FMO DATABASE

FMODB ID: YVQN2

Calculation Name: 3IC5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3IC5

Chain ID: A

ChEMBL ID:

UniProt ID: Q5LX24

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	115
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-793987.873591
FMO2-HF: Nuclear repulsion	752368.509344
FMO2-HF: Total energy	-41619.364248
FMO2-MP2: Total energy	-41740.194582

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.
-16.323	-15.181	7.771	-3.973	-4.939	0.029

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 : 0.044 / q_NPA : 0.007

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	1	MET	0	0.006	0.013	3.201	-1.693	1.163	-0.013	-1.312	-1.530	-0.001
4	A	2	ARG	1	0.803	0.900	1.863	-19.028	-20.929	7.785	-2.658	-3.226	0.030
5	A	3	TRP	0	0.021	0.030	5.956	-0.555	-0.555	0.000	0.000	0.000	0.000
6	A	4	ASN	0	-0.023	-0.025	9.662	0.361	0.361	0.000	0.000	0.000	0.000
7	A	5	ILE	0	-0.018	-0.013	10.871	-0.093	-0.093	0.000	0.000	0.000	0.000
8	A	6	CYS	0	-0.043	-0.007	13.745	-0.016	-0.016	0.000	0.000	0.000	0.000
9	A	7	VAL	0	-0.013	-0.010	16.178	0.035	0.035	0.000	0.000	0.000	0.000
10	A	8	VAL	0	0.032	0.015	18.633	-0.029	-0.029	0.000	0.000	0.000	0.000
11	A	9	GLY	0	0.040	0.025	22.083	0.007	0.007	0.000	0.000	0.000	0.000
12	A	10	ALA	0	-0.029	-0.028	21.974	0.028	0.028	0.000	0.000	0.000	0.000
13	A	11	GLY	0	0.055	0.033	23.024	0.002	0.002	0.000	0.000	0.000	0.000
14	A	12	LYS	1	0.977	0.982	23.757	-0.166	-0.166	0.000	0.000	0.000	0.000
15	A	13	ILE	0	0.045	0.017	22.943	0.027	0.027	0.000	0.000	0.000	0.000
16	A	14	GLY	0	0.074	0.040	20.812	0.039	0.039	0.000	0.000	0.000	0.000
17	A	15	GLN	0	-0.055	-0.041	19.181	0.048	0.048	0.000	0.000	0.000	0.000
18	A	16	MET	0	-0.044	-0.020	18.804	0.034	0.034	0.000	0.000	0.000	0.000
19	A	17	ILE	0	0.020	0.013	16.814	0.067	0.067	0.000	0.000	0.000	0.000
20	A	18	ALA	0	0.038	0.015	15.022	0.106	0.106	0.000	0.000	0.000	0.000
21	A	19	ALA	0	-0.010	-0.005	13.878	0.116	0.116	0.000	0.000	0.000	0.000
22	A	20	LEU	0	0.022	0.018	13.816	0.132	0.132	0.000	0.000	0.000	0.000
23	A	21	LEU	0	0.008	0.002	11.560	0.216	0.216	0.000	0.000	0.000	0.000
24	A	22	LYS	1	0.852	0.937	9.685	-0.043	-0.043	0.000	0.000	0.000	0.000
25	A	23	THR	0	-0.082	-0.047	9.254	0.247	0.247	0.000	0.000	0.000	0.000
26	A	24	SER	0	-0.032	-0.006	8.662	0.300	0.300	0.000	0.000	0.000	0.000
27	A	25	SER	0	0.016	-0.008	5.599	0.801	0.801	0.000	0.000	0.000	0.000
28	A	26	ASN	0	-0.043	-0.029	4.940	1.775	1.962	-0.001	-0.003	-0.183	0.000
29	A	27	TYR	0	0.037	0.026	7.034	-0.647	-0.647	0.000	0.000	0.000	0.000
30	A	28	SER	0	-0.003	0.008	5.935	1.411	1.411	0.000	0.000	0.000	0.000
31	A	29	VAL	0	-0.006	0.008	8.123	-0.183	-0.183	0.000	0.000	0.000	0.000
32	A	30	THR	0	-0.046	-0.017	11.337	-0.178	-0.178	0.000	0.000	0.000	0.000
33	A	31	VAL	0	0.003	0.006	14.022	0.030	0.030	0.000	0.000	0.000	0.000
34	A	32	ALA	0	0.005	-0.010	17.606	-0.047	-0.047	0.000	0.000	0.000	0.000
35	A	33	ASP	-1	-0.781	-0.887	20.652	0.096	0.096	0.000	0.000	0.000	0.000
36	A	34	HIS	0	0.081	0.041	24.210	-0.022	-0.022	0.000	0.000	0.000	0.000
37	A	35	ASP	-1	-0.872	-0.929	26.961	0.027	0.027	0.000	0.000	0.000	0.000
38	A	36	LEU	0	0.038	0.005	24.481	0.007	0.007	0.000	0.000	0.000	0.000
39	A	37	ALA	0	-0.015	0.003	24.807	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	38	ALA	0	-0.008	-0.009	25.394	0.010	0.010	0.000	0.000	0.000	0.000
41	A	39	LEU	0	-0.005	-0.011	20.086	0.019	0.019	0.000	0.000	0.000	0.000
42	A	40	ALA	0	0.021	0.005	20.606	0.005	0.005	0.000	0.000	0.000	0.000
43	A	41	VAL	0	-0.068	-0.035	21.863	0.001	0.001	0.000	0.000	0.000	0.000
44	A	42	LEU	0	0.040	0.015	17.349	0.022	0.022	0.000	0.000	0.000	0.000
45	A	43	ASN	0	0.021	0.027	17.029	0.030	0.030	0.000	0.000	0.000	0.000
46	A	44	ARG	1	0.927	0.973	17.488	-0.073	-0.073	0.000	0.000	0.000	0.000
47	A	45	MET	0	-0.055	0.005	16.906	0.002	0.002	0.000	0.000	0.000	0.000
48	A	46	GLY	0	0.018	0.008	13.967	0.077	0.077	0.000	0.000	0.000	0.000
49	A	47	VAL	0	-0.054	-0.019	12.263	0.045	0.045	0.000	0.000	0.000	0.000
50	A	48	ALA	0	0.016	0.018	11.707	-0.070	-0.070	0.000	0.000	0.000	0.000
51	A	49	THR	0	-0.034	-0.040	13.645	0.055	0.055	0.000	0.000	0.000	0.000
52	A	50	LYS	1	0.899	0.942	16.671	0.071	0.071	0.000	0.000	0.000	0.000
53	A	51	GLN	0	-0.024	-0.012	19.584	0.015	0.015	0.000	0.000	0.000	0.000
54	A	52	VAL	0	-0.035	-0.024	22.605	-0.013	-0.013	0.000	0.000	0.000	0.000
55	A	53	ASP	-1	-0.747	-0.876	25.381	0.015	0.015	0.000	0.000	0.000	0.000
56	A	54	ALA	0	-0.002	0.005	28.927	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	55	LYS	1	0.838	0.895	29.945	-0.011	-0.011	0.000	0.000	0.000	0.000
58	A	56	ASP	-1	-0.836	-0.903	30.295	-0.034	-0.034	0.000	0.000	0.000	0.000
59	A	57	GLU	-1	-0.788	-0.891	29.252	0.015	0.015	0.000	0.000	0.000	0.000
60	A	58	ALA	0	-0.011	0.007	28.558	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	59	GLY	0	0.037	0.020	27.223	-0.011	-0.011	0.000	0.000	0.000	0.000
62	A	60	LEU	0	-0.016	-0.008	24.021	-0.009	-0.009	0.000	0.000	0.000	0.000
63	A	61	ALA	0	0.028	0.000	23.703	0.000	0.000	0.000	0.000	0.000	0.000
64	A	62	LYS	1	0.849	0.922	23.130	0.052	0.052	0.000	0.000	0.000	0.000
65	A	63	ALA	0	-0.026	-0.007	20.931	-0.021	-0.021	0.000	0.000	0.000	0.000
66	A	64	LEU	0	0.009	-0.007	19.263	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	65	GLY	0	0.035	0.029	19.033	0.015	0.015	0.000	0.000	0.000	0.000
68	A	66	GLY	0	-0.028	-0.016	15.452	-0.023	-0.023	0.000	0.000	0.000	0.000
69	A	67	PHE	0	-0.060	-0.031	13.075	-0.051	-0.051	0.000	0.000	0.000	0.000
70	A	68	ASP	-1	-0.806	-0.894	12.133	0.140	0.140	0.000	0.000	0.000	0.000
71	A	69	ALA	0	-0.036	-0.028	15.394	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	70	VAL	0	-0.010	-0.002	16.840	0.011	0.011	0.000	0.000	0.000	0.000
73	A	71	ILE	0	0.003	0.001	16.873	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	72	SER	0	0.008	0.010	20.370	-0.018	-0.018	0.000	0.000	0.000	0.000
75	A	73	ALA	0	-0.038	-0.025	22.149	0.024	0.024	0.000	0.000	0.000	0.000
76	A	74	ALA	0	0.021	0.009	24.162	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	75	PRO	0	0.046	0.029	27.303	0.008	0.008	0.000	0.000	0.000	0.000
78	A	76	PHE	0	0.070	0.030	30.789	-0.005	-0.005	0.000	0.000	0.000	0.000
79	A	77	PHE	0	-0.010	-0.007	32.185	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	78	LEU	0	-0.025	-0.016	29.755	-0.009	-0.009	0.000	0.000	0.000	0.000
81	A	79	THR	0	0.011	-0.006	28.986	-0.005	-0.005	0.000	0.000	0.000	0.000
82	A	80	PRO	0	-0.023	-0.017	29.506	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	81	ILE	0	-0.003	0.012	29.200	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	82	ILE	0	-0.001	-0.005	24.484	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	83	ALA	0	0.020	0.021	25.712	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	84	LYS	1	0.829	0.901	26.942	-0.024	-0.024	0.000	0.000	0.000	0.000
87	A	85	ALA	0	0.005	-0.004	25.906	-0.009	-0.009	0.000	0.000	0.000	0.000
88	A	86	ALA	0	0.018	0.002	22.549	-0.012	-0.012	0.000	0.000	0.000	0.000
89	A	87	LYS	1	0.964	0.982	23.279	-0.038	-0.038	0.000	0.000	0.000	0.000
90	A	88	ALA	0	-0.070	-0.039	25.804	-0.009	-0.009	0.000	0.000	0.000	0.000
91	A	89	ALA	0	-0.027	-0.007	21.072	-0.014	-0.014	0.000	0.000	0.000	0.000
92	A	90	GLY	0	-0.054	-0.016	21.268	-0.016	-0.016	0.000	0.000	0.000	0.000
93	A	91	ALA	0	-0.015	0.012	19.049	0.006	0.006	0.000	0.000	0.000	0.000
94	A	92	HIS	0	-0.011	-0.013	18.227	0.005	0.005	0.000	0.000	0.000	0.000
95	A	93	TYR	0	-0.032	-0.056	20.686	0.005	0.005	0.000	0.000	0.000	0.000
96	A	94	PHE	0	0.000	0.000	20.730	0.011	0.011	0.000	0.000	0.000	0.000
97	A	95	ASP	-1	-0.735	-0.814	22.658	0.136	0.136	0.000	0.000	0.000	0.000
98	A	96	LEU	0	-0.020	0.004	21.570	-0.005	-0.005	0.000	0.000	0.000	0.000
99	A	97	THR	0	-0.056	-0.012	24.983	-0.017	-0.017	0.000	0.000	0.000	0.000
100	A	98	GLU	-1	-0.892	-0.969	26.183	0.126	0.126	0.000	0.000	0.000	0.000
101	A	99	ASP	-1	-0.883	-0.951	27.847	0.140	0.140	0.000	0.000	0.000	0.000
102	A	100	VAL	0	0.016	0.005	26.871	-0.007	-0.007	0.000	0.000	0.000	0.000
103	A	101	ALA	0	-0.029	-0.002	29.898	-0.006	-0.006	0.000	0.000	0.000	0.000
104	A	102	ALA	0	0.027	0.013	33.501	-0.008	-0.008	0.000	0.000	0.000	0.000
105	A	103	THR	0	0.016	-0.019	30.594	-0.012	-0.012	0.000	0.000	0.000	0.000
106	A	104	ASN	0	-0.001	-0.004	30.962	-0.006	-0.006	0.000	0.000	0.000	0.000
107	A	105	ALA	0	0.010	0.019	34.364	-0.005	-0.005	0.000	0.000	0.000	0.000
108	A	106	VAL	0	-0.021	-0.014	36.074	-0.006	-0.006	0.000	0.000	0.000	0.000
109	A	107	ARG	1	0.804	0.862	28.666	-0.145	-0.145	0.000	0.000	0.000	0.000
110	A	108	ALA	0	0.009	0.014	36.645	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	109	LEU	0	0.029	0.009	39.430	-0.004	-0.004	0.000	0.000	0.000	0.000
112	A	110	VAL	0	-0.077	-0.021	38.328	-0.005	-0.005	0.000	0.000	0.000	0.000
113	A	111	GLU	-1	-0.931	-0.960	38.275	0.080	0.080	0.000	0.000	0.000	0.000
114	A	112	ASP	-1	-0.996	-0.984	41.311	0.073	0.073	0.000	0.000	0.000	0.000
115	A	113	SER	0	-0.133	-0.072	44.517	-0.006	-0.006	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

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