FMO DATABASE

FMODB ID: LNNJ9

Calculation Name: 3UPS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3UPS

Chain ID: A

ChEMBL ID:

UniProt ID: Q5NLX3

Base Structure: X-ray

Registration Date: 2023-09-21

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

DOI:

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	108
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-791129.728911
FMO2-HF: Nuclear repulsion	749280.117409
FMO2-HF: Total energy	-41849.611502
FMO2-MP2: Total energy	-41971.32029

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:14:PHE)

Summations of interaction energy for fragment #1(A:14:PHE)

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.
-17.12	-7.228	10.046	-4.477	-15.462	0.016

Interaction energy analysis for fragmet #1(A:14:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.050 / q_NPA : -0.054

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	16	PRO	0	0.103	0.053	3.085	-3.557	-1.132	0.160	-1.005	-1.580	-0.002
4	A	17	GLU	-1	-0.812	-0.890	5.107	-0.828	-0.678	-0.001	-0.007	-0.142	0.000
5	A	18	MET	0	-0.088	-0.032	3.031	-2.300	0.330	1.421	-1.057	-2.994	0.011
6	A	19	LEU	0	0.003	0.002	2.252	-4.356	-1.831	2.810	-1.840	-3.495	-0.004
7	A	20	LEU	0	0.010	-0.003	2.873	2.786	1.458	0.095	1.504	-0.271	-0.001
8	A	21	LYS	1	0.838	0.910	5.534	0.474	0.474	0.000	0.000	0.000	0.000
9	A	22	LEU	0	-0.026	0.004	3.318	-0.251	0.397	0.034	-0.140	-0.542	0.000
10	A	23	VAL	0	0.022	0.000	5.504	0.391	0.391	0.000	0.000	0.000	0.000
11	A	24	THR	0	-0.044	-0.034	7.906	0.226	0.226	0.000	0.000	0.000	0.000
12	A	25	ASP	-1	-0.777	-0.873	8.723	-0.161	-0.161	0.000	0.000	0.000	0.000
13	A	26	SER	0	-0.028	-0.002	9.519	0.109	0.109	0.000	0.000	0.000	0.000
14	A	27	LEU	0	-0.059	-0.045	11.182	0.054	0.054	0.000	0.000	0.000	0.000
15	A	28	ASP	-1	-0.923	-0.956	13.401	-0.122	-0.122	0.000	0.000	0.000	0.000
16	A	29	ASP	-1	-0.941	-0.958	13.643	-0.032	-0.032	0.000	0.000	0.000	0.000
17	A	30	ASP	-1	-0.895	-0.947	15.266	-0.101	-0.101	0.000	0.000	0.000	0.000
18	A	31	GLN	0	-0.138	-0.081	17.383	0.005	0.005	0.000	0.000	0.000	0.000
19	A	32	ALA	0	-0.011	-0.010	16.934	0.007	0.007	0.000	0.000	0.000	0.000
20	A	33	LEU	0	-0.026	-0.018	18.877	0.012	0.012	0.000	0.000	0.000	0.000
21	A	34	GLU	-1	-0.989	-1.010	20.001	-0.220	-0.220	0.000	0.000	0.000	0.000
22	A	35	ILE	0	0.035	0.022	14.007	-0.021	-0.021	0.000	0.000	0.000	0.000
23	A	36	ALA	0	-0.018	0.001	17.076	0.007	0.007	0.000	0.000	0.000	0.000
24	A	37	THR	0	0.029	0.001	12.509	-0.074	-0.074	0.000	0.000	0.000	0.000
25	A	38	ILE	0	-0.050	-0.023	14.896	0.066	0.066	0.000	0.000	0.000	0.000
26	A	39	PRO	0	0.036	0.021	14.214	-0.079	-0.079	0.000	0.000	0.000	0.000
27	A	40	LEU	0	-0.026	-0.023	14.343	0.113	0.113	0.000	0.000	0.000	0.000
28	A	41	ALA	0	0.088	0.052	15.025	0.042	0.042	0.000	0.000	0.000	0.000
29	A	42	GLY	0	-0.060	-0.035	16.492	0.053	0.053	0.000	0.000	0.000	0.000
30	A	43	LYS	1	0.866	0.937	18.997	0.353	0.353	0.000	0.000	0.000	0.000
31	A	44	SER	0	-0.006	-0.015	18.142	0.024	0.024	0.000	0.000	0.000	0.000
32	A	45	SER	0	0.027	0.013	16.152	-0.013	-0.013	0.000	0.000	0.000	0.000
33	A	46	ILE	0	-0.090	-0.036	15.158	-0.045	-0.045	0.000	0.000	0.000	0.000
34	A	47	ALA	0	0.048	0.032	11.459	-0.056	-0.056	0.000	0.000	0.000	0.000
35	A	48	ASP	-1	-0.871	-0.931	9.000	-1.502	-1.502	0.000	0.000	0.000	0.000
36	A	49	TYR	0	-0.098	-0.084	8.848	0.355	0.355	0.000	0.000	0.000	0.000
37	A	50	MET	0	-0.040	-0.007	11.889	-0.048	-0.048	0.000	0.000	0.000	0.000
38	A	51	VAL	0	0.013	0.006	10.692	0.051	0.051	0.000	0.000	0.000	0.000
39	A	52	ILE	0	-0.019	-0.008	13.904	0.021	0.021	0.000	0.000	0.000	0.000
40	A	53	ALA	0	0.030	0.030	16.339	0.010	0.010	0.000	0.000	0.000	0.000
41	A	54	SER	0	-0.028	-0.001	18.271	0.012	0.012	0.000	0.000	0.000	0.000
42	A	55	GLY	0	0.095	0.025	20.607	0.000	0.000	0.000	0.000	0.000	0.000
43	A	56	ARG	1	0.944	0.974	22.337	0.100	0.100	0.000	0.000	0.000	0.000
44	A	57	SER	0	-0.047	-0.025	25.090	0.014	0.014	0.000	0.000	0.000	0.000
45	A	58	SER	0	0.101	0.042	24.774	-0.012	-0.012	0.000	0.000	0.000	0.000
46	A	59	ARG	1	0.963	0.973	24.391	0.082	0.082	0.000	0.000	0.000	0.000
47	A	60	GLN	0	-0.007	-0.007	21.037	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	61	VAL	0	0.105	0.061	20.220	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	62	THR	0	0.028	0.007	19.288	-0.020	-0.020	0.000	0.000	0.000	0.000
50	A	63	ALA	0	-0.061	-0.034	19.152	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	64	MET	0	-0.040	0.015	16.195	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	65	ALA	0	0.043	0.021	14.690	-0.017	-0.017	0.000	0.000	0.000	0.000
53	A	66	GLN	0	-0.059	-0.031	14.476	-0.033	-0.033	0.000	0.000	0.000	0.000
54	A	67	LYS	1	0.862	0.927	13.808	0.103	0.103	0.000	0.000	0.000	0.000
55	A	68	LEU	0	0.021	0.029	8.471	0.047	0.047	0.000	0.000	0.000	0.000
56	A	69	ALA	0	0.025	0.006	9.842	0.024	0.024	0.000	0.000	0.000	0.000
57	A	70	ASP	-1	-0.898	-0.943	11.067	0.001	0.001	0.000	0.000	0.000	0.000
58	A	71	ARG	1	0.853	0.910	7.859	0.164	0.164	0.000	0.000	0.000	0.000
59	A	72	ILE	0	0.059	0.035	6.020	0.355	0.355	0.000	0.000	0.000	0.000
60	A	73	LYS	1	0.961	1.004	6.810	0.576	0.576	0.000	0.000	0.000	0.000
61	A	74	ALA	0	-0.079	-0.044	8.391	0.087	0.087	0.000	0.000	0.000	0.000
62	A	75	ALA	0	-0.038	-0.015	3.165	-0.811	-0.120	0.152	-0.274	-0.569	0.002
63	A	76	THR	0	-0.024	-0.017	2.644	-3.591	-1.702	5.372	-1.599	-5.663	0.009
64	A	77	GLY	0	-0.031	-0.012	4.400	-1.498	-1.236	0.003	-0.059	-0.206	0.001
65	A	78	TYR	0	-0.027	-0.008	5.724	-0.184	-0.184	0.000	0.000	0.000	0.000
66	A	79	VAL	0	-0.049	-0.034	7.697	0.212	0.212	0.000	0.000	0.000	0.000
67	A	80	SER	0	0.031	0.008	10.214	-0.076	-0.076	0.000	0.000	0.000	0.000
68	A	81	LYS	1	0.913	0.982	11.988	0.409	0.409	0.000	0.000	0.000	0.000
69	A	82	ILE	0	-0.005	-0.009	15.400	-0.032	-0.032	0.000	0.000	0.000	0.000
70	A	83	GLU	-1	-0.920	-0.967	17.616	-0.275	-0.275	0.000	0.000	0.000	0.000
71	A	84	GLY	0	0.020	-0.007	20.670	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	85	LEU	0	0.010	0.029	19.397	0.013	0.013	0.000	0.000	0.000	0.000
73	A	86	PRO	0	-0.020	-0.026	23.607	0.000	0.000	0.000	0.000	0.000	0.000
74	A	87	ALA	0	-0.031	-0.024	25.896	0.005	0.005	0.000	0.000	0.000	0.000
75	A	88	ALA	0	0.051	0.044	23.130	-0.008	-0.008	0.000	0.000	0.000	0.000
76	A	89	ASP	-1	-0.923	-0.982	24.993	-0.145	-0.145	0.000	0.000	0.000	0.000
77	A	90	TRP	0	-0.083	-0.047	21.654	0.009	0.009	0.000	0.000	0.000	0.000
78	A	91	VAL	0	0.007	0.002	17.539	0.013	0.013	0.000	0.000	0.000	0.000
79	A	92	LEU	0	-0.030	0.004	16.539	-0.009	-0.009	0.000	0.000	0.000	0.000
80	A	93	LEU	0	-0.021	-0.008	10.840	0.032	0.032	0.000	0.000	0.000	0.000
81	A	94	ASP	-1	-0.875	-0.943	12.838	-0.887	-0.887	0.000	0.000	0.000	0.000
82	A	95	ALA	0	-0.007	-0.034	7.706	0.110	0.110	0.000	0.000	0.000	0.000
83	A	96	GLY	0	-0.001	0.010	7.794	-0.415	-0.415	0.000	0.000	0.000	0.000
84	A	97	ASP	-1	-0.851	-0.919	5.879	-3.570	-3.570	0.000	0.000	0.000	0.000
85	A	98	ILE	0	-0.051	-0.023	6.699	0.276	0.276	0.000	0.000	0.000	0.000
86	A	99	ILE	0	0.006	0.020	9.418	0.104	0.104	0.000	0.000	0.000	0.000
87	A	100	ILE	0	-0.026	-0.019	9.748	0.042	0.042	0.000	0.000	0.000	0.000
88	A	101	HIS	0	0.001	0.000	13.827	0.074	0.074	0.000	0.000	0.000	0.000
89	A	102	LEU	0	0.009	-0.003	15.308	0.010	0.010	0.000	0.000	0.000	0.000
90	A	103	PHE	0	-0.009	-0.018	18.926	0.020	0.020	0.000	0.000	0.000	0.000
91	A	104	ARG	1	0.936	0.974	22.686	0.135	0.135	0.000	0.000	0.000	0.000
92	A	105	PRO	0	0.050	0.027	24.941	0.004	0.004	0.000	0.000	0.000	0.000
93	A	106	GLU	-1	-0.826	-0.922	27.608	-0.120	-0.120	0.000	0.000	0.000	0.000
94	A	107	VAL	0	-0.017	-0.004	28.706	0.005	0.005	0.000	0.000	0.000	0.000
95	A	108	ARG	1	0.975	0.997	25.966	0.204	0.204	0.000	0.000	0.000	0.000
96	A	109	SER	0	-0.031	-0.024	29.349	0.001	0.001	0.000	0.000	0.000	0.000
97	A	110	PHE	0	-0.001	0.006	32.285	0.004	0.004	0.000	0.000	0.000	0.000
98	A	111	TYR	0	0.027	0.004	30.478	0.004	0.004	0.000	0.000	0.000	0.000
99	A	112	ASN	0	-0.055	-0.035	29.746	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	113	LEU	0	-0.019	-0.004	33.578	0.003	0.003	0.000	0.000	0.000	0.000
101	A	114	GLU	-1	-0.895	-0.942	36.681	-0.099	-0.099	0.000	0.000	0.000	0.000
102	A	115	ARG	1	0.951	0.969	29.975	0.155	0.155	0.000	0.000	0.000	0.000
103	A	116	MET	0	-0.066	-0.022	36.870	0.001	0.001	0.000	0.000	0.000	0.000
104	A	117	TRP	0	-0.058	-0.028	38.605	0.004	0.004	0.000	0.000	0.000	0.000
105	A	118	GLY	0	-0.012	0.005	40.211	0.005	0.005	0.000	0.000	0.000	0.000
106	A	119	PHE	0	-0.060	-0.037	39.379	0.003	0.003	0.000	0.000	0.000	0.000
107	A	120	GLY	0	-0.040	-0.021	38.451	-0.005	-0.005	0.000	0.000	0.000	0.000
108	A	121	ASP	-1	-0.962	-0.966	38.516	-0.105	-0.105	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:14:PHE)