FMO DATABASE

FMODB ID: 98942

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

Total energy (hartree)

FMO2-HF: Electronic energy	-946403.194419
FMO2-HF: Nuclear repulsion	900585.025746
FMO2-HF: Total energy	-45818.168673
FMO2-MP2: Total energy	-45954.198715

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.
-4.486	-0.041	0.069	-2.204	-2.308	-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 : 0.017 / q_NPA : -0.008

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

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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	0.044	0.029	2.935	-4.073	0.116	0.068	-2.162	-2.093	-0.003
4	A	8	LEU	0	-0.020	0.002	4.089	-0.254	0.002	0.001	-0.042	-0.215	0.000
5	A	9	PHE	0	-0.012	0.012	6.334	0.159	0.159	0.000	0.000	0.000	0.000
6	A	10	GLU	-1	-0.898	-0.960	8.187	0.015	0.015	0.000	0.000	0.000	0.000
7	A	11	VAL	0	-0.009	-0.003	10.344	-0.109	-0.109	0.000	0.000	0.000	0.000
8	A	12	ALA	0	0.024	0.022	13.169	0.051	0.051	0.000	0.000	0.000	0.000
9	A	13	VAL	0	-0.018	-0.004	16.238	-0.026	-0.026	0.000	0.000	0.000	0.000
10	A	14	LYS	1	0.837	0.905	19.399	0.164	0.164	0.000	0.000	0.000	0.000
11	A	15	VAL	0	-0.028	-0.005	22.598	0.001	0.001	0.000	0.000	0.000	0.000
12	A	16	LYS	1	0.805	0.886	25.687	0.095	0.095	0.000	0.000	0.000	0.000
13	A	17	ASN	0	-0.071	-0.061	29.024	0.008	0.008	0.000	0.000	0.000	0.000
14	A	18	LEU	0	0.023	0.033	25.030	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	19	GLU	-1	-0.773	-0.830	27.682	-0.020	-0.020	0.000	0.000	0.000	0.000
16	A	20	LYS	1	1.016	0.994	29.736	0.035	0.035	0.000	0.000	0.000	0.000
17	A	21	SER	0	0.022	0.014	25.154	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	22	SER	0	-0.001	-0.019	25.430	0.001	0.001	0.000	0.000	0.000	0.000
19	A	23	GLN	0	-0.071	-0.017	26.503	0.002	0.002	0.000	0.000	0.000	0.000
20	A	24	PHE	0	0.026	0.016	23.495	0.004	0.004	0.000	0.000	0.000	0.000
21	A	25	TYR	0	-0.008	-0.049	20.575	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	26	THR	0	-0.048	-0.033	23.530	0.006	0.006	0.000	0.000	0.000	0.000
23	A	27	GLU	-1	-0.858	-0.912	25.552	0.002	0.002	0.000	0.000	0.000	0.000
24	A	28	ILE	0	-0.058	-0.027	27.101	0.002	0.002	0.000	0.000	0.000	0.000
25	A	29	LEU	0	-0.009	-0.008	21.240	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	30	GLY	0	-0.025	0.014	23.039	0.003	0.003	0.000	0.000	0.000	0.000
27	A	31	PHE	0	-0.022	-0.020	18.657	0.010	0.010	0.000	0.000	0.000	0.000
28	A	32	GLU	-1	-0.843	-0.921	20.798	0.114	0.114	0.000	0.000	0.000	0.000
29	A	33	ALA	0	-0.002	-0.013	21.480	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	34	GLY	0	0.004	-0.001	20.711	0.017	0.017	0.000	0.000	0.000	0.000
31	A	35	LEU	0	-0.055	-0.029	21.666	0.009	0.009	0.000	0.000	0.000	0.000
32	A	36	LEU	0	0.027	0.028	23.153	-0.013	-0.013	0.000	0.000	0.000	0.000
33	A	37	ASP	-1	-0.785	-0.871	24.401	0.008	0.008	0.000	0.000	0.000	0.000
34	A	38	SER	0	0.020	-0.023	26.256	-0.010	-0.010	0.000	0.000	0.000	0.000
35	A	39	ALA	0	-0.039	-0.001	29.114	-0.005	-0.005	0.000	0.000	0.000	0.000
36	A	40	ARG	1	0.797	0.882	21.376	0.014	0.014	0.000	0.000	0.000	0.000
37	A	41	ARG	1	0.748	0.832	26.430	0.017	0.017	0.000	0.000	0.000	0.000
38	A	42	TRP	0	0.061	0.016	18.681	-0.011	-0.011	0.000	0.000	0.000	0.000
39	A	43	ASN	0	-0.020	-0.035	22.410	0.020	0.020	0.000	0.000	0.000	0.000
40	A	44	PHE	0	-0.005	0.009	16.918	-0.016	-0.016	0.000	0.000	0.000	0.000
41	A	45	LEU	0	0.005	-0.002	18.688	0.016	0.016	0.000	0.000	0.000	0.000
42	A	46	TRP	0	0.069	0.027	14.194	0.010	0.010	0.000	0.000	0.000	0.000
43	A	47	VAL	0	0.022	0.014	15.088	-0.021	-0.021	0.000	0.000	0.000	0.000
44	A	48	SER	0	0.021	0.005	15.868	0.022	0.022	0.000	0.000	0.000	0.000
45	A	49	GLY	0	0.049	0.028	17.185	0.044	0.044	0.000	0.000	0.000	0.000
46	A	50	ARG	1	0.799	0.879	14.484	-0.359	-0.359	0.000	0.000	0.000	0.000
47	A	51	ALA	0	-0.024	0.001	12.334	0.071	0.071	0.000	0.000	0.000	0.000
48	A	52	GLY	0	0.020	0.009	11.036	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	53	MET	0	-0.066	-0.016	12.375	0.037	0.037	0.000	0.000	0.000	0.000
50	A	54	VAL	0	0.008	0.011	13.682	-0.053	-0.053	0.000	0.000	0.000	0.000
51	A	55	VAL	0	-0.008	-0.003	15.446	0.031	0.031	0.000	0.000	0.000	0.000
52	A	56	LEU	0	0.004	0.015	17.993	-0.025	-0.025	0.000	0.000	0.000	0.000
53	A	57	GLN	0	0.033	0.012	18.758	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	58	GLU	-1	-0.757	-0.853	23.038	-0.048	-0.048	0.000	0.000	0.000	0.000
55	A	59	GLU	-1	-0.823	-0.886	24.076	-0.120	-0.120	0.000	0.000	0.000	0.000
56	A	60	LYS	1	0.909	0.944	27.548	0.040	0.040	0.000	0.000	0.000	0.000
57	A	61	GLU	-1	-0.919	-0.941	30.653	-0.073	-0.073	0.000	0.000	0.000	0.000
58	A	62	ASN	0	-0.041	-0.037	28.264	-0.005	-0.005	0.000	0.000	0.000	0.000
59	A	63	TRP	0	-0.017	-0.010	26.885	-0.009	-0.009	0.000	0.000	0.000	0.000
60	A	64	GLN	0	0.011	0.002	23.535	-0.013	-0.013	0.000	0.000	0.000	0.000
61	A	65	GLN	0	-0.062	-0.020	23.230	-0.006	-0.006	0.000	0.000	0.000	0.000
62	A	66	GLN	0	-0.021	-0.015	17.356	0.005	0.005	0.000	0.000	0.000	0.000
63	A	67	HIS	0	-0.028	-0.020	15.915	0.001	0.001	0.000	0.000	0.000	0.000
64	A	68	PHE	0	-0.001	-0.009	14.890	-0.032	-0.032	0.000	0.000	0.000	0.000
65	A	69	SER	0	-0.057	-0.019	14.402	0.022	0.022	0.000	0.000	0.000	0.000
66	A	70	PHE	0	0.036	0.016	14.024	-0.015	-0.015	0.000	0.000	0.000	0.000
67	A	71	ARG	1	0.909	0.965	12.225	0.123	0.123	0.000	0.000	0.000	0.000
68	A	72	VAL	0	0.035	0.016	14.579	0.036	0.036	0.000	0.000	0.000	0.000
69	A	73	GLU	-1	-0.924	-0.972	17.495	0.016	0.016	0.000	0.000	0.000	0.000
70	A	74	LYS	1	0.827	0.879	19.842	0.113	0.113	0.000	0.000	0.000	0.000
71	A	75	SER	0	-0.039	-0.038	22.518	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	76	GLU	-1	-0.825	-0.890	22.975	0.001	0.001	0.000	0.000	0.000	0.000
73	A	77	ILE	0	-0.031	-0.011	21.730	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	78	GLU	-1	-0.782	-0.890	25.063	-0.056	-0.056	0.000	0.000	0.000	0.000
75	A	79	PRO	0	-0.003	0.002	27.324	0.000	0.000	0.000	0.000	0.000	0.000
76	A	80	LEU	0	0.015	0.009	22.102	0.002	0.002	0.000	0.000	0.000	0.000
77	A	81	LYS	1	0.824	0.896	26.245	0.058	0.058	0.000	0.000	0.000	0.000
78	A	82	LYS	1	0.861	0.905	27.987	0.035	0.035	0.000	0.000	0.000	0.000
79	A	83	ALA	0	0.000	0.004	27.976	0.003	0.003	0.000	0.000	0.000	0.000
80	A	84	LEU	0	-0.019	0.000	24.714	0.003	0.003	0.000	0.000	0.000	0.000
81	A	85	GLU	-1	-0.808	-0.892	29.142	-0.042	-0.042	0.000	0.000	0.000	0.000
82	A	86	SER	0	-0.128	-0.063	32.323	0.004	0.004	0.000	0.000	0.000	0.000
83	A	87	LYS	1	0.818	0.900	28.372	0.014	0.014	0.000	0.000	0.000	0.000
84	A	88	GLY	0	-0.011	0.002	33.182	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	89	VAL	0	-0.050	-0.016	27.382	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	90	SER	0	-0.006	-0.009	30.720	0.001	0.001	0.000	0.000	0.000	0.000
87	A	91	VAL	0	-0.022	-0.012	26.419	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	92	HIS	0	-0.007	0.004	27.001	0.010	0.010	0.000	0.000	0.000	0.000
89	A	93	GLY	0	0.038	0.023	26.515	-0.011	-0.011	0.000	0.000	0.000	0.000
90	A	94	PRO	0	0.009	-0.011	25.887	0.009	0.009	0.000	0.000	0.000	0.000
91	A	95	VAL	0	-0.008	0.002	23.990	0.004	0.004	0.000	0.000	0.000	0.000
92	A	96	ASN	0	-0.041	-0.022	23.370	-0.007	-0.007	0.000	0.000	0.000	0.000
93	A	97	GLN	0	0.032	0.021	19.399	-0.008	-0.008	0.000	0.000	0.000	0.000
94	A	98	GLU	-1	-0.865	-0.936	20.371	-0.137	-0.137	0.000	0.000	0.000	0.000
95	A	99	TRP	0	-0.004	-0.015	15.949	-0.006	-0.006	0.000	0.000	0.000	0.000
96	A	100	MET	0	-0.032	-0.005	14.341	-0.022	-0.022	0.000	0.000	0.000	0.000
97	A	101	GLN	0	-0.056	-0.025	17.217	-0.007	-0.007	0.000	0.000	0.000	0.000
98	A	102	ALA	0	-0.016	0.010	17.070	0.019	0.019	0.000	0.000	0.000	0.000
99	A	103	VAL	0	0.000	-0.003	19.194	0.010	0.010	0.000	0.000	0.000	0.000
100	A	104	SER	0	-0.009	-0.025	18.678	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	105	LEU	0	-0.053	-0.006	21.163	0.014	0.014	0.000	0.000	0.000	0.000
102	A	106	TYR	0	-0.007	-0.011	19.406	-0.004	-0.004	0.000	0.000	0.000	0.000
103	A	107	PHE	0	0.026	0.002	21.654	0.014	0.014	0.000	0.000	0.000	0.000
104	A	108	ALA	0	0.022	0.017	24.534	-0.012	-0.012	0.000	0.000	0.000	0.000
105	A	109	ASP	-1	-0.702	-0.831	23.910	-0.095	-0.095	0.000	0.000	0.000	0.000
106	A	110	PRO	0	-0.050	-0.036	26.060	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	111	ASN	0	-0.070	-0.040	25.052	0.009	0.009	0.000	0.000	0.000	0.000
108	A	112	GLY	0	0.025	0.025	27.123	-0.006	-0.006	0.000	0.000	0.000	0.000
109	A	113	HIS	0	-0.012	-0.004	21.659	-0.018	-0.018	0.000	0.000	0.000	0.000
110	A	114	ALA	0	0.013	0.003	21.640	0.012	0.012	0.000	0.000	0.000	0.000
111	A	115	LEU	0	-0.019	-0.002	20.097	-0.021	-0.021	0.000	0.000	0.000	0.000
112	A	116	GLU	-1	-0.750	-0.837	17.832	-0.244	-0.244	0.000	0.000	0.000	0.000
113	A	117	PHE	0	-0.021	-0.005	18.371	0.002	0.002	0.000	0.000	0.000	0.000
114	A	118	THR	0	0.018	-0.017	15.097	-0.008	-0.008	0.000	0.000	0.000	0.000
115	A	119	ALA	0	0.013	0.014	16.464	0.008	0.008	0.000	0.000	0.000	0.000
116	A	120	LEU	0	0.009	0.004	13.003	0.004	0.004	0.000	0.000	0.000	0.000

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