FMO DATABASE

FMODB ID: 395RL

Calculation Name: 3LOD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LOD

Chain ID: A

ChEMBL ID:

UniProt ID: A6T8Z3

Base Structure: X-ray

Registration Date: 2023-09-20

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	145
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1322436.892147
FMO2-HF: Nuclear repulsion	1265869.739498
FMO2-HF: Total energy	-56567.152648
FMO2-MP2: Total energy	-56731.042885

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:ASN)

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

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.
-29.819	-28.556	11.596	-5.372	-7.488	0.042

Interaction energy analysis for fragmet #1(A:-1:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.051 / 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	1	MET	0	-0.086	-0.046	1.831	-11.506	-12.965	11.222	-4.915	-4.848	0.043
4	A	2	TYR	0	0.030	0.024	3.253	-6.251	-5.182	0.223	0.193	-1.486	0.006
5	A	3	THR	0	-0.026	-0.019	5.570	0.284	0.324	-0.001	0.001	-0.039	0.000
6	A	4	ILE	0	-0.003	-0.004	9.128	-0.331	-0.331	0.000	0.000	0.000	0.000
7	A	5	THR	0	-0.020	-0.004	12.367	0.036	0.036	0.000	0.000	0.000	0.000
8	A	6	ASP	-1	-0.813	-0.900	15.807	0.292	0.292	0.000	0.000	0.000	0.000
9	A	7	ILE	0	-0.025	-0.015	18.300	0.006	0.006	0.000	0.000	0.000	0.000
10	A	8	ALA	0	0.032	0.028	20.804	-0.009	-0.009	0.000	0.000	0.000	0.000
11	A	9	PRO	0	0.030	0.004	23.563	-0.018	-0.018	0.000	0.000	0.000	0.000
12	A	10	THR	0	-0.004	-0.023	25.270	-0.019	-0.019	0.000	0.000	0.000	0.000
13	A	11	ASP	-1	-0.858	-0.916	21.524	0.004	0.004	0.000	0.000	0.000	0.000
14	A	12	ALA	0	0.033	0.004	23.513	-0.022	-0.022	0.000	0.000	0.000	0.000
15	A	13	GLU	-1	-0.795	-0.880	16.425	-0.078	-0.078	0.000	0.000	0.000	0.000
16	A	14	PHE	0	-0.046	-0.017	19.545	-0.042	-0.042	0.000	0.000	0.000	0.000
17	A	15	ILE	0	0.008	-0.004	21.131	-0.036	-0.036	0.000	0.000	0.000	0.000
18	A	16	ALA	0	0.001	0.012	20.382	-0.022	-0.022	0.000	0.000	0.000	0.000
19	A	17	LEU	0	-0.008	-0.006	15.724	-0.049	-0.049	0.000	0.000	0.000	0.000
20	A	18	ILE	0	-0.009	0.001	19.780	-0.031	-0.031	0.000	0.000	0.000	0.000
21	A	19	ALA	0	0.020	0.018	23.010	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	20	ALA	0	0.008	0.002	20.409	-0.009	-0.009	0.000	0.000	0.000	0.000
23	A	21	LEU	0	-0.069	-0.038	20.826	-0.027	-0.027	0.000	0.000	0.000	0.000
24	A	22	ASP	-1	-0.798	-0.881	22.227	-0.210	-0.210	0.000	0.000	0.000	0.000
25	A	23	ALA	0	-0.010	0.009	24.679	0.005	0.005	0.000	0.000	0.000	0.000
26	A	24	TRP	0	-0.022	-0.010	21.008	-0.021	-0.021	0.000	0.000	0.000	0.000
27	A	25	GLN	0	-0.080	-0.057	24.230	0.005	0.005	0.000	0.000	0.000	0.000
28	A	26	GLU	-1	-0.861	-0.905	26.382	-0.205	-0.205	0.000	0.000	0.000	0.000
29	A	27	THR	0	-0.170	-0.079	26.300	0.015	0.015	0.000	0.000	0.000	0.000
30	A	37	LEU	0	0.061	0.011	29.091	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	38	ASP	-1	-0.926	-0.974	31.119	-0.033	-0.033	0.000	0.000	0.000	0.000
32	A	39	LEU	0	0.006	-0.003	25.652	0.010	0.010	0.000	0.000	0.000	0.000
33	A	40	SER	0	-0.078	-0.028	29.597	0.017	0.017	0.000	0.000	0.000	0.000
34	A	41	GLN	0	-0.029	-0.014	30.827	0.003	0.003	0.000	0.000	0.000	0.000
35	A	42	LEU	0	0.018	0.020	31.267	0.007	0.007	0.000	0.000	0.000	0.000
36	A	43	PRO	0	0.045	0.022	33.142	0.007	0.007	0.000	0.000	0.000	0.000
37	A	44	PRO	0	0.064	0.035	30.265	0.005	0.005	0.000	0.000	0.000	0.000
38	A	45	GLN	0	0.024	0.018	29.454	0.008	0.008	0.000	0.000	0.000	0.000
39	A	46	THR	0	-0.071	-0.040	29.983	0.012	0.012	0.000	0.000	0.000	0.000
40	A	47	VAL	0	0.013	0.012	25.887	-0.009	-0.009	0.000	0.000	0.000	0.000
41	A	48	ILE	0	-0.021	0.002	21.687	0.025	0.025	0.000	0.000	0.000	0.000
42	A	49	ALA	0	0.027	0.012	21.548	-0.034	-0.034	0.000	0.000	0.000	0.000
43	A	50	LEU	0	-0.012	-0.002	16.346	0.056	0.056	0.000	0.000	0.000	0.000
44	A	51	ALA	0	0.031	0.007	15.130	-0.099	-0.099	0.000	0.000	0.000	0.000
45	A	52	ILE	0	-0.037	-0.024	8.932	0.202	0.202	0.000	0.000	0.000	0.000
46	A	53	ARG	1	0.760	0.855	10.159	-0.474	-0.474	0.000	0.000	0.000	0.000
47	A	54	SER	0	0.065	0.030	6.459	0.728	0.728	0.000	0.000	0.000	0.000
48	A	55	PRO	0	-0.008	-0.021	3.717	0.133	0.351	0.000	-0.033	-0.185	0.000
49	A	56	GLN	0	-0.029	-0.009	6.667	0.065	0.065	0.000	0.000	0.000	0.000
50	A	57	GLY	0	0.046	0.034	9.620	0.161	0.161	0.000	0.000	0.000	0.000
51	A	58	GLU	-1	-0.938	-0.963	10.764	-0.976	-0.976	0.000	0.000	0.000	0.000
52	A	59	ALA	0	-0.006	0.009	11.193	0.019	0.019	0.000	0.000	0.000	0.000
53	A	60	VAL	0	0.011	0.011	8.938	-0.121	-0.121	0.000	0.000	0.000	0.000
54	A	61	GLY	0	0.009	-0.012	12.284	-0.184	-0.184	0.000	0.000	0.000	0.000
55	A	62	CYS	0	-0.035	-0.004	14.176	0.126	0.126	0.000	0.000	0.000	0.000
56	A	63	GLY	0	0.023	0.012	16.773	-0.076	-0.076	0.000	0.000	0.000	0.000
57	A	64	ALA	0	0.005	-0.001	19.365	0.057	0.057	0.000	0.000	0.000	0.000
58	A	65	ILE	0	-0.031	-0.012	22.342	-0.027	-0.027	0.000	0.000	0.000	0.000
59	A	66	VAL	0	0.010	0.013	25.003	0.018	0.018	0.000	0.000	0.000	0.000
60	A	67	LEU	0	-0.009	-0.004	27.430	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	68	SER	0	-0.049	-0.024	30.572	-0.006	-0.006	0.000	0.000	0.000	0.000
62	A	69	GLU	-1	-0.918	-0.980	34.191	0.057	0.057	0.000	0.000	0.000	0.000
63	A	70	GLU	-1	-0.915	-0.952	36.691	0.055	0.055	0.000	0.000	0.000	0.000
64	A	71	GLY	0	0.036	0.030	33.030	0.001	0.001	0.000	0.000	0.000	0.000
65	A	72	PHE	0	-0.008	0.000	31.571	0.004	0.004	0.000	0.000	0.000	0.000
66	A	73	GLY	0	0.055	0.019	28.268	0.010	0.010	0.000	0.000	0.000	0.000
67	A	74	GLU	-1	-0.842	-0.884	28.430	-0.063	-0.063	0.000	0.000	0.000	0.000
68	A	75	MET	0	-0.025	-0.007	20.511	0.000	0.000	0.000	0.000	0.000	0.000
69	A	76	LYS	1	0.868	0.909	24.035	0.027	0.027	0.000	0.000	0.000	0.000
70	A	77	ARG	1	0.789	0.851	22.975	0.179	0.179	0.000	0.000	0.000	0.000
71	A	78	VAL	0	0.034	0.025	17.387	0.009	0.009	0.000	0.000	0.000	0.000
72	A	79	TYR	0	0.029	0.014	16.910	-0.065	-0.065	0.000	0.000	0.000	0.000
73	A	80	ILE	0	-0.018	-0.011	10.713	0.059	0.059	0.000	0.000	0.000	0.000
74	A	81	ASP	-1	-0.737	-0.874	12.934	-1.107	-1.107	0.000	0.000	0.000	0.000
75	A	82	PRO	0	-0.028	-0.026	12.190	-0.259	-0.259	0.000	0.000	0.000	0.000
76	A	83	GLN	0	-0.065	-0.023	11.147	-0.164	-0.164	0.000	0.000	0.000	0.000
77	A	84	HIS	0	0.051	0.033	7.952	-0.906	-0.906	0.000	0.000	0.000	0.000
78	A	85	ARG	1	0.831	0.921	7.622	0.645	0.645	0.000	0.000	0.000	0.000
79	A	86	GLY	0	0.022	0.006	8.522	-0.320	-0.320	0.000	0.000	0.000	0.000
80	A	87	GLN	0	-0.052	-0.035	2.936	-5.271	-3.876	0.152	-0.618	-0.930	-0.007
81	A	88	GLN	0	-0.008	0.003	5.254	-0.995	-0.995	0.000	0.000	0.000	0.000
82	A	89	LEU	0	0.055	0.032	5.737	0.754	0.754	0.000	0.000	0.000	0.000
83	A	90	GLY	0	0.008	0.011	8.968	0.364	0.364	0.000	0.000	0.000	0.000
84	A	91	GLU	-1	-0.778	-0.886	10.258	-0.695	-0.695	0.000	0.000	0.000	0.000
85	A	92	LYS	1	0.838	0.927	6.578	-3.751	-3.751	0.000	0.000	0.000	0.000
86	A	93	LEU	0	0.016	-0.006	10.944	0.151	0.151	0.000	0.000	0.000	0.000
87	A	94	LEU	0	0.021	0.012	13.576	0.039	0.039	0.000	0.000	0.000	0.000
88	A	95	ALA	0	0.007	-0.001	14.108	0.027	0.027	0.000	0.000	0.000	0.000
89	A	96	ALA	0	0.011	0.013	14.153	0.040	0.040	0.000	0.000	0.000	0.000
90	A	97	LEU	0	-0.005	-0.007	16.217	-0.010	-0.010	0.000	0.000	0.000	0.000
91	A	98	GLU	-1	-0.747	-0.842	19.241	0.110	0.110	0.000	0.000	0.000	0.000
92	A	99	ALA	0	-0.072	-0.030	18.767	-0.006	-0.006	0.000	0.000	0.000	0.000
93	A	100	LYS	1	0.849	0.901	19.595	-0.378	-0.378	0.000	0.000	0.000	0.000
94	A	101	ALA	0	0.019	0.015	22.119	-0.022	-0.022	0.000	0.000	0.000	0.000
95	A	102	ARG	1	0.883	0.931	20.671	-0.250	-0.250	0.000	0.000	0.000	0.000
96	A	103	GLN	0	-0.072	-0.023	21.375	-0.022	-0.022	0.000	0.000	0.000	0.000
97	A	104	ARG	1	0.820	0.896	26.412	-0.172	-0.172	0.000	0.000	0.000	0.000
98	A	105	ASP	-1	-0.908	-0.935	28.799	0.155	0.155	0.000	0.000	0.000	0.000
99	A	106	CYS	0	-0.119	-0.038	27.510	-0.022	-0.022	0.000	0.000	0.000	0.000
100	A	107	HIS	0	0.034	0.004	28.598	0.015	0.015	0.000	0.000	0.000	0.000
101	A	108	THR	0	-0.054	-0.034	28.640	-0.006	-0.006	0.000	0.000	0.000	0.000
102	A	109	LEU	0	-0.028	-0.001	23.230	0.002	0.002	0.000	0.000	0.000	0.000
103	A	110	ARG	1	0.905	0.941	27.049	-0.012	-0.012	0.000	0.000	0.000	0.000
104	A	111	LEU	0	-0.032	-0.011	23.042	0.007	0.007	0.000	0.000	0.000	0.000
105	A	112	GLU	-1	-0.831	-0.911	27.212	-0.151	-0.151	0.000	0.000	0.000	0.000
106	A	113	THR	0	-0.051	-0.007	23.471	-0.016	-0.016	0.000	0.000	0.000	0.000
107	A	114	GLY	0	0.148	0.072	26.946	0.011	0.011	0.000	0.000	0.000	0.000
108	A	115	ILE	0	0.011	-0.013	26.717	-0.020	-0.020	0.000	0.000	0.000	0.000
109	A	116	HIS	0	0.006	0.006	26.893	-0.019	-0.019	0.000	0.000	0.000	0.000
110	A	117	GLN	0	-0.034	-0.010	22.652	-0.018	-0.018	0.000	0.000	0.000	0.000
111	A	118	HIS	0	0.059	0.021	21.939	-0.009	-0.009	0.000	0.000	0.000	0.000
112	A	119	ALA	0	-0.015	-0.011	16.642	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	120	ALA	0	-0.004	0.011	17.671	-0.013	-0.013	0.000	0.000	0.000	0.000
114	A	121	ILE	0	0.076	0.036	19.294	0.029	0.029	0.000	0.000	0.000	0.000
115	A	122	ALA	0	0.009	0.007	18.210	0.037	0.037	0.000	0.000	0.000	0.000
116	A	123	LEU	0	-0.061	-0.027	13.787	-0.003	-0.003	0.000	0.000	0.000	0.000
117	A	124	TYR	0	0.055	0.019	16.877	0.047	0.047	0.000	0.000	0.000	0.000
118	A	125	THR	0	-0.002	-0.008	19.856	0.048	0.048	0.000	0.000	0.000	0.000
119	A	126	ARG	1	0.773	0.869	12.093	0.686	0.686	0.000	0.000	0.000	0.000
120	A	127	ASN	0	-0.087	-0.044	14.649	0.081	0.081	0.000	0.000	0.000	0.000
121	A	128	GLY	0	0.039	0.014	18.470	0.048	0.048	0.000	0.000	0.000	0.000
122	A	129	TYR	0	-0.044	-0.026	20.243	0.014	0.014	0.000	0.000	0.000	0.000
123	A	130	GLN	0	-0.020	-0.013	23.922	-0.026	-0.026	0.000	0.000	0.000	0.000
124	A	131	THR	0	0.026	0.014	27.099	0.002	0.002	0.000	0.000	0.000	0.000
125	A	132	ARG	1	0.778	0.878	29.400	0.048	0.048	0.000	0.000	0.000	0.000
126	A	133	CYS	0	-0.015	-0.017	32.609	-0.011	-0.011	0.000	0.000	0.000	0.000
127	A	134	ALA	0	0.057	0.026	34.550	0.004	0.004	0.000	0.000	0.000	0.000
128	A	135	PHE	0	-0.036	-0.010	30.350	0.010	0.010	0.000	0.000	0.000	0.000
129	A	136	ALA	0	0.026	0.047	36.150	-0.006	-0.006	0.000	0.000	0.000	0.000
130	A	137	PRO	0	-0.019	-0.018	34.638	0.005	0.005	0.000	0.000	0.000	0.000
131	A	138	TYR	0	0.020	-0.045	30.785	-0.008	-0.008	0.000	0.000	0.000	0.000
132	A	139	GLN	0	0.004	-0.018	36.889	0.006	0.006	0.000	0.000	0.000	0.000
133	A	140	PRO	0	-0.042	-0.051	36.919	-0.006	-0.006	0.000	0.000	0.000	0.000
134	A	141	ASP	-1	-0.891	-0.935	35.433	-0.116	-0.116	0.000	0.000	0.000	0.000
135	A	142	PRO	0	-0.236	0.021	34.989	-0.008	-0.008	0.000	0.000	0.000	0.000
136	A	143	LEU	0	0.036	-0.042	32.387	0.004	0.004	0.000	0.000	0.000	0.000
137	A	144	SER	0	0.094	-0.006	31.097	-0.007	-0.007	0.000	0.000	0.000	0.000
138	A	145	VAL	0	-0.082	-0.051	27.283	0.006	0.006	0.000	0.000	0.000	0.000
139	A	146	PHE	0	0.018	0.018	28.736	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	147	MET	0	-0.046	-0.030	23.542	-0.012	-0.012	0.000	0.000	0.000	0.000
141	A	148	GLU	-1	-0.802	-0.883	27.016	0.003	0.003	0.000	0.000	0.000	0.000
142	A	149	LYS	1	0.861	0.916	19.876	-0.081	-0.081	0.000	0.000	0.000	0.000
143	A	150	PRO	0	-0.020	0.016	26.139	0.010	0.010	0.000	0.000	0.000	0.000
144	A	151	LEU	0	-0.027	-0.024	23.283	0.010	0.010	0.000	0.000	0.000	0.000
145	A	152	PHE	0	0.009	0.012	25.386	0.030	0.030	0.000	0.000	0.000	0.000

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