FMO DATABASE

FMODB ID: 82V9Y

Calculation Name: 3RKD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RKD

Chain ID: A

ChEMBL ID:

UniProt ID: P33426

Base Structure: X-ray

Registration Date: 2023-06-19

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	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	146
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1271715.972781
FMO2-HF: Nuclear repulsion	1218516.719611
FMO2-HF: Total energy	-53199.25317
FMO2-MP2: Total energy	-53358.953143

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:459:SER)

Summations of interaction energy for fragment #1(A:459:SER)

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.
0.626	3.521	-0.018	-1.328	-1.549	0.005

Interaction energy analysis for fragmet #1(A:459:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.044 / q_NPA : 0.027

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	461	PRO	0	0.029	0.009	3.805	0.352	2.944	-0.017	-1.293	-1.282	0.005
4	A	462	PHE	0	0.086	0.032	5.768	-0.307	-0.217	-0.001	-0.005	-0.084	0.000
5	A	463	SER	0	0.008	-0.011	8.341	-0.104	-0.104	0.000	0.000	0.000	0.000
6	A	464	VAL	0	-0.046	0.002	8.109	-0.115	-0.115	0.000	0.000	0.000	0.000
7	A	465	LEU	0	0.035	0.031	9.113	0.027	0.027	0.000	0.000	0.000	0.000
8	A	466	ARG	1	0.935	0.947	8.034	0.566	0.566	0.000	0.000	0.000	0.000
9	A	467	ALA	0	0.031	0.017	13.159	0.057	0.057	0.000	0.000	0.000	0.000
10	A	468	ASN	0	-0.053	-0.050	14.951	-0.006	-0.006	0.000	0.000	0.000	0.000
11	A	469	ASP	-1	-0.727	-0.818	10.596	0.032	0.032	0.000	0.000	0.000	0.000
12	A	470	VAL	0	0.002	-0.009	12.513	-0.015	-0.015	0.000	0.000	0.000	0.000
13	A	471	LEU	0	-0.027	-0.018	12.304	0.075	0.075	0.000	0.000	0.000	0.000
14	A	472	TRP	0	0.041	0.018	14.119	-0.036	-0.036	0.000	0.000	0.000	0.000
15	A	473	LEU	0	-0.039	-0.036	15.820	0.032	0.032	0.000	0.000	0.000	0.000
16	A	474	SER	0	0.012	0.009	18.459	-0.017	-0.017	0.000	0.000	0.000	0.000
17	A	475	LEU	0	-0.009	-0.018	20.573	0.000	0.000	0.000	0.000	0.000	0.000
18	A	476	THR	0	0.028	0.004	22.991	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	477	ALA	0	-0.016	0.002	25.333	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	478	ALA	0	-0.012	0.011	27.443	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	479	GLU	-1	-0.877	-0.945	29.184	0.049	0.049	0.000	0.000	0.000	0.000
22	A	480	TYR	0	-0.050	-0.044	32.315	0.000	0.000	0.000	0.000	0.000	0.000
23	A	481	ASP	-1	-0.727	-0.855	33.649	0.024	0.024	0.000	0.000	0.000	0.000
24	A	482	GLN	0	0.022	0.011	35.278	0.002	0.002	0.000	0.000	0.000	0.000
25	A	483	SER	0	-0.080	-0.047	37.690	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	484	THR	0	-0.058	-0.020	35.206	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	485	TYR	0	-0.119	-0.121	29.645	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	486	GLY	0	0.014	0.022	32.642	0.001	0.001	0.000	0.000	0.000	0.000
29	A	487	SER	0	-0.040	-0.015	34.930	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	488	SER	0	0.031	-0.002	38.232	0.002	0.002	0.000	0.000	0.000	0.000
31	A	489	THR	0	-0.014	-0.004	38.983	0.001	0.001	0.000	0.000	0.000	0.000
32	A	490	GLY	0	-0.034	-0.026	35.654	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	491	PRO	0	-0.028	0.020	34.957	0.000	0.000	0.000	0.000	0.000	0.000
34	A	492	VAL	0	-0.025	-0.025	30.133	0.001	0.001	0.000	0.000	0.000	0.000
35	A	493	TYR	0	-0.010	-0.016	29.081	0.000	0.000	0.000	0.000	0.000	0.000
36	A	494	VAL	0	-0.016	-0.018	27.921	0.002	0.002	0.000	0.000	0.000	0.000
37	A	495	SER	0	0.053	-0.001	25.432	0.003	0.003	0.000	0.000	0.000	0.000
38	A	496	ASP	-1	-0.869	-0.937	25.106	0.065	0.065	0.000	0.000	0.000	0.000
39	A	497	SER	0	-0.068	-0.027	22.955	0.001	0.001	0.000	0.000	0.000	0.000
40	A	498	VAL	0	0.021	0.014	19.294	0.008	0.008	0.000	0.000	0.000	0.000
41	A	499	THR	0	-0.037	-0.006	15.733	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	500	LEU	0	0.007	-0.003	14.298	-0.027	-0.027	0.000	0.000	0.000	0.000
43	A	501	VAL	0	0.029	0.009	10.226	0.074	0.074	0.000	0.000	0.000	0.000
44	A	502	ASN	0	-0.026	0.004	7.797	-0.127	-0.127	0.000	0.000	0.000	0.000
45	A	503	VAL	0	0.019	-0.011	8.756	0.172	0.172	0.000	0.000	0.000	0.000
46	A	504	ALA	0	-0.005	0.009	9.013	0.045	0.045	0.000	0.000	0.000	0.000
47	A	505	THR	0	-0.039	-0.027	3.734	-0.130	0.004	0.001	-0.028	-0.107	0.000
48	A	506	GLY	0	0.038	0.027	4.848	0.524	0.603	-0.001	-0.002	-0.076	0.000
49	A	507	ALA	0	-0.036	-0.007	5.035	0.041	0.041	0.000	0.000	0.000	0.000
50	A	508	GLN	0	0.007	-0.010	6.656	-0.506	-0.506	0.000	0.000	0.000	0.000
51	A	509	ALA	0	0.010	0.012	9.949	0.006	0.006	0.000	0.000	0.000	0.000
52	A	510	VAL	0	0.035	0.024	12.618	-0.012	-0.012	0.000	0.000	0.000	0.000
53	A	511	ALA	0	0.037	0.015	16.287	-0.029	-0.029	0.000	0.000	0.000	0.000
54	A	512	ARG	1	0.878	0.933	18.438	-0.105	-0.105	0.000	0.000	0.000	0.000
55	A	513	SER	0	-0.050	-0.032	16.459	-0.013	-0.013	0.000	0.000	0.000	0.000
56	A	514	LEU	0	0.027	0.029	12.893	0.010	0.010	0.000	0.000	0.000	0.000
57	A	515	ASP	-1	-0.828	-0.886	16.013	-0.141	-0.141	0.000	0.000	0.000	0.000
58	A	516	TRP	0	0.002	-0.034	16.697	-0.021	-0.021	0.000	0.000	0.000	0.000
59	A	517	THR	0	-0.084	-0.059	18.591	-0.015	-0.015	0.000	0.000	0.000	0.000
60	A	518	LYS	1	0.907	0.953	15.311	0.220	0.220	0.000	0.000	0.000	0.000
61	A	519	VAL	0	-0.044	0.003	14.200	-0.055	-0.055	0.000	0.000	0.000	0.000
62	A	520	THR	0	-0.061	-0.029	13.379	-0.033	-0.033	0.000	0.000	0.000	0.000
63	A	521	LEU	0	0.028	0.013	14.070	0.007	0.007	0.000	0.000	0.000	0.000
64	A	522	ASP	-1	-0.838	-0.950	14.697	-0.158	-0.158	0.000	0.000	0.000	0.000
65	A	523	GLY	0	-0.061	-0.032	14.916	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	524	ARG	1	0.934	0.975	16.004	0.175	0.175	0.000	0.000	0.000	0.000
67	A	525	PRO	0	0.039	0.022	18.354	0.004	0.004	0.000	0.000	0.000	0.000
68	A	526	LEU	0	0.004	0.013	17.693	0.012	0.012	0.000	0.000	0.000	0.000
69	A	527	SER	0	0.000	0.012	20.894	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	528	THR	0	-0.006	-0.022	24.309	0.008	0.008	0.000	0.000	0.000	0.000
71	A	529	ILE	0	0.005	0.009	26.839	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	530	GLN	0	-0.018	-0.014	30.057	0.002	0.002	0.000	0.000	0.000	0.000
73	A	531	GLN	0	0.008	-0.008	32.369	0.004	0.004	0.000	0.000	0.000	0.000
74	A	532	HIS	0	0.028	0.017	33.774	0.000	0.000	0.000	0.000	0.000	0.000
75	A	533	SER	0	-0.009	-0.003	36.508	0.001	0.001	0.000	0.000	0.000	0.000
76	A	534	LYS	1	0.898	0.978	31.582	-0.009	-0.009	0.000	0.000	0.000	0.000
77	A	535	THR	0	0.021	0.008	28.160	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	536	PHE	0	-0.010	-0.004	26.651	0.004	0.004	0.000	0.000	0.000	0.000
79	A	537	PHE	0	0.013	0.001	21.803	-0.010	-0.010	0.000	0.000	0.000	0.000
80	A	538	VAL	0	0.017	-0.003	23.566	0.014	0.014	0.000	0.000	0.000	0.000
81	A	539	LEU	0	-0.001	0.005	17.298	-0.013	-0.013	0.000	0.000	0.000	0.000
82	A	540	PRO	0	0.014	0.000	20.863	0.015	0.015	0.000	0.000	0.000	0.000
83	A	541	LEU	0	0.009	0.013	19.783	0.003	0.003	0.000	0.000	0.000	0.000
84	A	542	ARG	1	0.879	0.947	19.469	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	543	GLY	0	0.022	0.010	23.022	0.011	0.011	0.000	0.000	0.000	0.000
86	A	544	LYS	1	0.814	0.906	25.691	-0.035	-0.035	0.000	0.000	0.000	0.000
87	A	545	LEU	0	-0.027	-0.021	21.689	0.007	0.007	0.000	0.000	0.000	0.000
88	A	546	SER	0	-0.014	0.002	23.140	-0.005	-0.005	0.000	0.000	0.000	0.000
89	A	547	PHE	0	0.027	-0.009	23.503	0.014	0.014	0.000	0.000	0.000	0.000
90	A	548	TRP	0	-0.004	0.002	21.528	-0.007	-0.007	0.000	0.000	0.000	0.000
91	A	549	GLU	-1	-0.883	-0.932	26.858	0.092	0.092	0.000	0.000	0.000	0.000
92	A	550	ALA	0	-0.017	-0.012	25.193	0.004	0.004	0.000	0.000	0.000	0.000
93	A	551	GLY	0	-0.001	-0.002	26.123	-0.006	-0.006	0.000	0.000	0.000	0.000
94	A	552	THR	0	-0.032	-0.016	27.838	-0.010	-0.010	0.000	0.000	0.000	0.000
95	A	553	THR	0	-0.008	-0.014	28.749	0.006	0.006	0.000	0.000	0.000	0.000
96	A	554	LYS	1	0.926	0.985	30.860	-0.076	-0.076	0.000	0.000	0.000	0.000
97	A	555	ALA	0	0.017	-0.007	30.055	0.005	0.005	0.000	0.000	0.000	0.000
98	A	556	GLY	0	0.006	0.016	29.837	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	557	TYR	0	-0.046	-0.030	30.749	0.000	0.000	0.000	0.000	0.000	0.000
100	A	558	PRO	0	0.050	0.017	29.925	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	559	TYR	0	0.054	0.012	31.881	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	560	ASN	0	-0.010	0.001	33.590	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	561	TYR	0	-0.020	-0.025	33.774	0.000	0.000	0.000	0.000	0.000	0.000
104	A	562	ASN	0	-0.002	0.009	34.857	0.002	0.002	0.000	0.000	0.000	0.000
105	A	563	THR	0	0.045	0.026	34.592	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	564	THR	0	0.005	-0.015	32.841	0.003	0.003	0.000	0.000	0.000	0.000
107	A	565	ALA	0	-0.007	0.019	31.375	-0.002	-0.002	0.000	0.000	0.000	0.000
108	A	566	SER	0	0.014	0.013	25.747	0.007	0.007	0.000	0.000	0.000	0.000
109	A	567	ASP	-1	-0.819	-0.894	25.680	0.042	0.042	0.000	0.000	0.000	0.000
110	A	568	GLN	0	-0.049	-0.046	23.880	-0.005	-0.005	0.000	0.000	0.000	0.000
111	A	569	LEU	0	-0.005	0.012	19.035	0.009	0.009	0.000	0.000	0.000	0.000
112	A	570	LEU	0	0.012	0.014	23.116	-0.013	-0.013	0.000	0.000	0.000	0.000
113	A	571	VAL	0	0.025	0.011	20.223	0.012	0.012	0.000	0.000	0.000	0.000
114	A	572	GLU	-1	-0.771	-0.854	23.661	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	573	ASN	0	-0.035	-0.024	24.791	0.003	0.003	0.000	0.000	0.000	0.000
116	A	574	ALA	0	0.024	0.003	25.802	-0.006	-0.006	0.000	0.000	0.000	0.000
117	A	575	ALA	0	0.037	0.019	25.667	0.007	0.007	0.000	0.000	0.000	0.000
118	A	576	GLY	0	-0.002	-0.009	24.940	0.002	0.002	0.000	0.000	0.000	0.000
119	A	577	HIS	1	0.780	0.897	20.986	0.008	0.008	0.000	0.000	0.000	0.000
120	A	578	ARG	1	0.984	1.005	22.751	-0.023	-0.023	0.000	0.000	0.000	0.000
121	A	579	VAL	0	0.006	0.011	20.797	-0.008	-0.008	0.000	0.000	0.000	0.000
122	A	580	ALA	0	0.007	0.003	24.144	0.003	0.003	0.000	0.000	0.000	0.000
123	A	581	ILE	0	-0.016	-0.007	24.200	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	582	SER	0	0.039	0.019	26.997	-0.003	-0.003	0.000	0.000	0.000	0.000
125	A	583	THR	0	-0.021	-0.010	29.922	0.007	0.007	0.000	0.000	0.000	0.000
126	A	584	TYR	0	0.002	0.003	32.555	-0.004	-0.004	0.000	0.000	0.000	0.000
127	A	585	THR	0	0.056	0.027	35.912	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	586	THR	0	0.017	0.022	35.660	0.003	0.003	0.000	0.000	0.000	0.000
129	A	587	SER	0	-0.046	-0.022	34.078	0.003	0.003	0.000	0.000	0.000	0.000
130	A	588	LEU	0	-0.022	-0.021	29.835	0.002	0.002	0.000	0.000	0.000	0.000
131	A	589	GLY	0	0.006	0.012	34.126	0.003	0.003	0.000	0.000	0.000	0.000
132	A	590	ALA	0	0.016	0.007	35.617	0.000	0.000	0.000	0.000	0.000	0.000
133	A	591	GLY	0	0.036	0.034	33.897	0.000	0.000	0.000	0.000	0.000	0.000
134	A	592	PRO	0	0.010	0.004	32.018	-0.003	-0.003	0.000	0.000	0.000	0.000
135	A	593	VAL	0	-0.027	-0.010	30.328	0.001	0.001	0.000	0.000	0.000	0.000
136	A	594	SER	0	-0.013	-0.014	26.181	0.000	0.000	0.000	0.000	0.000	0.000
137	A	595	ILE	0	0.009	0.019	24.907	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	596	SER	0	-0.048	-0.008	22.080	0.019	0.019	0.000	0.000	0.000	0.000
139	A	597	ALA	0	0.044	0.007	20.954	-0.018	-0.018	0.000	0.000	0.000	0.000
140	A	598	VAL	0	-0.018	0.010	17.589	0.029	0.029	0.000	0.000	0.000	0.000
141	A	599	ALA	0	0.005	0.000	17.974	-0.025	-0.025	0.000	0.000	0.000	0.000
142	A	600	VAL	0	0.017	0.018	17.097	0.022	0.022	0.000	0.000	0.000	0.000
143	A	601	LEU	0	0.012	0.013	14.194	-0.018	-0.018	0.000	0.000	0.000	0.000
144	A	602	ALA	0	-0.002	-0.001	17.816	-0.006	-0.006	0.000	0.000	0.000	0.000
145	A	603	PRO	0	-0.012	-0.017	19.437	-0.009	-0.009	0.000	0.000	0.000	0.000
146	A	604	PRO	0	-0.049	0.004	18.945	0.011	0.011	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:459:SER)