FMO DATABASE

FMODB ID: 379ML

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1614890.180967
FMO2-HF: Nuclear repulsion	1548149.613233
FMO2-HF: Total energy	-66740.567734
FMO2-MP2: Total energy	-66935.83961

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.
-2.749	1.872	0.357	-2.525	-2.453	-0.009

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 : 0.058 / q_NPA : 0.034

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	0.041	0.039	3.815	-1.019	1.555	-0.015	-1.384	-1.176	0.005
4	A	106	VAL	0	-0.027	-0.025	5.616	0.053	0.053	0.000	0.000	0.000	0.000
5	A	107	ILE	0	-0.002	0.011	8.548	0.115	0.115	0.000	0.000	0.000	0.000
6	A	108	ILE	0	-0.022	-0.023	11.511	0.044	0.044	0.000	0.000	0.000	0.000
7	A	109	SER	0	-0.010	0.002	15.019	0.035	0.035	0.000	0.000	0.000	0.000
8	A	110	THR	0	-0.048	-0.080	18.167	0.006	0.006	0.000	0.000	0.000	0.000
9	A	111	LEU	0	0.035	-0.004	20.944	0.006	0.006	0.000	0.000	0.000	0.000
10	A	112	ASP	-1	-0.825	-0.852	22.415	-0.155	-0.155	0.000	0.000	0.000	0.000
11	A	113	GLY	0	-0.045	-0.013	22.731	0.010	0.010	0.000	0.000	0.000	0.000
12	A	114	ARG	1	0.925	0.982	18.063	0.164	0.164	0.000	0.000	0.000	0.000
13	A	115	ILE	0	-0.032	-0.006	13.565	-0.030	-0.030	0.000	0.000	0.000	0.000
14	A	116	ALA	0	-0.026	-0.013	13.499	0.032	0.032	0.000	0.000	0.000	0.000
15	A	117	ALA	0	0.025	0.008	8.114	-0.075	-0.075	0.000	0.000	0.000	0.000
16	A	118	LEU	0	-0.067	-0.033	8.721	0.122	0.122	0.000	0.000	0.000	0.000
17	A	119	ASP	-1	-0.839	-0.932	2.814	-3.550	-1.537	0.373	-1.137	-1.248	-0.014
18	A	120	ALA	0	-0.066	-0.034	4.407	0.009	0.043	-0.001	-0.004	-0.029	0.000
19	A	121	GLU	-1	-0.923	-0.945	6.019	0.509	0.509	0.000	0.000	0.000	0.000
20	A	122	ASN	0	-0.118	-0.058	8.154	-0.127	-0.127	0.000	0.000	0.000	0.000
21	A	123	ASP	-1	-0.839	-0.921	8.013	-0.134	-0.134	0.000	0.000	0.000	0.000
22	A	124	GLY	0	0.017	0.007	9.077	0.000	0.000	0.000	0.000	0.000	0.000
23	A	125	LYS	1	0.851	0.915	9.534	-0.025	-0.025	0.000	0.000	0.000	0.000
24	A	126	LYS	1	0.871	0.928	9.261	0.038	0.038	0.000	0.000	0.000	0.000
25	A	127	GLN	0	0.020	-0.001	5.933	0.041	0.041	0.000	0.000	0.000	0.000
26	A	128	TRP	0	0.014	0.005	7.950	0.122	0.122	0.000	0.000	0.000	0.000
27	A	129	ASP	-1	-0.828	-0.914	11.601	-0.226	-0.226	0.000	0.000	0.000	0.000
28	A	130	LEU	0	-0.030	0.008	14.611	0.041	0.041	0.000	0.000	0.000	0.000
29	A	131	ASP	-1	-0.788	-0.901	16.550	-0.196	-0.196	0.000	0.000	0.000	0.000
30	A	132	VAL	0	0.001	-0.014	19.848	0.012	0.012	0.000	0.000	0.000	0.000
31	A	133	GLY	0	0.001	0.012	22.614	0.005	0.005	0.000	0.000	0.000	0.000
32	A	134	SER	0	-0.106	-0.075	25.504	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	135	GLY	0	-0.010	0.008	26.787	0.001	0.001	0.000	0.000	0.000	0.000
34	A	136	SER	0	0.054	0.023	25.944	-0.014	-0.014	0.000	0.000	0.000	0.000
35	A	137	LEU	0	-0.026	-0.011	22.383	0.003	0.003	0.000	0.000	0.000	0.000
36	A	138	VAL	0	-0.051	-0.028	26.790	0.001	0.001	0.000	0.000	0.000	0.000
37	A	139	SER	0	-0.040	-0.018	30.383	0.006	0.006	0.000	0.000	0.000	0.000
38	A	140	SER	0	0.050	0.011	33.663	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	141	SER	0	-0.049	-0.021	37.385	0.003	0.003	0.000	0.000	0.000	0.000
40	A	142	LEU	0	-0.005	-0.010	40.746	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	143	SER	0	-0.048	-0.050	44.526	0.003	0.003	0.000	0.000	0.000	0.000
42	A	191	ASP	-1	-0.938	-0.975	53.888	-0.043	-0.043	0.000	0.000	0.000	0.000
43	A	192	VAL	0	-0.072	-0.055	48.756	0.001	0.001	0.000	0.000	0.000	0.000
44	A	193	VAL	0	0.057	0.042	47.984	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	194	LEU	0	0.003	0.000	43.449	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	195	VAL	0	0.003	0.008	41.854	0.000	0.000	0.000	0.000	0.000	0.000
47	A	196	GLY	0	0.037	-0.005	38.943	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	197	GLY	0	-0.011	0.007	36.545	0.004	0.004	0.000	0.000	0.000	0.000
49	A	198	LYS	1	0.937	0.976	30.960	0.119	0.119	0.000	0.000	0.000	0.000
50	A	199	SER	0	-0.043	-0.023	30.050	0.004	0.004	0.000	0.000	0.000	0.000
51	A	200	LEU	0	-0.011	-0.003	24.980	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	201	THR	0	-0.011	0.003	24.449	0.002	0.002	0.000	0.000	0.000	0.000
53	A	202	THR	0	0.018	-0.016	20.162	-0.021	-0.021	0.000	0.000	0.000	0.000
54	A	203	TYR	0	-0.031	-0.031	18.238	0.033	0.033	0.000	0.000	0.000	0.000
55	A	204	GLY	0	0.018	0.017	16.552	-0.040	-0.040	0.000	0.000	0.000	0.000
56	A	205	LEU	0	0.025	0.017	12.129	0.051	0.051	0.000	0.000	0.000	0.000
57	A	206	SER	0	0.039	0.040	10.740	-0.064	-0.064	0.000	0.000	0.000	0.000
58	A	207	ALA	0	-0.047	-0.033	5.731	-0.137	-0.137	0.000	0.000	0.000	0.000
59	A	208	TYR	0	-0.007	0.013	6.385	0.210	0.210	0.000	0.000	0.000	0.000
60	A	209	SER	0	-0.048	-0.049	7.963	0.033	0.033	0.000	0.000	0.000	0.000
61	A	210	GLY	0	-0.027	0.012	9.656	-0.030	-0.030	0.000	0.000	0.000	0.000
62	A	211	LYS	1	0.911	0.965	10.985	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	212	LEU	0	-0.014	-0.016	14.198	-0.030	-0.030	0.000	0.000	0.000	0.000
64	A	213	ARG	1	0.889	0.936	12.496	0.179	0.179	0.000	0.000	0.000	0.000
65	A	214	TYR	0	0.000	-0.029	17.914	0.017	0.017	0.000	0.000	0.000	0.000
66	A	215	ILE	0	-0.034	0.004	20.247	-0.022	-0.022	0.000	0.000	0.000	0.000
67	A	216	CYS	0	-0.046	-0.013	22.810	0.008	0.008	0.000	0.000	0.000	0.000
68	A	217	SER	0	0.016	-0.007	24.885	-0.012	-0.012	0.000	0.000	0.000	0.000
69	A	218	ALA	0	-0.024	-0.019	27.613	0.004	0.004	0.000	0.000	0.000	0.000
70	A	219	LEU	0	-0.002	-0.002	30.705	0.006	0.006	0.000	0.000	0.000	0.000
71	A	220	GLY	0	0.019	0.023	29.880	0.007	0.007	0.000	0.000	0.000	0.000
72	A	222	ARG	1	0.902	0.964	24.528	0.068	0.068	0.000	0.000	0.000	0.000
73	A	223	ARG	1	1.000	0.980	22.326	0.042	0.042	0.000	0.000	0.000	0.000
74	A	224	TRP	0	-0.042	-0.024	20.732	-0.007	-0.007	0.000	0.000	0.000	0.000
75	A	225	ASP	-1	-0.878	-0.934	21.962	0.057	0.057	0.000	0.000	0.000	0.000
76	A	226	SER	0	-0.081	-0.041	17.838	0.002	0.002	0.000	0.000	0.000	0.000
77	A	227	ASP	-1	-0.885	-0.964	17.710	0.141	0.141	0.000	0.000	0.000	0.000
78	A	228	GLU	-1	-0.839	-0.901	12.916	0.531	0.531	0.000	0.000	0.000	0.000
79	A	229	MET	0	-0.015	0.002	12.878	-0.031	-0.031	0.000	0.000	0.000	0.000
80	A	230	GLU	-1	-0.994	-1.009	14.152	-0.133	-0.133	0.000	0.000	0.000	0.000
81	A	231	GLU	-1	-0.926	-0.974	15.121	0.095	0.095	0.000	0.000	0.000	0.000
82	A	232	GLU	-1	-0.870	-0.909	13.209	0.334	0.334	0.000	0.000	0.000	0.000
83	A	233	GLU	-1	-0.937	-0.963	9.764	0.200	0.200	0.000	0.000	0.000	0.000
84	A	234	ASP	-1	-0.858	-0.910	6.772	-1.085	-1.085	0.000	0.000	0.000	0.000
85	A	235	ILE	0	-0.092	-0.075	9.174	0.068	0.068	0.000	0.000	0.000	0.000
86	A	236	LEU	0	0.029	0.024	9.241	-0.164	-0.164	0.000	0.000	0.000	0.000
87	A	237	LEU	0	-0.045	-0.014	11.753	0.098	0.098	0.000	0.000	0.000	0.000
88	A	238	LEU	0	0.041	0.014	14.833	-0.046	-0.046	0.000	0.000	0.000	0.000
89	A	239	GLN	0	0.034	0.029	16.933	0.028	0.028	0.000	0.000	0.000	0.000
90	A	240	ARG	1	0.839	0.923	20.652	0.150	0.150	0.000	0.000	0.000	0.000
91	A	241	THR	0	-0.031	-0.020	23.031	0.021	0.021	0.000	0.000	0.000	0.000
92	A	242	GLN	0	0.080	0.065	26.273	-0.014	-0.014	0.000	0.000	0.000	0.000
93	A	243	LYS	1	0.917	0.951	28.842	0.143	0.143	0.000	0.000	0.000	0.000
94	A	244	THR	0	0.028	-0.010	32.256	0.000	0.000	0.000	0.000	0.000	0.000
95	A	245	VAL	0	-0.005	0.003	34.980	0.002	0.002	0.000	0.000	0.000	0.000
96	A	246	ARG	1	0.950	0.980	38.765	0.057	0.057	0.000	0.000	0.000	0.000
97	A	247	ALA	0	0.026	0.021	41.444	0.001	0.001	0.000	0.000	0.000	0.000
98	A	248	VAL	0	-0.023	-0.023	45.040	0.001	0.001	0.000	0.000	0.000	0.000
99	A	249	GLY	0	-0.008	-0.002	47.705	0.000	0.000	0.000	0.000	0.000	0.000
100	A	250	PRO	0	0.042	0.019	51.473	0.001	0.001	0.000	0.000	0.000	0.000
101	A	251	ARG	1	0.921	0.979	53.407	0.039	0.039	0.000	0.000	0.000	0.000
102	A	252	SER	0	0.055	0.016	53.250	0.001	0.001	0.000	0.000	0.000	0.000
103	A	253	GLY	0	0.032	0.022	48.951	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	254	SER	0	-0.039	-0.027	48.568	0.001	0.001	0.000	0.000	0.000	0.000
105	A	255	GLU	-1	-0.873	-0.925	42.465	-0.056	-0.056	0.000	0.000	0.000	0.000
106	A	256	LYS	1	0.861	0.987	46.672	0.048	0.048	0.000	0.000	0.000	0.000
107	A	257	TRP	0	0.082	0.043	41.501	0.000	0.000	0.000	0.000	0.000	0.000
108	A	258	ASN	0	-0.074	-0.059	38.290	-0.004	-0.004	0.000	0.000	0.000	0.000
109	A	259	PHE	0	0.041	0.020	35.608	0.000	0.000	0.000	0.000	0.000	0.000
110	A	260	SER	0	-0.034	-0.011	32.591	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	261	VAL	0	0.025	0.009	30.409	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	262	GLY	0	0.040	0.013	27.087	0.005	0.005	0.000	0.000	0.000	0.000
113	A	263	HIS	0	-0.021	0.001	23.580	0.007	0.007	0.000	0.000	0.000	0.000
114	A	264	PHE	0	0.056	0.011	18.759	0.017	0.017	0.000	0.000	0.000	0.000
115	A	265	GLU	-1	-0.962	-0.976	19.129	-0.264	-0.264	0.000	0.000	0.000	0.000
116	A	266	LEU	0	0.027	0.008	12.044	0.002	0.002	0.000	0.000	0.000	0.000
117	A	267	ARG	1	0.922	0.961	15.504	0.327	0.327	0.000	0.000	0.000	0.000
118	A	268	TYR	0	-0.017	-0.027	6.831	0.020	0.020	0.000	0.000	0.000	0.000
119	A	269	ILE	0	-0.079	-0.047	11.819	0.078	0.078	0.000	0.000	0.000	0.000
120	A	270	PRO	0	0.017	0.014	10.095	-0.038	-0.038	0.000	0.000	0.000	0.000
121	A	271	ASP	-1	-0.884	-0.926	10.576	0.041	0.041	0.000	0.000	0.000	0.000
122	A	306	LEU	0	0.061	0.021	7.013	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	307	ASP	-1	-0.764	-0.827	10.575	-0.472	-0.472	0.000	0.000	0.000	0.000
124	A	308	THR	0	-0.084	-0.031	11.631	-0.029	-0.029	0.000	0.000	0.000	0.000
125	A	309	VAL	0	-0.014	-0.012	13.816	-0.063	-0.063	0.000	0.000	0.000	0.000
126	A	310	ILE	0	0.052	0.022	11.828	0.026	0.026	0.000	0.000	0.000	0.000
127	A	311	LYS	1	0.890	0.967	15.366	0.246	0.246	0.000	0.000	0.000	0.000
128	A	312	VAL	0	0.070	0.026	17.455	0.006	0.006	0.000	0.000	0.000	0.000
129	A	313	SER	0	-0.044	-0.014	19.828	0.020	0.020	0.000	0.000	0.000	0.000
130	A	314	VAL	0	0.038	-0.005	23.040	0.007	0.007	0.000	0.000	0.000	0.000
131	A	315	ALA	0	-0.035	-0.015	24.642	0.009	0.009	0.000	0.000	0.000	0.000
132	A	316	ASP	-1	-0.883	-0.955	25.020	-0.112	-0.112	0.000	0.000	0.000	0.000
133	A	317	TRP	0	-0.013	0.000	22.488	0.001	0.001	0.000	0.000	0.000	0.000
134	A	318	LYS	1	0.879	0.961	20.120	0.131	0.131	0.000	0.000	0.000	0.000
135	A	319	VAL	0	-0.004	-0.010	13.803	-0.015	-0.015	0.000	0.000	0.000	0.000
136	A	320	MET	0	-0.023	-0.011	16.081	0.008	0.008	0.000	0.000	0.000	0.000
137	A	321	ALA	0	0.079	0.054	13.417	-0.047	-0.047	0.000	0.000	0.000	0.000
138	A	322	PHE	0	-0.030	-0.016	15.331	0.055	0.055	0.000	0.000	0.000	0.000
139	A	323	SER	0	0.061	0.019	16.044	-0.012	-0.012	0.000	0.000	0.000	0.000
140	A	324	ARG	1	0.794	0.846	16.354	0.255	0.255	0.000	0.000	0.000	0.000
141	A	325	LYS	1	0.891	0.965	20.720	0.106	0.106	0.000	0.000	0.000	0.000
142	A	326	GLY	0	0.051	0.008	24.516	0.011	0.011	0.000	0.000	0.000	0.000
143	A	327	GLY	0	0.018	0.007	21.707	-0.018	-0.018	0.000	0.000	0.000	0.000
144	A	328	ARG	1	0.788	0.877	18.003	0.129	0.129	0.000	0.000	0.000	0.000
145	A	329	LEU	0	0.026	0.006	19.218	-0.017	-0.017	0.000	0.000	0.000	0.000
146	A	330	GLU	-1	-0.829	-0.881	14.911	-0.115	-0.115	0.000	0.000	0.000	0.000
147	A	331	TRP	0	0.043	0.029	10.439	0.037	0.037	0.000	0.000	0.000	0.000
148	A	332	GLU	-1	-0.930	-0.982	16.080	-0.182	-0.182	0.000	0.000	0.000	0.000
149	A	333	TYR	0	0.011	0.017	13.746	0.028	0.028	0.000	0.000	0.000	0.000
150	A	334	GLN	0	0.028	0.019	16.610	-0.015	-0.015	0.000	0.000	0.000	0.000
151	A	335	PHE	0	0.027	0.015	14.994	0.010	0.010	0.000	0.000	0.000	0.000
152	A	336	CYS	0	-0.075	-0.042	20.681	0.008	0.008	0.000	0.000	0.000	0.000
153	A	337	THR	0	-0.011	-0.018	22.012	0.011	0.011	0.000	0.000	0.000	0.000
154	A	338	PRO	0	0.032	0.024	22.912	-0.015	-0.015	0.000	0.000	0.000	0.000
155	A	339	ILE	0	0.023	0.013	18.633	-0.003	-0.003	0.000	0.000	0.000	0.000
156	A	340	ALA	0	-0.051	-0.020	21.311	0.010	0.010	0.000	0.000	0.000	0.000
157	A	341	SER	0	-0.082	-0.054	19.451	0.007	0.007	0.000	0.000	0.000	0.000
158	A	342	ALA	0	0.057	0.037	15.528	-0.005	-0.005	0.000	0.000	0.000	0.000
159	A	343	TRP	0	-0.042	-0.016	13.216	0.026	0.026	0.000	0.000	0.000	0.000
160	A	344	LEU	0	-0.012	0.000	9.451	-0.014	-0.014	0.000	0.000	0.000	0.000
161	A	345	VAL	0	-0.016	-0.010	7.420	0.161	0.161	0.000	0.000	0.000	0.000
162	A	346	ARG	1	0.882	0.918	6.235	0.960	0.960	0.000	0.000	0.000	0.000
163	A	347	ASP	-1	-0.783	-0.896	5.601	-2.001	-2.001	0.000	0.000	0.000	0.000
164	A	348	GLY	0	0.055	0.036	6.203	-0.250	-0.250	0.000	0.000	0.000	0.000
165	A	349	LYS	1	0.823	0.938	8.788	1.540	1.540	0.000	0.000	0.000	0.000
166	A	350	VAL	0	-0.032	-0.028	10.863	-0.185	-0.185	0.000	0.000	0.000	0.000
167	A	351	ILE	0	-0.027	-0.006	13.146	0.113	0.113	0.000	0.000	0.000	0.000
168	A	352	PRO	0	0.041	0.007	14.601	-0.055	-0.055	0.000	0.000	0.000	0.000
169	A	353	ILE	0	0.011	0.007	13.112	0.036	0.036	0.000	0.000	0.000	0.000
170	A	354	SER	0	-0.020	-0.004	17.208	0.041	0.041	0.000	0.000	0.000	0.000
171	A	355	LEU	0	0.011	-0.001	20.934	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:103:ALA)