FMO DATABASE

FMODB ID: 8944Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1280597.612297
FMO2-HF: Nuclear repulsion	1223843.746334
FMO2-HF: Total energy	-56753.865963
FMO2-MP2: Total energy	-56912.700631

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.
-2.403	-0.878	0.015	-0.672	-0.867	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 : 0.008 / q_NPA : -0.021

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	0.017	0.014	3.909	-2.396	-0.871	0.015	-0.672	-0.867	0.003
4	A	7	ASN	0	-0.002	-0.019	6.681	0.489	0.489	0.000	0.000	0.000	0.000
5	A	8	PRO	0	0.012	0.003	9.607	-0.128	-0.128	0.000	0.000	0.000	0.000
6	A	9	PHE	0	0.022	0.005	12.483	-0.020	-0.020	0.000	0.000	0.000	0.000
7	A	10	ASP	-1	-0.836	-0.892	10.566	-0.377	-0.377	0.000	0.000	0.000	0.000
8	A	11	GLN	0	0.000	0.001	13.861	0.048	0.048	0.000	0.000	0.000	0.000
9	A	12	ASP	-1	-0.822	-0.912	16.116	-0.152	-0.152	0.000	0.000	0.000	0.000
10	A	13	VAL	0	0.025	0.009	16.873	0.018	0.018	0.000	0.000	0.000	0.000
11	A	14	GLU	-1	-0.916	-0.925	17.136	-0.299	-0.299	0.000	0.000	0.000	0.000
12	A	15	LYS	1	0.893	0.943	19.089	0.234	0.234	0.000	0.000	0.000	0.000
13	A	16	ALA	0	0.038	0.023	21.975	0.012	0.012	0.000	0.000	0.000	0.000
14	A	17	THR	0	-0.041	-0.038	21.000	0.010	0.010	0.000	0.000	0.000	0.000
15	A	18	SER	0	0.063	0.050	23.119	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	19	GLU	-1	-0.795	-0.905	22.829	-0.167	-0.167	0.000	0.000	0.000	0.000
17	A	20	MET	0	-0.082	-0.043	26.213	0.010	0.010	0.000	0.000	0.000	0.000
18	A	21	ASN	0	-0.034	0.007	25.805	0.002	0.002	0.000	0.000	0.000	0.000
19	A	22	THR	0	-0.005	-0.007	29.421	0.002	0.002	0.000	0.000	0.000	0.000
20	A	23	ALA	0	-0.028	-0.018	31.400	0.005	0.005	0.000	0.000	0.000	0.000
21	A	24	GLU	-1	-0.833	-0.903	27.296	-0.062	-0.062	0.000	0.000	0.000	0.000
22	A	25	ASP	-1	-0.910	-0.945	26.805	-0.083	-0.083	0.000	0.000	0.000	0.000
23	A	26	TRP	0	-0.001	-0.052	27.479	0.003	0.003	0.000	0.000	0.000	0.000
24	A	27	GLY	0	-0.022	0.004	29.160	0.006	0.006	0.000	0.000	0.000	0.000
25	A	28	LEU	0	0.022	0.001	23.673	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	29	ILE	0	-0.020	-0.001	24.279	0.002	0.002	0.000	0.000	0.000	0.000
27	A	30	LEU	0	0.004	-0.009	25.373	0.009	0.009	0.000	0.000	0.000	0.000
28	A	31	ASP	-1	-0.874	-0.918	23.758	-0.063	-0.063	0.000	0.000	0.000	0.000
29	A	32	ILE	0	-0.071	-0.036	20.302	0.006	0.006	0.000	0.000	0.000	0.000
30	A	33	CYS	0	-0.072	-0.057	22.002	0.017	0.017	0.000	0.000	0.000	0.000
31	A	34	ASP	-1	-0.864	-0.928	24.095	0.004	0.004	0.000	0.000	0.000	0.000
32	A	35	LYS	1	0.842	0.912	15.850	0.133	0.133	0.000	0.000	0.000	0.000
33	A	36	VAL	0	-0.056	-0.040	19.269	0.021	0.021	0.000	0.000	0.000	0.000
34	A	37	GLY	0	-0.005	-0.005	20.007	0.024	0.024	0.000	0.000	0.000	0.000
35	A	38	GLN	0	-0.039	-0.003	19.150	0.012	0.012	0.000	0.000	0.000	0.000
36	A	39	SER	0	-0.040	-0.024	14.803	0.012	0.012	0.000	0.000	0.000	0.000
37	A	40	ARG	1	0.942	0.961	15.207	-0.224	-0.224	0.000	0.000	0.000	0.000
38	A	41	THR	0	-0.064	-0.056	11.284	-0.010	-0.010	0.000	0.000	0.000	0.000
39	A	42	GLY	0	0.055	0.058	14.565	0.011	0.011	0.000	0.000	0.000	0.000
40	A	43	PRO	0	0.022	0.005	16.887	-0.011	-0.011	0.000	0.000	0.000	0.000
41	A	44	LYS	1	0.853	0.926	14.608	-0.278	-0.278	0.000	0.000	0.000	0.000
42	A	45	ASP	-1	-0.886	-0.927	12.260	0.410	0.410	0.000	0.000	0.000	0.000
43	A	46	CYS	0	0.008	0.024	13.883	-0.067	-0.067	0.000	0.000	0.000	0.000
44	A	47	LEU	0	0.034	0.029	16.709	-0.033	-0.033	0.000	0.000	0.000	0.000
45	A	48	ARG	1	0.848	0.901	11.350	-0.397	-0.397	0.000	0.000	0.000	0.000
46	A	49	SER	0	-0.039	-0.034	13.771	-0.035	-0.035	0.000	0.000	0.000	0.000
47	A	50	ILE	0	0.024	-0.003	14.570	-0.030	-0.030	0.000	0.000	0.000	0.000
48	A	51	MET	0	0.015	0.006	17.161	-0.018	-0.018	0.000	0.000	0.000	0.000
49	A	52	ARG	1	0.940	0.982	9.379	0.171	0.171	0.000	0.000	0.000	0.000
50	A	53	ARG	1	0.793	0.878	16.194	0.180	0.180	0.000	0.000	0.000	0.000
51	A	54	VAL	0	-0.018	-0.017	19.052	0.003	0.003	0.000	0.000	0.000	0.000
52	A	55	ASN	0	-0.102	-0.068	18.478	0.005	0.005	0.000	0.000	0.000	0.000
53	A	56	HIS	0	-0.033	0.010	19.987	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	57	LYS	1	0.947	0.968	21.146	0.182	0.182	0.000	0.000	0.000	0.000
55	A	58	ASP	-1	-0.842	-0.927	23.912	-0.094	-0.094	0.000	0.000	0.000	0.000
56	A	59	PRO	0	-0.010	-0.027	25.581	0.001	0.001	0.000	0.000	0.000	0.000
57	A	60	HIS	0	-0.062	-0.028	28.037	0.011	0.011	0.000	0.000	0.000	0.000
58	A	61	VAL	0	-0.012	0.020	21.684	0.002	0.002	0.000	0.000	0.000	0.000
59	A	62	ALA	0	-0.007	-0.007	23.838	0.005	0.005	0.000	0.000	0.000	0.000
60	A	63	MET	0	-0.046	-0.033	24.847	0.011	0.011	0.000	0.000	0.000	0.000
61	A	64	GLN	0	0.008	0.006	25.556	0.005	0.005	0.000	0.000	0.000	0.000
62	A	65	ALA	0	0.029	0.016	21.799	0.005	0.005	0.000	0.000	0.000	0.000
63	A	66	LEU	0	-0.034	-0.017	23.631	0.013	0.013	0.000	0.000	0.000	0.000
64	A	67	THR	0	0.007	0.008	26.162	0.009	0.009	0.000	0.000	0.000	0.000
65	A	68	LEU	0	0.036	0.028	21.052	0.006	0.006	0.000	0.000	0.000	0.000
66	A	69	LEU	0	-0.015	-0.011	22.172	0.011	0.011	0.000	0.000	0.000	0.000
67	A	70	GLY	0	0.018	0.001	24.611	0.010	0.010	0.000	0.000	0.000	0.000
68	A	71	ALA	0	0.020	0.024	27.037	0.006	0.006	0.000	0.000	0.000	0.000
69	A	72	CYS	0	0.009	0.000	23.381	0.003	0.003	0.000	0.000	0.000	0.000
70	A	73	VAL	0	-0.062	-0.027	25.658	0.010	0.010	0.000	0.000	0.000	0.000
71	A	74	SER	0	-0.030	-0.011	27.755	0.003	0.003	0.000	0.000	0.000	0.000
72	A	75	ASN	0	-0.052	-0.039	28.452	0.003	0.003	0.000	0.000	0.000	0.000
73	A	76	CYS	0	-0.032	0.006	24.859	0.000	0.000	0.000	0.000	0.000	0.000
74	A	77	GLY	0	0.016	0.021	26.510	0.009	0.009	0.000	0.000	0.000	0.000
75	A	78	LYS	1	0.847	0.874	27.268	-0.067	-0.067	0.000	0.000	0.000	0.000
76	A	79	ILE	0	-0.007	-0.008	22.258	0.008	0.008	0.000	0.000	0.000	0.000
77	A	80	PHE	0	0.044	0.022	20.491	0.016	0.016	0.000	0.000	0.000	0.000
78	A	81	HIS	0	0.021	0.011	23.887	0.010	0.010	0.000	0.000	0.000	0.000
79	A	82	LEU	0	-0.014	-0.013	24.023	0.001	0.001	0.000	0.000	0.000	0.000
80	A	83	GLU	-1	-0.876	-0.919	18.744	0.232	0.232	0.000	0.000	0.000	0.000
81	A	84	VAL	0	0.028	0.027	21.505	0.005	0.005	0.000	0.000	0.000	0.000
82	A	85	CYS	0	-0.100	-0.031	23.650	-0.008	-0.008	0.000	0.000	0.000	0.000
83	A	86	SER	0	-0.018	-0.025	21.036	0.013	0.013	0.000	0.000	0.000	0.000
84	A	87	ARG	1	0.968	0.960	21.746	-0.136	-0.136	0.000	0.000	0.000	0.000
85	A	88	ASP	-1	-0.830	-0.906	16.580	0.230	0.230	0.000	0.000	0.000	0.000
86	A	89	PHE	0	0.057	0.029	19.291	-0.019	-0.019	0.000	0.000	0.000	0.000
87	A	90	ALA	0	0.050	0.014	21.413	-0.016	-0.016	0.000	0.000	0.000	0.000
88	A	91	SER	0	-0.032	-0.015	20.261	-0.009	-0.009	0.000	0.000	0.000	0.000
89	A	92	GLU	-1	-0.870	-0.926	17.261	-0.016	-0.016	0.000	0.000	0.000	0.000
90	A	93	VAL	0	0.004	0.008	20.944	-0.016	-0.016	0.000	0.000	0.000	0.000
91	A	94	SER	0	-0.014	-0.016	24.667	-0.009	-0.009	0.000	0.000	0.000	0.000
92	A	95	ASN	0	-0.026	-0.006	20.023	-0.011	-0.011	0.000	0.000	0.000	0.000
93	A	96	VAL	0	0.013	0.011	22.229	-0.011	-0.011	0.000	0.000	0.000	0.000
94	A	97	LEU	0	-0.041	-0.033	24.658	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	98	ASN	0	-0.026	-0.009	26.875	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	99	LYS	1	0.854	0.926	21.365	0.047	0.047	0.000	0.000	0.000	0.000
97	A	100	GLY	0	0.017	0.023	26.975	-0.007	-0.007	0.000	0.000	0.000	0.000
98	A	101	HIS	0	0.059	0.022	27.659	0.006	0.006	0.000	0.000	0.000	0.000
99	A	102	PRO	0	0.034	0.000	30.492	0.003	0.003	0.000	0.000	0.000	0.000
100	A	103	LYS	1	0.998	1.005	32.279	0.057	0.057	0.000	0.000	0.000	0.000
101	A	104	VAL	0	0.033	0.012	26.376	0.002	0.002	0.000	0.000	0.000	0.000
102	A	105	CYS	0	-0.048	-0.019	29.681	0.006	0.006	0.000	0.000	0.000	0.000
103	A	106	GLU	-1	-0.974	-0.979	30.901	-0.018	-0.018	0.000	0.000	0.000	0.000
104	A	107	LYS	1	0.936	0.973	30.353	0.018	0.018	0.000	0.000	0.000	0.000
105	A	108	LEU	0	0.032	0.014	25.975	0.004	0.004	0.000	0.000	0.000	0.000
106	A	109	LYS	1	0.874	0.930	29.412	0.012	0.012	0.000	0.000	0.000	0.000
107	A	110	ALA	0	-0.007	0.010	32.383	0.004	0.004	0.000	0.000	0.000	0.000
108	A	111	LEU	0	0.010	0.002	28.074	0.002	0.002	0.000	0.000	0.000	0.000
109	A	112	MET	0	-0.031	-0.006	29.093	0.004	0.004	0.000	0.000	0.000	0.000
110	A	113	VAL	0	-0.003	-0.003	31.744	0.004	0.004	0.000	0.000	0.000	0.000
111	A	114	GLU	-1	-0.864	-0.938	33.783	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	115	TRP	0	0.054	0.018	26.333	0.005	0.005	0.000	0.000	0.000	0.000
113	A	116	THR	0	-0.086	-0.025	32.939	0.003	0.003	0.000	0.000	0.000	0.000
114	A	117	ASP	-1	-0.834	-0.908	35.022	0.019	0.019	0.000	0.000	0.000	0.000
115	A	118	GLU	-1	-0.903	-0.959	32.712	0.027	0.027	0.000	0.000	0.000	0.000
116	A	119	PHE	0	-0.035	-0.045	29.027	0.004	0.004	0.000	0.000	0.000	0.000
117	A	120	LYS	1	0.792	0.906	34.800	-0.016	-0.016	0.000	0.000	0.000	0.000
118	A	121	ASN	0	-0.036	-0.020	38.150	0.000	0.000	0.000	0.000	0.000	0.000
119	A	122	ASP	-1	-0.773	-0.866	33.115	0.065	0.065	0.000	0.000	0.000	0.000
120	A	123	PRO	0	0.012	-0.004	34.792	0.002	0.002	0.000	0.000	0.000	0.000
121	A	124	GLN	0	-0.048	-0.017	29.837	0.003	0.003	0.000	0.000	0.000	0.000
122	A	125	LEU	0	-0.005	0.003	28.874	0.008	0.008	0.000	0.000	0.000	0.000
123	A	126	SER	0	0.040	0.024	31.332	-0.004	-0.004	0.000	0.000	0.000	0.000
124	A	127	LEU	0	-0.002	0.003	27.034	-0.005	-0.005	0.000	0.000	0.000	0.000
125	A	128	ILE	0	0.086	0.041	27.317	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	129	SER	0	-0.008	-0.020	30.513	-0.005	-0.005	0.000	0.000	0.000	0.000
127	A	130	ALA	0	-0.024	-0.011	31.596	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	131	MET	0	-0.023	-0.005	25.987	-0.005	-0.005	0.000	0.000	0.000	0.000
129	A	132	ILE	0	0.019	0.017	30.968	-0.005	-0.005	0.000	0.000	0.000	0.000
130	A	133	LYS	1	0.904	0.956	33.916	-0.036	-0.036	0.000	0.000	0.000	0.000
131	A	134	ASN	0	-0.020	-0.008	31.480	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	135	LEU	0	0.022	0.007	29.454	-0.003	-0.003	0.000	0.000	0.000	0.000
133	A	136	LYS	1	0.912	0.963	33.674	-0.018	-0.018	0.000	0.000	0.000	0.000
134	A	137	GLU	-1	-0.934	-0.965	36.681	0.029	0.029	0.000	0.000	0.000	0.000
135	A	138	GLN	0	-0.081	-0.036	31.220	-0.003	-0.003	0.000	0.000	0.000	0.000
136	A	139	GLY	0	0.017	0.017	36.341	-0.003	-0.003	0.000	0.000	0.000	0.000
137	A	140	VAL	0	-0.028	-0.002	33.075	-0.003	-0.003	0.000	0.000	0.000	0.000
138	A	141	THR	0	0.010	-0.003	36.477	0.002	0.002	0.000	0.000	0.000	0.000
139	A	142	PHE	0	0.018	-0.025	32.583	-0.002	-0.002	0.000	0.000	0.000	0.000
140	A	143	PRO	0	0.020	0.026	37.908	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)