FMO DATABASE

FMODB ID: KGYZ3

Calculation Name: 2V9U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2V9U

Chain ID: A

ChEMBL ID:

UniProt ID: A0QR29

Base Structure: X-ray

Registration Date: 2023-09-24

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	132
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1014991.136704
FMO2-HF: Nuclear repulsion	966489.076691
FMO2-HF: Total energy	-48502.060012
FMO2-MP2: Total energy	-48646.173367

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:GLY)

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

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.
-10.319	-13.22	13.551	-5.838	-4.811	-0.043

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / q_NPA : -0.006

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	ASP	-1	-0.796	-0.884	3.851	-4.605	-3.293	-0.005	-0.616	-0.691	0.002
4	A	4	ASN	0	-0.030	0.000	5.976	1.143	1.143	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.850	-0.918	9.157	-1.276	-1.276	0.000	0.000	0.000	0.000
6	A	6	LEU	0	-0.041	-0.001	11.503	0.141	0.141	0.000	0.000	0.000	0.000
7	A	7	SER	0	0.006	-0.021	15.300	-0.043	-0.043	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.058	-0.027	17.940	0.023	0.023	0.000	0.000	0.000	0.000
9	A	9	VAL	0	-0.024	0.003	21.682	-0.004	-0.004	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.779	-0.876	24.581	-0.248	-0.248	0.000	0.000	0.000	0.000
11	A	11	GLY	0	-0.009	-0.013	26.330	0.018	0.018	0.000	0.000	0.000	0.000
12	A	12	GLN	0	-0.110	-0.061	28.796	0.018	0.018	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.926	-0.959	28.165	-0.155	-0.155	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.796	0.892	24.090	0.239	0.239	0.000	0.000	0.000	0.000
15	A	15	THR	0	-0.022	-0.019	19.726	-0.010	-0.010	0.000	0.000	0.000	0.000
16	A	16	LEU	0	0.005	0.012	19.729	-0.017	-0.017	0.000	0.000	0.000	0.000
17	A	17	THR	0	0.027	0.012	13.399	0.021	0.021	0.000	0.000	0.000	0.000
18	A	18	VAL	0	-0.017	0.009	13.772	-0.009	-0.009	0.000	0.000	0.000	0.000
19	A	19	GLN	0	-0.002	-0.029	8.632	-0.297	-0.297	0.000	0.000	0.000	0.000
20	A	20	GLN	0	-0.038	-0.037	8.262	0.308	0.308	0.000	0.000	0.000	0.000
21	A	21	TRP	0	-0.005	-0.024	2.837	-1.614	-0.990	0.996	-0.521	-1.099	-0.004
22	A	22	ASP	-1	-0.830	-0.916	1.788	-8.880	-13.958	12.550	-4.638	-2.834	-0.041
23	A	23	THR	0	-0.052	-0.045	3.713	2.059	2.300	0.010	-0.063	-0.187	0.000
24	A	24	PHE	0	-0.069	-0.034	6.817	0.308	0.308	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.005	0.002	9.269	0.055	0.055	0.000	0.000	0.000	0.000
26	A	26	ASN	0	0.019	0.014	12.998	0.120	0.120	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.041	0.009	14.813	0.007	0.007	0.000	0.000	0.000	0.000
28	A	28	VAL	0	-0.049	-0.025	18.317	0.037	0.037	0.000	0.000	0.000	0.000
29	A	29	PHE	0	-0.012	-0.016	21.340	-0.006	-0.006	0.000	0.000	0.000	0.000
30	A	30	PRO	0	0.021	0.034	25.101	0.003	0.003	0.000	0.000	0.000	0.000
31	A	31	LEU	0	0.031	0.017	26.445	0.019	0.019	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.789	-0.880	28.461	-0.100	-0.100	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.807	0.885	27.378	0.070	0.070	0.000	0.000	0.000	0.000
34	A	34	ASN	0	0.013	0.029	31.257	0.012	0.012	0.000	0.000	0.000	0.000
35	A	35	ARG	1	0.998	0.988	30.209	0.057	0.057	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.037	-0.010	30.456	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	37	THR	0	-0.031	-0.029	27.102	-0.011	-0.011	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.770	0.871	23.025	0.139	0.139	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.749	-0.853	22.479	-0.155	-0.155	0.000	0.000	0.000	0.000
40	A	40	TRP	0	0.005	-0.003	17.206	0.037	0.037	0.000	0.000	0.000	0.000
41	A	41	PHE	0	-0.038	-0.010	16.330	0.016	0.016	0.000	0.000	0.000	0.000
42	A	42	HIS	0	0.026	0.025	11.274	0.127	0.127	0.000	0.000	0.000	0.000
43	A	43	SER	0	-0.019	-0.009	9.828	0.145	0.145	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.065	0.044	7.433	-0.122	-0.122	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.820	0.896	5.588	2.049	2.049	0.000	0.000	0.000	0.000
46	A	46	ALA	0	0.049	0.041	8.727	-0.377	-0.377	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.853	0.927	5.649	2.128	2.128	0.000	0.000	0.000	0.000
48	A	48	TYR	0	-0.022	-0.025	11.578	-0.073	-0.073	0.000	0.000	0.000	0.000
49	A	49	ILE	0	0.019	0.017	12.106	0.019	0.019	0.000	0.000	0.000	0.000
50	A	50	VAL	0	-0.022	0.004	16.001	-0.009	-0.009	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.010	0.013	19.693	0.030	0.030	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.027	0.007	21.926	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	53	PRO	0	-0.035	-0.018	25.718	0.007	0.007	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.047	0.016	27.934	-0.011	-0.011	0.000	0.000	0.000	0.000
55	A	55	ALA	0	-0.037	-0.011	22.927	-0.014	-0.014	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.890	-0.965	23.510	-0.208	-0.208	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.967	-0.990	25.029	-0.161	-0.161	0.000	0.000	0.000	0.000
58	A	58	PHE	0	-0.017	0.007	21.451	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.860	-0.933	24.595	-0.222	-0.222	0.000	0.000	0.000	0.000
60	A	60	GLY	0	-0.007	0.005	23.540	0.008	0.008	0.000	0.000	0.000	0.000
61	A	61	THR	0	-0.019	-0.006	21.704	0.007	0.007	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.036	-0.012	14.507	-0.034	-0.034	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.818	-0.879	17.146	-0.443	-0.443	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.040	-0.014	10.773	-0.127	-0.127	0.000	0.000	0.000	0.000
65	A	65	GLY	0	-0.010	-0.005	14.674	0.114	0.114	0.000	0.000	0.000	0.000
66	A	66	TYR	0	0.019	0.009	14.706	-0.073	-0.073	0.000	0.000	0.000	0.000
67	A	67	GLN	0	-0.022	-0.005	16.940	0.065	0.065	0.000	0.000	0.000	0.000
68	A	68	ILE	0	-0.002	-0.003	19.592	-0.012	-0.012	0.000	0.000	0.000	0.000
69	A	69	GLY	0	0.024	0.007	21.834	0.016	0.016	0.000	0.000	0.000	0.000
70	A	122	GLY	0	0.023	-0.011	23.965	0.001	0.001	0.000	0.000	0.000	0.000
71	A	123	PRO	0	-0.043	0.004	26.666	0.011	0.011	0.000	0.000	0.000	0.000
72	A	124	GLY	0	0.014	0.001	28.834	0.009	0.009	0.000	0.000	0.000	0.000
73	A	125	ILE	0	-0.023	-0.017	24.466	-0.010	-0.010	0.000	0.000	0.000	0.000
74	A	126	GLN	0	-0.029	-0.009	24.803	0.010	0.010	0.000	0.000	0.000	0.000
75	A	127	GLU	-1	-0.818	-0.884	20.698	-0.480	-0.480	0.000	0.000	0.000	0.000
76	A	128	VAL	0	-0.011	0.003	19.957	0.037	0.037	0.000	0.000	0.000	0.000
77	A	129	ALA	0	0.047	0.022	18.981	-0.062	-0.062	0.000	0.000	0.000	0.000
78	A	130	THR	0	-0.042	-0.045	15.416	0.061	0.061	0.000	0.000	0.000	0.000
79	A	131	PHE	0	-0.035	-0.019	12.711	0.038	0.038	0.000	0.000	0.000	0.000
80	A	132	SER	0	-0.036	-0.049	18.144	-0.044	-0.044	0.000	0.000	0.000	0.000
81	A	133	VAL	0	-0.031	-0.017	18.199	0.040	0.040	0.000	0.000	0.000	0.000
82	A	134	ASP	-1	-0.830	-0.897	20.697	-0.333	-0.333	0.000	0.000	0.000	0.000
83	A	135	VAL	0	-0.091	-0.052	18.352	-0.013	-0.013	0.000	0.000	0.000	0.000
84	A	136	SER	0	-0.007	-0.018	21.754	0.010	0.010	0.000	0.000	0.000	0.000
85	A	137	GLY	0	0.022	0.037	21.982	0.000	0.000	0.000	0.000	0.000	0.000
86	A	138	ALA	0	0.018	0.018	20.594	-0.035	-0.035	0.000	0.000	0.000	0.000
87	A	139	GLU	-1	-0.968	-0.990	15.131	-0.381	-0.381	0.000	0.000	0.000	0.000
88	A	140	GLY	0	0.028	0.017	15.065	0.057	0.057	0.000	0.000	0.000	0.000
89	A	141	GLY	0	-0.021	-0.020	12.300	-0.127	-0.127	0.000	0.000	0.000	0.000
90	A	142	VAL	0	-0.035	0.006	12.409	0.127	0.127	0.000	0.000	0.000	0.000
91	A	143	ALA	0	-0.029	-0.025	10.073	-0.241	-0.241	0.000	0.000	0.000	0.000
92	A	144	VAL	0	0.020	0.018	10.939	0.188	0.188	0.000	0.000	0.000	0.000
93	A	145	SER	0	-0.031	-0.028	11.004	-0.099	-0.099	0.000	0.000	0.000	0.000
94	A	146	ASN	0	-0.033	-0.025	12.967	0.040	0.040	0.000	0.000	0.000	0.000
95	A	147	ALA	0	0.081	0.048	15.278	0.057	0.057	0.000	0.000	0.000	0.000
96	A	148	HIS	0	-0.080	-0.056	17.300	-0.035	-0.035	0.000	0.000	0.000	0.000
97	A	149	GLY	0	0.034	0.024	20.122	-0.023	-0.023	0.000	0.000	0.000	0.000
98	A	150	THR	0	-0.060	-0.045	21.212	0.025	0.025	0.000	0.000	0.000	0.000
99	A	151	VAL	0	0.017	0.017	23.828	-0.007	-0.007	0.000	0.000	0.000	0.000
100	A	152	THR	0	-0.001	-0.027	26.293	0.013	0.013	0.000	0.000	0.000	0.000
101	A	153	GLY	0	0.025	0.017	29.506	-0.005	-0.005	0.000	0.000	0.000	0.000
102	A	154	ALA	0	-0.002	0.009	27.037	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	155	ALA	0	-0.041	-0.031	28.891	0.009	0.009	0.000	0.000	0.000	0.000
104	A	156	GLY	0	-0.030	-0.027	29.386	0.006	0.006	0.000	0.000	0.000	0.000
105	A	157	GLY	0	-0.038	-0.005	25.265	0.003	0.003	0.000	0.000	0.000	0.000
106	A	158	VAL	0	-0.014	-0.014	21.677	0.004	0.004	0.000	0.000	0.000	0.000
107	A	159	LEU	0	-0.029	-0.001	19.697	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	160	LEU	0	0.031	0.012	16.220	0.011	0.011	0.000	0.000	0.000	0.000
109	A	161	ARG	1	0.887	0.955	15.723	0.419	0.419	0.000	0.000	0.000	0.000
110	A	162	PRO	0	-0.009	0.012	11.318	0.065	0.065	0.000	0.000	0.000	0.000
111	A	163	PHE	0	-0.001	-0.007	13.472	-0.028	-0.028	0.000	0.000	0.000	0.000
112	A	164	ALA	0	0.041	0.027	11.885	-0.038	-0.038	0.000	0.000	0.000	0.000
113	A	165	ARG	1	0.755	0.846	13.983	0.541	0.541	0.000	0.000	0.000	0.000
114	A	166	LEU	0	0.031	0.018	17.267	-0.018	-0.018	0.000	0.000	0.000	0.000
115	A	167	ILE	0	-0.008	-0.009	19.071	0.026	0.026	0.000	0.000	0.000	0.000
116	A	168	ALA	0	0.026	0.020	22.902	-0.003	-0.003	0.000	0.000	0.000	0.000
117	A	169	SER	0	-0.038	-0.041	25.083	0.017	0.017	0.000	0.000	0.000	0.000
118	A	170	THR	0	-0.069	-0.057	28.226	0.014	0.014	0.000	0.000	0.000	0.000
119	A	171	GLY	0	-0.024	-0.006	28.541	0.015	0.015	0.000	0.000	0.000	0.000
120	A	172	ASP	-1	-0.827	-0.887	25.505	-0.258	-0.258	0.000	0.000	0.000	0.000
121	A	173	SER	0	-0.022	-0.013	22.783	-0.017	-0.017	0.000	0.000	0.000	0.000
122	A	174	VAL	0	0.009	0.011	17.842	0.016	0.016	0.000	0.000	0.000	0.000
123	A	175	THR	0	0.007	-0.009	17.143	-0.033	-0.033	0.000	0.000	0.000	0.000
124	A	176	THR	0	-0.035	-0.016	11.600	0.099	0.099	0.000	0.000	0.000	0.000
125	A	177	TYR	0	0.005	-0.016	14.044	0.013	0.013	0.000	0.000	0.000	0.000
126	A	178	GLY	0	0.019	0.020	11.199	-0.087	-0.087	0.000	0.000	0.000	0.000
127	A	179	GLU	-1	-0.948	-0.982	12.020	-0.332	-0.332	0.000	0.000	0.000	0.000
128	A	180	PRO	0	-0.066	-0.041	13.398	-0.061	-0.061	0.000	0.000	0.000	0.000
129	A	181	TRP	0	0.093	0.041	8.514	0.159	0.159	0.000	0.000	0.000	0.000
130	A	182	ASN	0	-0.007	-0.015	15.293	0.019	0.019	0.000	0.000	0.000	0.000
131	A	183	MET	0	-0.023	0.001	15.695	0.019	0.019	0.000	0.000	0.000	0.000
132	A	184	ASN	0	-0.003	0.013	19.849	0.036	0.036	0.000	0.000	0.000	0.000

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