FMO DATABASE

FMODB ID: JLZG9

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	OptH
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	-1321081.182224
FMO2-HF: Nuclear repulsion	1264515.577303
FMO2-HF: Total energy	-56565.60492
FMO2-MP2: Total energy	-56729.643282

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.
-28.425	-29.808	13.87	-4.672	-7.814	0.038

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 : 0.027 / q_NPA : -0.011

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	-0.078	-0.050	1.870	-9.349	-12.698	13.477	-4.759	-5.370	0.047
4	A	2	TYR	0	-0.008	0.007	3.161	-5.219	-5.204	0.047	1.019	-1.081	0.003
5	A	3	THR	0	-0.050	-0.027	5.798	0.631	0.660	-0.001	0.001	-0.028	0.000
6	A	4	ILE	0	0.020	0.003	9.264	-0.378	-0.378	0.000	0.000	0.000	0.000
7	A	5	THR	0	-0.051	-0.016	12.569	0.044	0.044	0.000	0.000	0.000	0.000
8	A	6	ASP	-1	-0.870	-0.938	15.987	0.381	0.381	0.000	0.000	0.000	0.000
9	A	7	ILE	0	-0.046	-0.024	18.912	-0.002	-0.002	0.000	0.000	0.000	0.000
10	A	8	ALA	0	0.016	0.021	21.084	-0.002	-0.002	0.000	0.000	0.000	0.000
11	A	9	PRO	0	0.034	-0.002	24.013	-0.026	-0.026	0.000	0.000	0.000	0.000
12	A	10	THR	0	0.000	-0.021	25.635	-0.022	-0.022	0.000	0.000	0.000	0.000
13	A	11	ASP	-1	-0.845	-0.910	21.911	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	12	ALA	0	0.031	-0.002	24.169	-0.021	-0.021	0.000	0.000	0.000	0.000
15	A	13	GLU	-1	-0.835	-0.926	16.910	-0.166	-0.166	0.000	0.000	0.000	0.000
16	A	14	PHE	0	-0.056	-0.014	20.327	-0.041	-0.041	0.000	0.000	0.000	0.000
17	A	15	ILE	0	0.007	-0.008	21.875	-0.035	-0.035	0.000	0.000	0.000	0.000
18	A	16	ALA	0	0.010	0.015	21.193	-0.021	-0.021	0.000	0.000	0.000	0.000
19	A	17	LEU	0	-0.009	-0.008	16.286	-0.051	-0.051	0.000	0.000	0.000	0.000
20	A	18	ILE	0	-0.015	0.000	19.998	-0.027	-0.027	0.000	0.000	0.000	0.000
21	A	19	ALA	0	0.023	0.016	22.964	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	20	ALA	0	0.003	0.005	20.218	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	21	LEU	0	-0.085	-0.048	20.604	-0.028	-0.028	0.000	0.000	0.000	0.000
24	A	22	ASP	-1	-0.835	-0.924	22.169	-0.203	-0.203	0.000	0.000	0.000	0.000
25	A	23	ALA	0	-0.009	0.007	24.683	0.004	0.004	0.000	0.000	0.000	0.000
26	A	24	TRP	0	-0.041	-0.018	21.369	-0.020	-0.020	0.000	0.000	0.000	0.000
27	A	25	GLN	0	-0.071	-0.052	24.238	0.013	0.013	0.000	0.000	0.000	0.000
28	A	26	GLU	-1	-0.863	-0.913	26.402	-0.209	-0.209	0.000	0.000	0.000	0.000
29	A	27	THR	0	-0.183	-0.085	26.480	0.001	0.001	0.000	0.000	0.000	0.000
30	A	37	LEU	0	0.064	0.020	29.299	0.000	0.000	0.000	0.000	0.000	0.000
31	A	38	ASP	-1	-0.899	-0.973	31.271	0.000	0.000	0.000	0.000	0.000	0.000
32	A	39	LEU	0	-0.010	-0.009	25.721	0.012	0.012	0.000	0.000	0.000	0.000
33	A	40	SER	0	-0.062	-0.024	29.933	0.017	0.017	0.000	0.000	0.000	0.000
34	A	41	GLN	0	-0.043	-0.016	31.210	0.001	0.001	0.000	0.000	0.000	0.000
35	A	42	LEU	0	-0.007	0.006	31.618	0.007	0.007	0.000	0.000	0.000	0.000
36	A	43	PRO	0	0.042	0.012	33.475	0.007	0.007	0.000	0.000	0.000	0.000
37	A	44	PRO	0	0.069	0.060	30.735	0.009	0.009	0.000	0.000	0.000	0.000
38	A	45	GLN	0	0.029	0.020	29.721	0.013	0.013	0.000	0.000	0.000	0.000
39	A	46	THR	0	-0.079	-0.061	30.234	0.019	0.019	0.000	0.000	0.000	0.000
40	A	47	VAL	0	0.019	0.017	26.169	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	48	ILE	0	-0.016	0.004	21.964	0.026	0.026	0.000	0.000	0.000	0.000
42	A	49	ALA	0	0.013	0.006	21.928	-0.034	-0.034	0.000	0.000	0.000	0.000
43	A	50	LEU	0	-0.022	-0.008	16.696	0.061	0.061	0.000	0.000	0.000	0.000
44	A	51	ALA	0	0.044	0.010	15.427	-0.109	-0.109	0.000	0.000	0.000	0.000
45	A	52	ILE	0	-0.027	-0.022	9.281	0.212	0.212	0.000	0.000	0.000	0.000
46	A	53	ARG	1	0.838	0.928	10.480	-0.546	-0.546	0.000	0.000	0.000	0.000
47	A	54	SER	0	0.065	0.026	7.147	0.738	0.738	0.000	0.000	0.000	0.000
48	A	55	PRO	0	-0.017	-0.027	3.542	0.036	0.277	0.001	-0.037	-0.206	0.000
49	A	56	GLN	0	-0.032	-0.004	6.866	0.104	0.104	0.000	0.000	0.000	0.000
50	A	57	GLY	0	0.030	0.021	10.030	0.183	0.183	0.000	0.000	0.000	0.000
51	A	58	GLU	-1	-0.953	-0.972	11.573	-1.095	-1.095	0.000	0.000	0.000	0.000
52	A	59	ALA	0	-0.015	0.001	11.884	0.017	0.017	0.000	0.000	0.000	0.000
53	A	60	VAL	0	0.007	0.012	9.481	-0.124	-0.124	0.000	0.000	0.000	0.000
54	A	61	GLY	0	0.011	-0.015	12.876	-0.188	-0.188	0.000	0.000	0.000	0.000
55	A	62	CYS	0	-0.029	-0.001	14.116	0.131	0.131	0.000	0.000	0.000	0.000
56	A	63	GLY	0	0.014	0.009	16.968	-0.071	-0.071	0.000	0.000	0.000	0.000
57	A	64	ALA	0	0.010	-0.002	19.550	0.059	0.059	0.000	0.000	0.000	0.000
58	A	65	ILE	0	-0.034	-0.008	22.481	-0.022	-0.022	0.000	0.000	0.000	0.000
59	A	66	VAL	0	0.007	0.009	25.365	0.013	0.013	0.000	0.000	0.000	0.000
60	A	67	LEU	0	-0.016	-0.010	27.888	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	68	SER	0	-0.049	-0.012	30.887	-0.014	-0.014	0.000	0.000	0.000	0.000
62	A	69	GLU	-1	-0.917	-0.977	34.476	0.117	0.117	0.000	0.000	0.000	0.000
63	A	70	GLU	-1	-0.904	-0.944	36.908	0.125	0.125	0.000	0.000	0.000	0.000
64	A	71	GLY	0	0.030	0.021	33.191	0.004	0.004	0.000	0.000	0.000	0.000
65	A	72	PHE	0	-0.019	-0.005	31.575	0.013	0.013	0.000	0.000	0.000	0.000
66	A	73	GLY	0	0.038	0.010	28.374	0.006	0.006	0.000	0.000	0.000	0.000
67	A	74	GLU	-1	-0.917	-0.958	28.238	0.009	0.009	0.000	0.000	0.000	0.000
68	A	75	MET	0	-0.045	-0.009	20.934	0.004	0.004	0.000	0.000	0.000	0.000
69	A	76	LYS	1	0.977	0.975	24.071	-0.035	-0.035	0.000	0.000	0.000	0.000
70	A	77	ARG	1	0.828	0.899	22.949	0.150	0.150	0.000	0.000	0.000	0.000
71	A	78	VAL	0	0.032	0.027	17.297	0.010	0.010	0.000	0.000	0.000	0.000
72	A	79	TYR	0	0.052	0.016	17.324	-0.095	-0.095	0.000	0.000	0.000	0.000
73	A	80	ILE	0	-0.022	-0.011	10.790	0.070	0.070	0.000	0.000	0.000	0.000
74	A	81	ASP	-1	-0.735	-0.886	12.712	-1.321	-1.321	0.000	0.000	0.000	0.000
75	A	82	PRO	0	-0.040	-0.031	12.156	-0.281	-0.281	0.000	0.000	0.000	0.000
76	A	83	GLN	0	-0.048	-0.010	11.421	-0.222	-0.222	0.000	0.000	0.000	0.000
77	A	84	HIS	0	0.047	0.031	7.994	-1.038	-1.038	0.000	0.000	0.000	0.000
78	A	85	ARG	1	0.814	0.918	7.653	0.720	0.720	0.000	0.000	0.000	0.000
79	A	86	GLY	0	0.008	-0.001	8.690	-0.381	-0.381	0.000	0.000	0.000	0.000
80	A	87	GLN	0	-0.026	-0.014	2.718	-7.098	-5.329	0.347	-0.887	-1.228	-0.012
81	A	88	GLN	0	0.014	0.008	4.927	-0.525	-0.613	-0.001	-0.009	0.099	0.000
82	A	89	LEU	0	0.050	0.030	5.566	0.830	0.830	0.000	0.000	0.000	0.000
83	A	90	GLY	0	-0.005	0.004	8.944	0.378	0.378	0.000	0.000	0.000	0.000
84	A	91	GLU	-1	-0.896	-0.961	10.128	0.270	0.270	0.000	0.000	0.000	0.000
85	A	92	LYS	1	0.886	0.957	6.688	-4.452	-4.452	0.000	0.000	0.000	0.000
86	A	93	LEU	0	0.002	-0.004	10.944	0.136	0.136	0.000	0.000	0.000	0.000
87	A	94	LEU	0	0.015	0.004	13.793	0.022	0.022	0.000	0.000	0.000	0.000
88	A	95	ALA	0	0.023	0.011	14.204	0.007	0.007	0.000	0.000	0.000	0.000
89	A	96	ALA	0	-0.005	0.006	14.402	0.025	0.025	0.000	0.000	0.000	0.000
90	A	97	LEU	0	-0.013	-0.011	16.441	-0.037	-0.037	0.000	0.000	0.000	0.000
91	A	98	GLU	-1	-0.804	-0.896	19.248	0.383	0.383	0.000	0.000	0.000	0.000
92	A	99	ALA	0	-0.069	-0.032	18.886	-0.020	-0.020	0.000	0.000	0.000	0.000
93	A	100	LYS	1	0.933	0.954	19.782	-0.526	-0.526	0.000	0.000	0.000	0.000
94	A	101	ALA	0	0.030	0.019	22.303	-0.037	-0.037	0.000	0.000	0.000	0.000
95	A	102	ARG	1	0.952	0.973	20.578	-0.535	-0.535	0.000	0.000	0.000	0.000
96	A	103	GLN	0	-0.081	-0.030	21.399	-0.036	-0.036	0.000	0.000	0.000	0.000
97	A	104	ARG	1	0.827	0.909	26.530	-0.279	-0.279	0.000	0.000	0.000	0.000
98	A	105	ASP	-1	-0.893	-0.926	28.970	0.254	0.254	0.000	0.000	0.000	0.000
99	A	106	CYS	0	-0.128	-0.042	27.649	-0.024	-0.024	0.000	0.000	0.000	0.000
100	A	107	HIS	0	0.031	0.008	28.625	0.033	0.033	0.000	0.000	0.000	0.000
101	A	108	THR	0	-0.028	-0.026	28.726	0.004	0.004	0.000	0.000	0.000	0.000
102	A	109	LEU	0	-0.021	-0.002	23.101	-0.006	-0.006	0.000	0.000	0.000	0.000
103	A	110	ARG	1	0.939	0.963	26.953	-0.092	-0.092	0.000	0.000	0.000	0.000
104	A	111	LEU	0	-0.027	-0.006	22.760	0.007	0.007	0.000	0.000	0.000	0.000
105	A	112	GLU	-1	-0.857	-0.936	26.945	-0.102	-0.102	0.000	0.000	0.000	0.000
106	A	113	THR	0	-0.048	-0.008	23.438	-0.018	-0.018	0.000	0.000	0.000	0.000
107	A	114	GLY	0	0.132	0.069	26.799	0.011	0.011	0.000	0.000	0.000	0.000
108	A	115	ILE	0	0.023	-0.005	26.558	-0.015	-0.015	0.000	0.000	0.000	0.000
109	A	116	HIS	0	0.001	0.002	26.933	-0.022	-0.022	0.000	0.000	0.000	0.000
110	A	117	GLN	0	-0.008	0.005	22.465	-0.018	-0.018	0.000	0.000	0.000	0.000
111	A	118	HIS	0	0.058	0.021	21.810	0.014	0.014	0.000	0.000	0.000	0.000
112	A	119	ALA	0	-0.013	-0.013	16.499	0.009	0.009	0.000	0.000	0.000	0.000
113	A	120	ALA	0	-0.008	0.010	17.487	0.011	0.011	0.000	0.000	0.000	0.000
114	A	121	ILE	0	0.084	0.042	19.106	0.050	0.050	0.000	0.000	0.000	0.000
115	A	122	ALA	0	0.000	0.008	18.003	0.050	0.050	0.000	0.000	0.000	0.000
116	A	123	LEU	0	-0.057	-0.021	13.515	0.021	0.021	0.000	0.000	0.000	0.000
117	A	124	TYR	0	0.036	0.006	16.617	0.067	0.067	0.000	0.000	0.000	0.000
118	A	125	THR	0	-0.004	-0.021	19.561	0.055	0.055	0.000	0.000	0.000	0.000
119	A	126	ARG	1	0.902	0.951	12.583	0.368	0.368	0.000	0.000	0.000	0.000
120	A	127	ASN	0	-0.072	-0.028	14.507	0.166	0.166	0.000	0.000	0.000	0.000
121	A	128	GLY	0	0.023	0.007	18.425	0.043	0.043	0.000	0.000	0.000	0.000
122	A	129	TYR	0	-0.038	-0.010	20.133	-0.008	-0.008	0.000	0.000	0.000	0.000
123	A	130	GLN	0	-0.001	-0.011	23.743	-0.035	-0.035	0.000	0.000	0.000	0.000
124	A	131	THR	0	0.010	0.007	26.865	0.004	0.004	0.000	0.000	0.000	0.000
125	A	132	ARG	1	0.901	0.958	29.108	-0.029	-0.029	0.000	0.000	0.000	0.000
126	A	133	CYS	0	-0.025	-0.016	32.312	-0.013	-0.013	0.000	0.000	0.000	0.000
127	A	134	ALA	0	0.065	0.024	34.266	0.007	0.007	0.000	0.000	0.000	0.000
128	A	135	PHE	0	-0.066	-0.026	29.940	0.012	0.012	0.000	0.000	0.000	0.000
129	A	136	ALA	0	0.018	0.051	35.890	-0.009	-0.009	0.000	0.000	0.000	0.000
130	A	137	PRO	0	-0.003	-0.013	34.598	0.009	0.009	0.000	0.000	0.000	0.000
131	A	138	TYR	0	0.024	-0.028	30.647	-0.014	-0.014	0.000	0.000	0.000	0.000
132	A	139	GLN	0	0.020	-0.020	36.759	0.006	0.006	0.000	0.000	0.000	0.000
133	A	140	PRO	0	-0.080	-0.050	36.700	-0.005	-0.005	0.000	0.000	0.000	0.000
134	A	141	ASP	-1	-0.925	-0.951	35.270	-0.094	-0.094	0.000	0.000	0.000	0.000
135	A	142	PRO	0	-0.155	0.014	34.920	-0.008	-0.008	0.000	0.000	0.000	0.000
136	A	143	LEU	0	0.019	-0.012	32.157	0.000	0.000	0.000	0.000	0.000	0.000
137	A	144	SER	0	0.104	0.007	30.917	-0.011	-0.011	0.000	0.000	0.000	0.000
138	A	145	VAL	0	-0.081	-0.046	27.085	0.007	0.007	0.000	0.000	0.000	0.000
139	A	146	PHE	0	0.011	0.015	28.504	0.001	0.001	0.000	0.000	0.000	0.000
140	A	147	MET	0	-0.047	-0.031	23.922	-0.011	-0.011	0.000	0.000	0.000	0.000
141	A	148	GLU	-1	-0.936	-0.977	26.813	0.107	0.107	0.000	0.000	0.000	0.000
142	A	149	LYS	1	0.887	0.943	20.140	-0.339	-0.339	0.000	0.000	0.000	0.000
143	A	150	PRO	0	-0.003	0.021	26.117	0.007	0.007	0.000	0.000	0.000	0.000
144	A	151	LEU	0	-0.039	-0.030	23.553	0.029	0.029	0.000	0.000	0.000	0.000
145	A	152	PHE	0	-0.001	0.002	25.756	0.046	0.046	0.000	0.000	0.000	0.000

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