FMO DATABASE

FMODB ID: 9M4R2

Calculation Name: 4YZY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YZY

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Z2B5

Base Structure: X-ray

Registration Date: 2023-09-26

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	171
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1615625.873777
FMO2-HF: Nuclear repulsion	1548882.609384
FMO2-HF: Total energy	-66743.264393
FMO2-MP2: Total energy	-66938.29744

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:103:ALA)

Summations of interaction energy for fragment #1(A:103: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.
-3.651	1.503	1.231	-3.138	-3.246	-0.021

Interaction energy analysis for fragmet #1(A:103:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.055 / q_NPA : 0.036

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	105	LEU	0	0.035	0.035	3.840	-0.848	1.528	-0.008	-1.278	-1.090	0.004
4	A	106	VAL	0	-0.004	-0.008	5.460	0.130	0.130	0.000	0.000	0.000	0.000
5	A	107	ILE	0	0.003	0.008	8.069	0.090	0.090	0.000	0.000	0.000	0.000
6	A	108	ILE	0	-0.023	-0.020	11.264	0.036	0.036	0.000	0.000	0.000	0.000
7	A	109	SER	0	0.042	0.023	14.756	0.029	0.029	0.000	0.000	0.000	0.000
8	A	110	THR	0	-0.018	-0.034	18.021	-0.003	-0.003	0.000	0.000	0.000	0.000
9	A	111	LEU	0	0.028	-0.003	20.792	0.009	0.009	0.000	0.000	0.000	0.000
10	A	112	ASP	-1	-0.745	-0.819	22.540	-0.122	-0.122	0.000	0.000	0.000	0.000
11	A	113	GLY	0	-0.049	-0.020	23.239	0.011	0.011	0.000	0.000	0.000	0.000
12	A	114	ARG	1	0.861	0.927	18.069	0.112	0.112	0.000	0.000	0.000	0.000
13	A	115	ILE	0	-0.005	0.005	13.360	-0.028	-0.028	0.000	0.000	0.000	0.000
14	A	116	ALA	0	-0.004	-0.014	13.256	0.046	0.046	0.000	0.000	0.000	0.000
15	A	117	ALA	0	0.017	0.017	7.936	-0.076	-0.076	0.000	0.000	0.000	0.000
16	A	118	LEU	0	-0.033	-0.011	8.308	0.134	0.134	0.000	0.000	0.000	0.000
17	A	119	ASP	-1	-0.758	-0.878	2.685	-5.433	-2.815	1.242	-1.840	-2.020	-0.025
18	A	120	ALA	0	-0.084	-0.050	4.611	0.236	0.272	-0.001	-0.004	-0.031	0.000
19	A	121	GLU	-1	-0.938	-0.935	6.212	0.462	0.462	0.000	0.000	0.000	0.000
20	A	122	ASN	0	-0.120	-0.094	7.918	-0.122	-0.122	0.000	0.000	0.000	0.000
21	A	123	ASP	-1	-0.832	-0.907	8.356	-0.115	-0.115	0.000	0.000	0.000	0.000
22	A	124	GLY	0	0.064	0.038	9.253	0.018	0.018	0.000	0.000	0.000	0.000
23	A	125	LYS	1	0.811	0.885	8.463	-0.174	-0.174	0.000	0.000	0.000	0.000
24	A	126	LYS	1	0.833	0.882	8.265	-0.041	-0.041	0.000	0.000	0.000	0.000
25	A	127	GLN	0	-0.020	-0.013	4.192	0.096	0.180	-0.001	-0.013	-0.069	0.000
26	A	128	TRP	0	0.006	0.015	7.153	0.107	0.107	0.000	0.000	0.000	0.000
27	A	129	ASP	-1	-0.825	-0.909	11.132	-0.153	-0.153	0.000	0.000	0.000	0.000
28	A	130	LEU	0	-0.036	0.004	14.200	0.041	0.041	0.000	0.000	0.000	0.000
29	A	131	ASP	-1	-0.815	-0.909	16.488	-0.140	-0.140	0.000	0.000	0.000	0.000
30	A	132	VAL	0	0.012	-0.010	19.839	0.008	0.008	0.000	0.000	0.000	0.000
31	A	133	GLY	0	0.011	0.018	22.392	0.004	0.004	0.000	0.000	0.000	0.000
32	A	134	SER	0	-0.102	-0.074	25.567	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	135	GLY	0	0.015	0.022	26.835	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	136	SER	0	0.047	0.027	25.858	-0.014	-0.014	0.000	0.000	0.000	0.000
35	A	137	LEU	0	-0.014	0.013	22.210	0.001	0.001	0.000	0.000	0.000	0.000
36	A	138	VAL	0	-0.010	0.000	26.662	0.001	0.001	0.000	0.000	0.000	0.000
37	A	139	SER	0	-0.019	-0.010	30.316	0.007	0.007	0.000	0.000	0.000	0.000
38	A	140	SER	0	-0.001	-0.012	33.477	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	141	SER	0	-0.021	-0.007	37.278	0.003	0.003	0.000	0.000	0.000	0.000
40	A	142	LEU	0	0.010	0.000	40.655	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	143	SER	0	-0.006	-0.009	44.462	0.002	0.002	0.000	0.000	0.000	0.000
42	A	191	ASP	-1	-0.842	-0.932	54.086	-0.036	-0.036	0.000	0.000	0.000	0.000
43	A	192	VAL	0	-0.046	-0.030	48.580	0.001	0.001	0.000	0.000	0.000	0.000
44	A	193	VAL	0	0.038	0.039	47.628	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	194	LEU	0	-0.002	-0.009	43.107	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	195	VAL	0	0.008	0.005	42.027	0.001	0.001	0.000	0.000	0.000	0.000
47	A	196	GLY	0	0.024	-0.003	38.533	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	197	GLY	0	-0.003	0.010	36.012	0.003	0.003	0.000	0.000	0.000	0.000
49	A	198	LYS	1	0.920	0.951	31.116	0.105	0.105	0.000	0.000	0.000	0.000
50	A	199	SER	0	-0.002	0.017	29.154	0.002	0.002	0.000	0.000	0.000	0.000
51	A	200	LEU	0	-0.029	-0.010	24.919	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	201	THR	0	-0.001	-0.014	24.541	0.007	0.007	0.000	0.000	0.000	0.000
53	A	202	THR	0	-0.009	-0.011	19.932	-0.022	-0.022	0.000	0.000	0.000	0.000
54	A	203	TYR	0	-0.034	-0.013	17.898	0.029	0.029	0.000	0.000	0.000	0.000
55	A	204	GLY	0	0.053	0.032	16.275	-0.039	-0.039	0.000	0.000	0.000	0.000
56	A	205	LEU	0	-0.021	-0.015	11.794	0.045	0.045	0.000	0.000	0.000	0.000
57	A	206	SER	0	-0.001	-0.010	9.957	-0.037	-0.037	0.000	0.000	0.000	0.000
58	A	207	ALA	0	-0.028	-0.029	4.440	-0.021	0.019	-0.001	-0.003	-0.036	0.000
59	A	208	TYR	0	-0.063	-0.009	5.605	0.307	0.307	0.000	0.000	0.000	0.000
60	A	209	SER	0	-0.046	-0.052	7.706	0.066	0.066	0.000	0.000	0.000	0.000
61	A	210	GLY	0	-0.012	-0.004	9.128	-0.046	-0.046	0.000	0.000	0.000	0.000
62	A	211	LYS	1	0.902	0.952	10.874	-0.125	-0.125	0.000	0.000	0.000	0.000
63	A	212	LEU	0	-0.031	-0.018	13.598	-0.030	-0.030	0.000	0.000	0.000	0.000
64	A	213	ARG	1	0.879	0.921	12.514	0.105	0.105	0.000	0.000	0.000	0.000
65	A	214	TYR	0	-0.006	-0.035	18.150	0.008	0.008	0.000	0.000	0.000	0.000
66	A	215	ILE	0	-0.037	-0.001	19.754	-0.020	-0.020	0.000	0.000	0.000	0.000
67	A	216	CYS	0	-0.079	-0.033	22.422	0.004	0.004	0.000	0.000	0.000	0.000
68	A	217	SER	0	0.014	-0.010	24.757	-0.011	-0.011	0.000	0.000	0.000	0.000
69	A	218	ALA	0	-0.001	-0.012	27.619	0.004	0.004	0.000	0.000	0.000	0.000
70	A	219	LEU	0	-0.011	0.003	30.760	0.004	0.004	0.000	0.000	0.000	0.000
71	A	220	GLY	0	0.028	0.026	30.234	0.007	0.007	0.000	0.000	0.000	0.000
72	A	222	ARG	1	0.901	0.976	24.354	0.034	0.034	0.000	0.000	0.000	0.000
73	A	223	ARG	1	0.913	0.924	20.826	0.015	0.015	0.000	0.000	0.000	0.000
74	A	224	TRP	0	-0.040	-0.025	20.416	-0.010	-0.010	0.000	0.000	0.000	0.000
75	A	225	ASP	-1	-0.888	-0.935	22.033	0.081	0.081	0.000	0.000	0.000	0.000
76	A	226	SER	0	-0.075	-0.038	18.145	0.010	0.010	0.000	0.000	0.000	0.000
77	A	227	ASP	-1	-0.890	-0.931	18.493	0.161	0.161	0.000	0.000	0.000	0.000
78	A	228	GLU	-1	-0.845	-0.910	12.973	0.583	0.583	0.000	0.000	0.000	0.000
79	A	229	MET	0	-0.034	-0.034	13.052	0.041	0.041	0.000	0.000	0.000	0.000
80	A	230	GLU	-1	-0.901	-0.943	14.312	-0.098	-0.098	0.000	0.000	0.000	0.000
81	A	231	GLU	-1	-0.955	-0.982	15.616	0.113	0.113	0.000	0.000	0.000	0.000
82	A	232	GLU	-1	-0.870	-0.917	12.892	0.264	0.264	0.000	0.000	0.000	0.000
83	A	233	GLU	-1	-0.807	-0.885	9.277	0.277	0.277	0.000	0.000	0.000	0.000
84	A	234	ASP	-1	-0.832	-0.897	6.897	-1.054	-1.054	0.000	0.000	0.000	0.000
85	A	235	ILE	0	0.019	0.013	9.023	0.083	0.083	0.000	0.000	0.000	0.000
86	A	236	LEU	0	-0.001	0.018	8.746	-0.115	-0.115	0.000	0.000	0.000	0.000
87	A	237	LEU	0	-0.048	-0.017	11.427	0.102	0.102	0.000	0.000	0.000	0.000
88	A	238	LEU	0	0.035	0.017	14.822	-0.035	-0.035	0.000	0.000	0.000	0.000
89	A	239	GLN	0	-0.020	-0.019	16.452	0.030	0.030	0.000	0.000	0.000	0.000
90	A	240	ARG	1	0.769	0.886	20.163	0.126	0.126	0.000	0.000	0.000	0.000
91	A	241	THR	0	0.002	-0.020	22.771	0.017	0.017	0.000	0.000	0.000	0.000
92	A	242	GLN	0	0.049	0.027	26.018	-0.009	-0.009	0.000	0.000	0.000	0.000
93	A	243	LYS	1	0.795	0.893	28.118	0.144	0.144	0.000	0.000	0.000	0.000
94	A	244	THR	0	0.023	-0.002	32.085	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	245	VAL	0	-0.015	-0.001	34.823	0.002	0.002	0.000	0.000	0.000	0.000
96	A	246	ARG	1	0.912	0.932	38.632	0.047	0.047	0.000	0.000	0.000	0.000
97	A	247	ALA	0	0.026	0.037	41.538	0.001	0.001	0.000	0.000	0.000	0.000
98	A	248	VAL	0	0.007	-0.010	45.180	0.001	0.001	0.000	0.000	0.000	0.000
99	A	249	GLY	0	0.036	0.022	47.841	0.000	0.000	0.000	0.000	0.000	0.000
100	A	250	PRO	0	-0.002	-0.002	51.663	0.001	0.001	0.000	0.000	0.000	0.000
101	A	251	ARG	1	0.827	0.916	53.348	0.034	0.034	0.000	0.000	0.000	0.000
102	A	252	SER	0	0.031	0.006	53.167	0.001	0.001	0.000	0.000	0.000	0.000
103	A	253	GLY	0	0.019	0.016	48.979	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	254	SER	0	-0.012	-0.003	47.730	0.000	0.000	0.000	0.000	0.000	0.000
105	A	255	GLU	-1	-0.827	-0.890	41.893	-0.049	-0.049	0.000	0.000	0.000	0.000
106	A	256	LYS	1	0.815	0.917	46.439	0.040	0.040	0.000	0.000	0.000	0.000
107	A	257	TRP	0	0.075	0.034	41.698	0.000	0.000	0.000	0.000	0.000	0.000
108	A	258	ASN	0	-0.061	-0.034	38.060	-0.004	-0.004	0.000	0.000	0.000	0.000
109	A	259	PHE	0	0.041	0.021	35.447	0.000	0.000	0.000	0.000	0.000	0.000
110	A	260	SER	0	-0.001	0.005	32.073	0.003	0.003	0.000	0.000	0.000	0.000
111	A	261	VAL	0	0.006	-0.001	30.436	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	262	GLY	0	-0.031	-0.017	27.136	0.001	0.001	0.000	0.000	0.000	0.000
113	A	263	HIS	0	-0.032	-0.012	23.071	0.013	0.013	0.000	0.000	0.000	0.000
114	A	264	PHE	0	0.081	0.026	18.637	0.015	0.015	0.000	0.000	0.000	0.000
115	A	265	GLU	-1	-0.828	-0.893	19.307	-0.222	-0.222	0.000	0.000	0.000	0.000
116	A	266	LEU	0	0.006	-0.002	12.137	0.006	0.006	0.000	0.000	0.000	0.000
117	A	267	ARG	1	0.906	0.955	15.231	0.300	0.300	0.000	0.000	0.000	0.000
118	A	268	TYR	0	-0.024	-0.042	7.193	-0.018	-0.018	0.000	0.000	0.000	0.000
119	A	269	ILE	0	-0.055	-0.030	12.250	0.062	0.062	0.000	0.000	0.000	0.000
120	A	270	PRO	0	0.002	0.010	10.487	-0.032	-0.032	0.000	0.000	0.000	0.000
121	A	271	ASP	-1	-0.898	-0.936	10.953	-0.012	-0.012	0.000	0.000	0.000	0.000
122	A	306	LEU	0	0.067	0.045	7.384	0.033	0.033	0.000	0.000	0.000	0.000
123	A	307	ASP	-1	-0.823	-0.867	10.586	-0.535	-0.535	0.000	0.000	0.000	0.000
124	A	308	THR	0	-0.061	-0.038	11.429	-0.079	-0.079	0.000	0.000	0.000	0.000
125	A	309	VAL	0	-0.021	-0.013	13.994	-0.051	-0.051	0.000	0.000	0.000	0.000
126	A	310	ILE	0	0.039	0.017	11.386	0.038	0.038	0.000	0.000	0.000	0.000
127	A	311	LYS	1	0.866	0.933	15.033	0.249	0.249	0.000	0.000	0.000	0.000
128	A	312	VAL	0	0.047	0.032	17.347	0.012	0.012	0.000	0.000	0.000	0.000
129	A	313	SER	0	-0.026	-0.011	19.331	0.016	0.016	0.000	0.000	0.000	0.000
130	A	314	VAL	0	0.027	-0.012	22.640	0.009	0.009	0.000	0.000	0.000	0.000
131	A	315	ALA	0	-0.031	-0.014	24.274	0.010	0.010	0.000	0.000	0.000	0.000
132	A	316	ASP	-1	-0.828	-0.921	24.732	-0.104	-0.104	0.000	0.000	0.000	0.000
133	A	317	TRP	0	-0.009	-0.002	22.123	0.003	0.003	0.000	0.000	0.000	0.000
134	A	318	LYS	1	0.841	0.936	19.491	0.120	0.120	0.000	0.000	0.000	0.000
135	A	319	VAL	0	0.005	0.001	13.199	-0.015	-0.015	0.000	0.000	0.000	0.000
136	A	320	MET	0	-0.024	-0.015	16.369	0.025	0.025	0.000	0.000	0.000	0.000
137	A	321	ALA	0	0.042	0.035	13.443	-0.049	-0.049	0.000	0.000	0.000	0.000
138	A	322	PHE	0	0.002	-0.011	15.402	0.062	0.062	0.000	0.000	0.000	0.000
139	A	323	SER	0	0.008	-0.030	16.308	-0.042	-0.042	0.000	0.000	0.000	0.000
140	A	324	ARG	1	0.774	0.830	16.735	0.282	0.282	0.000	0.000	0.000	0.000
141	A	325	LYS	1	0.904	0.966	20.799	0.115	0.115	0.000	0.000	0.000	0.000
142	A	326	GLY	0	0.031	0.015	24.635	0.010	0.010	0.000	0.000	0.000	0.000
143	A	327	GLY	0	0.038	0.008	21.625	-0.021	-0.021	0.000	0.000	0.000	0.000
144	A	328	ARG	1	0.831	0.913	17.839	0.141	0.141	0.000	0.000	0.000	0.000
145	A	329	LEU	0	0.030	0.010	19.562	-0.025	-0.025	0.000	0.000	0.000	0.000
146	A	330	GLU	-1	-0.804	-0.844	15.028	-0.136	-0.136	0.000	0.000	0.000	0.000
147	A	331	TRP	0	0.070	0.040	10.059	0.041	0.041	0.000	0.000	0.000	0.000
148	A	332	GLU	-1	-0.879	-0.942	15.847	-0.172	-0.172	0.000	0.000	0.000	0.000
149	A	333	TYR	0	0.041	0.023	13.687	0.028	0.028	0.000	0.000	0.000	0.000
150	A	334	GLN	0	-0.043	-0.012	16.224	-0.019	-0.019	0.000	0.000	0.000	0.000
151	A	335	PHE	0	0.031	0.017	14.360	0.016	0.016	0.000	0.000	0.000	0.000
152	A	336	CYS	0	-0.029	-0.022	19.979	0.007	0.007	0.000	0.000	0.000	0.000
153	A	337	THR	0	-0.061	-0.064	21.173	0.009	0.009	0.000	0.000	0.000	0.000
154	A	338	PRO	0	0.014	0.012	22.373	-0.014	-0.014	0.000	0.000	0.000	0.000
155	A	339	ILE	0	0.007	0.011	18.036	-0.004	-0.004	0.000	0.000	0.000	0.000
156	A	340	ALA	0	-0.042	-0.013	21.088	0.008	0.008	0.000	0.000	0.000	0.000
157	A	341	SER	0	-0.077	-0.048	19.247	0.003	0.003	0.000	0.000	0.000	0.000
158	A	342	ALA	0	0.038	0.021	15.152	0.004	0.004	0.000	0.000	0.000	0.000
159	A	343	TRP	0	-0.021	-0.011	12.955	0.033	0.033	0.000	0.000	0.000	0.000
160	A	344	LEU	0	-0.001	0.012	9.116	-0.009	-0.009	0.000	0.000	0.000	0.000
161	A	345	VAL	0	0.001	-0.009	7.122	0.173	0.173	0.000	0.000	0.000	0.000
162	A	346	ARG	1	0.890	0.914	5.997	1.239	1.239	0.000	0.000	0.000	0.000
163	A	347	ASP	-1	-0.755	-0.858	5.595	-1.932	-1.932	0.000	0.000	0.000	0.000
164	A	348	GLY	0	0.044	0.030	7.786	0.099	0.099	0.000	0.000	0.000	0.000
165	A	349	LYS	1	0.764	0.882	9.894	1.236	1.236	0.000	0.000	0.000	0.000
166	A	350	VAL	0	0.009	0.006	11.688	-0.149	-0.149	0.000	0.000	0.000	0.000
167	A	351	ILE	0	-0.001	-0.008	13.347	0.079	0.079	0.000	0.000	0.000	0.000
168	A	352	PRO	0	-0.006	0.002	14.852	-0.045	-0.045	0.000	0.000	0.000	0.000
169	A	353	ILE	0	-0.001	0.000	12.797	0.030	0.030	0.000	0.000	0.000	0.000
170	A	354	SER	0	-0.008	0.002	17.290	0.045	0.045	0.000	0.000	0.000	0.000
171	A	355	LEU	0	-0.016	-0.013	21.095	0.016	0.016	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:103:ALA)