FMO DATABASE

FMODB ID: KR6L3

Calculation Name: 2D4P-A-Xray310

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D4P

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SIW0

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:

Apendix: None

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	131
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1072105.78252
FMO2-HF: Nuclear repulsion	1022584.151376
FMO2-HF: Total energy	-49521.631144
FMO2-MP2: Total energy	-49668.628596

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:1:MET )

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

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.
-218.094	-205.727	34.989	-20.692	-26.66	-0.195

Interaction energy analysis for fragmet #1(A:1:MET )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.781 / q_NPA : 0.884

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	3	PHE	0	0.047	0.025	3.178	-3.871	0.699	1.460	-2.184	-3.847	-0.008
4	A	4	ARG	1	0.740	0.848	5.413	28.951	28.951	0.000	0.000	0.000	0.000
5	A	5	PRO	0	0.072	0.039	8.861	0.373	0.373	0.000	0.000	0.000	0.000
6	A	6	PHE	0	-0.040	-0.011	11.537	-0.851	-0.851	0.000	0.000	0.000	0.000
7	A	7	THR	0	-0.008	-0.036	13.170	0.856	0.856	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.773	-0.891	16.517	-12.817	-12.817	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.858	-0.910	17.060	-14.892	-14.892	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.794	-0.878	12.805	-22.291	-22.291	0.000	0.000	0.000	0.000
11	A	11	LEU	0	0.002	-0.007	14.443	-0.443	-0.443	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.862	-0.934	16.417	-15.174	-15.174	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.884	0.942	10.117	23.278	23.278	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.004	0.002	11.721	-0.667	-0.667	0.000	0.000	0.000	0.000
15	A	15	ASN	0	-0.018	-0.024	13.398	0.450	0.450	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.917	0.967	11.292	22.279	22.279	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.067	-0.008	8.334	-0.350	-0.350	0.000	0.000	0.000	0.000
18	A	18	ALA	0	-0.017	0.013	12.209	0.306	0.306	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.043	0.024	15.448	0.850	0.850	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.940	0.957	16.969	12.187	12.187	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.932	0.972	18.326	13.853	13.853	0.000	0.000	0.000	0.000
22	A	22	PRO	0	0.077	0.056	19.174	-0.658	-0.658	0.000	0.000	0.000	0.000
23	A	23	VAL	0	0.005	0.012	16.335	0.427	0.427	0.000	0.000	0.000	0.000
24	A	24	SER	0	0.020	0.005	19.708	-0.067	-0.067	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.098	0.034	21.231	-0.351	-0.351	0.000	0.000	0.000	0.000
26	A	26	GLY	0	-0.003	-0.001	22.436	-0.103	-0.103	0.000	0.000	0.000	0.000
27	A	27	ALA	0	0.005	-0.005	20.929	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.015	0.031	16.745	-0.124	-0.124	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.835	0.885	18.907	11.387	11.387	0.000	0.000	0.000	0.000
30	A	30	PHE	0	-0.065	-0.022	21.461	0.077	0.077	0.000	0.000	0.000	0.000
31	A	31	PHE	0	0.021	-0.010	17.071	0.046	0.046	0.000	0.000	0.000	0.000
32	A	32	ALA	0	0.016	0.021	16.837	-0.446	-0.446	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.920	0.960	17.888	11.460	11.460	0.000	0.000	0.000	0.000
34	A	34	THR	0	-0.074	-0.029	18.207	0.039	0.039	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.024	0.024	17.374	0.305	0.305	0.000	0.000	0.000	0.000
36	A	36	HIS	0	-0.034	-0.035	15.790	0.104	0.104	0.000	0.000	0.000	0.000
37	A	37	SER	0	-0.011	0.006	13.705	-0.300	-0.300	0.000	0.000	0.000	0.000
38	A	38	PHE	0	-0.039	-0.016	8.648	-0.688	-0.688	0.000	0.000	0.000	0.000
39	A	39	LEU	0	0.001	-0.005	7.589	1.213	1.213	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.009	0.003	3.294	-2.832	-2.282	0.508	-0.268	-0.788	0.003
41	A	41	GLU	-1	-0.811	-0.888	3.292	-30.280	-29.356	0.037	-0.299	-0.662	0.000
42	A	42	GLU	-1	-0.817	-0.903	1.708	-165.510	-163.481	27.239	-16.019	-13.249	-0.178
43	A	43	GLY	0	0.011	0.011	3.243	11.314	11.333	0.050	0.225	-0.294	-0.001
44	A	44	GLU	-1	-0.892	-0.960	5.768	-25.888	-25.888	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.866	-0.911	6.231	-22.312	-22.312	0.000	0.000	0.000	0.000
46	A	46	PRO	0	-0.030	-0.025	5.733	-4.688	-4.688	0.000	0.000	0.000	0.000
47	A	47	MET	0	0.001	-0.016	2.337	1.114	2.159	1.556	-0.436	-2.165	0.002
48	A	48	GLY	0	0.052	-0.001	5.383	1.602	1.693	0.000	-0.008	-0.082	0.000
49	A	49	PHE	0	-0.042	-0.009	7.158	-0.817	-0.817	0.000	0.000	0.000	0.000
50	A	50	ALA	0	0.027	0.013	9.701	0.797	0.797	0.000	0.000	0.000	0.000
51	A	51	LEU	0	-0.059	-0.024	12.097	0.041	0.041	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.018	-0.008	15.683	0.449	0.449	0.000	0.000	0.000	0.000
53	A	53	GLN	0	0.000	-0.011	17.425	0.298	0.298	0.000	0.000	0.000	0.000
54	A	54	ALA	0	0.035	0.027	20.678	0.048	0.048	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.036	-0.020	23.354	0.264	0.264	0.000	0.000	0.000	0.000
56	A	56	TRP	0	-0.003	0.009	26.488	0.057	0.057	0.000	0.000	0.000	0.000
57	A	57	GLN	0	-0.009	-0.024	28.392	-0.057	-0.057	0.000	0.000	0.000	0.000
58	A	58	GLY	0	-0.012	0.000	31.449	0.256	0.256	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.987	-0.992	32.907	-8.087	-8.087	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.032	0.031	29.138	-0.207	-0.207	0.000	0.000	0.000	0.000
61	A	61	THR	0	0.005	-0.017	24.800	0.251	0.251	0.000	0.000	0.000	0.000
62	A	62	THR	0	0.036	0.034	23.601	-0.097	-0.097	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.018	-0.004	18.016	0.026	0.026	0.000	0.000	0.000	0.000
64	A	64	LEU	0	0.001	0.006	20.638	-0.157	-0.157	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.009	-0.017	14.491	-0.347	-0.347	0.000	0.000	0.000	0.000
66	A	66	THR	0	-0.071	-0.025	17.696	0.497	0.497	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.743	0.829	15.168	15.561	15.561	0.000	0.000	0.000	0.000
68	A	68	ILE	0	0.028	0.029	9.844	-0.520	-0.520	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.836	-0.895	11.017	-15.690	-15.690	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.017	-0.020	7.234	-1.374	-1.374	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.810	0.909	5.248	28.284	28.284	0.000	0.000	0.000	0.000
72	A	72	SER	0	0.060	0.041	2.635	-0.309	0.339	0.122	-0.298	-0.471	-0.002
73	A	73	VAL	0	0.086	0.045	5.495	-0.306	-0.306	0.000	0.000	0.000	0.000
74	A	74	GLU	-1	-0.962	-0.972	2.995	-70.415	-67.188	0.701	-1.555	-2.372	-0.014
75	A	75	ALA	0	0.000	-0.014	2.646	-1.199	0.121	3.274	-2.175	-2.419	0.004
76	A	76	LEU	0	-0.013	-0.002	3.672	2.913	0.857	0.042	2.325	-0.311	-0.001
77	A	77	ARG	1	0.876	0.918	7.201	24.914	24.914	0.000	0.000	0.000	0.000
78	A	78	GLY	0	-0.015	-0.009	5.536	0.821	0.821	0.000	0.000	0.000	0.000
79	A	79	LEU	0	-0.028	-0.011	6.087	0.928	0.928	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.020	0.002	8.025	1.559	1.559	0.000	0.000	0.000	0.000
81	A	81	ARG	1	0.921	0.973	5.890	31.621	31.621	0.000	0.000	0.000	0.000
82	A	82	ALA	0	-0.048	-0.009	8.545	1.075	1.075	0.000	0.000	0.000	0.000
83	A	83	VAL	0	0.013	0.003	10.553	1.437	1.437	0.000	0.000	0.000	0.000
84	A	84	VAL	0	0.045	0.035	13.419	1.098	1.098	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.867	0.929	13.302	19.348	19.348	0.000	0.000	0.000	0.000
86	A	86	SER	0	-0.026	-0.017	14.706	1.018	1.018	0.000	0.000	0.000	0.000
87	A	87	ALA	0	0.016	0.002	16.445	0.851	0.851	0.000	0.000	0.000	0.000
88	A	88	TYR	0	0.014	-0.003	17.831	0.518	0.518	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.894	-0.937	17.815	-15.486	-15.486	0.000	0.000	0.000	0.000
90	A	90	ALA	0	-0.065	-0.025	20.621	0.522	0.522	0.000	0.000	0.000	0.000
91	A	91	GLY	0	-0.027	-0.004	22.661	0.528	0.528	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.096	-0.049	21.692	0.452	0.452	0.000	0.000	0.000	0.000
93	A	93	TYR	0	-0.038	-0.004	23.617	-0.158	-0.158	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.919	-0.960	22.923	-11.078	-11.078	0.000	0.000	0.000	0.000
95	A	95	VAL	0	0.024	0.006	17.019	-0.156	-0.156	0.000	0.000	0.000	0.000
96	A	96	ALA	0	0.023	0.018	20.465	0.112	0.112	0.000	0.000	0.000	0.000
97	A	97	LEU	0	0.018	-0.003	15.134	-0.438	-0.438	0.000	0.000	0.000	0.000
98	A	98	HIS	0	-0.018	-0.011	19.535	0.332	0.332	0.000	0.000	0.000	0.000
99	A	99	LEU	0	-0.011	-0.008	16.893	-0.387	-0.387	0.000	0.000	0.000	0.000
100	A	100	ASP	-1	-0.864	-0.930	18.943	-11.874	-11.874	0.000	0.000	0.000	0.000
101	A	101	PRO	0	0.058	0.013	18.826	-0.578	-0.578	0.000	0.000	0.000	0.000
102	A	102	GLU	-1	-0.944	-0.962	19.962	-11.532	-11.532	0.000	0.000	0.000	0.000
103	A	103	ARG	1	0.816	0.909	12.409	15.810	15.810	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.935	0.950	15.550	12.314	12.314	0.000	0.000	0.000	0.000
105	A	105	GLU	-1	-0.876	-0.933	8.737	-22.401	-22.401	0.000	0.000	0.000	0.000
106	A	106	LEU	0	-0.011	-0.013	11.520	-0.755	-0.755	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.923	-0.963	12.716	-13.259	-13.259	0.000	0.000	0.000	0.000
108	A	108	GLU	-1	-0.933	-0.965	12.223	-19.391	-19.391	0.000	0.000	0.000	0.000
109	A	109	ALA	0	-0.030	-0.037	9.982	-0.347	-0.347	0.000	0.000	0.000	0.000
110	A	110	LEU	0	-0.001	-0.010	11.843	-0.073	-0.073	0.000	0.000	0.000	0.000
111	A	111	LYS	1	0.982	1.004	14.981	13.878	13.878	0.000	0.000	0.000	0.000
112	A	112	ALA	0	-0.062	-0.032	12.794	0.272	0.272	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.821	-0.898	11.117	-23.410	-23.410	0.000	0.000	0.000	0.000
114	A	114	GLY	0	-0.016	0.001	14.570	0.398	0.398	0.000	0.000	0.000	0.000
115	A	115	PHE	0	-0.014	-0.001	15.128	0.665	0.665	0.000	0.000	0.000	0.000
116	A	116	ALA	0	-0.005	-0.002	19.142	0.071	0.071	0.000	0.000	0.000	0.000
117	A	117	LEU	0	-0.035	-0.027	19.734	-0.034	-0.034	0.000	0.000	0.000	0.000
118	A	118	GLY	0	0.018	0.032	23.571	0.377	0.377	0.000	0.000	0.000	0.000
119	A	119	PRO	0	-0.041	-0.031	26.816	-0.246	-0.246	0.000	0.000	0.000	0.000
120	A	120	LEU	0	0.015	-0.007	28.112	0.252	0.252	0.000	0.000	0.000	0.000
121	A	121	VAL	0	0.044	0.031	28.002	-0.254	-0.254	0.000	0.000	0.000	0.000
122	A	122	LEU	0	-0.020	-0.003	25.032	0.058	0.058	0.000	0.000	0.000	0.000
123	A	123	ALA	0	0.010	0.006	28.624	0.156	0.156	0.000	0.000	0.000	0.000
124	A	124	VAL	0	0.011	-0.006	27.912	-0.078	-0.078	0.000	0.000	0.000	0.000
125	A	125	ARG	1	0.979	0.989	31.337	7.679	7.679	0.000	0.000	0.000	0.000
126	A	126	VAL	0	-0.002	0.000	30.104	-0.068	-0.068	0.000	0.000	0.000	0.000
127	A	127	LEU	0	-0.029	-0.013	32.890	0.244	0.244	0.000	0.000	0.000	0.000
128	A	128	GLY	0	0.035	0.020	33.246	0.152	0.152	0.000	0.000	0.000	0.000
129	A	129	SER	0	-0.036	-0.017	32.139	-0.112	-0.112	0.000	0.000	0.000	0.000
130	A	130	ARG	1	0.971	0.969	34.376	7.688	7.688	0.000	0.000	0.000	0.000
131	A	131	NME	0	0.036	0.037	36.681	-0.151	-0.151	0.000	0.000	0.000	0.000

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