FMO DATABASE

FMODB ID: YY5N2

Calculation Name: 3R7G-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3R7G

Chain ID: A

ChEMBL ID:

UniProt ID: Q9NZ56

Base Structure: X-ray

Registration Date: 2023-06-20

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	154
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1542385.418834
FMO2-HF: Nuclear repulsion	1479149.070411
FMO2-HF: Total energy	-63236.348423
FMO2-MP2: Total energy	-63415.4307

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:37:ARG)

Summations of interaction energy for fragment #1(A:37: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.
-162.897	-170.292	45.215	-18.76	-19.057	-0.178

Interaction energy analysis for fragmet #1(A:37:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.863 / q_NPA : 0.900

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	39	ALA	0	0.014	0.004	2.474	3.493	8.186	0.316	-2.574	-2.435	0.004
4	A	40	LEU	0	0.008	0.019	1.799	-41.641	-45.185	17.985	-6.793	-7.648	-0.063
5	A	41	SER	0	-0.032	-0.047	3.040	17.391	17.224	0.022	0.711	-0.565	0.000
6	A	42	LEU	0	0.038	0.012	5.089	-0.357	-0.319	-0.001	-0.001	-0.035	0.000
7	A	43	GLU	-1	-0.745	-0.860	7.724	-25.948	-25.948	0.000	0.000	0.000	0.000
8	A	44	GLU	-1	-0.817	-0.841	1.733	-129.854	-139.886	26.828	-9.662	-7.134	-0.119
9	A	45	ILE	0	0.022	0.014	5.892	2.859	2.859	0.000	0.000	0.000	0.000
10	A	46	LEU	0	-0.005	0.005	8.215	2.130	2.130	0.000	0.000	0.000	0.000
11	A	47	ARG	1	0.817	0.890	8.448	31.158	31.158	0.000	0.000	0.000	0.000
12	A	48	LEU	0	-0.053	-0.026	5.540	1.297	1.297	0.000	0.000	0.000	0.000
13	A	49	TYR	0	-0.049	-0.059	9.882	1.092	1.092	0.000	0.000	0.000	0.000
14	A	50	ASN	0	-0.045	-0.003	12.726	1.475	1.475	0.000	0.000	0.000	0.000
15	A	51	GLN	0	-0.051	-0.026	14.597	2.182	2.182	0.000	0.000	0.000	0.000
16	A	52	PRO	0	0.003	0.018	15.136	-1.427	-1.427	0.000	0.000	0.000	0.000
17	A	53	ILE	0	-0.013	0.006	13.705	0.009	0.009	0.000	0.000	0.000	0.000
18	A	54	ASN	0	0.062	0.022	16.523	1.369	1.369	0.000	0.000	0.000	0.000
19	A	55	GLU	-1	-0.740	-0.860	19.173	-12.935	-12.935	0.000	0.000	0.000	0.000
20	A	56	GLU	-1	-0.804	-0.863	20.734	-13.677	-13.677	0.000	0.000	0.000	0.000
21	A	57	GLN	0	0.060	0.018	15.522	-0.152	-0.152	0.000	0.000	0.000	0.000
22	A	58	ALA	0	0.038	0.027	16.433	-0.877	-0.877	0.000	0.000	0.000	0.000
23	A	59	TRP	0	0.018	0.000	18.225	-0.218	-0.218	0.000	0.000	0.000	0.000
24	A	60	ALA	0	-0.014	-0.010	16.827	0.087	0.087	0.000	0.000	0.000	0.000
25	A	61	VAL	0	0.024	0.001	12.713	-0.360	-0.360	0.000	0.000	0.000	0.000
26	A	62	CYS	0	-0.006	0.013	15.193	0.014	0.014	0.000	0.000	0.000	0.000
27	A	63	TYR	0	0.021	0.007	18.191	0.607	0.607	0.000	0.000	0.000	0.000
28	A	64	GLN	0	-0.005	-0.025	15.142	1.377	1.377	0.000	0.000	0.000	0.000
29	A	65	CYS	0	-0.022	0.008	14.552	-0.329	-0.329	0.000	0.000	0.000	0.000
30	A	66	CYS	0	-0.037	-0.012	15.776	0.645	0.645	0.000	0.000	0.000	0.000
31	A	67	GLY	0	0.005	-0.016	19.156	0.718	0.718	0.000	0.000	0.000	0.000
32	A	68	SER	0	-0.015	-0.031	14.679	0.822	0.822	0.000	0.000	0.000	0.000
33	A	69	LEU	0	0.000	0.010	17.069	0.544	0.544	0.000	0.000	0.000	0.000
34	A	70	ARG	1	0.877	0.932	19.178	12.958	12.958	0.000	0.000	0.000	0.000
35	A	71	ALA	0	-0.046	-0.025	19.598	0.790	0.790	0.000	0.000	0.000	0.000
36	A	72	ALA	0	0.039	0.017	18.470	0.478	0.478	0.000	0.000	0.000	0.000
37	A	73	ALA	0	0.059	0.028	20.565	0.548	0.548	0.000	0.000	0.000	0.000
38	A	74	ARG	1	0.845	0.922	23.332	13.316	13.316	0.000	0.000	0.000	0.000
39	A	75	ARG	1	0.891	0.935	22.858	12.277	12.277	0.000	0.000	0.000	0.000
40	A	76	ARG	1	0.931	0.971	24.583	10.291	10.291	0.000	0.000	0.000	0.000
41	A	77	GLN	0	-0.001	0.009	20.003	-0.359	-0.359	0.000	0.000	0.000	0.000
42	A	78	PRO	0	0.004	-0.004	20.746	0.211	0.211	0.000	0.000	0.000	0.000
43	A	79	ARG	1	0.828	0.917	20.073	11.283	11.283	0.000	0.000	0.000	0.000
44	A	80	HIS	0	0.032	0.012	17.243	0.193	0.193	0.000	0.000	0.000	0.000
45	A	81	ARG	1	0.797	0.857	18.680	12.311	12.311	0.000	0.000	0.000	0.000
46	A	82	VAL	0	-0.018	-0.007	14.327	-0.773	-0.773	0.000	0.000	0.000	0.000
47	A	83	ARG	1	0.966	0.972	15.405	15.729	15.729	0.000	0.000	0.000	0.000
48	A	84	SER	0	0.044	0.002	11.535	0.384	0.384	0.000	0.000	0.000	0.000
49	A	85	ALA	0	0.086	0.034	10.671	-0.529	-0.529	0.000	0.000	0.000	0.000
50	A	86	ALA	0	0.017	0.024	7.547	-2.829	-2.829	0.000	0.000	0.000	0.000
51	A	87	GLN	0	-0.029	-0.018	7.903	-2.186	-2.186	0.000	0.000	0.000	0.000
52	A	88	ILE	0	0.010	0.020	9.877	-0.091	-0.091	0.000	0.000	0.000	0.000
53	A	89	ARG	1	0.848	0.914	4.843	34.140	34.140	0.000	0.000	0.000	0.000
54	A	90	VAL	0	0.046	0.022	6.255	4.978	4.978	0.000	0.000	0.000	0.000
55	A	91	TRP	0	-0.026	-0.023	6.298	-8.140	-8.140	0.000	0.000	0.000	0.000
56	A	92	ARG	1	0.886	0.932	3.006	39.797	40.354	0.025	-0.185	-0.396	0.001
57	A	93	ASP	-1	-0.836	-0.923	8.168	-21.188	-21.188	0.000	0.000	0.000	0.000
58	A	94	GLY	0	0.042	0.034	10.814	2.020	2.020	0.000	0.000	0.000	0.000
59	A	95	ALA	0	-0.022	0.001	11.913	1.313	1.313	0.000	0.000	0.000	0.000
60	A	96	VAL	0	0.018	-0.004	10.782	-2.286	-2.286	0.000	0.000	0.000	0.000
61	A	97	THR	0	-0.042	0.001	9.676	1.852	1.852	0.000	0.000	0.000	0.000
62	A	98	LEU	0	0.009	0.010	10.386	-2.091	-2.091	0.000	0.000	0.000	0.000
63	A	99	ALA	0	-0.019	0.002	9.466	0.943	0.943	0.000	0.000	0.000	0.000
64	A	100	PRO	0	0.014	-0.003	11.545	0.802	0.802	0.000	0.000	0.000	0.000
65	A	101	ALA	0	0.006	0.006	12.689	-1.729	-1.729	0.000	0.000	0.000	0.000
66	A	102	ALA	0	-0.015	-0.009	12.845	0.541	0.541	0.000	0.000	0.000	0.000
67	A	103	ASP	-1	-0.976	-0.981	14.603	-16.133	-16.133	0.000	0.000	0.000	0.000
68	A	119	GLN	0	0.038	0.000	27.953	-0.366	-0.366	0.000	0.000	0.000	0.000
69	A	120	CYS	0	-0.009	0.006	23.486	-0.381	-0.381	0.000	0.000	0.000	0.000
70	A	121	MET	0	0.007	0.026	25.934	0.038	0.038	0.000	0.000	0.000	0.000
71	A	122	GLU	-1	-0.829	-0.926	24.418	-12.452	-12.452	0.000	0.000	0.000	0.000
72	A	123	THR	0	0.072	0.019	24.421	-0.507	-0.507	0.000	0.000	0.000	0.000
73	A	124	GLU	-1	-0.696	-0.804	24.599	-11.811	-11.811	0.000	0.000	0.000	0.000
74	A	125	VAL	0	-0.048	-0.006	19.015	-0.475	-0.475	0.000	0.000	0.000	0.000
75	A	126	ILE	0	-0.037	-0.012	20.385	-0.668	-0.668	0.000	0.000	0.000	0.000
76	A	127	GLU	-1	-0.834	-0.885	22.231	-12.034	-12.034	0.000	0.000	0.000	0.000
77	A	128	SER	0	-0.043	-0.040	19.323	-0.556	-0.556	0.000	0.000	0.000	0.000
78	A	129	LEU	0	-0.024	-0.022	15.984	-0.768	-0.768	0.000	0.000	0.000	0.000
79	A	130	GLY	0	0.034	0.018	18.525	-0.546	-0.546	0.000	0.000	0.000	0.000
80	A	131	ILE	0	0.054	0.025	20.181	-0.202	-0.202	0.000	0.000	0.000	0.000
81	A	132	ILE	0	-0.045	-0.021	14.086	-0.501	-0.501	0.000	0.000	0.000	0.000
82	A	133	ILE	0	-0.038	-0.026	15.334	-1.017	-1.017	0.000	0.000	0.000	0.000
83	A	134	TYR	0	-0.030	-0.040	17.603	-0.503	-0.503	0.000	0.000	0.000	0.000
84	A	135	LYS	1	0.867	0.905	17.448	14.660	14.660	0.000	0.000	0.000	0.000
85	A	136	ALA	0	-0.060	-0.027	14.499	-0.618	-0.618	0.000	0.000	0.000	0.000
86	A	137	LEU	0	-0.045	-0.019	15.831	-0.262	-0.262	0.000	0.000	0.000	0.000
87	A	138	ASP	-1	-0.747	-0.865	19.291	-14.365	-14.365	0.000	0.000	0.000	0.000
88	A	139	TYR	0	-0.031	-0.023	13.411	-0.335	-0.335	0.000	0.000	0.000	0.000
89	A	140	GLY	0	-0.001	-0.008	17.779	-0.030	-0.030	0.000	0.000	0.000	0.000
90	A	141	LEU	0	-0.057	-0.006	19.880	0.540	0.540	0.000	0.000	0.000	0.000
91	A	142	LYS	1	0.770	0.862	23.097	11.196	11.196	0.000	0.000	0.000	0.000
92	A	143	GLU	-1	-0.906	-0.967	25.542	-11.700	-11.700	0.000	0.000	0.000	0.000
93	A	144	ASN	0	-0.105	-0.046	27.310	0.161	0.161	0.000	0.000	0.000	0.000
94	A	145	GLU	-1	-0.812	-0.887	26.804	-11.099	-11.099	0.000	0.000	0.000	0.000
95	A	146	GLU	-1	-0.810	-0.877	26.790	-11.404	-11.404	0.000	0.000	0.000	0.000
96	A	147	ARG	1	0.762	0.880	19.872	14.819	14.819	0.000	0.000	0.000	0.000
97	A	148	GLU	-1	-0.913	-0.950	26.356	-9.857	-9.857	0.000	0.000	0.000	0.000
98	A	149	LEU	0	-0.027	-0.022	23.658	-0.565	-0.565	0.000	0.000	0.000	0.000
99	A	150	SER	0	-0.040	-0.051	27.145	0.572	0.572	0.000	0.000	0.000	0.000
100	A	151	PRO	0	0.076	0.024	28.867	-0.220	-0.220	0.000	0.000	0.000	0.000
101	A	152	PRO	0	-0.023	-0.017	29.210	-0.060	-0.060	0.000	0.000	0.000	0.000
102	A	153	LEU	0	-0.007	0.001	22.384	-0.225	-0.225	0.000	0.000	0.000	0.000
103	A	154	GLU	-1	-0.915	-0.950	26.144	-10.406	-10.406	0.000	0.000	0.000	0.000
104	A	155	GLN	0	0.043	0.014	28.057	-0.017	-0.017	0.000	0.000	0.000	0.000
105	A	156	LEU	0	-0.048	-0.016	23.435	0.035	0.035	0.000	0.000	0.000	0.000
106	A	157	ILE	0	-0.006	-0.018	21.590	-0.208	-0.208	0.000	0.000	0.000	0.000
107	A	158	ASP	-1	-0.798	-0.875	25.290	-10.242	-10.242	0.000	0.000	0.000	0.000
108	A	159	HIS	0	-0.073	-0.050	28.621	0.418	0.418	0.000	0.000	0.000	0.000
109	A	160	MET	0	-0.128	-0.074	20.784	-0.068	-0.068	0.000	0.000	0.000	0.000
110	A	161	ALA	0	-0.032	-0.019	24.983	-0.132	-0.132	0.000	0.000	0.000	0.000
111	A	162	ASN	0	-0.112	-0.071	26.304	0.360	0.360	0.000	0.000	0.000	0.000
112	A	163	THR	0	-0.030	-0.039	28.651	0.137	0.137	0.000	0.000	0.000	0.000
113	A	164	VAL	0	-0.043	0.000	31.039	0.225	0.225	0.000	0.000	0.000	0.000
114	A	165	GLU	-1	-1.003	-0.987	33.731	-8.271	-8.271	0.000	0.000	0.000	0.000
115	A	192	ALA	0	0.029	0.004	33.313	-0.059	-0.059	0.000	0.000	0.000	0.000
116	A	193	ILE	0	-0.011	-0.001	26.628	0.066	0.066	0.000	0.000	0.000	0.000
117	A	194	ARG	1	0.942	0.967	29.413	9.085	9.085	0.000	0.000	0.000	0.000
118	A	195	SER	0	-0.064	-0.043	27.295	0.037	0.037	0.000	0.000	0.000	0.000
119	A	196	TYR	0	0.081	0.013	21.286	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	197	ARG	1	0.806	0.878	24.340	9.985	9.985	0.000	0.000	0.000	0.000
121	A	198	ASP	-1	-0.763	-0.844	26.824	-10.215	-10.215	0.000	0.000	0.000	0.000
122	A	199	VAL	0	0.098	0.051	22.126	0.148	0.148	0.000	0.000	0.000	0.000
123	A	200	MET	0	0.002	0.037	21.472	0.090	0.090	0.000	0.000	0.000	0.000
124	A	201	LYS	1	0.966	0.981	24.578	9.691	9.691	0.000	0.000	0.000	0.000
125	A	202	LEU	0	0.042	0.026	27.219	0.149	0.149	0.000	0.000	0.000	0.000
126	A	203	CYS	0	0.003	0.009	22.915	-0.176	-0.176	0.000	0.000	0.000	0.000
127	A	204	ALA	0	-0.023	0.000	25.041	-0.090	-0.090	0.000	0.000	0.000	0.000
128	A	205	ALA	0	-0.005	-0.008	26.975	0.131	0.131	0.000	0.000	0.000	0.000
129	A	206	HIS	1	0.824	0.912	24.453	12.579	12.579	0.000	0.000	0.000	0.000
130	A	207	LEU	0	-0.029	-0.008	25.003	0.036	0.036	0.000	0.000	0.000	0.000
131	A	208	PRO	0	-0.008	-0.009	29.093	0.266	0.266	0.000	0.000	0.000	0.000
132	A	209	THR	0	-0.002	-0.018	30.818	0.451	0.451	0.000	0.000	0.000	0.000
133	A	210	GLU	-1	-0.961	-0.969	29.694	-10.279	-10.279	0.000	0.000	0.000	0.000
134	A	211	SER	0	-0.050	-0.054	28.632	-0.262	-0.262	0.000	0.000	0.000	0.000
135	A	212	ASP	-1	-0.829	-0.886	26.804	-11.075	-11.075	0.000	0.000	0.000	0.000
136	A	213	ALA	0	0.008	0.010	24.407	-0.603	-0.603	0.000	0.000	0.000	0.000
137	A	214	PRO	0	-0.056	-0.033	21.969	-0.730	-0.730	0.000	0.000	0.000	0.000
138	A	215	ASN	0	0.010	0.004	20.517	-1.031	-1.031	0.000	0.000	0.000	0.000
139	A	216	HIS	0	-0.021	-0.017	20.317	-0.748	-0.748	0.000	0.000	0.000	0.000
140	A	217	TYR	0	0.020	-0.016	18.877	-0.794	-0.794	0.000	0.000	0.000	0.000
141	A	218	GLN	0	-0.003	0.012	15.280	-0.359	-0.359	0.000	0.000	0.000	0.000
142	A	219	ALA	0	-0.005	-0.007	15.405	-1.353	-1.353	0.000	0.000	0.000	0.000
143	A	220	VAL	0	0.007	0.007	16.227	-0.817	-0.817	0.000	0.000	0.000	0.000
144	A	221	CYS	0	-0.061	-0.016	12.610	-1.016	-1.016	0.000	0.000	0.000	0.000
145	A	222	ARG	1	0.860	0.908	11.607	16.649	16.649	0.000	0.000	0.000	0.000
146	A	223	ALA	0	-0.022	-0.003	11.868	-1.195	-1.195	0.000	0.000	0.000	0.000
147	A	224	LEU	0	0.047	0.026	11.010	-0.564	-0.564	0.000	0.000	0.000	0.000
148	A	225	PHE	0	-0.038	-0.001	3.983	-2.170	-1.851	0.000	-0.069	-0.249	0.000
149	A	226	ALA	0	-0.029	-0.027	8.408	-2.387	-2.387	0.000	0.000	0.000	0.000
150	A	227	GLU	-1	-0.825	-0.877	10.102	-20.707	-20.707	0.000	0.000	0.000	0.000
151	A	228	THR	0	-0.001	-0.033	7.520	-0.467	-0.467	0.000	0.000	0.000	0.000
152	A	229	MET	0	-0.111	-0.056	3.360	-6.031	-5.290	0.040	-0.187	-0.595	-0.001
153	A	230	GLU	-1	-0.968	-0.963	7.478	-20.039	-20.039	0.000	0.000	0.000	0.000
154	A	231	LEU	0	-0.106	-0.032	9.502	0.306	0.306	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:37:ARG)