FMO DATABASE

FMODB ID: ZV3JN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1562837.868992
FMO2-HF: Nuclear repulsion	1499069.181612
FMO2-HF: Total energy	-63768.68738
FMO2-MP2: Total energy	-63958.675705

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.
-11.244	-8.488	7.634	-3.887	-6.504	0.034

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 : 0.035 / q_NPA : 0.003

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	0.033	0.018	3.138	-1.811	0.756	0.129	-1.183	-1.514	0.005
4	A	32	LYS	1	0.970	0.992	2.090	-6.374	-6.649	7.405	-2.728	-4.402	0.026
5	A	33	GLN	0	-0.022	-0.018	3.569	-2.168	-1.704	0.100	0.024	-0.588	0.003
6	A	34	VAL	0	0.024	0.012	5.723	-0.248	-0.248	0.000	0.000	0.000	0.000
7	A	35	LEU	0	-0.008	-0.016	5.616	-0.307	-0.307	0.000	0.000	0.000	0.000
8	A	36	ALA	0	0.014	0.007	7.788	-0.245	-0.245	0.000	0.000	0.000	0.000
9	A	37	ASP	-1	-0.819	-0.906	9.490	0.514	0.514	0.000	0.000	0.000	0.000
10	A	38	ILE	0	-0.042	-0.012	11.047	-0.087	-0.087	0.000	0.000	0.000	0.000
11	A	39	ALA	0	0.022	0.003	12.653	-0.064	-0.064	0.000	0.000	0.000	0.000
12	A	40	LYS	1	0.904	0.961	12.368	-0.498	-0.498	0.000	0.000	0.000	0.000
13	A	41	GLN	0	0.002	0.023	15.467	-0.013	-0.013	0.000	0.000	0.000	0.000
14	A	42	VAL	0	0.014	-0.009	17.325	-0.029	-0.029	0.000	0.000	0.000	0.000
15	A	43	ASP	-1	-0.839	-0.926	17.998	0.108	0.108	0.000	0.000	0.000	0.000
16	A	44	PHE	0	-0.068	-0.029	19.861	-0.010	-0.010	0.000	0.000	0.000	0.000
17	A	45	TRP	0	-0.027	-0.043	19.653	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	46	PHE	0	0.030	0.014	22.775	-0.013	-0.013	0.000	0.000	0.000	0.000
19	A	47	GLY	0	0.045	0.037	24.132	-0.012	-0.012	0.000	0.000	0.000	0.000
20	A	48	ASP	-1	-0.796	-0.907	25.011	0.069	0.069	0.000	0.000	0.000	0.000
21	A	49	ALA	0	0.028	0.023	27.109	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	50	ASN	0	0.010	-0.007	25.896	0.001	0.001	0.000	0.000	0.000	0.000
23	A	51	LEU	0	-0.025	-0.002	27.960	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	52	HIS	0	0.028	0.018	29.973	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	53	LYS	1	0.743	0.871	30.508	-0.091	-0.091	0.000	0.000	0.000	0.000
26	A	54	ASP	-1	-0.830	-0.925	30.162	0.081	0.081	0.000	0.000	0.000	0.000
27	A	55	ARG	1	0.874	0.939	32.223	-0.052	-0.052	0.000	0.000	0.000	0.000
28	A	56	PHE	0	0.027	0.009	29.622	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	57	LEU	0	0.010	0.010	25.996	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	58	ARG	1	0.884	0.926	30.455	-0.067	-0.067	0.000	0.000	0.000	0.000
31	A	59	GLU	-1	-0.847	-0.908	33.032	0.041	0.041	0.000	0.000	0.000	0.000
32	A	60	GLN	0	-0.066	-0.042	30.580	-0.007	-0.007	0.000	0.000	0.000	0.000
33	A	61	ILE	0	-0.052	-0.012	28.675	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	62	GLU	-1	-0.922	-0.955	32.441	0.037	0.037	0.000	0.000	0.000	0.000
35	A	63	LYS	1	0.818	0.905	36.060	-0.046	-0.046	0.000	0.000	0.000	0.000
36	A	64	SER	0	0.001	-0.009	33.243	0.002	0.002	0.000	0.000	0.000	0.000
37	A	65	ARG	1	0.926	0.973	35.981	-0.024	-0.024	0.000	0.000	0.000	0.000
38	A	66	ASP	-1	-0.824	-0.893	32.891	0.019	0.019	0.000	0.000	0.000	0.000
39	A	67	GLY	0	-0.015	-0.009	31.437	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	68	TYR	0	0.011	-0.034	26.075	0.002	0.002	0.000	0.000	0.000	0.000
41	A	69	VAL	0	-0.016	-0.019	25.787	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	70	ASP	-1	-0.778	-0.861	25.617	0.045	0.045	0.000	0.000	0.000	0.000
43	A	71	ILE	0	-0.003	-0.009	19.316	0.012	0.012	0.000	0.000	0.000	0.000
44	A	72	SER	0	-0.039	-0.054	22.209	0.015	0.015	0.000	0.000	0.000	0.000
45	A	73	LEU	0	-0.031	-0.004	24.662	0.007	0.007	0.000	0.000	0.000	0.000
46	A	74	LEU	0	0.031	0.025	20.116	0.008	0.008	0.000	0.000	0.000	0.000
47	A	75	VAL	0	-0.020	0.000	19.418	0.018	0.018	0.000	0.000	0.000	0.000
48	A	76	SER	0	-0.047	-0.030	21.649	0.007	0.007	0.000	0.000	0.000	0.000
49	A	77	PHE	0	0.043	0.026	22.571	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	78	ASN	0	0.017	-0.019	22.261	0.011	0.011	0.000	0.000	0.000	0.000
51	A	79	LYS	1	0.891	0.938	18.657	-0.235	-0.235	0.000	0.000	0.000	0.000
52	A	80	MET	0	0.045	0.050	17.089	0.046	0.046	0.000	0.000	0.000	0.000
53	A	81	LYS	1	0.885	0.941	17.291	-0.098	-0.098	0.000	0.000	0.000	0.000
54	A	82	LYS	1	0.901	0.957	17.236	-0.225	-0.225	0.000	0.000	0.000	0.000
55	A	83	LEU	0	-0.032	0.007	12.307	0.030	0.030	0.000	0.000	0.000	0.000
56	A	84	THR	0	-0.029	-0.031	12.684	0.039	0.039	0.000	0.000	0.000	0.000
57	A	85	THR	0	0.050	0.022	15.020	-0.015	-0.015	0.000	0.000	0.000	0.000
58	A	86	ASP	-1	-0.820	-0.888	14.916	0.036	0.036	0.000	0.000	0.000	0.000
59	A	87	GLY	0	0.074	0.022	16.071	0.029	0.029	0.000	0.000	0.000	0.000
60	A	88	LYS	1	0.938	0.945	16.091	-0.005	-0.005	0.000	0.000	0.000	0.000
61	A	89	LEU	0	-0.077	-0.039	9.850	-0.020	-0.020	0.000	0.000	0.000	0.000
62	A	90	ILE	0	0.043	0.012	12.522	0.039	0.039	0.000	0.000	0.000	0.000
63	A	91	ALA	0	0.035	0.021	15.012	0.002	0.002	0.000	0.000	0.000	0.000
64	A	92	ARG	1	0.885	0.939	7.605	0.256	0.256	0.000	0.000	0.000	0.000
65	A	93	ALA	0	-0.051	-0.025	11.296	-0.020	-0.020	0.000	0.000	0.000	0.000
66	A	94	LEU	0	0.026	0.019	12.238	0.007	0.007	0.000	0.000	0.000	0.000
67	A	95	ARG	1	0.916	0.981	14.035	0.076	0.076	0.000	0.000	0.000	0.000
68	A	96	SER	0	-0.020	-0.012	13.716	-0.026	-0.026	0.000	0.000	0.000	0.000
69	A	97	SER	0	0.027	0.021	15.307	0.032	0.032	0.000	0.000	0.000	0.000
70	A	98	ALA	0	-0.004	0.007	18.141	-0.022	-0.022	0.000	0.000	0.000	0.000
71	A	99	VAL	0	-0.029	-0.009	21.251	-0.014	-0.014	0.000	0.000	0.000	0.000
72	A	100	VAL	0	0.012	-0.020	20.027	0.007	0.007	0.000	0.000	0.000	0.000
73	A	101	GLU	-1	-0.842	-0.905	21.376	0.006	0.006	0.000	0.000	0.000	0.000
74	A	102	LEU	0	-0.001	-0.031	18.497	0.005	0.005	0.000	0.000	0.000	0.000
75	A	103	ASP	-1	-0.796	-0.838	22.757	-0.007	-0.007	0.000	0.000	0.000	0.000
76	A	104	LEU	0	-0.064	-0.029	24.151	-0.004	-0.004	0.000	0.000	0.000	0.000
77	A	105	GLU	-1	-0.881	-0.955	23.670	-0.037	-0.037	0.000	0.000	0.000	0.000
78	A	106	GLY	0	-0.086	-0.027	20.239	0.001	0.001	0.000	0.000	0.000	0.000
79	A	107	THR	0	0.004	0.003	20.680	0.008	0.008	0.000	0.000	0.000	0.000
80	A	108	ARG	1	0.828	0.893	23.332	-0.012	-0.012	0.000	0.000	0.000	0.000
81	A	109	ILE	0	0.002	0.001	20.655	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	110	ARG	1	0.821	0.914	24.079	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	111	ARG	1	0.854	0.898	25.231	-0.064	-0.064	0.000	0.000	0.000	0.000
84	A	112	LYS	1	0.822	0.947	21.760	-0.018	-0.018	0.000	0.000	0.000	0.000
85	A	113	LYS	1	0.977	0.979	27.097	-0.028	-0.028	0.000	0.000	0.000	0.000
86	A	114	PRO	0	-0.002	0.001	29.723	0.005	0.005	0.000	0.000	0.000	0.000
87	A	115	LEU	0	-0.033	-0.012	30.659	0.002	0.002	0.000	0.000	0.000	0.000
88	A	116	GLY	0	0.040	0.019	33.370	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	117	GLU	-1	-0.904	-0.955	36.750	0.037	0.037	0.000	0.000	0.000	0.000
90	A	118	ARG	1	0.804	0.880	35.384	-0.062	-0.062	0.000	0.000	0.000	0.000
91	A	119	PRO	0	0.001	-0.003	33.643	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	120	LYS	1	0.897	0.936	37.005	-0.041	-0.041	0.000	0.000	0.000	0.000
93	A	121	ASP	-1	-0.800	-0.898	35.151	0.059	0.059	0.000	0.000	0.000	0.000
94	A	122	GLU	-1	-0.759	-0.841	33.782	0.076	0.076	0.000	0.000	0.000	0.000
95	A	123	ASP	-1	-0.887	-0.948	35.385	0.063	0.063	0.000	0.000	0.000	0.000
96	A	124	GLU	-1	-0.961	-0.977	37.847	0.057	0.057	0.000	0.000	0.000	0.000
97	A	125	ARG	1	0.738	0.849	30.768	-0.075	-0.075	0.000	0.000	0.000	0.000
98	A	126	THR	0	-0.114	-0.054	32.774	0.007	0.007	0.000	0.000	0.000	0.000
99	A	127	VAL	0	0.042	0.028	32.705	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	128	TYR	0	-0.096	-0.062	33.790	0.006	0.006	0.000	0.000	0.000	0.000
101	A	129	VAL	0	0.011	-0.007	31.476	0.001	0.001	0.000	0.000	0.000	0.000
102	A	130	GLU	-1	-0.858	-0.905	34.890	0.076	0.076	0.000	0.000	0.000	0.000
103	A	131	LEU	0	-0.075	-0.030	30.776	0.004	0.004	0.000	0.000	0.000	0.000
104	A	132	LEU	0	0.021	0.022	30.538	-0.005	-0.005	0.000	0.000	0.000	0.000
105	A	133	PRO	0	-0.007	-0.013	32.396	0.006	0.006	0.000	0.000	0.000	0.000
106	A	134	LYS	1	1.031	1.018	31.099	-0.094	-0.094	0.000	0.000	0.000	0.000
107	A	135	ASN	0	-0.027	-0.033	28.716	0.016	0.016	0.000	0.000	0.000	0.000
108	A	136	VAL	0	0.022	0.003	27.689	0.003	0.003	0.000	0.000	0.000	0.000
109	A	137	ASN	0	-0.028	-0.023	23.168	0.028	0.028	0.000	0.000	0.000	0.000
110	A	138	HIS	0	0.053	0.008	22.578	0.007	0.007	0.000	0.000	0.000	0.000
111	A	139	SER	0	0.000	-0.010	18.669	0.006	0.006	0.000	0.000	0.000	0.000
112	A	140	TRP	0	-0.060	-0.017	21.157	0.013	0.013	0.000	0.000	0.000	0.000
113	A	141	ILE	0	0.037	0.013	23.903	-0.002	-0.002	0.000	0.000	0.000	0.000
114	A	142	GLU	-1	-0.910	-0.942	18.362	0.296	0.296	0.000	0.000	0.000	0.000
115	A	143	ARG	1	0.955	0.982	19.859	-0.249	-0.249	0.000	0.000	0.000	0.000
116	A	144	VAL	0	-0.071	-0.041	21.688	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	145	PHE	0	0.064	0.013	25.108	-0.007	-0.007	0.000	0.000	0.000	0.000
118	A	146	GLY	0	0.043	0.043	21.831	-0.007	-0.007	0.000	0.000	0.000	0.000
119	A	147	LYS	1	0.878	0.930	22.855	-0.174	-0.174	0.000	0.000	0.000	0.000
120	A	148	CYS	0	-0.016	0.015	24.598	-0.007	-0.007	0.000	0.000	0.000	0.000
121	A	149	GLY	0	0.026	0.007	25.115	-0.012	-0.012	0.000	0.000	0.000	0.000
122	A	150	ASN	0	-0.035	-0.013	20.947	0.022	0.022	0.000	0.000	0.000	0.000
123	A	151	VAL	0	0.007	0.004	21.896	-0.011	-0.011	0.000	0.000	0.000	0.000
124	A	152	VAL	0	-0.018	0.001	22.880	0.012	0.012	0.000	0.000	0.000	0.000
125	A	153	TYR	0	-0.013	-0.023	24.804	0.004	0.004	0.000	0.000	0.000	0.000
126	A	154	ILE	0	0.021	0.026	23.724	-0.002	-0.002	0.000	0.000	0.000	0.000
127	A	155	SER	0	-0.028	-0.016	27.475	0.002	0.002	0.000	0.000	0.000	0.000
128	A	156	ILE	0	0.041	0.028	27.177	-0.002	-0.002	0.000	0.000	0.000	0.000
129	A	157	PRO	0	-0.026	-0.007	31.327	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	158	HIS	0	0.028	0.002	32.666	0.006	0.006	0.000	0.000	0.000	0.000
131	A	159	TYR	0	-0.020	-0.011	35.961	-0.003	-0.003	0.000	0.000	0.000	0.000
132	A	160	LYS	1	1.023	1.015	38.986	-0.051	-0.051	0.000	0.000	0.000	0.000
133	A	161	SER	0	-0.046	-0.020	40.575	-0.002	-0.002	0.000	0.000	0.000	0.000
134	A	162	THR	0	0.014	-0.022	40.584	0.001	0.001	0.000	0.000	0.000	0.000
135	A	163	GLY	0	0.050	0.052	36.557	0.001	0.001	0.000	0.000	0.000	0.000
136	A	164	ASP	-1	-0.900	-0.945	36.089	0.080	0.080	0.000	0.000	0.000	0.000
137	A	165	PRO	0	-0.078	-0.046	33.831	0.000	0.000	0.000	0.000	0.000	0.000
138	A	166	LYS	1	0.904	0.948	35.891	-0.075	-0.075	0.000	0.000	0.000	0.000
139	A	167	GLY	0	0.014	0.019	36.458	-0.003	-0.003	0.000	0.000	0.000	0.000
140	A	168	PHE	0	0.034	0.024	35.347	0.002	0.002	0.000	0.000	0.000	0.000
141	A	169	ALA	0	-0.043	-0.032	30.661	0.005	0.005	0.000	0.000	0.000	0.000
142	A	170	PHE	0	0.024	0.014	31.886	-0.004	-0.004	0.000	0.000	0.000	0.000
143	A	171	VAL	0	-0.036	-0.023	27.371	0.008	0.008	0.000	0.000	0.000	0.000
144	A	172	GLU	-1	-0.768	-0.860	29.013	0.086	0.086	0.000	0.000	0.000	0.000
145	A	173	PHE	0	0.016	-0.001	26.967	0.012	0.012	0.000	0.000	0.000	0.000
146	A	174	GLU	-1	-0.856	-0.927	26.641	0.072	0.072	0.000	0.000	0.000	0.000
147	A	175	THR	0	-0.053	-0.035	28.696	0.002	0.002	0.000	0.000	0.000	0.000
148	A	176	LYS	1	0.965	0.959	31.544	-0.049	-0.049	0.000	0.000	0.000	0.000
149	A	177	GLU	-1	-0.817	-0.905	32.851	0.060	0.060	0.000	0.000	0.000	0.000
150	A	178	GLN	0	-0.076	-0.041	26.644	0.012	0.012	0.000	0.000	0.000	0.000
151	A	179	ALA	0	0.039	0.042	30.853	0.004	0.004	0.000	0.000	0.000	0.000
152	A	180	ALA	0	0.037	0.014	32.945	0.002	0.002	0.000	0.000	0.000	0.000
153	A	181	LYS	1	0.888	0.951	28.869	-0.096	-0.096	0.000	0.000	0.000	0.000
154	A	182	ALA	0	-0.007	0.001	30.797	0.005	0.005	0.000	0.000	0.000	0.000
155	A	183	ILE	0	-0.032	-0.023	32.420	0.001	0.001	0.000	0.000	0.000	0.000
156	A	184	GLU	-1	-0.914	-0.941	34.739	0.074	0.074	0.000	0.000	0.000	0.000
157	A	185	PHE	0	-0.042	-0.038	30.916	0.001	0.001	0.000	0.000	0.000	0.000
158	A	186	LEU	0	-0.045	-0.003	34.289	0.001	0.001	0.000	0.000	0.000	0.000
159	A	187	ASN	0	-0.023	-0.019	37.018	-0.002	-0.002	0.000	0.000	0.000	0.000
160	A	188	ASN	0	-0.010	0.007	35.030	0.001	0.001	0.000	0.000	0.000	0.000
161	A	189	PRO	0	-0.037	-0.013	34.725	0.003	0.003	0.000	0.000	0.000	0.000

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