FMO DATABASE

FMODB ID: VQG41

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1162584.26014
FMO2-HF: Nuclear repulsion	1108509.603217
FMO2-HF: Total energy	-54074.656923
FMO2-MP2: Total energy	-54235.822819

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.
-19.411	-11.314	4.619	-4.691	-8.026	-0.012

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 : 0.036 / q_NPA : 0.005

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	0.049	0.007	3.244	0.669	2.580	0.061	-0.995	-0.977	-0.001
4	A	20	VAL	0	0.068	0.034	5.958	0.893	0.893	0.000	0.000	0.000	0.000
5	A	21	GLN	0	0.031	0.025	2.248	-4.401	-1.911	3.166	-2.182	-3.474	-0.016
6	A	22	ARG	1	0.860	0.937	2.619	-8.361	-4.869	1.377	-1.473	-3.396	0.004
7	A	23	ALA	0	0.016	0.006	3.873	-1.997	-1.793	0.015	-0.041	-0.179	0.001
8	A	24	LEU	0	0.031	0.028	6.691	-0.502	-0.502	0.000	0.000	0.000	0.000
9	A	25	GLY	0	0.016	0.005	5.005	-0.881	-0.881	0.000	0.000	0.000	0.000
10	A	26	LEU	0	-0.081	-0.052	5.931	-0.982	-0.982	0.000	0.000	0.000	0.000
11	A	27	LEU	0	-0.012	-0.014	8.503	-0.492	-0.492	0.000	0.000	0.000	0.000
12	A	28	VAL	0	-0.017	-0.003	8.379	-0.295	-0.295	0.000	0.000	0.000	0.000
13	A	29	HIS	0	-0.050	-0.003	9.911	-0.268	-0.268	0.000	0.000	0.000	0.000
14	A	30	ARG	1	0.787	0.851	11.424	-1.210	-1.210	0.000	0.000	0.000	0.000
15	A	31	GLU	-1	-0.725	-0.808	13.507	0.785	0.785	0.000	0.000	0.000	0.000
16	A	32	HIS	0	-0.058	-0.034	11.916	0.247	0.247	0.000	0.000	0.000	0.000
17	A	33	SER	0	0.035	0.030	15.330	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	34	LYS	1	0.867	0.907	15.834	-0.462	-0.462	0.000	0.000	0.000	0.000
19	A	35	LYS	1	0.887	0.946	16.046	-0.500	-0.500	0.000	0.000	0.000	0.000
20	A	36	GLU	-1	-0.845	-0.892	14.410	1.281	1.281	0.000	0.000	0.000	0.000
21	A	37	LEU	0	0.015	0.005	10.200	0.256	0.256	0.000	0.000	0.000	0.000
22	A	38	ASN	0	0.020	0.013	11.879	0.378	0.378	0.000	0.000	0.000	0.000
23	A	39	ARG	1	1.009	1.006	13.130	-1.026	-1.026	0.000	0.000	0.000	0.000
24	A	40	LYS	1	0.799	0.878	10.072	-1.750	-1.750	0.000	0.000	0.000	0.000
25	A	41	LEU	0	-0.048	-0.010	7.109	0.664	0.664	0.000	0.000	0.000	0.000
26	A	42	GLN	0	0.029	0.005	9.552	0.029	0.029	0.000	0.000	0.000	0.000
27	A	43	ALA	0	-0.059	-0.024	11.977	-0.048	-0.048	0.000	0.000	0.000	0.000
28	A	44	ARG	1	0.881	0.935	6.134	-3.892	-3.892	0.000	0.000	0.000	0.000
29	A	45	GLY	0	0.027	0.015	8.244	0.436	0.436	0.000	0.000	0.000	0.000
30	A	46	ILE	0	-0.077	-0.022	6.088	-0.105	-0.105	0.000	0.000	0.000	0.000
31	A	47	GLU	-1	-0.820	-0.924	10.515	0.741	0.741	0.000	0.000	0.000	0.000
32	A	48	PRO	0	0.025	0.005	13.818	0.063	0.063	0.000	0.000	0.000	0.000
33	A	49	GLU	-1	-0.900	-0.944	15.744	0.466	0.466	0.000	0.000	0.000	0.000
34	A	50	ALA	0	0.001	0.002	11.529	-0.020	-0.020	0.000	0.000	0.000	0.000
35	A	51	ALA	0	-0.036	-0.024	10.913	0.114	0.114	0.000	0.000	0.000	0.000
36	A	52	GLN	0	0.025	0.018	11.985	0.149	0.149	0.000	0.000	0.000	0.000
37	A	53	ALA	0	0.017	0.009	13.501	-0.028	-0.028	0.000	0.000	0.000	0.000
38	A	54	ALA	0	-0.032	-0.019	8.973	-0.073	-0.073	0.000	0.000	0.000	0.000
39	A	55	VAL	0	-0.023	-0.009	11.039	0.040	0.040	0.000	0.000	0.000	0.000
40	A	56	GLU	-1	-0.800	-0.901	13.177	0.561	0.561	0.000	0.000	0.000	0.000
41	A	57	ARG	1	0.769	0.870	11.378	-0.190	-0.190	0.000	0.000	0.000	0.000
42	A	58	LEU	0	-0.004	-0.011	8.964	-0.050	-0.050	0.000	0.000	0.000	0.000
43	A	59	ALA	0	-0.024	0.002	13.494	-0.050	-0.050	0.000	0.000	0.000	0.000
44	A	60	GLY	0	0.002	0.009	17.111	-0.064	-0.064	0.000	0.000	0.000	0.000
45	A	61	GLU	-1	-0.861	-0.908	13.140	0.118	0.118	0.000	0.000	0.000	0.000
46	A	62	GLY	0	0.015	0.018	16.883	-0.031	-0.031	0.000	0.000	0.000	0.000
47	A	63	TRP	0	0.008	0.000	12.716	0.056	0.056	0.000	0.000	0.000	0.000
48	A	64	GLN	0	-0.055	-0.043	14.344	0.012	0.012	0.000	0.000	0.000	0.000
49	A	65	ASP	-1	-0.763	-0.887	15.964	0.324	0.324	0.000	0.000	0.000	0.000
50	A	66	ASP	-1	-0.774	-0.904	19.487	0.717	0.717	0.000	0.000	0.000	0.000
51	A	67	VAL	0	0.004	0.009	21.110	-0.010	-0.010	0.000	0.000	0.000	0.000
52	A	68	ARG	1	0.779	0.851	17.054	-0.498	-0.498	0.000	0.000	0.000	0.000
53	A	69	PHE	0	-0.016	-0.002	18.107	0.007	0.007	0.000	0.000	0.000	0.000
54	A	70	ALA	0	0.033	0.025	20.524	-0.013	-0.013	0.000	0.000	0.000	0.000
55	A	71	ALA	0	0.057	0.022	23.891	-0.017	-0.017	0.000	0.000	0.000	0.000
56	A	72	SER	0	-0.113	-0.071	20.773	-0.008	-0.008	0.000	0.000	0.000	0.000
57	A	73	VAL	0	-0.008	-0.003	21.414	-0.013	-0.013	0.000	0.000	0.000	0.000
58	A	74	VAL	0	0.026	0.003	23.608	-0.019	-0.019	0.000	0.000	0.000	0.000
59	A	75	ARG	1	1.006	1.019	22.843	-0.317	-0.317	0.000	0.000	0.000	0.000
60	A	76	ASN	0	0.015	0.009	21.349	-0.046	-0.046	0.000	0.000	0.000	0.000
61	A	77	ARG	1	0.782	0.884	20.909	-0.531	-0.531	0.000	0.000	0.000	0.000
62	A	78	ALA	0	0.056	0.033	27.077	-0.016	-0.016	0.000	0.000	0.000	0.000
63	A	79	SER	0	-0.039	-0.030	27.664	-0.011	-0.011	0.000	0.000	0.000	0.000
64	A	80	SER	0	-0.046	-0.035	26.506	-0.008	-0.008	0.000	0.000	0.000	0.000
65	A	81	GLY	0	0.021	0.016	28.620	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	82	TYR	0	-0.059	-0.033	26.464	0.002	0.002	0.000	0.000	0.000	0.000
67	A	83	GLY	0	0.059	0.027	31.357	-0.011	-0.011	0.000	0.000	0.000	0.000
68	A	84	PRO	0	0.017	-0.003	32.382	0.021	0.021	0.000	0.000	0.000	0.000
69	A	85	LEU	0	-0.013	-0.007	33.156	0.011	0.011	0.000	0.000	0.000	0.000
70	A	86	HIS	0	-0.008	-0.003	26.256	-0.007	-0.007	0.000	0.000	0.000	0.000
71	A	87	ILE	0	-0.015	0.001	27.656	0.030	0.030	0.000	0.000	0.000	0.000
72	A	88	ARG	1	0.936	0.953	28.273	-0.228	-0.228	0.000	0.000	0.000	0.000
73	A	89	ALA	0	0.013	0.019	29.673	0.014	0.014	0.000	0.000	0.000	0.000
74	A	90	GLU	-1	-0.774	-0.843	22.774	0.574	0.574	0.000	0.000	0.000	0.000
75	A	91	LEU	0	0.001	0.010	24.083	0.054	0.054	0.000	0.000	0.000	0.000
76	A	92	GLY	0	0.089	0.054	25.505	0.018	0.018	0.000	0.000	0.000	0.000
77	A	93	THR	0	-0.112	-0.069	24.073	0.033	0.033	0.000	0.000	0.000	0.000
78	A	94	HIS	0	0.000	-0.002	18.794	0.091	0.091	0.000	0.000	0.000	0.000
79	A	95	GLY	0	-0.068	-0.035	22.193	0.037	0.037	0.000	0.000	0.000	0.000
80	A	96	LEU	0	-0.022	0.009	23.119	-0.018	-0.018	0.000	0.000	0.000	0.000
81	A	97	ASP	-1	-0.772	-0.884	26.577	0.306	0.306	0.000	0.000	0.000	0.000
82	A	98	SER	0	-0.003	-0.039	30.290	0.007	0.007	0.000	0.000	0.000	0.000
83	A	99	ASP	-1	-0.889	-0.902	32.787	0.217	0.217	0.000	0.000	0.000	0.000
84	A	100	ALA	0	0.022	0.007	27.610	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	101	VAL	0	-0.034	-0.022	28.362	0.005	0.005	0.000	0.000	0.000	0.000
86	A	102	SER	0	-0.043	-0.043	29.967	-0.009	-0.009	0.000	0.000	0.000	0.000
87	A	103	ALA	0	0.014	0.015	30.737	-0.012	-0.012	0.000	0.000	0.000	0.000
88	A	104	ALA	0	0.013	0.014	27.506	-0.005	-0.005	0.000	0.000	0.000	0.000
89	A	105	MET	0	-0.070	-0.032	29.271	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	106	ALA	0	-0.035	-0.009	31.976	-0.011	-0.011	0.000	0.000	0.000	0.000
91	A	107	THR	0	-0.038	-0.023	29.032	-0.007	-0.007	0.000	0.000	0.000	0.000
92	A	108	PHE	0	-0.057	-0.033	31.956	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	109	GLU	-1	-0.907	-0.939	33.403	0.139	0.139	0.000	0.000	0.000	0.000
94	A	110	GLY	0	-0.029	-0.018	36.156	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	111	ASP	-1	-0.844	-0.914	37.221	0.144	0.144	0.000	0.000	0.000	0.000
96	A	112	TRP	0	0.038	-0.012	31.580	0.007	0.007	0.000	0.000	0.000	0.000
97	A	113	THR	0	-0.019	-0.024	37.992	0.003	0.003	0.000	0.000	0.000	0.000
98	A	114	GLU	-1	-0.772	-0.862	40.354	0.121	0.121	0.000	0.000	0.000	0.000
99	A	115	ASN	0	-0.031	-0.013	33.679	-0.009	-0.009	0.000	0.000	0.000	0.000
100	A	116	ALA	0	-0.038	-0.015	37.219	0.005	0.005	0.000	0.000	0.000	0.000
101	A	117	LEU	0	0.009	-0.009	38.958	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	118	ASP	-1	-0.768	-0.847	36.874	0.141	0.141	0.000	0.000	0.000	0.000
103	A	119	LEU	0	-0.081	-0.038	34.196	0.001	0.001	0.000	0.000	0.000	0.000
104	A	120	ILE	0	-0.060	-0.025	37.384	0.000	0.000	0.000	0.000	0.000	0.000
105	A	121	ARG	1	0.830	0.882	40.451	-0.123	-0.123	0.000	0.000	0.000	0.000
106	A	122	ARG	1	0.821	0.884	33.938	-0.172	-0.172	0.000	0.000	0.000	0.000
107	A	123	ARG	1	0.845	0.940	37.381	-0.160	-0.160	0.000	0.000	0.000	0.000
108	A	124	PHE	0	-0.057	-0.048	39.982	0.001	0.001	0.000	0.000	0.000	0.000
109	A	125	GLY	0	0.049	0.047	43.236	-0.006	-0.006	0.000	0.000	0.000	0.000
110	A	126	GLU	-1	-0.875	-0.962	44.728	0.104	0.104	0.000	0.000	0.000	0.000
111	A	127	ASP	-1	-0.893	-0.940	47.237	0.084	0.084	0.000	0.000	0.000	0.000
112	A	128	GLY	0	-0.022	0.000	46.004	0.003	0.003	0.000	0.000	0.000	0.000
113	A	129	PRO	0	-0.074	-0.042	45.233	-0.002	-0.002	0.000	0.000	0.000	0.000
114	A	130	VAL	0	0.062	0.028	47.352	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	131	ASP	-1	-0.792	-0.879	50.146	0.107	0.107	0.000	0.000	0.000	0.000
116	A	132	LEU	0	0.007	-0.016	50.021	0.006	0.006	0.000	0.000	0.000	0.000
117	A	133	ALA	0	-0.011	-0.007	47.673	0.006	0.006	0.000	0.000	0.000	0.000
118	A	134	GLN	0	0.000	-0.015	45.697	0.011	0.011	0.000	0.000	0.000	0.000
119	A	135	ARG	1	0.898	0.937	45.122	-0.102	-0.102	0.000	0.000	0.000	0.000
120	A	136	ARG	1	0.943	0.972	45.632	-0.118	-0.118	0.000	0.000	0.000	0.000
121	A	137	LYS	1	0.830	0.905	39.681	-0.172	-0.172	0.000	0.000	0.000	0.000
122	A	138	ALA	0	0.038	0.025	40.770	0.011	0.011	0.000	0.000	0.000	0.000
123	A	139	ALA	0	0.033	0.009	40.917	0.008	0.008	0.000	0.000	0.000	0.000
124	A	140	ASP	-1	-0.782	-0.851	38.854	0.217	0.217	0.000	0.000	0.000	0.000
125	A	141	LEU	0	-0.046	-0.017	34.879	0.015	0.015	0.000	0.000	0.000	0.000
126	A	142	LEU	0	0.020	0.013	35.960	0.015	0.015	0.000	0.000	0.000	0.000
127	A	143	ALA	0	0.007	0.000	36.770	0.010	0.010	0.000	0.000	0.000	0.000
128	A	144	ARG	1	0.810	0.870	33.640	-0.226	-0.226	0.000	0.000	0.000	0.000
129	A	145	ARG	1	0.827	0.920	29.641	-0.265	-0.265	0.000	0.000	0.000	0.000
130	A	146	GLY	0	0.020	0.016	32.898	0.009	0.009	0.000	0.000	0.000	0.000
131	A	147	PHE	0	-0.001	-0.006	34.568	0.000	0.000	0.000	0.000	0.000	0.000
132	A	148	ASP	-1	-0.772	-0.841	37.233	0.174	0.174	0.000	0.000	0.000	0.000
133	A	149	GLY	0	0.033	-0.004	40.232	-0.005	-0.005	0.000	0.000	0.000	0.000
134	A	150	ASN	0	-0.002	0.004	43.595	-0.011	-0.011	0.000	0.000	0.000	0.000
135	A	151	SER	0	0.034	-0.013	40.980	-0.009	-0.009	0.000	0.000	0.000	0.000
136	A	152	ILE	0	-0.024	0.000	39.854	-0.005	-0.005	0.000	0.000	0.000	0.000
137	A	153	ARG	1	0.884	0.953	43.259	-0.141	-0.141	0.000	0.000	0.000	0.000
138	A	154	LEU	0	0.041	0.029	45.939	-0.005	-0.005	0.000	0.000	0.000	0.000
139	A	155	ALA	0	0.043	0.021	43.040	-0.005	-0.005	0.000	0.000	0.000	0.000
140	A	156	THR	0	-0.048	-0.048	44.406	-0.005	-0.005	0.000	0.000	0.000	0.000
141	A	157	ARG	1	0.843	0.929	46.340	-0.115	-0.115	0.000	0.000	0.000	0.000
142	A	158	PHE	0	-0.023	0.009	49.136	-0.005	-0.005	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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