FMO DATABASE

FMODB ID: JL1Q9

Calculation Name: 4I8B-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4I8B

Chain ID: A

ChEMBL ID:

UniProt ID: Q9U8F3

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	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	104
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-817820.624141
FMO2-HF: Nuclear repulsion	776822.699223
FMO2-HF: Total energy	-40997.924917
FMO2-MP2: Total energy	-41117.920403

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:2:SER)

Summations of interaction energy for fragment #1(A:2:SER)

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.
-20.902	-23.3	24.485	-11.362	-10.724	-0.009

Interaction energy analysis for fragmet #1(A:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.023 / q_NPA : -0.011

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	4	VAL	0	-0.007	-0.002	1.858	-10.872	-10.738	9.885	-5.042	-4.977	0.027
4	A	5	LEU	0	-0.041	-0.012	3.746	-1.577	-1.434	0.013	-0.007	-0.150	0.002
5	A	6	HIS	0	-0.005	-0.011	4.059	0.319	0.397	-0.001	-0.006	-0.070	0.000
6	A	7	ILE	0	0.008	0.004	8.556	0.043	0.043	0.000	0.000	0.000	0.000
7	A	8	GLU	-1	-0.879	-0.949	12.254	-0.538	-0.538	0.000	0.000	0.000	0.000
8	A	9	THR	0	0.045	0.031	14.878	0.006	0.006	0.000	0.000	0.000	0.000
9	A	10	ASP	-1	-0.706	-0.839	17.739	-0.067	-0.067	0.000	0.000	0.000	0.000
10	A	11	ASP	-1	-0.886	-0.934	20.110	-0.029	-0.029	0.000	0.000	0.000	0.000
11	A	12	ASP	-1	-0.932	-0.974	16.136	-0.085	-0.085	0.000	0.000	0.000	0.000
12	A	13	PHE	0	-0.040	-0.026	14.501	0.050	0.050	0.000	0.000	0.000	0.000
13	A	14	ASP	-1	-0.905	-0.954	17.116	0.052	0.052	0.000	0.000	0.000	0.000
14	A	15	SER	0	-0.046	-0.027	18.971	0.019	0.019	0.000	0.000	0.000	0.000
15	A	16	PHE	0	0.035	0.010	12.348	0.040	0.040	0.000	0.000	0.000	0.000
16	A	17	LEU	0	0.024	0.004	16.722	0.041	0.041	0.000	0.000	0.000	0.000
17	A	18	LYS	1	0.845	0.935	18.520	-0.042	-0.042	0.000	0.000	0.000	0.000
18	A	19	GLU	-1	-0.913	-0.949	17.825	0.121	0.121	0.000	0.000	0.000	0.000
19	A	20	ASN	0	-0.076	-0.038	15.350	0.068	0.068	0.000	0.000	0.000	0.000
20	A	21	LYS	1	0.902	0.931	18.081	-0.110	-0.110	0.000	0.000	0.000	0.000
21	A	22	ASP	-1	-0.933	-0.956	19.978	0.256	0.256	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.920	0.972	15.364	-0.364	-0.364	0.000	0.000	0.000	0.000
23	A	24	LEU	0	-0.051	-0.024	15.670	-0.041	-0.041	0.000	0.000	0.000	0.000
24	A	25	ILE	0	0.012	0.005	12.831	0.088	0.088	0.000	0.000	0.000	0.000
25	A	26	VAL	0	-0.016	-0.008	11.134	-0.093	-0.093	0.000	0.000	0.000	0.000
26	A	27	VAL	0	0.030	0.008	10.976	0.104	0.104	0.000	0.000	0.000	0.000
27	A	28	ASP	-1	-0.903	-0.951	9.843	-0.396	-0.396	0.000	0.000	0.000	0.000
28	A	29	PHE	0	0.029	0.014	11.937	-0.064	-0.064	0.000	0.000	0.000	0.000
29	A	30	PHE	0	0.001	-0.029	11.039	-0.047	-0.047	0.000	0.000	0.000	0.000
30	A	31	ALA	0	0.120	0.057	14.710	0.019	0.019	0.000	0.000	0.000	0.000
31	A	32	THR	0	0.037	0.008	15.466	-0.035	-0.035	0.000	0.000	0.000	0.000
32	A	33	TRP	0	0.006	-0.005	16.934	-0.043	-0.043	0.000	0.000	0.000	0.000
33	A	34	CYS	0	0.022	0.063	13.560	0.039	0.039	0.000	0.000	0.000	0.000
34	A	35	GLY	0	-0.006	-0.011	16.662	-0.054	-0.054	0.000	0.000	0.000	0.000
35	A	36	PRO	0	0.017	-0.018	16.623	-0.049	-0.049	0.000	0.000	0.000	0.000
36	A	38	LYS	1	0.954	0.980	12.210	0.465	0.465	0.000	0.000	0.000	0.000
37	A	39	LYS	1	0.914	0.962	12.200	0.188	0.188	0.000	0.000	0.000	0.000
38	A	40	ILE	0	0.015	0.014	11.663	-0.018	-0.018	0.000	0.000	0.000	0.000
39	A	41	ALA	0	0.019	0.015	8.041	0.033	0.033	0.000	0.000	0.000	0.000
40	A	42	PRO	0	0.027	0.011	6.745	-0.194	-0.194	0.000	0.000	0.000	0.000
41	A	43	ALA	0	0.006	0.013	6.460	0.100	0.100	0.000	0.000	0.000	0.000
42	A	44	PHE	0	0.014	0.004	6.448	0.313	0.313	0.000	0.000	0.000	0.000
43	A	45	GLU	-1	-0.931	-0.976	1.998	-8.822	-13.514	14.404	-5.341	-4.372	-0.030
44	A	46	ALA	0	-0.009	0.008	3.138	0.200	1.225	0.113	-0.544	-0.594	-0.006
45	A	47	LEU	0	0.004	-0.002	5.335	0.369	0.391	-0.001	-0.002	-0.019	0.000
46	A	48	SER	0	-0.035	-0.031	3.093	0.549	1.405	0.074	-0.407	-0.522	-0.002
47	A	49	ALA	0	-0.008	0.000	4.757	0.104	0.133	-0.001	-0.012	-0.016	0.000
48	A	50	ASP	-1	-0.796	-0.829	5.369	0.523	0.530	-0.001	-0.001	-0.004	0.000
49	A	51	ARG	1	0.944	0.950	6.214	-1.883	-1.883	0.000	0.000	0.000	0.000
50	A	52	SER	0	-0.136	-0.091	9.990	-0.127	-0.127	0.000	0.000	0.000	0.000
51	A	53	ALA	0	-0.013	-0.014	11.342	-0.126	-0.126	0.000	0.000	0.000	0.000
52	A	54	LEU	0	-0.018	0.010	9.659	0.164	0.164	0.000	0.000	0.000	0.000
53	A	55	TYR	0	-0.013	-0.019	6.377	-0.176	-0.176	0.000	0.000	0.000	0.000
54	A	56	VAL	0	0.026	0.019	7.041	0.366	0.366	0.000	0.000	0.000	0.000
55	A	57	LYS	1	0.889	0.960	6.333	1.197	1.197	0.000	0.000	0.000	0.000
56	A	58	VAL	0	0.030	0.003	9.045	-0.057	-0.057	0.000	0.000	0.000	0.000
57	A	59	ASP	-1	-0.879	-0.931	12.489	-0.386	-0.386	0.000	0.000	0.000	0.000
58	A	60	VAL	0	0.012	-0.034	14.810	0.039	0.039	0.000	0.000	0.000	0.000
59	A	61	ASP	-1	-0.923	-0.956	18.210	-0.212	-0.212	0.000	0.000	0.000	0.000
60	A	62	LYS	1	0.799	0.905	14.573	0.464	0.464	0.000	0.000	0.000	0.000
61	A	63	LEU	0	-0.055	-0.022	15.693	0.019	0.019	0.000	0.000	0.000	0.000
62	A	64	GLU	-1	-0.907	-0.951	19.106	-0.115	-0.115	0.000	0.000	0.000	0.000
63	A	65	GLU	-1	-0.928	-0.974	22.395	-0.041	-0.041	0.000	0.000	0.000	0.000
64	A	66	THR	0	-0.057	-0.061	17.851	0.025	0.025	0.000	0.000	0.000	0.000
65	A	67	ALA	0	-0.022	-0.018	19.737	0.017	0.017	0.000	0.000	0.000	0.000
66	A	68	ARG	1	0.923	0.975	20.879	0.075	0.075	0.000	0.000	0.000	0.000
67	A	69	LYS	1	0.929	0.981	22.094	-0.037	-0.037	0.000	0.000	0.000	0.000
68	A	70	TYR	0	-0.078	-0.051	19.242	0.021	0.021	0.000	0.000	0.000	0.000
69	A	71	ASP	-1	-0.956	-0.968	22.739	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	72	VAL	0	-0.041	-0.018	19.002	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	73	SER	0	0.000	-0.009	22.130	-0.010	-0.010	0.000	0.000	0.000	0.000
72	A	74	ALA	0	-0.026	0.000	22.488	-0.012	-0.012	0.000	0.000	0.000	0.000
73	A	75	MET	0	-0.016	0.040	17.089	0.006	0.006	0.000	0.000	0.000	0.000
74	A	76	PRO	0	-0.014	-0.041	14.709	-0.012	-0.012	0.000	0.000	0.000	0.000
75	A	77	THR	0	-0.013	-0.035	16.382	0.032	0.032	0.000	0.000	0.000	0.000
76	A	78	PHE	0	-0.032	-0.012	11.333	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	79	ILE	0	-0.004	0.013	15.507	0.005	0.005	0.000	0.000	0.000	0.000
78	A	80	VAL	0	-0.019	-0.011	15.669	0.046	0.046	0.000	0.000	0.000	0.000
79	A	81	ILE	0	0.010	0.006	16.720	-0.036	-0.036	0.000	0.000	0.000	0.000
80	A	82	LYS	1	0.909	0.936	17.873	-0.175	-0.175	0.000	0.000	0.000	0.000
81	A	83	ASN	0	-0.050	-0.024	20.429	-0.009	-0.009	0.000	0.000	0.000	0.000
82	A	84	GLY	0	0.026	0.013	20.758	-0.018	-0.018	0.000	0.000	0.000	0.000
83	A	85	GLU	-1	-0.901	-0.940	22.004	0.070	0.070	0.000	0.000	0.000	0.000
84	A	86	LYS	1	0.947	0.985	21.214	-0.021	-0.021	0.000	0.000	0.000	0.000
85	A	87	VAL	0	-0.070	-0.042	20.877	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	88	ASP	-1	-0.839	-0.918	20.344	0.111	0.111	0.000	0.000	0.000	0.000
87	A	89	THR	0	-0.036	-0.018	20.043	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	90	VAL	0	-0.018	0.007	17.775	0.000	0.000	0.000	0.000	0.000	0.000
89	A	91	VAL	0	0.049	0.024	18.661	-0.014	-0.014	0.000	0.000	0.000	0.000
90	A	92	GLY	0	0.022	0.016	19.184	0.006	0.006	0.000	0.000	0.000	0.000
91	A	93	ALA	0	-0.020	-0.024	16.124	0.013	0.013	0.000	0.000	0.000	0.000
92	A	94	SER	0	-0.016	0.004	17.140	0.001	0.001	0.000	0.000	0.000	0.000
93	A	95	ILE	0	0.061	0.016	10.814	0.013	0.013	0.000	0.000	0.000	0.000
94	A	96	GLU	-1	-0.845	-0.924	14.677	0.061	0.061	0.000	0.000	0.000	0.000
95	A	97	ASN	0	-0.029	-0.023	17.572	0.037	0.037	0.000	0.000	0.000	0.000
96	A	98	VAL	0	0.001	0.013	12.547	0.025	0.025	0.000	0.000	0.000	0.000
97	A	99	GLU	-1	-0.905	-0.956	13.636	0.268	0.268	0.000	0.000	0.000	0.000
98	A	100	ALA	0	-0.072	-0.040	15.596	0.023	0.023	0.000	0.000	0.000	0.000
99	A	101	ALA	0	0.010	0.003	17.862	0.006	0.006	0.000	0.000	0.000	0.000
100	A	102	ILE	0	0.031	0.013	12.446	0.000	0.000	0.000	0.000	0.000	0.000
101	A	103	ARG	1	0.946	0.962	16.770	-0.209	-0.209	0.000	0.000	0.000	0.000
102	A	104	LYS	1	0.871	0.960	18.934	-0.143	-0.143	0.000	0.000	0.000	0.000
103	A	105	HIS	1	0.806	0.882	19.586	-0.187	-0.187	0.000	0.000	0.000	0.000
104	A	106	LYS	1	0.893	0.969	13.351	-0.552	-0.552	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)