FMO DATABASE

FMODB ID: MNM3Z

Calculation Name: 3DML-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DML

Chain ID: A

ChEMBL ID:

UniProt ID: Q8KM22

Base Structure: X-ray

Registration Date: 2023-09-20

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	95
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-706039.95532
FMO2-HF: Nuclear repulsion	667740.364592
FMO2-HF: Total energy	-38299.590729
FMO2-MP2: Total energy	-38408.688429

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:2:GLU)

Summations of interaction energy for fragment #1(A:2:GLU)

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.
76.124	73.082	17.999	-6.795	-8.16	0.092

Interaction energy analysis for fragmet #1(A:2:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.869 / q_NPA : -0.956

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	4	ARG	1	0.774	0.865	3.885	-51.256	-49.802	0.002	-0.579	-0.876	0.003
4	A	5	LEU	0	-0.004	0.008	6.397	-0.507	-0.507	0.000	0.000	0.000	0.000
5	A	6	LEU	0	-0.003	-0.006	9.961	-2.228	-2.228	0.000	0.000	0.000	0.000
6	A	7	MET	0	-0.037	-0.002	12.283	-0.662	-0.662	0.000	0.000	0.000	0.000
7	A	8	PHE	0	0.008	-0.006	14.233	-0.692	-0.692	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.813	-0.939	18.524	14.174	14.174	0.000	0.000	0.000	0.000
9	A	10	GLN	0	0.030	0.009	21.820	-0.417	-0.417	0.000	0.000	0.000	0.000
10	A	11	PRO	0	0.027	0.007	25.302	-0.129	-0.129	0.000	0.000	0.000	0.000
11	A	12	GLY	0	0.002	0.007	28.190	-0.155	-0.155	0.000	0.000	0.000	0.000
12	A	13	CYS	0	-0.044	0.015	25.760	-0.212	-0.212	0.000	0.000	0.000	0.000
13	A	14	LEU	0	0.028	0.014	27.042	0.311	0.311	0.000	0.000	0.000	0.000
14	A	15	TYR	0	0.015	-0.007	25.923	-0.025	-0.025	0.000	0.000	0.000	0.000
15	A	16	CYS	0	-0.010	-0.009	22.850	0.584	0.584	0.000	0.000	0.000	0.000
16	A	17	ALA	0	0.010	0.008	23.611	0.256	0.256	0.000	0.000	0.000	0.000
17	A	18	ARG	1	0.914	0.969	26.166	-10.831	-10.831	0.000	0.000	0.000	0.000
18	A	19	TRP	0	0.062	0.034	15.761	-0.064	-0.064	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.839	-0.920	21.259	14.814	14.814	0.000	0.000	0.000	0.000
20	A	21	ALA	0	-0.038	-0.012	22.801	-0.081	-0.081	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.883	-0.915	24.711	11.817	11.817	0.000	0.000	0.000	0.000
22	A	23	ILE	0	-0.006	0.019	18.409	0.135	0.135	0.000	0.000	0.000	0.000
23	A	24	ALA	0	-0.024	-0.014	18.493	0.542	0.542	0.000	0.000	0.000	0.000
24	A	25	PRO	0	-0.049	-0.028	18.956	0.474	0.474	0.000	0.000	0.000	0.000
25	A	26	GLN	0	-0.035	-0.035	20.334	0.173	0.173	0.000	0.000	0.000	0.000
26	A	27	TYR	0	-0.028	-0.009	11.183	-0.235	-0.235	0.000	0.000	0.000	0.000
27	A	28	PRO	0	-0.010	0.000	13.978	1.129	1.129	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.015	-0.008	15.023	0.205	0.205	0.000	0.000	0.000	0.000
29	A	30	THR	0	-0.014	-0.007	15.481	0.262	0.262	0.000	0.000	0.000	0.000
30	A	31	ASP	-1	-0.811	-0.903	13.345	20.855	20.855	0.000	0.000	0.000	0.000
31	A	32	GLU	-1	-0.850	-0.939	11.517	22.812	22.812	0.000	0.000	0.000	0.000
32	A	33	GLY	0	0.015	-0.011	10.713	2.501	2.501	0.000	0.000	0.000	0.000
33	A	34	ARG	1	0.700	0.821	10.394	-20.014	-20.014	0.000	0.000	0.000	0.000
34	A	35	ALA	0	-0.012	0.007	7.317	2.170	2.170	0.000	0.000	0.000	0.000
35	A	36	ALA	0	0.021	0.017	6.004	7.256	7.256	0.000	0.000	0.000	0.000
36	A	37	PRO	0	0.001	0.025	6.032	-4.679	-4.679	0.000	0.000	0.000	0.000
37	A	38	VAL	0	-0.003	0.013	8.665	1.109	1.109	0.000	0.000	0.000	0.000
38	A	39	GLN	0	-0.047	-0.028	9.328	-0.177	-0.177	0.000	0.000	0.000	0.000
39	A	40	ARG	1	0.837	0.908	12.260	-15.829	-15.829	0.000	0.000	0.000	0.000
40	A	41	LEU	0	0.006	0.010	13.891	0.032	0.032	0.000	0.000	0.000	0.000
41	A	42	GLN	0	0.012	0.000	17.631	-0.775	-0.775	0.000	0.000	0.000	0.000
42	A	43	MET	0	-0.052	-0.027	20.687	0.224	0.224	0.000	0.000	0.000	0.000
43	A	44	ARG	1	0.807	0.879	21.936	-11.750	-11.750	0.000	0.000	0.000	0.000
44	A	45	ASP	-1	-0.839	-0.899	20.046	13.399	13.399	0.000	0.000	0.000	0.000
45	A	46	PRO	0	-0.063	-0.042	20.543	0.313	0.313	0.000	0.000	0.000	0.000
46	A	47	LEU	0	0.026	0.019	15.110	0.172	0.172	0.000	0.000	0.000	0.000
47	A	48	PRO	0	0.000	-0.002	12.648	-0.533	-0.533	0.000	0.000	0.000	0.000
48	A	49	PRO	0	-0.028	-0.031	13.802	0.573	0.573	0.000	0.000	0.000	0.000
49	A	50	GLY	0	0.009	0.012	11.700	0.903	0.903	0.000	0.000	0.000	0.000
50	A	51	LEU	0	-0.012	0.014	8.666	1.923	1.923	0.000	0.000	0.000	0.000
51	A	52	GLU	-1	-0.900	-0.945	10.564	18.922	18.922	0.000	0.000	0.000	0.000
52	A	53	LEU	0	-0.016	-0.025	11.341	1.948	1.948	0.000	0.000	0.000	0.000
53	A	54	ALA	0	-0.009	-0.001	13.813	-1.185	-1.185	0.000	0.000	0.000	0.000
54	A	55	ARG	1	0.806	0.872	15.316	-17.153	-17.153	0.000	0.000	0.000	0.000
55	A	56	PRO	0	0.047	0.029	17.584	0.746	0.746	0.000	0.000	0.000	0.000
56	A	57	VAL	0	0.030	0.028	17.552	0.077	0.077	0.000	0.000	0.000	0.000
57	A	58	THR	0	-0.010	-0.016	20.185	-0.445	-0.445	0.000	0.000	0.000	0.000
58	A	59	PHE	0	-0.027	-0.009	22.543	-0.780	-0.780	0.000	0.000	0.000	0.000
59	A	60	THR	0	0.016	0.047	22.201	0.478	0.478	0.000	0.000	0.000	0.000
60	A	61	PRO	0	0.037	-0.005	20.555	-0.760	-0.760	0.000	0.000	0.000	0.000
61	A	62	THR	0	-0.042	-0.036	16.978	-0.397	-0.397	0.000	0.000	0.000	0.000
62	A	63	PHE	0	0.008	-0.004	15.048	-0.024	-0.024	0.000	0.000	0.000	0.000
63	A	64	VAL	0	0.020	0.004	10.790	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	65	LEU	0	-0.015	0.014	7.193	0.130	0.130	0.000	0.000	0.000	0.000
65	A	66	MET	0	-0.042	-0.018	6.243	-2.132	-2.132	0.000	0.000	0.000	0.000
66	A	67	ALA	0	0.074	0.025	2.613	0.140	2.258	1.530	-1.660	-1.988	0.021
67	A	68	GLY	0	0.011	-0.001	1.767	-24.437	-30.975	16.451	-4.964	-4.948	0.065
68	A	69	ASP	-1	-0.908	-0.932	3.150	32.115	32.039	0.016	0.408	-0.348	0.003
69	A	70	VAL	0	0.003	0.000	6.340	-5.695	-5.695	0.000	0.000	0.000	0.000
70	A	71	GLU	-1	-0.773	-0.858	6.898	26.756	26.756	0.000	0.000	0.000	0.000
71	A	72	SER	0	-0.023	0.004	6.742	-2.399	-2.399	0.000	0.000	0.000	0.000
72	A	73	GLY	0	-0.012	-0.020	8.712	-3.243	-3.243	0.000	0.000	0.000	0.000
73	A	74	ARG	1	0.714	0.801	11.564	-18.002	-18.002	0.000	0.000	0.000	0.000
74	A	75	LEU	0	-0.014	0.011	14.287	-1.056	-1.056	0.000	0.000	0.000	0.000
75	A	76	GLU	-1	-0.797	-0.875	17.385	15.980	15.980	0.000	0.000	0.000	0.000
76	A	77	GLY	0	-0.001	0.001	20.442	-0.644	-0.644	0.000	0.000	0.000	0.000
77	A	78	TYR	0	-0.072	-0.081	21.692	0.899	0.899	0.000	0.000	0.000	0.000
78	A	79	PRO	0	-0.021	-0.015	23.842	-0.502	-0.502	0.000	0.000	0.000	0.000
79	A	80	GLY	0	0.033	0.022	25.149	-0.593	-0.593	0.000	0.000	0.000	0.000
80	A	81	GLU	-1	-0.793	-0.894	23.333	13.768	13.768	0.000	0.000	0.000	0.000
81	A	82	ASP	-1	-0.926	-0.961	22.751	12.829	12.829	0.000	0.000	0.000	0.000
82	A	83	PHE	0	-0.067	-0.039	23.535	0.067	0.067	0.000	0.000	0.000	0.000
83	A	84	PHE	0	0.001	-0.004	15.791	0.565	0.565	0.000	0.000	0.000	0.000
84	A	85	TRP	0	0.043	0.016	16.287	1.282	1.282	0.000	0.000	0.000	0.000
85	A	86	PRO	0	0.015	0.014	17.273	1.057	1.057	0.000	0.000	0.000	0.000
86	A	87	MET	0	-0.058	-0.035	17.778	0.390	0.390	0.000	0.000	0.000	0.000
87	A	88	LEU	0	0.011	0.020	11.884	1.051	1.051	0.000	0.000	0.000	0.000
88	A	89	ALA	0	0.066	0.034	12.934	2.099	2.099	0.000	0.000	0.000	0.000
89	A	90	ARG	1	0.811	0.906	13.273	-19.206	-19.206	0.000	0.000	0.000	0.000
90	A	91	LEU	0	-0.047	-0.021	11.107	0.333	0.333	0.000	0.000	0.000	0.000
91	A	92	ILE	0	0.040	0.015	8.085	2.394	2.394	0.000	0.000	0.000	0.000
92	A	93	GLY	0	0.012	0.005	8.945	2.448	2.448	0.000	0.000	0.000	0.000
93	A	94	GLN	0	-0.062	-0.023	11.061	-2.557	-2.557	0.000	0.000	0.000	0.000
94	A	95	ALA	0	-0.038	-0.013	5.586	-0.166	-0.166	0.000	0.000	0.000	0.000
95	A	96	GLU	-1	-1.011	-0.990	5.798	43.167	43.167	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:GLU)