FMO DATABASE

FMODB ID: Q13YY

Calculation Name: 4PUG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4PUG

Chain ID: A

ChEMBL ID:

UniProt ID: Q682I1

Base Structure: X-ray

Registration Date: 2023-06-20

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	94
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-666284.958887
FMO2-HF: Nuclear repulsion	628691.381401
FMO2-HF: Total energy	-37593.577486
FMO2-MP2: Total energy	-37703.216231

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:64:ALA)

Summations of interaction energy for fragment #1(A:64:ALA)

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.
-1.289	0.2	-0.023	-0.647	-0.819	0

Interaction energy analysis for fragmet #1(A:64:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.017

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	66	GLU	-1	-0.946	-0.957	3.801	-1.002	0.487	-0.023	-0.647	-0.819
4	A	67	ASN	0	-0.017	-0.013	5.877	0.256	0.256	0.000	0.000	0.000
5	A	68	ARG	1	0.788	0.844	8.632	-0.045	-0.045	0.000	0.000	0.000
6	A	69	ALA	0	-0.006	-0.007	9.499	0.000	0.000	0.000	0.000	0.000
7	A	70	SER	0	-0.064	-0.034	5.615	-0.103	-0.103	0.000	0.000	0.000
8	A	71	ARG	1	0.900	0.928	7.549	-0.053	-0.053	0.000	0.000	0.000
9	A	72	MET	0	-0.037	-0.003	10.015	-0.041	-0.041	0.000	0.000	0.000
10	A	73	ARG	1	0.897	0.941	8.989	-0.738	-0.738	0.000	0.000	0.000
11	A	74	GLU	-1	-0.925	-0.963	8.809	-0.057	-0.057	0.000	0.000	0.000
12	A	75	LYS	1	1.001	1.012	10.719	-0.048	-0.048	0.000	0.000	0.000
13	A	76	LEU	0	-0.045	-0.038	14.126	-0.019	-0.019	0.000	0.000	0.000
14	A	77	GLN	0	-0.030	-0.029	13.061	0.014	0.014	0.000	0.000	0.000
15	A	78	LYS	1	0.922	0.973	14.232	0.005	0.005	0.000	0.000	0.000
16	A	79	GLU	-1	-0.929	-0.975	15.873	0.010	0.010	0.000	0.000	0.000
17	A	80	LEU	0	-0.086	-0.047	18.638	-0.007	-0.007	0.000	0.000	0.000
18	A	81	GLU	-1	-0.928	-0.938	18.242	0.071	0.071	0.000	0.000	0.000
19	A	82	PRO	0	-0.105	-0.030	17.232	-0.005	-0.005	0.000	0.000	0.000
20	A	83	VAL	0	-0.016	-0.017	18.788	0.011	0.011	0.000	0.000	0.000
21	A	84	GLU	-1	-0.942	-0.981	19.066	0.230	0.230	0.000	0.000	0.000
22	A	85	LEU	0	0.004	0.005	14.076	-0.020	-0.020	0.000	0.000	0.000
23	A	86	VAL	0	-0.003	0.001	15.646	0.068	0.068	0.000	0.000	0.000
24	A	87	ILE	0	-0.019	-0.018	12.532	-0.046	-0.046	0.000	0.000	0.000
25	A	88	GLU	-1	-0.889	-0.942	14.401	0.334	0.334	0.000	0.000	0.000
26	A	89	ASP	-1	-0.814	-0.899	14.566	0.252	0.252	0.000	0.000	0.000
27	A	90	VAL	0	0.013	-0.005	16.662	0.001	0.001	0.000	0.000	0.000
28	A	91	SER	0	0.026	0.004	17.926	-0.042	-0.042	0.000	0.000	0.000
29	A	92	TYR	0	-0.033	-0.009	18.535	-0.036	-0.036	0.000	0.000	0.000
30	A	93	GLN	0	-0.060	-0.032	21.365	-0.007	-0.007	0.000	0.000	0.000
31	A	94	HIS	0	-0.038	-0.013	23.554	-0.021	-0.021	0.000	0.000	0.000
32	A	95	ALA	0	-0.023	0.001	22.294	-0.013	-0.013	0.000	0.000	0.000
33	A	96	GLY	0	0.069	0.049	22.581	0.007	0.007	0.000	0.000	0.000
34	A	97	HIS	0	0.038	-0.002	23.362	-0.004	-0.004	0.000	0.000	0.000
35	A	98	ALA	0	-0.002	0.000	23.899	-0.006	-0.006	0.000	0.000	0.000
36	A	99	GLY	0	-0.032	-0.014	24.980	-0.008	-0.008	0.000	0.000	0.000
37	A	100	MET	0	-0.024	-0.017	24.062	-0.009	-0.009	0.000	0.000	0.000
38	A	101	LYS	1	0.996	1.002	18.265	-0.078	-0.078	0.000	0.000	0.000
39	A	102	GLY	0	-0.010	-0.003	17.581	-0.009	-0.009	0.000	0.000	0.000
40	A	103	ARG	1	0.892	0.937	18.568	0.039	0.039	0.000	0.000	0.000
41	A	104	THR	0	0.012	0.013	20.018	-0.005	-0.005	0.000	0.000	0.000
42	A	105	ASP	-1	-0.821	-0.896	16.141	0.032	0.032	0.000	0.000	0.000
43	A	106	ASP	-1	-0.906	-0.959	16.746	0.066	0.066	0.000	0.000	0.000
44	A	107	GLU	-1	-0.827	-0.904	11.665	0.328	0.328	0.000	0.000	0.000
45	A	108	THR	0	0.044	0.024	16.241	-0.014	-0.014	0.000	0.000	0.000
46	A	109	HIS	0	-0.027	-0.040	19.288	-0.020	-0.020	0.000	0.000	0.000
47	A	110	PHE	0	0.033	0.015	13.751	0.029	0.029	0.000	0.000	0.000
48	A	111	ASN	0	-0.045	-0.009	19.069	-0.049	-0.049	0.000	0.000	0.000
49	A	112	VAL	0	0.017	0.004	17.306	0.034	0.034	0.000	0.000	0.000
50	A	113	LYS	1	0.923	0.967	19.360	-0.205	-0.205	0.000	0.000	0.000
51	A	114	ILE	0	0.008	0.001	18.939	0.022	0.022	0.000	0.000	0.000
52	A	115	VAL	0	-0.005	0.003	21.062	-0.025	-0.025	0.000	0.000	0.000
53	A	116	SER	0	0.060	0.008	21.856	0.004	0.004	0.000	0.000	0.000
54	A	117	LYS	1	1.041	0.994	23.702	-0.087	-0.087	0.000	0.000	0.000
55	A	118	GLY	0	0.041	0.043	25.215	-0.008	-0.008	0.000	0.000	0.000
56	A	119	PHE	0	-0.029	-0.045	23.169	-0.008	-0.008	0.000	0.000	0.000
57	A	120	GLU	-1	-0.907	-0.963	28.211	0.063	0.063	0.000	0.000	0.000
58	A	121	GLY	0	-0.023	0.001	31.397	-0.004	-0.004	0.000	0.000	0.000
59	A	122	MET	0	-0.114	-0.030	27.811	-0.003	-0.003	0.000	0.000	0.000
60	A	123	ASN	0	0.079	0.032	32.735	0.005	0.005	0.000	0.000	0.000
61	A	124	LEU	0	0.074	0.019	30.611	0.002	0.002	0.000	0.000	0.000
62	A	125	VAL	0	0.026	0.008	30.516	0.003	0.003	0.000	0.000	0.000
63	A	126	LYS	1	0.972	0.980	30.830	-0.039	-0.039	0.000	0.000	0.000
64	A	127	ARG	1	0.802	0.909	27.274	-0.078	-0.078	0.000	0.000	0.000
65	A	128	HIS	1	0.912	0.958	26.202	-0.088	-0.088	0.000	0.000	0.000
66	A	129	ARG	1	0.973	0.995	26.184	-0.033	-0.033	0.000	0.000	0.000
67	A	130	LEU	0	-0.015	0.011	23.926	-0.005	-0.005	0.000	0.000	0.000
68	A	131	VAL	0	0.023	0.001	20.609	-0.003	-0.003	0.000	0.000	0.000
69	A	132	TYR	0	0.033	0.004	21.554	0.001	0.001	0.000	0.000	0.000
70	A	133	HIS	0	-0.055	-0.020	23.031	-0.005	-0.005	0.000	0.000	0.000
71	A	134	LEU	0	-0.044	-0.025	19.037	-0.010	-0.010	0.000	0.000	0.000
72	A	135	LEU	0	0.008	-0.002	16.293	-0.002	-0.002	0.000	0.000	0.000
73	A	136	ARG	1	0.939	0.975	19.300	-0.015	-0.015	0.000	0.000	0.000
74	A	137	GLU	-1	-0.895	-0.941	16.295	-0.067	-0.067	0.000	0.000	0.000
75	A	138	GLU	-1	-0.758	-0.832	14.158	0.031	0.031	0.000	0.000	0.000
76	A	139	LEU	0	-0.079	-0.040	17.925	0.002	0.002	0.000	0.000	0.000
77	A	140	ASP	-1	-0.925	-0.941	21.398	0.001	0.001	0.000	0.000	0.000
78	A	141	THR	0	-0.082	-0.065	17.914	-0.009	-0.009	0.000	0.000	0.000
79	A	142	GLY	0	0.032	0.025	18.407	-0.009	-0.009	0.000	0.000	0.000
80	A	143	LEU	0	-0.067	-0.022	17.644	0.017	0.017	0.000	0.000	0.000
81	A	144	HIS	0	0.004	0.011	19.845	-0.012	-0.012	0.000	0.000	0.000
82	A	145	ALA	0	-0.025	-0.016	22.359	-0.005	-0.005	0.000	0.000	0.000
83	A	146	LEU	0	0.035	0.020	19.439	0.019	0.019	0.000	0.000	0.000
84	A	147	SER	0	-0.037	-0.007	22.417	-0.018	-0.018	0.000	0.000	0.000
85	A	148	ILE	0	0.014	-0.005	22.467	0.014	0.014	0.000	0.000	0.000
86	A	149	VAL	0	-0.036	-0.016	23.507	-0.016	-0.016	0.000	0.000	0.000
87	A	150	SER	0	-0.010	-0.009	23.779	0.009	0.009	0.000	0.000	0.000
88	A	151	LYS	1	0.895	0.943	25.246	-0.111	-0.111	0.000	0.000	0.000
89	A	152	THR	0	0.079	0.042	26.001	0.007	0.007	0.000	0.000	0.000
90	A	153	PRO	0	0.028	-0.015	25.745	0.002	0.002	0.000	0.000	0.000
91	A	154	SER	0	0.033	0.025	27.926	0.002	0.002	0.000	0.000	0.000
92	A	155	GLU	-1	-0.855	-0.903	30.249	0.083	0.083	0.000	0.000	0.000
93	A	156	SER	0	-0.064	-0.032	27.406	0.006	0.006	0.000	0.000	0.000
94	A	157	PRO	0	0.022	0.029	27.272	0.001	0.001	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:64:ALA)