Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: JQ7Y9

Calculation Name: 3CRM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CRM

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HUL9

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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2941683.850234
FMO2-HF: Nuclear repulsion 2849837.000543
FMO2-HF: Total energy -91846.849691
FMO2-MP2: Total energy -92114.795912


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:3:SER)


Summations of interaction energy for fragment #1(A:3: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.
0.1131.554-0.012-0.568-0.8590.003
Interaction energy analysis for fragmet #1(A:3:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.014
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   
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].
3A5PRO00.0370.0343.860-1.569-0.206-0.011-0.565-0.7860.003
4A6PRO00.0320.0236.0170.7230.7230.0000.0000.0000.000
5A7ALA0-0.001-0.0098.2100.1220.1220.0000.0000.0000.000
6A8ILE0-0.0050.00811.8870.0640.0640.0000.0000.0000.000
7A9PHE0-0.009-0.00515.1690.0280.0280.0000.0000.0000.000
8A10LEU00.0100.00517.9630.0110.0110.0000.0000.0000.000
9A11MET00.0140.02120.2020.0200.0200.0000.0000.0000.000
10A12GLY00.0670.01023.9250.0050.0050.0000.0000.0000.000
11A13PRO0-0.055-0.02427.376-0.001-0.0010.0000.0000.0000.000
12A14THR00.0400.01130.906-0.007-0.0070.0000.0000.0000.000
13A15ALA0-0.036-0.03733.1370.0050.0050.0000.0000.0000.000
14A16ALA0-0.0150.00130.2370.0020.0020.0000.0000.0000.000
15A17GLY00.0530.05330.769-0.001-0.0010.0000.0000.0000.000
16A18LYS10.8480.93726.4350.1440.1440.0000.0000.0000.000
17A19THR00.0330.00926.081-0.017-0.0170.0000.0000.0000.000
18A20ASP-1-0.827-0.91727.022-0.144-0.1440.0000.0000.0000.000
19A21LEU0-0.0030.00123.231-0.005-0.0050.0000.0000.0000.000
20A22ALA00.006-0.00922.504-0.019-0.0190.0000.0000.0000.000
21A23MET0-0.044-0.00522.909-0.018-0.0180.0000.0000.0000.000
22A24ALA00.0370.02224.591-0.009-0.0090.0000.0000.0000.000
23A25LEU0-0.022-0.02318.424-0.008-0.0080.0000.0000.0000.000
24A26ALA0-0.022-0.01420.114-0.027-0.0270.0000.0000.0000.000
25A27ASP-1-0.854-0.88521.614-0.197-0.1970.0000.0000.0000.000
26A28ALA0-0.051-0.01920.9500.0120.0120.0000.0000.0000.000
27A29LEU0-0.024-0.01514.737-0.021-0.0210.0000.0000.0000.000
28A30PRO00.0310.03514.3940.0210.0210.0000.0000.0000.000
29A31CYS0-0.008-0.00215.385-0.096-0.0960.0000.0000.0000.000
30A32GLU-1-0.793-0.87917.374-0.336-0.3360.0000.0000.0000.000
31A33LEU00.0000.02218.719-0.027-0.0270.0000.0000.0000.000
32A34ILE0-0.028-0.01618.0230.0140.0140.0000.0000.0000.000
33A35SER00.0260.02621.9770.0040.0040.0000.0000.0000.000
34A36VAL00.003-0.01421.421-0.007-0.0070.0000.0000.0000.000
35A37ASP-1-0.834-0.94124.811-0.107-0.1070.0000.0000.0000.000
36A38SER00.0030.00328.590-0.002-0.0020.0000.0000.0000.000
37A39ALA0-0.038-0.00830.9880.0070.0070.0000.0000.0000.000
38A40LEU00.0330.01129.9790.0010.0010.0000.0000.0000.000
39A41ILE0-0.040-0.01229.366-0.005-0.0050.0000.0000.0000.000
40A42TYR0-0.054-0.03531.870-0.001-0.0010.0000.0000.0000.000
41A43ARG10.8460.92834.5490.1060.1060.0000.0000.0000.000
42A44GLY0-0.0030.00337.8400.0050.0050.0000.0000.0000.000
43A45MET0-0.046-0.02437.8480.0060.0060.0000.0000.0000.000
44A46ASP-1-0.854-0.88837.307-0.107-0.1070.0000.0000.0000.000
45A47ILE0-0.012-0.01338.119-0.003-0.0030.0000.0000.0000.000
46A48GLY00.028-0.01240.169-0.001-0.0010.0000.0000.0000.000
47A49THR0-0.089-0.07835.3710.0000.0000.0000.0000.0000.000
48A50ALA0-0.104-0.05735.495-0.004-0.0040.0000.0000.0000.000
49A51LYS10.7570.87533.0380.1070.1070.0000.0000.0000.000
50A52PRO0-0.041-0.02229.8250.0040.0040.0000.0000.0000.000
51A53SER00.011-0.01633.022-0.002-0.0020.0000.0000.0000.000
52A54ARG11.0181.00534.1220.0910.0910.0000.0000.0000.000
53A55GLU-1-0.817-0.89634.461-0.112-0.1120.0000.0000.0000.000
54A56LEU0-0.016-0.00330.232-0.006-0.0060.0000.0000.0000.000
55A57LEU00.001-0.02229.332-0.013-0.0130.0000.0000.0000.000
56A58ALA0-0.040-0.01729.673-0.012-0.0120.0000.0000.0000.000
57A59ARG10.8800.95129.2660.1500.1500.0000.0000.0000.000
58A60TYR0-0.070-0.06725.350-0.006-0.0060.0000.0000.0000.000
59A61PRO00.0200.01325.4430.0000.0000.0000.0000.0000.000
60A62HIS0-0.041-0.01824.547-0.024-0.0240.0000.0000.0000.000
61A63ARG10.8250.88121.8370.3020.3020.0000.0000.0000.000
62A64LEU0-0.005-0.01322.9230.0000.0000.0000.0000.0000.000
63A65ILE00.0280.01626.7240.0080.0080.0000.0000.0000.000
64A66ASP-1-0.824-0.90029.968-0.125-0.1250.0000.0000.0000.000
65A67ILE0-0.0200.00227.9540.0030.0030.0000.0000.0000.000
66A68ARG10.8300.91628.6930.1330.1330.0000.0000.0000.000
67A69ASP-1-0.777-0.86434.509-0.077-0.0770.0000.0000.0000.000
68A70PRO00.007-0.00438.2990.0000.0000.0000.0000.0000.000
69A71ALA00.0520.04940.1830.0030.0030.0000.0000.0000.000
70A72GLU-1-0.848-0.90435.695-0.097-0.0970.0000.0000.0000.000
71A73SER0-0.022-0.01335.7280.0010.0010.0000.0000.0000.000
72A74TYR0-0.028-0.04626.653-0.010-0.0100.0000.0000.0000.000
73A75SER0-0.036-0.03929.9820.0000.0000.0000.0000.0000.000
74A76ALA00.011-0.01926.119-0.010-0.0100.0000.0000.0000.000
75A77ALA00.0130.01425.099-0.012-0.0120.0000.0000.0000.000
76A78GLU-1-0.742-0.83225.042-0.115-0.1150.0000.0000.0000.000
77A79PHE00.0230.02221.582-0.020-0.0200.0000.0000.0000.000
78A80ARG10.8400.89418.0460.0950.0950.0000.0000.0000.000
79A81ALA00.0100.00520.347-0.030-0.0300.0000.0000.0000.000
80A82ASP-1-0.771-0.87721.015-0.210-0.2100.0000.0000.0000.000
81A83ALA00.010-0.00419.978-0.032-0.0320.0000.0000.0000.000
82A84LEU0-0.012-0.00415.199-0.062-0.0620.0000.0000.0000.000
83A85ALA0-0.0030.00916.460-0.074-0.0740.0000.0000.0000.000
84A86ALA0-0.034-0.01818.022-0.038-0.0380.0000.0000.0000.000
85A87MET0-0.001-0.00114.073-0.050-0.0500.0000.0000.0000.000
86A88ALA00.0530.04813.034-0.129-0.1290.0000.0000.0000.000
87A89LYS10.9500.96713.8870.2450.2450.0000.0000.0000.000
88A90ALA0-0.024-0.00915.1390.0280.0280.0000.0000.0000.000
89A91THR00.0510.0139.086-0.067-0.0670.0000.0000.0000.000
90A92ALA0-0.042-0.01811.413-0.072-0.0720.0000.0000.0000.000
91A93ARG10.8330.91613.1780.4850.4850.0000.0000.0000.000
92A94GLY00.0230.01511.6440.0750.0750.0000.0000.0000.000
93A95ARG10.8190.91712.7340.4190.4190.0000.0000.0000.000
94A96ILE00.0270.01011.335-0.100-0.1000.0000.0000.0000.000
95A97PRO0-0.016-0.00712.3750.1420.1420.0000.0000.0000.000
96A98LEU00.0000.00615.033-0.016-0.0160.0000.0000.0000.000
97A99LEU00.0250.00616.6450.0430.0430.0000.0000.0000.000
98A100VAL00.0300.03619.8220.0210.0210.0000.0000.0000.000
99A101GLY00.0130.00223.1350.0100.0100.0000.0000.0000.000
100A102GLY00.010-0.00425.6280.0050.0050.0000.0000.0000.000
101A103THR0-0.0030.00827.2570.0140.0140.0000.0000.0000.000
102A104MET0-0.027-0.01124.992-0.011-0.0110.0000.0000.0000.000
103A105LEU00.0360.01424.490-0.002-0.0020.0000.0000.0000.000
104A106TYR00.001-0.00824.3250.0040.0040.0000.0000.0000.000
105A107TYR00.012-0.02119.5990.0030.0030.0000.0000.0000.000
106A108LYS10.8030.88919.9890.0190.0190.0000.0000.0000.000
107A109ALA0-0.0070.00221.1210.0120.0120.0000.0000.0000.000
108A110LEU0-0.0280.00117.4020.0010.0010.0000.0000.0000.000
109A111LEU0-0.023-0.01015.402-0.010-0.0100.0000.0000.0000.000
110A112GLU-1-0.799-0.86716.7090.0170.0170.0000.0000.0000.000
111A113GLY0-0.0210.00919.379-0.005-0.0050.0000.0000.0000.000
112A199LEU00.011-0.00812.2670.0010.0010.0000.0000.0000.000
113A200PRO0-0.0130.0079.0570.0730.0730.0000.0000.0000.000
114A201TYR0-0.034-0.0557.702-0.446-0.4460.0000.0000.0000.000
115A202THR0-0.009-0.0104.6960.7740.852-0.001-0.003-0.0730.000
116A203VAL0-0.014-0.0137.376-0.074-0.0740.0000.0000.0000.000
117A204ALA00.0240.03111.2300.1220.1220.0000.0000.0000.000
118A205GLN0-0.020-0.01713.491-0.004-0.0040.0000.0000.0000.000
119A206LEU00.0100.01017.1050.0300.0300.0000.0000.0000.000
120A207ALA0-0.013-0.00320.310-0.001-0.0010.0000.0000.0000.000
121A208ILE0-0.0120.00123.7810.0070.0070.0000.0000.0000.000
122A209ALA0-0.009-0.02827.0910.0020.0020.0000.0000.0000.000
123A210PRO0-0.0290.00030.7860.0000.0000.0000.0000.0000.000
124A211GLU-1-0.919-0.94132.850-0.056-0.0560.0000.0000.0000.000
125A212GLN0-0.014-0.00234.3090.0050.0050.0000.0000.0000.000
126A213ARG10.9300.93735.0720.0500.0500.0000.0000.0000.000
127A214GLN00.0310.01937.624-0.004-0.0040.0000.0000.0000.000
128A215VAL00.0720.04038.2220.0000.0000.0000.0000.0000.000
129A216LEU00.0300.02134.226-0.001-0.0010.0000.0000.0000.000
130A217HIS0-0.014-0.01338.005-0.002-0.0020.0000.0000.0000.000
131A218ALA00.0370.02840.9860.0010.0010.0000.0000.0000.000
132A219ARG10.9650.97736.8920.0820.0820.0000.0000.0000.000
133A220ILE0-0.013-0.01837.038-0.001-0.0010.0000.0000.0000.000
134A221ALA0-0.009-0.01140.7010.0000.0000.0000.0000.0000.000
135A222GLN00.0240.02442.507-0.001-0.0010.0000.0000.0000.000
136A223ARG10.9120.95135.6580.0850.0850.0000.0000.0000.000
137A224PHE00.0450.01642.2610.0000.0000.0000.0000.0000.000
138A225ARG10.9430.96143.9020.0460.0460.0000.0000.0000.000
139A226GLN00.0310.02744.1600.0000.0000.0000.0000.0000.000
140A227MET0-0.0380.00739.2090.0000.0000.0000.0000.0000.000
141A228LEU0-0.018-0.01344.5340.0000.0000.0000.0000.0000.000
142A229GLU-1-0.943-0.96848.179-0.049-0.0490.0000.0000.0000.000
143A230GLN0-0.062-0.03844.081-0.001-0.0010.0000.0000.0000.000
144A231GLY00.0530.03746.622-0.002-0.0020.0000.0000.0000.000
145A232PHE0-0.056-0.03543.1080.0000.0000.0000.0000.0000.000
146A233ILE00.014-0.00346.1500.0000.0000.0000.0000.0000.000
147A234ALA00.0960.05049.4200.0010.0010.0000.0000.0000.000
148A235GLU-1-0.767-0.83341.866-0.080-0.0800.0000.0000.0000.000
149A236VAL0-0.015-0.02345.058-0.001-0.0010.0000.0000.0000.000
150A237GLU-1-0.911-0.95647.093-0.046-0.0460.0000.0000.0000.000
151A238ALA0-0.025-0.00646.9590.0010.0010.0000.0000.0000.000
152A239LEU0-0.078-0.04543.035-0.001-0.0010.0000.0000.0000.000
153A240HIS0-0.034-0.04147.2130.0010.0010.0000.0000.0000.000
154A241ALA00.0050.00650.4910.0020.0020.0000.0000.0000.000
155A242ARG10.7110.80342.8440.0670.0670.0000.0000.0000.000
156A243SER00.0400.01549.7700.0000.0000.0000.0000.0000.000
157A244ASP-1-0.856-0.89545.785-0.057-0.0570.0000.0000.0000.000
158A245LEU0-0.058-0.01943.634-0.003-0.0030.0000.0000.0000.000
159A246HIS00.0670.01945.4730.0030.0030.0000.0000.0000.000
160A247ALA00.0370.01845.790-0.003-0.0030.0000.0000.0000.000
161A248GLY00.0020.00544.9020.0010.0010.0000.0000.0000.000
162A249LEU00.0020.02341.6460.0000.0000.0000.0000.0000.000
163A250PRO0-0.059-0.04536.7650.0010.0010.0000.0000.0000.000
164A251SER00.015-0.00238.082-0.001-0.0010.0000.0000.0000.000
165A252ILE00.0560.02939.117-0.001-0.0010.0000.0000.0000.000
166A253ARG10.8440.91238.5350.0570.0570.0000.0000.0000.000
167A254ALA0-0.0170.01137.5680.0000.0000.0000.0000.0000.000
168A255VAL0-0.045-0.04437.5760.0040.0040.0000.0000.0000.000
169A256GLY00.0160.00939.932-0.003-0.0030.0000.0000.0000.000
170A257TYR0-0.002-0.02639.5800.0010.0010.0000.0000.0000.000
171A258ARG10.8230.91043.6610.0450.0450.0000.0000.0000.000
172A259GLN0-0.026-0.02244.5570.0000.0000.0000.0000.0000.000
173A260VAL00.0290.00446.7290.0030.0030.0000.0000.0000.000
174A261TRP00.0450.03547.0740.0000.0000.0000.0000.0000.000
175A262ASP-1-0.804-0.89749.519-0.036-0.0360.0000.0000.0000.000
176A263TYR0-0.041-0.01851.5500.0020.0020.0000.0000.0000.000
177A264LEU00.0360.02250.8920.0010.0010.0000.0000.0000.000
178A265ASP-1-0.845-0.89753.037-0.038-0.0380.0000.0000.0000.000
179A266GLY0-0.0110.00055.5120.0020.0020.0000.0000.0000.000
180A267LYS10.7480.85952.9200.0370.0370.0000.0000.0000.000
181A268LEU0-0.062-0.02251.4740.0010.0010.0000.0000.0000.000
182A269SER00.030-0.01655.606-0.001-0.0010.0000.0000.0000.000
183A270TYR00.0730.01752.631-0.001-0.0010.0000.0000.0000.000
184A271ALA00.0120.01053.030-0.002-0.0020.0000.0000.0000.000
185A272GLU-1-0.740-0.83652.708-0.032-0.0320.0000.0000.0000.000
186A273MET00.0260.03949.324-0.002-0.0020.0000.0000.0000.000
187A274THR0-0.016-0.01848.643-0.003-0.0030.0000.0000.0000.000
188A275GLU-1-0.931-0.95847.898-0.036-0.0360.0000.0000.0000.000
189A276ARG10.8220.88447.6560.0320.0320.0000.0000.0000.000
190A277GLY00.0630.04144.747-0.001-0.0010.0000.0000.0000.000
191A278ILE0-0.0230.01943.245-0.003-0.0030.0000.0000.0000.000
192A279ILE0-0.019-0.01242.878-0.002-0.0020.0000.0000.0000.000
193A280ALA00.0290.01542.0420.0000.0000.0000.0000.0000.000
194A281THR0-0.004-0.02338.371-0.004-0.0040.0000.0000.0000.000
195A282ARG10.9010.94738.1020.0430.0430.0000.0000.0000.000
196A283GLN0-0.013-0.00838.4930.0020.0020.0000.0000.0000.000
197A284LEU0-0.0080.00833.5920.0020.0020.0000.0000.0000.000
198A285ALA00.0630.03233.911-0.002-0.0020.0000.0000.0000.000
199A286LYS10.8570.93333.8050.0350.0350.0000.0000.0000.000
200A287ARG10.9801.00433.5490.0590.0590.0000.0000.0000.000
201A288GLN00.0310.00330.0770.0050.0050.0000.0000.0000.000
202A289PHE00.053-0.00129.482-0.002-0.0020.0000.0000.0000.000
203A290THR0-0.083-0.04730.5580.0050.0050.0000.0000.0000.000
204A291TRP00.0240.00925.5660.0040.0040.0000.0000.0000.000
205A292LEU00.0210.00624.8260.0040.0040.0000.0000.0000.000
206A293ARG10.9030.95925.9610.0250.0250.0000.0000.0000.000
207A294SER0-0.042-0.01526.6070.0080.0080.0000.0000.0000.000
208A295TRP0-0.053-0.02819.1100.0170.0170.0000.0000.0000.000
209A296SER00.0300.01618.6760.0010.0010.0000.0000.0000.000
210A297HIS00.0450.00015.249-0.033-0.0330.0000.0000.0000.000
211A298LEU00.0000.01717.475-0.037-0.0370.0000.0000.0000.000
212A299HIS0-0.0030.01819.0810.0190.0190.0000.0000.0000.000
213A300TRP00.004-0.01420.786-0.017-0.0170.0000.0000.0000.000
214A301MET0-0.056-0.01523.242-0.009-0.0090.0000.0000.0000.000
215A302ASP-1-0.690-0.86726.159-0.076-0.0760.0000.0000.0000.000
216A303SER0-0.074-0.06529.949-0.004-0.0040.0000.0000.0000.000
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