FMO DATABASE

FMODB ID: N1GNQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1271642.784767
FMO2-HF: Nuclear repulsion	1218443.26642
FMO2-HF: Total energy	-53199.518346
FMO2-MP2: Total energy	-53359.156695

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.
0.625	3.542	-0.02	-1.322	-1.576	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 : 0.036 / q_NPA : 0.022

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	0.030	0.010	3.805	0.437	2.993	-0.018	-1.280	-1.258	0.005
4	A	462	PHE	0	0.077	0.029	5.792	-0.242	-0.159	-0.001	-0.005	-0.077	0.000
5	A	463	SER	0	0.012	-0.010	8.322	-0.090	-0.090	0.000	0.000	0.000	0.000
6	A	464	VAL	0	-0.049	-0.003	8.138	-0.106	-0.106	0.000	0.000	0.000	0.000
7	A	465	LEU	0	0.048	0.038	9.232	0.053	0.053	0.000	0.000	0.000	0.000
8	A	466	ARG	1	0.941	0.949	8.619	0.414	0.414	0.000	0.000	0.000	0.000
9	A	467	ALA	0	0.027	0.009	13.234	0.055	0.055	0.000	0.000	0.000	0.000
10	A	468	ASN	0	-0.047	-0.035	14.989	-0.012	-0.012	0.000	0.000	0.000	0.000
11	A	469	ASP	-1	-0.693	-0.773	10.314	0.151	0.151	0.000	0.000	0.000	0.000
12	A	470	VAL	0	-0.011	-0.014	12.559	-0.024	-0.024	0.000	0.000	0.000	0.000
13	A	471	LEU	0	-0.023	-0.014	12.356	0.078	0.078	0.000	0.000	0.000	0.000
14	A	472	TRP	0	0.044	0.017	14.204	-0.040	-0.040	0.000	0.000	0.000	0.000
15	A	473	LEU	0	-0.038	-0.034	15.919	0.029	0.029	0.000	0.000	0.000	0.000
16	A	474	SER	0	0.037	0.013	18.563	-0.009	-0.009	0.000	0.000	0.000	0.000
17	A	475	LEU	0	-0.043	-0.027	20.589	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	476	THR	0	0.015	-0.001	22.858	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	477	ALA	0	-0.013	0.000	25.284	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	478	ALA	0	-0.016	0.011	27.339	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	479	GLU	-1	-0.857	-0.936	29.134	0.043	0.043	0.000	0.000	0.000	0.000
22	A	480	TYR	0	-0.052	-0.045	32.298	0.000	0.000	0.000	0.000	0.000	0.000
23	A	481	ASP	-1	-0.729	-0.859	33.718	0.020	0.020	0.000	0.000	0.000	0.000
24	A	482	GLN	0	0.020	0.012	35.409	0.002	0.002	0.000	0.000	0.000	0.000
25	A	483	SER	0	-0.043	-0.026	37.803	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	484	THR	0	-0.061	-0.027	35.559	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	485	TYR	0	-0.125	-0.119	29.564	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	486	GLY	0	0.008	0.020	32.745	0.001	0.001	0.000	0.000	0.000	0.000
29	A	487	SER	0	-0.047	-0.024	35.067	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	488	SER	0	0.048	0.009	38.360	0.002	0.002	0.000	0.000	0.000	0.000
31	A	489	THR	0	-0.057	-0.027	39.352	0.001	0.001	0.000	0.000	0.000	0.000
32	A	490	GLY	0	-0.012	-0.015	35.778	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	491	PRO	0	-0.034	0.018	35.084	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	492	VAL	0	-0.028	-0.026	30.276	0.002	0.002	0.000	0.000	0.000	0.000
35	A	493	TYR	0	-0.006	-0.001	29.226	0.000	0.000	0.000	0.000	0.000	0.000
36	A	494	VAL	0	-0.019	-0.022	27.891	0.003	0.003	0.000	0.000	0.000	0.000
37	A	495	SER	0	0.063	0.011	25.378	0.002	0.002	0.000	0.000	0.000	0.000
38	A	496	ASP	-1	-0.802	-0.895	25.060	0.049	0.049	0.000	0.000	0.000	0.000
39	A	497	SER	0	-0.053	-0.018	22.915	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	498	VAL	0	0.014	0.008	19.350	0.008	0.008	0.000	0.000	0.000	0.000
41	A	499	THR	0	-0.032	-0.004	15.700	0.006	0.006	0.000	0.000	0.000	0.000
42	A	500	LEU	0	-0.002	-0.006	14.277	-0.023	-0.023	0.000	0.000	0.000	0.000
43	A	501	VAL	0	0.034	0.010	10.574	0.068	0.068	0.000	0.000	0.000	0.000
44	A	502	ASN	0	-0.038	-0.008	7.929	-0.096	-0.096	0.000	0.000	0.000	0.000
45	A	503	VAL	0	0.016	-0.013	8.814	0.179	0.179	0.000	0.000	0.000	0.000
46	A	504	ALA	0	-0.006	0.010	9.038	0.039	0.039	0.000	0.000	0.000	0.000
47	A	505	THR	0	-0.037	-0.031	3.729	-0.181	-0.041	0.001	-0.030	-0.111	0.000
48	A	506	GLY	0	0.036	0.028	4.858	0.559	0.636	-0.001	-0.002	-0.074	0.000
49	A	507	ALA	0	-0.039	-0.006	4.992	-0.101	-0.040	-0.001	-0.005	-0.056	0.000
50	A	508	GLN	0	0.001	-0.014	6.590	-0.498	-0.498	0.000	0.000	0.000	0.000
51	A	509	ALA	0	0.010	0.013	9.932	-0.016	-0.016	0.000	0.000	0.000	0.000
52	A	510	VAL	0	0.045	0.025	12.600	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	511	ALA	0	0.029	0.016	16.274	-0.029	-0.029	0.000	0.000	0.000	0.000
54	A	512	ARG	1	0.843	0.914	18.425	-0.082	-0.082	0.000	0.000	0.000	0.000
55	A	513	SER	0	-0.049	-0.028	16.640	-0.013	-0.013	0.000	0.000	0.000	0.000
56	A	514	LEU	0	0.030	0.029	13.159	0.001	0.001	0.000	0.000	0.000	0.000
57	A	515	ASP	-1	-0.801	-0.863	16.052	-0.150	-0.150	0.000	0.000	0.000	0.000
58	A	516	TRP	0	0.008	-0.031	16.728	-0.018	-0.018	0.000	0.000	0.000	0.000
59	A	517	THR	0	-0.079	-0.053	18.607	-0.011	-0.011	0.000	0.000	0.000	0.000
60	A	518	LYS	1	0.862	0.916	15.361	0.195	0.195	0.000	0.000	0.000	0.000
61	A	519	VAL	0	-0.045	0.001	14.121	-0.051	-0.051	0.000	0.000	0.000	0.000
62	A	520	THR	0	-0.049	-0.025	13.496	-0.027	-0.027	0.000	0.000	0.000	0.000
63	A	521	LEU	0	0.024	0.014	14.199	0.011	0.011	0.000	0.000	0.000	0.000
64	A	522	ASP	-1	-0.829	-0.936	14.791	-0.118	-0.118	0.000	0.000	0.000	0.000
65	A	523	GLY	0	-0.042	-0.025	14.920	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	524	ARG	1	0.910	0.967	16.004	0.150	0.150	0.000	0.000	0.000	0.000
67	A	525	PRO	0	0.045	0.023	18.354	0.005	0.005	0.000	0.000	0.000	0.000
68	A	526	LEU	0	0.003	0.012	17.541	0.014	0.014	0.000	0.000	0.000	0.000
69	A	527	SER	0	0.004	0.014	21.034	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	528	THR	0	0.000	-0.017	24.452	0.005	0.005	0.000	0.000	0.000	0.000
71	A	529	ILE	0	-0.024	-0.009	26.986	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	530	GLN	0	-0.013	-0.013	30.202	0.001	0.001	0.000	0.000	0.000	0.000
73	A	531	GLN	0	0.006	-0.009	31.947	0.004	0.004	0.000	0.000	0.000	0.000
74	A	532	HIS	0	0.052	0.031	33.825	0.000	0.000	0.000	0.000	0.000	0.000
75	A	533	SER	0	-0.010	-0.004	36.493	0.000	0.000	0.000	0.000	0.000	0.000
76	A	534	LYS	1	0.868	0.956	31.571	-0.007	-0.007	0.000	0.000	0.000	0.000
77	A	535	THR	0	0.018	0.002	28.240	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	536	PHE	0	-0.003	0.003	26.760	0.003	0.003	0.000	0.000	0.000	0.000
79	A	537	PHE	0	0.017	0.002	21.888	-0.009	-0.009	0.000	0.000	0.000	0.000
80	A	538	VAL	0	0.009	-0.006	23.695	0.013	0.013	0.000	0.000	0.000	0.000
81	A	539	LEU	0	0.003	0.009	17.242	-0.011	-0.011	0.000	0.000	0.000	0.000
82	A	540	PRO	0	0.019	0.002	20.988	0.014	0.014	0.000	0.000	0.000	0.000
83	A	541	LEU	0	0.004	0.012	19.798	0.006	0.006	0.000	0.000	0.000	0.000
84	A	542	ARG	1	0.869	0.929	19.765	-0.030	-0.030	0.000	0.000	0.000	0.000
85	A	543	GLY	0	0.018	0.010	23.081	0.011	0.011	0.000	0.000	0.000	0.000
86	A	544	LYS	1	0.810	0.902	25.762	-0.041	-0.041	0.000	0.000	0.000	0.000
87	A	545	LEU	0	-0.041	-0.020	22.022	0.008	0.008	0.000	0.000	0.000	0.000
88	A	546	SER	0	-0.007	0.005	23.179	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	547	PHE	0	0.028	-0.010	23.575	0.014	0.014	0.000	0.000	0.000	0.000
90	A	548	TRP	0	-0.007	0.003	21.395	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	549	GLU	-1	-0.829	-0.898	26.936	0.083	0.083	0.000	0.000	0.000	0.000
92	A	550	ALA	0	-0.008	-0.012	25.271	0.004	0.004	0.000	0.000	0.000	0.000
93	A	551	GLY	0	0.001	-0.004	26.178	-0.006	-0.006	0.000	0.000	0.000	0.000
94	A	552	THR	0	-0.036	-0.016	27.889	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	553	THR	0	0.000	-0.008	28.793	0.006	0.006	0.000	0.000	0.000	0.000
96	A	554	LYS	1	0.861	0.946	30.901	-0.073	-0.073	0.000	0.000	0.000	0.000
97	A	555	ALA	0	0.022	-0.004	30.115	0.005	0.005	0.000	0.000	0.000	0.000
98	A	556	GLY	0	0.009	0.017	29.906	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	557	TYR	0	-0.040	-0.026	30.821	0.001	0.001	0.000	0.000	0.000	0.000
100	A	558	PRO	0	0.048	0.016	30.049	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	559	TYR	0	0.049	0.014	31.974	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	560	ASN	0	-0.017	-0.005	33.564	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	561	TYR	0	-0.007	-0.011	33.849	0.001	0.001	0.000	0.000	0.000	0.000
104	A	562	ASN	0	-0.007	0.006	34.934	0.002	0.002	0.000	0.000	0.000	0.000
105	A	563	THR	0	0.048	0.023	34.816	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	564	THR	0	0.012	-0.006	32.907	0.003	0.003	0.000	0.000	0.000	0.000
107	A	565	ALA	0	-0.008	0.018	31.450	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	566	SER	0	0.002	0.002	25.814	0.006	0.006	0.000	0.000	0.000	0.000
109	A	567	ASP	-1	-0.820	-0.903	25.865	0.045	0.045	0.000	0.000	0.000	0.000
110	A	568	GLN	0	-0.042	-0.042	23.973	-0.006	-0.006	0.000	0.000	0.000	0.000
111	A	569	LEU	0	-0.004	0.013	19.186	0.008	0.008	0.000	0.000	0.000	0.000
112	A	570	LEU	0	0.009	0.013	23.241	-0.012	-0.012	0.000	0.000	0.000	0.000
113	A	571	VAL	0	0.028	0.008	20.212	0.010	0.010	0.000	0.000	0.000	0.000
114	A	572	GLU	-1	-0.745	-0.827	23.639	-0.005	-0.005	0.000	0.000	0.000	0.000
115	A	573	ASN	0	-0.016	-0.012	24.790	0.002	0.002	0.000	0.000	0.000	0.000
116	A	574	ALA	0	0.028	0.006	25.795	-0.006	-0.006	0.000	0.000	0.000	0.000
117	A	575	ALA	0	0.039	0.020	25.676	0.005	0.005	0.000	0.000	0.000	0.000
118	A	576	GLY	0	0.008	0.000	24.946	0.003	0.003	0.000	0.000	0.000	0.000
119	A	577	HIS	1	0.771	0.883	21.024	0.021	0.021	0.000	0.000	0.000	0.000
120	A	578	ARG	1	0.918	0.963	22.735	-0.013	-0.013	0.000	0.000	0.000	0.000
121	A	579	VAL	0	-0.004	0.003	20.743	-0.006	-0.006	0.000	0.000	0.000	0.000
122	A	580	ALA	0	0.007	0.003	24.108	0.003	0.003	0.000	0.000	0.000	0.000
123	A	581	ILE	0	-0.015	-0.007	24.188	0.000	0.000	0.000	0.000	0.000	0.000
124	A	582	SER	0	0.040	0.018	27.117	-0.003	-0.003	0.000	0.000	0.000	0.000
125	A	583	THR	0	-0.022	-0.011	30.025	0.007	0.007	0.000	0.000	0.000	0.000
126	A	584	TYR	0	-0.008	0.002	32.660	-0.004	-0.004	0.000	0.000	0.000	0.000
127	A	585	THR	0	0.055	0.019	36.016	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	586	THR	0	0.014	0.026	35.762	0.003	0.003	0.000	0.000	0.000	0.000
129	A	587	SER	0	-0.042	-0.020	34.230	0.002	0.002	0.000	0.000	0.000	0.000
130	A	588	LEU	0	-0.025	-0.023	29.998	0.002	0.002	0.000	0.000	0.000	0.000
131	A	589	GLY	0	0.013	0.014	34.216	0.002	0.002	0.000	0.000	0.000	0.000
132	A	590	ALA	0	0.014	-0.001	35.724	0.001	0.001	0.000	0.000	0.000	0.000
133	A	591	GLY	0	0.037	0.033	33.840	0.000	0.000	0.000	0.000	0.000	0.000
134	A	592	PRO	0	0.006	0.001	31.996	-0.003	-0.003	0.000	0.000	0.000	0.000
135	A	593	VAL	0	-0.047	-0.016	30.569	0.001	0.001	0.000	0.000	0.000	0.000
136	A	594	SER	0	-0.016	-0.013	26.099	0.000	0.000	0.000	0.000	0.000	0.000
137	A	595	ILE	0	0.002	0.013	25.109	0.000	0.000	0.000	0.000	0.000	0.000
138	A	596	SER	0	-0.027	0.003	22.085	0.012	0.012	0.000	0.000	0.000	0.000
139	A	597	ALA	0	0.040	0.005	21.037	-0.017	-0.017	0.000	0.000	0.000	0.000
140	A	598	VAL	0	-0.026	0.004	17.429	0.028	0.028	0.000	0.000	0.000	0.000
141	A	599	ALA	0	0.009	0.006	18.051	-0.025	-0.025	0.000	0.000	0.000	0.000
142	A	600	VAL	0	0.023	0.016	17.171	0.025	0.025	0.000	0.000	0.000	0.000
143	A	601	LEU	0	0.015	0.015	14.322	-0.021	-0.021	0.000	0.000	0.000	0.000
144	A	602	ALA	0	-0.007	0.002	17.896	-0.003	-0.003	0.000	0.000	0.000	0.000
145	A	603	PRO	0	0.002	-0.010	19.520	-0.007	-0.007	0.000	0.000	0.000	0.000
146	A	604	PRO	0	-0.054	-0.003	18.995	0.007	0.007	0.000	0.000	0.000	0.000

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