FMO DATABASE

FMODB ID: KG2R3

Calculation Name: 3RD6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RD6

Chain ID: A

ChEMBL ID:

UniProt ID: Q98FZ2

Base Structure: X-ray

Registration Date: 2023-09-21

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	147
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1320267.64057
FMO2-HF: Nuclear repulsion	1263969.520239
FMO2-HF: Total energy	-56298.12033
FMO2-MP2: Total energy	-56464.794111

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:3:HIS)

Summations of interaction energy for fragment #1(A:3:HIS)

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.
-163.291	-160.892	22.938	-14.17	-11.167	-0.142

Interaction energy analysis for fragmet #1(A:3:HIS)

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 : 0.903

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	5	VAL	0	0.005	0.001	3.820	-4.545	-1.625	-0.029	-1.605	-1.286	0.004
4	A	6	ILE	0	-0.002	0.025	6.363	2.978	2.978	0.000	0.000	0.000	0.000
5	A	7	HIS	0	0.016	0.004	9.190	1.128	1.128	0.000	0.000	0.000	0.000
6	A	8	SER	0	-0.038	-0.016	12.746	1.103	1.103	0.000	0.000	0.000	0.000
7	A	9	THR	0	-0.006	-0.020	16.188	-0.156	-0.156	0.000	0.000	0.000	0.000
8	A	10	PHE	0	0.013	0.031	19.193	0.174	0.174	0.000	0.000	0.000	0.000
9	A	11	THR	0	0.017	-0.010	22.353	-0.164	-0.164	0.000	0.000	0.000	0.000
10	A	12	ILE	0	-0.031	-0.012	25.211	0.148	0.148	0.000	0.000	0.000	0.000
11	A	13	GLU	-1	-0.875	-0.909	28.521	-9.490	-9.490	0.000	0.000	0.000	0.000
12	A	14	ARG	1	0.854	0.900	32.166	8.946	8.946	0.000	0.000	0.000	0.000
13	A	15	THR	0	-0.019	-0.006	34.655	-0.095	-0.095	0.000	0.000	0.000	0.000
14	A	16	TYR	0	-0.056	-0.022	33.736	-0.041	-0.041	0.000	0.000	0.000	0.000
15	A	17	PRO	0	0.016	0.007	39.969	0.069	0.069	0.000	0.000	0.000	0.000
16	A	18	GLN	0	0.022	0.013	41.090	0.033	0.033	0.000	0.000	0.000	0.000
17	A	19	SER	0	0.046	0.012	42.322	-0.091	-0.091	0.000	0.000	0.000	0.000
18	A	20	PRO	0	0.022	-0.014	39.710	-0.141	-0.141	0.000	0.000	0.000	0.000
19	A	21	ASP	-1	-0.821	-0.890	39.424	-7.467	-7.467	0.000	0.000	0.000	0.000
20	A	22	ARG	1	0.802	0.905	39.245	7.776	7.776	0.000	0.000	0.000	0.000
21	A	23	VAL	0	0.031	-0.003	35.294	-0.143	-0.143	0.000	0.000	0.000	0.000
22	A	24	PHE	0	0.032	0.038	34.001	-0.313	-0.313	0.000	0.000	0.000	0.000
23	A	25	HIS	0	0.013	0.020	35.297	-0.221	-0.221	0.000	0.000	0.000	0.000
24	A	26	ALA	0	-0.048	-0.027	35.495	-0.116	-0.116	0.000	0.000	0.000	0.000
25	A	27	PHE	0	-0.011	-0.029	28.567	-0.366	-0.366	0.000	0.000	0.000	0.000
26	A	28	ALA	0	0.005	0.002	31.696	-0.292	-0.292	0.000	0.000	0.000	0.000
27	A	29	ASP	-1	-0.819	-0.876	33.986	-8.357	-8.357	0.000	0.000	0.000	0.000
28	A	30	LYS	1	0.818	0.904	30.716	10.055	10.055	0.000	0.000	0.000	0.000
29	A	31	ALA	0	-0.002	-0.005	33.726	-0.173	-0.173	0.000	0.000	0.000	0.000
30	A	32	THR	0	0.011	-0.026	35.710	0.000	0.000	0.000	0.000	0.000	0.000
31	A	33	VAL	0	0.008	0.013	29.784	-0.146	-0.146	0.000	0.000	0.000	0.000
32	A	34	ARG	1	0.790	0.891	30.503	9.792	9.792	0.000	0.000	0.000	0.000
33	A	35	ARG	1	0.827	0.932	32.427	8.346	8.346	0.000	0.000	0.000	0.000
34	A	36	TRP	0	-0.040	-0.019	29.367	-0.117	-0.117	0.000	0.000	0.000	0.000
35	A	37	ARG	1	0.795	0.885	24.521	11.706	11.706	0.000	0.000	0.000	0.000
36	A	38	VAL	0	-0.066	-0.037	26.604	-0.396	-0.396	0.000	0.000	0.000	0.000
37	A	39	ASP	-1	-0.820	-0.907	29.115	-10.038	-10.038	0.000	0.000	0.000	0.000
38	A	40	GLY	0	-0.101	-0.064	31.916	0.062	0.062	0.000	0.000	0.000	0.000
39	A	41	ASP	-1	-0.892	-0.958	33.239	-7.935	-7.935	0.000	0.000	0.000	0.000
40	A	42	GLY	0	-0.093	-0.013	36.423	-0.117	-0.117	0.000	0.000	0.000	0.000
41	A	43	PHE	0	0.036	-0.026	33.185	0.198	0.198	0.000	0.000	0.000	0.000
42	A	44	THR	0	0.011	0.034	30.930	-0.131	-0.131	0.000	0.000	0.000	0.000
43	A	45	VAL	0	0.020	0.016	28.691	0.109	0.109	0.000	0.000	0.000	0.000
44	A	46	ALA	0	-0.046	-0.032	25.492	-0.117	-0.117	0.000	0.000	0.000	0.000
45	A	47	GLU	-1	-0.835	-0.908	24.558	-12.425	-12.425	0.000	0.000	0.000	0.000
46	A	48	PHE	0	0.071	0.015	26.093	-0.127	-0.127	0.000	0.000	0.000	0.000
47	A	49	SER	0	-0.034	0.016	26.243	0.755	0.755	0.000	0.000	0.000	0.000
48	A	50	PHE	0	-0.010	-0.019	26.805	-0.334	-0.334	0.000	0.000	0.000	0.000
49	A	51	ASP	-1	-0.853	-0.904	28.454	-9.884	-9.884	0.000	0.000	0.000	0.000
50	A	52	PHE	0	0.017	0.009	29.453	-0.261	-0.261	0.000	0.000	0.000	0.000
51	A	53	ARG	1	0.884	0.927	29.304	10.833	10.833	0.000	0.000	0.000	0.000
52	A	54	VAL	0	0.039	0.034	28.453	-0.395	-0.395	0.000	0.000	0.000	0.000
53	A	55	GLY	0	-0.045	-0.021	26.647	0.261	0.261	0.000	0.000	0.000	0.000
54	A	56	GLY	0	-0.034	-0.012	26.687	-0.208	-0.208	0.000	0.000	0.000	0.000
55	A	57	GLY	0	0.047	0.010	24.442	-0.386	-0.386	0.000	0.000	0.000	0.000
56	A	58	GLU	-1	-0.860	-0.907	23.632	-12.027	-12.027	0.000	0.000	0.000	0.000
57	A	59	VAL	0	-0.015	-0.006	21.461	-0.692	-0.692	0.000	0.000	0.000	0.000
58	A	60	SER	0	0.008	0.017	21.817	0.918	0.918	0.000	0.000	0.000	0.000
59	A	61	ARG	1	0.727	0.836	20.627	12.451	12.451	0.000	0.000	0.000	0.000
60	A	62	PHE	0	0.038	0.020	21.560	0.659	0.659	0.000	0.000	0.000	0.000
61	A	63	SER	0	0.060	0.032	21.902	-0.677	-0.677	0.000	0.000	0.000	0.000
62	A	64	TYR	0	0.026	0.022	23.485	0.573	0.573	0.000	0.000	0.000	0.000
63	A	65	GLY	0	0.017	0.009	25.197	-0.220	-0.220	0.000	0.000	0.000	0.000
64	A	66	GLY	0	-0.008	-0.016	25.892	0.022	0.022	0.000	0.000	0.000	0.000
65	A	67	GLY	0	-0.053	-0.016	22.200	-0.325	-0.325	0.000	0.000	0.000	0.000
66	A	68	PRO	0	0.000	-0.017	16.949	0.096	0.096	0.000	0.000	0.000	0.000
67	A	69	GLU	-1	-0.842	-0.906	18.828	-14.304	-14.304	0.000	0.000	0.000	0.000
68	A	70	VAL	0	-0.015	-0.018	17.434	-1.212	-1.212	0.000	0.000	0.000	0.000
69	A	71	ARG	1	0.870	0.910	16.580	17.033	17.033	0.000	0.000	0.000	0.000
70	A	72	LEU	0	-0.021	-0.007	16.593	-1.224	-1.224	0.000	0.000	0.000	0.000
71	A	73	ASP	-1	-0.800	-0.878	17.063	-16.420	-16.420	0.000	0.000	0.000	0.000
72	A	74	ALA	0	0.039	0.005	18.098	-0.849	-0.849	0.000	0.000	0.000	0.000
73	A	75	GLN	0	-0.049	-0.028	20.690	0.534	0.534	0.000	0.000	0.000	0.000
74	A	76	PHE	0	0.013	-0.001	22.789	-0.232	-0.232	0.000	0.000	0.000	0.000
75	A	77	GLN	0	-0.031	-0.025	22.169	-0.405	-0.405	0.000	0.000	0.000	0.000
76	A	78	ASP	-1	-0.818	-0.903	25.767	-9.975	-9.975	0.000	0.000	0.000	0.000
77	A	79	ILE	0	-0.011	0.008	28.990	-0.125	-0.125	0.000	0.000	0.000	0.000
78	A	80	VAL	0	-0.008	0.010	32.064	0.242	0.242	0.000	0.000	0.000	0.000
79	A	81	PRO	0	-0.009	-0.014	35.045	-0.080	-0.080	0.000	0.000	0.000	0.000
80	A	82	ASP	-1	-0.829	-0.944	37.400	-7.873	-7.873	0.000	0.000	0.000	0.000
81	A	83	GLN	0	-0.067	-0.029	36.158	0.144	0.144	0.000	0.000	0.000	0.000
82	A	84	ARG	1	0.824	0.889	29.821	9.851	9.851	0.000	0.000	0.000	0.000
83	A	85	ILE	0	0.000	0.000	28.017	0.055	0.055	0.000	0.000	0.000	0.000
84	A	86	VAL	0	0.017	0.020	24.093	-0.322	-0.322	0.000	0.000	0.000	0.000
85	A	87	PHE	0	0.020	0.014	21.819	0.222	0.222	0.000	0.000	0.000	0.000
86	A	88	SER	0	0.005	0.038	18.110	-0.520	-0.520	0.000	0.000	0.000	0.000
87	A	89	TYR	0	-0.035	-0.057	17.168	0.249	0.249	0.000	0.000	0.000	0.000
88	A	90	ARG	1	0.877	0.943	12.742	18.151	18.151	0.000	0.000	0.000	0.000
89	A	91	MET	0	0.006	0.029	13.226	1.243	1.243	0.000	0.000	0.000	0.000
90	A	92	ALA	0	-0.016	-0.012	12.156	-2.435	-2.435	0.000	0.000	0.000	0.000
91	A	93	ILE	0	0.047	0.042	12.766	1.862	1.862	0.000	0.000	0.000	0.000
92	A	94	GLY	0	-0.004	0.009	13.004	-1.194	-1.194	0.000	0.000	0.000	0.000
93	A	95	PRO	0	-0.037	-0.025	10.463	0.149	0.149	0.000	0.000	0.000	0.000
94	A	96	GLN	0	0.001	-0.001	6.956	-5.837	-5.837	0.000	0.000	0.000	0.000
95	A	97	PRO	0	0.001	0.005	6.414	2.812	2.812	0.000	0.000	0.000	0.000
96	A	98	MET	0	0.049	0.010	7.379	-3.325	-3.325	0.000	0.000	0.000	0.000
97	A	99	SER	0	0.016	0.003	9.571	-0.254	-0.254	0.000	0.000	0.000	0.000
98	A	100	ALA	0	-0.042	-0.013	10.593	1.018	1.018	0.000	0.000	0.000	0.000
99	A	101	SER	0	-0.011	0.007	12.709	-0.857	-0.857	0.000	0.000	0.000	0.000
100	A	102	LEU	0	-0.022	-0.014	15.746	0.307	0.307	0.000	0.000	0.000	0.000
101	A	103	THR	0	-0.021	-0.027	19.085	-0.237	-0.237	0.000	0.000	0.000	0.000
102	A	104	THR	0	0.001	0.001	22.307	0.316	0.316	0.000	0.000	0.000	0.000
103	A	105	VAL	0	-0.030	-0.014	25.597	-0.038	-0.038	0.000	0.000	0.000	0.000
104	A	106	GLU	-1	-0.947	-0.968	28.815	-9.992	-9.992	0.000	0.000	0.000	0.000
105	A	107	LEU	0	-0.025	-0.021	31.846	0.027	0.027	0.000	0.000	0.000	0.000
106	A	108	THR	0	0.019	0.008	35.380	0.197	0.197	0.000	0.000	0.000	0.000
107	A	109	PRO	0	0.014	-0.002	37.996	0.021	0.021	0.000	0.000	0.000	0.000
108	A	110	SER	0	-0.028	-0.011	40.767	-0.070	-0.070	0.000	0.000	0.000	0.000
109	A	111	GLY	0	-0.038	-0.015	42.695	0.084	0.084	0.000	0.000	0.000	0.000
110	A	112	ASP	-1	-0.931	-0.967	46.424	-6.625	-6.625	0.000	0.000	0.000	0.000
111	A	113	GLY	0	0.009	0.028	43.456	-0.004	-0.004	0.000	0.000	0.000	0.000
112	A	114	THR	0	-0.071	-0.048	38.294	-0.058	-0.058	0.000	0.000	0.000	0.000
113	A	115	ARG	1	0.890	0.925	34.933	8.659	8.659	0.000	0.000	0.000	0.000
114	A	116	LEU	0	0.004	0.008	30.651	-0.096	-0.096	0.000	0.000	0.000	0.000
115	A	117	THR	0	-0.008	-0.001	30.008	-0.191	-0.191	0.000	0.000	0.000	0.000
116	A	118	TYR	0	-0.006	-0.019	22.806	0.147	0.147	0.000	0.000	0.000	0.000
117	A	119	THR	0	0.024	0.002	23.002	-0.185	-0.185	0.000	0.000	0.000	0.000
118	A	120	GLU	-1	-0.771	-0.864	18.899	-15.345	-15.345	0.000	0.000	0.000	0.000
119	A	121	GLN	0	-0.018	0.001	17.816	-0.136	-0.136	0.000	0.000	0.000	0.000
120	A	122	GLY	0	0.016	-0.010	14.924	-0.198	-0.198	0.000	0.000	0.000	0.000
121	A	123	ALA	0	0.002	0.000	9.705	-0.116	-0.116	0.000	0.000	0.000	0.000
122	A	124	PHE	0	-0.045	-0.029	10.017	-0.368	-0.368	0.000	0.000	0.000	0.000
123	A	125	PHE	0	-0.031	-0.022	4.910	-1.755	-1.755	0.000	0.000	0.000	0.000
124	A	126	ASP	-1	-0.737	-0.852	1.718	-127.994	-128.677	22.968	-12.526	-9.759	-0.146
125	A	127	GLY	0	-0.007	0.034	4.454	4.151	4.313	-0.001	-0.039	-0.122	0.000
126	A	128	VAL	0	-0.030	-0.042	7.043	4.223	4.223	0.000	0.000	0.000	0.000
127	A	129	ASP	-1	-0.769	-0.873	9.727	-21.170	-21.170	0.000	0.000	0.000	0.000
128	A	130	SER	0	-0.003	-0.014	12.357	1.546	1.546	0.000	0.000	0.000	0.000
129	A	131	ALA	0	-0.017	0.012	14.912	1.191	1.191	0.000	0.000	0.000	0.000
130	A	132	LYS	1	0.870	0.908	15.676	19.198	19.198	0.000	0.000	0.000	0.000
131	A	133	GLY	0	0.069	0.032	18.528	0.668	0.668	0.000	0.000	0.000	0.000
132	A	134	ARG	1	0.854	0.908	14.153	19.404	19.404	0.000	0.000	0.000	0.000
133	A	135	GLU	-1	-0.848	-0.908	19.584	-11.976	-11.976	0.000	0.000	0.000	0.000
134	A	136	GLU	-1	-0.965	-0.981	22.389	-12.185	-12.185	0.000	0.000	0.000	0.000
135	A	137	GLY	0	0.035	0.018	22.976	0.535	0.535	0.000	0.000	0.000	0.000
136	A	138	THR	0	0.014	0.006	22.718	0.478	0.478	0.000	0.000	0.000	0.000
137	A	139	ARG	1	0.848	0.915	25.167	11.777	11.777	0.000	0.000	0.000	0.000
138	A	140	GLY	0	0.024	0.019	27.329	0.479	0.479	0.000	0.000	0.000	0.000
139	A	141	LEU	0	-0.007	-0.009	25.111	0.389	0.389	0.000	0.000	0.000	0.000
140	A	142	LEU	0	0.004	0.004	28.318	0.362	0.362	0.000	0.000	0.000	0.000
141	A	143	GLU	-1	-0.889	-0.928	30.971	-8.478	-8.478	0.000	0.000	0.000	0.000
142	A	144	ALA	0	0.002	-0.006	31.830	0.324	0.324	0.000	0.000	0.000	0.000
143	A	145	LEU	0	-0.013	-0.006	32.564	0.300	0.300	0.000	0.000	0.000	0.000
144	A	146	ALA	0	-0.019	-0.014	34.358	0.302	0.302	0.000	0.000	0.000	0.000
145	A	147	ALA	0	-0.014	-0.003	37.111	0.278	0.278	0.000	0.000	0.000	0.000
146	A	148	GLU	-1	-0.800	-0.872	36.288	-8.026	-8.026	0.000	0.000	0.000	0.000
147	A	149	LEU	0	-0.113	-0.044	37.498	0.405	0.405	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:HIS)