FMO DATABASE

FMODB ID: R9958

Calculation Name: 4DAM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4DAM

Chain ID: A

ChEMBL ID:

UniProt ID: Q9KYI9

Base Structure: X-ray

Registration Date: 2023-06-21

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	113
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-783694.586289
FMO2-HF: Nuclear repulsion	740672.9028
FMO2-HF: Total energy	-43021.683489
FMO2-MP2: Total energy	-43147.29584

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:0:SER)

Summations of interaction energy for fragment #1(A:0: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.
-3.532	-0.203	0.086	-1.661	-1.753	0.003

Interaction energy analysis for fragmet #1(A:0:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / q_NPA : 0.012

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	2	ASN	0	-0.028	-0.024	3.874	-1.381	1.266	-0.016	-1.488	-1.143	0.004
4	A	3	GLU	-1	-0.752	-0.859	3.025	1.611	2.295	0.103	-0.172	-0.614	-0.001
5	A	4	ILE	0	0.005	0.014	5.358	-0.099	-0.101	-0.001	-0.001	0.004	0.000
6	A	5	MET	0	-0.041	-0.013	7.721	0.331	0.331	0.000	0.000	0.000	0.000
7	A	6	ILE	0	-0.012	-0.004	10.101	-0.200	-0.200	0.000	0.000	0.000	0.000
8	A	7	CYS	0	-0.028	-0.026	13.787	0.075	0.075	0.000	0.000	0.000	0.000
9	A	8	ALA	0	-0.007	0.004	16.527	-0.046	-0.046	0.000	0.000	0.000	0.000
10	A	9	VAL	0	0.039	0.014	19.705	0.014	0.014	0.000	0.000	0.000	0.000
11	A	10	GLY	0	0.008	0.004	23.197	-0.015	-0.015	0.000	0.000	0.000	0.000
12	A	11	ASN	0	-0.027	-0.015	25.499	-0.006	-0.006	0.000	0.000	0.000	0.000
13	A	12	VAL	0	0.003	0.023	25.066	0.012	0.012	0.000	0.000	0.000	0.000
14	A	13	ALA	0	0.007	-0.005	26.885	-0.017	-0.017	0.000	0.000	0.000	0.000
15	A	14	THR	0	-0.035	-0.026	26.929	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	15	THR	0	0.039	0.012	27.881	0.010	0.010	0.000	0.000	0.000	0.000
17	A	16	PRO	0	-0.004	0.010	24.961	0.006	0.006	0.000	0.000	0.000	0.000
18	A	17	VAL	0	-0.043	-0.016	25.221	-0.015	-0.015	0.000	0.000	0.000	0.000
19	A	18	PHE	0	0.010	0.000	23.429	0.029	0.029	0.000	0.000	0.000	0.000
20	A	19	ARG	1	0.914	0.946	22.974	-0.270	-0.270	0.000	0.000	0.000	0.000
21	A	20	ASP	-1	-0.802	-0.897	22.697	0.286	0.286	0.000	0.000	0.000	0.000
22	A	21	LEU	0	-0.071	-0.037	19.072	-0.015	-0.015	0.000	0.000	0.000	0.000
23	A	22	ALA	0	0.039	0.016	21.471	0.005	0.005	0.000	0.000	0.000	0.000
24	A	23	ASN	0	0.014	0.015	16.168	-0.022	-0.022	0.000	0.000	0.000	0.000
25	A	24	GLY	0	0.000	-0.003	17.613	0.046	0.046	0.000	0.000	0.000	0.000
26	A	25	PRO	0	0.039	0.035	19.841	0.004	0.004	0.000	0.000	0.000	0.000
27	A	26	SER	0	-0.038	-0.035	17.671	0.047	0.047	0.000	0.000	0.000	0.000
28	A	27	VAL	0	0.007	0.005	19.491	-0.045	-0.045	0.000	0.000	0.000	0.000
29	A	28	ARG	1	0.938	0.988	19.622	-0.215	-0.215	0.000	0.000	0.000	0.000
30	A	29	PHE	0	0.030	0.007	20.934	-0.031	-0.031	0.000	0.000	0.000	0.000
31	A	30	ARG	1	0.923	0.983	22.066	-0.162	-0.162	0.000	0.000	0.000	0.000
32	A	31	LEU	0	0.016	0.020	20.409	-0.012	-0.012	0.000	0.000	0.000	0.000
33	A	32	ALA	0	-0.005	-0.011	23.604	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	33	VAL	0	0.013	-0.011	22.029	0.002	0.002	0.000	0.000	0.000	0.000
35	A	34	THR	0	-0.014	0.003	25.388	0.000	0.000	0.000	0.000	0.000	0.000
36	A	35	ALA	0	0.001	0.021	27.178	0.000	0.000	0.000	0.000	0.000	0.000
37	A	36	ARG	1	0.820	0.865	28.636	-0.113	-0.113	0.000	0.000	0.000	0.000
38	A	37	TYR	0	-0.012	-0.006	31.566	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	38	TRP	0	0.055	0.029	34.282	0.003	0.003	0.000	0.000	0.000	0.000
40	A	39	ASP	-1	-0.795	-0.915	37.564	0.039	0.039	0.000	0.000	0.000	0.000
41	A	40	ARG	1	0.783	0.874	39.116	-0.036	-0.036	0.000	0.000	0.000	0.000
42	A	41	GLU	-1	-0.796	-0.881	43.863	0.031	0.031	0.000	0.000	0.000	0.000
43	A	42	LYS	1	0.824	0.902	40.271	-0.048	-0.048	0.000	0.000	0.000	0.000
44	A	43	ASN	0	-0.052	-0.014	44.161	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	44	ALA	0	0.026	0.018	41.659	0.001	0.001	0.000	0.000	0.000	0.000
46	A	45	TRP	0	-0.008	-0.001	33.162	0.000	0.000	0.000	0.000	0.000	0.000
47	A	46	THR	0	-0.032	-0.006	36.753	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	47	ASP	-1	-0.790	-0.868	33.598	0.097	0.097	0.000	0.000	0.000	0.000
49	A	48	GLY	0	0.021	0.005	32.399	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	49	HIS	0	-0.014	-0.003	25.157	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	50	THR	0	-0.014	-0.017	27.566	0.001	0.001	0.000	0.000	0.000	0.000
52	A	51	ASN	0	-0.005	0.016	22.427	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	52	PHE	0	0.019	-0.016	23.431	0.000	0.000	0.000	0.000	0.000	0.000
54	A	53	PHE	0	0.016	0.008	17.895	0.005	0.005	0.000	0.000	0.000	0.000
55	A	54	THR	0	-0.032	-0.024	18.941	-0.030	-0.030	0.000	0.000	0.000	0.000
56	A	55	VAL	0	-0.017	0.007	17.183	0.060	0.060	0.000	0.000	0.000	0.000
57	A	56	TRP	0	0.013	-0.012	15.443	-0.057	-0.057	0.000	0.000	0.000	0.000
58	A	57	ALA	0	0.014	0.001	15.298	0.089	0.089	0.000	0.000	0.000	0.000
59	A	58	ASN	0	0.018	0.001	13.790	-0.102	-0.102	0.000	0.000	0.000	0.000
60	A	59	ARG	1	0.912	0.942	13.890	-0.555	-0.555	0.000	0.000	0.000	0.000
61	A	60	GLN	0	0.053	0.019	17.774	-0.014	-0.014	0.000	0.000	0.000	0.000
62	A	61	LEU	0	-0.005	0.010	15.152	-0.031	-0.031	0.000	0.000	0.000	0.000
63	A	62	ALA	0	-0.015	-0.006	18.499	-0.026	-0.026	0.000	0.000	0.000	0.000
64	A	63	THR	0	0.012	0.004	20.260	-0.020	-0.020	0.000	0.000	0.000	0.000
65	A	64	ASN	0	0.022	0.018	21.868	-0.029	-0.029	0.000	0.000	0.000	0.000
66	A	65	ALA	0	0.013	0.007	21.479	-0.020	-0.020	0.000	0.000	0.000	0.000
67	A	66	SER	0	-0.085	-0.056	23.467	-0.023	-0.023	0.000	0.000	0.000	0.000
68	A	67	GLY	0	0.020	0.020	25.862	-0.015	-0.015	0.000	0.000	0.000	0.000
69	A	68	SER	0	-0.065	-0.028	25.913	-0.013	-0.013	0.000	0.000	0.000	0.000
70	A	69	LEU	0	-0.025	0.004	22.987	0.004	0.004	0.000	0.000	0.000	0.000
71	A	70	ALA	0	0.006	0.001	27.641	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	71	VAL	0	-0.037	-0.026	29.689	0.007	0.007	0.000	0.000	0.000	0.000
73	A	72	GLY	0	0.027	0.012	30.634	-0.010	-0.010	0.000	0.000	0.000	0.000
74	A	73	ASP	-1	-0.805	-0.889	28.316	0.168	0.168	0.000	0.000	0.000	0.000
75	A	74	PRO	0	-0.013	0.002	28.071	0.013	0.013	0.000	0.000	0.000	0.000
76	A	75	VAL	0	0.002	-0.002	23.301	0.005	0.005	0.000	0.000	0.000	0.000
77	A	76	VAL	0	0.015	0.003	19.811	-0.007	-0.007	0.000	0.000	0.000	0.000
78	A	77	VAL	0	-0.014	-0.012	16.496	0.018	0.018	0.000	0.000	0.000	0.000
79	A	78	GLN	0	0.036	0.012	11.981	0.089	0.089	0.000	0.000	0.000	0.000
80	A	79	GLY	0	0.029	0.001	11.010	0.023	0.023	0.000	0.000	0.000	0.000
81	A	80	ARG	1	0.893	0.965	5.532	-2.581	-2.581	0.000	0.000	0.000	0.000
82	A	81	LEU	0	-0.002	-0.001	9.657	-0.102	-0.102	0.000	0.000	0.000	0.000
83	A	82	LYS	1	0.765	0.876	6.538	-1.327	-1.327	0.000	0.000	0.000	0.000
84	A	83	VAL	0	0.018	0.003	12.588	-0.040	-0.040	0.000	0.000	0.000	0.000
85	A	84	ARG	1	0.805	0.891	12.561	-0.527	-0.527	0.000	0.000	0.000	0.000
86	A	85	THR	0	0.018	-0.012	17.317	-0.024	-0.024	0.000	0.000	0.000	0.000
87	A	86	ASP	-1	-0.831	-0.907	20.221	0.234	0.234	0.000	0.000	0.000	0.000
88	A	87	VAL	0	-0.019	-0.013	23.181	-0.008	-0.008	0.000	0.000	0.000	0.000
89	A	88	ARG	1	0.791	0.882	22.334	-0.180	-0.180	0.000	0.000	0.000	0.000
90	A	89	GLU	-1	-0.825	-0.898	29.055	0.099	0.099	0.000	0.000	0.000	0.000
91	A	90	GLY	0	0.014	0.018	32.021	-0.007	-0.007	0.000	0.000	0.000	0.000
92	A	91	GLN	0	0.029	0.028	30.352	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	92	SER	0	-0.002	-0.003	25.902	0.014	0.014	0.000	0.000	0.000	0.000
94	A	93	ARG	1	0.811	0.882	25.646	-0.119	-0.119	0.000	0.000	0.000	0.000
95	A	94	THR	0	0.046	0.024	19.980	0.012	0.012	0.000	0.000	0.000	0.000
96	A	95	SER	0	-0.018	0.004	20.287	-0.013	-0.013	0.000	0.000	0.000	0.000
97	A	96	ALA	0	0.014	0.002	17.388	0.008	0.008	0.000	0.000	0.000	0.000
98	A	97	ASP	-1	-0.757	-0.830	15.241	0.379	0.379	0.000	0.000	0.000	0.000
99	A	98	ILE	0	-0.004	-0.014	13.589	0.026	0.026	0.000	0.000	0.000	0.000
100	A	99	ASP	-1	-0.811	-0.904	10.254	0.927	0.927	0.000	0.000	0.000	0.000
101	A	100	ALA	0	-0.030	-0.020	10.911	0.229	0.229	0.000	0.000	0.000	0.000
102	A	101	VAL	0	-0.073	-0.037	9.097	0.183	0.183	0.000	0.000	0.000	0.000
103	A	102	ALA	0	0.003	0.002	12.171	-0.083	-0.083	0.000	0.000	0.000	0.000
104	A	103	ILE	0	-0.009	-0.019	15.688	0.012	0.012	0.000	0.000	0.000	0.000
105	A	104	GLY	0	0.010	0.017	19.119	-0.012	-0.012	0.000	0.000	0.000	0.000
106	A	105	HIS	0	0.025	0.004	22.631	-0.003	-0.003	0.000	0.000	0.000	0.000
107	A	106	ASP	-1	-0.839	-0.908	25.711	0.157	0.157	0.000	0.000	0.000	0.000
108	A	107	LEU	0	0.033	0.005	26.802	-0.012	-0.012	0.000	0.000	0.000	0.000
109	A	108	ALA	0	-0.042	-0.004	28.611	-0.012	-0.012	0.000	0.000	0.000	0.000
110	A	109	ARG	1	0.702	0.812	26.431	-0.166	-0.166	0.000	0.000	0.000	0.000
111	A	110	GLY	0	0.025	0.018	31.709	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	111	THR	0	-0.015	0.006	32.242	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	112	ALA	0	0.007	0.007	30.909	0.008	0.008	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:SER)