FMO DATABASE

FMODB ID: GNVG1

Calculation Name: 3QD7-X-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3QD7

Chain ID: X

ChEMBL ID:

UniProt ID: P76053

Base Structure: X-ray

Registration Date: 2023-03-14

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	131
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1180709.431719
FMO2-HF: Nuclear repulsion	1128966.759067
FMO2-HF: Total energy	-51742.672652
FMO2-MP2: Total energy	-51894.37672

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(X:40:ASP)

Summations of interaction energy for fragment #1(X:40:ASP)

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.
0.30600000000001	4.74	4.921	-3.81	-5.545	-0.008

Interaction energy analysis for fragmet #1(X:40:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.905 / q_NPA : -0.952

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	X	42	LEU	0	0.005	0.011	2.594	-13.212	-8.917	0.630	-1.866	-3.059	0.014
4	X	43	GLN	0	0.050	0.008	4.059	-2.311	-2.249	-0.001	0.001	-0.062	0.000
5	X	44	LEU	0	-0.041	-0.014	5.109	-2.937	-2.937	0.000	0.000	0.000	0.000
6	X	45	ASP	-1	-0.839	-0.918	2.348	53.689	53.766	4.292	-1.945	-2.424	-0.022
7	X	46	ASN	0	-0.128	-0.075	5.402	-2.260	-2.260	0.000	0.000	0.000	0.000
8	X	47	PHE	0	0.043	0.009	7.793	-1.969	-1.969	0.000	0.000	0.000	0.000
9	X	48	LEU	0	-0.060	-0.003	10.500	-1.808	-1.808	0.000	0.000	0.000	0.000
10	X	49	THR	0	0.003	0.003	13.206	-0.489	-0.489	0.000	0.000	0.000	0.000
11	X	50	THR	0	-0.033	-0.032	16.398	-0.510	-0.510	0.000	0.000	0.000	0.000
12	X	51	GLY	0	0.001	0.008	19.440	-0.072	-0.072	0.000	0.000	0.000	0.000
13	X	52	PHE	0	0.022	-0.020	22.885	0.090	0.090	0.000	0.000	0.000	0.000
14	X	53	LEU	0	-0.060	-0.014	23.098	0.045	0.045	0.000	0.000	0.000	0.000
15	X	54	ASP	-1	-0.816	-0.903	24.790	11.461	11.461	0.000	0.000	0.000	0.000
16	X	55	ILE	0	-0.081	-0.054	27.010	0.119	0.119	0.000	0.000	0.000	0.000
17	X	56	ILE	0	0.043	0.019	26.058	-0.277	-0.277	0.000	0.000	0.000	0.000
18	X	57	PRO	0	0.028	0.032	30.024	-0.042	-0.042	0.000	0.000	0.000	0.000
19	X	58	LEU	0	-0.033	-0.005	32.688	0.139	0.139	0.000	0.000	0.000	0.000
20	X	59	SER	0	-0.065	-0.027	34.313	0.072	0.072	0.000	0.000	0.000	0.000
21	X	60	GLN	0	0.022	0.018	32.135	0.109	0.109	0.000	0.000	0.000	0.000
22	X	61	PRO	0	0.030	0.033	30.960	0.228	0.228	0.000	0.000	0.000	0.000
23	X	62	LEU	0	0.010	-0.011	24.013	0.078	0.078	0.000	0.000	0.000	0.000
24	X	63	GLU	-1	-0.964	-0.997	26.954	9.510	9.510	0.000	0.000	0.000	0.000
25	X	64	PHE	0	0.024	0.025	20.374	0.025	0.025	0.000	0.000	0.000	0.000
26	X	65	ARG	1	0.930	0.951	24.413	-10.031	-10.031	0.000	0.000	0.000	0.000
27	X	66	ARG	1	0.892	0.968	16.782	-16.011	-16.011	0.000	0.000	0.000	0.000
28	X	67	GLU	-1	-0.908	-0.964	23.778	11.347	11.347	0.000	0.000	0.000	0.000
29	X	68	GLY	0	-0.011	-0.008	24.750	0.390	0.390	0.000	0.000	0.000	0.000
30	X	69	LEU	0	-0.053	-0.015	22.129	0.264	0.264	0.000	0.000	0.000	0.000
31	X	70	GLN	0	0.017	0.006	25.319	-0.089	-0.089	0.000	0.000	0.000	0.000
32	X	71	HIS	0	0.042	-0.001	27.309	0.221	0.221	0.000	0.000	0.000	0.000
33	X	72	GLY	0	0.028	0.017	29.035	-0.112	-0.112	0.000	0.000	0.000	0.000
34	X	73	VAL	0	-0.061	-0.024	23.083	0.075	0.075	0.000	0.000	0.000	0.000
35	X	74	LEU	0	0.044	0.005	25.410	0.258	0.258	0.000	0.000	0.000	0.000
36	X	75	ASP	-1	-0.854	-0.922	27.550	9.369	9.369	0.000	0.000	0.000	0.000
37	X	76	LYS	1	0.765	0.904	19.904	-14.198	-14.198	0.000	0.000	0.000	0.000
38	X	77	LEU	0	-0.016	-0.009	23.081	0.230	0.230	0.000	0.000	0.000	0.000
39	X	78	ARG	1	0.973	0.992	25.877	-8.887	-8.887	0.000	0.000	0.000	0.000
40	X	79	SER	0	-0.051	-0.048	29.228	-0.216	-0.216	0.000	0.000	0.000	0.000
41	X	80	GLY	0	0.039	0.066	25.395	0.018	0.018	0.000	0.000	0.000	0.000
42	X	81	LYS	1	0.919	0.955	24.650	-11.931	-11.931	0.000	0.000	0.000	0.000
43	X	82	TYR	0	-0.005	-0.020	22.072	0.694	0.694	0.000	0.000	0.000	0.000
44	X	83	PRO	0	-0.033	-0.009	21.724	-0.358	-0.358	0.000	0.000	0.000	0.000
45	X	84	GLN	0	0.078	0.027	22.447	0.079	0.079	0.000	0.000	0.000	0.000
46	X	85	GLN	0	0.049	0.026	18.227	-0.200	-0.200	0.000	0.000	0.000	0.000
47	X	86	ALA	0	-0.029	-0.002	17.510	0.952	0.952	0.000	0.000	0.000	0.000
48	X	87	SER	0	-0.060	-0.036	18.987	-0.400	-0.400	0.000	0.000	0.000	0.000
49	X	88	LEU	0	0.064	0.049	15.620	0.237	0.237	0.000	0.000	0.000	0.000
50	X	89	ASN	0	-0.020	-0.024	18.894	-0.606	-0.606	0.000	0.000	0.000	0.000
51	X	90	LEU	0	0.058	0.013	17.718	0.287	0.287	0.000	0.000	0.000	0.000
52	X	91	LEU	0	-0.047	-0.018	21.415	-0.441	-0.441	0.000	0.000	0.000	0.000
53	X	92	ARG	1	0.899	0.937	24.420	-10.379	-10.379	0.000	0.000	0.000	0.000
54	X	93	GLN	0	0.074	0.057	20.341	0.032	0.032	0.000	0.000	0.000	0.000
55	X	94	PRO	0	0.042	0.027	20.953	-0.259	-0.259	0.000	0.000	0.000	0.000
56	X	95	VAL	0	0.065	0.018	20.028	0.510	0.510	0.000	0.000	0.000	0.000
57	X	96	GLU	-1	-0.812	-0.903	15.073	18.390	18.390	0.000	0.000	0.000	0.000
58	X	97	GLU	-1	-0.938	-0.970	16.061	18.114	18.114	0.000	0.000	0.000	0.000
59	X	98	CYS	0	-0.050	-0.017	15.941	0.618	0.618	0.000	0.000	0.000	0.000
60	X	99	ARG	1	0.848	0.907	11.968	-19.478	-19.478	0.000	0.000	0.000	0.000
61	X	100	LYS	1	0.933	0.974	11.649	-17.552	-17.552	0.000	0.000	0.000	0.000
62	X	101	MET	0	-0.009	-0.002	11.149	1.317	1.317	0.000	0.000	0.000	0.000
63	X	102	VAL	0	0.019	0.009	12.716	0.617	0.617	0.000	0.000	0.000	0.000
64	X	103	PHE	0	0.026	0.026	5.148	-0.271	-0.271	0.000	0.000	0.000	0.000
65	X	104	SER	0	-0.017	-0.004	7.843	0.949	0.949	0.000	0.000	0.000	0.000
66	X	105	PHE	0	-0.009	-0.009	8.921	0.723	0.723	0.000	0.000	0.000	0.000
67	X	106	ILE	0	-0.030	-0.016	10.448	-0.341	-0.341	0.000	0.000	0.000	0.000
68	X	107	GLN	0	0.023	0.010	5.200	1.736	1.736	0.000	0.000	0.000	0.000
69	X	108	GLN	0	-0.007	0.011	7.391	0.909	0.909	0.000	0.000	0.000	0.000
70	X	109	ALA	0	-0.011	-0.017	9.358	-1.101	-1.101	0.000	0.000	0.000	0.000
71	X	110	LEU	0	-0.035	-0.016	8.931	-1.529	-1.529	0.000	0.000	0.000	0.000
72	X	111	ALA	0	0.000	0.012	7.399	-1.055	-1.055	0.000	0.000	0.000	0.000
73	X	112	ASP	-1	-0.911	-0.945	9.422	21.471	21.471	0.000	0.000	0.000	0.000
74	X	113	GLY	0	-0.070	-0.034	12.787	-1.905	-1.905	0.000	0.000	0.000	0.000
75	X	114	LEU	0	-0.033	-0.026	14.405	-1.877	-1.877	0.000	0.000	0.000	0.000
76	X	115	ARG	1	0.934	0.966	15.845	-13.081	-13.081	0.000	0.000	0.000	0.000
77	X	116	ASN	0	-0.018	-0.014	18.566	-0.477	-0.477	0.000	0.000	0.000	0.000
78	X	117	VAL	0	0.025	0.029	15.746	0.062	0.062	0.000	0.000	0.000	0.000
79	X	118	LEU	0	-0.048	-0.021	19.019	-0.515	-0.515	0.000	0.000	0.000	0.000
80	X	119	ILE	0	0.031	0.017	17.159	0.431	0.431	0.000	0.000	0.000	0.000
81	X	120	ILE	0	-0.010	-0.008	20.784	-0.710	-0.710	0.000	0.000	0.000	0.000
82	X	121	HIS	0	0.052	0.012	23.086	0.398	0.398	0.000	0.000	0.000	0.000
83	X	122	GLY	0	-0.011	-0.009	24.525	-0.217	-0.217	0.000	0.000	0.000	0.000
84	X	123	LYS	1	0.901	0.951	28.220	-8.989	-8.989	0.000	0.000	0.000	0.000
85	X	124	GLY	0	0.033	0.023	31.527	-0.017	-0.017	0.000	0.000	0.000	0.000
86	X	125	ARG	1	0.894	0.934	32.915	-8.630	-8.630	0.000	0.000	0.000	0.000
87	X	126	ASP	-1	-0.793	-0.907	35.276	8.296	8.296	0.000	0.000	0.000	0.000
88	X	127	ASP	-1	-0.818	-0.921	33.275	8.920	8.920	0.000	0.000	0.000	0.000
89	X	128	LYS	1	0.935	0.971	31.664	-8.625	-8.625	0.000	0.000	0.000	0.000
90	X	129	SER	0	-0.022	0.006	31.877	0.177	0.177	0.000	0.000	0.000	0.000
91	X	130	HIS	0	0.023	-0.011	24.496	-0.107	-0.107	0.000	0.000	0.000	0.000
92	X	131	ALA	0	0.013	0.004	26.953	0.362	0.362	0.000	0.000	0.000	0.000
93	X	132	ASN	0	-0.008	-0.019	27.053	0.420	0.420	0.000	0.000	0.000	0.000
94	X	133	ILE	0	-0.002	0.014	24.730	0.200	0.200	0.000	0.000	0.000	0.000
95	X	134	VAL	0	0.012	-0.006	21.715	0.440	0.440	0.000	0.000	0.000	0.000
96	X	135	ARG	1	0.781	0.878	22.569	-9.684	-9.684	0.000	0.000	0.000	0.000
97	X	136	SER	0	0.014	0.010	23.895	0.124	0.124	0.000	0.000	0.000	0.000
98	X	137	TYR	0	0.043	0.021	19.790	0.153	0.153	0.000	0.000	0.000	0.000
99	X	138	VAL	0	-0.030	-0.007	19.041	0.635	0.635	0.000	0.000	0.000	0.000
100	X	139	ALA	0	-0.002	-0.001	19.540	0.459	0.459	0.000	0.000	0.000	0.000
101	X	140	ARG	1	0.890	0.970	18.665	-13.478	-13.478	0.000	0.000	0.000	0.000
102	X	141	TRP	0	-0.033	-0.017	15.337	0.462	0.462	0.000	0.000	0.000	0.000
103	X	142	LEU	0	-0.014	-0.006	15.421	0.920	0.920	0.000	0.000	0.000	0.000
104	X	143	THR	0	-0.056	-0.038	16.478	0.298	0.298	0.000	0.000	0.000	0.000
105	X	144	GLU	-1	-0.753	-0.883	14.241	17.245	17.245	0.000	0.000	0.000	0.000
106	X	145	PHE	0	-0.019	0.003	9.013	1.177	1.177	0.000	0.000	0.000	0.000
107	X	146	ASP	-1	-0.815	-0.922	12.567	17.805	17.805	0.000	0.000	0.000	0.000
108	X	147	ASP	-1	-0.862	-0.918	11.018	21.548	21.548	0.000	0.000	0.000	0.000
109	X	148	VAL	0	-0.032	0.002	14.061	-0.819	-0.819	0.000	0.000	0.000	0.000
110	X	149	GLN	0	0.006	-0.009	16.475	-0.488	-0.488	0.000	0.000	0.000	0.000
111	X	150	ALA	0	0.025	-0.001	19.956	-0.624	-0.624	0.000	0.000	0.000	0.000
112	X	151	TYR	0	-0.012	-0.007	20.344	0.331	0.331	0.000	0.000	0.000	0.000
113	X	152	CYS	0	-0.017	-0.007	23.051	-0.385	-0.385	0.000	0.000	0.000	0.000
114	X	153	THR	0	-0.019	0.011	25.946	0.224	0.224	0.000	0.000	0.000	0.000
115	X	154	ALA	0	0.023	0.026	26.746	-0.100	-0.100	0.000	0.000	0.000	0.000
116	X	155	LEU	0	0.056	0.018	28.451	-0.407	-0.407	0.000	0.000	0.000	0.000
117	X	156	PRO	0	0.017	-0.016	31.043	0.225	0.225	0.000	0.000	0.000	0.000
118	X	157	HIS	0	-0.017	0.002	31.190	-0.086	-0.086	0.000	0.000	0.000	0.000
119	X	158	HIS	0	0.030	0.034	27.269	0.077	0.077	0.000	0.000	0.000	0.000
120	X	159	GLY	0	0.045	0.022	27.819	0.368	0.368	0.000	0.000	0.000	0.000
121	X	160	GLY	0	-0.041	-0.016	30.003	-0.168	-0.168	0.000	0.000	0.000	0.000
122	X	161	SER	0	0.022	-0.010	29.572	0.282	0.282	0.000	0.000	0.000	0.000
123	X	162	GLY	0	-0.053	-0.018	29.030	0.069	0.069	0.000	0.000	0.000	0.000
124	X	163	ALA	0	0.005	0.011	25.131	0.372	0.372	0.000	0.000	0.000	0.000
125	X	164	CYS	0	-0.026	0.002	22.510	-0.228	-0.228	0.000	0.000	0.000	0.000
126	X	165	TYR	0	0.021	0.002	22.535	0.320	0.320	0.000	0.000	0.000	0.000
127	X	166	VAL	0	0.062	0.015	17.202	-0.161	-0.161	0.000	0.000	0.000	0.000
128	X	167	ALA	0	-0.064	-0.031	19.889	0.113	0.113	0.000	0.000	0.000	0.000
129	X	168	LEU	0	0.045	0.014	14.082	0.109	0.109	0.000	0.000	0.000	0.000
130	X	169	ARG	1	0.801	0.878	14.284	-19.337	-19.337	0.000	0.000	0.000	0.000
131	X	170	LYS	1	0.903	0.963	14.702	-15.641	-15.641	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(X:40:ASP)