FMO DATABASE

FMODB ID: R8628

Calculation Name: 1LMI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1LMI

Chain ID: A

ChEMBL ID:

UniProt ID: P9WIP1

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	131
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1035702.663168
FMO2-HF: Nuclear repulsion	987630.898028
FMO2-HF: Total energy	-48071.76514
FMO2-MP2: Total energy	-48212.723727

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:SER)

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

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.
-39.762	-39.252	18.977	-10.895	-8.591	-0.044

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.037 / q_NPA : -0.046

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	TYR	0	-0.061	0.002	2.178	-9.121	-4.600	3.694	-3.835	-4.380	0.030
4	A	4	PRO	0	0.000	-0.007	2.986	-4.220	-2.978	0.190	-0.657	-0.774	-0.006
5	A	5	ILE	0	-0.015	-0.005	6.329	0.297	0.297	0.000	0.000	0.000	0.000
6	A	6	THR	0	0.010	-0.006	9.278	-0.179	-0.179	0.000	0.000	0.000	0.000
7	A	7	GLY	0	-0.002	-0.004	12.099	0.114	0.114	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.863	0.941	15.889	0.149	0.149	0.000	0.000	0.000	0.000
9	A	9	LEU	0	0.024	0.013	19.369	0.018	0.018	0.000	0.000	0.000	0.000
10	A	10	GLY	0	-0.034	-0.019	21.122	0.023	0.023	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.052	-0.043	18.681	0.030	0.030	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.843	-0.928	18.348	-0.066	-0.066	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.051	-0.015	13.372	0.032	0.032	0.000	0.000	0.000	0.000
14	A	14	THR	0	-0.008	-0.013	14.579	-0.032	-0.032	0.000	0.000	0.000	0.000
15	A	15	MET	0	0.013	0.014	9.109	-0.044	-0.044	0.000	0.000	0.000	0.000
16	A	16	THR	0	-0.005	-0.013	10.318	-0.099	-0.099	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.799	-0.890	9.712	0.271	0.271	0.000	0.000	0.000	0.000
18	A	18	THR	0	-0.022	-0.026	11.316	-0.074	-0.074	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.047	-0.018	10.899	-0.009	-0.009	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.025	0.011	13.153	-0.039	-0.039	0.000	0.000	0.000	0.000
21	A	21	GLN	0	-0.048	-0.004	14.935	0.007	0.007	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.001	0.007	14.282	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	23	VAL	0	-0.031	-0.029	14.531	0.069	0.069	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.039	-0.005	12.998	-0.041	-0.041	0.000	0.000	0.000	0.000
25	A	25	GLY	0	0.024	0.023	15.177	0.033	0.033	0.000	0.000	0.000	0.000
26	A	26	TRP	0	0.025	0.001	14.539	-0.037	-0.037	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.910	0.964	17.218	0.144	0.144	0.000	0.000	0.000	0.000
28	A	28	VAL	0	0.016	0.012	17.955	-0.008	-0.008	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.023	-0.035	20.540	0.010	0.010	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.829	-0.890	23.618	-0.170	-0.170	0.000	0.000	0.000	0.000
31	A	31	LEU	0	0.020	0.022	21.114	0.001	0.001	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.805	0.908	24.751	0.175	0.175	0.000	0.000	0.000	0.000
33	A	33	SER	0	0.040	0.016	28.074	-0.012	-0.012	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.047	-0.060	30.039	0.014	0.014	0.000	0.000	0.000	0.000
35	A	35	THR	0	0.002	-0.006	31.957	0.000	0.000	0.000	0.000	0.000	0.000
36	A	36	ALA	0	-0.021	-0.005	31.473	0.008	0.008	0.000	0.000	0.000	0.000
37	A	37	VAL	0	0.019	0.002	33.015	-0.011	-0.011	0.000	0.000	0.000	0.000
38	A	38	ILE	0	-0.005	0.000	29.581	0.006	0.006	0.000	0.000	0.000	0.000
39	A	39	PRO	0	0.021	0.030	32.967	0.004	0.004	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.008	-0.005	34.052	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	41	TYR	0	-0.018	-0.025	27.328	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	42	PRO	0	-0.036	-0.013	31.070	0.009	0.009	0.000	0.000	0.000	0.000
43	A	43	VAL	0	-0.044	-0.024	31.166	-0.012	-0.012	0.000	0.000	0.000	0.000
44	A	44	ALA	0	-0.027	-0.015	30.364	0.013	0.013	0.000	0.000	0.000	0.000
45	A	45	GLY	0	-0.020	-0.015	30.552	0.005	0.005	0.000	0.000	0.000	0.000
46	A	46	GLN	0	-0.075	-0.027	30.732	0.020	0.020	0.000	0.000	0.000	0.000
47	A	47	VAL	0	0.038	0.021	29.321	-0.020	-0.020	0.000	0.000	0.000	0.000
48	A	48	TRP	0	-0.004	0.003	25.736	0.010	0.010	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.839	-0.908	26.144	-0.184	-0.184	0.000	0.000	0.000	0.000
50	A	50	ALA	0	0.022	0.013	22.391	-0.011	-0.011	0.000	0.000	0.000	0.000
51	A	51	THR	0	-0.024	-0.010	24.471	0.012	0.012	0.000	0.000	0.000	0.000
52	A	52	ALA	0	-0.002	-0.001	20.409	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	53	THR	0	-0.017	-0.025	21.184	0.017	0.017	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.016	0.005	18.055	-0.015	-0.015	0.000	0.000	0.000	0.000
55	A	55	ASN	0	-0.002	-0.023	19.419	0.017	0.017	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.048	0.032	19.396	0.009	0.009	0.000	0.000	0.000	0.000
57	A	57	ILE	0	0.003	0.001	17.717	0.019	0.019	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.815	0.894	17.941	-0.217	-0.217	0.000	0.000	0.000	0.000
59	A	59	GLY	0	0.055	0.021	19.038	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	60	SER	0	-0.022	-0.013	21.359	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	61	VAL	0	0.008	-0.004	17.613	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	62	THR	0	0.003	-0.008	19.359	0.005	0.005	0.000	0.000	0.000	0.000
63	A	63	PRO	0	-0.019	0.007	18.135	-0.033	-0.033	0.000	0.000	0.000	0.000
64	A	64	ALA	0	0.045	0.029	14.877	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.000	-0.013	16.022	-0.074	-0.074	0.000	0.000	0.000	0.000
66	A	66	SER	0	0.017	0.006	17.699	-0.040	-0.040	0.000	0.000	0.000	0.000
67	A	67	GLN	0	0.046	0.027	11.290	-0.144	-0.144	0.000	0.000	0.000	0.000
68	A	68	PHE	0	-0.029	-0.002	13.941	-0.109	-0.109	0.000	0.000	0.000	0.000
69	A	69	ASN	0	0.009	0.007	14.066	0.058	0.058	0.000	0.000	0.000	0.000
70	A	70	ALA	0	0.021	0.029	17.195	0.002	0.002	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.791	0.834	10.943	1.174	1.174	0.000	0.000	0.000	0.000
72	A	72	THR	0	-0.011	-0.030	18.611	0.031	0.031	0.000	0.000	0.000	0.000
73	A	73	ALA	0	-0.023	-0.024	18.259	-0.048	-0.048	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.859	-0.898	17.864	-0.447	-0.447	0.000	0.000	0.000	0.000
75	A	75	GLY	0	0.021	0.012	16.309	-0.040	-0.040	0.000	0.000	0.000	0.000
76	A	76	ILE	0	-0.031	-0.002	17.093	-0.045	-0.045	0.000	0.000	0.000	0.000
77	A	77	ASN	0	-0.011	-0.007	15.682	-0.078	-0.078	0.000	0.000	0.000	0.000
78	A	78	TYR	0	0.009	-0.013	18.633	0.009	0.009	0.000	0.000	0.000	0.000
79	A	79	ARG	1	0.840	0.900	16.730	0.592	0.592	0.000	0.000	0.000	0.000
80	A	80	VAL	0	-0.006	0.007	18.919	0.047	0.047	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.046	-0.023	21.038	-0.007	-0.007	0.000	0.000	0.000	0.000
82	A	82	TRP	0	-0.011	0.014	21.058	0.004	0.004	0.000	0.000	0.000	0.000
83	A	83	GLN	0	-0.025	-0.020	22.523	-0.018	-0.018	0.000	0.000	0.000	0.000
84	A	84	ALA	0	0.007	-0.010	25.130	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	85	ALA	0	0.029	0.014	27.975	0.015	0.015	0.000	0.000	0.000	0.000
86	A	86	GLY	0	0.010	0.018	29.787	-0.010	-0.010	0.000	0.000	0.000	0.000
87	A	87	PRO	0	-0.016	0.003	31.389	0.005	0.005	0.000	0.000	0.000	0.000
88	A	88	ASP	-1	-0.816	-0.912	31.159	-0.150	-0.150	0.000	0.000	0.000	0.000
89	A	89	THR	0	-0.015	-0.002	26.158	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	90	ILE	0	-0.060	-0.004	21.824	0.011	0.011	0.000	0.000	0.000	0.000
91	A	91	SER	0	0.009	-0.002	25.448	-0.013	-0.013	0.000	0.000	0.000	0.000
92	A	92	GLY	0	0.026	-0.005	23.080	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	93	ALA	0	-0.033	-0.011	23.532	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	94	THR	0	-0.008	-0.012	22.656	-0.012	-0.012	0.000	0.000	0.000	0.000
95	A	95	ILE	0	0.006	0.036	21.901	0.008	0.008	0.000	0.000	0.000	0.000
96	A	96	PRO	0	0.015	0.004	23.789	0.004	0.004	0.000	0.000	0.000	0.000
97	A	97	GLN	0	0.039	0.015	22.936	0.003	0.003	0.000	0.000	0.000	0.000
98	A	98	GLY	0	-0.052	-0.022	24.187	0.003	0.003	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.934	-0.959	25.829	-0.039	-0.039	0.000	0.000	0.000	0.000
100	A	100	GLN	0	-0.024	-0.037	24.027	-0.010	-0.010	0.000	0.000	0.000	0.000
101	A	101	SER	0	-0.023	0.004	23.515	0.001	0.001	0.000	0.000	0.000	0.000
102	A	102	THR	0	0.018	-0.005	23.818	-0.014	-0.014	0.000	0.000	0.000	0.000
103	A	103	GLY	0	0.041	0.026	25.526	0.007	0.007	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.807	0.911	25.344	0.143	0.143	0.000	0.000	0.000	0.000
105	A	105	ILE	0	-0.015	0.000	19.946	-0.009	-0.009	0.000	0.000	0.000	0.000
106	A	106	TYR	0	0.005	-0.028	23.958	0.005	0.005	0.000	0.000	0.000	0.000
107	A	107	PHE	0	0.020	0.000	19.596	-0.030	-0.030	0.000	0.000	0.000	0.000
108	A	108	ASP	-1	-0.749	-0.882	24.698	-0.232	-0.232	0.000	0.000	0.000	0.000
109	A	109	VAL	0	-0.036	-0.007	24.985	-0.023	-0.023	0.000	0.000	0.000	0.000
110	A	110	THR	0	0.000	-0.001	26.795	0.016	0.016	0.000	0.000	0.000	0.000
111	A	111	GLY	0	0.017	0.011	26.679	0.006	0.006	0.000	0.000	0.000	0.000
112	A	112	PRO	0	-0.027	-0.008	25.269	0.014	0.014	0.000	0.000	0.000	0.000
113	A	113	SER	0	0.022	0.016	25.244	-0.023	-0.023	0.000	0.000	0.000	0.000
114	A	114	PRO	0	-0.017	0.013	21.712	-0.008	-0.008	0.000	0.000	0.000	0.000
115	A	115	THR	0	-0.051	-0.041	21.244	0.021	0.021	0.000	0.000	0.000	0.000
116	A	116	ILE	0	0.001	0.005	15.286	0.018	0.018	0.000	0.000	0.000	0.000
117	A	117	VAL	0	-0.011	0.000	16.534	0.004	0.004	0.000	0.000	0.000	0.000
118	A	118	ALA	0	0.019	0.004	12.192	-0.010	-0.010	0.000	0.000	0.000	0.000
119	A	119	MET	0	-0.036	0.000	11.325	0.058	0.058	0.000	0.000	0.000	0.000
120	A	120	ASN	0	-0.027	-0.030	9.164	-0.123	-0.123	0.000	0.000	0.000	0.000
121	A	121	ASN	0	0.042	0.019	5.669	0.249	0.249	0.000	0.000	0.000	0.000
122	A	122	GLY	0	-0.032	-0.010	9.757	0.184	0.184	0.000	0.000	0.000	0.000
123	A	123	MET	0	-0.072	-0.032	6.557	0.324	0.324	0.000	0.000	0.000	0.000
124	A	124	GLU	-1	-0.837	-0.910	1.647	-26.645	-31.951	15.094	-6.401	-3.388	-0.068
125	A	125	ASP	-1	-0.757	-0.835	5.872	-0.789	-0.789	0.000	0.000	0.000	0.000
126	A	126	LEU	0	-0.012	-0.011	4.682	-0.530	-0.477	-0.001	-0.002	-0.049	0.000
127	A	127	LEU	0	0.005	-0.008	6.943	0.448	0.448	0.000	0.000	0.000	0.000
128	A	128	ILE	0	-0.002	0.000	9.593	-0.089	-0.089	0.000	0.000	0.000	0.000
129	A	129	TRP	0	-0.009	-0.013	12.767	0.075	0.075	0.000	0.000	0.000	0.000
130	A	130	GLU	-1	-0.819	-0.903	15.698	-0.378	-0.378	0.000	0.000	0.000	0.000
131	A	131	PRO	0	0.007	-0.003	18.011	0.050	0.050	0.000	0.000	0.000	0.000

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