FMO DATABASE

FMODB ID: YVN42

Calculation Name: 5IW9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5IW9

Chain ID: A

ChEMBL ID:

UniProt ID: P09425

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	OptHSide
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	126
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-974525.107734
FMO2-HF: Nuclear repulsion	923767.049359
FMO2-HF: Total energy	-50758.058375
FMO2-MP2: Total energy	-50905.765443

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:3:ASN)

Summations of interaction energy for fragment #1(A:3: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.
1.531	3.604	-0.02	-0.865	-1.188	0.002

Interaction energy analysis for fragmet #1(A:3:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / q_NPA : -0.016

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	5	ASN	0	-0.017	0.006	3.826	2.882	4.955	-0.020	-0.865	-1.188	0.002
4	A	6	LYS	1	0.966	0.977	6.242	-1.481	-1.481	0.000	0.000	0.000	0.000
5	A	7	LEU	0	0.035	0.021	8.107	0.095	0.095	0.000	0.000	0.000	0.000
6	A	8	TYR	0	-0.016	-0.008	11.723	-0.137	-0.137	0.000	0.000	0.000	0.000
7	A	9	SER	0	0.023	-0.001	14.014	-0.039	-0.039	0.000	0.000	0.000	0.000
8	A	10	ASP	-1	-0.964	-0.973	14.567	0.163	0.163	0.000	0.000	0.000	0.000
9	A	11	ILE	0	-0.042	-0.024	17.136	-0.041	-0.041	0.000	0.000	0.000	0.000
10	A	12	ASP	-1	-0.824	-0.912	19.474	0.128	0.128	0.000	0.000	0.000	0.000
11	A	13	PRO	0	-0.027	0.003	21.522	-0.042	-0.042	0.000	0.000	0.000	0.000
12	A	14	GLU	-1	-0.860	-0.948	25.205	0.139	0.139	0.000	0.000	0.000	0.000
13	A	15	MET	0	-0.052	-0.019	20.679	0.019	0.019	0.000	0.000	0.000	0.000
14	A	16	LYS	1	0.810	0.909	21.471	-0.010	-0.010	0.000	0.000	0.000	0.000
15	A	17	MET	0	0.008	0.020	22.327	0.015	0.015	0.000	0.000	0.000	0.000
16	A	18	ASP	-1	-0.799	-0.897	23.321	-0.104	-0.104	0.000	0.000	0.000	0.000
17	A	19	TRP	0	-0.051	-0.049	17.590	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	20	ASN	0	0.004	0.000	23.371	-0.015	-0.015	0.000	0.000	0.000	0.000
19	A	21	LYS	1	0.893	0.956	27.149	0.043	0.043	0.000	0.000	0.000	0.000
20	A	22	ASP	-1	-0.827	-0.914	30.372	-0.010	-0.010	0.000	0.000	0.000	0.000
21	A	23	VAL	0	-0.023	0.011	27.239	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	24	SER	0	-0.026	-0.031	30.465	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	25	ARG	1	0.879	0.928	32.049	0.018	0.018	0.000	0.000	0.000	0.000
24	A	26	SER	0	-0.023	-0.030	33.330	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	27	LEU	0	-0.044	-0.030	30.783	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	28	GLY	0	0.041	0.022	35.226	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	29	LEU	0	0.027	0.025	37.657	0.000	0.000	0.000	0.000	0.000	0.000
28	A	30	ARG	1	0.956	0.977	34.208	0.089	0.089	0.000	0.000	0.000	0.000
29	A	31	SER	0	-0.060	-0.025	38.458	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	32	ILE	0	0.061	0.035	40.402	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	33	LYS	1	0.832	0.921	43.172	0.032	0.032	0.000	0.000	0.000	0.000
32	A	34	ASN	0	-0.077	-0.054	41.846	0.001	0.001	0.000	0.000	0.000	0.000
33	A	35	SER	0	-0.045	-0.022	44.349	0.000	0.000	0.000	0.000	0.000	0.000
34	A	36	LEU	0	0.048	0.017	45.999	0.001	0.001	0.000	0.000	0.000	0.000
35	A	37	LEU	0	0.004	0.010	47.667	0.002	0.002	0.000	0.000	0.000	0.000
36	A	38	GLY	0	0.003	0.015	48.326	0.001	0.001	0.000	0.000	0.000	0.000
37	A	39	ILE	0	-0.001	0.004	49.258	0.001	0.001	0.000	0.000	0.000	0.000
38	A	40	ILE	0	-0.009	-0.019	52.020	0.002	0.002	0.000	0.000	0.000	0.000
39	A	41	THR	0	-0.059	-0.051	51.992	0.001	0.001	0.000	0.000	0.000	0.000
40	A	42	THR	0	-0.067	-0.024	52.443	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	43	ARG	1	0.824	0.894	55.057	0.041	0.041	0.000	0.000	0.000	0.000
42	A	44	LYS	1	0.853	0.936	58.406	0.044	0.044	0.000	0.000	0.000	0.000
43	A	45	GLY	0	0.020	0.022	59.063	0.002	0.002	0.000	0.000	0.000	0.000
44	A	46	SER	0	-0.129	-0.078	57.546	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	47	ARG	1	0.918	0.973	50.092	0.069	0.069	0.000	0.000	0.000	0.000
46	A	48	PRO	0	0.028	-0.004	55.329	0.000	0.000	0.000	0.000	0.000	0.000
47	A	49	PHE	0	-0.057	-0.039	51.692	0.000	0.000	0.000	0.000	0.000	0.000
48	A	50	ASP	-1	-0.811	-0.896	53.295	-0.068	-0.068	0.000	0.000	0.000	0.000
49	A	51	PRO	0	-0.035	-0.012	55.293	0.001	0.001	0.000	0.000	0.000	0.000
50	A	52	GLU	-1	-0.804	-0.891	57.340	-0.046	-0.046	0.000	0.000	0.000	0.000
51	A	53	PHE	0	-0.025	-0.003	50.014	0.001	0.001	0.000	0.000	0.000	0.000
52	A	54	GLY	0	-0.001	-0.003	55.175	0.000	0.000	0.000	0.000	0.000	0.000
53	A	55	CYS	0	-0.036	-0.003	56.094	0.002	0.002	0.000	0.000	0.000	0.000
54	A	56	ASP	-1	-0.970	-0.979	58.837	-0.038	-0.038	0.000	0.000	0.000	0.000
55	A	57	LEU	0	-0.004	-0.008	58.953	0.002	0.002	0.000	0.000	0.000	0.000
56	A	58	SER	0	0.028	0.017	62.966	0.000	0.000	0.000	0.000	0.000	0.000
57	A	59	ASP	-1	-0.745	-0.883	65.052	-0.035	-0.035	0.000	0.000	0.000	0.000
58	A	60	GLN	0	-0.011	-0.011	67.369	0.000	0.000	0.000	0.000	0.000	0.000
59	A	61	LEU	0	-0.074	-0.016	64.956	0.002	0.002	0.000	0.000	0.000	0.000
60	A	62	PHE	0	-0.015	-0.016	61.987	0.001	0.001	0.000	0.000	0.000	0.000
61	A	63	GLU	-1	-0.872	-0.926	67.937	-0.026	-0.026	0.000	0.000	0.000	0.000
62	A	64	ASN	0	-0.128	-0.067	71.342	0.001	0.001	0.000	0.000	0.000	0.000
63	A	65	MET	0	0.012	0.042	66.785	0.000	0.000	0.000	0.000	0.000	0.000
64	A	66	THR	0	0.009	-0.008	71.417	0.001	0.001	0.000	0.000	0.000	0.000
65	A	67	PRO	0	-0.001	-0.015	71.066	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	68	LEU	0	0.008	0.003	71.014	0.000	0.000	0.000	0.000	0.000	0.000
67	A	69	THR	0	0.030	0.025	66.818	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	70	ALA	0	0.045	0.024	65.378	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	71	ASP	-1	-0.747	-0.829	64.680	-0.022	-0.022	0.000	0.000	0.000	0.000
70	A	72	THR	0	-0.020	-0.026	65.353	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	73	VAL	0	0.011	0.003	61.264	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	74	GLU	-1	-0.798	-0.893	60.911	-0.021	-0.021	0.000	0.000	0.000	0.000
73	A	75	ARG	1	0.814	0.869	60.510	0.021	0.021	0.000	0.000	0.000	0.000
74	A	76	ASN	0	-0.029	-0.006	60.953	-0.004	-0.004	0.000	0.000	0.000	0.000
75	A	77	ILE	0	0.069	0.022	55.809	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	78	GLU	-1	-0.880	-0.945	56.366	-0.029	-0.029	0.000	0.000	0.000	0.000
77	A	79	SER	0	-0.085	-0.043	56.248	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	80	ALA	0	0.043	0.020	55.643	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	81	VAL	0	-0.002	-0.019	50.902	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	82	ARG	1	0.801	0.884	51.493	0.035	0.035	0.000	0.000	0.000	0.000
81	A	83	ASN	0	-0.047	-0.013	52.550	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	84	TYR	0	-0.070	-0.054	50.424	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	85	GLU	-1	-0.761	-0.840	45.225	-0.075	-0.075	0.000	0.000	0.000	0.000
84	A	86	PRO	0	0.018	0.008	45.619	0.004	0.004	0.000	0.000	0.000	0.000
85	A	87	ARG	1	0.780	0.852	39.999	0.080	0.080	0.000	0.000	0.000	0.000
86	A	88	ILE	0	-0.017	0.002	44.871	0.003	0.003	0.000	0.000	0.000	0.000
87	A	89	ASP	-1	-0.838	-0.936	47.370	-0.029	-0.029	0.000	0.000	0.000	0.000
88	A	90	LYS	1	0.849	0.938	49.004	0.016	0.016	0.000	0.000	0.000	0.000
89	A	91	LEU	0	-0.023	-0.016	51.085	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	92	ALA	0	-0.002	0.007	53.621	0.002	0.002	0.000	0.000	0.000	0.000
91	A	93	VAL	0	-0.021	-0.006	55.638	0.000	0.000	0.000	0.000	0.000	0.000
92	A	94	ASN	0	-0.073	-0.032	57.774	0.002	0.002	0.000	0.000	0.000	0.000
93	A	95	VAL	0	-0.030	-0.022	59.449	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	96	ILE	0	-0.026	-0.017	60.640	0.002	0.002	0.000	0.000	0.000	0.000
95	A	97	PRO	0	-0.008	-0.010	63.628	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	98	VAL	0	-0.013	-0.002	63.284	0.002	0.002	0.000	0.000	0.000	0.000
97	A	99	TYR	0	0.009	-0.023	66.471	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	100	ASP	-1	-0.977	-0.975	68.320	-0.013	-0.013	0.000	0.000	0.000	0.000
99	A	101	ASP	-1	-0.829	-0.896	64.075	-0.018	-0.018	0.000	0.000	0.000	0.000
100	A	102	TYR	0	-0.067	-0.023	66.506	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	103	THR	0	-0.048	-0.030	62.100	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	104	LEU	0	-0.001	0.000	61.833	0.001	0.001	0.000	0.000	0.000	0.000
103	A	105	ILE	0	-0.021	-0.006	57.872	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	106	VAL	0	0.010	0.010	56.238	0.001	0.001	0.000	0.000	0.000	0.000
105	A	107	GLU	-1	-0.834	-0.904	54.573	-0.013	-0.013	0.000	0.000	0.000	0.000
106	A	108	ILE	0	0.002	0.008	51.962	0.000	0.000	0.000	0.000	0.000	0.000
107	A	109	ARG	1	0.898	0.932	51.489	0.010	0.010	0.000	0.000	0.000	0.000
108	A	110	PHE	0	0.011	-0.013	45.272	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	111	SER	0	0.038	0.031	46.844	0.002	0.002	0.000	0.000	0.000	0.000
110	A	112	VAL	0	-0.006	0.007	41.161	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	113	ILE	0	0.012	-0.002	42.621	0.003	0.003	0.000	0.000	0.000	0.000
112	A	114	ASP	-1	-0.937	-0.966	38.680	-0.062	-0.062	0.000	0.000	0.000	0.000
113	A	115	ASN	0	-0.076	-0.030	39.048	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	116	PRO	0	0.030	0.037	42.207	0.002	0.002	0.000	0.000	0.000	0.000
115	A	117	ASP	-1	-0.918	-0.966	43.475	-0.008	-0.008	0.000	0.000	0.000	0.000
116	A	118	ASP	-1	-0.807	-0.887	42.045	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	119	ILE	0	-0.100	-0.052	45.553	-0.004	-0.004	0.000	0.000	0.000	0.000
118	A	120	GLU	-1	-0.809	-0.897	42.944	-0.020	-0.020	0.000	0.000	0.000	0.000
119	A	121	GLN	0	-0.022	-0.035	46.943	0.001	0.001	0.000	0.000	0.000	0.000
120	A	122	ILE	0	-0.074	-0.030	47.470	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	123	LYS	1	0.892	0.930	49.987	0.015	0.015	0.000	0.000	0.000	0.000
122	A	124	LEU	0	-0.018	0.001	50.723	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	125	GLN	0	-0.014	-0.019	54.366	0.002	0.002	0.000	0.000	0.000	0.000
124	A	126	LEU	0	-0.058	-0.021	56.105	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	127	ALA	0	0.090	0.024	59.324	0.002	0.002	0.000	0.000	0.000	0.000
126	A	128	SER	0	-0.017	0.012	62.079	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:3:ASN)