FMO DATABASE

FMODB ID: 43YKN

Calculation Name: 3GXV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GXV

Chain ID: A

ChEMBL ID:

UniProt ID: O25916

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	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	122
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1041421.688337
FMO2-HF: Nuclear repulsion	992282.986778
FMO2-HF: Total energy	-49138.701559
FMO2-MP2: Total energy	-49283.61386

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:1:MET)

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

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.
-14.127	-6.906	6.415	-4.058	-9.577	-0.014

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.026 / q_NPA : -0.022

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	3	HIS	0	0.067	0.002	3.081	-3.152	-0.999	0.111	-1.126	-1.138	0.000
4	A	4	LEU	0	0.002	0.002	5.722	0.156	0.156	0.000	0.000	0.000	0.000
5	A	5	LYS	1	0.890	0.933	2.370	-5.892	-4.751	3.498	-1.224	-3.414	0.002
6	A	6	HIS	0	0.047	0.020	2.701	-1.739	1.332	2.571	-1.492	-4.150	-0.015
7	A	7	LEU	0	-0.029	0.001	4.427	-0.342	-0.231	0.002	-0.008	-0.105	0.000
8	A	8	GLN	0	-0.026	-0.025	6.728	0.311	0.311	0.000	0.000	0.000	0.000
9	A	9	GLN	0	0.029	0.008	3.264	-1.453	-0.708	0.233	-0.208	-0.770	-0.001
10	A	10	LEU	0	-0.003	0.024	5.885	-0.375	-0.375	0.000	0.000	0.000	0.000
11	A	11	GLN	0	0.002	-0.004	8.107	0.042	0.042	0.000	0.000	0.000	0.000
12	A	12	ASN	0	-0.020	-0.007	7.769	-0.114	-0.114	0.000	0.000	0.000	0.000
13	A	13	ILE	0	0.038	0.020	5.901	-0.016	-0.016	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.737	-0.864	9.870	-0.272	-0.272	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.809	0.907	13.075	-0.120	-0.120	0.000	0.000	0.000	0.000
16	A	16	ILE	0	0.012	0.008	10.445	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.009	0.006	13.260	-0.009	-0.009	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.046	-0.027	15.675	0.013	0.013	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.001	0.005	17.543	0.000	0.000	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.028	0.004	18.133	0.007	0.007	0.000	0.000	0.000	0.000
21	A	21	ILE	0	-0.047	-0.013	19.701	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	22	VAL	0	-0.022	-0.007	22.032	0.007	0.007	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.055	-0.018	22.356	0.008	0.008	0.000	0.000	0.000	0.000
24	A	24	ALA	0	-0.028	-0.014	23.396	0.002	0.002	0.000	0.000	0.000	0.000
25	A	25	ASN	0	0.027	0.010	24.506	-0.012	-0.012	0.000	0.000	0.000	0.000
26	A	26	HIS	0	0.090	0.038	26.165	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.828	0.895	20.747	0.174	0.174	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.006	0.002	22.939	-0.026	-0.026	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.875	-0.930	24.064	-0.141	-0.141	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.831	-0.892	21.138	-0.223	-0.223	0.000	0.000	0.000	0.000
31	A	31	VAL	0	0.007	0.004	18.308	-0.030	-0.030	0.000	0.000	0.000	0.000
32	A	32	HIS	1	0.895	0.956	20.533	0.162	0.162	0.000	0.000	0.000	0.000
33	A	33	SER	0	-0.093	-0.030	22.951	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.013	-0.004	17.811	-0.019	-0.019	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.052	-0.022	15.892	-0.026	-0.026	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.801	-0.901	20.191	-0.168	-0.168	0.000	0.000	0.000	0.000
37	A	37	PRO	0	0.039	0.008	20.661	-0.021	-0.021	0.000	0.000	0.000	0.000
38	A	38	SER	0	-0.011	-0.016	20.606	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.831	-0.876	17.406	-0.378	-0.378	0.000	0.000	0.000	0.000
40	A	40	PHE	0	0.037	0.031	15.888	-0.066	-0.066	0.000	0.000	0.000	0.000
41	A	41	TYR	0	-0.102	-0.058	11.613	0.021	0.021	0.000	0.000	0.000	0.000
42	A	42	TYR	0	-0.079	-0.051	14.768	0.040	0.040	0.000	0.000	0.000	0.000
43	A	43	PRO	0	0.049	0.006	16.447	0.002	0.002	0.000	0.000	0.000	0.000
44	A	44	PRO	0	-0.039	-0.020	19.345	-0.008	-0.008	0.000	0.000	0.000	0.000
45	A	45	ASN	0	0.011	-0.008	14.896	0.039	0.039	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.032	0.024	18.882	-0.013	-0.013	0.000	0.000	0.000	0.000
47	A	47	LEU	0	-0.028	-0.025	20.844	0.001	0.001	0.000	0.000	0.000	0.000
48	A	48	PHE	0	0.056	0.029	21.291	0.005	0.005	0.000	0.000	0.000	0.000
49	A	49	PHE	0	0.009	-0.002	20.629	0.000	0.000	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.882	-0.940	22.714	-0.103	-0.103	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.042	-0.021	25.837	0.004	0.004	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.026	0.001	24.701	0.003	0.003	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.018	-0.001	24.859	0.000	0.000	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.826	0.907	27.745	0.092	0.092	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.016	0.008	29.140	0.004	0.004	0.000	0.000	0.000	0.000
56	A	56	HIS	0	-0.011	-0.026	28.854	0.009	0.009	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.993	-0.988	30.557	-0.111	-0.111	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.895	-0.933	33.307	-0.045	-0.045	0.000	0.000	0.000	0.000
59	A	59	ASP	-1	-0.942	-0.969	34.312	-0.061	-0.061	0.000	0.000	0.000	0.000
60	A	60	CYS	0	-0.104	-0.032	34.102	0.008	0.008	0.000	0.000	0.000	0.000
61	A	61	PRO	0	0.000	-0.011	31.797	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	62	ILE	0	-0.001	0.003	25.763	0.003	0.003	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.810	-0.918	27.569	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.805	-0.922	26.621	0.060	0.060	0.000	0.000	0.000	0.000
65	A	65	ASN	0	-0.098	-0.051	28.652	0.004	0.004	0.000	0.000	0.000	0.000
66	A	66	PHE	0	0.022	-0.010	31.635	0.001	0.001	0.000	0.000	0.000	0.000
67	A	67	ILE	0	-0.016	0.011	25.973	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.752	0.843	27.484	-0.058	-0.058	0.000	0.000	0.000	0.000
69	A	69	GLN	0	-0.053	-0.016	31.103	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.805	0.893	32.600	0.040	0.040	0.000	0.000	0.000	0.000
71	A	71	MET	0	0.013	0.039	29.099	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	72	PRO	0	-0.014	-0.020	29.731	0.003	0.003	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.974	0.990	32.677	0.007	0.007	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.920	-0.943	33.403	-0.035	-0.035	0.000	0.000	0.000	0.000
75	A	75	LYS	1	0.800	0.901	28.292	0.039	0.039	0.000	0.000	0.000	0.000
76	A	76	GLN	0	0.072	0.025	29.533	-0.006	-0.006	0.000	0.000	0.000	0.000
77	A	77	ILE	0	-0.035	-0.023	23.537	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	78	LYS	1	0.958	0.972	23.768	-0.028	-0.028	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.769	-0.873	24.839	0.077	0.077	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.926	-0.967	21.478	0.168	0.168	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.799	-0.887	19.609	0.112	0.112	0.000	0.000	0.000	0.000
82	A	82	LEU	0	-0.011	-0.007	20.556	-0.009	-0.009	0.000	0.000	0.000	0.000
83	A	83	VAL	0	0.022	0.008	22.269	0.000	0.000	0.000	0.000	0.000	0.000
84	A	84	ALA	0	-0.030	-0.013	17.420	0.010	0.010	0.000	0.000	0.000	0.000
85	A	85	ILE	0	-0.054	-0.018	17.573	0.013	0.013	0.000	0.000	0.000	0.000
86	A	86	PHE	0	0.025	-0.001	18.980	-0.010	-0.010	0.000	0.000	0.000	0.000
87	A	87	ALA	0	-0.029	-0.004	19.898	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	88	ALA	0	-0.034	0.005	15.072	0.035	0.035	0.000	0.000	0.000	0.000
89	A	89	SER	0	-0.019	-0.016	15.235	-0.020	-0.020	0.000	0.000	0.000	0.000
90	A	90	PRO	0	0.026	0.012	15.342	-0.018	-0.018	0.000	0.000	0.000	0.000
91	A	91	ILE	0	-0.045	-0.017	12.047	0.022	0.022	0.000	0.000	0.000	0.000
92	A	92	ASP	-1	-0.909	-0.942	16.257	-0.099	-0.099	0.000	0.000	0.000	0.000
93	A	93	ASN	0	-0.038	-0.046	15.981	-0.046	-0.046	0.000	0.000	0.000	0.000
94	A	94	ILE	0	0.054	0.025	14.127	-0.047	-0.047	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.917	-0.954	14.475	-0.408	-0.408	0.000	0.000	0.000	0.000
96	A	96	ALA	0	0.003	0.001	10.625	-0.041	-0.041	0.000	0.000	0.000	0.000
97	A	97	TYR	0	0.046	0.016	8.038	0.003	0.003	0.000	0.000	0.000	0.000
98	A	98	VAL	0	0.024	0.005	11.056	-0.040	-0.040	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.886	-0.925	12.767	-0.908	-0.908	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.888	-0.958	6.256	-2.103	-2.103	0.000	0.000	0.000	0.000
101	A	101	ILE	0	-0.047	-0.017	10.291	-0.029	-0.029	0.000	0.000	0.000	0.000
102	A	102	LYS	1	0.840	0.910	12.322	0.425	0.425	0.000	0.000	0.000	0.000
103	A	103	ASN	0	-0.036	-0.034	11.608	0.027	0.027	0.000	0.000	0.000	0.000
104	A	104	ALA	0	-0.012	-0.012	10.185	0.034	0.034	0.000	0.000	0.000	0.000
105	A	105	SER	0	-0.082	-0.066	12.140	0.084	0.084	0.000	0.000	0.000	0.000
106	A	106	ILE	0	0.015	0.003	15.727	0.054	0.054	0.000	0.000	0.000	0.000
107	A	107	LYS	1	0.893	0.948	11.800	1.155	1.155	0.000	0.000	0.000	0.000
108	A	108	ARG	1	0.893	0.953	13.571	0.524	0.524	0.000	0.000	0.000	0.000
109	A	109	LYS	1	0.890	0.946	16.758	0.407	0.407	0.000	0.000	0.000	0.000
110	A	110	LEU	0	-0.007	0.012	18.253	0.038	0.038	0.000	0.000	0.000	0.000
111	A	111	PHE	0	0.011	-0.009	14.314	0.021	0.021	0.000	0.000	0.000	0.000
112	A	112	GLY	0	0.012	0.016	19.466	0.039	0.039	0.000	0.000	0.000	0.000
113	A	113	LEU	0	0.007	0.009	22.221	0.032	0.032	0.000	0.000	0.000	0.000
114	A	114	ALA	0	0.000	-0.008	21.668	0.022	0.022	0.000	0.000	0.000	0.000
115	A	115	ASN	0	-0.031	-0.011	20.607	0.005	0.005	0.000	0.000	0.000	0.000
116	A	116	THR	0	0.067	0.004	24.405	0.021	0.021	0.000	0.000	0.000	0.000
117	A	117	ILE	0	-0.035	-0.003	26.652	0.017	0.017	0.000	0.000	0.000	0.000
118	A	118	ARG	1	0.843	0.926	21.896	0.278	0.278	0.000	0.000	0.000	0.000
119	A	119	GLU	-1	-0.892	-0.950	26.467	-0.166	-0.166	0.000	0.000	0.000	0.000
120	A	120	GLN	0	-0.042	-0.011	30.029	0.016	0.016	0.000	0.000	0.000	0.000
121	A	121	ALA	0	-0.039	-0.003	31.857	0.008	0.008	0.000	0.000	0.000	0.000
122	A	122	HIS	0	-0.090	-0.044	32.984	0.016	0.016	0.000	0.000	0.000	0.000

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