FMO DATABASE

FMODB ID: LN4Z9

Calculation Name: 3GHJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GHJ

Chain ID: A

ChEMBL ID:

UniProt ID: B0BGV9

Base Structure: X-ray

Registration Date: 2023-09-23

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	116
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-945868.478305
FMO2-HF: Nuclear repulsion	900050.456853
FMO2-HF: Total energy	-45818.021452
FMO2-MP2: Total energy	-45953.996344

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:5:ILE)

Summations of interaction energy for fragment #1(A:5:ILE)

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.
-5.235	-0.184	0.345	-2.471	-2.925	-0.003

Interaction energy analysis for fragmet #1(A:5:ILE)

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 : -0.017

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	7	GLY	0	0.040	0.033	2.477	-4.477	0.066	0.326	-2.298	-2.571	-0.002
4	A	8	LEU	0	-0.021	0.001	3.647	-0.514	-0.006	0.019	-0.173	-0.354	-0.001
5	A	9	PHE	0	-0.024	0.003	6.101	0.198	0.198	0.000	0.000	0.000	0.000
6	A	10	GLU	-1	-0.893	-0.956	8.079	-0.050	-0.050	0.000	0.000	0.000	0.000
7	A	11	VAL	0	-0.014	-0.001	10.279	-0.112	-0.112	0.000	0.000	0.000	0.000
8	A	12	ALA	0	0.010	0.012	13.037	0.058	0.058	0.000	0.000	0.000	0.000
9	A	13	VAL	0	-0.002	0.004	16.165	-0.026	-0.026	0.000	0.000	0.000	0.000
10	A	14	LYS	1	0.839	0.915	19.218	0.196	0.196	0.000	0.000	0.000	0.000
11	A	15	VAL	0	-0.028	-0.005	22.448	0.001	0.001	0.000	0.000	0.000	0.000
12	A	16	LYS	1	0.901	0.943	25.414	0.113	0.113	0.000	0.000	0.000	0.000
13	A	17	ASN	0	-0.054	-0.043	28.825	0.009	0.009	0.000	0.000	0.000	0.000
14	A	18	LEU	0	0.016	0.020	24.918	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	19	GLU	-1	-0.775	-0.845	27.781	-0.043	-0.043	0.000	0.000	0.000	0.000
16	A	20	LYS	1	1.012	0.998	30.003	0.054	0.054	0.000	0.000	0.000	0.000
17	A	21	SER	0	0.026	0.015	25.162	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	22	SER	0	-0.007	-0.023	25.273	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	23	GLN	0	-0.063	-0.015	26.352	0.001	0.001	0.000	0.000	0.000	0.000
20	A	24	PHE	0	0.024	0.024	23.664	0.003	0.003	0.000	0.000	0.000	0.000
21	A	25	TYR	0	-0.012	-0.053	20.290	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	26	THR	0	-0.041	-0.025	23.486	0.005	0.005	0.000	0.000	0.000	0.000
23	A	27	GLU	-1	-0.876	-0.917	25.515	-0.020	-0.020	0.000	0.000	0.000	0.000
24	A	28	ILE	0	-0.051	-0.026	26.740	0.004	0.004	0.000	0.000	0.000	0.000
25	A	29	LEU	0	-0.021	-0.020	20.873	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	30	GLY	0	-0.017	0.016	22.794	0.003	0.003	0.000	0.000	0.000	0.000
27	A	31	PHE	0	-0.035	-0.026	18.352	0.008	0.008	0.000	0.000	0.000	0.000
28	A	32	GLU	-1	-0.911	-0.964	20.949	0.073	0.073	0.000	0.000	0.000	0.000
29	A	33	ALA	0	0.018	0.002	21.604	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	34	GLY	0	0.041	0.008	20.691	0.015	0.015	0.000	0.000	0.000	0.000
31	A	35	LEU	0	-0.071	-0.021	21.197	0.010	0.010	0.000	0.000	0.000	0.000
32	A	36	LEU	0	0.011	0.017	22.730	-0.015	-0.015	0.000	0.000	0.000	0.000
33	A	37	ASP	-1	-0.782	-0.876	24.384	-0.016	-0.016	0.000	0.000	0.000	0.000
34	A	38	SER	0	0.018	-0.025	26.156	-0.010	-0.010	0.000	0.000	0.000	0.000
35	A	39	ALA	0	-0.035	-0.001	28.783	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	40	ARG	1	0.820	0.893	20.828	0.041	0.041	0.000	0.000	0.000	0.000
37	A	41	ARG	1	0.733	0.828	26.380	0.038	0.038	0.000	0.000	0.000	0.000
38	A	42	TRP	0	0.043	0.002	18.566	-0.015	-0.015	0.000	0.000	0.000	0.000
39	A	43	ASN	0	-0.015	-0.025	22.298	0.022	0.022	0.000	0.000	0.000	0.000
40	A	44	PHE	0	-0.021	0.001	16.690	-0.018	-0.018	0.000	0.000	0.000	0.000
41	A	45	LEU	0	0.014	0.002	18.594	0.021	0.021	0.000	0.000	0.000	0.000
42	A	46	TRP	0	0.023	0.001	13.976	0.002	0.002	0.000	0.000	0.000	0.000
43	A	47	VAL	0	0.016	0.009	14.864	-0.009	-0.009	0.000	0.000	0.000	0.000
44	A	48	SER	0	0.011	-0.009	15.750	0.020	0.020	0.000	0.000	0.000	0.000
45	A	49	GLY	0	0.063	0.044	16.831	0.036	0.036	0.000	0.000	0.000	0.000
46	A	50	ARG	1	0.888	0.930	14.742	-0.301	-0.301	0.000	0.000	0.000	0.000
47	A	51	ALA	0	-0.029	-0.008	12.342	0.060	0.060	0.000	0.000	0.000	0.000
48	A	52	GLY	0	0.030	0.015	10.900	-0.028	-0.028	0.000	0.000	0.000	0.000
49	A	53	MET	0	-0.055	-0.007	12.332	0.050	0.050	0.000	0.000	0.000	0.000
50	A	54	VAL	0	0.006	0.010	13.627	-0.058	-0.058	0.000	0.000	0.000	0.000
51	A	55	VAL	0	-0.001	0.004	15.221	0.036	0.036	0.000	0.000	0.000	0.000
52	A	56	LEU	0	-0.019	0.004	17.785	-0.024	-0.024	0.000	0.000	0.000	0.000
53	A	57	GLN	0	0.032	0.008	18.610	0.004	0.004	0.000	0.000	0.000	0.000
54	A	58	GLU	-1	-0.760	-0.853	22.692	-0.070	-0.070	0.000	0.000	0.000	0.000
55	A	59	GLU	-1	-0.821	-0.904	24.058	-0.149	-0.149	0.000	0.000	0.000	0.000
56	A	60	LYS	1	0.890	0.928	27.442	0.061	0.061	0.000	0.000	0.000	0.000
57	A	61	GLU	-1	-0.961	-0.971	30.009	-0.084	-0.084	0.000	0.000	0.000	0.000
58	A	62	ASN	0	-0.026	-0.017	27.752	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	63	TRP	0	-0.050	-0.025	26.734	-0.010	-0.010	0.000	0.000	0.000	0.000
60	A	64	GLN	0	0.008	-0.006	23.124	-0.015	-0.015	0.000	0.000	0.000	0.000
61	A	65	GLN	0	-0.048	-0.010	22.863	-0.009	-0.009	0.000	0.000	0.000	0.000
62	A	66	GLN	0	-0.031	-0.021	17.053	0.006	0.006	0.000	0.000	0.000	0.000
63	A	67	HIS	0	-0.041	-0.026	16.165	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	68	PHE	0	-0.003	-0.004	14.473	-0.040	-0.040	0.000	0.000	0.000	0.000
65	A	69	SER	0	-0.030	-0.006	14.050	0.021	0.021	0.000	0.000	0.000	0.000
66	A	70	PHE	0	0.016	0.006	13.610	-0.030	-0.030	0.000	0.000	0.000	0.000
67	A	71	ARG	1	0.936	0.976	12.035	0.200	0.200	0.000	0.000	0.000	0.000
68	A	72	VAL	0	0.025	0.011	14.809	0.035	0.035	0.000	0.000	0.000	0.000
69	A	73	GLU	-1	-0.910	-0.957	18.099	-0.012	-0.012	0.000	0.000	0.000	0.000
70	A	74	LYS	1	0.859	0.890	19.787	0.135	0.135	0.000	0.000	0.000	0.000
71	A	75	SER	0	-0.053	-0.040	22.378	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	76	GLU	-1	-0.822	-0.898	22.947	-0.016	-0.016	0.000	0.000	0.000	0.000
73	A	77	ILE	0	-0.037	-0.014	21.530	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	78	GLU	-1	-0.808	-0.905	25.023	-0.073	-0.073	0.000	0.000	0.000	0.000
75	A	79	PRO	0	0.007	0.007	27.516	0.000	0.000	0.000	0.000	0.000	0.000
76	A	80	LEU	0	0.013	0.010	22.244	0.002	0.002	0.000	0.000	0.000	0.000
77	A	81	LYS	1	0.865	0.921	26.391	0.075	0.075	0.000	0.000	0.000	0.000
78	A	82	LYS	1	0.878	0.930	28.187	0.049	0.049	0.000	0.000	0.000	0.000
79	A	83	ALA	0	0.002	0.003	28.208	0.003	0.003	0.000	0.000	0.000	0.000
80	A	84	LEU	0	0.006	0.011	24.642	0.003	0.003	0.000	0.000	0.000	0.000
81	A	85	GLU	-1	-0.822	-0.899	29.110	-0.060	-0.060	0.000	0.000	0.000	0.000
82	A	86	SER	0	-0.137	-0.072	32.374	0.004	0.004	0.000	0.000	0.000	0.000
83	A	87	LYS	1	0.810	0.901	28.179	0.038	0.038	0.000	0.000	0.000	0.000
84	A	88	GLY	0	-0.011	0.001	33.040	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	89	VAL	0	-0.046	-0.017	27.406	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	90	SER	0	-0.025	-0.018	30.888	0.002	0.002	0.000	0.000	0.000	0.000
87	A	91	VAL	0	-0.017	-0.006	26.473	-0.009	-0.009	0.000	0.000	0.000	0.000
88	A	92	HIS	0	0.006	0.010	26.692	0.012	0.012	0.000	0.000	0.000	0.000
89	A	93	GLY	0	0.019	0.025	26.513	-0.011	-0.011	0.000	0.000	0.000	0.000
90	A	94	PRO	0	-0.015	-0.032	25.922	0.009	0.009	0.000	0.000	0.000	0.000
91	A	95	VAL	0	-0.010	-0.004	24.217	0.006	0.006	0.000	0.000	0.000	0.000
92	A	96	ASN	0	0.001	-0.002	23.691	-0.011	-0.011	0.000	0.000	0.000	0.000
93	A	97	GLN	0	0.015	0.009	19.686	-0.004	-0.004	0.000	0.000	0.000	0.000
94	A	98	GLU	-1	-0.910	-0.966	21.139	-0.148	-0.148	0.000	0.000	0.000	0.000
95	A	99	TRP	0	0.000	-0.004	16.052	-0.007	-0.007	0.000	0.000	0.000	0.000
96	A	100	MET	0	-0.014	0.001	14.770	-0.017	-0.017	0.000	0.000	0.000	0.000
97	A	101	GLN	0	-0.052	-0.022	17.646	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	102	ALA	0	-0.014	0.009	17.447	0.010	0.010	0.000	0.000	0.000	0.000
99	A	103	VAL	0	-0.010	0.001	19.508	0.014	0.014	0.000	0.000	0.000	0.000
100	A	104	SER	0	-0.004	-0.021	19.061	-0.007	-0.007	0.000	0.000	0.000	0.000
101	A	105	LEU	0	-0.047	-0.005	21.419	0.017	0.017	0.000	0.000	0.000	0.000
102	A	106	TYR	0	-0.001	-0.008	19.754	-0.007	-0.007	0.000	0.000	0.000	0.000
103	A	107	PHE	0	0.024	0.006	21.575	0.017	0.017	0.000	0.000	0.000	0.000
104	A	108	ALA	0	0.028	0.023	23.981	-0.014	-0.014	0.000	0.000	0.000	0.000
105	A	109	ASP	-1	-0.713	-0.833	23.463	-0.129	-0.129	0.000	0.000	0.000	0.000
106	A	110	PRO	0	-0.022	-0.022	25.603	0.001	0.001	0.000	0.000	0.000	0.000
107	A	111	ASN	0	-0.081	-0.041	24.985	0.012	0.012	0.000	0.000	0.000	0.000
108	A	112	GLY	0	0.026	0.020	27.196	-0.004	-0.004	0.000	0.000	0.000	0.000
109	A	113	HIS	0	-0.019	-0.007	21.396	-0.019	-0.019	0.000	0.000	0.000	0.000
110	A	114	ALA	0	-0.001	-0.006	21.448	0.014	0.014	0.000	0.000	0.000	0.000
111	A	115	LEU	0	-0.020	-0.004	19.642	-0.026	-0.026	0.000	0.000	0.000	0.000
112	A	116	GLU	-1	-0.743	-0.861	18.074	-0.287	-0.287	0.000	0.000	0.000	0.000
113	A	117	PHE	0	-0.025	-0.001	18.192	-0.005	-0.005	0.000	0.000	0.000	0.000
114	A	118	THR	0	0.024	-0.008	15.318	-0.006	-0.006	0.000	0.000	0.000	0.000
115	A	119	ALA	0	0.008	0.016	16.607	0.005	0.005	0.000	0.000	0.000	0.000
116	A	120	LEU	0	-0.016	-0.013	13.105	-0.006	-0.006	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:5:ILE)