FMO DATABASE

FMODB ID: J39Q9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1271512.675048
FMO2-HF: Nuclear repulsion	1218313.075283
FMO2-HF: Total energy	-53199.599765
FMO2-MP2: Total energy	-53359.229554

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.
0.678	3.071	-0.014	-1.085	-1.293	0.003

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 : 0.057 / q_NPA : 0.029

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	0.015	0.007	3.910	0.776	2.842	-0.013	-1.040	-1.013	0.003
4	A	462	PHE	0	0.055	0.024	5.952	-0.267	-0.267	0.000	0.000	0.000	0.000
5	A	463	SER	0	0.005	-0.002	8.567	-0.094	-0.094	0.000	0.000	0.000	0.000
6	A	464	VAL	0	-0.025	0.002	8.247	-0.148	-0.148	0.000	0.000	0.000	0.000
7	A	465	LEU	0	0.050	0.040	9.500	0.025	0.025	0.000	0.000	0.000	0.000
8	A	466	ARG	1	0.941	0.948	8.988	0.394	0.394	0.000	0.000	0.000	0.000
9	A	467	ALA	0	0.032	0.010	13.469	0.058	0.058	0.000	0.000	0.000	0.000
10	A	468	ASN	0	-0.032	-0.026	14.992	-0.016	-0.016	0.000	0.000	0.000	0.000
11	A	469	ASP	-1	-0.707	-0.793	10.380	0.303	0.303	0.000	0.000	0.000	0.000
12	A	470	VAL	0	0.008	0.009	12.878	-0.021	-0.021	0.000	0.000	0.000	0.000
13	A	471	LEU	0	-0.026	-0.009	12.397	0.106	0.106	0.000	0.000	0.000	0.000
14	A	472	TRP	0	0.067	0.028	14.290	-0.057	-0.057	0.000	0.000	0.000	0.000
15	A	473	LEU	0	-0.044	-0.032	15.549	0.039	0.039	0.000	0.000	0.000	0.000
16	A	474	SER	0	0.028	0.006	18.267	-0.017	-0.017	0.000	0.000	0.000	0.000
17	A	475	LEU	0	-0.011	-0.004	20.377	0.004	0.004	0.000	0.000	0.000	0.000
18	A	476	THR	0	0.004	-0.012	22.646	-0.006	-0.006	0.000	0.000	0.000	0.000
19	A	477	ALA	0	-0.018	-0.011	24.894	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	478	ALA	0	0.001	0.021	26.954	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	479	GLU	-1	-0.867	-0.936	28.857	0.053	0.053	0.000	0.000	0.000	0.000
22	A	480	TYR	0	-0.033	-0.037	31.778	0.002	0.002	0.000	0.000	0.000	0.000
23	A	481	ASP	-1	-0.688	-0.815	33.489	0.035	0.035	0.000	0.000	0.000	0.000
24	A	482	GLN	0	0.027	0.012	35.198	0.003	0.003	0.000	0.000	0.000	0.000
25	A	483	SER	0	-0.040	-0.024	37.397	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	484	THR	0	-0.072	-0.062	35.458	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	485	TYR	0	-0.135	-0.106	29.602	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	486	GLY	0	0.014	0.020	32.308	0.002	0.002	0.000	0.000	0.000	0.000
29	A	487	SER	0	-0.041	-0.027	34.612	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	488	SER	0	0.032	-0.004	38.234	0.002	0.002	0.000	0.000	0.000	0.000
31	A	489	THR	0	-0.048	-0.021	39.502	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	490	GLY	0	0.000	-0.006	35.678	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	491	PRO	0	-0.036	0.017	34.783	0.001	0.001	0.000	0.000	0.000	0.000
34	A	492	VAL	0	-0.036	-0.027	29.958	0.003	0.003	0.000	0.000	0.000	0.000
35	A	493	TYR	0	-0.003	-0.003	28.865	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	494	VAL	0	-0.016	-0.019	27.523	0.005	0.005	0.000	0.000	0.000	0.000
37	A	495	SER	0	0.057	0.014	25.203	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	496	ASP	-1	-0.771	-0.867	24.419	0.076	0.076	0.000	0.000	0.000	0.000
39	A	497	SER	0	-0.050	-0.012	23.151	0.004	0.004	0.000	0.000	0.000	0.000
40	A	498	VAL	0	-0.006	0.008	19.325	0.008	0.008	0.000	0.000	0.000	0.000
41	A	499	THR	0	-0.030	-0.009	15.882	0.011	0.011	0.000	0.000	0.000	0.000
42	A	500	LEU	0	0.008	0.000	14.183	-0.028	-0.028	0.000	0.000	0.000	0.000
43	A	501	VAL	0	0.019	-0.002	10.291	0.069	0.069	0.000	0.000	0.000	0.000
44	A	502	ASN	0	-0.023	-0.018	8.085	-0.138	-0.138	0.000	0.000	0.000	0.000
45	A	503	VAL	0	0.010	-0.010	9.061	0.212	0.212	0.000	0.000	0.000	0.000
46	A	504	ALA	0	-0.007	0.008	9.019	-0.013	-0.013	0.000	0.000	0.000	0.000
47	A	505	THR	0	-0.047	-0.031	3.724	-0.496	-0.328	0.001	-0.033	-0.136	0.000
48	A	506	GLY	0	0.023	0.025	4.927	1.022	1.091	-0.001	-0.001	-0.066	0.000
49	A	507	ALA	0	-0.026	-0.001	4.518	-0.455	-0.365	-0.001	-0.011	-0.078	0.000
50	A	508	GLN	0	-0.003	-0.017	6.251	-0.513	-0.513	0.000	0.000	0.000	0.000
51	A	509	ALA	0	0.009	0.010	9.854	-0.020	-0.020	0.000	0.000	0.000	0.000
52	A	510	VAL	0	0.036	0.013	12.730	-0.010	-0.010	0.000	0.000	0.000	0.000
53	A	511	ALA	0	0.019	0.019	16.459	-0.024	-0.024	0.000	0.000	0.000	0.000
54	A	512	ARG	1	0.846	0.901	18.667	-0.107	-0.107	0.000	0.000	0.000	0.000
55	A	513	SER	0	-0.054	-0.028	17.105	-0.018	-0.018	0.000	0.000	0.000	0.000
56	A	514	LEU	0	0.030	0.027	13.139	0.010	0.010	0.000	0.000	0.000	0.000
57	A	515	ASP	-1	-0.784	-0.853	16.265	-0.065	-0.065	0.000	0.000	0.000	0.000
58	A	516	TRP	0	0.009	-0.022	17.004	-0.010	-0.010	0.000	0.000	0.000	0.000
59	A	517	THR	0	-0.077	-0.054	18.625	-0.016	-0.016	0.000	0.000	0.000	0.000
60	A	518	LYS	1	0.840	0.899	15.162	0.080	0.080	0.000	0.000	0.000	0.000
61	A	519	VAL	0	-0.035	0.005	14.016	-0.026	-0.026	0.000	0.000	0.000	0.000
62	A	520	THR	0	-0.065	-0.036	13.448	-0.041	-0.041	0.000	0.000	0.000	0.000
63	A	521	LEU	0	0.017	0.011	14.240	0.031	0.031	0.000	0.000	0.000	0.000
64	A	522	ASP	-1	-0.828	-0.928	14.761	-0.100	-0.100	0.000	0.000	0.000	0.000
65	A	523	GLY	0	-0.011	0.001	15.150	-0.016	-0.016	0.000	0.000	0.000	0.000
66	A	524	ARG	1	0.876	0.940	16.116	0.128	0.128	0.000	0.000	0.000	0.000
67	A	525	PRO	0	0.043	0.013	18.169	0.009	0.009	0.000	0.000	0.000	0.000
68	A	526	LEU	0	-0.001	0.015	17.242	0.007	0.007	0.000	0.000	0.000	0.000
69	A	527	SER	0	0.013	0.013	20.589	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	528	THR	0	-0.008	-0.015	24.090	0.009	0.009	0.000	0.000	0.000	0.000
71	A	529	ILE	0	-0.015	-0.003	26.680	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	530	GLN	0	-0.016	-0.020	29.982	0.000	0.000	0.000	0.000	0.000	0.000
73	A	531	GLN	0	0.015	0.001	31.390	0.003	0.003	0.000	0.000	0.000	0.000
74	A	532	HIS	0	0.028	0.024	33.329	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	533	SER	0	0.003	0.005	36.191	0.001	0.001	0.000	0.000	0.000	0.000
76	A	534	LYS	1	0.856	0.953	31.450	-0.031	-0.031	0.000	0.000	0.000	0.000
77	A	535	THR	0	0.020	0.000	28.441	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	536	PHE	0	-0.015	0.000	26.539	0.004	0.004	0.000	0.000	0.000	0.000
79	A	537	PHE	0	0.017	0.002	21.762	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	538	VAL	0	0.007	-0.003	23.253	0.011	0.011	0.000	0.000	0.000	0.000
81	A	539	LEU	0	-0.001	0.002	17.279	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	540	PRO	0	0.035	0.011	21.036	0.010	0.010	0.000	0.000	0.000	0.000
83	A	541	LEU	0	-0.011	0.007	19.919	0.011	0.011	0.000	0.000	0.000	0.000
84	A	542	ARG	1	0.862	0.924	19.672	-0.041	-0.041	0.000	0.000	0.000	0.000
85	A	543	GLY	0	0.026	0.014	23.283	0.010	0.010	0.000	0.000	0.000	0.000
86	A	544	LYS	1	0.807	0.894	26.090	-0.047	-0.047	0.000	0.000	0.000	0.000
87	A	545	LEU	0	-0.036	-0.015	22.489	0.009	0.009	0.000	0.000	0.000	0.000
88	A	546	SER	0	0.001	0.015	23.132	-0.009	-0.009	0.000	0.000	0.000	0.000
89	A	547	PHE	0	0.019	-0.014	23.697	0.017	0.017	0.000	0.000	0.000	0.000
90	A	548	TRP	0	0.009	0.010	21.598	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	549	GLU	-1	-0.814	-0.894	26.770	0.086	0.086	0.000	0.000	0.000	0.000
92	A	550	ALA	0	-0.001	-0.002	24.937	0.002	0.002	0.000	0.000	0.000	0.000
93	A	551	GLY	0	-0.011	-0.005	25.849	-0.006	-0.006	0.000	0.000	0.000	0.000
94	A	552	THR	0	-0.055	-0.024	27.440	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	553	THR	0	0.010	-0.007	28.637	0.006	0.006	0.000	0.000	0.000	0.000
96	A	554	LYS	1	0.835	0.931	30.921	-0.076	-0.076	0.000	0.000	0.000	0.000
97	A	555	ALA	0	0.027	-0.003	29.907	0.005	0.005	0.000	0.000	0.000	0.000
98	A	556	GLY	0	0.008	0.012	29.984	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	557	TYR	0	-0.032	-0.022	30.844	0.001	0.001	0.000	0.000	0.000	0.000
100	A	558	PRO	0	0.026	0.019	30.074	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	559	TYR	0	0.050	0.007	32.019	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	560	ASN	0	-0.019	-0.006	33.260	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	561	TYR	0	-0.008	-0.006	33.549	0.001	0.001	0.000	0.000	0.000	0.000
104	A	562	ASN	0	0.011	0.009	34.618	0.002	0.002	0.000	0.000	0.000	0.000
105	A	563	THR	0	0.022	0.014	35.137	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	564	THR	0	0.027	-0.001	33.113	0.004	0.004	0.000	0.000	0.000	0.000
107	A	565	ALA	0	-0.009	0.018	31.473	0.000	0.000	0.000	0.000	0.000	0.000
108	A	566	SER	0	-0.009	-0.001	25.907	0.005	0.005	0.000	0.000	0.000	0.000
109	A	567	ASP	-1	-0.810	-0.897	26.103	0.059	0.059	0.000	0.000	0.000	0.000
110	A	568	GLN	0	-0.050	-0.048	24.074	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	569	LEU	0	-0.010	0.011	19.207	0.006	0.006	0.000	0.000	0.000	0.000
112	A	570	LEU	0	0.009	0.012	23.312	-0.010	-0.010	0.000	0.000	0.000	0.000
113	A	571	VAL	0	0.015	0.000	20.158	0.009	0.009	0.000	0.000	0.000	0.000
114	A	572	GLU	-1	-0.750	-0.833	23.589	0.027	0.027	0.000	0.000	0.000	0.000
115	A	573	ASN	0	-0.025	-0.019	24.852	0.008	0.008	0.000	0.000	0.000	0.000
116	A	574	ALA	0	0.038	0.017	26.072	-0.008	-0.008	0.000	0.000	0.000	0.000
117	A	575	ALA	0	0.024	0.009	25.881	0.007	0.007	0.000	0.000	0.000	0.000
118	A	576	GLY	0	0.023	0.013	24.934	0.001	0.001	0.000	0.000	0.000	0.000
119	A	577	HIS	1	0.779	0.881	21.189	-0.032	-0.032	0.000	0.000	0.000	0.000
120	A	578	ARG	1	0.888	0.934	22.677	-0.039	-0.039	0.000	0.000	0.000	0.000
121	A	579	VAL	0	0.009	0.014	20.340	-0.005	-0.005	0.000	0.000	0.000	0.000
122	A	580	ALA	0	0.003	0.000	23.648	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	581	ILE	0	0.008	0.000	23.926	0.003	0.003	0.000	0.000	0.000	0.000
124	A	582	SER	0	0.021	0.018	26.913	-0.005	-0.005	0.000	0.000	0.000	0.000
125	A	583	THR	0	-0.021	-0.029	30.047	0.006	0.006	0.000	0.000	0.000	0.000
126	A	584	TYR	0	-0.001	0.000	32.762	-0.004	-0.004	0.000	0.000	0.000	0.000
127	A	585	THR	0	0.045	0.023	36.070	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	586	THR	0	0.015	0.033	35.759	0.004	0.004	0.000	0.000	0.000	0.000
129	A	587	SER	0	-0.053	-0.031	33.972	0.002	0.002	0.000	0.000	0.000	0.000
130	A	588	LEU	0	-0.013	-0.013	29.772	0.001	0.001	0.000	0.000	0.000	0.000
131	A	589	GLY	0	0.030	0.021	34.124	0.001	0.001	0.000	0.000	0.000	0.000
132	A	590	ALA	0	0.001	-0.003	35.620	0.001	0.001	0.000	0.000	0.000	0.000
133	A	591	GLY	0	0.029	0.021	33.915	0.002	0.002	0.000	0.000	0.000	0.000
134	A	592	PRO	0	0.007	0.014	31.882	-0.004	-0.004	0.000	0.000	0.000	0.000
135	A	593	VAL	0	-0.029	-0.026	30.208	0.001	0.001	0.000	0.000	0.000	0.000
136	A	594	SER	0	-0.015	-0.010	25.813	0.003	0.003	0.000	0.000	0.000	0.000
137	A	595	ILE	0	-0.011	0.012	25.116	-0.002	-0.002	0.000	0.000	0.000	0.000
138	A	596	SER	0	-0.020	0.002	22.174	0.012	0.012	0.000	0.000	0.000	0.000
139	A	597	ALA	0	0.030	0.001	21.090	-0.018	-0.018	0.000	0.000	0.000	0.000
140	A	598	VAL	0	-0.038	-0.013	17.638	0.032	0.032	0.000	0.000	0.000	0.000
141	A	599	ALA	0	0.022	0.017	18.314	-0.030	-0.030	0.000	0.000	0.000	0.000
142	A	600	VAL	0	0.021	0.004	17.228	0.031	0.031	0.000	0.000	0.000	0.000
143	A	601	LEU	0	0.015	0.017	14.661	-0.025	-0.025	0.000	0.000	0.000	0.000
144	A	602	ALA	0	-0.018	-0.006	17.994	-0.011	-0.011	0.000	0.000	0.000	0.000
145	A	603	PRO	0	0.011	-0.008	19.439	0.000	0.000	0.000	0.000	0.000	0.000
146	A	604	PRO	0	-0.058	-0.003	18.968	0.004	0.004	0.000	0.000	0.000	0.000

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