FMO DATABASE

FMODB ID: R8RZ8

Calculation Name: 4WKR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4WKR

Chain ID: A

ChEMBL ID:

UniProt ID: Q4G0J3

Base Structure: X-ray

Registration Date: 2023-09-24

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	161
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1568023.270714
FMO2-HF: Nuclear repulsion	1504253.344589
FMO2-HF: Total energy	-63769.926125
FMO2-MP2: Total energy	-63959.796765

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:29:SER)

Summations of interaction energy for fragment #1(A:29: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.
-14.881	-10.361	7.968	-5.371	-7.117	0.032

Interaction energy analysis for fragmet #1(A:29:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.087 / q_NPA : 0.044

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	31	VAL	0	0.037	0.023	2.819	-3.581	0.051	0.676	-1.998	-2.310	0.011
4	A	32	LYS	1	0.974	0.989	1.910	-8.991	-8.812	7.268	-3.140	-4.307	0.020
5	A	33	GLN	0	-0.024	-0.017	3.835	-1.979	-1.270	0.024	-0.233	-0.500	0.001
6	A	34	VAL	0	0.039	0.018	5.676	0.052	0.052	0.000	0.000	0.000	0.000
7	A	35	LEU	0	-0.027	-0.013	5.794	-0.198	-0.198	0.000	0.000	0.000	0.000
8	A	36	ALA	0	0.027	0.015	7.664	-0.138	-0.138	0.000	0.000	0.000	0.000
9	A	37	ASP	-1	-0.824	-0.905	9.294	-0.255	-0.255	0.000	0.000	0.000	0.000
10	A	38	ILE	0	-0.017	-0.011	11.080	-0.020	-0.020	0.000	0.000	0.000	0.000
11	A	39	ALA	0	0.013	0.010	12.460	-0.027	-0.027	0.000	0.000	0.000	0.000
12	A	40	LYS	1	0.901	0.954	12.540	0.106	0.106	0.000	0.000	0.000	0.000
13	A	41	GLN	0	-0.003	0.009	15.122	-0.020	-0.020	0.000	0.000	0.000	0.000
14	A	42	VAL	0	-0.003	-0.006	17.062	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	43	ASP	-1	-0.763	-0.910	17.858	0.035	0.035	0.000	0.000	0.000	0.000
16	A	44	PHE	0	-0.046	-0.008	19.291	-0.005	-0.005	0.000	0.000	0.000	0.000
17	A	45	TRP	0	-0.029	-0.032	19.360	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	46	PHE	0	0.034	0.012	22.600	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	47	GLY	0	0.084	0.053	23.771	0.001	0.001	0.000	0.000	0.000	0.000
20	A	48	ASP	-1	-0.819	-0.897	24.791	0.008	0.008	0.000	0.000	0.000	0.000
21	A	49	ALA	0	0.029	0.020	27.050	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	50	ASN	0	0.007	-0.006	25.653	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	51	LEU	0	-0.019	-0.002	27.742	0.000	0.000	0.000	0.000	0.000	0.000
24	A	52	HIS	0	0.015	0.013	29.677	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	53	LYS	1	0.693	0.839	30.235	0.003	0.003	0.000	0.000	0.000	0.000
26	A	54	ASP	-1	-0.784	-0.878	29.891	0.000	0.000	0.000	0.000	0.000	0.000
27	A	55	ARG	1	0.855	0.912	31.863	0.000	0.000	0.000	0.000	0.000	0.000
28	A	56	PHE	0	0.000	0.002	29.388	0.001	0.001	0.000	0.000	0.000	0.000
29	A	57	LEU	0	-0.004	-0.007	25.373	0.001	0.001	0.000	0.000	0.000	0.000
30	A	58	ARG	1	0.870	0.921	29.901	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	59	GLU	-1	-0.808	-0.881	32.488	0.002	0.002	0.000	0.000	0.000	0.000
32	A	60	GLN	0	-0.040	-0.023	30.178	0.000	0.000	0.000	0.000	0.000	0.000
33	A	61	ILE	0	-0.037	0.015	28.446	0.001	0.001	0.000	0.000	0.000	0.000
34	A	62	GLU	-1	-0.903	-0.969	32.455	0.004	0.004	0.000	0.000	0.000	0.000
35	A	63	LYS	1	0.808	0.889	35.862	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	64	SER	0	0.002	-0.003	32.997	0.000	0.000	0.000	0.000	0.000	0.000
37	A	65	ARG	1	0.922	0.966	35.286	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	66	ASP	-1	-0.809	-0.892	32.914	0.010	0.010	0.000	0.000	0.000	0.000
39	A	67	GLY	0	-0.025	-0.003	31.757	0.001	0.001	0.000	0.000	0.000	0.000
40	A	68	TYR	0	-0.079	-0.073	25.900	0.002	0.002	0.000	0.000	0.000	0.000
41	A	69	VAL	0	0.025	0.021	25.867	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	70	ASP	-1	-0.780	-0.885	25.611	0.020	0.020	0.000	0.000	0.000	0.000
43	A	71	ILE	0	0.015	0.001	19.292	0.001	0.001	0.000	0.000	0.000	0.000
44	A	72	SER	0	-0.027	-0.040	22.067	0.003	0.003	0.000	0.000	0.000	0.000
45	A	73	LEU	0	-0.034	-0.003	24.167	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	74	LEU	0	0.023	0.025	20.010	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	75	VAL	0	-0.025	-0.008	19.059	0.000	0.000	0.000	0.000	0.000	0.000
48	A	76	SER	0	-0.051	-0.034	21.335	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	77	PHE	0	0.064	0.037	22.056	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	78	ASN	0	0.001	-0.025	21.696	0.005	0.005	0.000	0.000	0.000	0.000
51	A	79	LYS	1	0.878	0.939	17.963	0.029	0.029	0.000	0.000	0.000	0.000
52	A	80	MET	0	0.064	0.049	16.796	0.005	0.005	0.000	0.000	0.000	0.000
53	A	81	LYS	1	0.881	0.932	16.777	0.008	0.008	0.000	0.000	0.000	0.000
54	A	82	LYS	1	0.906	0.965	17.043	0.035	0.035	0.000	0.000	0.000	0.000
55	A	83	LEU	0	-0.023	0.014	12.154	-0.013	-0.013	0.000	0.000	0.000	0.000
56	A	84	THR	0	-0.031	-0.048	12.129	0.068	0.068	0.000	0.000	0.000	0.000
57	A	85	THR	0	0.038	0.022	14.508	-0.010	-0.010	0.000	0.000	0.000	0.000
58	A	86	ASP	-1	-0.784	-0.866	14.724	0.045	0.045	0.000	0.000	0.000	0.000
59	A	87	GLY	0	0.068	0.020	15.793	0.017	0.017	0.000	0.000	0.000	0.000
60	A	88	LYS	1	0.931	0.945	15.797	-0.023	-0.023	0.000	0.000	0.000	0.000
61	A	89	LEU	0	-0.073	-0.035	9.277	0.004	0.004	0.000	0.000	0.000	0.000
62	A	90	ILE	0	0.035	0.007	12.312	0.033	0.033	0.000	0.000	0.000	0.000
63	A	91	ALA	0	0.040	0.022	14.732	0.004	0.004	0.000	0.000	0.000	0.000
64	A	92	ARG	1	0.893	0.938	7.579	0.020	0.020	0.000	0.000	0.000	0.000
65	A	93	ALA	0	-0.037	-0.011	11.216	0.010	0.010	0.000	0.000	0.000	0.000
66	A	94	LEU	0	0.002	-0.004	12.133	-0.012	-0.012	0.000	0.000	0.000	0.000
67	A	95	ARG	1	0.913	0.969	13.898	-0.045	-0.045	0.000	0.000	0.000	0.000
68	A	96	SER	0	-0.033	-0.014	13.507	-0.014	-0.014	0.000	0.000	0.000	0.000
69	A	97	SER	0	0.010	0.023	14.930	0.010	0.010	0.000	0.000	0.000	0.000
70	A	98	ALA	0	-0.009	0.014	17.709	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	99	VAL	0	-0.019	-0.006	20.640	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	100	VAL	0	-0.003	-0.013	20.193	0.005	0.005	0.000	0.000	0.000	0.000
73	A	101	GLU	-1	-0.813	-0.883	21.714	0.023	0.023	0.000	0.000	0.000	0.000
74	A	102	LEU	0	-0.015	-0.033	18.163	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	103	ASP	-1	-0.800	-0.856	22.868	0.012	0.012	0.000	0.000	0.000	0.000
76	A	104	LEU	0	-0.001	-0.004	24.053	0.001	0.001	0.000	0.000	0.000	0.000
77	A	105	GLU	-1	-0.912	-0.965	23.543	0.006	0.006	0.000	0.000	0.000	0.000
78	A	106	GLY	0	-0.081	-0.013	20.608	0.002	0.002	0.000	0.000	0.000	0.000
79	A	107	THR	0	0.014	-0.003	20.585	0.005	0.005	0.000	0.000	0.000	0.000
80	A	108	ARG	1	0.790	0.875	23.235	-0.012	-0.012	0.000	0.000	0.000	0.000
81	A	109	ILE	0	-0.015	-0.016	20.895	0.003	0.003	0.000	0.000	0.000	0.000
82	A	110	ARG	1	0.855	0.921	24.367	-0.019	-0.019	0.000	0.000	0.000	0.000
83	A	111	ARG	1	0.771	0.830	25.372	-0.010	-0.010	0.000	0.000	0.000	0.000
84	A	112	LYS	1	0.771	0.921	21.004	-0.036	-0.036	0.000	0.000	0.000	0.000
85	A	113	LYS	1	0.983	0.972	26.774	-0.018	-0.018	0.000	0.000	0.000	0.000
86	A	114	PRO	0	0.018	0.011	29.286	0.000	0.000	0.000	0.000	0.000	0.000
87	A	115	LEU	0	-0.011	-0.006	30.494	0.001	0.001	0.000	0.000	0.000	0.000
88	A	116	GLY	0	0.035	0.014	33.226	0.000	0.000	0.000	0.000	0.000	0.000
89	A	117	GLU	-1	-0.916	-0.954	36.684	0.005	0.005	0.000	0.000	0.000	0.000
90	A	118	ARG	1	0.792	0.884	35.139	0.001	0.001	0.000	0.000	0.000	0.000
91	A	119	PRO	0	0.013	0.006	33.257	0.000	0.000	0.000	0.000	0.000	0.000
92	A	120	LYS	1	0.858	0.908	36.589	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	121	ASP	-1	-0.779	-0.880	34.873	0.001	0.001	0.000	0.000	0.000	0.000
94	A	122	GLU	-1	-0.760	-0.844	33.314	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	123	ASP	-1	-0.880	-0.937	35.160	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	124	GLU	-1	-0.924	-0.955	37.194	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	125	ARG	1	0.748	0.844	30.700	0.001	0.001	0.000	0.000	0.000	0.000
98	A	126	THR	0	-0.130	-0.064	32.257	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	127	VAL	0	0.016	0.009	32.428	0.001	0.001	0.000	0.000	0.000	0.000
100	A	128	TYR	0	-0.088	-0.066	33.199	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	129	VAL	0	0.005	-0.007	30.950	0.000	0.000	0.000	0.000	0.000	0.000
102	A	130	GLU	-1	-0.839	-0.889	34.176	-0.013	-0.013	0.000	0.000	0.000	0.000
103	A	131	LEU	0	-0.057	-0.029	30.316	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	132	LEU	0	0.021	0.024	30.094	0.001	0.001	0.000	0.000	0.000	0.000
105	A	133	PRO	0	-0.009	-0.016	32.327	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	134	LYS	1	0.941	0.967	31.011	0.018	0.018	0.000	0.000	0.000	0.000
107	A	135	ASN	0	-0.012	-0.025	28.285	-0.005	-0.005	0.000	0.000	0.000	0.000
108	A	136	VAL	0	0.008	0.003	27.135	0.000	0.000	0.000	0.000	0.000	0.000
109	A	137	ASN	0	-0.006	-0.011	22.650	-0.010	-0.010	0.000	0.000	0.000	0.000
110	A	138	HIS	0	0.048	0.008	22.161	-0.005	-0.005	0.000	0.000	0.000	0.000
111	A	139	SER	0	0.004	-0.013	18.417	0.000	0.000	0.000	0.000	0.000	0.000
112	A	140	TRP	0	-0.053	-0.004	20.770	-0.009	-0.009	0.000	0.000	0.000	0.000
113	A	141	ILE	0	0.056	0.024	23.690	0.000	0.000	0.000	0.000	0.000	0.000
114	A	142	GLU	-1	-0.885	-0.918	18.102	-0.095	-0.095	0.000	0.000	0.000	0.000
115	A	143	ARG	1	0.898	0.936	18.867	0.083	0.083	0.000	0.000	0.000	0.000
116	A	144	VAL	0	-0.063	-0.022	21.134	0.002	0.002	0.000	0.000	0.000	0.000
117	A	145	PHE	0	0.062	0.002	24.742	0.003	0.003	0.000	0.000	0.000	0.000
118	A	146	GLY	0	0.026	0.014	21.591	0.004	0.004	0.000	0.000	0.000	0.000
119	A	147	LYS	1	0.861	0.931	22.631	0.042	0.042	0.000	0.000	0.000	0.000
120	A	148	CYS	0	-0.004	0.027	24.470	0.003	0.003	0.000	0.000	0.000	0.000
121	A	149	GLY	0	0.021	0.005	25.335	0.004	0.004	0.000	0.000	0.000	0.000
122	A	150	ASN	0	-0.032	-0.015	21.314	-0.006	-0.006	0.000	0.000	0.000	0.000
123	A	151	VAL	0	-0.015	-0.005	22.127	0.003	0.003	0.000	0.000	0.000	0.000
124	A	152	VAL	0	-0.025	-0.015	22.932	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	153	TYR	0	-0.023	-0.018	24.908	0.001	0.001	0.000	0.000	0.000	0.000
126	A	154	ILE	0	0.021	0.019	23.383	-0.001	-0.001	0.000	0.000	0.000	0.000
127	A	155	SER	0	-0.042	-0.007	27.148	0.000	0.000	0.000	0.000	0.000	0.000
128	A	156	ILE	0	0.060	0.027	26.914	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	157	PRO	0	-0.016	0.002	31.131	0.000	0.000	0.000	0.000	0.000	0.000
130	A	158	HIS	0	0.027	0.006	32.326	-0.003	-0.003	0.000	0.000	0.000	0.000
131	A	159	TYR	0	-0.015	-0.012	35.872	0.002	0.002	0.000	0.000	0.000	0.000
132	A	160	LYS	1	0.996	1.002	38.644	0.006	0.006	0.000	0.000	0.000	0.000
133	A	161	SER	0	-0.027	-0.025	40.707	0.000	0.000	0.000	0.000	0.000	0.000
134	A	162	THR	0	0.055	0.028	40.557	0.000	0.000	0.000	0.000	0.000	0.000
135	A	163	GLY	0	0.050	0.037	36.703	0.000	0.000	0.000	0.000	0.000	0.000
136	A	164	ASP	-1	-0.833	-0.916	35.704	-0.017	-0.017	0.000	0.000	0.000	0.000
137	A	165	PRO	0	-0.102	-0.045	33.376	0.001	0.001	0.000	0.000	0.000	0.000
138	A	166	LYS	1	0.896	0.936	35.450	0.010	0.010	0.000	0.000	0.000	0.000
139	A	167	GLY	0	0.017	0.025	36.207	0.001	0.001	0.000	0.000	0.000	0.000
140	A	168	PHE	0	0.020	0.015	34.925	0.000	0.000	0.000	0.000	0.000	0.000
141	A	169	ALA	0	-0.056	-0.035	30.512	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	170	PHE	0	0.025	0.014	31.687	0.001	0.001	0.000	0.000	0.000	0.000
143	A	171	VAL	0	-0.034	-0.019	27.129	-0.002	-0.002	0.000	0.000	0.000	0.000
144	A	172	GLU	-1	-0.730	-0.838	28.895	-0.003	-0.003	0.000	0.000	0.000	0.000
145	A	173	PHE	0	0.022	0.005	26.781	-0.003	-0.003	0.000	0.000	0.000	0.000
146	A	174	GLU	-1	-0.834	-0.910	26.473	0.003	0.003	0.000	0.000	0.000	0.000
147	A	175	THR	0	-0.062	-0.045	28.541	0.000	0.000	0.000	0.000	0.000	0.000
148	A	176	LYS	1	0.945	0.956	31.701	-0.003	-0.003	0.000	0.000	0.000	0.000
149	A	177	GLU	-1	-0.816	-0.899	32.869	0.000	0.000	0.000	0.000	0.000	0.000
150	A	178	GLN	0	-0.057	-0.025	26.494	-0.003	-0.003	0.000	0.000	0.000	0.000
151	A	179	ALA	0	0.045	0.034	30.682	-0.002	-0.002	0.000	0.000	0.000	0.000
152	A	180	ALA	0	0.029	0.008	32.484	-0.001	-0.001	0.000	0.000	0.000	0.000
153	A	181	LYS	1	0.915	0.959	28.977	0.006	0.006	0.000	0.000	0.000	0.000
154	A	182	ALA	0	-0.018	-0.012	30.435	-0.002	-0.002	0.000	0.000	0.000	0.000
155	A	183	ILE	0	-0.025	-0.019	32.068	-0.001	-0.001	0.000	0.000	0.000	0.000
156	A	184	GLU	-1	-0.925	-0.959	34.059	-0.006	-0.006	0.000	0.000	0.000	0.000
157	A	185	PHE	0	-0.046	-0.025	30.598	-0.001	-0.001	0.000	0.000	0.000	0.000
158	A	186	LEU	0	-0.034	-0.001	33.685	-0.001	-0.001	0.000	0.000	0.000	0.000
159	A	187	ASN	0	-0.025	-0.009	36.320	0.001	0.001	0.000	0.000	0.000	0.000
160	A	188	ASN	0	-0.043	-0.012	34.267	0.000	0.000	0.000	0.000	0.000	0.000
161	A	189	PRO	0	-0.034	-0.020	34.625	-0.002	-0.002	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:29:SER)