FMO DATABASE

FMODB ID: Z6G6N

Calculation Name: 4LEU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4LEU

Chain ID: A

ChEMBL ID:

UniProt ID: Q9STF9

Base Structure: X-ray

Registration Date: 2023-06-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

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. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	182
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-2010083.148798
FMO2-HF: Nuclear repulsion	1934693.522615
FMO2-HF: Total energy	-75389.626184
FMO2-MP2: Total energy	-75608.053808

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:71:LYS)

Summations of interaction energy for fragment #1(A:71:LYS)

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.
-96.163	-95.476	-0.076	1.217	-1.827	0

Interaction energy analysis for fragmet #1(A:71:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.990 / q_NPA : 0.999

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].
3	A	73	ILE	0	0.029	0.019	2.918	-1.629	-0.980	-0.075	1.219	-1.792
4	A	74	GLY	0	0.059	0.037	5.733	3.191	3.191	0.000	0.000	0.000
5	A	75	LYS	1	0.989	0.970	8.839	17.682	17.682	0.000	0.000	0.000
6	A	76	GLU	-1	-0.869	-0.932	12.419	-17.882	-17.882	0.000	0.000	0.000
7	A	77	ALA	0	0.072	0.031	8.811	0.684	0.684	0.000	0.000	0.000
8	A	78	LEU	0	0.008	0.001	9.151	0.408	0.408	0.000	0.000	0.000
9	A	79	PHE	0	-0.039	-0.009	11.540	1.194	1.194	0.000	0.000	0.000
10	A	80	VAL	0	0.026	0.005	13.283	1.148	1.148	0.000	0.000	0.000
11	A	81	ILE	0	0.009	0.018	8.405	0.806	0.806	0.000	0.000	0.000
12	A	82	LEU	0	-0.022	-0.020	13.056	0.988	0.988	0.000	0.000	0.000
13	A	83	GLY	0	-0.023	-0.006	15.629	1.077	1.077	0.000	0.000	0.000
14	A	84	LEU	0	-0.008	-0.011	14.114	0.902	0.902	0.000	0.000	0.000
15	A	85	LYS	1	0.891	0.918	13.356	21.555	21.555	0.000	0.000	0.000
16	A	86	ARG	1	0.893	0.960	17.748	14.461	14.461	0.000	0.000	0.000
17	A	87	LEU	0	-0.064	-0.043	20.731	0.800	0.800	0.000	0.000	0.000
18	A	88	LYS	1	0.903	0.966	19.162	16.295	16.295	0.000	0.000	0.000
19	A	89	GLU	-1	-0.909	-0.958	21.800	-12.598	-12.598	0.000	0.000	0.000
20	A	90	ASP	-1	-0.881	-0.927	25.289	-10.401	-10.401	0.000	0.000	0.000
21	A	91	ASP	-1	-0.870	-0.949	26.072	-12.125	-12.125	0.000	0.000	0.000
22	A	92	GLU	-1	-0.973	-0.973	26.796	-9.897	-9.897	0.000	0.000	0.000
23	A	93	LYS	1	0.867	0.921	26.110	10.474	10.474	0.000	0.000	0.000
24	A	94	LEU	0	0.010	0.015	19.867	-0.464	-0.464	0.000	0.000	0.000
25	A	95	ASP	-1	-0.814	-0.905	22.660	-12.624	-12.624	0.000	0.000	0.000
26	A	96	LYS	1	0.936	0.976	24.434	10.786	10.786	0.000	0.000	0.000
27	A	97	PHE	0	-0.013	-0.010	17.512	-0.046	-0.046	0.000	0.000	0.000
28	A	98	ILE	0	0.050	0.016	18.897	-0.519	-0.519	0.000	0.000	0.000
29	A	99	LYS	1	0.839	0.913	20.690	11.238	11.238	0.000	0.000	0.000
30	A	100	THR	0	-0.088	-0.030	23.161	0.367	0.367	0.000	0.000	0.000
31	A	101	HIS	0	-0.041	-0.050	18.764	0.065	0.065	0.000	0.000	0.000
32	A	102	VAL	0	0.004	0.017	15.492	-0.778	-0.778	0.000	0.000	0.000
33	A	103	PHE	0	0.027	0.006	17.012	-0.638	-0.638	0.000	0.000	0.000
34	A	104	ARG	1	0.892	0.958	18.557	15.228	15.228	0.000	0.000	0.000
35	A	105	LEU	0	-0.030	-0.001	12.829	-0.194	-0.194	0.000	0.000	0.000
36	A	106	LEU	0	0.080	0.041	13.251	0.312	0.312	0.000	0.000	0.000
37	A	107	LYS	1	0.981	0.995	11.029	21.915	21.915	0.000	0.000	0.000
38	A	108	LEU	0	-0.002	-0.017	7.496	-1.547	-1.547	0.000	0.000	0.000
39	A	109	ASP	-1	-0.888	-0.941	7.552	-29.971	-29.971	0.000	0.000	0.000
40	A	110	MET	0	-0.033	-0.002	9.313	-1.412	-1.412	0.000	0.000	0.000
41	A	111	LEU	0	0.018	0.006	7.199	-0.443	-0.443	0.000	0.000	0.000
42	A	112	ALA	0	-0.027	-0.007	4.876	-4.952	-4.952	0.000	0.000	0.000
43	A	113	VAL	0	-0.050	-0.024	5.887	-2.000	-2.000	0.000	0.000	0.000
44	A	114	ILE	0	-0.032	-0.012	8.271	0.608	0.608	0.000	0.000	0.000
45	A	115	GLY	0	0.088	0.056	4.662	0.102	0.140	-0.001	-0.002	-0.035
46	A	116	GLU	-1	-0.818	-0.871	5.611	-39.709	-39.709	0.000	0.000	0.000
47	A	117	LEU	0	-0.066	-0.041	7.169	2.961	2.961	0.000	0.000	0.000
48	A	118	GLU	-1	-0.836	-0.927	7.729	-31.624	-31.624	0.000	0.000	0.000
49	A	119	ARG	1	0.791	0.873	5.595	37.194	37.194	0.000	0.000	0.000
50	A	120	GLN	0	-0.086	-0.054	8.175	4.756	4.756	0.000	0.000	0.000
51	A	121	GLU	-1	-0.867	-0.925	11.253	-19.354	-19.354	0.000	0.000	0.000
52	A	122	GLU	-1	-0.876	-0.930	13.011	-16.618	-16.618	0.000	0.000	0.000
53	A	123	THR	0	0.031	-0.001	14.428	0.171	0.171	0.000	0.000	0.000
54	A	124	ALA	0	-0.001	0.000	15.575	0.128	0.128	0.000	0.000	0.000
55	A	125	LEU	0	-0.010	-0.010	15.344	0.377	0.377	0.000	0.000	0.000
56	A	126	ALA	0	0.027	0.023	12.301	-0.143	-0.143	0.000	0.000	0.000
57	A	127	ILE	0	0.025	0.011	13.719	-0.169	-0.169	0.000	0.000	0.000
58	A	128	LYS	1	0.963	0.988	16.697	14.679	14.679	0.000	0.000	0.000
59	A	129	MET	0	-0.012	-0.005	12.420	0.854	0.854	0.000	0.000	0.000
60	A	130	PHE	0	0.053	0.021	13.884	0.138	0.138	0.000	0.000	0.000
61	A	131	GLU	-1	-0.970	-0.992	15.175	-14.081	-14.081	0.000	0.000	0.000
62	A	132	VAL	0	-0.075	-0.032	16.834	0.705	0.705	0.000	0.000	0.000
63	A	133	ILE	0	0.019	-0.004	11.797	0.473	0.473	0.000	0.000	0.000
64	A	134	GLN	0	-0.029	-0.014	16.090	1.009	1.009	0.000	0.000	0.000
65	A	135	LYS	1	0.889	0.951	18.657	14.178	14.178	0.000	0.000	0.000
66	A	136	GLN	0	-0.066	-0.027	16.570	0.683	0.683	0.000	0.000	0.000
67	A	137	GLU	-1	-0.920	-0.965	19.572	-13.084	-13.084	0.000	0.000	0.000
68	A	138	TRP	0	-0.024	-0.027	13.142	-0.418	-0.418	0.000	0.000	0.000
69	A	139	TYR	0	-0.031	-0.011	15.401	-1.225	-1.225	0.000	0.000	0.000
70	A	140	GLN	0	0.030	0.003	16.636	1.186	1.186	0.000	0.000	0.000
71	A	141	PRO	0	-0.045	-0.004	16.173	-1.272	-1.272	0.000	0.000	0.000
72	A	142	ASP	-1	-0.841	-0.928	12.015	-24.607	-24.607	0.000	0.000	0.000
73	A	143	VAL	0	0.038	0.010	14.089	-0.456	-0.456	0.000	0.000	0.000
74	A	144	PHE	0	0.014	0.003	9.211	-0.520	-0.520	0.000	0.000	0.000
75	A	145	MET	0	-0.003	0.017	9.848	-1.177	-1.177	0.000	0.000	0.000
76	A	146	TYR	0	-0.021	-0.022	10.885	0.291	0.291	0.000	0.000	0.000
77	A	147	LYS	1	0.845	0.926	9.549	28.037	28.037	0.000	0.000	0.000
78	A	148	ASP	-1	-0.936	-0.969	7.044	-38.794	-38.794	0.000	0.000	0.000
79	A	149	LEU	0	-0.012	0.005	9.849	0.842	0.842	0.000	0.000	0.000
80	A	150	ILE	0	-0.027	-0.015	12.354	1.162	1.162	0.000	0.000	0.000
81	A	151	VAL	0	-0.009	-0.005	11.681	1.020	1.020	0.000	0.000	0.000
82	A	152	SER	0	-0.037	-0.021	11.114	1.416	1.416	0.000	0.000	0.000
83	A	153	LEU	0	-0.031	-0.027	13.053	1.083	1.083	0.000	0.000	0.000
84	A	154	ALA	0	0.020	0.009	16.557	0.833	0.833	0.000	0.000	0.000
85	A	155	LYS	1	0.916	0.972	11.399	25.482	25.482	0.000	0.000	0.000
86	A	156	SER	0	-0.038	-0.007	16.366	0.301	0.301	0.000	0.000	0.000
87	A	157	LYS	1	0.879	0.934	18.573	13.961	13.961	0.000	0.000	0.000
88	A	158	ARG	1	0.848	0.941	19.363	15.843	15.843	0.000	0.000	0.000
89	A	159	MET	0	0.004	-0.009	20.684	-0.651	-0.651	0.000	0.000	0.000
90	A	160	ASP	-1	-0.841	-0.906	22.857	-11.746	-11.746	0.000	0.000	0.000
91	A	161	GLU	-1	-0.891	-0.965	20.488	-13.495	-13.495	0.000	0.000	0.000
92	A	162	ALA	0	-0.002	0.003	18.853	-0.378	-0.378	0.000	0.000	0.000
93	A	163	MET	0	-0.010	-0.007	19.777	-0.465	-0.465	0.000	0.000	0.000
94	A	164	ALA	0	-0.018	0.003	22.743	0.103	0.103	0.000	0.000	0.000
95	A	165	LEU	0	-0.019	-0.026	16.996	0.121	0.121	0.000	0.000	0.000
96	A	166	TRP	0	-0.032	-0.023	17.690	-0.743	-0.743	0.000	0.000	0.000
97	A	167	GLU	-1	-0.867	-0.947	20.585	-11.718	-11.718	0.000	0.000	0.000
98	A	168	LYS	1	0.840	0.933	20.139	14.613	14.613	0.000	0.000	0.000
99	A	169	MET	0	0.020	0.010	17.960	-0.283	-0.283	0.000	0.000	0.000
100	A	170	LYS	1	0.831	0.919	20.349	12.128	12.128	0.000	0.000	0.000
101	A	171	LYS	1	0.886	0.945	23.426	11.901	11.901	0.000	0.000	0.000
102	A	172	GLU	-1	-0.913	-0.946	20.791	-14.157	-14.157	0.000	0.000	0.000
103	A	173	ASN	0	-0.104	-0.044	23.090	0.023	0.023	0.000	0.000	0.000
104	A	174	LEU	0	-0.004	0.007	17.485	-0.282	-0.282	0.000	0.000	0.000
105	A	175	PHE	0	0.004	-0.019	19.728	0.475	0.475	0.000	0.000	0.000
106	A	176	PRO	0	-0.028	-0.009	17.191	-0.798	-0.798	0.000	0.000	0.000
107	A	177	ASP	-1	-0.751	-0.861	14.611	-19.796	-19.796	0.000	0.000	0.000
108	A	178	SER	0	0.067	0.013	17.891	-0.035	-0.035	0.000	0.000	0.000
109	A	179	GLN	0	-0.047	-0.026	11.970	-0.655	-0.655	0.000	0.000	0.000
110	A	180	THR	0	0.014	0.008	14.154	-0.942	-0.942	0.000	0.000	0.000
111	A	181	TYR	0	0.063	0.029	15.353	0.090	0.090	0.000	0.000	0.000
112	A	182	THR	0	-0.036	-0.026	17.567	0.566	0.566	0.000	0.000	0.000
113	A	183	GLU	-1	-0.919	-0.959	11.108	-25.629	-25.629	0.000	0.000	0.000
114	A	184	VAL	0	0.034	0.025	15.827	0.063	0.063	0.000	0.000	0.000
115	A	185	ILE	0	0.004	0.020	17.506	0.595	0.595	0.000	0.000	0.000
116	A	186	ARG	1	0.919	0.951	15.805	17.751	17.751	0.000	0.000	0.000
117	A	187	GLY	0	0.001	-0.003	17.801	0.337	0.337	0.000	0.000	0.000
118	A	188	PHE	0	0.067	0.027	18.520	0.334	0.334	0.000	0.000	0.000
119	A	189	LEU	0	-0.042	-0.021	21.887	0.595	0.595	0.000	0.000	0.000
120	A	190	ARG	1	0.850	0.934	19.790	14.477	14.477	0.000	0.000	0.000
121	A	191	ASP	-1	-0.827	-0.930	21.169	-14.507	-14.507	0.000	0.000	0.000
122	A	192	GLY	0	-0.086	-0.037	23.632	0.444	0.444	0.000	0.000	0.000
123	A	193	CYS	0	-0.010	0.013	24.937	0.467	0.467	0.000	0.000	0.000
124	A	194	PRO	0	0.024	-0.005	26.229	-0.240	-0.240	0.000	0.000	0.000
125	A	195	ALA	0	0.008	0.012	28.326	-0.018	-0.018	0.000	0.000	0.000
126	A	196	ASP	-1	-0.788	-0.908	24.274	-12.103	-12.103	0.000	0.000	0.000
127	A	197	ALA	0	-0.019	-0.012	23.883	-0.264	-0.264	0.000	0.000	0.000
128	A	198	MET	0	-0.026	-0.024	24.934	-0.156	-0.156	0.000	0.000	0.000
129	A	199	ASN	0	-0.002	0.005	26.241	0.110	0.110	0.000	0.000	0.000
130	A	200	VAL	0	0.035	0.027	20.733	-0.016	-0.016	0.000	0.000	0.000
131	A	201	TYR	0	-0.057	-0.080	24.082	-0.255	-0.255	0.000	0.000	0.000
132	A	202	GLU	-1	-0.893	-0.968	25.869	-9.795	-9.795	0.000	0.000	0.000
133	A	203	ASP	-1	-0.888	-0.933	24.451	-11.972	-11.972	0.000	0.000	0.000
134	A	204	MET	0	-0.047	-0.033	22.770	-0.236	-0.236	0.000	0.000	0.000
135	A	205	LEU	0	-0.049	-0.017	24.863	0.049	0.049	0.000	0.000	0.000
136	A	206	LYS	1	0.883	0.946	28.067	10.803	10.803	0.000	0.000	0.000
137	A	207	SER	0	-0.028	0.004	23.915	-0.034	-0.034	0.000	0.000	0.000
138	A	208	PRO	0	-0.025	-0.017	24.624	0.365	0.365	0.000	0.000	0.000
139	A	209	ASP	-1	-0.946	-0.962	22.304	-13.227	-13.227	0.000	0.000	0.000
140	A	210	PRO	0	-0.023	-0.020	25.806	0.124	0.124	0.000	0.000	0.000
141	A	211	PRO	0	0.010	0.019	25.278	-0.454	-0.454	0.000	0.000	0.000
142	A	212	GLU	-1	-0.902	-0.950	21.134	-14.393	-14.393	0.000	0.000	0.000
143	A	213	GLU	-1	-0.807	-0.939	24.779	-10.767	-10.767	0.000	0.000	0.000
144	A	214	LEU	0	-0.052	-0.023	18.922	0.025	0.025	0.000	0.000	0.000
145	A	215	PRO	0	0.041	0.011	21.519	0.045	0.045	0.000	0.000	0.000
146	A	216	PHE	0	0.063	0.027	23.058	0.151	0.151	0.000	0.000	0.000
147	A	217	ARG	1	0.928	0.989	24.725	11.742	11.742	0.000	0.000	0.000
148	A	218	VAL	0	-0.098	-0.045	20.867	0.048	0.048	0.000	0.000	0.000
149	A	219	LEU	0	0.028	0.012	24.189	0.241	0.241	0.000	0.000	0.000
150	A	220	LEU	0	0.020	0.021	26.590	0.319	0.319	0.000	0.000	0.000
151	A	221	LYS	1	0.968	1.003	24.247	12.608	12.608	0.000	0.000	0.000
152	A	222	GLY	0	-0.057	-0.034	26.520	0.110	0.110	0.000	0.000	0.000
153	A	223	LEU	0	0.017	0.005	27.395	0.202	0.202	0.000	0.000	0.000
154	A	224	LEU	0	-0.035	-0.004	30.610	0.385	0.385	0.000	0.000	0.000
155	A	225	PRO	0	-0.037	-0.026	31.565	0.301	0.301	0.000	0.000	0.000
156	A	226	HIS	0	-0.002	0.004	31.400	0.367	0.367	0.000	0.000	0.000
157	A	227	PRO	0	0.076	0.029	34.942	-0.098	-0.098	0.000	0.000	0.000
158	A	228	LEU	0	0.004	0.000	37.089	0.057	0.057	0.000	0.000	0.000
159	A	229	LEU	0	0.002	0.007	31.809	0.019	0.019	0.000	0.000	0.000
160	A	230	ARG	1	0.911	0.954	32.452	9.264	9.264	0.000	0.000	0.000
161	A	231	ASN	0	-0.018	-0.023	33.708	-0.124	-0.124	0.000	0.000	0.000
162	A	232	LYS	1	0.896	0.966	33.716	9.171	9.171	0.000	0.000	0.000
163	A	233	VAL	0	0.031	0.014	29.627	0.002	0.002	0.000	0.000	0.000
164	A	234	LYS	1	0.901	0.953	32.670	8.236	8.236	0.000	0.000	0.000
165	A	235	LYS	1	0.966	0.985	34.578	7.888	7.888	0.000	0.000	0.000
166	A	236	ASP	-1	-0.787	-0.869	32.837	-9.196	-9.196	0.000	0.000	0.000
167	A	237	PHE	0	0.030	0.007	29.368	-0.047	-0.047	0.000	0.000	0.000
168	A	238	GLU	-1	-0.937	-0.977	33.236	-8.090	-8.090	0.000	0.000	0.000
169	A	239	GLU	-1	-1.030	-1.012	36.066	-8.242	-8.242	0.000	0.000	0.000
170	A	240	LEU	0	-0.013	0.013	31.250	0.019	0.019	0.000	0.000	0.000
171	A	241	PHE	0	-0.085	-0.047	29.177	-0.135	-0.135	0.000	0.000	0.000
172	A	242	PRO	0	0.063	0.049	34.679	0.038	0.038	0.000	0.000	0.000
173	A	243	GLU	-1	-0.937	-0.970	36.963	-7.975	-7.975	0.000	0.000	0.000
174	A	244	LYS	1	0.928	0.956	29.529	10.370	10.370	0.000	0.000	0.000
175	A	245	HIS	0	-0.063	-0.047	34.481	0.002	0.002	0.000	0.000	0.000
176	A	246	ALA	0	-0.048	-0.001	35.642	0.037	0.037	0.000	0.000	0.000
177	A	247	TYR	0	-0.064	-0.044	33.396	-0.030	-0.030	0.000	0.000	0.000
178	A	248	ASP	-1	-0.928	-0.964	30.191	-10.400	-10.400	0.000	0.000	0.000
179	A	249	PRO	0	0.041	0.042	32.679	-0.166	-0.166	0.000	0.000	0.000
180	A	250	PRO	0	-0.025	-0.009	29.118	-0.230	-0.230	0.000	0.000	0.000
181	A	251	GLU	-1	-0.976	-1.022	30.254	-8.842	-8.842	0.000	0.000	0.000
182	A	252	GLU	-1	-1.008	-0.991	31.737	-9.237	-9.237	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:71:LYS)