FMO DATABASE

FMODB ID: MMKRZ

Calculation Name: 3RKD-A-Xray313

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	146
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1271488.646118
FMO2-HF: Nuclear repulsion	1218289.958257
FMO2-HF: Total energy	-53198.687861
FMO2-MP2: Total energy	-53358.375473

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.
0.204	3.005	-0.01	-1.299	-1.491	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 : 0.026

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	0.291	2.799	-0.012	-1.261	-1.235	0.005
4	A	462	PHE	0	0.081	0.029	5.768	-0.310	-0.225	0.000	-0.006	-0.079	0.000
5	A	463	SER	0	0.005	-0.011	8.341	-0.104	-0.104	0.000	0.000	0.000	0.000
6	A	464	VAL	0	-0.041	0.004	8.109	-0.106	-0.106	0.000	0.000	0.000	0.000
7	A	465	LEU	0	0.029	0.028	9.110	0.025	0.025	0.000	0.000	0.000	0.000
8	A	466	ARG	1	0.943	0.950	8.032	0.435	0.435	0.000	0.000	0.000	0.000
9	A	467	ALA	0	0.043	0.026	13.157	0.046	0.046	0.000	0.000	0.000	0.000
10	A	468	ASN	0	-0.062	-0.055	14.950	-0.003	-0.003	0.000	0.000	0.000	0.000
11	A	469	ASP	-1	-0.733	-0.821	10.595	0.029	0.029	0.000	0.000	0.000	0.000
12	A	470	VAL	0	0.003	-0.009	12.513	-0.011	-0.011	0.000	0.000	0.000	0.000
13	A	471	LEU	0	-0.027	-0.018	12.303	0.059	0.059	0.000	0.000	0.000	0.000
14	A	472	TRP	0	0.039	0.016	14.119	-0.028	-0.028	0.000	0.000	0.000	0.000
15	A	473	LEU	0	-0.032	-0.033	15.820	0.023	0.023	0.000	0.000	0.000	0.000
16	A	474	SER	0	0.000	0.005	18.459	-0.013	-0.013	0.000	0.000	0.000	0.000
17	A	475	LEU	0	-0.004	-0.016	20.573	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	476	THR	0	0.027	0.003	22.993	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	477	ALA	0	-0.018	0.001	25.333	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	478	ALA	0	-0.009	0.013	27.442	-0.005	-0.005	0.000	0.000	0.000	0.000
21	A	479	GLU	-1	-0.877	-0.946	29.184	0.028	0.028	0.000	0.000	0.000	0.000
22	A	480	TYR	0	-0.054	-0.045	32.314	0.000	0.000	0.000	0.000	0.000	0.000
23	A	481	ASP	-1	-0.725	-0.854	33.647	0.011	0.011	0.000	0.000	0.000	0.000
24	A	482	GLN	0	0.026	0.012	35.277	0.001	0.001	0.000	0.000	0.000	0.000
25	A	483	SER	0	-0.088	-0.049	37.689	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	484	THR	0	-0.059	-0.022	35.207	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	485	TYR	0	-0.114	-0.120	29.645	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	486	GLY	0	0.018	0.024	32.640	0.001	0.001	0.000	0.000	0.000	0.000
29	A	487	SER	0	-0.042	-0.017	34.928	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	488	SER	0	0.028	-0.002	38.231	0.002	0.002	0.000	0.000	0.000	0.000
31	A	489	THR	0	-0.014	-0.004	38.977	0.001	0.001	0.000	0.000	0.000	0.000
32	A	490	GLY	0	-0.034	-0.026	35.652	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	491	PRO	0	-0.030	0.019	34.955	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	492	VAL	0	-0.015	-0.021	30.131	0.001	0.001	0.000	0.000	0.000	0.000
35	A	493	TYR	0	-0.019	-0.018	29.080	0.000	0.000	0.000	0.000	0.000	0.000
36	A	494	VAL	0	-0.014	-0.016	27.920	0.002	0.002	0.000	0.000	0.000	0.000
37	A	495	SER	0	0.051	-0.002	25.432	0.002	0.002	0.000	0.000	0.000	0.000
38	A	496	ASP	-1	-0.864	-0.936	25.106	0.034	0.034	0.000	0.000	0.000	0.000
39	A	497	SER	0	-0.073	-0.028	22.955	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	498	VAL	0	0.022	0.014	19.293	0.006	0.006	0.000	0.000	0.000	0.000
41	A	499	THR	0	-0.038	-0.007	15.733	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	500	LEU	0	0.007	-0.003	14.298	-0.018	-0.018	0.000	0.000	0.000	0.000
43	A	501	VAL	0	0.029	0.008	10.227	0.059	0.059	0.000	0.000	0.000	0.000
44	A	502	ASN	0	-0.021	0.006	7.797	-0.102	-0.102	0.000	0.000	0.000	0.000
45	A	503	VAL	0	0.017	-0.011	8.756	0.130	0.130	0.000	0.000	0.000	0.000
46	A	504	ALA	0	-0.006	0.009	9.014	0.030	0.030	0.000	0.000	0.000	0.000
47	A	505	THR	0	-0.040	-0.027	3.735	-0.125	0.003	0.002	-0.029	-0.101	0.000
48	A	506	GLY	0	0.037	0.026	4.851	0.359	0.439	0.000	-0.003	-0.076	0.000
49	A	507	ALA	0	-0.043	-0.009	5.034	0.023	0.023	0.000	0.000	0.000	0.000
50	A	508	GLN	0	0.011	-0.008	6.656	-0.438	-0.438	0.000	0.000	0.000	0.000
51	A	509	ALA	0	0.005	0.011	9.949	0.004	0.004	0.000	0.000	0.000	0.000
52	A	510	VAL	0	0.034	0.022	12.618	-0.013	-0.013	0.000	0.000	0.000	0.000
53	A	511	ALA	0	0.040	0.017	16.287	-0.023	-0.023	0.000	0.000	0.000	0.000
54	A	512	ARG	1	0.878	0.934	18.438	-0.060	-0.060	0.000	0.000	0.000	0.000
55	A	513	SER	0	-0.055	-0.035	16.459	-0.011	-0.011	0.000	0.000	0.000	0.000
56	A	514	LEU	0	0.027	0.028	12.893	0.005	0.005	0.000	0.000	0.000	0.000
57	A	515	ASP	-1	-0.832	-0.889	16.013	-0.128	-0.128	0.000	0.000	0.000	0.000
58	A	516	TRP	0	0.003	-0.033	16.697	-0.015	-0.015	0.000	0.000	0.000	0.000
59	A	517	THR	0	-0.081	-0.057	18.591	-0.011	-0.011	0.000	0.000	0.000	0.000
60	A	518	LYS	1	0.903	0.951	15.425	0.191	0.191	0.000	0.000	0.000	0.000
61	A	519	VAL	0	-0.050	0.000	14.197	-0.044	-0.044	0.000	0.000	0.000	0.000
62	A	520	THR	0	-0.061	-0.029	13.377	-0.028	-0.028	0.000	0.000	0.000	0.000
63	A	521	LEU	0	0.031	0.013	14.067	0.005	0.005	0.000	0.000	0.000	0.000
64	A	522	ASP	-1	-0.827	-0.939	14.695	-0.122	-0.122	0.000	0.000	0.000	0.000
65	A	523	GLY	0	-0.070	-0.036	14.915	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	524	ARG	1	0.938	0.976	16.002	0.133	0.133	0.000	0.000	0.000	0.000
67	A	525	PRO	0	0.030	0.016	18.354	0.003	0.003	0.000	0.000	0.000	0.000
68	A	526	LEU	0	0.008	0.015	17.690	0.012	0.012	0.000	0.000	0.000	0.000
69	A	527	SER	0	0.012	0.019	20.891	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	528	THR	0	-0.015	-0.027	24.305	0.007	0.007	0.000	0.000	0.000	0.000
71	A	529	ILE	0	0.011	0.012	26.836	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	530	GLN	0	-0.024	-0.017	30.054	0.001	0.001	0.000	0.000	0.000	0.000
73	A	531	GLN	0	0.011	-0.008	32.367	0.003	0.003	0.000	0.000	0.000	0.000
74	A	532	HIS	0	0.026	0.016	33.772	0.000	0.000	0.000	0.000	0.000	0.000
75	A	533	SER	0	-0.012	-0.004	36.508	0.000	0.000	0.000	0.000	0.000	0.000
76	A	534	LYS	1	0.894	0.976	31.582	0.001	0.001	0.000	0.000	0.000	0.000
77	A	535	THR	0	0.022	0.008	28.160	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	536	PHE	0	-0.013	-0.006	26.648	0.002	0.002	0.000	0.000	0.000	0.000
79	A	537	PHE	0	0.013	0.001	21.800	-0.007	-0.007	0.000	0.000	0.000	0.000
80	A	538	VAL	0	0.020	-0.002	23.565	0.011	0.011	0.000	0.000	0.000	0.000
81	A	539	LEU	0	-0.002	0.004	17.295	-0.009	-0.009	0.000	0.000	0.000	0.000
82	A	540	PRO	0	0.033	0.010	20.861	0.013	0.013	0.000	0.000	0.000	0.000
83	A	541	LEU	0	0.005	0.010	19.782	0.003	0.003	0.000	0.000	0.000	0.000
84	A	542	ARG	1	0.885	0.951	19.469	-0.008	-0.008	0.000	0.000	0.000	0.000
85	A	543	GLY	0	0.013	0.005	23.022	0.009	0.009	0.000	0.000	0.000	0.000
86	A	544	LYS	1	0.812	0.905	25.690	-0.025	-0.025	0.000	0.000	0.000	0.000
87	A	545	LEU	0	-0.025	-0.019	21.689	0.006	0.006	0.000	0.000	0.000	0.000
88	A	546	SER	0	-0.014	0.003	23.141	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	547	PHE	0	0.025	-0.009	23.503	0.010	0.010	0.000	0.000	0.000	0.000
90	A	548	TRP	0	-0.004	0.001	21.530	-0.005	-0.005	0.000	0.000	0.000	0.000
91	A	549	GLU	-1	-0.884	-0.933	26.858	0.059	0.059	0.000	0.000	0.000	0.000
92	A	550	ALA	0	-0.019	-0.012	25.191	0.003	0.003	0.000	0.000	0.000	0.000
93	A	551	GLY	0	0.000	-0.001	26.126	-0.004	-0.004	0.000	0.000	0.000	0.000
94	A	552	THR	0	-0.035	-0.018	27.840	-0.007	-0.007	0.000	0.000	0.000	0.000
95	A	553	THR	0	-0.007	-0.014	28.750	0.004	0.004	0.000	0.000	0.000	0.000
96	A	554	LYS	1	0.924	0.984	30.862	-0.049	-0.049	0.000	0.000	0.000	0.000
97	A	555	ALA	0	0.021	-0.006	30.055	0.003	0.003	0.000	0.000	0.000	0.000
98	A	556	GLY	0	0.001	0.015	29.837	-0.004	-0.004	0.000	0.000	0.000	0.000
99	A	557	TYR	0	-0.043	-0.029	30.749	0.000	0.000	0.000	0.000	0.000	0.000
100	A	558	PRO	0	0.054	0.019	29.924	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	559	TYR	0	0.053	0.011	31.881	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	560	ASN	0	-0.009	0.001	33.589	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	561	TYR	0	-0.024	-0.025	33.773	0.001	0.001	0.000	0.000	0.000	0.000
104	A	562	ASN	0	-0.003	0.008	34.857	0.002	0.002	0.000	0.000	0.000	0.000
105	A	563	THR	0	0.043	0.024	34.591	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	564	THR	0	0.004	-0.016	32.841	0.002	0.002	0.000	0.000	0.000	0.000
107	A	565	ALA	0	-0.006	0.020	31.373	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	566	SER	0	0.020	0.016	25.746	0.005	0.005	0.000	0.000	0.000	0.000
109	A	567	ASP	-1	-0.825	-0.897	25.679	0.028	0.028	0.000	0.000	0.000	0.000
110	A	568	GLN	0	-0.039	-0.039	23.878	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	569	LEU	0	-0.011	0.008	19.032	0.007	0.007	0.000	0.000	0.000	0.000
112	A	570	LEU	0	0.011	0.016	23.114	-0.010	-0.010	0.000	0.000	0.000	0.000
113	A	571	VAL	0	0.019	0.007	20.224	0.009	0.009	0.000	0.000	0.000	0.000
114	A	572	GLU	-1	-0.767	-0.852	23.661	-0.012	-0.012	0.000	0.000	0.000	0.000
115	A	573	ASN	0	-0.032	-0.021	24.791	0.000	0.000	0.000	0.000	0.000	0.000
116	A	574	ALA	0	0.022	0.001	25.801	-0.004	-0.004	0.000	0.000	0.000	0.000
117	A	575	ALA	0	0.034	0.017	25.667	0.004	0.004	0.000	0.000	0.000	0.000
118	A	576	GLY	0	-0.003	-0.010	24.941	0.003	0.003	0.000	0.000	0.000	0.000
119	A	577	HIS	1	0.781	0.899	20.986	0.021	0.021	0.000	0.000	0.000	0.000
120	A	578	ARG	1	0.979	1.003	22.751	-0.005	-0.005	0.000	0.000	0.000	0.000
121	A	579	VAL	0	0.014	0.014	20.797	-0.005	-0.005	0.000	0.000	0.000	0.000
122	A	580	ALA	0	0.005	0.002	24.144	0.002	0.002	0.000	0.000	0.000	0.000
123	A	581	ILE	0	-0.016	-0.007	24.199	0.000	0.000	0.000	0.000	0.000	0.000
124	A	582	SER	0	0.041	0.020	26.996	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	583	THR	0	-0.021	-0.010	29.921	0.005	0.005	0.000	0.000	0.000	0.000
126	A	584	TYR	0	0.001	0.002	32.554	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	585	THR	0	0.052	0.026	35.911	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	586	THR	0	0.020	0.022	35.660	0.002	0.002	0.000	0.000	0.000	0.000
129	A	587	SER	0	-0.051	-0.023	34.078	0.002	0.002	0.000	0.000	0.000	0.000
130	A	588	LEU	0	-0.016	-0.019	29.835	0.002	0.002	0.000	0.000	0.000	0.000
131	A	589	GLY	0	0.004	0.011	34.126	0.001	0.001	0.000	0.000	0.000	0.000
132	A	590	ALA	0	0.015	0.006	35.617	0.000	0.000	0.000	0.000	0.000	0.000
133	A	591	GLY	0	0.037	0.035	33.897	0.000	0.000	0.000	0.000	0.000	0.000
134	A	592	PRO	0	0.008	0.003	32.018	-0.002	-0.002	0.000	0.000	0.000	0.000
135	A	593	VAL	0	-0.026	-0.011	30.328	0.001	0.001	0.000	0.000	0.000	0.000
136	A	594	SER	0	-0.012	-0.013	26.181	0.000	0.000	0.000	0.000	0.000	0.000
137	A	595	ILE	0	0.004	0.017	24.906	0.000	0.000	0.000	0.000	0.000	0.000
138	A	596	SER	0	-0.047	-0.007	22.081	0.013	0.013	0.000	0.000	0.000	0.000
139	A	597	ALA	0	0.041	0.006	20.954	-0.012	-0.012	0.000	0.000	0.000	0.000
140	A	598	VAL	0	-0.015	0.010	17.589	0.021	0.021	0.000	0.000	0.000	0.000
141	A	599	ALA	0	0.002	-0.002	17.974	-0.018	-0.018	0.000	0.000	0.000	0.000
142	A	600	VAL	0	0.010	0.014	17.097	0.017	0.017	0.000	0.000	0.000	0.000
143	A	601	LEU	0	0.007	0.010	14.191	-0.014	-0.014	0.000	0.000	0.000	0.000
144	A	602	ALA	0	-0.006	-0.006	17.814	-0.003	-0.003	0.000	0.000	0.000	0.000
145	A	603	PRO	0	-0.045	-0.039	19.435	-0.006	-0.006	0.000	0.000	0.000	0.000
146	A	604	PRO	-1	-0.965	-0.950	18.946	-0.054	-0.054	0.000	0.000	0.000	0.000

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