FMO DATABASE

FMODB ID: 2JKYR

Calculation Name: 1WBA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WBA

Chain ID: A

ChEMBL ID:

UniProt ID: P15465

Base Structure: X-ray

Registration Date: 2023-06-21

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	170
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1763208.051491
FMO2-HF: Nuclear repulsion	1697166.733915
FMO2-HF: Total energy	-66041.317576
FMO2-MP2: Total energy	-66235.300382

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:2:ASP)

Summations of interaction energy for fragment #1(A:2:ASP)

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.
-211.157	-207.974	18.026	-11.049	-10.161	0.087

Interaction energy analysis for fragmet #1(A:2:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.792 / q_NPA : -0.877

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	4	PRO	0	-0.098	-0.056	3.773	-3.867	-1.414	0.000	-1.378	-1.076	0.008
4	A	5	VAL	0	-0.008	0.000	6.249	-0.060	-0.060	0.000	0.000	0.000	0.000
5	A	6	TYR	0	0.017	-0.002	8.169	-3.600	-3.600	0.000	0.000	0.000	0.000
6	A	7	ASP	-1	-0.779	-0.895	11.745	17.907	17.907	0.000	0.000	0.000	0.000
7	A	8	ALA	0	-0.018	-0.024	15.153	0.166	0.166	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.924	-0.959	17.993	13.884	13.884	0.000	0.000	0.000	0.000
9	A	10	GLY	0	-0.035	-0.023	15.851	-0.411	-0.411	0.000	0.000	0.000	0.000
10	A	11	ASN	0	-0.037	-0.008	15.500	0.265	0.265	0.000	0.000	0.000	0.000
11	A	12	LYS	1	0.953	0.983	9.013	-23.562	-23.562	0.000	0.000	0.000	0.000
12	A	13	LEU	0	0.058	0.022	10.601	-1.544	-1.544	0.000	0.000	0.000	0.000
13	A	14	VAL	0	-0.064	-0.012	11.496	0.943	0.943	0.000	0.000	0.000	0.000
14	A	15	ASN	0	0.003	-0.010	11.767	-0.505	-0.505	0.000	0.000	0.000	0.000
15	A	16	ARG	1	0.873	0.916	13.405	-16.937	-16.937	0.000	0.000	0.000	0.000
16	A	17	GLY	0	-0.007	0.015	15.833	-1.040	-1.040	0.000	0.000	0.000	0.000
17	A	18	LYS	1	0.871	0.926	17.398	-12.039	-12.039	0.000	0.000	0.000	0.000
18	A	19	TYR	0	-0.036	-0.027	15.486	-0.016	-0.016	0.000	0.000	0.000	0.000
19	A	20	THR	0	0.020	0.013	18.681	-0.015	-0.015	0.000	0.000	0.000	0.000
20	A	21	ILE	0	-0.011	0.004	16.580	0.587	0.587	0.000	0.000	0.000	0.000
21	A	22	VAL	0	-0.009	-0.010	19.046	-0.786	-0.786	0.000	0.000	0.000	0.000
22	A	23	SER	0	-0.029	-0.034	19.645	1.197	1.197	0.000	0.000	0.000	0.000
23	A	24	PHE	0	-0.007	-0.030	18.226	-0.411	-0.411	0.000	0.000	0.000	0.000
24	A	25	SER	0	0.037	0.016	20.365	-0.209	-0.209	0.000	0.000	0.000	0.000
25	A	26	ASP	-1	-0.813	-0.863	23.266	12.099	12.099	0.000	0.000	0.000	0.000
26	A	27	GLY	0	0.020	0.020	24.383	-0.433	-0.433	0.000	0.000	0.000	0.000
27	A	28	ALA	0	-0.011	0.008	25.517	-0.150	-0.150	0.000	0.000	0.000	0.000
28	A	29	GLY	0	0.040	0.008	23.470	0.720	0.720	0.000	0.000	0.000	0.000
29	A	30	ILE	0	-0.034	-0.011	20.240	-0.203	-0.203	0.000	0.000	0.000	0.000
30	A	31	ASP	-1	-0.740	-0.831	23.948	10.142	10.142	0.000	0.000	0.000	0.000
31	A	32	VAL	0	-0.019	-0.017	26.696	0.391	0.391	0.000	0.000	0.000	0.000
32	A	33	VAL	0	-0.043	-0.027	29.047	-0.398	-0.398	0.000	0.000	0.000	0.000
33	A	34	ALA	0	0.031	0.024	31.906	0.209	0.209	0.000	0.000	0.000	0.000
34	A	35	THR	0	-0.079	-0.050	31.266	0.063	0.063	0.000	0.000	0.000	0.000
35	A	36	GLY	0	0.037	0.006	34.267	0.001	0.001	0.000	0.000	0.000	0.000
36	A	37	ASN	0	-0.046	-0.023	36.490	-0.415	-0.415	0.000	0.000	0.000	0.000
37	A	38	GLU	-1	-0.747	-0.799	32.022	10.124	10.124	0.000	0.000	0.000	0.000
38	A	39	ASN	0	0.052	0.008	36.798	-0.120	-0.120	0.000	0.000	0.000	0.000
39	A	40	PRO	0	-0.011	-0.026	37.293	0.237	0.237	0.000	0.000	0.000	0.000
40	A	41	GLU	-1	-0.917	-0.943	37.680	7.589	7.589	0.000	0.000	0.000	0.000
41	A	42	ASP	-1	-0.952	-0.975	34.694	9.231	9.231	0.000	0.000	0.000	0.000
42	A	43	PRO	0	-0.059	-0.008	32.433	0.167	0.167	0.000	0.000	0.000	0.000
43	A	44	LEU	0	0.027	0.004	30.709	0.333	0.333	0.000	0.000	0.000	0.000
44	A	45	SER	0	-0.028	-0.034	28.351	0.552	0.552	0.000	0.000	0.000	0.000
45	A	46	ILE	0	-0.025	-0.012	22.655	-0.116	-0.116	0.000	0.000	0.000	0.000
46	A	47	VAL	0	-0.031	-0.030	25.153	0.234	0.234	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.876	0.920	23.919	-12.343	-12.343	0.000	0.000	0.000	0.000
48	A	49	SER	0	-0.043	-0.044	25.653	-0.600	-0.600	0.000	0.000	0.000	0.000
49	A	50	THR	0	-0.021	-0.028	28.827	0.066	0.066	0.000	0.000	0.000	0.000
50	A	51	ARG	1	0.835	0.894	31.763	-10.124	-10.124	0.000	0.000	0.000	0.000
51	A	52	ASN	0	0.011	0.008	30.923	0.049	0.049	0.000	0.000	0.000	0.000
52	A	53	ILE	0	-0.020	0.015	28.368	0.009	0.009	0.000	0.000	0.000	0.000
53	A	54	MET	0	0.000	-0.021	24.988	0.443	0.443	0.000	0.000	0.000	0.000
54	A	55	TYR	0	-0.004	0.015	25.140	-0.042	-0.042	0.000	0.000	0.000	0.000
55	A	56	ALA	0	0.009	0.012	22.230	0.638	0.638	0.000	0.000	0.000	0.000
56	A	57	THR	0	-0.038	-0.025	18.505	0.021	0.021	0.000	0.000	0.000	0.000
57	A	58	SER	0	0.008	-0.008	18.775	0.270	0.270	0.000	0.000	0.000	0.000
58	A	59	ILE	0	-0.009	0.019	12.291	0.312	0.312	0.000	0.000	0.000	0.000
59	A	60	SER	0	-0.010	-0.017	14.051	-0.312	-0.312	0.000	0.000	0.000	0.000
60	A	61	SER	0	0.037	0.012	11.149	0.611	0.611	0.000	0.000	0.000	0.000
61	A	62	GLU	-1	-0.891	-0.918	12.062	18.071	18.071	0.000	0.000	0.000	0.000
62	A	63	ASP	-1	-0.772	-0.870	12.798	17.177	17.177	0.000	0.000	0.000	0.000
63	A	64	LYS	1	0.828	0.905	14.547	-16.790	-16.790	0.000	0.000	0.000	0.000
64	A	65	THR	0	0.027	0.004	15.455	-1.140	-1.140	0.000	0.000	0.000	0.000
65	A	66	PRO	0	-0.060	-0.013	15.473	0.806	0.806	0.000	0.000	0.000	0.000
66	A	67	PRO	0	0.013	0.018	13.938	-0.339	-0.339	0.000	0.000	0.000	0.000
67	A	68	GLN	0	0.041	0.006	13.237	1.166	1.166	0.000	0.000	0.000	0.000
68	A	69	PRO	0	0.051	0.027	8.263	-0.433	-0.433	0.000	0.000	0.000	0.000
69	A	70	ARG	1	0.937	0.968	10.386	-17.565	-17.565	0.000	0.000	0.000	0.000
70	A	71	ASN	0	-0.064	-0.048	9.018	-1.446	-1.446	0.000	0.000	0.000	0.000
71	A	72	ILE	0	0.006	0.007	7.669	0.769	0.769	0.000	0.000	0.000	0.000
72	A	73	LEU	0	-0.012	0.002	2.401	-2.503	-1.294	0.540	-0.573	-1.176	0.002
73	A	74	GLU	-1	-0.754	-0.870	2.926	47.575	50.030	0.424	-1.168	-1.711	0.011
74	A	75	ASN	0	-0.029	-0.030	1.680	-32.863	-35.968	17.064	-7.893	-6.066	0.066
75	A	76	MET	0	-0.057	-0.003	4.533	-8.873	-8.793	-0.001	-0.023	-0.056	0.000
76	A	77	ARG	1	0.854	0.916	6.211	-24.883	-24.883	0.000	0.000	0.000	0.000
77	A	78	LEU	0	-0.005	-0.004	8.814	-1.368	-1.368	0.000	0.000	0.000	0.000
78	A	79	LYS	1	0.842	0.898	12.085	-18.952	-18.952	0.000	0.000	0.000	0.000
79	A	80	ILE	0	0.035	0.030	14.173	0.268	0.268	0.000	0.000	0.000	0.000
80	A	81	ASN	0	0.042	0.029	17.553	-0.860	-0.860	0.000	0.000	0.000	0.000
81	A	82	PHE	0	0.047	0.022	21.062	0.476	0.476	0.000	0.000	0.000	0.000
82	A	83	ALA	0	0.005	-0.002	22.241	-0.382	-0.382	0.000	0.000	0.000	0.000
83	A	84	THR	0	-0.021	-0.019	24.234	-0.212	-0.212	0.000	0.000	0.000	0.000
84	A	85	ASP	-1	-0.827	-0.884	27.753	9.799	9.799	0.000	0.000	0.000	0.000
85	A	86	PRO	0	-0.010	-0.008	30.709	0.152	0.152	0.000	0.000	0.000	0.000
86	A	87	HIS	1	0.913	0.937	27.805	-10.536	-10.536	0.000	0.000	0.000	0.000
87	A	88	LYS	1	0.848	0.915	27.444	-9.357	-9.357	0.000	0.000	0.000	0.000
88	A	89	GLY	0	0.037	0.021	25.550	-0.294	-0.294	0.000	0.000	0.000	0.000
89	A	90	ASP	-1	-0.799	-0.872	25.618	11.021	11.021	0.000	0.000	0.000	0.000
90	A	91	VAL	0	-0.051	-0.039	20.787	0.604	0.604	0.000	0.000	0.000	0.000
91	A	92	TRP	0	0.003	-0.004	17.865	-0.041	-0.041	0.000	0.000	0.000	0.000
92	A	93	SER	0	-0.063	-0.042	21.038	0.271	0.271	0.000	0.000	0.000	0.000
93	A	94	VAL	0	0.039	0.021	18.932	-0.013	-0.013	0.000	0.000	0.000	0.000
94	A	95	VAL	0	-0.003	0.002	22.148	-0.183	-0.183	0.000	0.000	0.000	0.000
95	A	96	ASP	-1	-0.829	-0.909	25.362	12.784	12.784	0.000	0.000	0.000	0.000
96	A	97	PHE	0	-0.022	-0.003	26.880	-0.466	-0.466	0.000	0.000	0.000	0.000
97	A	98	GLN	0	0.014	0.034	29.643	-0.130	-0.130	0.000	0.000	0.000	0.000
98	A	99	PRO	0	-0.010	-0.018	32.456	-0.167	-0.167	0.000	0.000	0.000	0.000
99	A	100	ASP	-1	-0.809	-0.909	29.911	10.289	10.289	0.000	0.000	0.000	0.000
100	A	101	GLY	0	0.018	0.020	27.071	0.320	0.320	0.000	0.000	0.000	0.000
101	A	102	GLN	0	-0.065	-0.050	21.039	0.814	0.814	0.000	0.000	0.000	0.000
102	A	103	GLN	0	-0.022	-0.001	23.445	0.300	0.300	0.000	0.000	0.000	0.000
103	A	104	LEU	0	-0.032	-0.016	19.328	0.241	0.241	0.000	0.000	0.000	0.000
104	A	105	LYS	1	0.865	0.934	23.348	-11.381	-11.381	0.000	0.000	0.000	0.000
105	A	106	LEU	0	-0.040	-0.003	24.851	0.643	0.643	0.000	0.000	0.000	0.000
106	A	107	ALA	0	-0.013	-0.008	24.253	-0.203	-0.203	0.000	0.000	0.000	0.000
107	A	108	GLY	0	-0.037	-0.025	26.296	-0.325	-0.325	0.000	0.000	0.000	0.000
108	A	109	ARG	1	0.835	0.910	29.267	-10.687	-10.687	0.000	0.000	0.000	0.000
109	A	110	TYR	0	0.012	-0.017	29.293	-0.344	-0.344	0.000	0.000	0.000	0.000
110	A	111	PRO	0	0.013	0.014	29.734	0.324	0.324	0.000	0.000	0.000	0.000
111	A	112	ASN	0	-0.015	-0.020	29.368	0.079	0.079	0.000	0.000	0.000	0.000
112	A	113	GLN	0	0.052	0.017	24.319	0.048	0.048	0.000	0.000	0.000	0.000
113	A	114	VAL	0	-0.007	0.000	20.767	-0.044	-0.044	0.000	0.000	0.000	0.000
114	A	115	LYS	1	0.964	0.982	20.493	-13.658	-13.658	0.000	0.000	0.000	0.000
115	A	116	GLY	0	0.022	-0.008	17.251	0.305	0.305	0.000	0.000	0.000	0.000
116	A	117	ALA	0	-0.080	-0.013	13.383	-0.647	-0.647	0.000	0.000	0.000	0.000
117	A	118	PHE	0	0.021	0.015	13.387	0.499	0.499	0.000	0.000	0.000	0.000
118	A	119	THR	0	0.011	0.000	7.705	0.395	0.395	0.000	0.000	0.000	0.000
119	A	120	ILE	0	0.005	0.001	7.766	-3.138	-3.138	0.000	0.000	0.000	0.000
120	A	121	GLN	0	0.020	-0.003	5.509	2.191	2.191	0.000	0.000	0.000	0.000
121	A	122	LYS	1	0.822	0.862	4.369	-64.905	-64.814	-0.001	-0.014	-0.076	0.000
122	A	123	GLY	0	-0.042	-0.011	8.784	-0.440	-0.440	0.000	0.000	0.000	0.000
123	A	124	SER	0	-0.019	-0.019	12.522	-2.240	-2.240	0.000	0.000	0.000	0.000
124	A	125	ASN	0	0.037	0.011	13.012	2.024	2.024	0.000	0.000	0.000	0.000
125	A	126	THR	0	-0.009	0.014	14.799	-0.687	-0.687	0.000	0.000	0.000	0.000
126	A	127	PRO	0	0.050	0.030	13.665	1.385	1.385	0.000	0.000	0.000	0.000
127	A	128	ARG	1	0.868	0.937	12.473	-18.882	-18.882	0.000	0.000	0.000	0.000
128	A	129	THR	0	0.003	0.017	12.737	-1.481	-1.481	0.000	0.000	0.000	0.000
129	A	130	TYR	0	0.021	0.016	7.543	0.235	0.235	0.000	0.000	0.000	0.000
130	A	131	LYS	1	0.949	0.990	10.089	-31.855	-31.855	0.000	0.000	0.000	0.000
131	A	132	LEU	0	-0.005	-0.007	11.200	2.388	2.388	0.000	0.000	0.000	0.000
132	A	133	LEU	0	0.015	0.011	8.871	-0.736	-0.736	0.000	0.000	0.000	0.000
133	A	134	PHE	0	0.033	0.006	12.531	-0.230	-0.230	0.000	0.000	0.000	0.000
134	A	135	CYS	0	-0.026	-0.002	10.837	0.265	0.265	0.000	0.000	0.000	0.000
135	A	136	PRO	0	0.030	0.010	13.667	-0.362	-0.362	0.000	0.000	0.000	0.000
136	A	137	VAL	0	-0.031	-0.035	16.357	0.833	0.833	0.000	0.000	0.000	0.000
137	A	138	GLY	0	0.016	0.014	17.151	-0.806	-0.806	0.000	0.000	0.000	0.000
138	A	139	SER	0	-0.038	-0.021	16.931	-0.984	-0.984	0.000	0.000	0.000	0.000
139	A	140	PRO	0	0.024	0.016	13.981	1.429	1.429	0.000	0.000	0.000	0.000
140	A	142	LYS	1	0.867	0.939	13.120	-16.455	-16.455	0.000	0.000	0.000	0.000
141	A	143	ASN	0	0.040	0.020	13.436	3.194	3.194	0.000	0.000	0.000	0.000
142	A	144	ILE	0	-0.015	-0.005	15.037	-1.377	-1.377	0.000	0.000	0.000	0.000
143	A	145	GLY	0	0.065	0.029	17.041	0.675	0.675	0.000	0.000	0.000	0.000
144	A	146	ILE	0	-0.058	-0.031	19.856	-0.290	-0.290	0.000	0.000	0.000	0.000
145	A	147	SER	0	0.017	0.016	23.568	-0.171	-0.171	0.000	0.000	0.000	0.000
146	A	148	THR	0	-0.045	-0.025	26.912	-0.014	-0.014	0.000	0.000	0.000	0.000
147	A	149	ASP	-1	-0.751	-0.851	30.410	9.901	9.901	0.000	0.000	0.000	0.000
148	A	150	PRO	0	0.024	0.000	33.142	-0.048	-0.048	0.000	0.000	0.000	0.000
149	A	151	GLU	-1	-0.810	-0.899	35.736	8.959	8.959	0.000	0.000	0.000	0.000
150	A	152	GLY	0	-0.005	0.004	34.655	-0.059	-0.059	0.000	0.000	0.000	0.000
151	A	153	LYS	1	0.861	0.932	31.561	-9.261	-9.261	0.000	0.000	0.000	0.000
152	A	154	LYS	1	0.877	0.924	27.261	-10.477	-10.477	0.000	0.000	0.000	0.000
153	A	155	ARG	1	0.863	0.915	26.366	-9.930	-9.930	0.000	0.000	0.000	0.000
154	A	156	LEU	0	0.003	0.012	19.949	0.307	0.307	0.000	0.000	0.000	0.000
155	A	157	VAL	0	-0.009	-0.003	21.857	-0.343	-0.343	0.000	0.000	0.000	0.000
156	A	158	VAL	0	-0.005	-0.010	17.513	1.001	1.001	0.000	0.000	0.000	0.000
157	A	159	SER	0	-0.008	-0.024	18.784	-0.696	-0.696	0.000	0.000	0.000	0.000
158	A	160	TYR	0	0.021	-0.012	16.337	0.370	0.370	0.000	0.000	0.000	0.000
159	A	161	GLN	0	0.017	0.007	17.645	1.162	1.162	0.000	0.000	0.000	0.000
160	A	162	SER	0	-0.061	-0.003	18.322	-0.843	-0.843	0.000	0.000	0.000	0.000
161	A	163	ASP	-1	-0.862	-0.926	18.174	16.925	16.925	0.000	0.000	0.000	0.000
162	A	164	PRO	0	-0.045	-0.028	14.838	-0.051	-0.051	0.000	0.000	0.000	0.000
163	A	165	LEU	0	-0.005	0.001	16.992	-0.534	-0.534	0.000	0.000	0.000	0.000
164	A	166	VAL	0	-0.002	0.009	15.211	1.132	1.132	0.000	0.000	0.000	0.000
165	A	167	VAL	0	-0.038	-0.020	14.734	-1.336	-1.336	0.000	0.000	0.000	0.000
166	A	168	LYS	1	0.828	0.907	15.432	-17.178	-17.178	0.000	0.000	0.000	0.000
167	A	169	PHE	0	0.018	0.016	11.587	-0.986	-0.986	0.000	0.000	0.000	0.000
168	A	170	HIS	0	0.059	0.022	16.631	-0.172	-0.172	0.000	0.000	0.000	0.000
169	A	171	ARG	1	0.989	0.994	17.511	-15.174	-15.174	0.000	0.000	0.000	0.000
170	A	172	HIS	0	0.031	0.028	20.342	-0.705	-0.705	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:2:ASP)