FMO DATABASE

FMODB ID: 526YZ

Calculation Name: 4YMR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YMR

Chain ID: A

ChEMBL ID:

UniProt ID: Q3UR97

Base Structure: X-ray

Registration Date: 2023-09-19

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	134
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1025930.891541
FMO2-HF: Nuclear repulsion	974585.267591
FMO2-HF: Total energy	-51345.62395
FMO2-MP2: Total energy	-51496.908646

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:230:VAL)

Summations of interaction energy for fragment #1(A:230:VAL)

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.
-10.765	-8.668	18.709	-7.647	-13.159	-0.048

Interaction energy analysis for fragmet #1(A:230:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.070 / q_NPA : 0.038

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	232	PRO	0	-0.025	-0.016	2.522	-2.093	1.466	0.247	-1.739	-2.067	0.006
4	A	233	GLU	-1	-0.856	-0.925	3.496	-0.472	0.494	0.025	-0.236	-0.754	0.000
5	A	234	LEU	0	0.016	0.010	2.515	-0.768	0.573	0.687	-0.424	-1.604	0.000
6	A	235	ARG	1	0.882	0.947	5.230	1.889	2.016	-0.001	-0.007	-0.119	0.000
7	A	236	ARG	1	0.896	0.945	8.332	0.649	0.649	0.000	0.000	0.000	0.000
8	A	237	ALA	0	0.051	0.023	7.564	0.160	0.160	0.000	0.000	0.000	0.000
9	A	238	GLN	0	0.019	0.017	9.065	0.066	0.066	0.000	0.000	0.000	0.000
10	A	239	SER	0	-0.061	-0.028	10.872	0.095	0.095	0.000	0.000	0.000	0.000
11	A	240	LEU	0	-0.003	-0.007	12.073	0.054	0.054	0.000	0.000	0.000	0.000
12	A	241	THR	0	0.014	-0.013	12.151	0.057	0.057	0.000	0.000	0.000	0.000
13	A	242	CYS	0	-0.087	-0.039	14.490	0.031	0.031	0.000	0.000	0.000	0.000
14	A	243	THR	0	-0.063	-0.031	16.992	0.027	0.027	0.000	0.000	0.000	0.000
15	A	244	GLY	0	0.051	0.039	18.012	0.021	0.021	0.000	0.000	0.000	0.000
16	A	245	LEU	0	-0.059	-0.020	17.001	0.022	0.022	0.000	0.000	0.000	0.000
17	A	246	TYR	0	0.010	-0.034	16.132	-0.026	-0.026	0.000	0.000	0.000	0.000
18	A	247	ARG	1	0.960	0.981	15.490	0.048	0.048	0.000	0.000	0.000	0.000
19	A	248	GLU	-1	-0.856	-0.918	14.276	-0.240	-0.240	0.000	0.000	0.000	0.000
20	A	249	ALA	0	-0.003	-0.006	11.966	-0.020	-0.020	0.000	0.000	0.000	0.000
21	A	250	LEU	0	-0.012	0.000	10.733	-0.029	-0.029	0.000	0.000	0.000	0.000
22	A	251	ALA	0	0.030	0.007	10.691	0.017	0.017	0.000	0.000	0.000	0.000
23	A	252	LEU	0	-0.019	-0.002	7.716	0.035	0.035	0.000	0.000	0.000	0.000
24	A	253	TRP	0	0.025	0.005	6.096	-0.063	-0.063	0.000	0.000	0.000	0.000
25	A	254	ALA	0	-0.009	0.007	6.715	0.085	0.085	0.000	0.000	0.000	0.000
26	A	255	ASN	0	-0.006	-0.001	6.210	0.132	0.132	0.000	0.000	0.000	0.000
27	A	256	ALA	0	0.043	0.020	2.424	-0.101	-0.091	1.963	-0.669	-1.305	0.000
28	A	257	TRP	0	-0.013	0.000	3.022	-0.549	-0.075	0.198	0.142	-0.814	-0.008
29	A	258	GLN	0	-0.030	-0.024	5.623	-0.023	-0.023	0.000	0.000	0.000	0.000
30	A	259	LEU	0	-0.021	-0.019	2.635	-1.003	0.120	0.419	-0.343	-1.200	-0.003
31	A	260	GLN	0	-0.052	-0.058	2.211	-1.096	-0.035	1.456	-0.693	-1.824	-0.005
32	A	261	THR	0	-0.019	0.007	4.755	-0.016	0.009	-0.001	-0.013	-0.011	0.000
33	A	262	GLN	0	-0.021	-0.008	8.063	-0.071	-0.071	0.000	0.000	0.000	0.000
34	A	263	LEU	0	-0.047	-0.012	6.382	-0.086	-0.086	0.000	0.000	0.000	0.000
35	A	264	GLY	0	0.042	0.008	6.700	0.278	0.278	0.000	0.000	0.000	0.000
36	A	265	THR	0	-0.058	-0.018	8.354	-0.140	-0.140	0.000	0.000	0.000	0.000
37	A	266	PRO	0	-0.070	-0.009	6.770	-0.040	-0.040	0.000	0.000	0.000	0.000
38	A	267	SER	0	0.076	0.027	6.381	0.093	0.093	0.000	0.000	0.000	0.000
39	A	268	GLY	0	0.000	-0.016	8.166	-0.054	-0.054	0.000	0.000	0.000	0.000
40	A	269	PRO	0	-0.036	-0.030	8.173	0.003	0.003	0.000	0.000	0.000	0.000
41	A	270	ASP	-1	-0.841	-0.919	9.553	-0.061	-0.061	0.000	0.000	0.000	0.000
42	A	271	ARG	1	0.854	0.908	3.273	-0.515	-0.140	0.021	-0.067	-0.329	0.000
43	A	272	PRO	0	0.033	0.042	6.230	-0.058	-0.058	0.000	0.000	0.000	0.000
44	A	273	LEU	0	0.019	0.014	7.771	-0.023	-0.023	0.000	0.000	0.000	0.000
45	A	274	LEU	0	-0.002	0.010	6.988	-0.017	-0.017	0.000	0.000	0.000	0.000
46	A	275	THR	0	-0.007	-0.021	5.364	-0.046	-0.046	0.000	0.000	0.000	0.000
47	A	276	LEU	0	-0.027	-0.009	7.503	0.003	0.003	0.000	0.000	0.000	0.000
48	A	277	ALA	0	-0.004	0.005	10.972	0.005	0.005	0.000	0.000	0.000	0.000
49	A	278	GLY	0	0.030	0.014	10.186	0.000	0.000	0.000	0.000	0.000	0.000
50	A	279	LEU	0	0.001	-0.013	9.465	0.012	0.012	0.000	0.000	0.000	0.000
51	A	280	ALA	0	0.007	0.005	12.312	0.011	0.011	0.000	0.000	0.000	0.000
52	A	281	VAL	0	0.017	0.010	14.896	0.008	0.008	0.000	0.000	0.000	0.000
53	A	282	CYS	0	-0.040	-0.014	13.379	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	283	HIS	0	-0.033	-0.048	15.139	0.015	0.015	0.000	0.000	0.000	0.000
55	A	284	GLN	0	-0.041	-0.016	17.834	0.007	0.007	0.000	0.000	0.000	0.000
56	A	285	GLU	-1	-0.872	-0.914	19.259	-0.097	-0.097	0.000	0.000	0.000	0.000
57	A	286	LEU	0	-0.119	-0.046	17.440	0.001	0.001	0.000	0.000	0.000	0.000
58	A	287	GLU	-1	-0.951	-0.956	21.458	-0.031	-0.031	0.000	0.000	0.000	0.000
59	A	288	ASP	-1	-0.880	-0.942	19.545	-0.020	-0.020	0.000	0.000	0.000	0.000
60	A	289	PRO	0	0.029	-0.002	20.789	0.000	0.000	0.000	0.000	0.000	0.000
61	A	290	GLY	0	-0.032	-0.018	22.247	0.002	0.002	0.000	0.000	0.000	0.000
62	A	291	GLU	-1	-0.879	-0.949	17.446	0.033	0.033	0.000	0.000	0.000	0.000
63	A	292	ALA	0	0.026	0.023	17.420	0.002	0.002	0.000	0.000	0.000	0.000
64	A	293	ARG	1	0.936	0.971	18.397	-0.008	-0.008	0.000	0.000	0.000	0.000
65	A	294	ALA	0	-0.001	0.000	17.837	0.004	0.004	0.000	0.000	0.000	0.000
66	A	295	CYS	0	-0.031	-0.014	14.273	0.009	0.009	0.000	0.000	0.000	0.000
67	A	296	SER	0	-0.011	-0.015	15.334	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	297	GLU	-1	-0.899	-0.930	17.894	0.034	0.034	0.000	0.000	0.000	0.000
69	A	298	LYS	1	0.922	0.967	13.301	-0.101	-0.101	0.000	0.000	0.000	0.000
70	A	299	ALA	0	0.027	0.004	14.453	0.009	0.009	0.000	0.000	0.000	0.000
71	A	300	LEU	0	0.018	0.003	15.356	0.002	0.002	0.000	0.000	0.000	0.000
72	A	301	GLN	0	-0.031	-0.022	17.400	0.016	0.016	0.000	0.000	0.000	0.000
73	A	302	LEU	0	-0.081	-0.050	11.633	0.009	0.009	0.000	0.000	0.000	0.000
74	A	303	LEU	0	-0.035	-0.024	15.928	0.001	0.001	0.000	0.000	0.000	0.000
75	A	304	GLY	0	0.001	0.016	17.848	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	305	ASP	-1	-0.818	-0.879	17.870	0.089	0.089	0.000	0.000	0.000	0.000
77	A	306	LYS	1	0.916	0.960	19.428	-0.058	-0.058	0.000	0.000	0.000	0.000
78	A	307	ARG	1	0.821	0.876	14.133	-0.100	-0.100	0.000	0.000	0.000	0.000
79	A	308	PRO	0	-0.010	-0.003	17.020	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	309	HIS	0	0.082	0.049	12.966	0.006	0.006	0.000	0.000	0.000	0.000
81	A	310	PRO	0	-0.001	-0.001	11.301	-0.008	-0.008	0.000	0.000	0.000	0.000
82	A	311	PHE	0	0.037	-0.003	12.576	0.001	0.001	0.000	0.000	0.000	0.000
83	A	312	LEU	0	0.002	0.015	16.765	-0.011	-0.011	0.000	0.000	0.000	0.000
84	A	313	ALA	0	0.046	0.014	19.339	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	314	PRO	0	-0.016	0.000	17.495	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	315	PHE	0	0.025	-0.002	18.793	-0.008	-0.008	0.000	0.000	0.000	0.000
87	A	316	LEU	0	-0.021	0.015	22.610	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	317	GLU	-1	-0.761	-0.854	24.106	0.051	0.051	0.000	0.000	0.000	0.000
89	A	318	ALA	0	-0.064	-0.035	24.087	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	319	HIS	0	0.039	0.038	26.031	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	320	VAL	0	0.033	0.026	28.340	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	321	ARG	1	0.819	0.884	27.437	-0.048	-0.048	0.000	0.000	0.000	0.000
93	A	322	LEU	0	-0.042	-0.042	27.690	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	323	SER	0	0.006	0.000	31.455	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	324	TRP	0	0.000	0.020	34.067	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	325	ARG	1	0.886	0.946	34.080	-0.009	-0.009	0.000	0.000	0.000	0.000
97	A	326	LEU	0	-0.022	-0.014	34.105	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	327	GLY	0	-0.005	0.016	37.489	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	328	LEU	0	-0.043	-0.027	35.682	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	329	ASP	-1	-0.813	-0.897	37.502	0.016	0.016	0.000	0.000	0.000	0.000
101	A	330	LYS	1	0.839	0.908	34.069	-0.027	-0.027	0.000	0.000	0.000	0.000
102	A	331	ARG	1	0.898	0.912	33.467	-0.011	-0.011	0.000	0.000	0.000	0.000
103	A	332	GLN	0	0.003	0.008	32.547	0.002	0.002	0.000	0.000	0.000	0.000
104	A	333	SER	0	-0.013	-0.041	29.176	0.001	0.001	0.000	0.000	0.000	0.000
105	A	334	GLU	-1	-0.808	-0.887	29.111	0.034	0.034	0.000	0.000	0.000	0.000
106	A	335	ALA	0	0.008	0.009	30.505	0.004	0.004	0.000	0.000	0.000	0.000
107	A	336	GLN	0	-0.009	-0.002	25.690	0.003	0.003	0.000	0.000	0.000	0.000
108	A	337	LEU	0	0.030	0.005	24.598	0.004	0.004	0.000	0.000	0.000	0.000
109	A	338	GLN	0	-0.036	-0.031	27.141	0.005	0.005	0.000	0.000	0.000	0.000
110	A	339	ALA	0	0.033	0.031	28.541	0.000	0.000	0.000	0.000	0.000	0.000
111	A	340	LEU	0	-0.017	-0.023	22.004	0.003	0.003	0.000	0.000	0.000	0.000
112	A	341	GLN	0	-0.013	0.001	24.338	0.011	0.011	0.000	0.000	0.000	0.000
113	A	342	GLU	-1	-0.950	-0.969	26.460	0.053	0.053	0.000	0.000	0.000	0.000
114	A	343	ALA	0	-0.036	-0.013	26.243	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	344	GLY	0	-0.030	-0.013	24.337	0.003	0.003	0.000	0.000	0.000	0.000
116	A	345	LEU	0	-0.066	-0.032	20.600	0.009	0.009	0.000	0.000	0.000	0.000
117	A	346	THR	0	-0.016	-0.013	19.523	0.013	0.013	0.000	0.000	0.000	0.000
118	A	347	SER	0	-0.030	-0.018	21.001	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	348	THR	0	0.042	-0.004	22.858	-0.010	-0.010	0.000	0.000	0.000	0.000
120	A	349	PRO	0	-0.026	-0.021	25.252	0.004	0.004	0.000	0.000	0.000	0.000
121	A	350	PRO	0	0.000	0.059	21.897	0.011	0.011	0.000	0.000	0.000	0.000
122	A	351	PRO	0	0.049	0.027	17.452	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	352	SER	0	0.000	0.000	19.669	-0.020	-0.020	0.000	0.000	0.000	0.000
124	A	353	LEU	0	0.035	0.000	18.491	0.011	0.011	0.000	0.000	0.000	0.000
125	A	354	LYS	1	0.964	0.975	17.934	-0.049	-0.049	0.000	0.000	0.000	0.000
126	A	355	GLU	-1	-0.823	-0.894	16.374	0.188	0.188	0.000	0.000	0.000	0.000
127	A	356	LEU	0	0.033	0.004	13.637	0.025	0.025	0.000	0.000	0.000	0.000
128	A	357	LEU	0	-0.059	-0.017	13.081	0.003	0.003	0.000	0.000	0.000	0.000
129	A	358	ILE	0	-0.051	-0.033	13.748	-0.017	-0.017	0.000	0.000	0.000	0.000
130	A	359	LYS	1	0.839	0.903	11.720	-0.262	-0.262	0.000	0.000	0.000	0.000
131	A	360	GLU	-1	-0.841	-0.880	7.493	0.213	0.213	0.000	0.000	0.000	0.000
132	A	361	VAL	0	0.000	0.002	4.788	-0.169	-0.094	-0.001	-0.002	-0.071	0.000
133	A	362	LEU	0	-0.046	-0.025	6.689	-0.207	-0.207	0.000	0.000	0.000	0.000
134	A	363	ASP	-1	-0.810	-0.896	1.881	-6.526	-13.565	13.696	-3.596	-3.061	-0.038

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Interactive mode: IFIE and PIEDA for fragment #1(A:230:VAL)