FMO DATABASE

FMODB ID: GN9K1

Calculation Name: 4LDD-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4LDD

Chain ID: C

ChEMBL ID:

UniProt ID: Q05128

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	143
LigandResidueName
LigandFragmentNumber	0
LigandCharge	DLY=1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1246929.818536
FMO2-HF: Nuclear repulsion	1192893.797142
FMO2-HF: Total energy	-54036.021394
FMO2-MP2: Total energy	-54196.056474

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(C:45:ASP)

Summations of interaction energy for fragment #1(C:45:ASP)

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.
-93.188	-89.64	0.29	-1.588	-2.248	-0.004

Interaction energy analysis for fragmet #1(C:45:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.957 / q_NPA : -0.985

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	C	47	PRO	0	-0.053	-0.046	3.807	-4.118	-2.209	-0.027	-0.897	-0.985	0.003
4	C	48	SER	0	0.000	0.018	6.416	-0.268	-0.268	0.000	0.000	0.000	0.000
5	C	49	ASN	0	0.026	0.019	8.904	0.918	0.918	0.000	0.000	0.000	0.000
6	C	50	PRO	0	-0.008	-0.014	12.517	-0.214	-0.214	0.000	0.000	0.000	0.000
7	C	51	LEU	0	-0.004	0.001	14.883	-0.650	-0.650	0.000	0.000	0.000	0.000
8	C	52	ARG	1	0.903	0.951	17.826	-13.103	-13.103	0.000	0.000	0.000	0.000
9	C	53	PRO	0	-0.015	0.003	20.765	-0.040	-0.040	0.000	0.000	0.000	0.000
10	C	54	ILE	0	-0.002	-0.006	22.170	-0.377	-0.377	0.000	0.000	0.000	0.000
11	C	55	ALA	0	-0.005	-0.010	25.354	0.191	0.191	0.000	0.000	0.000	0.000
12	C	56	ASP	-1	-0.803	-0.893	27.291	9.846	9.846	0.000	0.000	0.000	0.000
13	C	57	ASP	-1	-0.903	-0.952	28.836	9.006	9.006	0.000	0.000	0.000	0.000
14	C	58	THR	0	-0.085	-0.055	30.997	-0.304	-0.304	0.000	0.000	0.000	0.000
15	C	59	ILE	0	-0.084	-0.036	28.691	-0.075	-0.075	0.000	0.000	0.000	0.000
16	C	60	ASP	-1	-0.791	-0.875	33.206	7.550	7.550	0.000	0.000	0.000	0.000
17	C	61	HIS	0	-0.078	-0.058	35.564	-0.043	-0.043	0.000	0.000	0.000	0.000
18	C	62	ALA	0	0.049	0.022	36.537	0.049	0.049	0.000	0.000	0.000	0.000
19	C	63	SER	0	-0.031	-0.041	37.289	-0.122	-0.122	0.000	0.000	0.000	0.000
20	C	64	HIS	1	0.778	0.872	32.075	-8.918	-8.918	0.000	0.000	0.000	0.000
21	C	65	THR	0	0.013	0.014	36.393	0.054	0.054	0.000	0.000	0.000	0.000
22	C	66	PRO	0	0.005	0.008	38.654	-0.038	-0.038	0.000	0.000	0.000	0.000
23	C	67	GLY	0	0.051	0.025	39.036	0.153	0.153	0.000	0.000	0.000	0.000
24	C	68	SER	0	-0.041	-0.023	39.119	0.141	0.141	0.000	0.000	0.000	0.000
25	C	69	VAL	0	-0.016	0.010	36.224	0.051	0.051	0.000	0.000	0.000	0.000
26	C	70	SER	0	0.004	0.010	33.486	0.190	0.190	0.000	0.000	0.000	0.000
27	C	71	SER	0	-0.002	-0.002	31.148	-0.156	-0.156	0.000	0.000	0.000	0.000
28	C	72	ALA	0	-0.019	-0.001	27.732	0.242	0.242	0.000	0.000	0.000	0.000
29	C	73	PHE	0	0.031	-0.001	24.482	-0.112	-0.112	0.000	0.000	0.000	0.000
30	C	74	ILE	0	-0.006	-0.004	21.760	0.437	0.437	0.000	0.000	0.000	0.000
31	C	75	LEU	0	0.001	0.002	17.828	-0.232	-0.232	0.000	0.000	0.000	0.000
32	C	76	GLU	-1	-0.822	-0.902	19.050	12.112	12.112	0.000	0.000	0.000	0.000
33	C	77	ALA	0	-0.004	-0.008	15.409	-0.161	-0.161	0.000	0.000	0.000	0.000
34	C	78	MET	0	0.056	0.050	16.804	0.372	0.372	0.000	0.000	0.000	0.000
35	C	79	VAL	0	-0.028	0.000	12.350	0.414	0.414	0.000	0.000	0.000	0.000
36	C	80	ASN	0	0.023	0.014	14.101	-1.361	-1.361	0.000	0.000	0.000	0.000
37	C	81	VAL	0	0.002	0.012	10.065	1.224	1.224	0.000	0.000	0.000	0.000
38	C	82	ILE	0	0.034	0.013	10.438	-1.524	-1.524	0.000	0.000	0.000	0.000
39	C	83	SER	0	0.008	-0.010	9.459	2.952	2.952	0.000	0.000	0.000	0.000
40	C	84	GLY	0	0.009	0.015	10.060	-1.307	-1.307	0.000	0.000	0.000	0.000
41	C	85	PRO	0	0.000	0.009	11.789	-0.306	-0.306	0.000	0.000	0.000	0.000
42	C	86	LYS	1	0.964	0.988	15.372	-15.839	-15.839	0.000	0.000	0.000	0.000
43	C	87	VAL	0	0.029	0.006	14.659	1.047	1.047	0.000	0.000	0.000	0.000
44	C	88	LEU	0	-0.085	-0.056	12.109	-0.678	-0.678	0.000	0.000	0.000	0.000
45	C	89	MET	0	-0.010	-0.005	14.984	-1.149	-1.149	0.000	0.000	0.000	0.000
46	C	90	LYS	1	0.963	0.971	15.926	-11.747	-11.747	0.000	0.000	0.000	0.000
47	C	91	GLN	0	-0.048	-0.054	18.104	-0.856	-0.856	0.000	0.000	0.000	0.000
48	C	92	ILE	0	-0.004	0.001	14.865	-0.464	-0.464	0.000	0.000	0.000	0.000
49	C	93	PRO	0	0.039	0.021	16.763	0.589	0.589	0.000	0.000	0.000	0.000
50	C	94	ILE	0	-0.039	-0.021	12.304	0.348	0.348	0.000	0.000	0.000	0.000
51	C	95	TRP	0	0.037	0.017	16.519	-0.133	-0.133	0.000	0.000	0.000	0.000
52	C	96	LEU	0	-0.003	-0.011	13.791	0.506	0.506	0.000	0.000	0.000	0.000
53	C	97	PRO	0	0.018	0.018	17.897	-0.353	-0.353	0.000	0.000	0.000	0.000
54	C	98	LEU	0	0.009	-0.003	18.639	0.387	0.387	0.000	0.000	0.000	0.000
55	C	99	GLY	0	0.001	0.003	21.031	0.191	0.191	0.000	0.000	0.000	0.000
56	C	100	VAL	0	-0.004	-0.009	24.217	-0.274	-0.274	0.000	0.000	0.000	0.000
57	C	101	ALA	0	-0.010	-0.009	27.870	0.202	0.202	0.000	0.000	0.000	0.000
58	C	102	ASP	-1	-0.800	-0.881	29.716	8.885	8.885	0.000	0.000	0.000	0.000
59	C	103	GLN	0	0.009	0.002	32.875	0.197	0.197	0.000	0.000	0.000	0.000
60	C	104	LYS	1	0.835	0.911	35.219	-8.832	-8.832	0.000	0.000	0.000	0.000
61	C	105	THR	0	-0.013	-0.001	31.751	-0.120	-0.120	0.000	0.000	0.000	0.000
62	C	106	TYR	0	-0.018	-0.027	29.573	-0.078	-0.078	0.000	0.000	0.000	0.000
63	C	107	SER	0	0.078	0.057	33.152	0.081	0.081	0.000	0.000	0.000	0.000
64	C	108	PHE	0	0.064	0.015	31.044	0.361	0.361	0.000	0.000	0.000	0.000
65	C	109	ASP	-1	-0.834	-0.907	31.750	8.753	8.753	0.000	0.000	0.000	0.000
66	C	110	SER	0	-0.012	-0.019	31.944	0.203	0.203	0.000	0.000	0.000	0.000
67	C	111	THR	0	-0.035	-0.018	27.170	0.471	0.471	0.000	0.000	0.000	0.000
68	C	112	THR	0	0.011	-0.005	27.198	0.523	0.523	0.000	0.000	0.000	0.000
69	C	113	ALA	0	-0.006	0.002	27.519	0.319	0.319	0.000	0.000	0.000	0.000
70	C	114	ALA	0	-0.004	-0.002	25.716	0.333	0.333	0.000	0.000	0.000	0.000
71	C	115	ILE	0	-0.012	-0.001	22.166	0.653	0.653	0.000	0.000	0.000	0.000
72	C	116	MET	0	0.028	0.021	22.776	0.644	0.644	0.000	0.000	0.000	0.000
73	C	117	LEU	0	-0.055	-0.011	24.757	0.138	0.138	0.000	0.000	0.000	0.000
74	C	118	ALA	0	-0.015	-0.013	20.528	0.133	0.133	0.000	0.000	0.000	0.000
75	C	119	SER	0	-0.018	-0.007	17.647	-0.436	-0.436	0.000	0.000	0.000	0.000
76	C	120	TYR	0	-0.004	-0.014	15.156	0.553	0.553	0.000	0.000	0.000	0.000
77	C	121	THR	0	0.006	0.010	10.108	0.728	0.728	0.000	0.000	0.000	0.000
78	C	122	ILE	0	0.033	0.013	8.703	-0.250	-0.250	0.000	0.000	0.000	0.000
79	C	123	THR	0	0.002	-0.003	5.169	2.249	2.249	0.000	0.000	0.000	0.000
80	C	124	HIS	1	0.886	0.962	3.724	-35.637	-35.333	0.001	-0.044	-0.261	0.000
81	C	125	PHE	0	0.075	0.067	2.759	3.171	4.410	0.319	-0.639	-0.919	-0.007
82	C	126	GLY	0	-0.006	0.006	5.157	-2.690	-2.705	-0.001	0.000	0.017	0.000
83	C	127	DLY	2	1.021	1.066	7.878	-43.279	-43.279	0.000	0.000	0.000	0.000
84	C	128	ALA	-1	-0.064	-0.174	14.749	19.657	19.657	0.000	0.000	0.000	0.000
85	C	129	THR	0	-0.070	-0.040	10.627	2.013	2.013	0.000	0.000	0.000	0.000
86	C	130	ASN	0	0.036	0.028	12.128	0.730	0.730	0.000	0.000	0.000	0.000
87	C	131	PRO	0	0.003	0.047	9.374	1.301	1.301	0.000	0.000	0.000	0.000
88	C	132	LEU	0	-0.015	-0.014	8.394	-1.764	-1.764	0.000	0.000	0.000	0.000
89	C	133	VAL	0	0.008	0.001	7.683	2.578	2.578	0.000	0.000	0.000	0.000
90	C	134	ARG	1	0.914	0.967	7.562	-31.814	-31.814	0.000	0.000	0.000	0.000
91	C	135	VAL	0	0.042	0.047	9.320	1.519	1.519	0.000	0.000	0.000	0.000
92	C	136	ASN	0	-0.025	-0.049	8.442	-0.380	-0.380	0.000	0.000	0.000	0.000
93	C	137	ARG	1	0.832	0.915	12.687	-14.373	-14.373	0.000	0.000	0.000	0.000
94	C	138	LEU	0	-0.024	-0.010	13.545	0.222	0.222	0.000	0.000	0.000	0.000
95	C	139	GLY	0	0.002	0.003	17.140	-0.888	-0.888	0.000	0.000	0.000	0.000
96	C	140	PRO	0	0.003	0.004	19.579	0.535	0.535	0.000	0.000	0.000	0.000
97	C	141	GLY	0	0.034	0.022	21.554	-0.091	-0.091	0.000	0.000	0.000	0.000
98	C	142	ILE	0	-0.038	-0.039	22.043	-0.472	-0.472	0.000	0.000	0.000	0.000
99	C	143	PRO	0	0.037	0.005	25.325	0.176	0.176	0.000	0.000	0.000	0.000
100	C	144	ASP	-1	-0.878	-0.927	26.469	10.650	10.650	0.000	0.000	0.000	0.000
101	C	145	HIS	0	0.047	0.035	25.168	-0.067	-0.067	0.000	0.000	0.000	0.000
102	C	146	PRO	0	0.047	0.020	25.565	0.529	0.529	0.000	0.000	0.000	0.000
103	C	147	LEU	0	-0.010	0.012	22.837	0.276	0.276	0.000	0.000	0.000	0.000
104	C	148	ARG	1	0.963	0.976	16.951	-16.077	-16.077	0.000	0.000	0.000	0.000
105	C	149	LEU	0	0.000	0.011	15.864	0.393	0.393	0.000	0.000	0.000	0.000
106	C	150	LEU	0	0.012	0.006	18.875	0.437	0.437	0.000	0.000	0.000	0.000
107	C	151	ARG	1	0.818	0.939	21.827	-12.683	-12.683	0.000	0.000	0.000	0.000
108	C	152	ILE	0	-0.063	-0.042	16.275	0.064	0.064	0.000	0.000	0.000	0.000
109	C	153	GLY	0	0.082	0.053	16.935	0.601	0.601	0.000	0.000	0.000	0.000
110	C	154	ASN	0	-0.055	-0.029	12.434	1.741	1.741	0.000	0.000	0.000	0.000
111	C	155	GLN	0	-0.018	-0.022	13.704	-1.061	-1.061	0.000	0.000	0.000	0.000
112	C	156	ALA	0	-0.018	-0.004	11.667	0.822	0.822	0.000	0.000	0.000	0.000
113	C	157	PHE	0	0.031	0.019	12.357	-1.299	-1.299	0.000	0.000	0.000	0.000
114	C	158	LEU	0	0.073	0.026	12.298	1.580	1.580	0.000	0.000	0.000	0.000
115	C	159	GLN	0	0.048	0.005	9.361	1.300	1.300	0.000	0.000	0.000	0.000
116	C	160	GLU	-1	-0.954	-0.975	12.757	14.834	14.834	0.000	0.000	0.000	0.000
117	C	161	PHE	0	-0.044	-0.020	15.840	-0.811	-0.811	0.000	0.000	0.000	0.000
118	C	162	VAL	0	-0.027	-0.003	13.611	-0.429	-0.429	0.000	0.000	0.000	0.000
119	C	163	LEU	0	-0.016	-0.008	11.565	0.128	0.128	0.000	0.000	0.000	0.000
120	C	164	PRO	0	0.027	0.010	16.230	-0.300	-0.300	0.000	0.000	0.000	0.000
121	C	165	PRO	0	0.036	0.029	17.633	0.644	0.644	0.000	0.000	0.000	0.000
122	C	166	VAL	0	-0.025	-0.014	17.528	-0.620	-0.620	0.000	0.000	0.000	0.000
123	C	167	GLN	0	-0.015	-0.016	15.102	1.312	1.312	0.000	0.000	0.000	0.000
124	C	168	LEU	0	0.016	0.029	11.565	-0.284	-0.284	0.000	0.000	0.000	0.000
125	C	169	PRO	0	-0.019	-0.022	10.682	0.521	0.521	0.000	0.000	0.000	0.000
126	C	170	GLN	0	0.016	0.009	8.039	-1.632	-1.632	0.000	0.000	0.000	0.000
127	C	171	TYR	0	-0.001	-0.012	4.688	1.343	1.415	-0.001	-0.004	-0.067	0.000
128	C	172	PHE	0	-0.034	-0.012	5.561	-2.487	-2.487	0.000	0.000	0.000	0.000
129	C	173	THR	0	0.035	0.015	4.983	4.710	4.749	-0.001	-0.004	-0.033	0.000
130	C	174	PHE	0	0.010	-0.012	6.438	-2.939	-2.939	0.000	0.000	0.000	0.000
131	C	175	ASP	-1	-0.839	-0.909	9.095	18.351	18.351	0.000	0.000	0.000	0.000
132	C	176	LEU	0	-0.058	-0.026	12.457	-1.030	-1.030	0.000	0.000	0.000	0.000
133	C	177	THR	0	-0.022	-0.015	14.385	-0.687	-0.687	0.000	0.000	0.000	0.000
134	C	178	ALA	0	0.031	0.006	18.013	-0.660	-0.660	0.000	0.000	0.000	0.000
135	C	179	LEU	0	-0.019	-0.008	16.987	0.612	0.612	0.000	0.000	0.000	0.000
136	C	180	LYS	1	0.866	0.958	19.813	-11.297	-11.297	0.000	0.000	0.000	0.000
137	C	181	LEU	0	-0.024	-0.011	22.088	0.419	0.419	0.000	0.000	0.000	0.000
138	C	182	ILE	0	0.033	0.014	24.227	-0.445	-0.445	0.000	0.000	0.000	0.000
139	C	183	THR	0	-0.030	-0.035	26.072	0.096	0.096	0.000	0.000	0.000	0.000
140	C	184	GLN	0	0.008	0.002	28.789	-0.169	-0.169	0.000	0.000	0.000	0.000
141	C	185	PRO	0	0.012	0.008	31.325	0.166	0.166	0.000	0.000	0.000	0.000
142	C	186	LEU	0	-0.030	-0.009	31.187	0.017	0.017	0.000	0.000	0.000	0.000
143	C	187	PRO	0	0.031	0.021	35.514	-0.029	-0.029	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:45:ASP)