FMO DATABASE

FMODB ID: RLYR8

Calculation Name: 2D5X-B-Xray547

Preferred Name:

Target Type:

Ligand Name: protoporphyrin ix containing fe | 2-[4-({[(3,5-dichlorophenyl)amino]carbonyl}amino)phenoxy]-2-methylpropanoic acid | carbon monoxide

Ligand 3-letter code: HEM | L35 | CMO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2D5X

Chain ID: B

ChEMBL ID:

UniProt ID: P01958

Base Structure: X-ray

Registration Date: 2025-10-05

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	146
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1321678.136299
FMO2-HF: Nuclear repulsion	1266493.831178
FMO2-HF: Total energy	-55184.305121
FMO2-MP2: Total energy	-55348.847404

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(A:1:VAL)

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

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.
9.2260000000001	16.359	7.28	-4.293	-10.121	-0.027

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.876 / q_NPA : 0.930

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	LEU	0	-0.011	0.006	2.219	6.707	9.340	1.494	-1.379	-2.749	-0.006
4	A	4	SER	0	0.059	0.032	3.774	-0.612	-0.494	0.010	-0.020	-0.108	0.000
8	A	8	LYS	1	0.815	0.894	4.793	48.308	48.408	-0.001	-0.005	-0.094	0.000
78	A	78	LEU	0	0.034	0.016	3.104	-3.769	-2.971	0.069	-0.168	-0.699	-0.001
79	A	79	ASP	-1	-0.855	-0.906	3.030	-69.419	-68.076	0.153	-0.647	-0.849	-0.006
80	A	80	ASN	0	-0.019	-0.016	5.098	0.816	0.857	-0.001	-0.001	-0.039	0.000
81	A	81	LEU	0	0.027	0.040	2.478	3.884	4.144	1.158	-0.261	-1.158	-0.001
130	A	130	TYR	0	-0.005	-0.036	4.851	-5.403	-5.308	-0.001	-0.001	-0.094	0.000
132	A	132	LYS	1	0.801	0.880	2.208	36.139	35.454	2.923	-0.612	-1.625	-0.001
133	A	133	VAL	0	-0.035	-0.005	2.801	-10.220	-8.239	0.972	-1.071	-1.882	-0.012
134	A	134	VAL	0	-0.010	0.001	3.754	-0.636	-0.479	0.002	0.027	-0.185	0.000
136	A	136	GLY	0	-0.011	-0.009	2.585	-0.550	-0.160	0.496	-0.366	-0.519	0.000
137	A	137	VAL	0	-0.020	-0.015	3.456	2.220	2.122	0.006	0.211	-0.120	0.000
5	A	5	GLY	0	0.032	0.003	7.612	-0.961	-0.961	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.902	-0.948	10.036	-20.570	-20.570	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.730	-0.833	6.272	-35.306	-35.306	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.017	0.013	7.937	1.091	1.091	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.020	0.010	10.960	1.200	1.200	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.007	-0.008	6.074	0.698	0.698	0.000	0.000	0.000	0.000
12	A	12	LEU	0	-0.030	-0.011	9.123	0.984	0.984	0.000	0.000	0.000	0.000
13	A	13	ALA	0	0.041	0.029	11.437	1.191	1.191	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.044	-0.012	12.125	1.215	1.215	0.000	0.000	0.000	0.000
15	A	15	TRP	0	-0.032	-0.043	11.382	0.308	0.308	0.000	0.000	0.000	0.000
16	A	16	ASP	-1	-0.887	-0.949	13.841	-17.594	-17.594	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.911	0.962	16.686	15.927	15.927	0.000	0.000	0.000	0.000
18	A	18	VAL	0	-0.048	-0.010	14.407	0.665	0.665	0.000	0.000	0.000	0.000
19	A	19	ASN	0	0.052	0.027	17.664	-0.030	-0.030	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.755	-0.881	15.691	-16.815	-16.815	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.860	-0.913	18.876	-11.294	-11.294	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.935	-0.967	22.320	-11.002	-11.002	0.000	0.000	0.000	0.000
23	A	23	VAL	0	0.020	0.004	16.483	0.043	0.043	0.000	0.000	0.000	0.000
24	A	24	GLY	0	0.041	0.012	18.615	-0.392	-0.392	0.000	0.000	0.000	0.000
25	A	25	GLY	0	-0.015	-0.012	19.568	0.033	0.033	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.746	-0.809	21.427	-12.218	-12.218	0.000	0.000	0.000	0.000
27	A	27	ALA	0	0.012	0.000	17.191	0.120	0.120	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.013	-0.003	19.308	-0.074	-0.074	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.048	-0.002	20.899	0.297	0.297	0.000	0.000	0.000	0.000
30	A	30	ARG	1	0.859	0.896	20.931	12.617	12.617	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.018	0.000	18.233	0.090	0.090	0.000	0.000	0.000	0.000
32	A	32	LEU	0	0.000	0.005	21.358	0.299	0.299	0.000	0.000	0.000	0.000
33	A	33	VAL	0	-0.023	-0.004	24.872	0.501	0.501	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.032	-0.017	22.343	0.304	0.304	0.000	0.000	0.000	0.000
35	A	35	TYR	0	0.012	0.007	19.604	-0.176	-0.176	0.000	0.000	0.000	0.000
36	A	36	PRO	0	0.038	0.029	24.046	-0.173	-0.173	0.000	0.000	0.000	0.000
37	A	37	TRP	0	0.020	0.004	21.875	0.430	0.430	0.000	0.000	0.000	0.000
38	A	38	THR	0	-0.042	-0.040	21.140	0.040	0.040	0.000	0.000	0.000	0.000
39	A	39	GLN	0	-0.012	-0.026	24.151	0.110	0.110	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.969	1.005	26.325	10.942	10.942	0.000	0.000	0.000	0.000
41	A	41	PHE	0	-0.057	-0.026	23.209	0.058	0.058	0.000	0.000	0.000	0.000
42	A	42	PHE	0	-0.031	-0.027	21.329	-0.286	-0.286	0.000	0.000	0.000	0.000
43	A	43	ASP	-1	-0.813	-0.891	27.526	-9.351	-9.351	0.000	0.000	0.000	0.000
44	A	44	SER	0	-0.047	-0.024	29.628	0.223	0.223	0.000	0.000	0.000	0.000
45	A	45	PHE	0	-0.039	-0.054	24.914	0.061	0.061	0.000	0.000	0.000	0.000
46	A	46	GLY	0	-0.008	0.020	30.658	0.107	0.107	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.827	-0.896	33.423	-8.505	-8.505	0.000	0.000	0.000	0.000
48	A	48	LEU	0	0.015	-0.005	28.335	-0.296	-0.296	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.023	-0.029	31.722	-0.104	-0.104	0.000	0.000	0.000	0.000
50	A	50	ASN	0	0.009	0.006	33.644	0.020	0.020	0.000	0.000	0.000	0.000
51	A	51	PRO	0	0.063	0.012	30.243	-0.110	-0.110	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.010	0.019	30.981	-0.184	-0.184	0.000	0.000	0.000	0.000
53	A	53	ALA	0	0.006	0.013	33.119	-0.059	-0.059	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.026	-0.002	27.065	-0.149	-0.149	0.000	0.000	0.000	0.000
55	A	55	MET	0	-0.051	-0.012	24.628	-0.301	-0.301	0.000	0.000	0.000	0.000
56	A	56	GLY	0	-0.001	0.004	28.863	-0.065	-0.065	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.037	-0.030	29.353	-0.083	-0.083	0.000	0.000	0.000	0.000
58	A	58	PRO	0	0.034	-0.001	28.904	-0.370	-0.370	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.885	0.961	28.145	9.025	9.025	0.000	0.000	0.000	0.000
60	A	60	VAL	0	0.031	0.029	24.486	-0.466	-0.466	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.980	0.995	23.918	9.494	9.494	0.000	0.000	0.000	0.000
62	A	62	ALA	0	0.004	0.004	23.742	-0.483	-0.483	0.000	0.000	0.000	0.000
63	A	63	HIS	0	-0.018	-0.021	20.908	-0.078	-0.078	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.078	0.032	20.012	-0.667	-0.667	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.860	0.921	18.865	11.043	11.043	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.881	0.955	18.891	11.513	11.513	0.000	0.000	0.000	0.000
67	A	67	VAL	0	0.022	0.018	15.284	-0.835	-0.835	0.000	0.000	0.000	0.000
68	A	68	LEU	0	0.011	0.029	14.328	-1.427	-1.427	0.000	0.000	0.000	0.000
69	A	69	HIS	1	0.833	0.904	14.109	15.408	15.408	0.000	0.000	0.000	0.000
70	A	70	SER	0	-0.056	-0.039	13.358	-1.027	-1.027	0.000	0.000	0.000	0.000
71	A	71	PHE	0	0.039	0.005	8.867	-1.932	-1.932	0.000	0.000	0.000	0.000
72	A	72	GLY	0	0.068	0.043	9.640	-2.110	-2.110	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.892	-0.946	11.467	-19.894	-19.894	0.000	0.000	0.000	0.000
74	A	74	GLY	0	0.005	-0.002	7.731	-1.411	-1.411	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.011	-0.008	6.785	-4.069	-4.069	0.000	0.000	0.000	0.000
76	A	76	HIS	1	0.832	0.912	7.811	20.437	20.437	0.000	0.000	0.000	0.000
77	A	77	HIS	1	0.858	0.924	8.169	26.003	26.003	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.943	0.970	6.074	33.215	33.215	0.000	0.000	0.000	0.000
83	A	83	GLY	0	0.016	0.009	8.611	2.620	2.620	0.000	0.000	0.000	0.000
84	A	84	THR	0	-0.055	-0.040	8.860	2.218	2.218	0.000	0.000	0.000	0.000
85	A	85	PHE	0	0.014	-0.004	7.757	1.349	1.349	0.000	0.000	0.000	0.000
86	A	86	ALA	0	0.017	0.029	11.542	1.264	1.264	0.000	0.000	0.000	0.000
87	A	87	ALA	0	0.051	0.012	13.842	0.793	0.793	0.000	0.000	0.000	0.000
88	A	88	LEU	0	-0.003	-0.002	13.605	0.858	0.858	0.000	0.000	0.000	0.000
89	A	89	SER	0	0.005	0.001	13.271	0.675	0.675	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.803	-0.895	15.256	-13.165	-13.165	0.000	0.000	0.000	0.000
91	A	91	LEU	0	-0.035	-0.016	18.801	0.762	0.762	0.000	0.000	0.000	0.000
92	A	92	HIS	0	-0.028	-0.043	16.606	1.056	1.056	0.000	0.000	0.000	0.000
93	A	93	CYS	0	-0.036	0.010	16.411	0.297	0.297	0.000	0.000	0.000	0.000
94	A	94	ASP	-1	-0.828	-0.904	19.297	-13.764	-13.764	0.000	0.000	0.000	0.000
95	A	95	LYS	1	0.753	0.872	22.212	13.338	13.338	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.010	-0.010	21.024	0.462	0.462	0.000	0.000	0.000	0.000
97	A	97	HIS	1	0.849	0.944	21.904	12.823	12.823	0.000	0.000	0.000	0.000
98	A	98	VAL	0	0.008	0.010	18.476	0.341	0.341	0.000	0.000	0.000	0.000
99	A	99	ASP	-1	-0.822	-0.898	18.758	-15.754	-15.754	0.000	0.000	0.000	0.000
100	A	100	PRO	0	0.047	0.009	13.875	-0.303	-0.303	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.861	-0.911	14.018	-19.593	-19.593	0.000	0.000	0.000	0.000
102	A	102	ASN	0	-0.034	-0.035	15.560	0.070	0.070	0.000	0.000	0.000	0.000
103	A	103	PHE	0	-0.003	0.004	12.000	0.051	0.051	0.000	0.000	0.000	0.000
104	A	104	ARG	1	0.910	0.948	10.671	20.316	20.316	0.000	0.000	0.000	0.000
105	A	105	LEU	0	-0.029	0.003	12.614	-0.122	-0.122	0.000	0.000	0.000	0.000
106	A	106	LEU	0	0.009	0.000	14.370	0.208	0.208	0.000	0.000	0.000	0.000
107	A	107	GLY	0	0.029	0.010	11.147	-0.041	-0.041	0.000	0.000	0.000	0.000
108	A	108	ASN	0	0.049	0.010	11.887	-1.241	-1.241	0.000	0.000	0.000	0.000
109	A	109	VAL	0	-0.022	0.004	13.749	0.680	0.680	0.000	0.000	0.000	0.000
110	A	110	LEU	0	-0.009	-0.001	11.031	0.626	0.626	0.000	0.000	0.000	0.000
111	A	111	VAL	0	-0.006	-0.001	10.654	0.329	0.329	0.000	0.000	0.000	0.000
112	A	112	VAL	0	-0.001	0.002	13.321	0.720	0.720	0.000	0.000	0.000	0.000
113	A	113	VAL	0	-0.056	-0.020	16.919	0.752	0.752	0.000	0.000	0.000	0.000
114	A	114	LEU	0	-0.003	-0.001	11.856	0.526	0.526	0.000	0.000	0.000	0.000
115	A	115	ALA	0	0.030	0.010	15.917	0.520	0.520	0.000	0.000	0.000	0.000
116	A	116	ARG	1	0.788	0.861	17.527	12.553	12.553	0.000	0.000	0.000	0.000
117	A	117	HIS	0	-0.078	-0.046	19.074	0.535	0.535	0.000	0.000	0.000	0.000
118	A	118	PHE	0	0.003	0.003	16.349	0.280	0.280	0.000	0.000	0.000	0.000
119	A	119	GLY	0	0.015	0.017	19.648	0.321	0.321	0.000	0.000	0.000	0.000
120	A	120	LYS	1	0.911	0.935	19.410	10.481	10.481	0.000	0.000	0.000	0.000
121	A	121	ASP	-1	-0.886	-0.930	18.533	-13.441	-13.441	0.000	0.000	0.000	0.000
122	A	122	PHE	0	-0.067	-0.035	11.694	-1.162	-1.162	0.000	0.000	0.000	0.000
123	A	123	THR	0	0.000	-0.015	15.327	-0.127	-0.127	0.000	0.000	0.000	0.000
124	A	124	PRO	0	0.041	0.008	14.158	-1.003	-1.003	0.000	0.000	0.000	0.000
125	A	125	GLU	-1	-0.843	-0.900	12.026	-18.205	-18.205	0.000	0.000	0.000	0.000
126	A	126	LEU	0	0.015	0.020	9.849	-2.347	-2.347	0.000	0.000	0.000	0.000
127	A	127	GLN	0	0.010	0.004	9.685	-1.081	-1.081	0.000	0.000	0.000	0.000
128	A	128	ALA	0	-0.013	-0.008	9.297	-1.780	-1.780	0.000	0.000	0.000	0.000
129	A	129	SER	0	-0.040	-0.052	5.836	-2.409	-2.409	0.000	0.000	0.000	0.000
131	A	131	GLN	0	-0.020	-0.009	6.614	-0.002	-0.002	0.000	0.000	0.000	0.000
135	A	135	ALA	0	0.010	0.015	5.118	1.675	1.675	0.000	0.000	0.000	0.000
138	A	138	ALA	0	0.008	0.007	6.581	2.248	2.248	0.000	0.000	0.000	0.000
139	A	139	ASN	0	-0.011	-0.007	5.942	5.248	5.248	0.000	0.000	0.000	0.000
140	A	140	ALA	0	-0.051	-0.017	6.601	1.452	1.452	0.000	0.000	0.000	0.000
141	A	141	LEU	0	0.006	-0.009	8.381	2.212	2.212	0.000	0.000	0.000	0.000
142	A	142	ALA	0	0.007	0.021	10.703	1.910	1.910	0.000	0.000	0.000	0.000
143	A	143	HIS	0	0.064	0.036	10.922	-1.005	-1.005	0.000	0.000	0.000	0.000
144	A	144	LYS	1	0.804	0.871	12.639	16.249	16.249	0.000	0.000	0.000	0.000
145	A	145	TYR	0	-0.075	-0.062	15.431	1.446	1.446	0.000	0.000	0.000	0.000
146	A	146	HIS	-1	-0.961	-0.955	10.418	-16.803	-16.803	0.000	0.000	0.000	0.000

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