FMO DATABASE

FMODB ID: YZGZ2

Calculation Name: 1R62-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1R62

Chain ID: A

ChEMBL ID:

UniProt ID: P0AFB5

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	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	136
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1233895.154268
FMO2-HF: Nuclear repulsion	1181275.359741
FMO2-HF: Total energy	-52619.794527
FMO2-MP2: Total energy	-52777.020395

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:194:ARG)

Summations of interaction energy for fragment #1(A:194:ARG)

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.
-72.284	-71.028	9.343	-5.556	-5.043	-0.056

Interaction energy analysis for fragmet #1(A:194:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.909 / q_NPA : 0.949

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	196	THR	0	-0.027	-0.016	3.895	3.679	5.242	-0.014	-0.777	-0.773	0.001
4	A	197	GLU	-1	-0.815	-0.890	6.701	-27.088	-27.088	0.000	0.000	0.000	0.000
5	A	198	SER	0	0.014	-0.007	8.552	0.829	0.829	0.000	0.000	0.000	0.000
6	A	199	ILE	0	0.042	0.023	8.969	-0.050	-0.050	0.000	0.000	0.000	0.000
7	A	200	HIS	0	0.062	0.045	11.196	0.860	0.860	0.000	0.000	0.000	0.000
8	A	201	LYS	1	0.768	0.863	11.026	23.591	23.591	0.000	0.000	0.000	0.000
9	A	202	VAL	0	0.006	0.018	8.827	0.089	0.089	0.000	0.000	0.000	0.000
10	A	203	ALA	0	0.014	0.006	11.967	0.813	0.813	0.000	0.000	0.000	0.000
11	A	204	GLU	-1	-0.748	-0.829	15.307	-12.801	-12.801	0.000	0.000	0.000	0.000
12	A	205	ARG	1	0.766	0.879	9.706	22.145	22.145	0.000	0.000	0.000	0.000
13	A	206	VAL	0	0.023	0.012	14.480	0.599	0.599	0.000	0.000	0.000	0.000
14	A	207	VAL	0	-0.001	-0.002	17.107	0.655	0.655	0.000	0.000	0.000	0.000
15	A	208	THR	0	-0.039	-0.030	19.498	0.704	0.704	0.000	0.000	0.000	0.000
16	A	209	LEU	0	-0.040	-0.006	16.727	0.560	0.560	0.000	0.000	0.000	0.000
17	A	210	VAL	0	0.053	0.009	20.403	0.463	0.463	0.000	0.000	0.000	0.000
18	A	211	SER	0	-0.083	-0.048	22.723	0.598	0.598	0.000	0.000	0.000	0.000
19	A	212	MET	0	-0.049	-0.021	22.620	0.404	0.404	0.000	0.000	0.000	0.000
20	A	213	GLU	-1	-0.841	-0.882	22.952	-11.734	-11.734	0.000	0.000	0.000	0.000
21	A	214	LEU	0	-0.035	-0.010	26.008	0.076	0.076	0.000	0.000	0.000	0.000
22	A	215	PRO	0	0.007	0.006	28.680	0.152	0.152	0.000	0.000	0.000	0.000
23	A	216	ASP	-1	-0.914	-0.952	32.382	-8.221	-8.221	0.000	0.000	0.000	0.000
24	A	217	ASN	0	-0.093	-0.040	34.908	-0.043	-0.043	0.000	0.000	0.000	0.000
25	A	218	VAL	0	0.005	0.006	28.949	0.012	0.012	0.000	0.000	0.000	0.000
26	A	219	ARG	1	0.798	0.877	30.074	8.655	8.655	0.000	0.000	0.000	0.000
27	A	220	LEU	0	0.029	0.007	22.451	-0.132	-0.132	0.000	0.000	0.000	0.000
28	A	221	ILE	0	-0.046	-0.015	26.064	-0.024	-0.024	0.000	0.000	0.000	0.000
29	A	222	ARG	1	0.820	0.878	21.150	11.979	11.979	0.000	0.000	0.000	0.000
30	A	223	ASP	-1	-0.780	-0.864	22.465	-10.591	-10.591	0.000	0.000	0.000	0.000
31	A	224	TYR	0	-0.022	-0.047	18.963	-0.345	-0.345	0.000	0.000	0.000	0.000
32	A	225	ASP	-1	-0.734	-0.824	19.225	-12.939	-12.939	0.000	0.000	0.000	0.000
33	A	226	PRO	0	-0.039	-0.037	18.900	-0.716	-0.716	0.000	0.000	0.000	0.000
34	A	227	SER	0	-0.092	-0.059	19.892	-0.252	-0.252	0.000	0.000	0.000	0.000
35	A	228	LEU	0	-0.020	0.001	14.367	-0.450	-0.450	0.000	0.000	0.000	0.000
36	A	229	PRO	0	-0.056	-0.032	13.597	-0.545	-0.545	0.000	0.000	0.000	0.000
37	A	230	GLU	-1	-0.799	-0.876	10.396	-22.729	-22.729	0.000	0.000	0.000	0.000
38	A	231	LEU	0	-0.035	-0.022	7.805	0.008	0.008	0.000	0.000	0.000	0.000
39	A	232	ALA	0	-0.024	-0.010	4.656	-1.821	-1.748	-0.001	-0.022	-0.050	0.000
40	A	233	HIS	0	-0.020	-0.025	3.418	3.576	4.405	0.041	-0.287	-0.583	0.000
41	A	234	ASP	-1	-0.815	-0.904	1.926	-51.423	-52.959	9.310	-4.400	-3.374	-0.057
42	A	235	PRO	0	0.005	-0.027	3.665	4.311	4.540	0.008	-0.067	-0.169	0.000
43	A	236	ASP	-1	-0.776	-0.866	6.843	-22.543	-22.543	0.000	0.000	0.000	0.000
44	A	237	GLN	0	-0.059	-0.032	7.031	3.079	3.079	0.000	0.000	0.000	0.000
45	A	238	ILE	0	0.005	-0.008	7.136	2.299	2.299	0.000	0.000	0.000	0.000
46	A	239	GLU	-1	-0.826	-0.906	9.730	-16.593	-16.593	0.000	0.000	0.000	0.000
47	A	240	GLN	0	0.023	0.017	11.996	2.228	2.228	0.000	0.000	0.000	0.000
48	A	241	VAL	0	-0.043	-0.017	11.485	1.240	1.240	0.000	0.000	0.000	0.000
49	A	242	LEU	0	0.014	0.003	13.467	1.097	1.097	0.000	0.000	0.000	0.000
50	A	243	LEU	0	0.012	0.015	15.846	0.922	0.922	0.000	0.000	0.000	0.000
51	A	244	ASN	0	-0.080	-0.048	16.907	1.412	1.412	0.000	0.000	0.000	0.000
52	A	245	ILE	0	-0.011	-0.002	16.950	0.600	0.600	0.000	0.000	0.000	0.000
53	A	246	VAL	0	0.023	0.012	19.710	0.552	0.552	0.000	0.000	0.000	0.000
54	A	247	ARG	1	0.831	0.882	19.716	13.256	13.256	0.000	0.000	0.000	0.000
55	A	248	ASN	0	-0.078	-0.048	23.003	0.277	0.277	0.000	0.000	0.000	0.000
56	A	249	ALA	0	0.037	0.030	24.272	0.389	0.389	0.000	0.000	0.000	0.000
57	A	250	LEU	0	-0.004	-0.004	25.305	0.372	0.372	0.000	0.000	0.000	0.000
58	A	251	GLN	0	-0.061	-0.039	27.541	0.450	0.450	0.000	0.000	0.000	0.000
59	A	252	ALA	0	-0.054	-0.010	28.812	0.269	0.269	0.000	0.000	0.000	0.000
60	A	253	LEU	0	-0.022	0.002	29.599	0.264	0.264	0.000	0.000	0.000	0.000
61	A	254	GLY	0	0.014	0.012	31.941	0.295	0.295	0.000	0.000	0.000	0.000
62	A	255	PRO	0	-0.044	-0.047	33.884	-0.026	-0.026	0.000	0.000	0.000	0.000
63	A	256	GLU	-1	-0.923	-0.953	36.863	-7.126	-7.126	0.000	0.000	0.000	0.000
64	A	257	GLY	0	-0.007	0.009	33.579	0.069	0.069	0.000	0.000	0.000	0.000
65	A	258	GLY	0	-0.006	-0.029	33.628	0.089	0.089	0.000	0.000	0.000	0.000
66	A	259	GLU	-1	-0.853	-0.890	29.295	-9.174	-9.174	0.000	0.000	0.000	0.000
67	A	260	ILE	0	0.019	0.006	24.143	-0.057	-0.057	0.000	0.000	0.000	0.000
68	A	261	ILE	0	-0.010	-0.009	24.536	-0.062	-0.062	0.000	0.000	0.000	0.000
69	A	262	LEU	0	0.006	0.013	17.549	-0.273	-0.273	0.000	0.000	0.000	0.000
70	A	263	ARG	1	0.767	0.854	20.924	10.990	10.990	0.000	0.000	0.000	0.000
71	A	264	THR	0	-0.043	-0.052	16.051	-0.417	-0.417	0.000	0.000	0.000	0.000
72	A	265	ARG	1	0.810	0.873	18.153	12.324	12.324	0.000	0.000	0.000	0.000
73	A	266	THR	0	-0.007	-0.014	17.679	-0.911	-0.911	0.000	0.000	0.000	0.000
74	A	267	ALA	0	-0.037	-0.013	17.728	0.768	0.768	0.000	0.000	0.000	0.000
75	A	268	PHE	0	0.020	-0.014	18.852	-0.576	-0.576	0.000	0.000	0.000	0.000
76	A	269	GLN	0	-0.062	-0.041	21.077	0.544	0.544	0.000	0.000	0.000	0.000
77	A	270	LEU	0	0.064	0.059	16.861	0.530	0.530	0.000	0.000	0.000	0.000
78	A	271	THR	0	-0.011	-0.019	19.580	-0.498	-0.498	0.000	0.000	0.000	0.000
79	A	272	LEU	0	-0.007	-0.004	14.212	0.148	0.148	0.000	0.000	0.000	0.000
80	A	273	HIS	0	0.006	-0.004	14.801	0.573	0.573	0.000	0.000	0.000	0.000
81	A	274	GLY	0	0.019	0.023	18.803	0.079	0.079	0.000	0.000	0.000	0.000
82	A	275	GLU	-1	-0.812	-0.867	17.271	-16.068	-16.068	0.000	0.000	0.000	0.000
83	A	276	ARG	1	0.885	0.935	20.269	11.785	11.785	0.000	0.000	0.000	0.000
84	A	277	TYR	0	-0.014	-0.019	13.650	-0.638	-0.638	0.000	0.000	0.000	0.000
85	A	278	ARG	1	0.892	0.915	18.256	15.195	15.195	0.000	0.000	0.000	0.000
86	A	279	LEU	0	0.004	0.003	16.230	0.584	0.584	0.000	0.000	0.000	0.000
87	A	280	ALA	0	0.045	0.026	14.188	-1.034	-1.034	0.000	0.000	0.000	0.000
88	A	281	ALA	0	0.043	0.028	12.844	0.621	0.621	0.000	0.000	0.000	0.000
89	A	282	ARG	1	0.771	0.868	14.759	11.797	11.797	0.000	0.000	0.000	0.000
90	A	283	ILE	0	-0.018	-0.023	12.912	-0.064	-0.064	0.000	0.000	0.000	0.000
91	A	284	ASP	-1	-0.755	-0.835	16.858	-12.384	-12.384	0.000	0.000	0.000	0.000
92	A	285	VAL	0	-0.002	-0.003	19.193	-0.178	-0.178	0.000	0.000	0.000	0.000
93	A	286	GLU	-1	-0.814	-0.887	21.821	-9.626	-9.626	0.000	0.000	0.000	0.000
94	A	287	ASP	-1	-0.817	-0.900	25.512	-10.004	-10.004	0.000	0.000	0.000	0.000
95	A	288	ASN	0	-0.035	-0.025	28.369	0.376	0.376	0.000	0.000	0.000	0.000
96	A	289	GLY	0	0.081	0.032	31.983	-0.007	-0.007	0.000	0.000	0.000	0.000
97	A	290	PRO	0	-0.022	-0.001	34.790	0.047	0.047	0.000	0.000	0.000	0.000
98	A	291	GLY	0	0.014	0.022	36.950	0.115	0.115	0.000	0.000	0.000	0.000
99	A	292	ILE	0	-0.070	-0.032	32.771	-0.360	-0.360	0.000	0.000	0.000	0.000
100	A	313	GLY	0	0.111	0.054	24.988	0.208	0.208	0.000	0.000	0.000	0.000
101	A	314	LEU	0	-0.026	-0.018	21.136	-0.345	-0.345	0.000	0.000	0.000	0.000
102	A	315	GLY	0	0.082	0.044	19.916	-0.509	-0.509	0.000	0.000	0.000	0.000
103	A	316	LEU	0	0.032	0.017	18.807	-0.669	-0.669	0.000	0.000	0.000	0.000
104	A	317	SER	0	-0.072	-0.045	19.127	-0.254	-0.254	0.000	0.000	0.000	0.000
105	A	318	ILE	0	-0.008	-0.006	15.065	-0.503	-0.503	0.000	0.000	0.000	0.000
106	A	319	ALA	0	0.020	0.012	14.706	-0.977	-0.977	0.000	0.000	0.000	0.000
107	A	320	ARG	1	0.976	0.977	14.324	11.707	11.707	0.000	0.000	0.000	0.000
108	A	321	ASN	0	0.031	0.029	13.996	-1.353	-1.353	0.000	0.000	0.000	0.000
109	A	322	LEU	0	0.014	0.004	10.132	-0.969	-0.969	0.000	0.000	0.000	0.000
110	A	323	ILE	0	-0.006	0.013	9.433	-1.849	-1.849	0.000	0.000	0.000	0.000
111	A	324	ASP	-1	-0.909	-0.960	11.213	-16.748	-16.748	0.000	0.000	0.000	0.000
112	A	325	GLN	0	-0.055	-0.029	8.138	-2.269	-2.269	0.000	0.000	0.000	0.000
113	A	326	HIS	0	-0.026	-0.011	5.303	-4.911	-4.813	-0.001	-0.003	-0.094	0.000
114	A	327	SER	0	-0.063	-0.028	8.056	0.335	0.335	0.000	0.000	0.000	0.000
115	A	328	GLY	0	0.023	0.011	11.405	0.775	0.775	0.000	0.000	0.000	0.000
116	A	329	LYS	1	0.783	0.897	12.790	14.002	14.002	0.000	0.000	0.000	0.000
117	A	330	ILE	0	0.003	-0.007	15.525	-0.298	-0.298	0.000	0.000	0.000	0.000
118	A	331	GLU	-1	-0.871	-0.895	18.318	-11.934	-11.934	0.000	0.000	0.000	0.000
119	A	332	PHE	0	0.004	-0.015	21.906	-0.177	-0.177	0.000	0.000	0.000	0.000
120	A	333	THR	0	-0.027	-0.002	24.773	0.344	0.344	0.000	0.000	0.000	0.000
121	A	334	SER	0	0.034	0.016	28.049	-0.084	-0.084	0.000	0.000	0.000	0.000
122	A	335	TRP	0	-0.039	-0.004	28.066	0.200	0.200	0.000	0.000	0.000	0.000
123	A	336	PRO	0	0.007	-0.015	34.048	-0.012	-0.012	0.000	0.000	0.000	0.000
124	A	337	GLY	0	0.014	0.024	35.866	-0.051	-0.051	0.000	0.000	0.000	0.000
125	A	338	HIS	1	0.835	0.911	30.375	8.645	8.645	0.000	0.000	0.000	0.000
126	A	339	THR	0	-0.065	-0.046	28.052	0.050	0.050	0.000	0.000	0.000	0.000
127	A	340	GLU	-1	-0.777	-0.887	23.927	-10.966	-10.966	0.000	0.000	0.000	0.000
128	A	341	PHE	0	0.002	0.010	20.741	-0.033	-0.033	0.000	0.000	0.000	0.000
129	A	342	SER	0	0.002	-0.023	19.878	-0.024	-0.024	0.000	0.000	0.000	0.000
130	A	343	VAL	0	0.000	0.003	13.425	-0.139	-0.139	0.000	0.000	0.000	0.000
131	A	344	TYR	0	-0.042	-0.053	14.922	0.210	0.210	0.000	0.000	0.000	0.000
132	A	345	LEU	0	0.033	0.019	8.629	-0.627	-0.627	0.000	0.000	0.000	0.000
133	A	346	PRO	0	0.020	0.016	9.857	1.029	1.029	0.000	0.000	0.000	0.000
134	A	347	ILE	0	0.008	0.015	10.320	-1.217	-1.217	0.000	0.000	0.000	0.000
135	A	348	ARG	1	0.914	0.942	12.138	17.595	17.595	0.000	0.000	0.000	0.000
136	A	349	LYS	1	0.861	0.947	14.354	19.664	19.664	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:194:ARG)