FMO DATABASE

FMODB ID: LJVL9

Calculation Name: 3A6M-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3A6M

Chain ID: B

ChEMBL ID:

UniProt ID: Q56236

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:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	164
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1151018.548426
FMO2-HF: Nuclear repulsion	1087439.058538
FMO2-HF: Total energy	-63579.489888
FMO2-MP2: Total energy	-63768.037626

3D Structure Molmil

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(B:7:GLU)

Summations of interaction energy for fragment #1(B:7:GLU)

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.
20.149	24.555	14.745	-9.863	-9.287	-0.053

Interaction energy analysis for fragmet #1(B:7:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.920 / q_NPA : -0.957

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	B	9	THR	0	-0.026	-0.035	3.475	-16.288	-12.965	0.120	-1.577	-1.865	0.014
4	B	10	LEU	0	-0.049	0.003	1.602	-4.070	-7.096	9.709	-3.826	-2.857	-0.003
5	B	11	GLU	-1	-0.781	-0.909	2.358	23.484	27.468	4.917	-4.454	-4.447	-0.064
6	B	12	LYS	1	0.860	0.926	5.264	-44.203	-44.078	-0.001	-0.006	-0.118	0.000
7	B	13	ASP	-1	-0.966	-0.976	6.886	23.659	23.659	0.000	0.000	0.000	0.000
8	B	14	LEU	0	0.021	0.012	7.549	-2.608	-2.608	0.000	0.000	0.000	0.000
9	B	15	GLU	-1	-0.958	-0.976	8.909	26.356	26.356	0.000	0.000	0.000	0.000
10	B	16	ALA	0	-0.012	-0.006	11.703	-1.155	-1.155	0.000	0.000	0.000	0.000
11	B	17	VAL	0	0.028	0.004	13.647	-1.184	-1.184	0.000	0.000	0.000	0.000
12	B	18	GLY	0	-0.021	-0.009	14.878	-0.945	-0.945	0.000	0.000	0.000	0.000
13	B	19	GLN	0	-0.003	-0.006	16.697	-1.098	-1.098	0.000	0.000	0.000	0.000
14	B	20	GLU	-1	-0.938	-0.964	18.487	12.384	12.384	0.000	0.000	0.000	0.000
15	B	21	ALA	0	-0.024	-0.012	20.207	-0.653	-0.653	0.000	0.000	0.000	0.000
16	B	22	GLN	0	-0.007	0.002	19.961	0.114	0.114	0.000	0.000	0.000	0.000
17	B	23	ALA	0	0.039	0.012	22.330	-0.403	-0.403	0.000	0.000	0.000	0.000
18	B	24	LEU	0	-0.071	-0.049	24.399	-0.561	-0.561	0.000	0.000	0.000	0.000
19	B	25	GLU	-1	-0.852	-0.921	26.009	9.550	9.550	0.000	0.000	0.000	0.000
20	B	26	GLU	-1	-0.924	-0.957	27.707	10.226	10.226	0.000	0.000	0.000	0.000
21	B	27	ARG	1	0.887	0.948	24.649	-11.262	-11.262	0.000	0.000	0.000	0.000
22	B	28	LEU	0	-0.044	-0.022	30.909	-0.355	-0.355	0.000	0.000	0.000	0.000
23	B	29	LYS	1	0.842	0.916	31.047	-9.733	-9.733	0.000	0.000	0.000	0.000
24	B	30	ALA	0	0.111	0.062	32.980	-0.187	-0.187	0.000	0.000	0.000	0.000
25	B	31	ALA	0	-0.004	0.003	34.837	-0.279	-0.279	0.000	0.000	0.000	0.000
26	B	32	GLU	-1	-0.934	-0.973	35.916	8.048	8.048	0.000	0.000	0.000	0.000
27	B	33	GLU	-1	-0.916	-0.952	36.922	8.371	8.371	0.000	0.000	0.000	0.000
28	B	34	GLU	-1	-0.797	-0.903	38.987	6.823	6.823	0.000	0.000	0.000	0.000
29	B	35	LEU	0	-0.072	-0.033	40.257	-0.259	-0.259	0.000	0.000	0.000	0.000
30	B	36	LYS	1	0.847	0.926	38.835	-7.921	-7.921	0.000	0.000	0.000	0.000
31	B	37	GLY	0	0.045	0.014	43.574	-0.137	-0.137	0.000	0.000	0.000	0.000
32	B	38	LEU	0	-0.072	-0.030	44.702	-0.162	-0.162	0.000	0.000	0.000	0.000
33	B	39	LYS	1	0.907	0.931	46.652	-6.571	-6.571	0.000	0.000	0.000	0.000
34	B	40	ASP	-1	-0.818	-0.898	49.075	6.204	6.204	0.000	0.000	0.000	0.000
35	B	41	LYS	1	0.758	0.876	45.712	-6.941	-6.941	0.000	0.000	0.000	0.000
36	B	42	TYR	0	0.029	0.015	51.596	-0.078	-0.078	0.000	0.000	0.000	0.000
37	B	43	LEU	0	0.036	0.018	53.289	-0.108	-0.108	0.000	0.000	0.000	0.000
38	B	44	ARG	1	0.947	0.969	53.933	-5.908	-5.908	0.000	0.000	0.000	0.000
39	B	45	LEU	0	0.018	0.020	55.042	-0.087	-0.087	0.000	0.000	0.000	0.000
40	B	46	LEU	0	0.002	-0.004	57.344	-0.088	-0.088	0.000	0.000	0.000	0.000
41	B	47	ALA	0	-0.012	-0.003	59.296	-0.093	-0.093	0.000	0.000	0.000	0.000
42	B	48	ASP	-1	-0.889	-0.949	60.635	5.088	5.088	0.000	0.000	0.000	0.000
43	B	49	PHE	0	-0.013	-0.020	61.307	-0.087	-0.087	0.000	0.000	0.000	0.000
44	B	50	ASP	-1	-0.847	-0.908	63.172	4.752	4.752	0.000	0.000	0.000	0.000
45	B	51	ASN	0	-0.001	0.018	64.752	-0.128	-0.128	0.000	0.000	0.000	0.000
46	B	52	TYR	0	0.040	-0.010	66.694	-0.080	-0.080	0.000	0.000	0.000	0.000
47	B	53	ARG	1	0.859	0.942	62.788	-4.933	-4.933	0.000	0.000	0.000	0.000
48	B	54	LYS	1	0.853	0.917	66.556	-4.751	-4.751	0.000	0.000	0.000	0.000
49	B	55	ARG	1	0.830	0.942	68.702	-4.593	-4.593	0.000	0.000	0.000	0.000
50	B	56	MET	0	0.004	-0.011	71.684	-0.036	-0.036	0.000	0.000	0.000	0.000
51	B	57	GLU	-1	-0.913	-0.936	74.364	3.982	3.982	0.000	0.000	0.000	0.000
52	B	58	GLU	-1	-0.940	-0.966	76.555	3.918	3.918	0.000	0.000	0.000	0.000
53	B	59	GLU	-1	-0.882	-0.963	73.887	4.266	4.266	0.000	0.000	0.000	0.000
54	B	60	LEU	0	-0.026	-0.026	76.861	-0.042	-0.042	0.000	0.000	0.000	0.000
55	B	61	LYS	1	0.884	0.939	79.344	-3.754	-3.754	0.000	0.000	0.000	0.000
56	B	62	ALA	0	0.006	0.001	80.840	-0.057	-0.057	0.000	0.000	0.000	0.000
57	B	63	ARG	1	0.910	0.942	78.149	-4.082	-4.082	0.000	0.000	0.000	0.000
58	B	64	GLU	-1	-0.852	-0.908	81.873	3.640	3.640	0.000	0.000	0.000	0.000
59	B	65	ARG	1	0.939	0.958	85.209	-3.713	-3.713	0.000	0.000	0.000	0.000
60	B	66	GLU	-1	-0.869	-0.899	81.205	3.929	3.929	0.000	0.000	0.000	0.000
61	B	67	GLY	0	0.019	0.015	85.445	-0.026	-0.026	0.000	0.000	0.000	0.000
62	B	68	VAL	0	0.021	-0.001	87.281	-0.041	-0.041	0.000	0.000	0.000	0.000
63	B	69	LEU	0	-0.027	-0.011	87.682	-0.042	-0.042	0.000	0.000	0.000	0.000
64	B	70	LYS	1	0.938	0.970	85.568	-3.760	-3.760	0.000	0.000	0.000	0.000
65	B	71	ALA	0	-0.001	-0.004	89.415	-0.021	-0.021	0.000	0.000	0.000	0.000
66	B	72	LEU	0	0.034	0.008	92.557	-0.032	-0.032	0.000	0.000	0.000	0.000
67	B	73	ARG	1	0.899	0.947	87.525	-3.667	-3.667	0.000	0.000	0.000	0.000
68	B	74	ALA	0	0.010	0.001	93.012	-0.024	-0.024	0.000	0.000	0.000	0.000
69	B	75	LEU	0	0.000	-0.009	94.900	-0.029	-0.029	0.000	0.000	0.000	0.000
70	B	76	LEU	0	-0.010	0.008	96.538	-0.036	-0.036	0.000	0.000	0.000	0.000
71	B	77	PRO	0	0.049	0.030	98.175	-0.033	-0.033	0.000	0.000	0.000	0.000
72	B	78	VAL	0	-0.025	-0.001	101.153	-0.036	-0.036	0.000	0.000	0.000	0.000
73	B	79	LEU	0	-0.017	-0.012	102.931	-0.033	-0.033	0.000	0.000	0.000	0.000
74	B	80	ASP	-1	-0.860	-0.927	101.616	3.165	3.165	0.000	0.000	0.000	0.000
75	B	81	ASP	-1	-0.882	-0.946	104.873	3.068	3.068	0.000	0.000	0.000	0.000
76	B	82	LEU	0	-0.086	-0.039	106.810	-0.039	-0.039	0.000	0.000	0.000	0.000
77	B	83	ASP	-1	-0.862	-0.924	108.055	2.958	2.958	0.000	0.000	0.000	0.000
78	B	84	ARG	1	0.836	0.906	104.717	-3.093	-3.093	0.000	0.000	0.000	0.000
79	B	85	ALA	0	-0.081	-0.054	110.559	-0.030	-0.030	0.000	0.000	0.000	0.000
80	B	86	LEU	0	-0.010	-0.020	112.884	-0.035	-0.035	0.000	0.000	0.000	0.000
81	B	87	GLU	-1	-0.910	-0.938	111.882	2.890	2.890	0.000	0.000	0.000	0.000
82	B	88	PHE	0	-0.066	-0.044	111.570	-0.018	-0.018	0.000	0.000	0.000	0.000
83	B	89	ALA	0	-0.063	-0.032	116.802	-0.028	-0.028	0.000	0.000	0.000	0.000
84	B	90	GLU	-1	-0.897	-0.935	118.452	2.686	2.686	0.000	0.000	0.000	0.000
85	B	91	ALA	0	-0.080	-0.020	120.026	-0.025	-0.025	0.000	0.000	0.000	0.000
86	B	92	SER	0	-0.048	-0.036	120.975	-0.024	-0.024	0.000	0.000	0.000	0.000
87	B	93	PRO	0	0.069	0.043	121.363	0.022	0.022	0.000	0.000	0.000	0.000
88	B	94	GLU	-1	-0.882	-0.939	121.785	2.623	2.623	0.000	0.000	0.000	0.000
89	B	95	SER	0	-0.083	-0.061	118.189	0.024	0.024	0.000	0.000	0.000	0.000
90	B	96	ILE	0	0.081	0.044	115.728	0.031	0.031	0.000	0.000	0.000	0.000
91	B	97	ARG	1	0.872	0.930	116.272	-2.696	-2.696	0.000	0.000	0.000	0.000
92	B	98	GLN	0	0.005	-0.007	115.403	0.020	0.020	0.000	0.000	0.000	0.000
93	B	99	GLY	0	0.061	0.039	112.906	0.028	0.028	0.000	0.000	0.000	0.000
94	B	100	VAL	0	0.047	0.021	111.455	0.034	0.034	0.000	0.000	0.000	0.000
95	B	101	ARG	1	0.909	0.963	110.906	-2.808	-2.808	0.000	0.000	0.000	0.000
96	B	102	ALA	0	0.019	0.009	109.294	0.027	0.027	0.000	0.000	0.000	0.000
97	B	103	ILE	0	0.056	0.033	106.609	0.036	0.036	0.000	0.000	0.000	0.000
98	B	104	ARG	1	0.818	0.900	105.959	-2.936	-2.936	0.000	0.000	0.000	0.000
99	B	105	ASP	-1	-0.801	-0.900	105.615	3.021	3.021	0.000	0.000	0.000	0.000
100	B	106	GLY	0	-0.040	-0.017	103.448	0.036	0.036	0.000	0.000	0.000	0.000
101	B	107	PHE	0	0.036	0.006	100.502	0.042	0.042	0.000	0.000	0.000	0.000
102	B	108	PHE	0	-0.035	-0.009	100.477	0.029	0.029	0.000	0.000	0.000	0.000
103	B	109	ARG	1	0.913	0.959	99.140	-3.105	-3.105	0.000	0.000	0.000	0.000
104	B	110	ILE	0	0.038	0.021	96.571	0.041	0.041	0.000	0.000	0.000	0.000
105	B	111	LEU	0	-0.012	-0.006	95.618	0.044	0.044	0.000	0.000	0.000	0.000
106	B	112	ALA	0	0.045	0.022	94.763	0.039	0.039	0.000	0.000	0.000	0.000
107	B	113	GLY	0	-0.023	0.011	93.016	0.045	0.045	0.000	0.000	0.000	0.000
108	B	114	LEU	0	-0.131	-0.068	90.793	0.055	0.055	0.000	0.000	0.000	0.000
109	B	115	GLY	0	-0.014	-0.006	90.292	0.035	0.035	0.000	0.000	0.000	0.000
110	B	116	VAL	0	-0.077	-0.045	91.368	0.011	0.011	0.000	0.000	0.000	0.000
111	B	117	GLU	-1	-0.834	-0.903	93.214	3.421	3.421	0.000	0.000	0.000	0.000
112	B	118	GLU	-1	-0.864	-0.927	96.451	3.102	3.102	0.000	0.000	0.000	0.000
113	B	119	VAL	0	-0.060	-0.032	97.247	0.014	0.014	0.000	0.000	0.000	0.000
114	B	120	PRO	0	0.029	0.019	98.658	-0.030	-0.030	0.000	0.000	0.000	0.000
115	B	121	GLY	0	0.062	0.026	101.581	-0.007	-0.007	0.000	0.000	0.000	0.000
116	B	122	GLU	-1	-0.832	-0.914	105.261	2.861	2.861	0.000	0.000	0.000	0.000
117	B	123	GLY	0	-0.024	-0.003	108.017	0.008	0.008	0.000	0.000	0.000	0.000
118	B	124	GLU	-1	-0.920	-0.965	103.064	3.136	3.136	0.000	0.000	0.000	0.000
119	B	125	ALA	0	-0.026	-0.011	102.117	-0.024	-0.024	0.000	0.000	0.000	0.000
120	B	126	PHE	0	0.012	-0.004	102.406	0.022	0.022	0.000	0.000	0.000	0.000
121	B	127	ASP	-1	-0.777	-0.891	97.097	3.343	3.343	0.000	0.000	0.000	0.000
122	B	128	PRO	0	-0.016	-0.002	97.513	-0.004	-0.004	0.000	0.000	0.000	0.000
123	B	129	ARG	1	0.815	0.910	91.813	-3.388	-3.388	0.000	0.000	0.000	0.000
124	B	130	TYR	0	0.014	-0.022	93.115	0.021	0.021	0.000	0.000	0.000	0.000
125	B	131	HIS	0	-0.061	-0.030	98.420	-0.028	-0.028	0.000	0.000	0.000	0.000
126	B	132	GLU	-1	-0.875	-0.938	101.592	3.096	3.096	0.000	0.000	0.000	0.000
127	B	133	ALA	0	-0.014	-0.010	103.854	-0.026	-0.026	0.000	0.000	0.000	0.000
128	B	134	VAL	0	-0.022	-0.023	107.016	-0.002	-0.002	0.000	0.000	0.000	0.000
129	B	135	GLY	0	-0.026	-0.013	109.830	-0.025	-0.025	0.000	0.000	0.000	0.000
130	B	136	LEU	0	-0.050	-0.010	111.997	0.023	0.023	0.000	0.000	0.000	0.000
131	B	137	LEU	0	0.008	-0.008	114.456	-0.021	-0.021	0.000	0.000	0.000	0.000
132	B	138	PRO	0	-0.014	0.010	115.432	0.021	0.021	0.000	0.000	0.000	0.000
133	B	139	GLY	0	0.041	0.013	114.503	0.013	0.013	0.000	0.000	0.000	0.000
134	B	140	GLU	-1	-0.926	-0.970	110.811	2.922	2.922	0.000	0.000	0.000	0.000
135	B	141	PRO	0	0.044	0.028	111.352	0.014	0.014	0.000	0.000	0.000	0.000
136	B	142	GLY	0	-0.031	-0.013	107.770	0.022	0.022	0.000	0.000	0.000	0.000
137	B	143	LYS	1	0.888	0.963	106.228	-2.965	-2.965	0.000	0.000	0.000	0.000
138	B	144	VAL	0	-0.025	0.002	105.112	-0.029	-0.029	0.000	0.000	0.000	0.000
139	B	145	ALA	0	0.023	0.008	108.178	-0.007	-0.007	0.000	0.000	0.000	0.000
140	B	146	LYS	1	0.799	0.870	111.045	-2.847	-2.847	0.000	0.000	0.000	0.000
141	B	147	VAL	0	0.018	0.018	106.542	0.018	0.018	0.000	0.000	0.000	0.000
142	B	148	PHE	0	-0.043	-0.020	109.292	-0.018	-0.018	0.000	0.000	0.000	0.000
143	B	149	GLN	0	-0.069	-0.041	104.642	0.016	0.016	0.000	0.000	0.000	0.000
144	B	150	ARG	1	0.888	0.938	103.844	-3.023	-3.023	0.000	0.000	0.000	0.000
145	B	151	GLY	0	0.064	0.040	101.167	0.002	0.002	0.000	0.000	0.000	0.000
146	B	152	PHE	0	-0.032	-0.011	97.303	-0.012	-0.012	0.000	0.000	0.000	0.000
147	B	153	ARG	1	0.859	0.931	92.266	-3.430	-3.430	0.000	0.000	0.000	0.000
148	B	154	MET	0	-0.004	0.010	88.138	-0.007	-0.007	0.000	0.000	0.000	0.000
149	B	155	GLY	0	-0.019	-0.015	88.665	0.039	0.039	0.000	0.000	0.000	0.000
150	B	156	GLU	-1	-0.911	-0.954	85.514	3.640	3.640	0.000	0.000	0.000	0.000
151	B	157	ALA	0	-0.025	-0.004	88.167	-0.028	-0.028	0.000	0.000	0.000	0.000
152	B	158	LEU	0	0.025	-0.002	89.874	-0.023	-0.023	0.000	0.000	0.000	0.000
153	B	159	VAL	0	-0.057	-0.023	93.544	0.004	0.004	0.000	0.000	0.000	0.000
154	B	160	ARG	1	0.896	0.928	95.001	-3.152	-3.152	0.000	0.000	0.000	0.000
155	B	161	PRO	0	0.062	0.044	98.160	0.005	0.005	0.000	0.000	0.000	0.000
156	B	162	ALA	0	-0.024	-0.008	100.140	-0.022	-0.022	0.000	0.000	0.000	0.000
157	B	163	ARG	1	0.929	0.979	103.487	-2.976	-2.976	0.000	0.000	0.000	0.000
158	B	164	VAL	0	-0.009	-0.014	105.819	-0.020	-0.020	0.000	0.000	0.000	0.000
159	B	165	ALA	0	0.020	0.024	108.143	-0.003	-0.003	0.000	0.000	0.000	0.000
160	B	166	VAL	0	0.002	-0.003	107.492	0.011	0.011	0.000	0.000	0.000	0.000
161	B	167	GLY	0	0.045	0.026	110.438	-0.027	-0.027	0.000	0.000	0.000	0.000
162	B	168	GLU	-1	-0.934	-0.980	112.558	2.740	2.740	0.000	0.000	0.000	0.000
163	B	169	GLU	-1	-0.952	-0.979	112.358	2.853	2.853	0.000	0.000	0.000	0.000
164	B	170	LYS	1	0.952	0.972	115.251	-2.668	-2.668	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(B:7:GLU)