FMO DATABASE

FMODB ID: QVKJY

Calculation Name: 3LMB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LMB

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-22

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	164
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1648324.615737
FMO2-HF: Nuclear repulsion	1582466.696565
FMO2-HF: Total energy	-65857.919172
FMO2-MP2: Total energy	-66045.386317

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:MET)

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

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.
-6.908	-1.33	2.606	-3.282	-4.9	-0.012

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : 0.010

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	3	ALA	0	0.027	0.022	3.644	-0.027	3.311	0.376	-1.731	-1.982	-0.001
4	A	4	SER	0	0.011	0.003	6.160	0.478	0.478	0.000	0.000	0.000	0.000
5	A	5	LEU	0	-0.090	-0.032	7.597	-0.092	-0.092	0.000	0.000	0.000	0.000
6	A	6	THR	0	0.054	0.016	10.039	-0.074	-0.074	0.000	0.000	0.000	0.000
7	A	7	PRO	0	0.103	0.033	13.647	0.011	0.011	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.817	-0.915	15.916	-0.024	-0.024	0.000	0.000	0.000	0.000
9	A	9	GLN	0	-0.030	-0.005	12.255	0.028	0.028	0.000	0.000	0.000	0.000
10	A	10	VAL	0	0.026	0.014	10.711	0.026	0.026	0.000	0.000	0.000	0.000
11	A	11	SER	0	0.039	0.031	13.450	-0.005	-0.005	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.797	0.881	16.680	0.011	0.011	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.916	0.972	8.777	-0.301	-0.301	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.006	0.026	15.213	0.001	0.001	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.936	0.966	17.045	0.007	0.007	0.000	0.000	0.000	0.000
16	A	16	GLN	0	-0.075	-0.054	17.708	-0.005	-0.005	0.000	0.000	0.000	0.000
17	A	17	PHE	0	0.042	0.025	16.554	0.001	0.001	0.000	0.000	0.000	0.000
18	A	18	PHE	0	-0.002	-0.017	18.633	0.000	0.000	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.004	0.000	21.959	0.001	0.001	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.931	-0.944	19.777	0.061	0.061	0.000	0.000	0.000	0.000
21	A	21	HIS	0	-0.014	-0.011	18.434	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.027	-0.006	21.866	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	23	PRO	0	0.055	0.036	24.898	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.015	-0.011	27.461	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	25	SER	0	0.004	-0.011	25.746	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	26	GLN	0	0.010	-0.002	26.117	0.001	0.001	0.000	0.000	0.000	0.000
27	A	27	PHE	0	-0.029	-0.011	29.594	0.000	0.000	0.000	0.000	0.000	0.000
28	A	28	MET	0	-0.059	-0.014	30.290	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.050	0.017	31.282	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.077	-0.038	25.459	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.852	-0.912	25.965	-0.018	-0.018	0.000	0.000	0.000	0.000
32	A	32	ILE	0	-0.027	-0.029	19.731	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.874	-0.905	24.093	-0.041	-0.041	0.000	0.000	0.000	0.000
34	A	34	SER	0	0.008	-0.009	23.757	0.001	0.001	0.000	0.000	0.000	0.000
35	A	35	TYR	0	-0.064	-0.086	14.498	-0.005	-0.005	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.858	-0.912	20.190	-0.085	-0.085	0.000	0.000	0.000	0.000
37	A	37	GLY	0	-0.023	-0.009	16.451	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.853	-0.914	17.248	-0.162	-0.162	0.000	0.000	0.000	0.000
39	A	39	THR	0	-0.035	-0.028	20.056	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.057	-0.011	19.269	0.005	0.005	0.000	0.000	0.000	0.000
41	A	41	ILE	0	-0.016	-0.004	21.856	0.001	0.001	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.021	0.005	22.223	0.005	0.005	0.000	0.000	0.000	0.000
43	A	43	THR	0	-0.020	-0.021	26.099	0.002	0.002	0.000	0.000	0.000	0.000
44	A	44	ALA	0	0.040	0.026	29.367	0.002	0.002	0.000	0.000	0.000	0.000
45	A	45	PRO	0	-0.008	0.006	31.915	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	46	LEU	0	0.012	-0.001	35.519	0.000	0.000	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.965	-0.980	38.238	-0.011	-0.011	0.000	0.000	0.000	0.000
48	A	48	PRO	0	0.060	0.040	35.553	0.000	0.000	0.000	0.000	0.000	0.000
49	A	49	ASN	0	-0.085	-0.037	33.629	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	50	ILE	0	0.039	0.054	37.213	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	51	ASN	0	-0.014	-0.020	40.818	0.002	0.002	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.777	-0.883	43.226	-0.017	-0.017	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.766	0.863	45.755	0.020	0.020	0.000	0.000	0.000	0.000
54	A	54	GLN	0	-0.020	-0.013	45.198	0.000	0.000	0.000	0.000	0.000	0.000
55	A	55	THR	0	0.001	0.018	42.375	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.029	0.002	37.093	0.001	0.001	0.000	0.000	0.000	0.000
57	A	57	PHE	0	-0.004	-0.007	37.074	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.034	0.001	36.930	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	59	GLY	0	0.033	0.018	34.883	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	60	SER	0	0.018	-0.002	33.089	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.023	-0.011	32.014	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	62	TYR	0	0.005	-0.027	29.089	-0.005	-0.005	0.000	0.000	0.000	0.000
63	A	63	ASN	0	-0.029	-0.027	28.731	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	64	ALA	0	0.036	0.021	27.276	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.019	0.005	26.459	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	66	VAL	0	-0.015	0.005	24.665	-0.009	-0.009	0.000	0.000	0.000	0.000
67	A	67	MET	0	0.008	-0.001	22.778	-0.008	-0.008	0.000	0.000	0.000	0.000
68	A	68	ALA	0	0.033	0.029	21.738	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	69	CYS	0	-0.011	-0.003	21.020	-0.010	-0.010	0.000	0.000	0.000	0.000
70	A	70	TRP	0	-0.033	-0.012	16.461	-0.025	-0.025	0.000	0.000	0.000	0.000
71	A	71	GLY	0	0.025	0.000	17.360	-0.020	-0.020	0.000	0.000	0.000	0.000
72	A	72	MET	0	0.021	0.026	16.405	-0.020	-0.020	0.000	0.000	0.000	0.000
73	A	73	VAL	0	-0.007	0.000	14.293	-0.030	-0.030	0.000	0.000	0.000	0.000
74	A	74	TYR	0	0.018	0.017	12.955	-0.060	-0.060	0.000	0.000	0.000	0.000
75	A	75	LEU	0	-0.034	-0.029	11.743	-0.030	-0.030	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.835	0.903	11.212	0.221	0.221	0.000	0.000	0.000	0.000
77	A	77	THR	0	-0.007	-0.011	8.545	-0.133	-0.133	0.000	0.000	0.000	0.000
78	A	78	GLN	0	-0.014	-0.015	6.940	-0.144	-0.144	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.800	-0.851	7.030	-0.129	-0.129	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.828	-0.920	5.578	-0.424	-0.424	0.000	0.000	0.000	0.000
81	A	81	ASN	0	-0.148	-0.078	2.194	-2.621	-1.616	1.781	-0.831	-1.955	-0.002
82	A	82	ILE	0	0.016	0.026	2.770	-3.075	-1.871	0.450	-0.720	-0.934	-0.009
83	A	83	ALA	0	-0.027	-0.010	5.164	0.625	0.656	-0.001	0.000	-0.029	0.000
84	A	84	CYS	0	-0.056	-0.034	7.678	-0.035	-0.035	0.000	0.000	0.000	0.000
85	A	85	ASN	0	-0.010	-0.004	10.946	0.079	0.079	0.000	0.000	0.000	0.000
86	A	86	GLN	0	0.058	0.013	14.348	-0.068	-0.068	0.000	0.000	0.000	0.000
87	A	87	VAL	0	-0.019	0.003	16.148	0.031	0.031	0.000	0.000	0.000	0.000
88	A	88	VAL	0	0.037	0.013	19.932	-0.019	-0.019	0.000	0.000	0.000	0.000
89	A	89	THR	0	-0.130	-0.061	22.381	0.006	0.006	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.883	-0.939	24.460	-0.070	-0.070	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.063	0.031	26.038	-0.009	-0.009	0.000	0.000	0.000	0.000
92	A	92	ASN	0	-0.091	-0.033	28.374	0.011	0.011	0.000	0.000	0.000	0.000
93	A	93	MET	0	-0.010	0.027	31.035	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	94	LYS	1	0.908	0.969	33.507	0.043	0.043	0.000	0.000	0.000	0.000
95	A	95	TYR	0	-0.030	-0.035	35.336	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	96	ILE	0	-0.074	-0.034	37.338	0.002	0.002	0.000	0.000	0.000	0.000
97	A	97	ALA	0	0.005	-0.009	40.006	0.002	0.002	0.000	0.000	0.000	0.000
98	A	98	PRO	0	0.026	0.020	40.253	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	99	VAL	0	0.030	0.022	36.343	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	100	TYR	0	0.031	-0.011	39.608	0.001	0.001	0.000	0.000	0.000	0.000
101	A	101	GLY	0	0.033	0.021	39.731	0.002	0.002	0.000	0.000	0.000	0.000
102	A	102	ARG	1	0.794	0.890	31.431	0.026	0.026	0.000	0.000	0.000	0.000
103	A	103	ILE	0	0.009	0.011	31.807	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	104	ARG	1	0.797	0.846	30.428	0.046	0.046	0.000	0.000	0.000	0.000
105	A	105	ALA	0	-0.040	-0.008	27.524	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	106	ILE	0	0.018	0.016	26.308	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	107	CYS	0	-0.021	-0.016	22.408	-0.005	-0.005	0.000	0.000	0.000	0.000
108	A	108	HIS	0	0.053	0.033	22.310	0.009	0.009	0.000	0.000	0.000	0.000
109	A	109	ALA	0	0.011	-0.007	17.476	-0.007	-0.007	0.000	0.000	0.000	0.000
110	A	110	PRO	0	-0.025	-0.015	17.209	0.009	0.009	0.000	0.000	0.000	0.000
111	A	111	ASP	-1	-0.866	-0.937	18.546	-0.168	-0.168	0.000	0.000	0.000	0.000
112	A	112	GLU	-1	-0.913	-0.954	16.584	-0.229	-0.229	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.926	-0.970	16.256	-0.248	-0.248	0.000	0.000	0.000	0.000
114	A	114	GLU	-1	-0.866	-0.947	17.570	-0.220	-0.220	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.043	-0.016	13.377	-0.034	-0.034	0.000	0.000	0.000	0.000
116	A	116	ALA	0	0.001	0.009	12.924	-0.082	-0.082	0.000	0.000	0.000	0.000
117	A	117	ASN	0	-0.045	-0.024	13.482	-0.064	-0.064	0.000	0.000	0.000	0.000
118	A	118	PHE	0	-0.026	-0.006	12.760	-0.004	-0.004	0.000	0.000	0.000	0.000
119	A	119	PHE	0	0.038	-0.013	9.098	-0.044	-0.044	0.000	0.000	0.000	0.000
120	A	120	ASP	-1	-0.779	-0.861	10.677	-0.464	-0.464	0.000	0.000	0.000	0.000
121	A	121	HIS	0	-0.035	-0.032	12.435	0.082	0.082	0.000	0.000	0.000	0.000
122	A	122	PHE	0	-0.034	-0.025	8.207	0.086	0.086	0.000	0.000	0.000	0.000
123	A	123	GLU	-1	-0.922	-0.945	7.655	-0.939	-0.939	0.000	0.000	0.000	0.000
124	A	124	ARG	1	0.814	0.887	10.678	0.407	0.407	0.000	0.000	0.000	0.000
125	A	125	LYS	1	0.825	0.900	14.098	0.257	0.257	0.000	0.000	0.000	0.000
126	A	126	GLY	0	-0.049	-0.016	13.022	0.049	0.049	0.000	0.000	0.000	0.000
127	A	127	LYS	1	0.944	0.963	14.089	0.160	0.160	0.000	0.000	0.000	0.000
128	A	128	ALA	0	0.018	0.030	14.505	-0.012	-0.012	0.000	0.000	0.000	0.000
129	A	129	ARG	1	0.891	0.947	16.443	0.137	0.137	0.000	0.000	0.000	0.000
130	A	130	ILE	0	0.074	0.056	16.542	-0.010	-0.010	0.000	0.000	0.000	0.000
131	A	131	SER	0	0.006	-0.019	19.302	0.016	0.016	0.000	0.000	0.000	0.000
132	A	132	LEU	0	0.000	0.014	19.162	-0.007	-0.007	0.000	0.000	0.000	0.000
133	A	133	GLU	-1	-0.838	-0.906	23.049	-0.077	-0.077	0.000	0.000	0.000	0.000
134	A	134	ALA	0	0.021	0.003	25.264	-0.004	-0.004	0.000	0.000	0.000	0.000
135	A	135	ALA	0	-0.050	-0.018	27.318	0.005	0.005	0.000	0.000	0.000	0.000
136	A	136	ILE	0	0.001	0.009	30.225	0.000	0.000	0.000	0.000	0.000	0.000
137	A	137	TYR	0	0.072	0.022	31.128	0.001	0.001	0.000	0.000	0.000	0.000
138	A	138	ASN	0	-0.012	-0.023	35.488	0.002	0.002	0.000	0.000	0.000	0.000
139	A	139	ASP	-1	-0.852	-0.928	37.763	-0.037	-0.037	0.000	0.000	0.000	0.000
140	A	140	ALA	0	0.005	0.001	35.925	-0.002	-0.002	0.000	0.000	0.000	0.000
141	A	141	CYS	0	-0.047	-0.023	34.941	0.000	0.000	0.000	0.000	0.000	0.000
142	A	142	VAL	0	-0.016	0.014	31.957	-0.002	-0.002	0.000	0.000	0.000	0.000
143	A	143	MET	0	0.013	0.013	29.086	0.000	0.000	0.000	0.000	0.000	0.000
144	A	144	LYS	1	0.864	0.916	28.000	0.058	0.058	0.000	0.000	0.000	0.000
145	A	145	ILE	0	-0.024	-0.004	27.169	0.005	0.005	0.000	0.000	0.000	0.000
146	A	146	GLU	-1	-0.855	-0.912	30.220	-0.057	-0.057	0.000	0.000	0.000	0.000
147	A	147	PRO	0	-0.019	-0.016	33.294	0.003	0.003	0.000	0.000	0.000	0.000
148	A	148	GLU	-1	-0.861	-0.959	35.725	-0.053	-0.053	0.000	0.000	0.000	0.000
149	A	149	THR	0	-0.026	0.000	36.098	0.004	0.004	0.000	0.000	0.000	0.000
150	A	150	LYS	1	0.856	0.921	36.855	0.044	0.044	0.000	0.000	0.000	0.000
151	A	151	PRO	0	0.010	0.030	34.502	0.002	0.002	0.000	0.000	0.000	0.000
152	A	152	SER	0	-0.002	-0.005	36.600	0.002	0.002	0.000	0.000	0.000	0.000
153	A	153	VAL	0	-0.036	-0.022	33.446	0.002	0.002	0.000	0.000	0.000	0.000
154	A	154	LYS	1	0.901	0.942	31.591	0.069	0.069	0.000	0.000	0.000	0.000
155	A	155	PHE	0	0.003	-0.010	25.287	0.005	0.005	0.000	0.000	0.000	0.000
156	A	156	ASN	0	0.037	0.027	27.532	-0.004	-0.004	0.000	0.000	0.000	0.000
157	A	157	GLY	0	0.045	0.018	24.859	0.008	0.008	0.000	0.000	0.000	0.000
158	A	158	GLN	0	-0.002	-0.001	22.575	-0.010	-0.010	0.000	0.000	0.000	0.000
159	A	159	TYR	0	-0.006	-0.022	18.526	0.017	0.017	0.000	0.000	0.000	0.000
160	A	160	ALA	0	-0.017	-0.013	17.965	-0.013	-0.013	0.000	0.000	0.000	0.000
161	A	161	ILE	0	0.024	0.029	11.083	0.026	0.026	0.000	0.000	0.000	0.000
162	A	162	LEU	0	-0.032	-0.043	14.407	0.002	0.002	0.000	0.000	0.000	0.000
163	A	163	LYS	1	0.934	0.988	9.687	0.451	0.451	0.000	0.000	0.000	0.000
164	A	164	ASN	0	-0.023	0.003	11.236	0.097	0.097	0.000	0.000	0.000	0.000

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