FMO DATABASE

FMODB ID: 6Y9MZ

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	OptH
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	-1562335.383113
FMO2-HF: Nuclear repulsion	1498567.961932
FMO2-HF: Total energy	-63767.42118
FMO2-MP2: Total energy	-63957.457843

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.
-3.499	0.668	4.773	-3.523	-5.417	-0.002

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 : 0.059 / q_NPA : 0.009

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	0.039	0.022	2.798	-1.527	0.880	0.273	-1.191	-1.489	-0.004
4	A	32	LYS	1	0.975	0.990	1.928	-3.309	-2.041	4.489	-2.232	-3.525	0.002
5	A	33	GLN	0	0.008	0.006	3.748	-0.102	0.390	0.011	-0.100	-0.403	0.000
6	A	34	VAL	0	0.037	0.025	5.658	0.488	0.488	0.000	0.000	0.000	0.000
7	A	35	LEU	0	-0.011	-0.024	6.286	0.214	0.214	0.000	0.000	0.000	0.000
8	A	36	ALA	0	0.013	0.008	7.903	0.128	0.128	0.000	0.000	0.000	0.000
9	A	37	ASP	-1	-0.838	-0.929	9.607	-0.363	-0.363	0.000	0.000	0.000	0.000
10	A	38	ILE	0	-0.036	-0.007	10.378	0.056	0.056	0.000	0.000	0.000	0.000
11	A	39	ALA	0	0.031	0.009	12.686	0.039	0.039	0.000	0.000	0.000	0.000
12	A	40	LYS	1	0.911	0.962	11.827	0.182	0.182	0.000	0.000	0.000	0.000
13	A	41	GLN	0	-0.027	-0.005	15.504	0.019	0.019	0.000	0.000	0.000	0.000
14	A	42	VAL	0	0.004	-0.016	17.298	0.016	0.016	0.000	0.000	0.000	0.000
15	A	43	ASP	-1	-0.844	-0.930	18.035	-0.045	-0.045	0.000	0.000	0.000	0.000
16	A	44	PHE	0	-0.064	-0.023	19.976	0.013	0.013	0.000	0.000	0.000	0.000
17	A	45	TRP	0	-0.034	-0.040	19.752	0.001	0.001	0.000	0.000	0.000	0.000
18	A	46	PHE	0	0.027	0.009	22.983	0.004	0.004	0.000	0.000	0.000	0.000
19	A	47	GLY	0	0.031	0.029	24.236	0.007	0.007	0.000	0.000	0.000	0.000
20	A	48	ASP	-1	-0.862	-0.956	25.093	-0.017	-0.017	0.000	0.000	0.000	0.000
21	A	49	ALA	0	0.028	0.021	27.097	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	50	ASN	0	-0.006	-0.015	26.013	0.000	0.000	0.000	0.000	0.000	0.000
23	A	51	LEU	0	-0.022	0.002	27.946	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	52	HIS	0	0.039	0.017	30.015	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	53	LYS	1	0.812	0.932	30.539	0.017	0.017	0.000	0.000	0.000	0.000
26	A	54	ASP	-1	-0.865	-0.953	29.882	-0.056	-0.056	0.000	0.000	0.000	0.000
27	A	55	ARG	1	0.953	0.988	32.191	0.031	0.031	0.000	0.000	0.000	0.000
28	A	56	PHE	0	0.053	0.029	29.136	0.000	0.000	0.000	0.000	0.000	0.000
29	A	57	LEU	0	0.022	0.015	25.813	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	58	ARG	1	0.899	0.943	30.348	0.034	0.034	0.000	0.000	0.000	0.000
31	A	59	GLU	-1	-0.911	-0.953	32.993	-0.038	-0.038	0.000	0.000	0.000	0.000
32	A	60	GLN	0	-0.064	-0.041	30.579	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	61	ILE	0	-0.029	-0.011	29.440	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	62	GLU	-1	-0.940	-0.960	32.469	-0.034	-0.034	0.000	0.000	0.000	0.000
35	A	63	LYS	1	0.818	0.916	36.064	0.045	0.045	0.000	0.000	0.000	0.000
36	A	64	SER	0	-0.020	-0.015	33.819	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	65	ARG	1	0.935	0.979	36.024	0.037	0.037	0.000	0.000	0.000	0.000
38	A	66	ASP	-1	-0.891	-0.947	33.123	-0.059	-0.059	0.000	0.000	0.000	0.000
39	A	67	GLY	0	-0.029	-0.023	31.642	0.000	0.000	0.000	0.000	0.000	0.000
40	A	68	TYR	0	0.103	0.066	26.746	0.000	0.000	0.000	0.000	0.000	0.000
41	A	69	VAL	0	-0.043	-0.028	25.771	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	70	ASP	-1	-0.798	-0.883	25.565	-0.124	-0.124	0.000	0.000	0.000	0.000
43	A	71	ILE	0	0.009	-0.004	19.359	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	72	SER	0	-0.049	-0.056	22.053	-0.012	-0.012	0.000	0.000	0.000	0.000
45	A	73	LEU	0	-0.011	0.010	24.487	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	74	LEU	0	0.040	0.051	20.046	0.000	0.000	0.000	0.000	0.000	0.000
47	A	75	VAL	0	-0.031	0.002	19.609	-0.007	-0.007	0.000	0.000	0.000	0.000
48	A	76	SER	0	-0.065	-0.072	21.351	0.000	0.000	0.000	0.000	0.000	0.000
49	A	77	PHE	0	0.028	0.013	22.341	0.008	0.008	0.000	0.000	0.000	0.000
50	A	78	ASN	0	0.007	-0.020	21.865	-0.018	-0.018	0.000	0.000	0.000	0.000
51	A	79	LYS	1	0.949	0.969	19.047	0.090	0.090	0.000	0.000	0.000	0.000
52	A	80	MET	0	0.039	0.051	16.912	-0.033	-0.033	0.000	0.000	0.000	0.000
53	A	81	LYS	1	0.915	0.961	16.869	0.097	0.097	0.000	0.000	0.000	0.000
54	A	82	LYS	1	0.904	0.961	16.762	0.121	0.121	0.000	0.000	0.000	0.000
55	A	83	LEU	0	-0.034	0.001	11.842	-0.035	-0.035	0.000	0.000	0.000	0.000
56	A	84	THR	0	-0.019	-0.021	12.452	-0.061	-0.061	0.000	0.000	0.000	0.000
57	A	85	THR	0	0.025	0.002	14.591	0.026	0.026	0.000	0.000	0.000	0.000
58	A	86	ASP	-1	-0.789	-0.871	14.588	-0.290	-0.290	0.000	0.000	0.000	0.000
59	A	87	GLY	0	0.062	0.019	15.856	-0.013	-0.013	0.000	0.000	0.000	0.000
60	A	88	LYS	1	0.925	0.935	16.240	0.287	0.287	0.000	0.000	0.000	0.000
61	A	89	LEU	0	-0.057	-0.028	9.398	-0.008	-0.008	0.000	0.000	0.000	0.000
62	A	90	ILE	0	0.026	0.008	12.647	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	91	ALA	0	0.035	0.021	14.993	0.019	0.019	0.000	0.000	0.000	0.000
64	A	92	ARG	1	0.899	0.943	8.601	0.518	0.518	0.000	0.000	0.000	0.000
65	A	93	ALA	0	-0.052	-0.027	11.484	0.028	0.028	0.000	0.000	0.000	0.000
66	A	94	LEU	0	0.020	0.020	12.501	0.029	0.029	0.000	0.000	0.000	0.000
67	A	95	ARG	1	0.914	0.979	14.873	0.166	0.166	0.000	0.000	0.000	0.000
68	A	96	SER	0	-0.021	-0.012	14.044	0.018	0.018	0.000	0.000	0.000	0.000
69	A	97	SER	0	0.005	-0.012	15.780	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	98	ALA	0	0.005	0.003	18.563	0.002	0.002	0.000	0.000	0.000	0.000
71	A	99	VAL	0	-0.032	-0.004	21.498	0.002	0.002	0.000	0.000	0.000	0.000
72	A	100	VAL	0	-0.022	-0.026	20.095	-0.008	-0.008	0.000	0.000	0.000	0.000
73	A	101	GLU	-1	-0.923	-0.963	21.745	-0.057	-0.057	0.000	0.000	0.000	0.000
74	A	102	LEU	0	0.001	-0.034	19.068	-0.006	-0.006	0.000	0.000	0.000	0.000
75	A	103	ASP	-1	-0.890	-0.923	23.242	-0.074	-0.074	0.000	0.000	0.000	0.000
76	A	104	LEU	0	-0.043	-0.002	24.786	-0.010	-0.010	0.000	0.000	0.000	0.000
77	A	105	GLU	-1	-0.874	-0.966	24.511	-0.118	-0.118	0.000	0.000	0.000	0.000
78	A	106	GLY	0	-0.096	-0.026	20.744	-0.010	-0.010	0.000	0.000	0.000	0.000
79	A	107	THR	0	-0.002	-0.004	21.005	-0.013	-0.013	0.000	0.000	0.000	0.000
80	A	108	ARG	1	0.955	0.981	23.580	0.083	0.083	0.000	0.000	0.000	0.000
81	A	109	ILE	0	-0.003	0.006	20.902	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	110	ARG	1	0.895	0.956	24.246	0.063	0.063	0.000	0.000	0.000	0.000
83	A	111	ARG	1	0.935	0.954	25.469	0.032	0.032	0.000	0.000	0.000	0.000
84	A	112	LYS	1	0.862	0.982	22.359	0.040	0.040	0.000	0.000	0.000	0.000
85	A	113	LYS	1	0.969	0.967	27.474	0.019	0.019	0.000	0.000	0.000	0.000
86	A	114	PRO	0	-0.011	0.000	30.043	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	115	LEU	0	-0.034	-0.012	30.727	0.002	0.002	0.000	0.000	0.000	0.000
88	A	116	GLY	0	0.044	0.021	33.518	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	117	GLU	-1	-0.930	-0.967	36.882	-0.013	-0.013	0.000	0.000	0.000	0.000
90	A	118	ARG	1	0.827	0.903	35.239	0.016	0.016	0.000	0.000	0.000	0.000
91	A	119	PRO	0	-0.004	-0.005	33.728	0.001	0.001	0.000	0.000	0.000	0.000
92	A	120	LYS	1	0.913	0.947	37.028	0.006	0.006	0.000	0.000	0.000	0.000
93	A	121	ASP	-1	-0.846	-0.929	35.239	0.005	0.005	0.000	0.000	0.000	0.000
94	A	122	GLU	-1	-0.821	-0.893	33.810	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	123	ASP	-1	-0.880	-0.948	35.297	0.001	0.001	0.000	0.000	0.000	0.000
96	A	124	GLU	-1	-0.972	-0.980	37.722	0.017	0.017	0.000	0.000	0.000	0.000
97	A	125	ARG	1	0.794	0.889	29.913	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	126	THR	0	-0.121	-0.056	32.641	0.001	0.001	0.000	0.000	0.000	0.000
99	A	127	VAL	0	0.060	0.037	32.444	0.001	0.001	0.000	0.000	0.000	0.000
100	A	128	TYR	0	-0.029	-0.008	33.574	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	129	VAL	0	-0.001	-0.012	31.240	0.003	0.003	0.000	0.000	0.000	0.000
102	A	130	GLU	-1	-0.908	-0.956	34.599	0.007	0.007	0.000	0.000	0.000	0.000
103	A	131	LEU	0	-0.083	-0.031	30.397	0.003	0.003	0.000	0.000	0.000	0.000
104	A	132	LEU	0	0.019	0.022	29.863	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	133	PRO	0	-0.006	-0.017	32.013	-0.003	-0.003	0.000	0.000	0.000	0.000
106	A	134	LYS	1	1.037	1.023	30.686	0.016	0.016	0.000	0.000	0.000	0.000
107	A	135	ASN	0	-0.028	-0.034	28.439	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	136	VAL	0	0.006	-0.003	27.312	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	137	ASN	0	-0.025	-0.021	23.028	0.001	0.001	0.000	0.000	0.000	0.000
110	A	138	HIS	0	0.054	0.004	22.243	0.003	0.003	0.000	0.000	0.000	0.000
111	A	139	SER	0	0.005	-0.001	18.338	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	140	TRP	0	-0.012	0.012	20.825	0.015	0.015	0.000	0.000	0.000	0.000
113	A	141	ILE	0	0.037	0.009	23.540	0.009	0.009	0.000	0.000	0.000	0.000
114	A	142	GLU	-1	-0.948	-0.971	18.298	0.035	0.035	0.000	0.000	0.000	0.000
115	A	143	ARG	1	0.963	0.999	19.837	-0.049	-0.049	0.000	0.000	0.000	0.000
116	A	144	VAL	0	-0.089	-0.056	21.353	0.013	0.013	0.000	0.000	0.000	0.000
117	A	145	PHE	0	0.067	0.016	24.812	0.004	0.004	0.000	0.000	0.000	0.000
118	A	146	GLY	0	0.038	0.044	21.588	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	147	LYS	1	0.874	0.928	22.621	-0.081	-0.081	0.000	0.000	0.000	0.000
120	A	148	CYS	0	-0.016	0.015	24.342	0.003	0.003	0.000	0.000	0.000	0.000
121	A	149	GLY	0	0.006	0.004	24.935	-0.005	-0.005	0.000	0.000	0.000	0.000
122	A	150	ASN	0	-0.026	-0.008	20.607	0.004	0.004	0.000	0.000	0.000	0.000
123	A	151	VAL	0	0.010	0.008	21.756	-0.006	-0.006	0.000	0.000	0.000	0.000
124	A	152	VAL	0	-0.028	-0.003	22.766	-0.007	-0.007	0.000	0.000	0.000	0.000
125	A	153	TYR	0	-0.002	-0.019	24.728	-0.010	-0.010	0.000	0.000	0.000	0.000
126	A	154	ILE	0	0.016	0.020	23.671	0.005	0.005	0.000	0.000	0.000	0.000
127	A	155	SER	0	-0.041	-0.018	27.291	-0.008	-0.008	0.000	0.000	0.000	0.000
128	A	156	ILE	0	0.046	0.027	26.877	0.004	0.004	0.000	0.000	0.000	0.000
129	A	157	PRO	0	-0.036	-0.010	31.083	-0.005	-0.005	0.000	0.000	0.000	0.000
130	A	158	HIS	0	0.030	0.002	32.331	0.003	0.003	0.000	0.000	0.000	0.000
131	A	159	TYR	0	-0.031	-0.016	35.716	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	160	LYS	1	1.015	1.013	38.752	0.018	0.018	0.000	0.000	0.000	0.000
133	A	161	SER	0	-0.060	-0.035	40.369	0.003	0.003	0.000	0.000	0.000	0.000
134	A	162	THR	0	0.016	-0.003	40.357	-0.003	-0.003	0.000	0.000	0.000	0.000
135	A	163	GLY	0	0.064	0.063	36.299	0.001	0.001	0.000	0.000	0.000	0.000
136	A	164	ASP	-1	-0.896	-0.966	35.802	-0.020	-0.020	0.000	0.000	0.000	0.000
137	A	165	PRO	0	-0.072	-0.043	33.536	0.000	0.000	0.000	0.000	0.000	0.000
138	A	166	LYS	1	0.911	0.956	35.590	0.017	0.017	0.000	0.000	0.000	0.000
139	A	167	GLY	0	0.019	0.025	36.127	0.002	0.002	0.000	0.000	0.000	0.000
140	A	168	PHE	0	0.029	0.026	35.042	0.002	0.002	0.000	0.000	0.000	0.000
141	A	169	ALA	0	-0.043	-0.033	30.503	-0.004	-0.004	0.000	0.000	0.000	0.000
142	A	170	PHE	0	0.013	0.008	31.665	0.002	0.002	0.000	0.000	0.000	0.000
143	A	171	VAL	0	-0.028	-0.026	27.132	-0.005	-0.005	0.000	0.000	0.000	0.000
144	A	172	GLU	-1	-0.848	-0.931	28.887	-0.004	-0.004	0.000	0.000	0.000	0.000
145	A	173	PHE	0	0.026	0.010	26.596	0.000	0.000	0.000	0.000	0.000	0.000
146	A	174	GLU	-1	-0.865	-0.934	26.616	0.007	0.007	0.000	0.000	0.000	0.000
147	A	175	THR	0	-0.043	-0.023	28.650	0.007	0.007	0.000	0.000	0.000	0.000
148	A	176	LYS	1	0.981	0.969	31.499	-0.021	-0.021	0.000	0.000	0.000	0.000
149	A	177	GLU	-1	-0.816	-0.907	32.708	0.029	0.029	0.000	0.000	0.000	0.000
150	A	178	GLN	0	-0.096	-0.056	26.980	0.003	0.003	0.000	0.000	0.000	0.000
151	A	179	ALA	0	0.042	0.045	30.725	0.002	0.002	0.000	0.000	0.000	0.000
152	A	180	ALA	0	0.041	0.011	32.795	0.000	0.000	0.000	0.000	0.000	0.000
153	A	181	LYS	1	0.937	0.975	28.719	-0.058	-0.058	0.000	0.000	0.000	0.000
154	A	182	ALA	0	0.003	-0.001	30.456	0.004	0.004	0.000	0.000	0.000	0.000
155	A	183	ILE	0	-0.042	-0.024	32.190	0.000	0.000	0.000	0.000	0.000	0.000
156	A	184	GLU	-1	-0.920	-0.939	34.534	0.050	0.050	0.000	0.000	0.000	0.000
157	A	185	PHE	0	-0.029	-0.036	30.821	0.002	0.002	0.000	0.000	0.000	0.000
158	A	186	LEU	0	-0.058	-0.007	34.001	0.000	0.000	0.000	0.000	0.000	0.000
159	A	187	ASN	0	-0.017	-0.018	36.724	-0.002	-0.002	0.000	0.000	0.000	0.000
160	A	188	ASN	0	0.011	0.016	34.838	0.001	0.001	0.000	0.000	0.000	0.000
161	A	189	PRO	0	-0.064	-0.026	34.085	-0.001	-0.001	0.000	0.000	0.000	0.000

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