FMO DATABASE

FMODB ID: 3J3QL

Calculation Name: 1YHF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YHF

Chain ID: A

ChEMBL ID:

UniProt ID: Q99YR1

Base Structure: X-ray

Registration Date: 2023-09-20

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	OptAll
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	114
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-861168.464106
FMO2-HF: Nuclear repulsion	816404.365218
FMO2-HF: Total energy	-44764.098888
FMO2-MP2: Total energy	-44891.909735

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:ASN)

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

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.
-4.979	-2.315	0.005	-1.203	-1.466	0

Interaction energy analysis for fragmet #1(A:-1:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.019

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	1	MET	0	-0.017	0.003	3.221	-1.561	1.036	0.006	-1.192	-1.411
4	A	2	SER	0	0.025	-0.004	4.726	-1.352	-1.285	-0.001	-0.011	-0.055
5	A	3	TYR	0	-0.016	-0.018	7.082	0.320	0.320	0.000	0.000	0.000
6	A	4	ILE	0	0.019	0.019	9.916	0.195	0.195	0.000	0.000	0.000
7	A	5	ASN	0	-0.020	-0.004	10.391	-0.575	-0.575	0.000	0.000	0.000
8	A	6	ASN	0	-0.013	-0.018	12.418	0.044	0.044	0.000	0.000	0.000
9	A	7	ILE	0	0.046	0.034	12.581	0.112	0.112	0.000	0.000	0.000
10	A	8	GLU	-1	-0.806	-0.876	11.773	-1.541	-1.541	0.000	0.000	0.000
11	A	9	HIS	0	-0.034	-0.027	6.636	-0.676	-0.676	0.000	0.000	0.000
12	A	10	ALA	0	-0.053	-0.031	7.567	-0.006	-0.006	0.000	0.000	0.000
13	A	11	LYS	1	0.826	0.908	9.672	1.350	1.350	0.000	0.000	0.000
14	A	12	VAL	0	-0.014	-0.005	13.311	0.067	0.067	0.000	0.000	0.000
15	A	13	LEU	0	-0.017	-0.012	15.135	0.007	0.007	0.000	0.000	0.000
16	A	14	ASP	-1	-0.787	-0.870	18.732	-0.465	-0.465	0.000	0.000	0.000
17	A	15	LEU	0	-0.006	-0.015	19.025	-0.010	-0.010	0.000	0.000	0.000
18	A	16	THR	0	-0.024	-0.019	22.330	0.021	0.021	0.000	0.000	0.000
19	A	17	GLN	0	-0.013	-0.017	23.298	0.033	0.033	0.000	0.000	0.000
20	A	18	GLU	-1	-0.850	-0.916	17.610	-0.902	-0.902	0.000	0.000	0.000
21	A	19	VAL	0	-0.050	-0.029	21.835	-0.010	-0.010	0.000	0.000	0.000
22	A	20	MET	0	0.083	0.065	24.588	0.025	0.025	0.000	0.000	0.000
23	A	21	ILE	0	0.020	0.027	27.876	0.011	0.011	0.000	0.000	0.000
24	A	22	GLU	-1	-0.938	-0.971	30.497	-0.303	-0.303	0.000	0.000	0.000
25	A	23	GLN	0	-0.023	-0.013	33.068	0.021	0.021	0.000	0.000	0.000
26	A	24	ASP	-1	-0.907	-0.943	36.554	-0.166	-0.166	0.000	0.000	0.000
27	A	25	GLN	0	-0.114	-0.063	32.844	0.000	0.000	0.000	0.000	0.000
28	A	26	MET	0	0.008	-0.004	30.222	0.002	0.002	0.000	0.000	0.000
29	A	27	LEU	0	-0.007	0.013	26.789	-0.002	-0.002	0.000	0.000	0.000
30	A	28	SER	0	-0.015	-0.017	24.652	0.014	0.014	0.000	0.000	0.000
31	A	29	ARG	1	0.741	0.850	17.069	0.763	0.763	0.000	0.000	0.000
32	A	30	THR	0	-0.004	-0.005	19.036	-0.014	-0.014	0.000	0.000	0.000
33	A	31	LEU	0	0.026	0.036	15.231	-0.044	-0.044	0.000	0.000	0.000
34	A	32	VAL	0	-0.028	-0.021	14.739	-0.056	-0.056	0.000	0.000	0.000
35	A	33	GLN	0	0.020	0.007	16.847	0.004	0.004	0.000	0.000	0.000
36	A	34	ARG	1	0.889	0.970	13.625	0.033	0.033	0.000	0.000	0.000
37	A	35	GLN	0	0.023	0.006	19.876	-0.011	-0.011	0.000	0.000	0.000
38	A	36	ASP	-1	-0.775	-0.893	19.957	0.065	0.065	0.000	0.000	0.000
39	A	37	LEU	0	-0.017	-0.008	17.582	-0.020	-0.020	0.000	0.000	0.000
40	A	38	GLY	0	-0.021	-0.014	20.613	0.006	0.006	0.000	0.000	0.000
41	A	39	ILE	0	-0.011	-0.003	17.288	0.007	0.007	0.000	0.000	0.000
42	A	40	THR	0	-0.005	-0.009	19.614	-0.038	-0.038	0.000	0.000	0.000
43	A	41	VAL	0	0.018	0.028	20.204	0.025	0.025	0.000	0.000	0.000
44	A	42	PHE	0	0.021	-0.018	22.845	0.001	0.001	0.000	0.000	0.000
45	A	43	SER	0	-0.027	-0.023	26.348	-0.001	-0.001	0.000	0.000	0.000
46	A	44	LEU	0	-0.006	-0.003	29.323	0.010	0.010	0.000	0.000	0.000
47	A	45	ASP	-1	-0.763	-0.873	32.971	-0.205	-0.205	0.000	0.000	0.000
48	A	46	LYS	1	0.900	0.929	35.973	0.169	0.169	0.000	0.000	0.000
49	A	47	GLY	0	-0.038	-0.015	39.227	0.004	0.004	0.000	0.000	0.000
50	A	48	GLN	0	-0.033	0.010	35.977	0.017	0.017	0.000	0.000	0.000
51	A	49	GLU	-1	-0.947	-0.997	37.015	-0.112	-0.112	0.000	0.000	0.000
52	A	50	ILE	0	-0.044	-0.011	30.922	-0.005	-0.005	0.000	0.000	0.000
53	A	51	GLY	0	0.099	0.050	35.180	0.005	0.005	0.000	0.000	0.000
54	A	52	ARG	1	0.774	0.885	36.760	0.066	0.066	0.000	0.000	0.000
55	A	53	HIS	0	-0.030	-0.015	32.719	0.004	0.004	0.000	0.000	0.000
56	A	54	SER	0	0.024	0.007	35.855	-0.005	-0.005	0.000	0.000	0.000
57	A	55	SER	0	-0.023	-0.029	30.032	-0.004	-0.004	0.000	0.000	0.000
58	A	56	PRO	0	-0.029	-0.017	29.175	0.005	0.005	0.000	0.000	0.000
59	A	57	GLY	0	0.018	-0.010	28.715	0.016	0.016	0.000	0.000	0.000
60	A	58	ASP	-1	-0.829	-0.885	29.123	-0.063	-0.063	0.000	0.000	0.000
61	A	59	ALA	0	-0.010	-0.016	27.841	-0.011	-0.011	0.000	0.000	0.000
62	A	60	MET	0	-0.021	0.004	24.537	0.010	0.010	0.000	0.000	0.000
63	A	61	VAL	0	0.012	-0.005	27.225	-0.018	-0.018	0.000	0.000	0.000
64	A	62	THR	0	-0.005	-0.019	26.361	0.013	0.013	0.000	0.000	0.000
65	A	63	ILE	0	-0.009	-0.003	27.926	-0.025	-0.025	0.000	0.000	0.000
66	A	64	LEU	0	-0.065	-0.038	24.335	-0.007	-0.007	0.000	0.000	0.000
67	A	65	SER	0	0.011	-0.019	28.523	-0.002	-0.002	0.000	0.000	0.000
68	A	66	GLY	0	0.056	0.045	31.697	0.007	0.007	0.000	0.000	0.000
69	A	67	LEU	0	-0.003	-0.020	35.317	0.003	0.003	0.000	0.000	0.000
70	A	68	ALA	0	0.003	0.010	34.810	0.002	0.002	0.000	0.000	0.000
71	A	69	GLU	-1	-0.846	-0.907	36.905	-0.107	-0.107	0.000	0.000	0.000
72	A	70	ILE	0	0.000	-0.006	33.659	-0.002	-0.002	0.000	0.000	0.000
73	A	71	THR	0	-0.046	-0.012	37.737	0.009	0.009	0.000	0.000	0.000
74	A	72	ILE	0	-0.001	-0.015	36.293	-0.002	-0.002	0.000	0.000	0.000
75	A	73	ASP	-1	-0.862	-0.952	39.632	-0.048	-0.048	0.000	0.000	0.000
76	A	74	GLN	0	-0.072	-0.034	42.329	-0.002	-0.002	0.000	0.000	0.000
77	A	75	GLU	-1	-0.847	-0.873	42.962	-0.074	-0.074	0.000	0.000	0.000
78	A	76	THR	0	-0.023	-0.017	42.018	-0.003	-0.003	0.000	0.000	0.000
79	A	77	TYR	0	-0.039	-0.048	38.795	0.000	0.000	0.000	0.000	0.000
80	A	78	ARG	1	0.820	0.888	39.395	0.103	0.103	0.000	0.000	0.000
81	A	79	VAL	0	-0.027	-0.012	34.097	0.002	0.002	0.000	0.000	0.000
82	A	80	ALA	0	0.031	0.006	36.155	-0.005	-0.005	0.000	0.000	0.000
83	A	81	GLU	-1	-0.877	-0.943	32.046	-0.274	-0.274	0.000	0.000	0.000
84	A	82	GLY	0	-0.021	0.000	30.841	0.009	0.009	0.000	0.000	0.000
85	A	83	GLN	0	-0.052	-0.009	31.887	0.012	0.012	0.000	0.000	0.000
86	A	84	THR	0	0.011	0.000	28.912	-0.021	-0.021	0.000	0.000	0.000
87	A	85	ILE	0	-0.009	0.016	31.535	0.015	0.015	0.000	0.000	0.000
88	A	86	VAL	0	0.007	-0.009	30.031	-0.013	-0.013	0.000	0.000	0.000
89	A	87	MET	0	-0.015	0.006	31.161	0.012	0.012	0.000	0.000	0.000
90	A	88	PRO	0	0.001	-0.001	32.521	-0.001	-0.001	0.000	0.000	0.000
91	A	89	ALA	0	0.011	0.010	32.190	-0.001	-0.001	0.000	0.000	0.000
92	A	90	GLY	0	-0.028	-0.008	33.713	0.005	0.005	0.000	0.000	0.000
93	A	91	ILE	0	-0.028	-0.017	36.566	0.001	0.001	0.000	0.000	0.000
94	A	92	PRO	0	-0.020	-0.004	36.913	-0.007	-0.007	0.000	0.000	0.000
95	A	93	HIS	1	0.896	0.943	32.600	0.097	0.097	0.000	0.000	0.000
96	A	94	ALA	0	0.001	0.006	36.584	0.002	0.002	0.000	0.000	0.000
97	A	95	LEU	0	0.003	-0.002	32.016	-0.002	-0.002	0.000	0.000	0.000
98	A	96	TYR	0	0.030	0.021	36.211	0.001	0.001	0.000	0.000	0.000
99	A	97	ALA	0	0.028	0.022	36.299	-0.004	-0.004	0.000	0.000	0.000
100	A	98	VAL	0	-0.004	-0.004	37.867	0.006	0.006	0.000	0.000	0.000
101	A	99	GLU	-1	-0.975	-0.989	38.274	-0.179	-0.179	0.000	0.000	0.000
102	A	100	ALA	0	0.007	0.004	35.473	-0.001	-0.001	0.000	0.000	0.000
103	A	101	PHE	0	-0.037	-0.012	31.599	-0.004	-0.004	0.000	0.000	0.000
104	A	102	GLN	0	0.010	-0.002	27.747	0.000	0.000	0.000	0.000	0.000
105	A	103	MET	0	-0.025	-0.007	27.545	0.020	0.020	0.000	0.000	0.000
106	A	104	LEU	0	-0.007	0.005	20.926	-0.035	-0.035	0.000	0.000	0.000
107	A	105	LEU	0	-0.003	0.012	24.337	0.032	0.032	0.000	0.000	0.000
108	A	106	VAL	0	0.002	-0.014	21.506	-0.033	-0.033	0.000	0.000	0.000
109	A	107	VAL	0	-0.016	-0.015	23.462	0.026	0.026	0.000	0.000	0.000
110	A	108	VAL	0	0.025	0.009	23.033	0.003	0.003	0.000	0.000	0.000
111	A	109	LYS	1	0.771	0.896	23.009	0.073	0.073	0.000	0.000	0.000
112	A	110	PRO	0	0.006	-0.006	25.430	0.012	0.012	0.000	0.000	0.000
113	A	111	GLU	-1	-0.922	-0.954	23.216	0.161	0.161	0.000	0.000	0.000
114	A	112	ALA	0	-0.051	-0.017	20.615	-0.009	-0.009	0.000	0.000	0.000

Top

Graph

Manual

About

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