FMO DATABASE

FMODB ID: 4L9VN

Calculation Name: 5IBK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5IBK

Chain ID: A

ChEMBL ID:

UniProt ID: Q969H0

Base Structure: X-ray

Registration Date: 2023-09-26

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	144
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1200725.452423
FMO2-HF: Nuclear repulsion	1143961.394591
FMO2-HF: Total energy	-56764.057832
FMO2-MP2: Total energy	-56928.016941

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:GLY)

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

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.
-1.831	-0.816	-0.014	-0.401	-0.601	-0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / 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	1	MET	0	-0.014	0.002	3.805	-0.091	0.924	-0.014	-0.401	-0.601	-0.001
4	A	2	PRO	0	0.005	0.004	6.313	0.430	0.430	0.000	0.000	0.000	0.000
5	A	3	SER	0	-0.051	-0.040	9.499	-0.108	-0.108	0.000	0.000	0.000	0.000
6	A	4	ILE	0	-0.008	0.007	12.772	0.038	0.038	0.000	0.000	0.000	0.000
7	A	5	LYS	1	0.870	0.920	16.252	0.119	0.119	0.000	0.000	0.000	0.000
8	A	6	LEU	0	-0.002	0.013	19.432	0.002	0.002	0.000	0.000	0.000	0.000
9	A	7	GLN	0	-0.047	-0.035	22.162	0.009	0.009	0.000	0.000	0.000	0.000
10	A	8	SER	0	0.000	-0.024	25.772	-0.003	-0.003	0.000	0.000	0.000	0.000
11	A	9	SER	0	-0.001	-0.016	27.980	0.005	0.005	0.000	0.000	0.000	0.000
12	A	10	ASP	-1	-0.830	-0.889	30.148	-0.071	-0.071	0.000	0.000	0.000	0.000
13	A	11	GLY	0	0.002	0.010	30.254	0.006	0.006	0.000	0.000	0.000	0.000
14	A	12	GLU	-1	-0.831	-0.894	26.432	-0.073	-0.073	0.000	0.000	0.000	0.000
15	A	13	ILE	0	-0.015	-0.010	22.094	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	14	PHE	0	-0.038	-0.021	20.307	0.007	0.007	0.000	0.000	0.000	0.000
17	A	15	GLU	-1	-0.867	-0.915	15.060	-0.137	-0.137	0.000	0.000	0.000	0.000
18	A	16	VAL	0	-0.017	-0.018	14.714	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	17	ASP	-1	-0.845	-0.914	8.895	-0.904	-0.904	0.000	0.000	0.000	0.000
20	A	18	VAL	0	0.007	-0.015	10.089	0.052	0.052	0.000	0.000	0.000	0.000
21	A	19	GLU	-1	-0.927	-0.971	7.261	-1.407	-1.407	0.000	0.000	0.000	0.000
22	A	20	ILE	0	-0.035	-0.014	11.039	0.095	0.095	0.000	0.000	0.000	0.000
23	A	21	ALA	0	0.004	-0.005	13.262	0.074	0.074	0.000	0.000	0.000	0.000
24	A	22	LYS	1	0.811	0.896	14.162	0.442	0.442	0.000	0.000	0.000	0.000
25	A	23	GLN	0	-0.009	-0.009	14.117	0.063	0.063	0.000	0.000	0.000	0.000
26	A	24	SER	0	-0.086	-0.048	17.606	0.035	0.035	0.000	0.000	0.000	0.000
27	A	25	VAL	0	0.039	0.012	20.212	-0.016	-0.016	0.000	0.000	0.000	0.000
28	A	26	THR	0	-0.013	-0.022	22.064	0.000	0.000	0.000	0.000	0.000	0.000
29	A	27	ILE	0	0.037	0.007	18.988	0.006	0.006	0.000	0.000	0.000	0.000
30	A	28	LYS	1	0.841	0.907	17.130	0.270	0.270	0.000	0.000	0.000	0.000
31	A	29	THR	0	-0.069	-0.050	19.781	0.003	0.003	0.000	0.000	0.000	0.000
32	A	30	MET	0	-0.016	-0.017	23.012	0.010	0.010	0.000	0.000	0.000	0.000
33	A	31	LEU	0	-0.013	-0.003	17.171	0.001	0.001	0.000	0.000	0.000	0.000
34	A	32	GLU	-1	-0.845	-0.891	17.131	-0.301	-0.301	0.000	0.000	0.000	0.000
35	A	33	ASP	-1	-0.869	-0.905	20.719	-0.156	-0.156	0.000	0.000	0.000	0.000
36	A	34	LEU	0	-0.087	-0.039	24.462	0.015	0.015	0.000	0.000	0.000	0.000
37	A	35	GLY	0	-0.015	0.015	22.400	0.011	0.011	0.000	0.000	0.000	0.000
38	A	36	MET	0	-0.092	-0.051	23.476	0.014	0.014	0.000	0.000	0.000	0.000
39	A	37	ASP	-1	-0.791	-0.901	18.286	-0.215	-0.215	0.000	0.000	0.000	0.000
40	A	44	PRO	0	-0.039	-0.039	21.910	0.013	0.013	0.000	0.000	0.000	0.000
41	A	45	VAL	0	-0.013	-0.006	21.317	0.009	0.009	0.000	0.000	0.000	0.000
42	A	46	PRO	0	-0.027	0.003	24.048	0.002	0.002	0.000	0.000	0.000	0.000
43	A	47	LEU	0	0.021	-0.003	23.793	-0.005	-0.005	0.000	0.000	0.000	0.000
44	A	48	PRO	0	0.014	-0.004	28.272	0.005	0.005	0.000	0.000	0.000	0.000
45	A	49	ASN	0	-0.038	-0.025	30.620	0.003	0.003	0.000	0.000	0.000	0.000
46	A	50	VAL	0	-0.002	0.008	26.845	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	51	ASN	0	0.016	0.034	29.539	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	52	ALA	0	0.045	-0.005	27.568	-0.009	-0.009	0.000	0.000	0.000	0.000
49	A	53	ALA	0	-0.044	-0.014	26.944	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	54	ILE	0	0.030	0.006	27.394	-0.009	-0.009	0.000	0.000	0.000	0.000
51	A	55	LEU	0	0.032	0.021	22.830	-0.011	-0.011	0.000	0.000	0.000	0.000
52	A	56	LYS	1	0.810	0.899	22.990	0.066	0.066	0.000	0.000	0.000	0.000
53	A	57	LYS	1	0.813	0.918	22.617	0.087	0.087	0.000	0.000	0.000	0.000
54	A	58	VAL	0	0.045	0.013	21.614	-0.012	-0.012	0.000	0.000	0.000	0.000
55	A	59	ILE	0	0.056	0.042	17.610	-0.021	-0.021	0.000	0.000	0.000	0.000
56	A	60	GLN	0	-0.016	0.001	18.144	-0.023	-0.023	0.000	0.000	0.000	0.000
57	A	61	TRP	0	-0.019	-0.025	19.128	-0.014	-0.014	0.000	0.000	0.000	0.000
58	A	62	CYS	0	0.007	-0.001	16.906	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	63	THR	0	-0.025	-0.024	13.771	-0.052	-0.052	0.000	0.000	0.000	0.000
60	A	64	HIS	1	0.835	0.926	14.565	0.155	0.155	0.000	0.000	0.000	0.000
61	A	65	HIS	1	0.705	0.819	16.732	0.213	0.213	0.000	0.000	0.000	0.000
62	A	66	LYS	1	0.856	0.926	7.800	0.908	0.908	0.000	0.000	0.000	0.000
63	A	67	ASP	-1	-0.865	-0.907	9.912	-0.720	-0.720	0.000	0.000	0.000	0.000
64	A	68	ASP	-1	-0.791	-0.878	12.798	-0.180	-0.180	0.000	0.000	0.000	0.000
65	A	69	PRO	0	-0.048	-0.027	16.279	-0.007	-0.007	0.000	0.000	0.000	0.000
66	A	70	GLY	0	-0.027	0.027	17.569	0.017	0.017	0.000	0.000	0.000	0.000
67	A	71	GLY	0	0.021	-0.004	19.205	-0.012	-0.012	0.000	0.000	0.000	0.000
68	A	72	SER	0	-0.016	-0.027	22.390	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	73	GLY	0	0.012	0.014	24.030	0.000	0.000	0.000	0.000	0.000	0.000
70	A	82	THR	0	-0.013	-0.003	25.800	0.004	0.004	0.000	0.000	0.000	0.000
71	A	83	ASP	-1	-0.850	-0.942	28.513	-0.090	-0.090	0.000	0.000	0.000	0.000
72	A	84	ASP	-1	-0.945	-0.944	30.551	-0.069	-0.069	0.000	0.000	0.000	0.000
73	A	85	ILE	0	-0.013	-0.006	28.200	-0.007	-0.007	0.000	0.000	0.000	0.000
74	A	86	PRO	0	0.055	0.032	24.187	0.008	0.008	0.000	0.000	0.000	0.000
75	A	87	VAL	0	0.065	0.012	26.583	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	88	TRP	0	-0.001	0.004	21.650	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	89	ASP	-1	-0.754	-0.874	23.651	-0.146	-0.146	0.000	0.000	0.000	0.000
78	A	90	GLN	0	-0.067	-0.043	26.049	0.008	0.008	0.000	0.000	0.000	0.000
79	A	91	GLU	-1	-0.869	-0.960	27.733	-0.058	-0.058	0.000	0.000	0.000	0.000
80	A	92	PHE	0	-0.042	-0.002	24.378	0.003	0.003	0.000	0.000	0.000	0.000
81	A	93	LEU	0	0.011	0.007	27.329	0.001	0.001	0.000	0.000	0.000	0.000
82	A	94	LYS	1	0.827	0.957	30.315	0.067	0.067	0.000	0.000	0.000	0.000
83	A	95	VAL	0	-0.059	-0.027	30.942	0.002	0.002	0.000	0.000	0.000	0.000
84	A	96	ASP	-1	-0.813	-0.881	33.986	-0.057	-0.057	0.000	0.000	0.000	0.000
85	A	97	GLN	0	0.023	-0.032	35.822	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	98	GLY	0	0.006	0.018	37.112	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	99	THR	0	0.001	-0.033	31.271	-0.005	-0.005	0.000	0.000	0.000	0.000
88	A	100	LEU	0	-0.003	0.000	31.975	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	101	PHE	0	0.010	0.001	33.058	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	102	GLU	-1	-0.849	-0.939	32.515	-0.076	-0.076	0.000	0.000	0.000	0.000
91	A	103	LEU	0	-0.015	-0.009	27.095	-0.007	-0.007	0.000	0.000	0.000	0.000
92	A	104	ILE	0	-0.020	-0.006	29.292	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	105	LEU	0	-0.028	-0.015	31.050	-0.005	-0.005	0.000	0.000	0.000	0.000
94	A	106	ALA	0	0.021	0.014	27.632	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	107	ALA	0	0.002	0.002	26.191	-0.009	-0.009	0.000	0.000	0.000	0.000
96	A	108	ASN	0	-0.024	-0.014	26.956	-0.007	-0.007	0.000	0.000	0.000	0.000
97	A	109	TYR	0	-0.020	0.003	28.139	0.000	0.000	0.000	0.000	0.000	0.000
98	A	110	LEU	0	-0.014	-0.002	23.607	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	111	ASP	-1	-0.885	-0.914	24.014	-0.173	-0.173	0.000	0.000	0.000	0.000
100	A	112	ILE	0	0.025	0.016	21.061	-0.017	-0.017	0.000	0.000	0.000	0.000
101	A	113	LYS	1	0.874	0.912	23.509	0.136	0.136	0.000	0.000	0.000	0.000
102	A	114	GLY	0	0.054	0.028	23.213	0.011	0.011	0.000	0.000	0.000	0.000
103	A	115	LEU	0	0.036	0.020	23.513	0.013	0.013	0.000	0.000	0.000	0.000
104	A	116	LEU	0	0.051	0.034	25.185	0.014	0.014	0.000	0.000	0.000	0.000
105	A	117	ASP	-1	-0.813	-0.886	27.342	-0.113	-0.113	0.000	0.000	0.000	0.000
106	A	118	VAL	0	-0.022	-0.011	25.886	0.011	0.011	0.000	0.000	0.000	0.000
107	A	119	THR	0	0.014	-0.006	28.390	0.010	0.010	0.000	0.000	0.000	0.000
108	A	120	CYS	0	-0.017	-0.010	30.708	0.009	0.009	0.000	0.000	0.000	0.000
109	A	121	LYS	1	0.802	0.886	31.948	0.089	0.089	0.000	0.000	0.000	0.000
110	A	122	THR	0	-0.011	-0.019	31.494	0.006	0.006	0.000	0.000	0.000	0.000
111	A	123	VAL	0	0.037	0.012	34.147	0.006	0.006	0.000	0.000	0.000	0.000
112	A	124	ALA	0	0.010	0.001	36.752	0.005	0.005	0.000	0.000	0.000	0.000
113	A	125	ASN	0	-0.026	-0.018	34.760	0.006	0.006	0.000	0.000	0.000	0.000
114	A	126	MET	0	-0.015	0.005	38.050	0.002	0.002	0.000	0.000	0.000	0.000
115	A	127	ILE	0	0.008	0.020	40.381	0.004	0.004	0.000	0.000	0.000	0.000
116	A	128	LYS	1	0.860	0.928	37.668	0.063	0.063	0.000	0.000	0.000	0.000
117	A	129	GLY	0	-0.020	-0.011	43.371	0.001	0.001	0.000	0.000	0.000	0.000
118	A	130	LYS	1	0.854	0.942	43.071	0.045	0.045	0.000	0.000	0.000	0.000
119	A	131	THR	0	-0.019	-0.041	48.347	0.000	0.000	0.000	0.000	0.000	0.000
120	A	132	PRO	0	0.071	0.010	50.708	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	133	GLU	-1	-0.793	-0.876	51.381	-0.030	-0.030	0.000	0.000	0.000	0.000
122	A	134	GLU	-1	-0.818	-0.876	49.155	-0.032	-0.032	0.000	0.000	0.000	0.000
123	A	135	ILE	0	-0.003	0.010	45.912	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	136	ARG	1	0.801	0.885	47.414	0.029	0.029	0.000	0.000	0.000	0.000
125	A	137	LYS	1	0.876	0.926	49.468	0.028	0.028	0.000	0.000	0.000	0.000
126	A	138	THR	0	-0.063	-0.024	43.278	0.000	0.000	0.000	0.000	0.000	0.000
127	A	139	PHE	0	-0.032	-0.019	40.342	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	140	ASN	0	-0.043	-0.010	45.344	0.001	0.001	0.000	0.000	0.000	0.000
129	A	141	ILE	0	-0.024	-0.004	46.870	0.000	0.000	0.000	0.000	0.000	0.000
130	A	142	LYS	1	0.857	0.923	49.994	0.036	0.036	0.000	0.000	0.000	0.000
131	A	143	ASN	0	0.026	-0.002	53.410	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	144	ASP	-1	-0.858	-0.921	54.815	-0.032	-0.032	0.000	0.000	0.000	0.000
133	A	145	PHE	0	-0.031	0.003	54.353	0.000	0.000	0.000	0.000	0.000	0.000
134	A	146	THR	0	0.021	-0.008	59.022	0.001	0.001	0.000	0.000	0.000	0.000
135	A	147	GLU	-1	-0.957	-0.991	62.084	-0.021	-0.021	0.000	0.000	0.000	0.000
136	A	148	GLU	-1	-0.952	-0.971	63.837	-0.022	-0.022	0.000	0.000	0.000	0.000
137	A	149	GLU	-1	-0.812	-0.912	59.794	-0.026	-0.026	0.000	0.000	0.000	0.000
138	A	150	GLU	-1	-0.878	-0.923	57.737	-0.030	-0.030	0.000	0.000	0.000	0.000
139	A	151	ALA	0	-0.041	-0.038	59.914	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	152	GLN	0	-0.047	-0.022	60.229	-0.001	-0.001	0.000	0.000	0.000	0.000
141	A	153	VAL	0	-0.018	-0.005	54.944	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	154	ARG	1	0.830	0.923	56.718	0.026	0.026	0.000	0.000	0.000	0.000
143	A	155	LYS	1	0.801	0.903	57.711	0.028	0.028	0.000	0.000	0.000	0.000
144	A	156	GLU	-1	-0.831	-0.895	54.478	-0.030	-0.030	0.000	0.000	0.000	0.000

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