FMO DATABASE

FMODB ID: Q16NY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1136907.509326
FMO2-HF: Nuclear repulsion	1085705.693774
FMO2-HF: Total energy	-51201.815552
FMO2-MP2: Total energy	-51349.913438

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.
-0.655	1.17	-0.013	-1.186	-0.627	0.006

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 : 0.041 / 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	199	VAL	0	-0.018	-0.010	3.788	-1.378	0.447	-0.013	-1.186	-0.627	0.006
4	A	200	THR	0	0.000	-0.028	6.702	-0.050	-0.050	0.000	0.000	0.000	0.000
5	A	201	ASP	-1	-0.808	-0.877	8.492	-0.807	-0.807	0.000	0.000	0.000	0.000
6	A	202	ALA	0	-0.002	-0.010	11.676	-0.019	-0.019	0.000	0.000	0.000	0.000
7	A	203	LEU	0	-0.014	0.013	13.583	0.030	0.030	0.000	0.000	0.000	0.000
8	A	204	SER	0	-0.034	-0.021	16.808	0.041	0.041	0.000	0.000	0.000	0.000
9	A	205	LEU	0	0.002	-0.006	18.579	0.010	0.010	0.000	0.000	0.000	0.000
10	A	206	MET	0	0.021	0.022	22.360	0.016	0.016	0.000	0.000	0.000	0.000
11	A	207	TYR	0	-0.026	-0.027	25.316	0.009	0.009	0.000	0.000	0.000	0.000
12	A	208	SER	0	0.069	0.006	28.420	0.013	0.013	0.000	0.000	0.000	0.000
13	A	209	THR	0	-0.013	-0.001	31.875	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	210	SER	0	-0.006	0.000	33.616	0.005	0.005	0.000	0.000	0.000	0.000
15	A	211	THR	0	-0.087	-0.048	28.917	0.002	0.002	0.000	0.000	0.000	0.000
16	A	212	GLY	0	0.071	0.020	30.357	-0.014	-0.014	0.000	0.000	0.000	0.000
17	A	213	GLY	0	0.014	0.030	32.478	0.000	0.000	0.000	0.000	0.000	0.000
18	A	214	PRO	0	-0.018	-0.002	33.682	0.007	0.007	0.000	0.000	0.000	0.000
19	A	215	ALA	0	0.040	0.017	37.194	0.000	0.000	0.000	0.000	0.000	0.000
20	A	216	SER	0	-0.017	-0.031	39.705	0.003	0.003	0.000	0.000	0.000	0.000
21	A	217	ILE	0	-0.044	0.003	33.813	0.000	0.000	0.000	0.000	0.000	0.000
22	A	218	ALA	0	0.019	0.000	38.241	0.005	0.005	0.000	0.000	0.000	0.000
23	A	219	ALA	0	0.012	0.010	39.547	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	220	ASN	0	-0.066	-0.035	40.206	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	221	ALA	0	0.043	0.017	39.158	0.003	0.003	0.000	0.000	0.000	0.000
26	A	222	LEU	0	-0.001	0.000	33.447	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	223	THR	0	0.025	0.021	36.105	0.002	0.002	0.000	0.000	0.000	0.000
28	A	224	ASP	-1	-0.833	-0.900	31.433	-0.159	-0.159	0.000	0.000	0.000	0.000
29	A	225	PHE	0	0.003	-0.013	28.973	0.005	0.005	0.000	0.000	0.000	0.000
30	A	226	ASP	-1	-0.763	-0.823	30.334	-0.204	-0.204	0.000	0.000	0.000	0.000
31	A	227	LEU	0	-0.025	-0.028	25.187	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	228	SER	0	-0.080	-0.061	27.512	-0.019	-0.019	0.000	0.000	0.000	0.000
33	A	229	GLY	0	0.034	0.006	29.029	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	230	ALA	0	-0.013	0.012	26.108	0.005	0.005	0.000	0.000	0.000	0.000
35	A	231	LEU	0	0.001	0.013	24.915	-0.013	-0.013	0.000	0.000	0.000	0.000
36	A	232	THR	0	-0.001	-0.014	20.152	0.004	0.004	0.000	0.000	0.000	0.000
37	A	233	VAL	0	-0.020	-0.001	19.356	0.006	0.006	0.000	0.000	0.000	0.000
38	A	234	ASN	0	0.015	-0.006	12.925	-0.013	-0.013	0.000	0.000	0.000	0.000
39	A	235	SER	0	0.011	0.003	16.122	0.055	0.055	0.000	0.000	0.000	0.000
40	A	236	VAL	0	-0.029	-0.002	9.566	-0.028	-0.028	0.000	0.000	0.000	0.000
41	A	237	GLY	0	0.052	0.039	12.952	0.005	0.005	0.000	0.000	0.000	0.000
42	A	238	THR	0	-0.020	-0.028	13.521	0.078	0.078	0.000	0.000	0.000	0.000
43	A	239	GLY	0	-0.016	-0.008	15.166	0.085	0.085	0.000	0.000	0.000	0.000
44	A	240	LEU	0	-0.015	0.008	14.848	0.064	0.064	0.000	0.000	0.000	0.000
45	A	241	THR	0	0.001	0.000	18.030	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	242	LYS	1	0.862	0.938	21.267	0.335	0.335	0.000	0.000	0.000	0.000
47	A	243	SER	0	-0.023	-0.039	24.265	0.009	0.009	0.000	0.000	0.000	0.000
48	A	244	ALA	0	0.042	0.013	27.606	0.001	0.001	0.000	0.000	0.000	0.000
49	A	245	ALA	0	-0.049	-0.011	28.939	0.012	0.012	0.000	0.000	0.000	0.000
50	A	246	GLY	0	0.038	0.015	26.890	0.010	0.010	0.000	0.000	0.000	0.000
51	A	247	ILE	0	-0.051	-0.022	20.085	-0.015	-0.015	0.000	0.000	0.000	0.000
52	A	248	GLN	0	0.013	0.026	22.951	0.026	0.026	0.000	0.000	0.000	0.000
53	A	249	LEU	0	0.009	0.001	18.548	-0.047	-0.047	0.000	0.000	0.000	0.000
54	A	250	ALA	0	-0.032	-0.008	18.488	0.037	0.037	0.000	0.000	0.000	0.000
55	A	251	ALA	0	0.072	0.011	19.619	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	252	GLY	0	0.014	0.008	18.922	-0.028	-0.028	0.000	0.000	0.000	0.000
57	A	253	LYS	1	0.820	0.900	13.124	0.825	0.825	0.000	0.000	0.000	0.000
58	A	254	SER	0	0.095	0.063	16.565	-0.028	-0.028	0.000	0.000	0.000	0.000
59	A	255	GLY	0	0.004	-0.001	14.599	-0.050	-0.050	0.000	0.000	0.000	0.000
60	A	256	LEU	0	-0.030	-0.003	13.186	0.031	0.031	0.000	0.000	0.000	0.000
61	A	257	TYR	0	-0.007	-0.040	13.412	-0.162	-0.162	0.000	0.000	0.000	0.000
62	A	258	GLN	0	0.009	0.018	13.255	0.109	0.109	0.000	0.000	0.000	0.000
63	A	259	ILE	0	-0.016	-0.029	15.189	-0.064	-0.064	0.000	0.000	0.000	0.000
64	A	260	THR	0	0.001	-0.006	18.242	0.033	0.033	0.000	0.000	0.000	0.000
65	A	261	MET	0	-0.037	0.011	20.156	-0.027	-0.027	0.000	0.000	0.000	0.000
66	A	262	THR	0	-0.044	-0.021	22.807	0.023	0.023	0.000	0.000	0.000	0.000
67	A	263	VAL	0	0.038	0.016	25.528	-0.008	-0.008	0.000	0.000	0.000	0.000
68	A	264	LYS	1	0.869	0.950	28.903	0.118	0.118	0.000	0.000	0.000	0.000
69	A	265	ASN	0	0.094	0.025	31.328	-0.010	-0.010	0.000	0.000	0.000	0.000
70	A	266	ASN	0	0.047	0.004	34.094	0.004	0.004	0.000	0.000	0.000	0.000
71	A	267	THR	0	0.018	0.031	36.698	0.003	0.003	0.000	0.000	0.000	0.000
72	A	268	VAL	0	0.001	0.021	38.463	0.004	0.004	0.000	0.000	0.000	0.000
73	A	269	THR	0	-0.032	-0.007	38.109	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	270	THR	0	0.050	0.029	39.876	0.004	0.004	0.000	0.000	0.000	0.000
75	A	271	GLY	0	0.029	0.030	40.252	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	272	ASN	0	-0.064	-0.063	36.772	0.002	0.002	0.000	0.000	0.000	0.000
77	A	273	TYR	0	0.006	-0.007	32.854	-0.005	-0.005	0.000	0.000	0.000	0.000
78	A	274	LEU	0	-0.013	-0.004	33.590	0.002	0.002	0.000	0.000	0.000	0.000
79	A	275	LEU	0	-0.024	-0.019	27.507	-0.009	-0.009	0.000	0.000	0.000	0.000
80	A	276	ARG	1	0.888	0.918	29.282	0.138	0.138	0.000	0.000	0.000	0.000
81	A	277	VAL	0	-0.012	-0.003	23.233	-0.012	-0.012	0.000	0.000	0.000	0.000
82	A	278	LYS	1	0.838	0.905	26.703	0.162	0.162	0.000	0.000	0.000	0.000
83	A	279	TYR	0	0.023	-0.010	22.713	-0.032	-0.032	0.000	0.000	0.000	0.000
84	A	280	GLY	0	0.026	0.027	25.957	0.011	0.011	0.000	0.000	0.000	0.000
85	A	281	SER	0	-0.042	-0.032	28.206	0.001	0.001	0.000	0.000	0.000	0.000
86	A	282	SER	0	-0.020	0.005	26.746	0.013	0.013	0.000	0.000	0.000	0.000
87	A	283	ASP	-1	-0.936	-0.978	28.547	-0.127	-0.127	0.000	0.000	0.000	0.000
88	A	284	PHE	0	0.012	0.005	24.842	0.008	0.008	0.000	0.000	0.000	0.000
89	A	285	VAL	0	0.023	-0.003	28.039	-0.010	-0.010	0.000	0.000	0.000	0.000
90	A	286	VAL	0	-0.005	-0.005	27.826	0.006	0.006	0.000	0.000	0.000	0.000
91	A	287	ALA	0	0.012	0.015	30.598	-0.005	-0.005	0.000	0.000	0.000	0.000
92	A	288	CYS	0	-0.048	-0.015	30.394	0.002	0.002	0.000	0.000	0.000	0.000
93	A	289	PRO	0	0.048	0.023	33.159	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	290	ALA	0	-0.019	0.009	35.465	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	291	SER	0	0.014	-0.010	36.420	0.007	0.007	0.000	0.000	0.000	0.000
96	A	292	SER	0	0.015	-0.016	37.349	-0.004	-0.004	0.000	0.000	0.000	0.000
97	A	293	LEU	0	-0.032	-0.012	35.419	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	294	THR	0	-0.011	0.012	32.160	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	295	ALA	0	0.019	0.030	33.898	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	296	GLY	0	0.006	-0.030	31.641	-0.008	-0.008	0.000	0.000	0.000	0.000
101	A	297	GLY	0	0.033	0.018	29.866	0.010	0.010	0.000	0.000	0.000	0.000
102	A	298	THR	0	-0.073	-0.056	23.606	-0.016	-0.016	0.000	0.000	0.000	0.000
103	A	299	ILE	0	0.029	0.035	24.572	0.014	0.014	0.000	0.000	0.000	0.000
104	A	300	SER	0	0.005	-0.003	19.454	-0.036	-0.036	0.000	0.000	0.000	0.000
105	A	301	LEU	0	-0.030	-0.011	19.744	0.030	0.030	0.000	0.000	0.000	0.000
106	A	302	LEU	0	0.040	0.042	14.506	-0.048	-0.048	0.000	0.000	0.000	0.000
107	A	303	ILE	0	-0.008	-0.003	17.728	0.040	0.040	0.000	0.000	0.000	0.000
108	A	304	TYR	0	0.024	0.007	17.542	-0.054	-0.054	0.000	0.000	0.000	0.000
109	A	305	CYS	0	-0.036	-0.007	18.513	0.023	0.023	0.000	0.000	0.000	0.000
110	A	306	ASN	0	0.023	0.002	19.440	-0.024	-0.024	0.000	0.000	0.000	0.000
111	A	307	VAL	0	-0.051	-0.021	19.410	0.004	0.004	0.000	0.000	0.000	0.000
112	A	308	LEU	0	-0.041	-0.038	22.244	0.010	0.010	0.000	0.000	0.000	0.000
113	A	309	GLY	0	-0.021	-0.010	24.581	0.007	0.007	0.000	0.000	0.000	0.000
114	A	310	VAL	0	-0.045	-0.018	25.406	0.013	0.013	0.000	0.000	0.000	0.000
115	A	311	VAL	0	0.066	0.027	25.762	-0.003	-0.003	0.000	0.000	0.000	0.000
116	A	312	SER	0	-0.013	-0.016	27.340	-0.011	-0.011	0.000	0.000	0.000	0.000
117	A	313	LEU	0	-0.043	-0.021	28.590	0.009	0.009	0.000	0.000	0.000	0.000
118	A	314	ASP	-1	-0.742	-0.838	23.131	-0.240	-0.240	0.000	0.000	0.000	0.000
119	A	315	VAL	0	-0.038	-0.031	23.939	-0.026	-0.026	0.000	0.000	0.000	0.000
120	A	316	LEU	0	-0.003	0.009	19.631	0.019	0.019	0.000	0.000	0.000	0.000
121	A	317	LYS	1	0.938	0.972	24.210	0.175	0.175	0.000	0.000	0.000	0.000
122	A	318	PHE	0	0.060	0.006	21.681	0.002	0.002	0.000	0.000	0.000	0.000
123	A	319	SER	0	-0.009	-0.012	27.836	0.010	0.010	0.000	0.000	0.000	0.000
124	A	320	LEU	0	0.036	0.000	28.823	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	321	CYS	0	-0.033	0.019	32.338	0.002	0.002	0.000	0.000	0.000	0.000
126	A	322	ASN	0	0.007	0.004	35.220	0.003	0.003	0.000	0.000	0.000	0.000
127	A	323	ASP	-1	-0.778	-0.895	37.779	-0.069	-0.069	0.000	0.000	0.000	0.000
128	A	324	GLY	0	0.026	0.019	40.406	0.004	0.004	0.000	0.000	0.000	0.000
129	A	325	ALA	0	-0.043	-0.024	41.533	0.003	0.003	0.000	0.000	0.000	0.000
130	A	326	ALA	0	-0.005	0.002	40.580	-0.004	-0.004	0.000	0.000	0.000	0.000
131	A	327	LEU	0	-0.034	-0.009	34.820	0.001	0.001	0.000	0.000	0.000	0.000
132	A	328	SER	0	0.016	0.002	38.313	-0.004	-0.004	0.000	0.000	0.000	0.000
133	A	329	ASN	0	-0.069	-0.040	37.135	-0.004	-0.004	0.000	0.000	0.000	0.000
134	A	330	TYR	0	-0.022	-0.027	31.731	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	331	ILE	0	-0.011	0.003	27.797	-0.007	-0.007	0.000	0.000	0.000	0.000
136	A	332	ILE	0	-0.002	-0.006	26.753	0.004	0.004	0.000	0.000	0.000	0.000
137	A	333	ASN	0	-0.039	0.000	22.333	-0.026	-0.026	0.000	0.000	0.000	0.000
138	A	334	ILE	0	0.024	0.011	21.559	0.015	0.015	0.000	0.000	0.000	0.000
139	A	335	THR	0	0.004	0.009	15.579	-0.032	-0.032	0.000	0.000	0.000	0.000
140	A	336	ALA	0	0.018	0.017	16.607	0.041	0.041	0.000	0.000	0.000	0.000
141	A	337	ALA	0	0.020	0.002	11.091	-0.083	-0.083	0.000	0.000	0.000	0.000
142	A	338	LYS	1	0.878	0.957	11.374	0.836	0.836	0.000	0.000	0.000	0.000
143	A	339	ILE	0	-0.003	-0.021	8.925	-0.286	-0.286	0.000	0.000	0.000	0.000
144	A	340	ASN	0	-0.031	0.014	8.649	0.063	0.063	0.000	0.000	0.000	0.000

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