FMO DATABASE

FMODB ID: LJM29

Calculation Name: 3V67-A-Xray320

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3V67

Chain ID: A

ChEMBL ID:
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UniProt ID: Q87KW6

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	134
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1221346.639177
FMO2-HF: Nuclear repulsion	1167198.049432
FMO2-HF: Total energy	-54148.589744
FMO2-MP2: Total energy	-54308.618533

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:40:ACE )

Summations of interaction energy for fragment #1(A:40:ACE )

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.
-0.719	0.478	0.394	-0.745	-0.846	-0.001

Interaction energy analysis for fragmet #1(A:40:ACE )

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 : 0.000

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	42	ARG	1	0.892	0.917	2.522	-0.593	0.604	0.394	-0.745	-0.846	-0.001
4	A	43	LYS	1	0.976	0.983	5.584	0.726	0.726	0.000	0.000	0.000	0.000
5	A	44	ALA	0	0.012	0.024	9.327	0.155	0.155	0.000	0.000	0.000	0.000
6	A	45	ARG	1	0.935	0.967	11.797	0.248	0.248	0.000	0.000	0.000	0.000
7	A	46	ASP	-1	-0.753	-0.874	14.590	-0.169	-0.169	0.000	0.000	0.000	0.000
8	A	47	ILE	0	-0.088	-0.042	17.999	0.008	0.008	0.000	0.000	0.000	0.000
9	A	48	PRO	0	-0.001	0.005	19.413	-0.001	-0.001	0.000	0.000	0.000	0.000
10	A	49	ASP	-1	-0.792	-0.893	22.573	-0.068	-0.068	0.000	0.000	0.000	0.000
11	A	50	GLU	-1	-0.912	-0.956	25.486	-0.042	-0.042	0.000	0.000	0.000	0.000
12	A	51	HIS	0	-0.038	-0.027	20.732	0.007	0.007	0.000	0.000	0.000	0.000
13	A	52	TYR	0	0.019	-0.001	22.673	0.006	0.006	0.000	0.000	0.000	0.000
14	A	53	GLN	0	0.067	0.033	24.215	0.005	0.005	0.000	0.000	0.000	0.000
15	A	54	ARG	1	0.922	0.974	26.241	0.010	0.010	0.000	0.000	0.000	0.000
16	A	55	ILE	0	-0.038	-0.032	21.162	0.007	0.007	0.000	0.000	0.000	0.000
17	A	56	ILE	0	0.019	0.006	25.470	0.005	0.005	0.000	0.000	0.000	0.000
18	A	57	GLU	-1	-0.866	-0.929	27.957	-0.009	-0.009	0.000	0.000	0.000	0.000
19	A	58	THR	0	-0.104	-0.059	26.992	0.007	0.007	0.000	0.000	0.000	0.000
20	A	59	ARG	1	0.836	0.886	26.654	0.024	0.024	0.000	0.000	0.000	0.000
21	A	60	ASP	-1	-0.807	-0.883	28.689	-0.012	-0.012	0.000	0.000	0.000	0.000
22	A	61	ALA	0	-0.048	-0.015	32.140	0.002	0.002	0.000	0.000	0.000	0.000
23	A	62	ILE	0	-0.061	-0.037	27.862	0.003	0.003	0.000	0.000	0.000	0.000
24	A	63	GLN	0	0.056	0.018	30.843	0.001	0.001	0.000	0.000	0.000	0.000
25	A	64	ASN	0	0.036	0.015	33.094	0.001	0.001	0.000	0.000	0.000	0.000
26	A	65	LYS	1	0.860	0.956	34.638	-0.024	-0.024	0.000	0.000	0.000	0.000
27	A	66	TYR	0	-0.098	-0.074	32.634	0.003	0.003	0.000	0.000	0.000	0.000
28	A	67	SER	0	0.065	0.049	36.130	0.001	0.001	0.000	0.000	0.000	0.000
29	A	68	LYS	1	0.935	0.969	37.822	-0.014	-0.014	0.000	0.000	0.000	0.000
30	A	69	GLU	-1	-0.927	-0.962	36.138	0.025	0.025	0.000	0.000	0.000	0.000
31	A	70	THR	0	0.068	0.028	36.986	0.000	0.000	0.000	0.000	0.000	0.000
32	A	71	ASP	-1	-0.858	-0.917	34.827	0.035	0.035	0.000	0.000	0.000	0.000
33	A	72	LEU	0	0.078	0.019	27.825	0.002	0.002	0.000	0.000	0.000	0.000
34	A	73	GLY	0	0.048	0.025	30.468	0.004	0.004	0.000	0.000	0.000	0.000
35	A	74	ARG	1	0.884	0.940	31.544	-0.028	-0.028	0.000	0.000	0.000	0.000
36	A	75	ILE	0	-0.014	-0.003	30.417	0.002	0.002	0.000	0.000	0.000	0.000
37	A	76	LEU	0	-0.018	-0.002	26.049	0.002	0.002	0.000	0.000	0.000	0.000
38	A	77	PHE	0	0.013	0.011	28.760	0.004	0.004	0.000	0.000	0.000	0.000
39	A	78	ARG	1	0.948	0.962	30.832	-0.028	-0.028	0.000	0.000	0.000	0.000
40	A	79	VAL	0	-0.027	0.003	27.137	0.001	0.001	0.000	0.000	0.000	0.000
41	A	80	GLU	-1	-0.884	-0.897	24.066	0.092	0.092	0.000	0.000	0.000	0.000
42	A	81	GLY	0	0.056	0.020	27.705	0.007	0.007	0.000	0.000	0.000	0.000
43	A	82	ASN	0	-0.006	-0.005	30.374	0.001	0.001	0.000	0.000	0.000	0.000
44	A	83	ARG	1	0.745	0.882	23.140	-0.093	-0.093	0.000	0.000	0.000	0.000
45	A	84	ALA	0	0.053	0.030	28.367	0.002	0.002	0.000	0.000	0.000	0.000
46	A	85	GLY	0	0.023	0.006	27.518	0.001	0.001	0.000	0.000	0.000	0.000
47	A	86	LYS	1	0.927	0.955	22.345	-0.144	-0.144	0.000	0.000	0.000	0.000
48	A	87	HIS	0	0.008	-0.003	22.559	0.011	0.011	0.000	0.000	0.000	0.000
49	A	88	ASP	-1	-0.802	-0.849	24.394	0.063	0.063	0.000	0.000	0.000	0.000
50	A	89	PRO	0	0.048	0.030	23.752	0.008	0.008	0.000	0.000	0.000	0.000
51	A	90	ARG	1	0.873	0.907	23.799	-0.060	-0.060	0.000	0.000	0.000	0.000
52	A	91	PRO	0	0.055	0.035	21.928	0.013	0.013	0.000	0.000	0.000	0.000
53	A	92	ARG	1	0.827	0.917	19.729	-0.147	-0.147	0.000	0.000	0.000	0.000
54	A	93	VAL	0	0.029	0.020	20.767	0.002	0.002	0.000	0.000	0.000	0.000
55	A	94	PHE	0	-0.067	-0.033	17.605	0.020	0.020	0.000	0.000	0.000	0.000
56	A	95	PHE	0	0.083	0.021	20.787	-0.014	-0.014	0.000	0.000	0.000	0.000
57	A	96	SER	0	0.008	0.035	18.531	0.014	0.014	0.000	0.000	0.000	0.000
58	A	97	ASP	-1	-0.735	-0.836	20.586	0.023	0.023	0.000	0.000	0.000	0.000
59	A	98	TYR	0	0.018	-0.014	20.693	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	99	ASN	0	-0.024	-0.017	20.881	-0.015	-0.015	0.000	0.000	0.000	0.000
61	A	100	GLY	0	0.004	0.019	16.915	0.004	0.004	0.000	0.000	0.000	0.000
62	A	101	ASN	0	-0.073	-0.047	16.604	0.036	0.036	0.000	0.000	0.000	0.000
63	A	102	VAL	0	-0.017	-0.019	15.681	-0.009	-0.009	0.000	0.000	0.000	0.000
64	A	103	LEU	0	-0.033	-0.016	18.769	0.005	0.005	0.000	0.000	0.000	0.000
65	A	104	THR	0	-0.107	-0.127	20.549	0.003	0.003	0.000	0.000	0.000	0.000
66	A	105	THR	0	-0.024	-0.002	23.422	0.001	0.001	0.000	0.000	0.000	0.000
67	A	106	ASP	-1	-0.925	-0.950	22.167	0.171	0.171	0.000	0.000	0.000	0.000
68	A	107	LYS	1	0.924	0.968	22.065	-0.103	-0.103	0.000	0.000	0.000	0.000
69	A	108	ARG	1	0.910	0.910	22.002	-0.080	-0.080	0.000	0.000	0.000	0.000
70	A	109	SER	0	-0.063	-0.020	18.550	0.020	0.020	0.000	0.000	0.000	0.000
71	A	110	ASN	0	0.128	0.043	17.031	0.031	0.031	0.000	0.000	0.000	0.000
72	A	111	PHE	0	-0.050	-0.026	10.769	0.020	0.020	0.000	0.000	0.000	0.000
73	A	112	GLN	0	0.023	0.017	13.255	0.034	0.034	0.000	0.000	0.000	0.000
74	A	113	LEU	0	0.061	0.045	14.705	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	114	ARG	1	0.961	0.991	10.946	-0.445	-0.445	0.000	0.000	0.000	0.000
76	A	115	ALA	0	-0.037	-0.012	9.754	0.055	0.055	0.000	0.000	0.000	0.000
77	A	116	MET	0	0.003	0.009	10.749	-0.034	-0.034	0.000	0.000	0.000	0.000
78	A	117	GLN	0	0.101	0.050	11.685	-0.056	-0.056	0.000	0.000	0.000	0.000
79	A	118	ASN	0	0.005	0.026	4.984	-0.094	-0.094	0.000	0.000	0.000	0.000
80	A	119	PHE	0	-0.019	0.030	8.810	-0.129	-0.129	0.000	0.000	0.000	0.000
81	A	120	VAL	0	0.049	0.016	10.443	-0.083	-0.083	0.000	0.000	0.000	0.000
82	A	121	THR	0	-0.053	-0.029	9.913	-0.024	-0.024	0.000	0.000	0.000	0.000
83	A	122	SER	0	-0.080	-0.081	7.271	-0.081	-0.081	0.000	0.000	0.000	0.000
84	A	123	ILE	0	-0.095	-0.034	9.203	-0.126	-0.126	0.000	0.000	0.000	0.000
85	A	124	GLU	-1	-0.955	-0.967	10.968	-0.600	-0.600	0.000	0.000	0.000	0.000
86	A	125	ASP	-1	-0.826	-0.933	13.937	-0.125	-0.125	0.000	0.000	0.000	0.000
87	A	126	TYR	0	0.002	-0.007	15.753	0.014	0.014	0.000	0.000	0.000	0.000
88	A	127	ASN	0	-0.060	-0.022	19.258	0.012	0.012	0.000	0.000	0.000	0.000
89	A	128	LYS	1	0.931	0.963	18.743	0.194	0.194	0.000	0.000	0.000	0.000
90	A	129	PRO	0	-0.004	0.025	17.943	-0.017	-0.017	0.000	0.000	0.000	0.000
91	A	130	LYS	1	0.849	0.929	14.473	0.207	0.207	0.000	0.000	0.000	0.000
92	A	131	GLN	0	0.030	-0.006	14.197	0.064	0.064	0.000	0.000	0.000	0.000
93	A	132	ARG	1	0.919	0.964	7.283	0.542	0.542	0.000	0.000	0.000	0.000
94	A	133	LEU	0	0.008	0.007	9.594	0.081	0.081	0.000	0.000	0.000	0.000
95	A	134	TYR	0	-0.069	-0.075	6.535	0.036	0.036	0.000	0.000	0.000	0.000
96	A	135	GLY	0	0.025	0.011	8.653	-0.008	-0.008	0.000	0.000	0.000	0.000
97	A	136	ARG	1	0.980	0.985	10.483	-0.191	-0.191	0.000	0.000	0.000	0.000
98	A	137	TYR	0	-0.020	0.002	12.505	-0.046	-0.046	0.000	0.000	0.000	0.000
99	A	138	MET	0	0.009	0.021	12.196	0.030	0.030	0.000	0.000	0.000	0.000
100	A	139	ILE	0	-0.022	-0.005	12.057	0.022	0.022	0.000	0.000	0.000	0.000
101	A	140	ALA	0	0.011	0.007	13.930	-0.041	-0.041	0.000	0.000	0.000	0.000
102	A	141	GLY	0	0.022	0.035	16.619	0.026	0.026	0.000	0.000	0.000	0.000
103	A	142	PRO	0	0.034	0.013	16.633	-0.026	-0.026	0.000	0.000	0.000	0.000
104	A	143	VAL	0	0.007	-0.016	19.158	-0.013	-0.013	0.000	0.000	0.000	0.000
105	A	144	PRO	0	0.052	0.034	22.904	0.010	0.010	0.000	0.000	0.000	0.000
106	A	145	ILE	0	-0.039	-0.018	25.424	0.002	0.002	0.000	0.000	0.000	0.000
107	A	146	VAL	0	0.058	0.036	27.729	0.001	0.001	0.000	0.000	0.000	0.000
108	A	147	LEU	0	-0.057	-0.039	27.999	0.003	0.003	0.000	0.000	0.000	0.000
109	A	148	ALA	0	-0.004	-0.006	31.552	0.001	0.001	0.000	0.000	0.000	0.000
110	A	149	ASP	-1	-0.899	-0.943	34.324	0.004	0.004	0.000	0.000	0.000	0.000
111	A	150	SER	0	-0.054	-0.014	29.905	0.000	0.000	0.000	0.000	0.000	0.000
112	A	151	GLU	-1	-0.926	-0.963	28.090	-0.017	-0.017	0.000	0.000	0.000	0.000
113	A	152	LEU	0	-0.062	-0.036	24.739	0.003	0.003	0.000	0.000	0.000	0.000
114	A	153	LEU	0	-0.027	-0.004	19.857	-0.010	-0.010	0.000	0.000	0.000	0.000
115	A	154	MET	0	-0.034	-0.006	22.033	0.015	0.015	0.000	0.000	0.000	0.000
116	A	155	TYR	0	-0.001	-0.040	16.232	-0.015	-0.015	0.000	0.000	0.000	0.000
117	A	156	VAL	0	0.008	0.003	18.756	0.012	0.012	0.000	0.000	0.000	0.000
118	A	157	GLY	0	0.011	0.009	16.790	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	158	PHE	0	-0.004	-0.025	16.931	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	159	LYS	1	0.920	0.964	16.755	-0.120	-0.120	0.000	0.000	0.000	0.000
121	A	160	TRP	0	0.018	-0.003	14.950	-0.016	-0.016	0.000	0.000	0.000	0.000
122	A	161	ASN	0	-0.064	-0.065	16.920	0.029	0.029	0.000	0.000	0.000	0.000
123	A	162	GLU	-1	-0.950	-0.967	15.980	0.033	0.033	0.000	0.000	0.000	0.000
124	A	163	PRO	0	0.036	0.024	18.717	0.005	0.005	0.000	0.000	0.000	0.000
125	A	164	PRO	0	0.014	0.017	21.891	0.003	0.003	0.000	0.000	0.000	0.000
126	A	165	PRO	0	0.003	0.008	23.049	-0.007	-0.007	0.000	0.000	0.000	0.000
127	A	166	LEU	0	0.019	0.009	24.221	0.002	0.002	0.000	0.000	0.000	0.000
128	A	167	LEU	0	-0.005	0.002	25.793	-0.004	-0.004	0.000	0.000	0.000	0.000
129	A	168	LEU	0	-0.013	-0.011	26.671	0.004	0.004	0.000	0.000	0.000	0.000
130	A	169	ARG	1	0.858	0.908	27.875	0.025	0.025	0.000	0.000	0.000	0.000
131	A	170	LEU	0	0.058	0.030	28.934	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	171	PHE	0	-0.023	-0.016	30.993	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	172	ASP	-1	-0.810	-0.899	33.662	-0.037	-0.037	0.000	0.000	0.000	0.000
134	A	173	NME	0	-0.072	-0.016	35.139	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:40:ACE )