FMO DATABASE

FMODB ID: 5G97Z

Calculation Name: 2D2M-D-Xray547

Preferred Name:

Target Type:

Ligand Name: protoporphyrin ix containing fe | oxygen molecule

Ligand 3-letter code: HEM | OXY

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2D2M

Chain ID: D

ChEMBL ID:

UniProt ID: Q7M419

Base Structure: X-ray

Registration Date: 2025-10-06

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	144
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1155592.315254
FMO2-HF: Nuclear repulsion	1102582.618361
FMO2-HF: Total energy	-53009.696893
FMO2-MP2: Total energy	-53160.839682

3D Structure Molmil

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(D:1:GLU)

Summations of interaction energy for fragment #1(D:1: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.
-10.594	-8.189	0.099	-0.909	-1.595	-0.002

Interaction energy analysis for fragmet #1(D:1:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.102 / q_NPA : -0.070

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	D	3	CYS	0	-0.037	0.018	3.754	-2.604	-1.247	0.001	-0.460	-0.899	0.002
4	D	4	SER	0	-0.064	-0.057	2.664	-0.931	-0.146	0.098	-0.368	-0.514	-0.003
5	D	5	ARG	1	0.851	0.894	3.930	11.171	11.434	0.000	-0.081	-0.182	-0.001
6	D	6	GLY	0	0.056	0.030	6.892	1.770	1.770	0.000	0.000	0.000	0.000
7	D	7	ASP	-1	-0.802	-0.868	5.219	-16.546	-16.546	0.000	0.000	0.000	0.000
8	D	8	ALA	0	0.035	0.010	8.091	1.784	1.784	0.000	0.000	0.000	0.000
9	D	9	GLU	-1	-0.854	-0.911	10.050	-4.790	-4.790	0.000	0.000	0.000	0.000
10	D	10	VAL	0	-0.040	-0.011	11.693	0.781	0.781	0.000	0.000	0.000	0.000
11	D	11	VAL	0	0.027	0.012	11.747	0.614	0.614	0.000	0.000	0.000	0.000
12	D	12	ILE	0	0.006	0.003	13.914	0.491	0.491	0.000	0.000	0.000	0.000
13	D	13	SER	0	-0.024	-0.005	15.853	0.540	0.540	0.000	0.000	0.000	0.000
14	D	14	GLU	-1	-0.836	-0.919	16.335	-2.671	-2.671	0.000	0.000	0.000	0.000
15	D	15	TRP	0	-0.053	-0.038	18.062	0.301	0.301	0.000	0.000	0.000	0.000
16	D	16	ASP	-1	-0.865	-0.946	19.818	-2.071	-2.071	0.000	0.000	0.000	0.000
17	D	17	GLN	0	-0.099	-0.050	19.860	0.312	0.312	0.000	0.000	0.000	0.000
18	D	18	VAL	0	-0.031	-0.011	22.461	0.176	0.176	0.000	0.000	0.000	0.000
19	D	19	PHE	0	-0.029	-0.026	23.157	0.208	0.208	0.000	0.000	0.000	0.000
20	D	20	ASN	0	0.094	0.059	25.753	0.006	0.006	0.000	0.000	0.000	0.000
21	D	21	ALA	0	-0.031	-0.029	26.829	0.080	0.080	0.000	0.000	0.000	0.000
22	D	22	ALA	0	-0.110	-0.070	30.055	0.063	0.063	0.000	0.000	0.000	0.000
23	D	23	MET	0	-0.003	0.013	28.835	0.095	0.095	0.000	0.000	0.000	0.000
24	D	24	ALA	0	0.008	0.019	27.786	0.037	0.037	0.000	0.000	0.000	0.000
25	D	25	GLY	0	-0.028	-0.013	29.773	0.045	0.045	0.000	0.000	0.000	0.000
26	D	26	SER	0	-0.082	-0.055	32.346	0.081	0.081	0.000	0.000	0.000	0.000
27	D	27	SER	0	-0.050	-0.033	32.162	0.076	0.076	0.000	0.000	0.000	0.000
28	D	28	GLU	-1	-0.749	-0.860	28.188	-1.013	-1.013	0.000	0.000	0.000	0.000
29	D	29	SER	0	-0.029	-0.002	29.848	-0.006	-0.006	0.000	0.000	0.000	0.000
30	D	30	ALA	0	0.023	0.007	32.319	0.025	0.025	0.000	0.000	0.000	0.000
31	D	31	VAL	0	0.026	0.009	26.157	0.029	0.029	0.000	0.000	0.000	0.000
32	D	32	GLY	0	0.059	0.009	27.896	-0.008	-0.008	0.000	0.000	0.000	0.000
33	D	33	VAL	0	-0.057	-0.040	28.954	0.033	0.033	0.000	0.000	0.000	0.000
34	D	34	ALA	0	0.037	0.037	28.741	0.041	0.041	0.000	0.000	0.000	0.000
35	D	35	ILE	0	-0.021	0.000	23.675	0.012	0.012	0.000	0.000	0.000	0.000
36	D	36	PHE	0	0.012	-0.007	26.621	0.053	0.053	0.000	0.000	0.000	0.000
37	D	37	ASP	-1	-0.915	-0.954	28.998	-0.379	-0.379	0.000	0.000	0.000	0.000
38	D	38	ALA	0	0.014	0.008	25.763	0.065	0.065	0.000	0.000	0.000	0.000
39	D	39	PHE	0	0.015	0.014	24.221	0.061	0.061	0.000	0.000	0.000	0.000
40	D	40	PHE	0	-0.028	0.001	26.347	0.072	0.072	0.000	0.000	0.000	0.000
41	D	41	ALA	0	-0.029	-0.007	29.038	0.063	0.063	0.000	0.000	0.000	0.000
42	D	42	SER	0	-0.073	-0.039	24.490	0.062	0.062	0.000	0.000	0.000	0.000
43	D	43	SER	0	-0.025	-0.036	25.065	0.085	0.085	0.000	0.000	0.000	0.000
44	D	44	GLY	0	-0.010	0.004	26.301	0.064	0.064	0.000	0.000	0.000	0.000
45	D	45	VAL	0	-0.039	-0.018	27.261	0.018	0.018	0.000	0.000	0.000	0.000
46	D	46	SER	0	-0.026	-0.012	30.236	-0.024	-0.024	0.000	0.000	0.000	0.000
47	D	47	PRO	0	0.062	0.020	33.322	-0.011	-0.011	0.000	0.000	0.000	0.000
48	D	48	SER	0	-0.040	-0.038	34.388	-0.021	-0.021	0.000	0.000	0.000	0.000
49	D	49	MET	0	-0.030	0.008	30.787	0.014	0.014	0.000	0.000	0.000	0.000
50	D	50	PHE	0	0.000	0.006	28.320	-0.024	-0.024	0.000	0.000	0.000	0.000
51	D	51	PRO	0	0.006	-0.010	33.595	0.023	0.023	0.000	0.000	0.000	0.000
52	D	52	GLY	0	0.010	-0.004	36.329	-0.023	-0.023	0.000	0.000	0.000	0.000
53	D	53	GLY	0	-0.038	-0.003	37.325	0.017	0.017	0.000	0.000	0.000	0.000
54	D	54	GLY	0	-0.017	-0.008	35.283	0.019	0.019	0.000	0.000	0.000	0.000
55	D	55	ASP	-1	-0.828	-0.928	36.226	-0.323	-0.323	0.000	0.000	0.000	0.000
56	D	56	SER	0	0.019	0.006	36.767	-0.012	-0.012	0.000	0.000	0.000	0.000
57	D	57	ASN	0	-0.083	-0.041	37.941	-0.020	-0.020	0.000	0.000	0.000	0.000
58	D	58	ASN	0	0.063	0.045	39.475	-0.010	-0.010	0.000	0.000	0.000	0.000
59	D	59	PRO	0	0.013	-0.003	39.248	-0.032	-0.032	0.000	0.000	0.000	0.000
60	D	60	GLU	-1	-0.893	-0.952	38.622	-0.391	-0.391	0.000	0.000	0.000	0.000
61	D	61	PHE	0	-0.021	0.004	32.448	-0.037	-0.037	0.000	0.000	0.000	0.000
62	D	62	LEU	0	0.007	0.007	34.490	-0.055	-0.055	0.000	0.000	0.000	0.000
63	D	63	ALA	0	-0.016	-0.014	34.013	-0.059	-0.059	0.000	0.000	0.000	0.000
64	D	64	GLN	0	0.008	-0.004	29.578	-0.030	-0.030	0.000	0.000	0.000	0.000
65	D	65	VAL	0	-0.018	0.006	30.024	-0.063	-0.063	0.000	0.000	0.000	0.000
66	D	66	SER	0	0.005	0.006	29.071	-0.103	-0.103	0.000	0.000	0.000	0.000
67	D	67	ARG	1	0.874	0.934	28.771	0.529	0.529	0.000	0.000	0.000	0.000
68	D	68	VAL	0	-0.028	-0.002	25.200	-0.063	-0.063	0.000	0.000	0.000	0.000
69	D	69	VAL	0	0.020	0.014	24.546	-0.105	-0.105	0.000	0.000	0.000	0.000
70	D	70	SER	0	0.005	0.005	23.917	-0.169	-0.169	0.000	0.000	0.000	0.000
71	D	71	GLY	0	0.004	-0.003	23.546	-0.111	-0.111	0.000	0.000	0.000	0.000
72	D	72	ALA	0	-0.005	-0.004	20.152	-0.140	-0.140	0.000	0.000	0.000	0.000
73	D	73	ASP	-1	-0.821	-0.881	19.160	-2.166	-2.166	0.000	0.000	0.000	0.000
74	D	74	ILE	0	-0.015	-0.014	19.427	-0.241	-0.241	0.000	0.000	0.000	0.000
75	D	75	ALA	0	-0.023	-0.009	16.614	-0.171	-0.171	0.000	0.000	0.000	0.000
76	D	76	ILE	0	0.033	0.005	15.095	-0.522	-0.522	0.000	0.000	0.000	0.000
77	D	77	ASN	0	-0.015	-0.030	14.887	-0.746	-0.746	0.000	0.000	0.000	0.000
78	D	78	SER	0	-0.026	-0.004	15.191	0.122	0.122	0.000	0.000	0.000	0.000
79	D	79	LEU	0	-0.014	-0.006	10.532	-0.448	-0.448	0.000	0.000	0.000	0.000
80	D	80	THR	0	-0.039	-0.018	9.998	-1.221	-1.221	0.000	0.000	0.000	0.000
81	D	81	ASN	0	-0.079	-0.037	11.445	-0.302	-0.302	0.000	0.000	0.000	0.000
82	D	82	ARG	1	0.897	0.953	6.543	10.093	10.093	0.000	0.000	0.000	0.000
83	D	83	ALA	0	0.061	0.033	11.572	0.508	0.508	0.000	0.000	0.000	0.000
84	D	84	THR	0	-0.026	-0.026	14.806	0.335	0.335	0.000	0.000	0.000	0.000
85	D	85	CYS	0	0.015	0.033	13.005	0.272	0.272	0.000	0.000	0.000	0.000
86	D	86	ASP	-1	-0.814	-0.894	12.423	-2.713	-2.713	0.000	0.000	0.000	0.000
87	D	87	SER	0	-0.074	-0.032	15.100	0.442	0.442	0.000	0.000	0.000	0.000
88	D	88	LEU	0	0.015	0.004	18.090	0.240	0.240	0.000	0.000	0.000	0.000
89	D	89	LEU	0	-0.007	0.008	13.995	0.213	0.213	0.000	0.000	0.000	0.000
90	D	90	SER	0	-0.018	0.000	18.178	0.300	0.300	0.000	0.000	0.000	0.000
91	D	91	HIS	0	-0.025	-0.009	19.958	0.175	0.175	0.000	0.000	0.000	0.000
92	D	92	LEU	0	0.033	0.010	20.088	0.125	0.125	0.000	0.000	0.000	0.000
93	D	93	ASN	0	-0.014	0.009	19.177	0.171	0.171	0.000	0.000	0.000	0.000
94	D	94	ALA	0	-0.042	-0.022	21.939	0.114	0.114	0.000	0.000	0.000	0.000
95	D	95	GLN	0	-0.030	-0.024	25.196	0.010	0.010	0.000	0.000	0.000	0.000
96	D	96	HIS	0	-0.013	-0.026	23.698	0.049	0.049	0.000	0.000	0.000	0.000
97	D	97	ARG	1	0.830	0.921	21.225	0.057	0.057	0.000	0.000	0.000	0.000
98	D	98	ALA	0	-0.071	-0.018	26.744	0.056	0.056	0.000	0.000	0.000	0.000
99	D	99	ILE	0	-0.024	-0.002	28.205	0.001	0.001	0.000	0.000	0.000	0.000
100	D	100	SER	0	-0.011	-0.016	29.282	0.023	0.023	0.000	0.000	0.000	0.000
101	D	101	GLY	0	-0.007	-0.013	29.599	0.006	0.006	0.000	0.000	0.000	0.000
102	D	102	VAL	0	-0.027	0.000	23.780	-0.004	-0.004	0.000	0.000	0.000	0.000
103	D	103	THR	0	0.038	0.020	24.020	0.031	0.031	0.000	0.000	0.000	0.000
104	D	104	GLY	0	0.052	0.019	19.787	-0.094	-0.094	0.000	0.000	0.000	0.000
105	D	105	ALA	0	-0.018	-0.013	19.239	-0.070	-0.070	0.000	0.000	0.000	0.000
106	D	106	ALA	0	0.035	0.026	20.666	-0.076	-0.076	0.000	0.000	0.000	0.000
107	D	107	VAL	0	0.011	0.005	18.424	-0.120	-0.120	0.000	0.000	0.000	0.000
108	D	108	THR	0	-0.053	-0.029	15.613	-0.131	-0.131	0.000	0.000	0.000	0.000
109	D	109	HIS	0	0.047	0.033	17.941	-0.084	-0.084	0.000	0.000	0.000	0.000
110	D	110	LEU	0	-0.025	-0.006	21.076	-0.097	-0.097	0.000	0.000	0.000	0.000
111	D	111	SER	0	-0.067	-0.049	16.527	-0.131	-0.131	0.000	0.000	0.000	0.000
112	D	112	GLN	0	0.045	0.015	15.557	-0.082	-0.082	0.000	0.000	0.000	0.000
113	D	113	ALA	0	-0.025	-0.002	18.774	-0.042	-0.042	0.000	0.000	0.000	0.000
114	D	114	ILE	0	-0.010	-0.008	19.367	-0.031	-0.031	0.000	0.000	0.000	0.000
115	D	115	SER	0	-0.023	-0.030	15.988	-0.157	-0.157	0.000	0.000	0.000	0.000
116	D	116	SER	0	-0.008	-0.002	18.501	-0.018	-0.018	0.000	0.000	0.000	0.000
117	D	117	VAL	0	-0.024	-0.009	21.430	0.040	0.040	0.000	0.000	0.000	0.000
118	D	118	VAL	0	0.003	0.004	18.995	0.038	0.038	0.000	0.000	0.000	0.000
119	D	119	ALA	0	0.033	0.004	19.702	0.006	0.006	0.000	0.000	0.000	0.000
120	D	120	GLN	0	-0.115	-0.049	21.469	0.142	0.142	0.000	0.000	0.000	0.000
121	D	121	VAL	0	-0.043	-0.017	24.916	0.068	0.068	0.000	0.000	0.000	0.000
122	D	122	LEU	0	-0.039	-0.013	20.330	0.034	0.034	0.000	0.000	0.000	0.000
123	D	123	PRO	0	0.006	-0.008	21.949	-0.106	-0.106	0.000	0.000	0.000	0.000
124	D	124	SER	0	-0.056	-0.034	20.960	0.072	0.072	0.000	0.000	0.000	0.000
125	D	125	ALA	0	-0.007	0.027	17.881	-0.157	-0.157	0.000	0.000	0.000	0.000
126	D	126	HIS	0	0.039	0.016	10.547	0.326	0.326	0.000	0.000	0.000	0.000
127	D	127	ILE	0	0.004	-0.023	13.358	-0.432	-0.432	0.000	0.000	0.000	0.000
128	D	128	ASP	-1	-0.898	-0.938	9.945	-2.039	-2.039	0.000	0.000	0.000	0.000
129	D	129	ALA	0	-0.019	-0.015	8.797	-0.592	-0.592	0.000	0.000	0.000	0.000
130	D	130	TRP	0	-0.014	-0.028	9.866	-0.594	-0.594	0.000	0.000	0.000	0.000
131	D	131	GLU	-1	-0.801	-0.882	12.049	-1.656	-1.656	0.000	0.000	0.000	0.000
132	D	132	TYR	0	-0.093	-0.047	6.619	0.181	0.181	0.000	0.000	0.000	0.000
133	D	134	MET	0	0.028	0.020	10.265	0.395	0.395	0.000	0.000	0.000	0.000
134	D	135	ALA	0	0.018	0.017	9.708	0.515	0.515	0.000	0.000	0.000	0.000
135	D	136	TYR	0	-0.070	-0.074	8.485	0.121	0.121	0.000	0.000	0.000	0.000
136	D	137	ILE	0	0.040	0.007	10.430	0.517	0.517	0.000	0.000	0.000	0.000
137	D	138	ALA	0	0.011	-0.005	14.142	0.355	0.355	0.000	0.000	0.000	0.000
138	D	139	ALA	0	-0.034	-0.013	11.629	0.329	0.329	0.000	0.000	0.000	0.000
139	D	140	GLY	0	0.006	-0.007	13.652	0.218	0.218	0.000	0.000	0.000	0.000
140	D	141	ILE	0	-0.028	-0.021	15.144	0.204	0.204	0.000	0.000	0.000	0.000
141	D	142	GLY	0	0.022	0.004	17.446	0.126	0.126	0.000	0.000	0.000	0.000
142	D	143	ALA	0	-0.011	0.011	16.023	0.248	0.248	0.000	0.000	0.000	0.000
143	D	144	GLY	0	-0.033	-0.018	17.639	-0.036	-0.036	0.000	0.000	0.000	0.000
144	D	145	LEU	-1	-0.842	-0.914	20.374	0.336	0.336	0.000	0.000	0.000	0.000

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