FMO DATABASE

FMODB ID: NNJJQ

Calculation Name: 3LDZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LDZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q92783

Base Structure: X-ray

Registration Date: 2023-09-23

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	140
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1288417.647038
FMO2-HF: Nuclear repulsion	1231663.388409
FMO2-HF: Total energy	-56754.258629
FMO2-MP2: Total energy	-56913.121057

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:4:PHE)

Summations of interaction energy for fragment #1(A:4:PHE)

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.
-2.175	-0.631	0.028	-0.528	-1.043	0.003

Interaction energy analysis for fragmet #1(A:4:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : -0.019

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	6	THR	0	0.003	0.006	3.863	-2.079	-0.535	0.028	-0.528	-1.043	0.003
4	A	7	ASN	0	0.000	-0.009	6.323	0.509	0.509	0.000	0.000	0.000	0.000
5	A	8	PRO	0	0.008	0.009	9.224	-0.148	-0.148	0.000	0.000	0.000	0.000
6	A	9	PHE	0	0.025	0.006	12.123	-0.015	-0.015	0.000	0.000	0.000	0.000
7	A	10	ASP	-1	-0.802	-0.875	10.406	-0.318	-0.318	0.000	0.000	0.000	0.000
8	A	11	GLN	0	0.007	0.010	13.638	0.060	0.060	0.000	0.000	0.000	0.000
9	A	12	ASP	-1	-0.792	-0.891	15.426	-0.191	-0.191	0.000	0.000	0.000	0.000
10	A	13	VAL	0	0.041	0.016	16.631	0.020	0.020	0.000	0.000	0.000	0.000
11	A	14	GLU	-1	-0.895	-0.915	16.622	-0.296	-0.296	0.000	0.000	0.000	0.000
12	A	15	LYS	1	0.823	0.905	18.671	0.257	0.257	0.000	0.000	0.000	0.000
13	A	16	ALA	0	0.029	0.009	21.599	0.013	0.013	0.000	0.000	0.000	0.000
14	A	17	THR	0	-0.032	-0.029	20.677	0.011	0.011	0.000	0.000	0.000	0.000
15	A	18	SER	0	0.042	0.015	22.729	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	19	GLU	-1	-0.746	-0.872	22.248	-0.166	-0.166	0.000	0.000	0.000	0.000
17	A	20	MET	0	-0.093	-0.041	25.680	0.009	0.009	0.000	0.000	0.000	0.000
18	A	21	ASN	0	-0.024	0.033	25.361	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	22	THR	0	-0.012	-0.012	28.923	0.003	0.003	0.000	0.000	0.000	0.000
20	A	23	ALA	0	-0.023	-0.017	30.779	0.006	0.006	0.000	0.000	0.000	0.000
21	A	24	GLU	-1	-0.782	-0.869	26.894	-0.061	-0.061	0.000	0.000	0.000	0.000
22	A	25	ASP	-1	-0.871	-0.926	26.145	-0.091	-0.091	0.000	0.000	0.000	0.000
23	A	26	TRP	0	-0.018	-0.056	27.112	0.003	0.003	0.000	0.000	0.000	0.000
24	A	27	GLY	0	-0.010	0.012	29.184	0.006	0.006	0.000	0.000	0.000	0.000
25	A	28	LEU	0	0.027	0.001	23.173	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	29	ILE	0	-0.030	-0.010	24.119	0.002	0.002	0.000	0.000	0.000	0.000
27	A	30	LEU	0	0.004	0.013	25.383	0.010	0.010	0.000	0.000	0.000	0.000
28	A	31	ASP	-1	-0.885	-0.932	23.508	-0.077	-0.077	0.000	0.000	0.000	0.000
29	A	32	ILE	0	-0.074	-0.050	20.086	0.005	0.005	0.000	0.000	0.000	0.000
30	A	33	CYS	0	-0.050	-0.045	22.021	0.018	0.018	0.000	0.000	0.000	0.000
31	A	34	ASP	-1	-0.845	-0.896	23.797	-0.011	-0.011	0.000	0.000	0.000	0.000
32	A	35	LYS	1	0.852	0.913	15.749	0.168	0.168	0.000	0.000	0.000	0.000
33	A	36	VAL	0	-0.056	-0.043	18.937	0.017	0.017	0.000	0.000	0.000	0.000
34	A	37	GLY	0	-0.013	-0.007	20.005	0.024	0.024	0.000	0.000	0.000	0.000
35	A	38	GLN	0	-0.068	-0.033	18.851	0.015	0.015	0.000	0.000	0.000	0.000
36	A	39	SER	0	-0.030	-0.015	14.440	0.008	0.008	0.000	0.000	0.000	0.000
37	A	40	ARG	1	0.934	0.959	15.405	-0.212	-0.212	0.000	0.000	0.000	0.000
38	A	41	THR	0	-0.081	-0.064	11.199	0.001	0.001	0.000	0.000	0.000	0.000
39	A	42	GLY	0	0.063	0.041	14.490	0.010	0.010	0.000	0.000	0.000	0.000
40	A	43	PRO	0	0.041	0.013	16.751	-0.013	-0.013	0.000	0.000	0.000	0.000
41	A	44	LYS	1	0.815	0.903	14.657	-0.290	-0.290	0.000	0.000	0.000	0.000
42	A	45	ASP	-1	-0.861	-0.910	12.476	0.362	0.362	0.000	0.000	0.000	0.000
43	A	46	CYS	0	0.007	0.021	13.821	-0.064	-0.064	0.000	0.000	0.000	0.000
44	A	47	LEU	0	0.026	0.028	16.623	-0.027	-0.027	0.000	0.000	0.000	0.000
45	A	48	ARG	1	0.841	0.897	11.276	-0.432	-0.432	0.000	0.000	0.000	0.000
46	A	49	SER	0	-0.060	-0.047	13.637	-0.036	-0.036	0.000	0.000	0.000	0.000
47	A	50	ILE	0	0.028	0.003	14.495	-0.031	-0.031	0.000	0.000	0.000	0.000
48	A	51	MET	0	0.018	0.012	17.108	-0.018	-0.018	0.000	0.000	0.000	0.000
49	A	52	ARG	1	0.929	0.972	9.255	0.110	0.110	0.000	0.000	0.000	0.000
50	A	53	ARG	1	0.755	0.851	16.019	0.172	0.172	0.000	0.000	0.000	0.000
51	A	54	VAL	0	0.006	-0.007	18.938	0.003	0.003	0.000	0.000	0.000	0.000
52	A	55	ASN	0	-0.111	-0.072	18.001	0.004	0.004	0.000	0.000	0.000	0.000
53	A	56	HIS	0	-0.038	-0.006	19.660	0.001	0.001	0.000	0.000	0.000	0.000
54	A	57	LYS	1	0.945	0.964	20.873	0.165	0.165	0.000	0.000	0.000	0.000
55	A	58	ASP	-1	-0.828	-0.913	23.652	-0.087	-0.087	0.000	0.000	0.000	0.000
56	A	59	PRO	0	-0.021	-0.032	25.534	0.002	0.002	0.000	0.000	0.000	0.000
57	A	60	HIS	0	-0.084	-0.040	28.028	0.011	0.011	0.000	0.000	0.000	0.000
58	A	61	VAL	0	-0.015	0.012	21.464	0.003	0.003	0.000	0.000	0.000	0.000
59	A	62	ALA	0	0.016	0.008	23.555	0.004	0.004	0.000	0.000	0.000	0.000
60	A	63	MET	0	-0.036	-0.026	24.562	0.011	0.011	0.000	0.000	0.000	0.000
61	A	64	GLN	0	0.011	0.014	25.304	0.003	0.003	0.000	0.000	0.000	0.000
62	A	65	ALA	0	0.010	0.006	21.530	0.003	0.003	0.000	0.000	0.000	0.000
63	A	66	LEU	0	-0.041	-0.020	23.398	0.013	0.013	0.000	0.000	0.000	0.000
64	A	67	THR	0	-0.039	-0.023	26.020	0.008	0.008	0.000	0.000	0.000	0.000
65	A	68	LEU	0	0.053	0.032	20.863	0.006	0.006	0.000	0.000	0.000	0.000
66	A	69	LEU	0	-0.020	-0.008	21.925	0.009	0.009	0.000	0.000	0.000	0.000
67	A	70	GLY	0	0.012	-0.001	24.441	0.010	0.010	0.000	0.000	0.000	0.000
68	A	71	ALA	0	0.006	0.022	26.949	0.006	0.006	0.000	0.000	0.000	0.000
69	A	72	CYS	0	0.019	0.002	23.094	0.002	0.002	0.000	0.000	0.000	0.000
70	A	73	VAL	0	-0.054	-0.027	25.334	0.009	0.009	0.000	0.000	0.000	0.000
71	A	74	SER	0	-0.036	-0.025	27.377	0.004	0.004	0.000	0.000	0.000	0.000
72	A	75	ASN	0	-0.066	-0.033	28.109	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	76	CYS	0	-0.046	-0.005	24.411	0.000	0.000	0.000	0.000	0.000	0.000
74	A	77	GLY	0	0.031	0.027	26.131	0.009	0.009	0.000	0.000	0.000	0.000
75	A	78	LYS	1	0.858	0.881	26.892	-0.064	-0.064	0.000	0.000	0.000	0.000
76	A	79	ILE	0	-0.015	-0.011	21.993	0.011	0.011	0.000	0.000	0.000	0.000
77	A	80	PHE	0	0.034	0.020	20.254	0.019	0.019	0.000	0.000	0.000	0.000
78	A	81	HIS	0	-0.005	0.000	23.691	0.011	0.011	0.000	0.000	0.000	0.000
79	A	82	LEU	0	0.006	-0.003	24.140	0.002	0.002	0.000	0.000	0.000	0.000
80	A	83	GLU	-1	-0.851	-0.914	18.641	0.240	0.240	0.000	0.000	0.000	0.000
81	A	84	VAL	0	0.015	0.022	21.477	0.005	0.005	0.000	0.000	0.000	0.000
82	A	85	CYS	0	-0.096	-0.022	23.610	-0.008	-0.008	0.000	0.000	0.000	0.000
83	A	86	SER	0	-0.027	-0.019	20.539	0.009	0.009	0.000	0.000	0.000	0.000
84	A	87	ARG	1	0.966	0.950	21.492	-0.151	-0.151	0.000	0.000	0.000	0.000
85	A	88	ASP	-1	-0.813	-0.896	16.390	0.257	0.257	0.000	0.000	0.000	0.000
86	A	89	PHE	0	0.067	0.029	19.054	-0.020	-0.020	0.000	0.000	0.000	0.000
87	A	90	ALA	0	0.038	0.023	21.448	-0.015	-0.015	0.000	0.000	0.000	0.000
88	A	91	SER	0	-0.014	0.000	19.948	-0.009	-0.009	0.000	0.000	0.000	0.000
89	A	92	GLU	-1	-0.872	-0.916	17.109	0.009	0.009	0.000	0.000	0.000	0.000
90	A	93	VAL	0	0.032	0.012	20.704	-0.017	-0.017	0.000	0.000	0.000	0.000
91	A	94	SER	0	-0.042	-0.034	24.366	-0.009	-0.009	0.000	0.000	0.000	0.000
92	A	95	ASN	0	-0.038	-0.019	19.762	-0.011	-0.011	0.000	0.000	0.000	0.000
93	A	96	VAL	0	0.013	0.010	21.707	-0.011	-0.011	0.000	0.000	0.000	0.000
94	A	97	LEU	0	-0.029	-0.030	24.132	-0.007	-0.007	0.000	0.000	0.000	0.000
95	A	98	ASN	0	-0.033	-0.004	26.690	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	99	LYS	1	0.838	0.909	21.241	0.019	0.019	0.000	0.000	0.000	0.000
97	A	100	GLY	0	0.023	0.031	26.585	-0.008	-0.008	0.000	0.000	0.000	0.000
98	A	101	HIS	0	0.047	0.014	27.237	0.005	0.005	0.000	0.000	0.000	0.000
99	A	102	PRO	0	0.034	0.003	30.252	0.002	0.002	0.000	0.000	0.000	0.000
100	A	103	LYS	1	1.007	1.008	32.076	0.050	0.050	0.000	0.000	0.000	0.000
101	A	104	VAL	0	0.027	0.014	25.970	0.002	0.002	0.000	0.000	0.000	0.000
102	A	105	CYS	0	-0.026	-0.015	29.150	0.006	0.006	0.000	0.000	0.000	0.000
103	A	106	GLU	-1	-0.968	-0.980	30.318	-0.014	-0.014	0.000	0.000	0.000	0.000
104	A	107	LYS	1	0.864	0.920	30.360	0.014	0.014	0.000	0.000	0.000	0.000
105	A	108	LEU	0	0.034	0.020	25.482	0.004	0.004	0.000	0.000	0.000	0.000
106	A	109	LYS	1	0.858	0.924	29.093	0.005	0.005	0.000	0.000	0.000	0.000
107	A	110	ALA	0	-0.002	0.004	31.994	0.004	0.004	0.000	0.000	0.000	0.000
108	A	111	LEU	0	0.015	0.012	27.824	0.002	0.002	0.000	0.000	0.000	0.000
109	A	112	MET	0	-0.029	-0.002	28.877	0.004	0.004	0.000	0.000	0.000	0.000
110	A	113	VAL	0	-0.003	0.000	31.287	0.004	0.004	0.000	0.000	0.000	0.000
111	A	114	GLU	-1	-0.816	-0.898	33.334	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	115	TRP	0	0.073	0.023	26.069	0.004	0.004	0.000	0.000	0.000	0.000
113	A	116	THR	0	-0.095	-0.051	32.583	0.004	0.004	0.000	0.000	0.000	0.000
114	A	117	ASP	-1	-0.849	-0.914	34.795	0.019	0.019	0.000	0.000	0.000	0.000
115	A	118	GLU	-1	-0.889	-0.942	32.219	0.026	0.026	0.000	0.000	0.000	0.000
116	A	119	PHE	0	-0.010	-0.031	28.703	0.003	0.003	0.000	0.000	0.000	0.000
117	A	120	LYS	1	0.770	0.880	34.548	-0.017	-0.017	0.000	0.000	0.000	0.000
118	A	121	ASN	0	-0.023	-0.009	37.741	0.000	0.000	0.000	0.000	0.000	0.000
119	A	122	ASP	-1	-0.771	-0.865	32.901	0.064	0.064	0.000	0.000	0.000	0.000
120	A	123	PRO	0	0.026	0.001	34.324	0.003	0.003	0.000	0.000	0.000	0.000
121	A	124	GLN	0	-0.044	-0.001	29.609	0.002	0.002	0.000	0.000	0.000	0.000
122	A	125	LEU	0	0.013	0.003	28.684	0.009	0.009	0.000	0.000	0.000	0.000
123	A	126	SER	0	-0.005	-0.010	30.982	-0.003	-0.003	0.000	0.000	0.000	0.000
124	A	127	LEU	0	0.006	0.016	27.248	-0.005	-0.005	0.000	0.000	0.000	0.000
125	A	128	ILE	0	0.074	0.032	27.328	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	129	SER	0	-0.015	-0.021	30.508	-0.005	-0.005	0.000	0.000	0.000	0.000
127	A	130	ALA	0	-0.014	-0.005	31.652	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	131	MET	0	-0.034	-0.004	25.507	-0.004	-0.004	0.000	0.000	0.000	0.000
129	A	132	ILE	0	0.028	0.015	30.722	-0.004	-0.004	0.000	0.000	0.000	0.000
130	A	133	LYS	1	0.838	0.912	33.679	-0.042	-0.042	0.000	0.000	0.000	0.000
131	A	134	ASN	0	-0.021	-0.026	31.690	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	135	LEU	0	0.028	0.021	29.387	-0.002	-0.002	0.000	0.000	0.000	0.000
133	A	136	LYS	1	0.904	0.960	33.491	-0.023	-0.023	0.000	0.000	0.000	0.000
134	A	137	GLU	-1	-0.872	-0.913	36.322	0.038	0.038	0.000	0.000	0.000	0.000
135	A	138	GLN	0	-0.071	-0.030	31.071	-0.002	-0.002	0.000	0.000	0.000	0.000
136	A	139	GLY	0	0.006	0.009	36.224	-0.003	-0.003	0.000	0.000	0.000	0.000
137	A	140	VAL	0	-0.040	-0.016	33.024	-0.004	-0.004	0.000	0.000	0.000	0.000
138	A	141	THR	0	0.019	0.001	36.391	0.002	0.002	0.000	0.000	0.000	0.000
139	A	142	PHE	0	0.024	-0.020	32.515	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	143	PRO	0	0.019	0.030	37.921	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:PHE)