FMO DATABASE

FMODB ID: 5J6ZZ

Calculation Name: 3DFG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DFG

Chain ID: A

ChEMBL ID:

UniProt ID: Q8P9X1

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	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	142
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1160367.194712
FMO2-HF: Nuclear repulsion	1106293.328896
FMO2-HF: Total energy	-54073.865816
FMO2-MP2: Total energy	-54235.095561

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:17:GLN)

Summations of interaction energy for fragment #1(A:17:GLN)

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.
-23.11	-15.506	5.356	-5.037	-7.922	-0.004

Interaction energy analysis for fragmet #1(A:17:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : -0.012

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	19	PRO	0	0.067	0.010	3.393	0.914	2.632	0.048	-0.842	-0.924	0.001
4	A	20	VAL	0	0.069	0.036	6.094	0.953	0.953	0.000	0.000	0.000	0.000
5	A	21	GLN	0	0.026	0.019	2.067	-4.217	-2.141	3.720	-2.221	-3.575	-0.016
6	A	22	ARG	1	0.891	0.958	2.378	-11.825	-8.245	1.584	-1.908	-3.256	0.011
7	A	23	ALA	0	0.015	0.004	4.272	-0.930	-0.700	0.004	-0.066	-0.167	0.000
8	A	24	LEU	0	0.031	0.025	6.593	-0.196	-0.196	0.000	0.000	0.000	0.000
9	A	25	GLY	0	0.017	0.003	5.156	-0.557	-0.557	0.000	0.000	0.000	0.000
10	A	26	LEU	0	-0.087	-0.049	6.015	-0.452	-0.452	0.000	0.000	0.000	0.000
11	A	27	LEU	0	-0.003	-0.015	8.803	-0.391	-0.391	0.000	0.000	0.000	0.000
12	A	28	VAL	0	-0.022	0.007	8.058	-0.252	-0.252	0.000	0.000	0.000	0.000
13	A	29	HIS	0	-0.055	-0.007	10.530	-0.174	-0.174	0.000	0.000	0.000	0.000
14	A	30	ARG	1	0.811	0.888	12.095	-1.306	-1.306	0.000	0.000	0.000	0.000
15	A	31	GLU	-1	-0.837	-0.902	14.056	0.642	0.642	0.000	0.000	0.000	0.000
16	A	32	HIS	0	-0.079	-0.044	12.369	0.352	0.352	0.000	0.000	0.000	0.000
17	A	33	SER	0	0.040	0.014	15.728	-0.061	-0.061	0.000	0.000	0.000	0.000
18	A	34	LYS	1	0.969	0.968	16.348	-0.263	-0.263	0.000	0.000	0.000	0.000
19	A	35	LYS	1	0.912	0.963	16.422	-0.500	-0.500	0.000	0.000	0.000	0.000
20	A	36	GLU	-1	-0.863	-0.934	14.780	1.264	1.264	0.000	0.000	0.000	0.000
21	A	37	LEU	0	0.008	-0.005	10.811	0.268	0.268	0.000	0.000	0.000	0.000
22	A	38	ASN	0	0.051	0.054	11.990	0.327	0.327	0.000	0.000	0.000	0.000
23	A	39	ARG	1	1.013	1.006	13.469	-1.167	-1.167	0.000	0.000	0.000	0.000
24	A	40	LYS	1	0.843	0.911	10.711	-1.958	-1.958	0.000	0.000	0.000	0.000
25	A	41	LEU	0	-0.025	-0.012	7.225	0.565	0.565	0.000	0.000	0.000	0.000
26	A	42	GLN	0	0.014	-0.014	9.786	0.082	0.082	0.000	0.000	0.000	0.000
27	A	43	ALA	0	-0.049	-0.008	12.241	-0.068	-0.068	0.000	0.000	0.000	0.000
28	A	44	ARG	1	0.853	0.920	6.145	-5.256	-5.256	0.000	0.000	0.000	0.000
29	A	45	GLY	0	0.031	0.011	8.977	0.197	0.197	0.000	0.000	0.000	0.000
30	A	46	ILE	0	-0.085	-0.020	6.283	-0.153	-0.153	0.000	0.000	0.000	0.000
31	A	47	GLU	-1	-0.839	-0.929	10.584	0.525	0.525	0.000	0.000	0.000	0.000
32	A	48	PRO	0	0.035	0.009	13.626	0.035	0.035	0.000	0.000	0.000	0.000
33	A	49	GLU	-1	-0.896	-0.947	15.732	0.217	0.217	0.000	0.000	0.000	0.000
34	A	50	ALA	0	0.002	0.004	11.624	-0.044	-0.044	0.000	0.000	0.000	0.000
35	A	51	ALA	0	-0.045	-0.029	11.187	0.031	0.031	0.000	0.000	0.000	0.000
36	A	52	GLN	0	-0.002	-0.008	12.243	0.142	0.142	0.000	0.000	0.000	0.000
37	A	53	ALA	0	0.012	0.011	13.812	-0.032	-0.032	0.000	0.000	0.000	0.000
38	A	54	ALA	0	-0.035	-0.019	9.353	-0.090	-0.090	0.000	0.000	0.000	0.000
39	A	55	VAL	0	-0.014	-0.012	11.377	0.019	0.019	0.000	0.000	0.000	0.000
40	A	56	GLU	-1	-0.873	-0.947	13.506	0.264	0.264	0.000	0.000	0.000	0.000
41	A	57	ARG	1	0.922	0.978	11.168	0.381	0.381	0.000	0.000	0.000	0.000
42	A	58	LEU	0	-0.002	-0.011	9.201	-0.035	-0.035	0.000	0.000	0.000	0.000
43	A	59	ALA	0	-0.045	-0.014	13.524	-0.022	-0.022	0.000	0.000	0.000	0.000
44	A	60	GLY	0	0.003	0.006	17.115	-0.037	-0.037	0.000	0.000	0.000	0.000
45	A	61	GLU	-1	-1.013	-1.012	13.161	-0.445	-0.445	0.000	0.000	0.000	0.000
46	A	62	GLY	0	0.005	0.016	16.902	-0.038	-0.038	0.000	0.000	0.000	0.000
47	A	63	TRP	0	-0.011	-0.012	12.032	0.074	0.074	0.000	0.000	0.000	0.000
48	A	64	GLN	0	-0.074	-0.055	14.732	0.037	0.037	0.000	0.000	0.000	0.000
49	A	65	ASP	-1	-0.785	-0.894	16.579	0.210	0.210	0.000	0.000	0.000	0.000
50	A	66	ASP	-1	-0.771	-0.903	20.099	0.605	0.605	0.000	0.000	0.000	0.000
51	A	67	VAL	0	-0.005	0.014	21.784	0.009	0.009	0.000	0.000	0.000	0.000
52	A	68	ARG	1	0.934	0.963	17.467	-0.316	-0.316	0.000	0.000	0.000	0.000
53	A	69	PHE	0	-0.017	0.000	18.646	0.022	0.022	0.000	0.000	0.000	0.000
54	A	70	ALA	0	0.044	0.035	21.028	0.014	0.014	0.000	0.000	0.000	0.000
55	A	71	ALA	0	0.062	0.029	24.456	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	72	SER	0	-0.120	-0.086	21.122	0.011	0.011	0.000	0.000	0.000	0.000
57	A	73	VAL	0	-0.010	-0.002	21.986	0.005	0.005	0.000	0.000	0.000	0.000
58	A	74	VAL	0	0.022	0.011	24.043	-0.007	-0.007	0.000	0.000	0.000	0.000
59	A	75	ARG	1	1.008	1.008	22.606	-0.337	-0.337	0.000	0.000	0.000	0.000
60	A	76	ASN	0	0.000	-0.019	21.393	-0.060	-0.060	0.000	0.000	0.000	0.000
61	A	77	ARG	1	0.801	0.897	21.116	-0.596	-0.596	0.000	0.000	0.000	0.000
62	A	78	ALA	0	0.032	0.025	27.267	-0.015	-0.015	0.000	0.000	0.000	0.000
63	A	79	SER	0	-0.055	-0.019	27.676	-0.009	-0.009	0.000	0.000	0.000	0.000
64	A	80	SER	0	-0.031	-0.020	27.009	0.001	0.001	0.000	0.000	0.000	0.000
65	A	81	GLY	0	-0.019	-0.016	29.112	0.008	0.008	0.000	0.000	0.000	0.000
66	A	82	TYR	0	-0.055	-0.022	27.429	0.005	0.005	0.000	0.000	0.000	0.000
67	A	83	GLY	0	0.036	0.014	31.495	-0.013	-0.013	0.000	0.000	0.000	0.000
68	A	84	PRO	0	0.030	-0.002	32.580	0.022	0.022	0.000	0.000	0.000	0.000
69	A	85	LEU	0	-0.006	-0.005	33.399	0.008	0.008	0.000	0.000	0.000	0.000
70	A	86	HIS	0	0.002	0.017	26.648	-0.008	-0.008	0.000	0.000	0.000	0.000
71	A	87	ILE	0	0.018	0.011	27.992	0.029	0.029	0.000	0.000	0.000	0.000
72	A	88	ARG	1	0.959	0.982	28.622	-0.226	-0.226	0.000	0.000	0.000	0.000
73	A	89	ALA	0	0.007	0.012	30.007	0.009	0.009	0.000	0.000	0.000	0.000
74	A	90	GLU	-1	-0.812	-0.894	23.174	0.622	0.622	0.000	0.000	0.000	0.000
75	A	91	LEU	0	0.004	0.010	24.694	0.046	0.046	0.000	0.000	0.000	0.000
76	A	92	GLY	0	0.076	0.049	25.953	0.010	0.010	0.000	0.000	0.000	0.000
77	A	93	THR	0	-0.108	-0.064	24.419	0.026	0.026	0.000	0.000	0.000	0.000
78	A	94	HIS	0	-0.014	-0.002	19.104	0.081	0.081	0.000	0.000	0.000	0.000
79	A	95	GLY	0	-0.054	-0.028	22.889	0.010	0.010	0.000	0.000	0.000	0.000
80	A	96	LEU	0	-0.017	0.013	23.602	-0.026	-0.026	0.000	0.000	0.000	0.000
81	A	97	ASP	-1	-0.815	-0.909	26.988	0.250	0.250	0.000	0.000	0.000	0.000
82	A	98	SER	0	0.018	-0.020	30.696	0.005	0.005	0.000	0.000	0.000	0.000
83	A	99	ASP	-1	-0.889	-0.937	33.477	0.183	0.183	0.000	0.000	0.000	0.000
84	A	100	ALA	0	0.025	0.018	28.095	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	101	VAL	0	-0.049	-0.031	29.251	0.009	0.009	0.000	0.000	0.000	0.000
86	A	102	SER	0	-0.061	-0.039	30.743	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	103	ALA	0	0.020	0.021	31.004	-0.008	-0.008	0.000	0.000	0.000	0.000
88	A	104	ALA	0	0.014	0.011	28.208	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	105	MET	0	-0.088	-0.039	29.964	0.005	0.005	0.000	0.000	0.000	0.000
90	A	106	ALA	0	-0.018	-0.001	32.664	-0.007	-0.007	0.000	0.000	0.000	0.000
91	A	107	THR	0	-0.066	-0.037	29.775	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	108	PHE	0	-0.076	-0.034	32.534	0.004	0.004	0.000	0.000	0.000	0.000
93	A	109	GLU	-1	-0.880	-0.945	33.658	0.142	0.142	0.000	0.000	0.000	0.000
94	A	110	GLY	0	-0.050	-0.012	35.856	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	111	ASP	-1	-0.799	-0.901	37.389	0.158	0.158	0.000	0.000	0.000	0.000
96	A	112	TRP	0	0.026	-0.023	31.735	0.011	0.011	0.000	0.000	0.000	0.000
97	A	113	THR	0	-0.013	-0.012	38.241	0.006	0.006	0.000	0.000	0.000	0.000
98	A	114	GLU	-1	-0.878	-0.946	40.608	0.154	0.154	0.000	0.000	0.000	0.000
99	A	115	ASN	0	-0.008	0.000	34.321	-0.010	-0.010	0.000	0.000	0.000	0.000
100	A	116	ALA	0	-0.043	-0.015	37.656	0.009	0.009	0.000	0.000	0.000	0.000
101	A	117	LEU	0	-0.006	-0.013	39.248	0.001	0.001	0.000	0.000	0.000	0.000
102	A	118	ASP	-1	-0.820	-0.889	36.846	0.205	0.205	0.000	0.000	0.000	0.000
103	A	119	LEU	0	-0.070	-0.025	34.882	0.006	0.006	0.000	0.000	0.000	0.000
104	A	120	ILE	0	-0.062	-0.041	37.853	0.001	0.001	0.000	0.000	0.000	0.000
105	A	121	ARG	1	0.953	0.993	41.208	-0.158	-0.158	0.000	0.000	0.000	0.000
106	A	122	ARG	1	0.849	0.914	33.819	-0.246	-0.246	0.000	0.000	0.000	0.000
107	A	123	ARG	1	0.862	0.949	37.175	-0.234	-0.234	0.000	0.000	0.000	0.000
108	A	124	PHE	0	-0.058	-0.061	40.183	0.002	0.002	0.000	0.000	0.000	0.000
109	A	125	GLY	0	0.063	0.054	43.455	-0.007	-0.007	0.000	0.000	0.000	0.000
110	A	126	GLU	-1	-0.899	-0.978	45.259	0.137	0.137	0.000	0.000	0.000	0.000
111	A	127	ASP	-1	-0.928	-0.948	47.563	0.117	0.117	0.000	0.000	0.000	0.000
112	A	128	GLY	0	-0.097	-0.041	46.153	0.001	0.001	0.000	0.000	0.000	0.000
113	A	129	PRO	0	-0.096	-0.044	45.569	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	130	VAL	0	0.098	0.042	47.638	-0.005	-0.005	0.000	0.000	0.000	0.000
115	A	131	ASP	-1	-0.840	-0.919	50.053	0.145	0.145	0.000	0.000	0.000	0.000
116	A	132	LEU	0	0.006	-0.017	50.252	0.007	0.007	0.000	0.000	0.000	0.000
117	A	133	ALA	0	-0.001	-0.004	47.912	0.007	0.007	0.000	0.000	0.000	0.000
118	A	134	GLN	0	0.051	0.018	45.779	0.010	0.010	0.000	0.000	0.000	0.000
119	A	135	ARG	1	0.960	0.992	45.320	-0.135	-0.135	0.000	0.000	0.000	0.000
120	A	136	ARG	1	0.942	0.970	45.832	-0.151	-0.151	0.000	0.000	0.000	0.000
121	A	137	LYS	1	0.925	0.977	39.888	-0.218	-0.218	0.000	0.000	0.000	0.000
122	A	138	ALA	0	0.021	0.012	41.102	0.014	0.014	0.000	0.000	0.000	0.000
123	A	139	ALA	0	0.023	0.005	41.204	0.008	0.008	0.000	0.000	0.000	0.000
124	A	140	ASP	-1	-0.856	-0.920	38.875	0.271	0.271	0.000	0.000	0.000	0.000
125	A	141	LEU	0	-0.057	-0.031	35.055	0.017	0.017	0.000	0.000	0.000	0.000
126	A	142	LEU	0	0.024	0.008	36.335	0.017	0.017	0.000	0.000	0.000	0.000
127	A	143	ALA	0	0.022	0.015	37.296	0.007	0.007	0.000	0.000	0.000	0.000
128	A	144	ARG	1	0.836	0.912	33.653	-0.291	-0.291	0.000	0.000	0.000	0.000
129	A	145	ARG	1	0.842	0.932	31.207	-0.327	-0.327	0.000	0.000	0.000	0.000
130	A	146	GLY	0	0.049	0.037	33.042	0.010	0.010	0.000	0.000	0.000	0.000
131	A	147	PHE	0	-0.019	-0.010	34.787	-0.004	-0.004	0.000	0.000	0.000	0.000
132	A	148	ASP	-1	-0.784	-0.858	37.745	0.194	0.194	0.000	0.000	0.000	0.000
133	A	149	GLY	0	0.024	-0.009	40.734	-0.004	-0.004	0.000	0.000	0.000	0.000
134	A	150	ASN	0	-0.020	-0.012	44.137	-0.010	-0.010	0.000	0.000	0.000	0.000
135	A	151	SER	0	0.034	-0.019	41.380	-0.008	-0.008	0.000	0.000	0.000	0.000
136	A	152	ILE	0	-0.025	-0.001	40.188	-0.003	-0.003	0.000	0.000	0.000	0.000
137	A	153	ARG	1	0.928	0.974	43.661	-0.160	-0.160	0.000	0.000	0.000	0.000
138	A	154	LEU	0	0.047	0.039	45.996	-0.005	-0.005	0.000	0.000	0.000	0.000
139	A	155	ALA	0	0.048	0.016	43.487	-0.005	-0.005	0.000	0.000	0.000	0.000
140	A	156	THR	0	-0.089	-0.047	44.860	-0.003	-0.003	0.000	0.000	0.000	0.000
141	A	157	ARG	1	0.907	0.946	46.315	-0.148	-0.148	0.000	0.000	0.000	0.000
142	A	158	PHE	0	-0.027	-0.009	49.696	-0.005	-0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:17:GLN)