FMO DATABASE

FMODB ID: YVN82

Calculation Name: 1UFB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1UFB

Chain ID: A

ChEMBL ID:

UniProt ID: P83963

Base Structure: X-ray

Registration Date: 2023-09-22

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1078784.735321
FMO2-HF: Nuclear repulsion	1029892.007993
FMO2-HF: Total energy	-48892.727327
FMO2-MP2: Total energy	-49038.166539

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:1:MET)

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

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.
-7.084	-3.474	12.832	-4.447	-11.995	0.006

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : 0.002

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

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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	3	ARG	1	0.932	0.970	3.383	0.426	2.461	0.002	-0.936	-1.101	0.003
4	A	4	ALA	0	0.063	0.060	2.263	0.136	1.189	2.267	-1.259	-2.061	0.000
5	A	5	ARG	1	0.936	0.944	2.153	-4.390	-6.583	9.862	-1.587	-6.083	0.006
6	A	6	ASP	-1	-0.758	-0.871	4.806	-0.882	-0.740	-0.001	-0.017	-0.123	0.000
7	A	7	TRP	0	-0.049	-0.019	7.047	0.281	0.281	0.000	0.000	0.000	0.000
8	A	8	LEU	0	0.026	0.013	6.467	0.075	0.075	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.992	-0.995	8.730	0.172	0.172	0.000	0.000	0.000	0.000
10	A	10	GLN	0	-0.073	-0.030	10.377	-0.024	-0.024	0.000	0.000	0.000	0.000
11	A	11	ALA	0	0.002	0.013	11.806	0.003	0.003	0.000	0.000	0.000	0.000
12	A	12	ARG	1	0.955	0.971	7.493	-0.381	-0.381	0.000	0.000	0.000	0.000
13	A	13	HIS	0	-0.044	-0.013	13.838	0.006	0.006	0.000	0.000	0.000	0.000
14	A	14	ASN	0	0.031	0.018	16.250	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	15	LEU	0	0.036	0.018	16.851	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.960	0.973	14.282	-0.098	-0.098	0.000	0.000	0.000	0.000
17	A	17	HIS	0	0.015	0.016	19.861	0.000	0.000	0.000	0.000	0.000	0.000
18	A	18	ALA	0	0.009	0.008	21.506	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	19	GLN	0	-0.016	-0.013	21.113	0.006	0.006	0.000	0.000	0.000	0.000
20	A	20	GLY	0	-0.015	-0.005	23.993	0.000	0.000	0.000	0.000	0.000	0.000
21	A	21	SER	0	-0.046	-0.047	25.687	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.023	-0.001	26.918	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	23	GLY	0	-0.031	-0.010	28.592	0.000	0.000	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.047	-0.019	29.354	0.000	0.000	0.000	0.000	0.000	0.000
25	A	25	GLY	0	-0.011	0.003	31.993	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.927	-0.952	30.594	-0.020	-0.020	0.000	0.000	0.000	0.000
27	A	27	TYR	0	0.000	-0.017	30.120	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	28	ALA	0	0.053	0.031	29.731	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	29	TRP	0	0.002	-0.011	26.214	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	30	ALA	0	0.034	0.024	25.915	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	31	CYS	0	-0.030	-0.003	24.902	0.002	0.002	0.000	0.000	0.000	0.000
32	A	32	PHE	0	-0.075	-0.024	23.742	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	33	ALA	0	-0.020	-0.004	22.076	-0.008	-0.008	0.000	0.000	0.000	0.000
34	A	34	ALA	0	0.060	0.031	20.627	0.001	0.001	0.000	0.000	0.000	0.000
35	A	35	GLN	0	0.024	0.007	19.966	0.002	0.002	0.000	0.000	0.000	0.000
36	A	36	GLN	0	-0.077	-0.053	18.994	-0.021	-0.021	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.028	-0.011	16.331	-0.017	-0.017	0.000	0.000	0.000	0.000
38	A	38	ALA	0	0.053	0.025	15.018	0.010	0.010	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.754	-0.839	15.003	-0.185	-0.185	0.000	0.000	0.000	0.000
40	A	40	ALA	0	-0.020	-0.017	12.973	-0.042	-0.042	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.039	0.019	10.641	-0.036	-0.036	0.000	0.000	0.000	0.000
42	A	42	LEU	0	0.051	0.022	9.933	0.064	0.064	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.806	0.916	10.548	0.250	0.250	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.017	-0.002	7.016	-0.232	-0.232	0.000	0.000	0.000	0.000
45	A	45	LEU	0	0.016	0.002	5.769	0.001	0.001	0.000	0.000	0.000	0.000
46	A	46	HIS	1	0.783	0.850	7.159	0.214	0.214	0.000	0.000	0.000	0.000
47	A	47	LEU	0	-0.050	-0.011	5.259	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	48	ALA	0	-0.015	-0.011	2.816	-1.821	-0.899	0.463	-0.374	-1.011	-0.001
49	A	49	ARG	1	0.778	0.903	3.723	-0.343	-0.115	0.002	0.024	-0.253	0.000
50	A	50	GLY	0	-0.023	-0.006	6.008	0.117	0.117	0.000	0.000	0.000	0.000
51	A	51	GLN	0	0.045	0.042	7.762	0.188	0.188	0.000	0.000	0.000	0.000
52	A	52	VAL	0	0.010	0.005	9.331	-0.160	-0.160	0.000	0.000	0.000	0.000
53	A	53	ALA	0	0.014	0.013	11.589	0.103	0.103	0.000	0.000	0.000	0.000
54	A	54	TRP	0	-0.003	-0.018	13.755	-0.027	-0.027	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.012	0.004	16.817	0.027	0.027	0.000	0.000	0.000	0.000
56	A	56	HIS	1	0.786	0.841	18.451	0.155	0.155	0.000	0.000	0.000	0.000
57	A	57	SER	0	0.034	0.069	20.639	0.014	0.014	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.051	0.017	18.129	-0.012	-0.012	0.000	0.000	0.000	0.000
59	A	59	LEU	0	-0.027	-0.017	18.963	0.008	0.008	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.878	-0.944	19.800	-0.115	-0.115	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.091	-0.034	14.269	-0.015	-0.015	0.000	0.000	0.000	0.000
62	A	62	LEU	0	0.005	0.001	15.222	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	63	ALA	0	-0.009	0.012	17.242	0.011	0.011	0.000	0.000	0.000	0.000
64	A	64	ASP	-1	-0.915	-0.957	16.142	-0.170	-0.170	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.111	-0.058	11.681	-0.028	-0.028	0.000	0.000	0.000	0.000
66	A	66	PRO	0	-0.039	-0.022	11.205	0.000	0.000	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.889	-0.941	14.517	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.924	-0.952	12.948	0.109	0.109	0.000	0.000	0.000	0.000
69	A	69	VAL	0	-0.081	-0.034	11.893	0.042	0.042	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.918	-0.964	14.640	0.029	0.029	0.000	0.000	0.000	0.000
71	A	71	VAL	0	-0.011	-0.008	16.400	0.015	0.015	0.000	0.000	0.000	0.000
72	A	72	PRO	0	0.017	0.014	17.393	-0.009	-0.009	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.844	-0.942	20.645	-0.011	-0.011	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.927	-0.977	21.145	0.031	0.031	0.000	0.000	0.000	0.000
75	A	75	LEU	0	0.014	0.010	16.440	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	76	VAL	0	0.019	0.021	20.609	-0.011	-0.011	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.859	-0.953	23.051	-0.022	-0.022	0.000	0.000	0.000	0.000
78	A	78	ALA	0	0.016	0.003	21.346	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	79	ALA	0	0.007	-0.024	20.903	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	80	LYS	1	0.829	0.932	22.479	0.018	0.018	0.000	0.000	0.000	0.000
81	A	81	VAL	0	-0.033	-0.008	25.919	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	82	LEU	0	0.001	-0.010	20.525	-0.005	-0.005	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.746	-0.864	22.628	-0.080	-0.080	0.000	0.000	0.000	0.000
84	A	84	LYS	1	0.858	0.934	24.987	0.031	0.031	0.000	0.000	0.000	0.000
85	A	85	TYR	0	0.018	-0.008	25.596	0.000	0.000	0.000	0.000	0.000	0.000
86	A	86	TYR	0	0.027	0.035	22.875	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	87	ILE	0	0.018	0.002	25.570	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	88	PRO	0	0.035	0.000	28.937	0.002	0.002	0.000	0.000	0.000	0.000
89	A	89	THR	0	0.008	0.012	27.832	0.002	0.002	0.000	0.000	0.000	0.000
90	A	90	ARG	1	0.866	0.939	26.541	0.087	0.087	0.000	0.000	0.000	0.000
91	A	91	TYR	0	-0.032	-0.007	29.371	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	92	PRO	0	-0.012	-0.023	34.167	0.002	0.002	0.000	0.000	0.000	0.000
93	A	93	ASP	-1	-0.896	-0.936	36.306	-0.054	-0.054	0.000	0.000	0.000	0.000
94	A	94	ALA	0	-0.010	0.017	34.209	0.000	0.000	0.000	0.000	0.000	0.000
95	A	95	HIS	1	0.797	0.871	34.425	0.038	0.038	0.000	0.000	0.000	0.000
96	A	96	PRO	0	0.022	0.021	39.073	0.000	0.000	0.000	0.000	0.000	0.000
97	A	97	ALA	0	0.039	0.017	42.375	0.000	0.000	0.000	0.000	0.000	0.000
98	A	98	GLY	0	-0.020	-0.024	42.046	0.001	0.001	0.000	0.000	0.000	0.000
99	A	99	PRO	0	0.025	0.013	38.716	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	100	ALA	0	0.047	0.018	34.271	0.002	0.002	0.000	0.000	0.000	0.000
101	A	101	ALA	0	0.058	0.001	34.799	0.002	0.002	0.000	0.000	0.000	0.000
102	A	102	ARG	1	0.916	0.973	35.849	0.025	0.025	0.000	0.000	0.000	0.000
103	A	103	HIS	0	-0.108	-0.047	36.505	0.004	0.004	0.000	0.000	0.000	0.000
104	A	104	TYR	0	0.050	0.043	31.610	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	105	THR	0	0.000	0.001	34.056	0.002	0.002	0.000	0.000	0.000	0.000
106	A	106	ARG	1	0.919	0.935	32.100	-0.013	-0.013	0.000	0.000	0.000	0.000
107	A	107	LEU	0	0.000	-0.004	31.142	0.002	0.002	0.000	0.000	0.000	0.000
108	A	108	GLU	-1	-0.798	-0.903	30.606	-0.014	-0.014	0.000	0.000	0.000	0.000
109	A	109	ALA	0	-0.007	0.000	28.039	0.000	0.000	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.865	-0.938	26.570	0.020	0.020	0.000	0.000	0.000	0.000
111	A	111	GLU	-1	-0.887	-0.925	25.816	0.004	0.004	0.000	0.000	0.000	0.000
112	A	112	ALA	0	-0.035	-0.029	24.901	0.002	0.002	0.000	0.000	0.000	0.000
113	A	113	LEU	0	-0.035	-0.035	22.029	0.001	0.001	0.000	0.000	0.000	0.000
114	A	114	ASP	-1	-0.873	-0.923	20.969	0.038	0.038	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.067	-0.043	20.825	0.008	0.008	0.000	0.000	0.000	0.000
116	A	116	ALA	0	0.002	-0.001	18.427	0.003	0.003	0.000	0.000	0.000	0.000
117	A	117	GLN	0	0.016	0.003	14.934	0.011	0.011	0.000	0.000	0.000	0.000
118	A	118	LYS	1	0.917	0.963	15.879	-0.016	-0.016	0.000	0.000	0.000	0.000
119	A	119	ILE	0	-0.014	0.004	14.413	0.010	0.010	0.000	0.000	0.000	0.000
120	A	120	LEU	0	-0.030	-0.030	11.216	0.021	0.021	0.000	0.000	0.000	0.000
121	A	121	ALA	0	-0.014	0.006	11.019	0.037	0.037	0.000	0.000	0.000	0.000
122	A	122	PHE	0	0.046	0.039	11.470	0.015	0.015	0.000	0.000	0.000	0.000
123	A	123	VAL	0	-0.030	-0.028	8.008	0.036	0.036	0.000	0.000	0.000	0.000
124	A	124	GLU	-1	-0.969	-1.013	6.904	0.295	0.295	0.000	0.000	0.000	0.000
125	A	125	GLU	-1	-0.933	-0.966	6.753	0.014	0.014	0.000	0.000	0.000	0.000
126	A	126	LYS	1	0.859	0.952	8.506	-0.137	-0.137	0.000	0.000	0.000	0.000
127	A	127	LEU	0	-0.080	-0.027	3.005	-0.837	0.586	0.237	-0.298	-1.363	-0.002

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