FMO DATABASE

FMODB ID: L7ZV9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1613641.400637
FMO2-HF: Nuclear repulsion	1546899.825709
FMO2-HF: Total energy	-66741.574928
FMO2-MP2: Total energy	-66936.728519

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.
-2.722	2.156	0.269	-2.663	-2.485	-0.007

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 : 0.056 / q_NPA : 0.032

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	0.038	0.038	3.815	-1.182	1.530	-0.017	-1.459	-1.236	0.006
4	A	106	VAL	0	-0.029	-0.020	5.801	0.029	0.029	0.000	0.000	0.000	0.000
5	A	107	ILE	0	0.007	0.013	8.591	0.116	0.116	0.000	0.000	0.000	0.000
6	A	108	ILE	0	-0.024	-0.024	11.659	0.041	0.041	0.000	0.000	0.000	0.000
7	A	109	SER	0	0.023	0.016	15.165	0.033	0.033	0.000	0.000	0.000	0.000
8	A	110	THR	0	-0.012	-0.025	18.299	0.002	0.002	0.000	0.000	0.000	0.000
9	A	111	LEU	0	0.029	-0.002	21.073	0.005	0.005	0.000	0.000	0.000	0.000
10	A	112	ASP	-1	-0.787	-0.838	22.876	-0.137	-0.137	0.000	0.000	0.000	0.000
11	A	113	GLY	0	-0.046	-0.020	22.869	0.009	0.009	0.000	0.000	0.000	0.000
12	A	114	ARG	1	0.835	0.925	18.241	0.140	0.140	0.000	0.000	0.000	0.000
13	A	115	ILE	0	0.005	0.013	13.642	-0.027	-0.027	0.000	0.000	0.000	0.000
14	A	116	ALA	0	-0.018	-0.011	13.579	0.031	0.031	0.000	0.000	0.000	0.000
15	A	117	ALA	0	0.029	0.013	8.188	-0.073	-0.073	0.000	0.000	0.000	0.000
16	A	118	LEU	0	-0.054	-0.023	8.762	0.116	0.116	0.000	0.000	0.000	0.000
17	A	119	ASP	-1	-0.782	-0.890	2.902	-3.366	-1.230	0.287	-1.201	-1.223	-0.013
18	A	120	ALA	0	-0.069	-0.041	4.619	0.041	0.071	-0.001	-0.003	-0.026	0.000
19	A	121	GLU	-1	-0.922	-0.941	6.308	0.491	0.491	0.000	0.000	0.000	0.000
20	A	122	ASN	0	-0.125	-0.070	8.322	-0.134	-0.134	0.000	0.000	0.000	0.000
21	A	123	ASP	-1	-0.811	-0.926	8.057	-0.063	-0.063	0.000	0.000	0.000	0.000
22	A	124	GLY	0	0.047	0.040	9.126	-0.011	-0.011	0.000	0.000	0.000	0.000
23	A	125	LYS	1	0.796	0.881	9.569	-0.087	-0.087	0.000	0.000	0.000	0.000
24	A	126	LYS	1	0.830	0.893	9.281	0.014	0.014	0.000	0.000	0.000	0.000
25	A	127	GLN	0	-0.010	-0.013	5.104	0.115	0.115	0.000	0.000	0.000	0.000
26	A	128	TRP	0	0.009	0.002	7.743	0.100	0.100	0.000	0.000	0.000	0.000
27	A	129	ASP	-1	-0.814	-0.904	11.612	-0.182	-0.182	0.000	0.000	0.000	0.000
28	A	130	LEU	0	-0.035	0.015	14.652	0.038	0.038	0.000	0.000	0.000	0.000
29	A	131	ASP	-1	-0.807	-0.913	16.577	-0.172	-0.172	0.000	0.000	0.000	0.000
30	A	132	VAL	0	0.001	-0.016	19.890	0.010	0.010	0.000	0.000	0.000	0.000
31	A	133	GLY	0	0.018	0.020	22.651	0.005	0.005	0.000	0.000	0.000	0.000
32	A	134	SER	0	-0.102	-0.075	25.641	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	135	GLY	0	-0.005	0.012	26.860	0.001	0.001	0.000	0.000	0.000	0.000
34	A	136	SER	0	0.051	0.013	26.026	-0.013	-0.013	0.000	0.000	0.000	0.000
35	A	137	LEU	0	-0.038	-0.015	22.600	0.002	0.002	0.000	0.000	0.000	0.000
36	A	138	VAL	0	-0.044	-0.028	26.901	0.001	0.001	0.000	0.000	0.000	0.000
37	A	139	SER	0	-0.012	0.001	30.500	0.006	0.006	0.000	0.000	0.000	0.000
38	A	140	SER	0	0.029	0.004	33.772	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	141	SER	0	-0.026	-0.013	37.497	0.004	0.004	0.000	0.000	0.000	0.000
40	A	142	LEU	0	-0.014	-0.009	40.852	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	143	SER	0	-0.009	-0.024	44.633	0.003	0.003	0.000	0.000	0.000	0.000
42	A	191	ASP	-1	-0.937	-0.976	54.016	-0.041	-0.041	0.000	0.000	0.000	0.000
43	A	192	VAL	0	-0.072	-0.052	48.788	0.001	0.001	0.000	0.000	0.000	0.000
44	A	193	VAL	0	0.057	0.044	47.992	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	194	LEU	0	-0.008	-0.007	43.630	0.000	0.000	0.000	0.000	0.000	0.000
46	A	195	VAL	0	0.012	0.012	42.018	0.000	0.000	0.000	0.000	0.000	0.000
47	A	196	GLY	0	0.038	-0.002	39.028	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	197	GLY	0	-0.014	0.006	36.620	0.003	0.003	0.000	0.000	0.000	0.000
49	A	198	LYS	1	0.934	0.974	31.188	0.114	0.114	0.000	0.000	0.000	0.000
50	A	199	SER	0	-0.018	-0.012	29.225	0.007	0.007	0.000	0.000	0.000	0.000
51	A	200	LEU	0	-0.036	-0.014	25.228	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	201	THR	0	-0.010	-0.002	24.859	0.002	0.002	0.000	0.000	0.000	0.000
53	A	202	THR	0	0.006	-0.017	20.185	-0.021	-0.021	0.000	0.000	0.000	0.000
54	A	203	TYR	0	-0.032	-0.031	18.267	0.036	0.036	0.000	0.000	0.000	0.000
55	A	204	GLY	0	0.024	0.023	16.548	-0.039	-0.039	0.000	0.000	0.000	0.000
56	A	205	LEU	0	-0.016	-0.007	12.135	0.050	0.050	0.000	0.000	0.000	0.000
57	A	206	SER	0	-0.022	-0.015	10.780	-0.062	-0.062	0.000	0.000	0.000	0.000
58	A	207	ALA	0	-0.039	-0.034	5.689	-0.138	-0.138	0.000	0.000	0.000	0.000
59	A	208	TYR	0	-0.017	0.008	6.311	0.232	0.232	0.000	0.000	0.000	0.000
60	A	209	SER	0	-0.042	-0.043	7.734	0.020	0.020	0.000	0.000	0.000	0.000
61	A	210	GLY	0	-0.024	0.012	9.579	-0.030	-0.030	0.000	0.000	0.000	0.000
62	A	211	LYS	1	0.928	0.966	11.005	-0.017	-0.017	0.000	0.000	0.000	0.000
63	A	212	LEU	0	-0.021	-0.012	14.143	-0.030	-0.030	0.000	0.000	0.000	0.000
64	A	213	ARG	1	0.897	0.936	11.931	0.148	0.148	0.000	0.000	0.000	0.000
65	A	214	TYR	0	-0.011	-0.045	17.854	0.010	0.010	0.000	0.000	0.000	0.000
66	A	215	ILE	0	-0.038	0.002	20.230	-0.021	-0.021	0.000	0.000	0.000	0.000
67	A	216	CYS	0	-0.035	-0.013	22.802	0.006	0.006	0.000	0.000	0.000	0.000
68	A	217	SER	0	0.017	-0.007	24.907	-0.012	-0.012	0.000	0.000	0.000	0.000
69	A	218	ALA	0	-0.023	-0.020	27.636	0.003	0.003	0.000	0.000	0.000	0.000
70	A	219	LEU	0	-0.010	-0.003	30.713	0.005	0.005	0.000	0.000	0.000	0.000
71	A	220	GLY	0	0.025	0.023	29.880	0.007	0.007	0.000	0.000	0.000	0.000
72	A	222	ARG	1	0.902	0.974	24.657	0.060	0.060	0.000	0.000	0.000	0.000
73	A	223	ARG	1	0.996	0.980	22.259	0.041	0.041	0.000	0.000	0.000	0.000
74	A	224	TRP	0	-0.049	-0.030	20.671	-0.007	-0.007	0.000	0.000	0.000	0.000
75	A	225	ASP	-1	-0.884	-0.931	21.992	0.058	0.058	0.000	0.000	0.000	0.000
76	A	226	SER	0	-0.076	-0.041	18.095	0.000	0.000	0.000	0.000	0.000	0.000
77	A	227	ASP	-1	-0.882	-0.958	17.756	0.135	0.135	0.000	0.000	0.000	0.000
78	A	228	GLU	-1	-0.832	-0.919	12.909	0.513	0.513	0.000	0.000	0.000	0.000
79	A	229	MET	0	-0.019	0.008	12.917	-0.019	-0.019	0.000	0.000	0.000	0.000
80	A	230	GLU	-1	-1.037	-1.035	14.096	-0.125	-0.125	0.000	0.000	0.000	0.000
81	A	231	GLU	-1	-0.894	-0.963	15.121	0.101	0.101	0.000	0.000	0.000	0.000
82	A	232	GLU	-1	-0.885	-0.917	13.004	0.329	0.329	0.000	0.000	0.000	0.000
83	A	233	GLU	-1	-0.884	-0.914	9.636	0.158	0.158	0.000	0.000	0.000	0.000
84	A	234	ASP	-1	-0.841	-0.897	6.800	-1.007	-1.007	0.000	0.000	0.000	0.000
85	A	235	ILE	0	-0.010	-0.013	9.180	0.075	0.075	0.000	0.000	0.000	0.000
86	A	236	LEU	0	0.000	0.017	9.136	-0.167	-0.167	0.000	0.000	0.000	0.000
87	A	237	LEU	0	-0.039	-0.007	11.739	0.098	0.098	0.000	0.000	0.000	0.000
88	A	238	LEU	0	0.039	0.014	15.073	-0.044	-0.044	0.000	0.000	0.000	0.000
89	A	239	GLN	0	-0.010	-0.011	16.998	0.027	0.027	0.000	0.000	0.000	0.000
90	A	240	ARG	1	0.813	0.924	20.724	0.143	0.143	0.000	0.000	0.000	0.000
91	A	241	THR	0	-0.014	-0.013	23.113	0.021	0.021	0.000	0.000	0.000	0.000
92	A	242	GLN	0	0.053	0.037	26.368	-0.013	-0.013	0.000	0.000	0.000	0.000
93	A	243	LYS	1	0.928	0.958	28.936	0.148	0.148	0.000	0.000	0.000	0.000
94	A	244	THR	0	0.035	-0.005	32.359	0.001	0.001	0.000	0.000	0.000	0.000
95	A	245	VAL	0	-0.024	-0.006	35.076	0.002	0.002	0.000	0.000	0.000	0.000
96	A	246	ARG	1	0.876	0.929	38.863	0.053	0.053	0.000	0.000	0.000	0.000
97	A	247	ALA	0	0.016	0.020	41.538	0.001	0.001	0.000	0.000	0.000	0.000
98	A	248	VAL	0	-0.054	-0.030	45.139	0.002	0.002	0.000	0.000	0.000	0.000
99	A	249	GLY	0	0.004	0.005	47.793	0.000	0.000	0.000	0.000	0.000	0.000
100	A	250	PRO	0	0.040	0.020	51.563	0.000	0.000	0.000	0.000	0.000	0.000
101	A	251	ARG	1	0.920	0.973	53.492	0.036	0.036	0.000	0.000	0.000	0.000
102	A	252	SER	0	0.063	0.021	53.321	0.001	0.001	0.000	0.000	0.000	0.000
103	A	253	GLY	0	0.039	0.017	49.006	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	254	SER	0	-0.032	-0.026	48.636	0.001	0.001	0.000	0.000	0.000	0.000
105	A	255	GLU	-1	-0.823	-0.890	42.351	-0.054	-0.054	0.000	0.000	0.000	0.000
106	A	256	LYS	1	0.844	0.965	46.759	0.044	0.044	0.000	0.000	0.000	0.000
107	A	257	TRP	0	0.074	0.040	41.939	0.000	0.000	0.000	0.000	0.000	0.000
108	A	258	ASN	0	-0.054	-0.045	38.442	-0.004	-0.004	0.000	0.000	0.000	0.000
109	A	259	PHE	0	0.047	0.023	35.811	0.000	0.000	0.000	0.000	0.000	0.000
110	A	260	SER	0	-0.002	0.002	32.696	0.000	0.000	0.000	0.000	0.000	0.000
111	A	261	VAL	0	-0.007	-0.001	30.504	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	262	GLY	0	0.024	0.008	27.237	0.004	0.004	0.000	0.000	0.000	0.000
113	A	263	HIS	0	-0.090	-0.040	23.375	0.013	0.013	0.000	0.000	0.000	0.000
114	A	264	PHE	0	0.078	0.025	18.845	0.015	0.015	0.000	0.000	0.000	0.000
115	A	265	GLU	-1	-0.874	-0.913	19.271	-0.244	-0.244	0.000	0.000	0.000	0.000
116	A	266	LEU	0	0.023	0.007	12.426	0.003	0.003	0.000	0.000	0.000	0.000
117	A	267	ARG	1	0.914	0.959	15.454	0.320	0.320	0.000	0.000	0.000	0.000
118	A	268	TYR	0	-0.007	-0.028	6.881	-0.006	-0.006	0.000	0.000	0.000	0.000
119	A	269	ILE	0	-0.063	-0.042	11.814	0.073	0.073	0.000	0.000	0.000	0.000
120	A	270	PRO	0	0.006	0.014	10.065	-0.037	-0.037	0.000	0.000	0.000	0.000
121	A	271	ASP	-1	-0.891	-0.931	10.555	0.018	0.018	0.000	0.000	0.000	0.000
122	A	306	LEU	0	0.082	0.052	7.019	0.015	0.015	0.000	0.000	0.000	0.000
123	A	307	ASP	-1	-0.809	-0.870	10.575	-0.452	-0.452	0.000	0.000	0.000	0.000
124	A	308	THR	0	-0.088	-0.032	11.644	-0.027	-0.027	0.000	0.000	0.000	0.000
125	A	309	VAL	0	0.000	-0.002	13.827	-0.061	-0.061	0.000	0.000	0.000	0.000
126	A	310	ILE	0	0.049	0.022	11.637	0.027	0.027	0.000	0.000	0.000	0.000
127	A	311	LYS	1	0.901	0.964	15.473	0.226	0.226	0.000	0.000	0.000	0.000
128	A	312	VAL	0	0.057	0.023	17.579	0.006	0.006	0.000	0.000	0.000	0.000
129	A	313	SER	0	-0.022	-0.003	19.918	0.017	0.017	0.000	0.000	0.000	0.000
130	A	314	VAL	0	0.026	-0.010	23.127	0.007	0.007	0.000	0.000	0.000	0.000
131	A	315	ALA	0	-0.044	-0.018	24.721	0.009	0.009	0.000	0.000	0.000	0.000
132	A	316	ASP	-1	-0.834	-0.925	25.272	-0.101	-0.101	0.000	0.000	0.000	0.000
133	A	317	TRP	0	-0.023	-0.010	22.562	0.003	0.003	0.000	0.000	0.000	0.000
134	A	318	LYS	1	0.823	0.914	20.186	0.115	0.115	0.000	0.000	0.000	0.000
135	A	319	VAL	0	-0.013	-0.019	13.968	-0.017	-0.017	0.000	0.000	0.000	0.000
136	A	320	MET	0	-0.030	-0.015	16.164	0.010	0.010	0.000	0.000	0.000	0.000
137	A	321	ALA	0	0.078	0.054	13.542	-0.045	-0.045	0.000	0.000	0.000	0.000
138	A	322	PHE	0	-0.024	-0.020	15.433	0.052	0.052	0.000	0.000	0.000	0.000
139	A	323	SER	0	0.064	0.006	16.152	-0.010	-0.010	0.000	0.000	0.000	0.000
140	A	324	ARG	1	0.781	0.848	16.448	0.244	0.244	0.000	0.000	0.000	0.000
141	A	325	LYS	1	0.902	0.956	20.732	0.097	0.097	0.000	0.000	0.000	0.000
142	A	326	GLY	0	0.040	0.012	24.528	0.010	0.010	0.000	0.000	0.000	0.000
143	A	327	GLY	0	0.023	0.010	21.818	-0.017	-0.017	0.000	0.000	0.000	0.000
144	A	328	ARG	1	0.806	0.893	18.234	0.109	0.109	0.000	0.000	0.000	0.000
145	A	329	LEU	0	0.004	0.004	19.325	-0.015	-0.015	0.000	0.000	0.000	0.000
146	A	330	GLU	-1	-0.812	-0.875	15.046	-0.095	-0.095	0.000	0.000	0.000	0.000
147	A	331	TRP	0	0.048	0.032	10.207	0.033	0.033	0.000	0.000	0.000	0.000
148	A	332	GLU	-1	-0.881	-0.943	16.161	-0.166	-0.166	0.000	0.000	0.000	0.000
149	A	333	TYR	0	0.024	0.024	14.001	0.026	0.026	0.000	0.000	0.000	0.000
150	A	334	GLN	0	0.001	0.009	16.671	-0.012	-0.012	0.000	0.000	0.000	0.000
151	A	335	PHE	0	0.039	0.026	15.120	0.010	0.010	0.000	0.000	0.000	0.000
152	A	336	CYS	0	-0.067	-0.039	20.725	0.006	0.006	0.000	0.000	0.000	0.000
153	A	337	THR	0	-0.048	-0.050	21.964	0.011	0.011	0.000	0.000	0.000	0.000
154	A	338	PRO	0	0.030	0.016	23.047	-0.013	-0.013	0.000	0.000	0.000	0.000
155	A	339	ILE	0	0.025	0.016	18.793	-0.003	-0.003	0.000	0.000	0.000	0.000
156	A	340	ALA	0	-0.066	-0.027	21.466	0.008	0.008	0.000	0.000	0.000	0.000
157	A	341	SER	0	-0.089	-0.061	19.810	0.006	0.006	0.000	0.000	0.000	0.000
158	A	342	ALA	0	0.061	0.041	15.746	-0.002	-0.002	0.000	0.000	0.000	0.000
159	A	343	TRP	0	-0.045	-0.021	13.343	0.029	0.029	0.000	0.000	0.000	0.000
160	A	344	LEU	0	-0.023	-0.011	9.890	-0.003	-0.003	0.000	0.000	0.000	0.000
161	A	345	VAL	0	-0.013	-0.001	7.311	0.149	0.149	0.000	0.000	0.000	0.000
162	A	346	ARG	1	0.903	0.919	6.180	0.972	0.972	0.000	0.000	0.000	0.000
163	A	347	ASP	-1	-0.785	-0.869	5.671	-1.853	-1.853	0.000	0.000	0.000	0.000
164	A	348	GLY	0	0.082	0.047	6.260	-0.261	-0.261	0.000	0.000	0.000	0.000
165	A	349	LYS	1	0.787	0.884	8.852	1.357	1.357	0.000	0.000	0.000	0.000
166	A	350	VAL	0	-0.007	-0.009	10.804	-0.164	-0.164	0.000	0.000	0.000	0.000
167	A	351	ILE	0	-0.032	-0.008	13.161	0.116	0.116	0.000	0.000	0.000	0.000
168	A	352	PRO	0	0.043	0.012	14.780	-0.049	-0.049	0.000	0.000	0.000	0.000
169	A	353	ILE	0	0.015	0.011	13.136	0.036	0.036	0.000	0.000	0.000	0.000
170	A	354	SER	0	-0.027	-0.007	17.399	0.041	0.041	0.000	0.000	0.000	0.000
171	A	355	LEU	0	0.013	0.006	21.097	0.004	0.004	0.000	0.000	0.000	0.000

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