FMO DATABASE

FMODB ID: 823ZY

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:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
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
LigandCharge	DLY=1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1249531.30535
FMO2-HF: Nuclear repulsion	1195494.415629
FMO2-HF: Total energy	-54036.889722
FMO2-MP2: Total energy	-54196.887323

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.
-92.239	-89.7	3.139	-2.547	-3.132	-0.011

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 : -0.984 / q_NPA : -0.996

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	-0.035	-0.032	3.885	-5.193	-3.522	-0.009	-0.880	-0.782	0.004
4	C	48	SER	0	-0.021	-0.003	6.699	0.232	0.232	0.000	0.000	0.000	0.000
5	C	49	ASN	0	0.023	0.015	9.334	1.073	1.073	0.000	0.000	0.000	0.000
6	C	50	PRO	0	-0.006	-0.001	12.956	0.052	0.052	0.000	0.000	0.000	0.000
7	C	51	LEU	0	-0.008	0.009	15.028	-0.735	-0.735	0.000	0.000	0.000	0.000
8	C	52	ARG	1	0.878	0.934	17.814	-13.280	-13.280	0.000	0.000	0.000	0.000
9	C	53	PRO	0	-0.001	0.005	20.591	0.058	0.058	0.000	0.000	0.000	0.000
10	C	54	ILE	0	0.005	0.000	21.878	-0.380	-0.380	0.000	0.000	0.000	0.000
11	C	55	ALA	0	-0.002	-0.005	25.090	0.210	0.210	0.000	0.000	0.000	0.000
12	C	56	ASP	-1	-0.793	-0.881	26.890	9.989	9.989	0.000	0.000	0.000	0.000
13	C	57	ASP	-1	-0.908	-0.953	28.369	9.216	9.216	0.000	0.000	0.000	0.000
14	C	58	THR	0	-0.062	-0.048	30.736	-0.323	-0.323	0.000	0.000	0.000	0.000
15	C	59	ILE	0	-0.096	-0.049	28.210	-0.127	-0.127	0.000	0.000	0.000	0.000
16	C	60	ASP	-1	-0.754	-0.842	32.811	7.665	7.665	0.000	0.000	0.000	0.000
17	C	61	HIS	0	-0.086	-0.055	35.170	0.122	0.122	0.000	0.000	0.000	0.000
18	C	62	ALA	0	0.045	0.013	36.216	0.042	0.042	0.000	0.000	0.000	0.000
19	C	63	SER	0	-0.059	-0.067	36.972	-0.104	-0.104	0.000	0.000	0.000	0.000
20	C	64	HIS	1	0.805	0.885	31.810	-8.847	-8.847	0.000	0.000	0.000	0.000
21	C	65	THR	0	0.016	0.023	36.232	0.043	0.043	0.000	0.000	0.000	0.000
22	C	66	PRO	0	0.002	0.002	38.395	-0.055	-0.055	0.000	0.000	0.000	0.000
23	C	67	GLY	0	0.045	0.026	38.423	0.123	0.123	0.000	0.000	0.000	0.000
24	C	68	SER	0	-0.017	-0.012	38.501	0.090	0.090	0.000	0.000	0.000	0.000
25	C	69	VAL	0	-0.060	-0.006	35.876	0.006	0.006	0.000	0.000	0.000	0.000
26	C	70	SER	0	0.029	0.023	32.911	0.196	0.196	0.000	0.000	0.000	0.000
27	C	71	SER	0	-0.026	-0.028	30.539	-0.174	-0.174	0.000	0.000	0.000	0.000
28	C	72	ALA	0	0.020	0.023	26.854	0.252	0.252	0.000	0.000	0.000	0.000
29	C	73	PHE	0	0.017	-0.003	24.181	-0.164	-0.164	0.000	0.000	0.000	0.000
30	C	74	ILE	0	-0.020	-0.014	21.007	0.401	0.401	0.000	0.000	0.000	0.000
31	C	75	LEU	0	0.001	0.010	17.194	-0.224	-0.224	0.000	0.000	0.000	0.000
32	C	76	GLU	-1	-0.816	-0.897	19.079	12.066	12.066	0.000	0.000	0.000	0.000
33	C	77	ALA	0	-0.001	-0.010	14.947	-0.110	-0.110	0.000	0.000	0.000	0.000
34	C	78	MET	0	0.033	0.040	16.266	0.466	0.466	0.000	0.000	0.000	0.000
35	C	79	VAL	0	-0.021	-0.007	12.328	0.486	0.486	0.000	0.000	0.000	0.000
36	C	80	ASN	0	-0.009	0.001	14.562	-1.524	-1.524	0.000	0.000	0.000	0.000
37	C	81	VAL	0	0.001	0.009	10.190	1.352	1.352	0.000	0.000	0.000	0.000
38	C	82	ILE	0	0.021	0.000	10.525	-1.665	-1.665	0.000	0.000	0.000	0.000
39	C	83	SER	0	0.004	-0.027	9.483	3.154	3.154	0.000	0.000	0.000	0.000
40	C	84	GLY	0	0.020	0.021	9.921	-1.864	-1.864	0.000	0.000	0.000	0.000
41	C	85	PRO	0	-0.001	0.002	11.701	0.012	0.012	0.000	0.000	0.000	0.000
42	C	86	LYS	1	0.936	0.977	14.655	-16.967	-16.967	0.000	0.000	0.000	0.000
43	C	87	VAL	0	0.034	0.015	14.483	1.222	1.222	0.000	0.000	0.000	0.000
44	C	88	LEU	0	-0.081	-0.050	11.853	-0.623	-0.623	0.000	0.000	0.000	0.000
45	C	89	MET	0	0.001	0.005	15.059	-1.068	-1.068	0.000	0.000	0.000	0.000
46	C	90	LYS	1	0.954	0.968	16.034	-12.063	-12.063	0.000	0.000	0.000	0.000
47	C	91	GLN	0	-0.029	-0.043	18.363	-0.825	-0.825	0.000	0.000	0.000	0.000
48	C	92	ILE	0	0.012	0.017	14.768	-0.514	-0.514	0.000	0.000	0.000	0.000
49	C	93	PRO	0	0.035	0.018	16.686	0.608	0.608	0.000	0.000	0.000	0.000
50	C	94	ILE	0	-0.031	-0.020	11.574	0.143	0.143	0.000	0.000	0.000	0.000
51	C	95	TRP	0	0.023	0.014	15.820	-0.313	-0.313	0.000	0.000	0.000	0.000
52	C	96	LEU	0	-0.001	-0.013	13.108	0.588	0.588	0.000	0.000	0.000	0.000
53	C	97	PRO	0	0.019	0.011	17.188	-0.329	-0.329	0.000	0.000	0.000	0.000
54	C	98	LEU	0	0.017	-0.003	18.275	0.401	0.401	0.000	0.000	0.000	0.000
55	C	99	GLY	0	-0.006	0.005	20.397	0.174	0.174	0.000	0.000	0.000	0.000
56	C	100	VAL	0	-0.014	-0.014	23.513	-0.255	-0.255	0.000	0.000	0.000	0.000
57	C	101	ALA	0	-0.012	-0.005	27.154	0.239	0.239	0.000	0.000	0.000	0.000
58	C	102	ASP	-1	-0.799	-0.888	29.262	8.838	8.838	0.000	0.000	0.000	0.000
59	C	103	GLN	0	0.006	-0.002	32.531	0.209	0.209	0.000	0.000	0.000	0.000
60	C	104	LYS	1	0.836	0.911	34.732	-8.864	-8.864	0.000	0.000	0.000	0.000
61	C	105	THR	0	-0.024	-0.006	31.712	-0.105	-0.105	0.000	0.000	0.000	0.000
62	C	106	TYR	0	-0.009	-0.028	29.497	-0.012	-0.012	0.000	0.000	0.000	0.000
63	C	107	SER	0	0.031	0.019	32.859	0.115	0.115	0.000	0.000	0.000	0.000
64	C	108	PHE	0	0.070	0.028	30.744	0.367	0.367	0.000	0.000	0.000	0.000
65	C	109	ASP	-1	-0.769	-0.862	31.159	8.882	8.882	0.000	0.000	0.000	0.000
66	C	110	SER	0	-0.021	-0.018	31.425	0.224	0.224	0.000	0.000	0.000	0.000
67	C	111	THR	0	-0.035	-0.015	26.782	0.474	0.474	0.000	0.000	0.000	0.000
68	C	112	THR	0	0.007	-0.008	26.795	0.523	0.523	0.000	0.000	0.000	0.000
69	C	113	ALA	0	-0.007	-0.002	27.071	0.350	0.350	0.000	0.000	0.000	0.000
70	C	114	ALA	0	-0.002	0.001	25.510	0.364	0.364	0.000	0.000	0.000	0.000
71	C	115	ILE	0	0.011	0.010	21.681	0.687	0.687	0.000	0.000	0.000	0.000
72	C	116	MET	0	0.024	0.018	22.631	0.659	0.659	0.000	0.000	0.000	0.000
73	C	117	LEU	0	-0.028	-0.005	24.709	0.133	0.133	0.000	0.000	0.000	0.000
74	C	118	ALA	0	-0.025	-0.003	20.287	0.128	0.128	0.000	0.000	0.000	0.000
75	C	119	SER	0	-0.010	-0.001	18.052	-0.561	-0.561	0.000	0.000	0.000	0.000
76	C	120	TYR	0	-0.029	-0.034	15.039	0.696	0.696	0.000	0.000	0.000	0.000
77	C	121	THR	0	0.010	0.015	10.143	0.606	0.606	0.000	0.000	0.000	0.000
78	C	122	ILE	0	0.014	0.006	8.276	-0.486	-0.486	0.000	0.000	0.000	0.000
79	C	123	THR	0	0.019	0.005	4.597	1.931	1.966	-0.001	-0.021	-0.013	0.000
80	C	124	HIS	1	0.870	0.938	3.086	-37.102	-36.534	0.010	-0.146	-0.432	0.001
81	C	125	PHE	0	0.056	0.030	2.207	2.466	2.620	3.142	-1.484	-1.813	-0.016
82	C	126	GLY	0	-0.008	-0.028	4.825	-3.448	-3.445	-0.001	-0.004	0.002	0.000
83	C	127	DLY	1	0.952	0.966	7.728	-19.703	-19.703	0.000	0.000	0.000	0.000
84	C	128	ALA	0	0.011	0.007	10.885	-0.791	-0.791	0.000	0.000	0.000	0.000
85	C	129	THR	0	-0.024	-0.019	9.868	0.793	0.793	0.000	0.000	0.000	0.000
86	C	130	ASN	0	0.037	0.023	10.928	1.512	1.512	0.000	0.000	0.000	0.000
87	C	131	PRO	0	0.025	0.046	9.191	1.196	1.196	0.000	0.000	0.000	0.000
88	C	132	LEU	0	-0.014	-0.003	8.054	-1.722	-1.722	0.000	0.000	0.000	0.000
89	C	133	VAL	0	0.008	0.002	7.191	2.372	2.372	0.000	0.000	0.000	0.000
90	C	134	ARG	1	0.871	0.932	7.669	-30.459	-30.459	0.000	0.000	0.000	0.000
91	C	135	VAL	0	0.047	0.045	8.732	1.515	1.515	0.000	0.000	0.000	0.000
92	C	136	ASN	0	0.009	-0.022	8.269	0.106	0.106	0.000	0.000	0.000	0.000
93	C	137	ARG	1	0.820	0.899	12.489	-14.696	-14.696	0.000	0.000	0.000	0.000
94	C	138	LEU	0	-0.022	-0.010	13.423	0.042	0.042	0.000	0.000	0.000	0.000
95	C	139	GLY	0	0.039	0.008	17.029	-0.925	-0.925	0.000	0.000	0.000	0.000
96	C	140	PRO	0	0.005	0.014	19.657	0.560	0.560	0.000	0.000	0.000	0.000
97	C	141	GLY	0	0.029	0.024	21.694	-0.019	-0.019	0.000	0.000	0.000	0.000
98	C	142	ILE	0	-0.030	-0.019	22.138	-0.463	-0.463	0.000	0.000	0.000	0.000
99	C	143	PRO	0	0.037	0.003	25.279	0.188	0.188	0.000	0.000	0.000	0.000
100	C	144	ASP	-1	-0.877	-0.933	26.463	10.720	10.720	0.000	0.000	0.000	0.000
101	C	145	HIS	0	0.022	0.030	25.180	-0.029	-0.029	0.000	0.000	0.000	0.000
102	C	146	PRO	0	0.029	0.016	25.565	0.485	0.485	0.000	0.000	0.000	0.000
103	C	147	LEU	0	-0.007	0.005	22.339	0.347	0.347	0.000	0.000	0.000	0.000
104	C	148	ARG	1	0.969	0.980	16.711	-15.845	-15.845	0.000	0.000	0.000	0.000
105	C	149	LEU	0	-0.009	0.002	15.223	0.334	0.334	0.000	0.000	0.000	0.000
106	C	150	LEU	0	-0.006	0.000	18.302	0.410	0.410	0.000	0.000	0.000	0.000
107	C	151	ARG	1	0.828	0.932	21.511	-12.487	-12.487	0.000	0.000	0.000	0.000
108	C	152	ILE	0	-0.026	-0.019	16.341	-0.023	-0.023	0.000	0.000	0.000	0.000
109	C	153	GLY	0	0.057	0.039	16.482	1.019	1.019	0.000	0.000	0.000	0.000
110	C	154	ASN	0	-0.076	-0.045	12.016	2.049	2.049	0.000	0.000	0.000	0.000
111	C	155	GLN	0	-0.016	-0.021	13.135	-1.143	-1.143	0.000	0.000	0.000	0.000
112	C	156	ALA	0	-0.019	-0.005	11.134	1.000	1.000	0.000	0.000	0.000	0.000
113	C	157	PHE	0	0.032	0.019	11.730	-1.322	-1.322	0.000	0.000	0.000	0.000
114	C	158	LEU	0	0.057	0.027	11.588	1.520	1.520	0.000	0.000	0.000	0.000
115	C	159	GLN	0	0.023	-0.009	8.751	1.226	1.226	0.000	0.000	0.000	0.000
116	C	160	GLU	-1	-0.939	-0.979	12.023	15.217	15.217	0.000	0.000	0.000	0.000
117	C	161	PHE	0	-0.046	-0.013	15.335	-0.858	-0.858	0.000	0.000	0.000	0.000
118	C	162	VAL	0	-0.040	-0.013	12.799	-0.348	-0.348	0.000	0.000	0.000	0.000
119	C	163	LEU	0	0.002	0.004	11.203	0.251	0.251	0.000	0.000	0.000	0.000
120	C	164	PRO	0	0.043	0.016	15.742	-0.368	-0.368	0.000	0.000	0.000	0.000
121	C	165	PRO	0	0.026	0.030	17.011	0.712	0.712	0.000	0.000	0.000	0.000
122	C	166	VAL	0	-0.045	-0.028	17.790	-0.472	-0.472	0.000	0.000	0.000	0.000
123	C	167	GLN	0	0.011	0.001	14.494	1.295	1.295	0.000	0.000	0.000	0.000
124	C	168	LEU	0	-0.015	0.004	11.206	-0.352	-0.352	0.000	0.000	0.000	0.000
125	C	169	PRO	0	0.000	-0.015	11.030	0.528	0.528	0.000	0.000	0.000	0.000
126	C	170	GLN	0	0.032	0.027	7.452	-1.509	-1.509	0.000	0.000	0.000	0.000
127	C	171	TYR	0	0.001	0.001	4.731	0.999	1.072	-0.001	-0.007	-0.065	0.000
128	C	172	PHE	0	-0.027	-0.002	5.764	-2.758	-2.758	0.000	0.000	0.000	0.000
129	C	173	THR	0	0.033	0.020	5.219	5.114	5.149	-0.001	-0.005	-0.029	0.000
130	C	174	PHE	0	0.009	-0.015	6.780	-2.977	-2.977	0.000	0.000	0.000	0.000
131	C	175	ASP	-1	-0.837	-0.904	9.568	18.531	18.531	0.000	0.000	0.000	0.000
132	C	176	LEU	0	-0.012	-0.014	12.913	-0.973	-0.973	0.000	0.000	0.000	0.000
133	C	177	THR	0	-0.023	-0.006	14.453	-0.730	-0.730	0.000	0.000	0.000	0.000
134	C	178	ALA	0	0.021	0.001	18.083	-0.671	-0.671	0.000	0.000	0.000	0.000
135	C	179	LEU	0	-0.027	-0.011	16.669	0.692	0.692	0.000	0.000	0.000	0.000
136	C	180	LYS	1	0.822	0.917	19.529	-11.495	-11.495	0.000	0.000	0.000	0.000
137	C	181	LEU	0	-0.020	-0.011	21.459	0.486	0.486	0.000	0.000	0.000	0.000
138	C	182	ILE	0	0.035	0.018	23.736	-0.449	-0.449	0.000	0.000	0.000	0.000
139	C	183	THR	0	-0.027	-0.034	25.532	0.132	0.132	0.000	0.000	0.000	0.000
140	C	184	GLN	0	0.005	0.005	28.242	-0.185	-0.185	0.000	0.000	0.000	0.000
141	C	185	PRO	0	0.017	0.010	30.861	0.139	0.139	0.000	0.000	0.000	0.000
142	C	186	LEU	0	-0.030	-0.008	30.457	0.053	0.053	0.000	0.000	0.000	0.000
143	C	187	PRO	0	0.026	0.019	34.886	-0.039	-0.039	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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