FMO DATABASE

FMODB ID: 5JY1Z

Calculation Name: 1U61-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1U61

Chain ID: A

ChEMBL ID:

UniProt ID: Q81J58

Base Structure: X-ray

Registration Date: 2023-09-23

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	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	127
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1118599.311772
FMO2-HF: Nuclear repulsion	1068635.931454
FMO2-HF: Total energy	-49963.380318
FMO2-MP2: Total energy	-50112.58719

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:ILE)

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

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.
-3.729	-0.281	3.244	-1.4	-5.291	-0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.024 / q_NPA : -0.029

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	ALA	0	0.017	-0.010	3.240	-0.917	1.282	0.134	-0.788	-1.545	0.000
4	A	5	LYS	1	0.866	0.930	3.699	0.834	1.007	0.012	0.010	-0.195	0.000
5	A	6	GLN	0	-0.061	-0.033	6.050	0.174	0.174	0.000	0.000	0.000	0.000
6	A	7	LEU	0	-0.069	-0.003	2.692	-0.566	0.083	0.421	-0.155	-0.914	0.000
7	A	8	ASN	0	0.003	0.000	5.761	-0.154	-0.154	0.000	0.000	0.000	0.000
8	A	9	SER	0	0.068	-0.009	8.100	-0.064	-0.064	0.000	0.000	0.000	0.000
9	A	10	LEU	0	0.001	0.021	10.758	-0.039	-0.039	0.000	0.000	0.000	0.000
10	A	11	ALA	0	-0.009	-0.007	6.379	-0.021	-0.021	0.000	0.000	0.000	0.000
11	A	12	LEU	0	-0.007	0.008	5.426	-0.108	-0.108	0.000	0.000	0.000	0.000
12	A	13	ALA	0	0.028	0.010	7.408	-0.070	-0.070	0.000	0.000	0.000	0.000
13	A	14	TYR	0	-0.022	-0.006	7.737	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	15	MET	0	-0.035	-0.009	5.537	-0.051	-0.051	0.000	0.000	0.000	0.000
15	A	16	GLY	0	0.051	-0.001	7.817	-0.020	-0.020	0.000	0.000	0.000	0.000
16	A	17	ASP	-1	-0.955	-0.970	10.576	-0.196	-0.196	0.000	0.000	0.000	0.000
17	A	18	ALA	0	-0.009	0.001	10.578	0.019	0.019	0.000	0.000	0.000	0.000
18	A	19	VAL	0	-0.041	-0.019	9.230	0.018	0.018	0.000	0.000	0.000	0.000
19	A	20	TYR	0	0.010	-0.019	12.195	0.029	0.029	0.000	0.000	0.000	0.000
20	A	21	GLU	-1	-0.754	-0.858	15.448	-0.158	-0.158	0.000	0.000	0.000	0.000
21	A	22	GLN	0	-0.076	-0.033	12.897	0.013	0.013	0.000	0.000	0.000	0.000
22	A	23	TYR	0	-0.050	-0.053	14.196	0.011	0.011	0.000	0.000	0.000	0.000
23	A	24	ILE	0	-0.006	0.012	18.198	0.029	0.029	0.000	0.000	0.000	0.000
24	A	25	ARG	1	0.788	0.868	19.675	0.190	0.190	0.000	0.000	0.000	0.000
25	A	26	TYR	0	0.000	0.005	20.320	0.017	0.017	0.000	0.000	0.000	0.000
26	A	27	HIS	0	-0.002	-0.010	22.117	0.011	0.011	0.000	0.000	0.000	0.000
27	A	28	LEU	0	-0.023	-0.021	24.284	0.017	0.017	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.079	-0.044	23.774	0.014	0.014	0.000	0.000	0.000	0.000
29	A	30	GLN	0	-0.016	0.008	25.939	0.012	0.012	0.000	0.000	0.000	0.000
30	A	31	LYS	1	0.845	0.925	27.883	0.128	0.128	0.000	0.000	0.000	0.000
31	A	32	GLY	0	0.008	0.012	29.926	0.009	0.009	0.000	0.000	0.000	0.000
32	A	33	LYS	1	0.869	0.920	31.755	0.098	0.098	0.000	0.000	0.000	0.000
33	A	34	VAL	0	0.007	0.015	31.164	0.004	0.004	0.000	0.000	0.000	0.000
34	A	35	ARG	1	0.975	0.988	33.327	0.063	0.063	0.000	0.000	0.000	0.000
35	A	36	PRO	0	0.085	0.025	30.890	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	37	ASN	0	-0.023	-0.021	30.493	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	38	GLN	0	-0.007	-0.005	32.152	0.004	0.004	0.000	0.000	0.000	0.000
38	A	39	LEU	0	0.037	0.033	27.002	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	40	HIS	0	0.065	0.044	24.385	-0.009	-0.009	0.000	0.000	0.000	0.000
40	A	41	ARG	1	0.971	0.979	26.789	0.078	0.078	0.000	0.000	0.000	0.000
41	A	42	LEU	0	-0.020	-0.022	28.935	0.000	0.000	0.000	0.000	0.000	0.000
42	A	43	GLY	0	0.116	0.071	24.613	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	44	THR	0	-0.013	-0.005	24.269	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	45	SER	0	-0.117	-0.070	25.766	0.000	0.000	0.000	0.000	0.000	0.000
45	A	46	PHE	0	0.039	0.015	22.976	0.001	0.001	0.000	0.000	0.000	0.000
46	A	47	VAL	0	0.025	0.018	19.857	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	48	SER	0	-0.044	-0.001	21.209	0.005	0.005	0.000	0.000	0.000	0.000
48	A	49	ALA	0	0.063	0.011	22.137	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	50	LYS	1	0.945	0.951	23.175	0.073	0.073	0.000	0.000	0.000	0.000
50	A	51	ALA	0	0.007	0.024	24.158	0.001	0.001	0.000	0.000	0.000	0.000
51	A	52	GLN	0	0.054	0.013	17.951	-0.022	-0.022	0.000	0.000	0.000	0.000
52	A	53	ALA	0	-0.006	-0.001	21.754	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	54	LYS	1	0.902	0.971	23.541	0.116	0.116	0.000	0.000	0.000	0.000
54	A	55	VAL	0	0.001	0.005	21.049	0.003	0.003	0.000	0.000	0.000	0.000
55	A	56	VAL	0	0.013	0.001	19.649	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	57	TYR	0	-0.028	-0.027	22.336	0.004	0.004	0.000	0.000	0.000	0.000
57	A	58	HIS	0	0.102	0.067	25.793	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	59	LEU	0	-0.022	-0.008	19.867	0.001	0.001	0.000	0.000	0.000	0.000
59	A	60	LEU	0	-0.041	-0.029	21.450	0.001	0.001	0.000	0.000	0.000	0.000
60	A	61	GLU	-1	-0.983	-0.979	24.626	-0.099	-0.099	0.000	0.000	0.000	0.000
61	A	62	THR	0	-0.055	-0.043	26.883	0.002	0.002	0.000	0.000	0.000	0.000
62	A	63	ALA	0	0.009	0.018	25.102	0.000	0.000	0.000	0.000	0.000	0.000
63	A	64	PHE	0	-0.011	-0.005	20.825	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	65	LEU	0	-0.055	-0.028	17.749	-0.020	-0.020	0.000	0.000	0.000	0.000
65	A	66	THR	0	0.050	0.000	17.681	0.013	0.013	0.000	0.000	0.000	0.000
66	A	67	GLU	-1	-0.882	-0.954	19.099	-0.142	-0.142	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.817	-0.881	12.434	-0.431	-0.431	0.000	0.000	0.000	0.000
68	A	69	GLU	-1	-0.718	-0.810	14.542	-0.348	-0.348	0.000	0.000	0.000	0.000
69	A	70	GLU	-1	-0.844	-0.928	15.613	-0.155	-0.155	0.000	0.000	0.000	0.000
70	A	71	ALA	0	-0.080	-0.036	15.603	0.022	0.022	0.000	0.000	0.000	0.000
71	A	72	VAL	0	-0.016	-0.001	11.048	0.025	0.025	0.000	0.000	0.000	0.000
72	A	73	LEU	0	0.028	0.028	13.498	0.019	0.019	0.000	0.000	0.000	0.000
73	A	74	ARG	1	0.938	0.963	16.291	0.130	0.130	0.000	0.000	0.000	0.000
74	A	75	ARG	1	0.924	0.949	12.479	0.104	0.104	0.000	0.000	0.000	0.000
75	A	76	GLY	0	0.063	0.030	13.942	0.021	0.021	0.000	0.000	0.000	0.000
76	A	77	ARG	1	0.789	0.902	14.778	0.101	0.101	0.000	0.000	0.000	0.000
77	A	78	ASN	0	-0.062	-0.049	16.603	0.012	0.012	0.000	0.000	0.000	0.000
78	A	79	ALA	0	0.035	0.016	16.403	0.004	0.004	0.000	0.000	0.000	0.000
79	A	80	ASN	0	0.001	0.000	17.344	0.029	0.029	0.000	0.000	0.000	0.000
80	A	81	SER	0	0.068	0.055	17.057	-0.004	-0.004	0.000	0.000	0.000	0.000
81	A	82	GLY	0	-0.016	0.001	18.266	0.008	0.008	0.000	0.000	0.000	0.000
82	A	83	THR	0	-0.012	0.010	21.689	0.002	0.002	0.000	0.000	0.000	0.000
83	A	84	VAL	0	-0.027	-0.019	22.055	-0.008	-0.008	0.000	0.000	0.000	0.000
84	A	85	PRO	0	0.018	0.018	22.208	0.007	0.007	0.000	0.000	0.000	0.000
85	A	86	LYS	1	1.009	0.988	24.935	0.039	0.039	0.000	0.000	0.000	0.000
86	A	87	ASN	0	-0.041	-0.029	28.708	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	88	THR	0	-0.012	0.013	24.801	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	89	ASP	-1	-0.792	-0.878	28.102	-0.063	-0.063	0.000	0.000	0.000	0.000
89	A	90	VAL	0	0.041	0.016	25.009	-0.007	-0.007	0.000	0.000	0.000	0.000
90	A	91	GLN	0	0.051	0.023	24.349	-0.013	-0.013	0.000	0.000	0.000	0.000
91	A	92	THR	0	-0.031	-0.029	24.255	-0.010	-0.010	0.000	0.000	0.000	0.000
92	A	93	TYR	0	0.010	-0.009	18.347	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	94	ARG	1	0.849	0.923	20.009	0.045	0.045	0.000	0.000	0.000	0.000
94	A	95	HIS	0	0.055	0.024	19.253	-0.012	-0.012	0.000	0.000	0.000	0.000
95	A	96	SER	0	-0.033	-0.006	18.924	-0.014	-0.014	0.000	0.000	0.000	0.000
96	A	97	THR	0	0.002	0.000	14.982	-0.011	-0.011	0.000	0.000	0.000	0.000
97	A	98	ALA	0	-0.049	-0.017	14.675	-0.028	-0.028	0.000	0.000	0.000	0.000
98	A	99	PHE	0	0.018	0.006	14.851	-0.038	-0.038	0.000	0.000	0.000	0.000
99	A	100	GLU	-1	-0.797	-0.896	13.053	-0.237	-0.237	0.000	0.000	0.000	0.000
100	A	101	ALA	0	0.001	-0.005	10.416	-0.069	-0.069	0.000	0.000	0.000	0.000
101	A	102	LEU	0	-0.015	-0.006	10.049	-0.095	-0.095	0.000	0.000	0.000	0.000
102	A	103	ILE	0	-0.006	0.006	11.356	-0.080	-0.080	0.000	0.000	0.000	0.000
103	A	104	GLY	0	0.010	0.002	7.998	-0.087	-0.087	0.000	0.000	0.000	0.000
104	A	105	TYR	0	-0.088	-0.073	6.639	-0.321	-0.321	0.000	0.000	0.000	0.000
105	A	106	HIS	0	0.041	0.000	7.106	-0.321	-0.321	0.000	0.000	0.000	0.000
106	A	107	HIS	0	-0.010	0.001	6.029	-0.005	-0.005	0.000	0.000	0.000	0.000
107	A	108	LEU	0	-0.047	-0.028	2.342	-1.130	-0.766	2.678	-0.454	-2.588	-0.001
108	A	109	LEU	0	-0.044	-0.013	4.667	-0.818	-0.755	-0.001	-0.013	-0.049	0.000
109	A	110	ASN	0	-0.066	-0.027	6.289	0.399	0.399	0.000	0.000	0.000	0.000
110	A	111	ASN	0	0.010	0.007	9.253	0.178	0.178	0.000	0.000	0.000	0.000
111	A	112	ARG	1	0.934	0.958	12.291	0.513	0.513	0.000	0.000	0.000	0.000
112	A	113	GLU	-1	-0.909	-0.941	14.282	-0.265	-0.265	0.000	0.000	0.000	0.000
113	A	114	ARG	1	0.842	0.882	15.091	0.319	0.319	0.000	0.000	0.000	0.000
114	A	115	LEU	0	-0.007	-0.011	11.751	0.028	0.028	0.000	0.000	0.000	0.000
115	A	116	ASP	-1	-0.800	-0.886	15.372	-0.324	-0.324	0.000	0.000	0.000	0.000
116	A	117	GLU	-1	-0.881	-0.919	18.551	-0.232	-0.232	0.000	0.000	0.000	0.000
117	A	118	ILE	0	-0.036	-0.018	15.634	0.028	0.028	0.000	0.000	0.000	0.000
118	A	119	VAL	0	0.001	0.003	16.267	0.029	0.029	0.000	0.000	0.000	0.000
119	A	120	TYR	0	-0.051	-0.048	19.180	0.033	0.033	0.000	0.000	0.000	0.000
120	A	121	LYS	1	0.870	0.957	22.226	0.179	0.179	0.000	0.000	0.000	0.000
121	A	122	ALA	0	-0.007	-0.015	20.698	0.018	0.018	0.000	0.000	0.000	0.000
122	A	123	ILE	0	-0.015	-0.019	21.697	0.017	0.017	0.000	0.000	0.000	0.000
123	A	124	ALA	0	0.002	0.005	24.657	0.014	0.014	0.000	0.000	0.000	0.000
124	A	125	VAL	0	0.029	0.017	25.812	0.011	0.011	0.000	0.000	0.000	0.000
125	A	126	LEU	0	-0.114	-0.062	23.769	0.014	0.014	0.000	0.000	0.000	0.000
126	A	127	GLU	-1	-0.840	-0.905	27.872	-0.126	-0.126	0.000	0.000	0.000	0.000
127	A	128	GLU	-1	-1.030	-0.986	30.459	-0.098	-0.098	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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