILE	0	0.034	0.037	24.716	0.014	0.014	0.000	0.000	0.000	0.000
104	A	300	SER	0	-0.016	-0.021	19.788	-0.034	-0.034	0.000	0.000	0.000	0.000
105	A	301	LEU	0	-0.016	0.007	19.908	0.029	0.029	0.000	0.000	0.000	0.000
106	A	302	LEU	0	0.025	0.022	14.510	-0.041	-0.041	0.000	0.000	0.000	0.000
107	A	303	ILE	0	-0.001	0.007	17.616	0.038	0.038	0.000	0.000	0.000	0.000
108	A	304	TYR	0	-0.004	-0.008	17.272	-0.041	-0.041	0.000	0.000	0.000	0.000
109	A	305	CYS	0	-0.028	0.002	18.115	0.005	0.005	0.000	0.000	0.000	0.000
110	A	306	ASN	0	0.001	-0.004	18.977	-0.009	-0.009	0.000	0.000	0.000	0.000
111	A	307	VAL	0	-0.032	-0.018	19.355	0.010	0.010	0.000	0.000	0.000	0.000
112	A	308	LEU	0	-0.022	-0.023	22.041	0.014	0.014	0.000	0.000	0.000	0.000
113	A	309	GLY	0	-0.021	-0.005	24.690	0.008	0.008	0.000	0.000	0.000	0.000
114	A	310	VAL	0	-0.036	-0.019	25.606	0.007	0.007	0.000	0.000	0.000	0.000
115	A	311	VAL	0	0.073	0.031	25.505	0.000	0.000	0.000	0.000	0.000	0.000
116	A	312	SER	0	-0.010	-0.004	27.318	-0.009	-0.009	0.000	0.000	0.000	0.000
117	A	313	LEU	0	-0.048	-0.020	28.433	0.008	0.008	0.000	0.000	0.000	0.000
118	A	314	ASP	-1	-0.743	-0.845	23.172	-0.198	-0.198	0.000	0.000	0.000	0.000
119	A	315	VAL	0	-0.030	-0.024	23.934	-0.024	-0.024	0.000	0.000	0.000	0.000
120	A	316	LEU	0	-0.001	0.012	19.204	0.018	0.018	0.000	0.000	0.000	0.000
121	A	317	LYS	1	0.939	0.983	23.727	0.149	0.149	0.000	0.000	0.000	0.000
122	A	318	PHE	0	0.044	0.000	21.534	0.001	0.001	0.000	0.000	0.000	0.000
123	A	319	SER	0	-0.012	-0.022	27.726	0.008	0.008	0.000	0.000	0.000	0.000
124	A	320	LEU	0	0.016	-0.007	28.931	0.000	0.000	0.000	0.000	0.000	0.000
125	A	321	CYS	0	-0.024	-0.009	32.482	0.001	0.001	0.000	0.000	0.000	0.000
126	A	322	ASN	0	0.000	-0.003	35.307	0.002	0.002	0.000	0.000	0.000	0.000
127	A	323	ASP	-1	-0.775	-0.877	38.055	-0.061	-0.061	0.000	0.000	0.000	0.000
128	A	324	GLY	0	0.023	0.019	40.820	0.004	0.004	0.000	0.000	0.000	0.000
129	A	325	ALA	0	-0.047	-0.024	41.619	0.002	0.002	0.000	0.000	0.000	0.000
130	A	326	ALA	0	-0.001	0.004	40.771	-0.003	-0.003	0.000	0.000	0.000	0.000
131	A	327	LEU	0	-0.044	-0.016	35.059	0.000	0.000	0.000	0.000	0.000	0.000
132	A	328	SER	0	0.038	0.011	38.309	-0.004	-0.004	0.000	0.000	0.000	0.000
133	A	329	ASN	0	-0.069	-0.039	37.692	-0.005	-0.005	0.000	0.000	0.000	0.000
134	A	330	TYR	0	-0.024	-0.025	32.090	-0.002	-0.002	0.000	0.000	0.000	0.000
135	A	331	ILE	0	-0.012	-0.005	28.046	-0.006	-0.006	0.000	0.000	0.000	0.000
136	A	332	ILE	0	0.005	0.004	26.990	0.004	0.004	0.000	0.000	0.000	0.000
137	A	333	ASN	0	-0.024	-0.008	22.693	-0.024	-0.024	0.000	0.000	0.000	0.000
138	A	334	ILE	0	0.041	0.020	21.977	0.012	0.012	0.000	0.000	0.000	0.000
139	A	335	THR	0	-0.039	-0.022	16.003	-0.039	-0.039	0.000	0.000	0.000	0.000
140	A	336	ALA	0	0.027	0.024	16.675	0.048	0.048	0.000	0.000	0.000	0.000
141	A	337	ALA	0	0.034	0.006	11.142	-0.081	-0.081	0.000	0.000	0.000	0.000
142	A	338	LYS	1	0.861	0.936	10.920	0.679	0.679	0.000	0.000	0.000	0.000
143	A	339	ILE	0	-0.016	-0.018	8.356	-0.229	-0.229	0.000	0.000	0.000	0.000
144	A	340	ASN	0	-0.051	-0.012	8.202	0.038	0.038	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:197:GLY)